o&&(n.val=o);var p;p=c.geo.origin.fixedLineage?c.geo.origin.windowOffset:{left:c.geo.origin.windowOffset.left+c.geo.window.scroll.left,top:c.geo.origin.windowOffset.top+c.geo.window.scroll.top},d.coord={left:p.left+(d.coord.left-c.geo.origin.windowOffset.left),top:p.top+(d.coord.top-c.geo.origin.windowOffset.top)},e.__sideChange(e.__instance._$tooltip,d.side),c.geo.origin.fixedLineage?e.__instance._$tooltip.css("position","fixed"):e.__instance._$tooltip.css("position",""),e.__instance._$tooltip.css({left:d.coord.left,top:d.coord.top,height:d.size.height,width:d.size.width}).find(".tooltipster-arrow").css({left:"",top:""}).css(n.prop,n.val),e.__instance._$tooltip.appendTo(e.__instance.option("parent")),e.__instance._trigger({type:"repositioned",event:b,position:d})},__sideChange:function(a,b){a.removeClass("tooltipster-bottom").removeClass("tooltipster-left").removeClass("tooltipster-right").removeClass("tooltipster-top").addClass("tooltipster-"+b)},__targetFind:function(a){var b={},c=this.__instance._$origin[0].getClientRects();if(c.length>1){var d=this.__instance._$origin.css("opacity");1==d&&(this.__instance._$origin.css("opacity",.99),c=this.__instance._$origin[0].getClientRects(),this.__instance._$origin.css("opacity",1))}if(c.length<2)b.top=Math.floor(a.geo.origin.windowOffset.left+a.geo.origin.size.width/2),b.bottom=b.top,b.left=Math.floor(a.geo.origin.windowOffset.top+a.geo.origin.size.height/2),b.right=b.left;else{var e=c[0];b.top=Math.floor(e.left+(e.right-e.left)/2),e=c.length>2?c[Math.ceil(c.length/2)-1]:c[0],b.right=Math.floor(e.top+(e.bottom-e.top)/2),e=c[c.length-1],b.bottom=Math.floor(e.left+(e.right-e.left)/2),e=c.length>2?c[Math.ceil((c.length+1)/2)-1]:c[c.length-1],b.left=Math.floor(e.top+(e.bottom-e.top)/2)}return b}}}),a});
\ No newline at end of file
diff --git a/app/assets/javascripts/vendor.js b/app/assets/javascripts/vendor.js
index 68827662c..76dfe4056 100644
--- a/app/assets/javascripts/vendor.js
+++ b/app/assets/javascripts/vendor.js
@@ -6,35 +6,22 @@
//
// WARNING: THE FIRST BLANK LINE MARKS THE END OF WHAT'S TO BE PROCESSED, ANY BLANK LINE SHOULD
// GO AFTER THE REQUIRES BELOW.
-//
+// Jquery 2 dependencies
//= require jquery2
//= require jquery-migrate-1.3.0.min
//= require jquery_ujs
//= require jquery-ui
+// popper is required by bootstrap 4
//= require popper
//= require bootstrap-sprockets
-//
-//= require jquery.blockUI
-//= require facebox
-//= require thickbox
-//= require fg.menu
-//= require jquery.tools.min
+// Other
//= require jquery.dataTables
-//= require dataTables.fixedHeader
//= require chosen.jquery
-//= require ajax-chosen
-//= require jquery.cookie
//= require autocomplete
-//= require jquery.hoverIntent
-//= require jquery.simple.tree
-//= require jquery.scrollTo-1.4.0-min
-//= require jquery.rating.pack
-//= require history/jquery.history
+// Alertify is used the admin page
//= require alertify
-//= require jquery.tooltip
-//= require Chart.min
-//= require select2
//= require jquery.readyselector
+// can be removed used only in the ontology bridge form
//= require trumbowyg
//= require sharer.min
diff --git a/app/assets/stylesheets/account.scss b/app/assets/stylesheets/account.scss
index 3112a95d4..c96f1b072 100644
--- a/app/assets/stylesheets/account.scss
+++ b/app/assets/stylesheets/account.scss
@@ -1,223 +1,255 @@
-.account-page-center{
- display: flex;
- justify-content: center;
- margin: 30px 0;
+.account-page-center {
+ display: flex;
+ justify-content: center;
+ margin: 30px 0;
+}
+.account-page-center svg path {
+ fill: var(--primary-color)
}
-.account-page-title{
- font-size: 18px;
- font-weight: 700;
+
+.clipboard .copy svg path {
+ fill: none;
}
-.account-page-sub-container{
- display: flex;
+.account-page-title {
+ font-size: 18px;
+ font-weight: 700;
}
-.account-page-first-row{
- width: 566px;
- margin-right: 20px;
+
+.account-page-sub-container {
+ display: flex;
+}
+
+.account-page-first-row {
+ width: 566px;
+ margin-right: 20px;
+}
+
+.account-page-second-row {
+ width: 566px;
+}
+
+#account-page-title-line {
+ width: 93px;
+ margin-top: 3px;
+ border: 0.5px solid var(--primary-color);
+ border-radius: 5px;
+ margin-bottom: 0px !important;
+}
+
+.account-page-card {
+ border: 1px solid #DFDFDF;
+ border-radius: 5px;
+ padding: 20px 20px;
+ margin-top: 20px;
+}
+
+.account-page-card-title {
+ font-size: 16px;
+ font-weight: 600;
+}
+
+.account-page-personal-informations-title-bar {
+ display: flex;
+ align-items: center;
+ justify-content: space-between;
+}
+
+.account-page-rounded-button {
+ display: flex;
+ justify-content: center;
+ border: 0.5px solid var(--primary-color);
+ padding: 10px;
+ border-radius: 50px;
+ width: 40px;
+}
+
+.account-page-info-column {
+ display: flex;
+}
+
+.account-page-info-column .title {
+ margin-right: 9px;
+ font-size: 15px;
+ color: #666666;
+}
+
+.account-page-info-column .info {
+ font-size: 15px;
+ font-weight: 600;
+}
+
+.account-page-card-desc {
+ font-size: 13px;
+ color: #666666;
+ margin: 8px 0;
+}
+
+.apikey {
+ font-size: 17px;
+ font-weight: 600;
+}
+
+.account-page-card-container {
+ display: flex;
+ justify-content: space-between;
+ align-items: center;
+}
+
+.account-page-no-ontology {
+ display: flex;
+ align-items: center;
+ justify-content: center;
+ flex-direction: column;
+ padding: 37px;
+}
+
+.account-page-no-ontology p {
+ color: #bbbbbb;
+ font-size: 16px;
+ margin: 26px 0;
+}
+
+.account-page-upload-ontology-button {
+ width: 220px;
+ font-size: 16px;
+ font-weight: 500;
+ color: var(--primary-color);
+ background-color: white;
+ padding: 16px;
+ border: 1px solid var(--primary-color);
+ border-radius: 5px;
+ text-align: center;
}
-.account-page-second-row{
- width: 566px;
-}
-
-#account-page-title-line{
- width: 93px;
- margin-top: 3px;
- border: 0.5px solid var(--primary-color);
- border-radius: 5px;
- margin-bottom: 0px !important ;
-}
-.account-page-card{
- border: 1px solid #DFDFDF;
- border-radius: 5px;
- padding: 20px 20px;
- margin-top: 20px;
-}
-.account-page-card-title{
- font-size: 16px;
- font-weight: 600;
-}
-.account-page-personal-informations-title-bar{
- display: flex;
- align-items: center;
- justify-content:space-between;
-}
-.account-page-rounded-button{
- display: flex;
- justify-content: center;
- border: 0.5px solid var(--primary-color);
- padding: 10px;
- border-radius: 50px;
- width: 40px;
-}
-.account-page-info-column{
- display: flex;
-}
-.account-page-info-column .title{
- margin-right: 9px;
- font-size: 15px;
- color: #666666;
-}
-
-.account-page-info-column .info{
- font-size: 15px;
- font-weight: 600;
-}
-.account-page-card-desc{
- font-size: 13px;
- color: #666666;
- margin: 8px 0;
-}
-.apikey{
- font-size: 17px;
- font-weight: 600;
-}
-.account-page-card-container{
- display: flex;
- justify-content: space-between;
- align-items: center;
-}
-.account-page-no-ontology{
- display: flex;
- align-items: center;
- justify-content: center;
- flex-direction: column;
- padding: 37px;
-}
-.account-page-no-ontology p{
- color: #bbbbbb;
- font-size: 16px;
- margin: 26px 0;
-}
-.account-page-upload-ontology-button{
- width: 220px;
- font-size: 16px;
- font-weight: 500;
- color: var(--primary-color);
- background-color: white;
- padding: 16px;
- border: 1px solid var(--primary-color);
- border-radius: 5px;
- text-align: center;
-}
-.account-page-select-ontology-set-button{
- display: flex;
- justify-content: space-between;
- align-items: center;
- width: 200px;
- border: 1px solid var(--primary-color);
- padding: 16px;
- border-radius: 5px;
- font-size: 16px;
- font-weight: 500;
- color: var(--primary-color);
-}
-.account-page-select-ontology-set-button p{
- margin-bottom: 0 !important;
-}
-.account-page-api-documentation-link{
- display: flex;
- margin-top: 10px;
-}
-.account-page-api-documentation-link a{
- font-size: 15px;
- font-weight: 500;
- color: var(--primary-color);
- text-decoration: none;
-}
-.account-page-api-documentation-link a svg{
- margin-left: 10px;
- margin-bottom: 5px;
-}
-svg path{
- fill: var(--primary-color);
-}
-
-.account-page-subscribe-button{
- border: 1px solid var(--primary-color);
- text-decoration: none;
- color: var(--primary-color);
- border-radius: 5px;
- padding: 12px 20px;
- font-size: 14px;
- font-weight: 500;
-}
-
-.account-page-subscription{
- margin-top: 10px;
- display: flex;
- justify-content: space-between;
-}
-.account-page-subscription a{
- font-size: 15px;
- font-weight: 400;
- color: var(--primary-color);
-}
-.account-page-subscription div{
- display: flex;
-}
-.account-page-subscription div .notes{
- margin-right: 23px;
- color: #666666 !important;
- font-weight: 400;
-}
-.account-page-subscription div .subscribe_to_notes{
- color: #EB4335 !important;
- font-weight: 400 !important;
- border: unset !important;
- background-color: unset !important;
- vertical-align: top;
- padding: unset !important;
- box-shadow: unset !important;
-}
-.account-page-small-cards-container{
- display: flex;
- flex-wrap: wrap;
-}
-.account-page-submitted-ontology{
- background-color: #F6F6F6;
- padding: 10px;
- border-radius: 5px;
- margin-right: 10px;
- margin-top: 10px;
-}
-
-.account-page-submitted-ontology a{
- color: #777777 !important;
- font-weight: 500;
- font-size: 15px;
-}
-.no-margin{
- margin: 0 !important;
-}
-.change-password{
- margin-top: 14px;
- display: flex;
- justify-content: center;
+.account-page-select-ontology-set-button {
+ display: flex;
+ justify-content: space-between;
+ align-items: center;
+ width: 200px;
+ border: 1px solid var(--primary-color);
+ padding: 16px;
+ border-radius: 5px;
+ font-size: 16px;
+ font-weight: 500;
+ color: var(--primary-color);
}
+
+.account-page-select-ontology-set-button p {
+ margin-bottom: 0 !important;
+}
+
+.account-page-api-documentation-link {
+ display: flex;
+ margin-top: 10px;
+}
+
+.account-page-api-documentation-link a {
+ font-size: 15px;
+ font-weight: 500;
+ color: var(--primary-color);
+ text-decoration: none;
+}
+
+.account-page-api-documentation-link a svg {
+ margin-left: 10px;
+ margin-bottom: 5px;
+}
+
+.account-page-subscribe-button {
+ border: 1px solid var(--primary-color);
+ text-decoration: none;
+ color: var(--primary-color);
+ border-radius: 5px;
+ padding: 12px 20px;
+ font-size: 14px;
+ font-weight: 500;
+}
+
+.account-page-subscription {
+ margin-top: 10px;
+ display: flex;
+ justify-content: space-between;
+}
+
+.account-page-subscription a {
+ font-size: 15px;
+ font-weight: 400;
+ color: var(--primary-color);
+}
+
+.account-page-subscription > div {
+ display: flex;
+}
+
+.account-page-subscription div .notes {
+ margin-right: 23px;
+ color: #666666 !important;
+ font-weight: 400;
+}
+
+.account-page-subscription div .subscribe_to_notes {
+ color: var(--error-color) !important;
+ font-weight: 400 !important;
+ border: unset !important;
+ background-color: unset !important;
+ vertical-align: top;
+ padding: unset !important;
+ box-shadow: unset !important;
+}
+
+.account-page-small-cards-container {
+ display: flex;
+ flex-wrap: wrap;
+}
+
+.account-page-submitted-ontology {
+ background-color: #F6F6F6;
+ padding: 10px;
+ border-radius: 5px;
+ margin-right: 10px;
+ margin-top: 10px;
+}
+
+.account-page-submitted-ontology a {
+ color: #777777 !important;
+ font-weight: 500;
+ font-size: 15px;
+}
+
+.no-margin {
+ margin: 0 !important;
+}
+
+.change-password {
+ margin-top: 14px;
+ display: flex;
+ justify-content: center;
+}
+
@media only screen and (max-width: 1200px) {
- .account-page-first-row{
- width: 47vw;
- margin-right: 20px;
- }
-
- .account-page-second-row{
- width: 47vw;
- }
+ .account-page-first-row {
+ width: 47vw;
+ margin-right: 20px;
+ }
+
+ .account-page-second-row {
+ width: 47vw;
+ }
}
@media only screen and (max-width: 950px) {
- .account-page-first-row{
- width: 80vw;
- margin-right: 20px;
- }
-
- .account-page-second-row{
- width: 80vw;
- }
- .account-page-sub-container{
- display:block;
- }
+ .account-page-first-row {
+ width: 80vw;
+ margin-right: 20px;
+ }
+
+ .account-page-second-row {
+ width: 80vw;
+ }
+ .account-page-sub-container {
+ display: block;
+ }
}
\ No newline at end of file
diff --git a/app/assets/stylesheets/admin.scss b/app/assets/stylesheets/admin.scss
index 440605d04..c52a938c8 100644
--- a/app/assets/stylesheets/admin.scss
+++ b/app/assets/stylesheets/admin.scss
@@ -8,6 +8,27 @@
margin-bottom: 30px;
}
+.analytics {
+ .card-header-1{
+ color: white; font-size: 60px; font-weight: 600; word-wrap: break-word
+ }
+
+ .card-header-2{
+ color: white; font-size: 14px; font-weight: 400; word-wrap: break-word
+ }
+
+ .card-header-3{
+ color: white; opacity: 0.6; font-size: 14px; font-weight: 400; word-wrap: break-word
+ }
+}
+
+.yasgui .autocompleteWrapper, .yasgui .tabContextButton{
+ display: none !important;
+}
+.yasqe .yasqe_buttons .yasqe_share{
+ display: none !important;
+}
+
.alert-box span {
font-weight: bold;
text-transform: uppercase;
@@ -50,6 +71,7 @@ table.dataTable tbody tr.selected {
.ontologies_list_container {
padding: 1em;
+ position: relative;
}
/* Datatables */
@@ -106,10 +128,7 @@ table.dataTable tbody tr.selected {
display: none;
}
-/* to fix facebox default sizing in chrome */
-#facebox .body {
- width: 375px !important;
-}
+
.zebra td {
padding: 8px 12px 8px 12px !important;
@@ -133,9 +152,7 @@ table.dataTable tbody tr.selected {
}
.site-admin-page-section {
- display: flex;
margin-top: 15px;
-
.admin-action-item {
margin-right: 8px;
}
@@ -166,3 +183,8 @@ div.groupFormError {
padding-top: 3px;
}
+
+div.groupFormError {
+ color: red;
+ padding-top: 3px;
+}
\ No newline at end of file
diff --git a/app/assets/stylesheets/agent_tooltip.scss b/app/assets/stylesheets/agent_tooltip.scss
new file mode 100644
index 000000000..7460f746e
--- /dev/null
+++ b/app/assets/stylesheets/agent_tooltip.scss
@@ -0,0 +1,43 @@
+.agent-container{
+ display: flex;
+ align-items: center;
+ margin: 10px;
+}
+.agent-circle{
+ width: 70px;
+ height: 70px;
+ background-color: var(--light-color);
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ border-radius: 35px;
+ margin-right: 12px;
+}
+.agent-name{
+ font-size: 18px;
+ font-weight: 600;
+ margin-bottom: 3px;
+}
+.agent-dependency{
+ font-size: 16px;
+ font-weight: 400;
+ color: #767676;
+ margin-bottom: 5px;
+ display: flex;
+ align-items: center;
+}
+.agent-type-icon path{
+ fill: var(--primary-color)
+}
+.agent-dependency-icon{
+ width: 20px;
+ height: 20px;
+ margin-right: 5px;
+}
+.agent-dependency-icon.ror{
+ width: 30px;
+ height: 30px;
+}
+.agent-dependency-icon path{
+ fill: #C0C0C0
+}
\ No newline at end of file
diff --git a/app/assets/stylesheets/agents.scss b/app/assets/stylesheets/agents.scss
index c469fae57..08e47fb87 100644
--- a/app/assets/stylesheets/agents.scss
+++ b/app/assets/stylesheets/agents.scss
@@ -1,3 +1,32 @@
+.agents-inputs input {
+ @extend .form-control !optional;
+ height: 100% !important;
+}
+.agent-chip{
+ display: flex;
+ justify-content: center;
+ align-items: center;
+}
+
+.agent-chip-circle svg{
+ height: 15px;
+}
+
+.agent-chip-circle{
+ height: 30px;
+ width: 30px;
+ background-color: rgba(128, 128, 128, 0.08);
+ border-radius: 15px;
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ margin-right:10px;
+}
+
+.agent-chip-name{
+ color: #8C8E8D;
+ font-size: 15px;
+}
.agents-inputs input {
@extend .form-control !optional;
}
\ No newline at end of file
diff --git a/app/assets/stylesheets/annotator.scss b/app/assets/stylesheets/annotator.scss
index d07f55d7c..8cb42cc98 100644
--- a/app/assets/stylesheets/annotator.scss
+++ b/app/assets/stylesheets/annotator.scss
@@ -1,78 +1,236 @@
-div#semanticTypes_chzn.chzn-container input.default {
- font-style: oblique !important;
+.annotator-page-container{
+ display:flex;
+ justify-content:center;
}
-
-div#semanticTypes_chzn.chzn-container-active input.default {
- font-style: normal !important;
+.annotator-page-container a{
+ color: var(--primary-color) !important;
}
-
-div#annotations_filter, div#annotations_info {
- display: none;
+.annotator-page-subcontainer{
+ width: 1248px;
+ padding: 20px 50px;
}
-
-.result_count {
- font-weight: bold;
+.annotator-page-title{
+ font-size: 25px;
+ font-weight: 700;
+}
+.annotator-page-title .line{
+ height: 2px;
+ width: 57px;
+ background-color: var(--primary-color);
+ border-radius: 10px;
+}
+.annotator-page-decription{
+ color: #888888;
+ margin-top: 20px;
+}
+.annotator-page-inputs{
+ margin-top: 20px;
+}
+.annotator-page-inputs .inputs{
+ display: flex;
+}
+.annotator-page-text-area{
+ box-shadow: 2px 30px 60px rgba(0, 0, 0, 0.1);
+ border-radius: 8px;
+ width: 630px;
+ margin-right: 30px;
+}
+.annotator-page-text-area textarea{
+ font-size: 16px;
+ outline: none;
+ padding: 20px;
+ width: 630px;
+ border: none;
+ margin-right: 30px;
+}
+.annotator-page-text-area .insert-sample-text-button{
+ display: flex;
+ justify-content: flex-end;
+ padding: 10px 20px 20px 20px;
+}
+.annotator-page-text-area .insert-sample-text-button .button{
+ display: flex;
+ align-items: center;
+}
+.annotator-page-text-area .insert-sample-text-button .button:hover{
+ cursor: pointer;
+}
+.annotator-page-text-area .insert-sample-text-button .button .text{
+ font-size: 14px;
+ font-weight: 500;
+ color: var(--primary-color);
+ margin-right: 10px;
+}
+.annotator-page-text-area .insert-sample-text-button .button svg{
+ width: 16px;
+ height: 16px;
+}
+.annotator-page-text-area .insert-sample-text-button .button svg path{
+ fill: var(--primary-color);
+}
+.annotator-page-options{
+ width: 100%;
}
-#annotations th {
- padding-right: 6px;
+.annotator-page-options .section-text{
+ font-weight: 600;
+
+}
+.annotator-page-options .title{
+ margin-top: 10px;
+ color: #888888;
+ font-size: 14px;
+ font-weight: 500;
+ margin-bottom: 5px;
}
-#annotations span[class="popup_container"] {
- padding-left: 1.7em;
+.annotator-page-options .chips{
+ display: flex;
+}
+.annotator-page-options input{
+ accent-color: var(--primary-color) revert;
+}
+.annotator-page-options .radios{
+ display: flex;
}
-#annotator_parameters {
- color: gray;
- font-weight: bold;
+.annotator-page-options .advanced-options-button{
+ display: flex;
+ align-items: center;
+ margin-top: 15px;
+}
+.annotator-page-options .advanced-options-button:hover{
+ cursor: pointer;
+}
+.annotator-page-options .advanced-options-button .text{
+ margin-left: 10px;
+ color: var(--primary-color);
+ font-size: 14px;
}
-#annotations_container {
- display: none;
- margin-top: 10px;
- margin-bottom: 25px;
+.annotator-page-options .advanced-options-button svg path{
+ fill: var(--primary-color);
+}
+.annotator-page-button{
+ margin-top: 27px;
+ width: 630px;
}
-#annotations_container #result_counts {
- float: right;
- font-style: oblique;
+.annotator-page-options .chips{
+ display: flex;
+ flex-wrap: wrap;
+}
+.annotator-page-options .select-ontologies{
+ margin: 10px 0;
+}
+.annotator-page-options .preftitle{
+ font-size: 14px;
+ color: #666666;
+ margin-bottom: 5px;
+}
+.annotator-page-container .advanced-options-button{
+ color: var(--primary-color);
+ font-size: 14px;
+ margin-top: 5px !important;
+}
+.annotator-page-container .advanced-options-button:hover{
+ cursor: pointer;
+}
+.annotator-page-container .advanced-options-button svg{
+ margin-left: 5px;
+}
+.annotator-page-container .advanced-options-button svg path{
+ fill: var(--primary-color);
+}
+.annotator-page-container .advanced-options-button.hide-button svg{
+ transform: scaleY(-1);
+}
+.annotation-context{
color: gray;
+ font-weight: 400;
}
-
-#annotator-help i {
- margin-left: .25em;
+.annotator-page-container .highlighted-annotation{
+ color: black;
+ font-weight: 600;
+}
+.annotator-page-results .cont{
+ margin-top: 40px;
+ display: flex;
+ justify-content: space-between;
+ align-items: center;
+}
+.annotator-page-results .title{
+ font-size: 18px;
+ font-weight: 600;
+}
+.annotator-page-results .details{
+ color: #888888;
+}
+.annotator-page-container .more-advanced-options{
+ margin-top: 20px;
+}
+.annotator-page-container .more-advanced-options .filters_line{
+ display: flex;
+ margin-top: 20px;
+}
+.annotator-page-container .more-advanced-options .filters_line div{
+ width: 100%;
}
-/* AnnotatorPlus */
-
-.annotatorplus {
-
- #annotator-help > i.fa.fa-question-circle {
- margin-left: .25em;
- vertical-align: middle;
- }
-
- #download_links {
- margin-top: 1.5em;
- }
-
- #annotator_parameters {
- font-weight: normal;
- }
+.annotator-page-container .more-advanced-options .filters_line > :not(:first-child) {
+ margin-left: 20px;
+}
+.annotator-page-container .more-advanced-options .chips{
+ display: flex;
+ margin-top: 20px;
+}
+.annotation-parent{
+ display: flex;
+ white-space: nowrap;
+}
+.annotation-parent div, .annotation-parent a{
+ margin-right: 11px;
+}
+.annotation-parent .text{
+ margin-right: 8px;
+}
- .annotator_spinner {
- display: none;
-
- img {
- margin-left: 3px;
- vertical-align: middle;
- }
- }
+.annotation-parent a{
+ text-decoration: underline !important;
+}
+.annotator-page-options .prefrences{
+ margin-top: 10px;
+}
- .annotator_error {
- color: red;
- font-style: italic;
- margin-left: 3px;
- vertical-align: middle;
- }
-}
\ No newline at end of file
+.annotation-parent .level{
+ font-weight: 600;
+ color: var(--primary-color);
+}
+.annotation-parent .gray{
+ color: #888888;
+}
+.annotator-table-container{
+ margin-top: 20px;
+}
+.annotator-table-container .class{
+ width: 250px;
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+.annotation-parent + div{
+ margin-top: 5px;
+}
+.annotator-bottom-actions{
+ margin-top: 20px;
+ display: flex;
+}
+.annotator-bottom-actions div{
+ display: inline-block;
+}
+.annotator-bottom-actions div + div{
+ margin-left: 20px;
+}
+.annotator-bottom-actions .rdf-button svg, .annotator-doc svg{
+ width: 21px;
+}
diff --git a/app/assets/stylesheets/application.css.scss.erb b/app/assets/stylesheets/application.css.scss.erb
old mode 100644
new mode 100755
index 28f3f1469..65c233fbd
--- a/app/assets/stylesheets/application.css.scss.erb
+++ b/app/assets/stylesheets/application.css.scss.erb
@@ -11,16 +11,12 @@
*= require jquery-ui
*= require alertify
*= require chosen
- *= require facebox
- *= require fg.menu
*= require jquery-ui-1.8.1.custom
*= require jquery.autocomplete
- *= require jquery.rating
- *= require jquery.tooltip
- *= require thickbox
- *= require select2
*= require trumbowyg
+ *= require flag-icon
*= require theme-variables
+ *= require summary
*/
/* BioPortal */
@@ -37,19 +33,32 @@
@import "recommender";
@import "search";
@import "submissions";
-@import "tree";
@import "ontolobridge";
@import "fair_assement";
@import "instances_table";
-@import "file_uploader";
@import "register";
@import "lostpassword";
@import "flatpickr/dist/themes/light";
+@import "tom-select/dist/scss/tom-select";
+@import "tippy.js/dist/tippy";
+@import 'tippy.js/themes/light-border';
+@import '@triply/yasgui/build/yasgui.min';
+//@import 'highlight.js/styles/default.min';
+@import 'highlight.js/styles/intellij-light';
@import "feedback";
@import "login";
@import "components/index";
@import "account";
@import "agents";
+@import "upload_ontology";
+@import "edit-ontology";
+@import "nav_bar";
+@import "ontology_details_header";
+@import "ontology_viewer";
+@import "browse";
+@import "agent_tooltip";
+@import "content_finder";
+@import "tools";
/* Bootstrap and Font Awesome */
diff --git a/app/assets/stylesheets/bioportal.scss b/app/assets/stylesheets/bioportal.scss
index f3b3a6e25..a13fd8843 100644
--- a/app/assets/stylesheets/bioportal.scss
+++ b/app/assets/stylesheets/bioportal.scss
@@ -1,3 +1,18 @@
+.turbo-progress-bar {
+ height: 5px;
+ background-color: var(--admin-color);
+}
+
+a{
+ text-decoration: none !important;
+}
+p {
+ margin-bottom: 0;
+}
+
+body{
+ position: relative;
+}
.alignright {
float:right;
@@ -6,6 +21,73 @@
float:left;
}
+.admin-border{
+ border: 1px solid;
+ border-radius: 5px;
+ border-color: var(--admin-color) !important;
+}
+
+.admin-background{
+ background-color: var(--bg-info-light-color) !important;
+ border-color: var(--admin-color) !important;
+ color: var(--admin-color) !important;
+ border-radius: 5px;
+}
+
+.container-gradient {
+ background: linear-gradient(-45deg, var(--admin-color), var(--primary-color), var(--admin-color));
+ background-size: 400% 400%;
+ animation: gradient 15s ease infinite;
+ .header-component{
+ color: white;
+ }
+
+ .field-description_text{
+ color: white !important;
+ opacity: 0.7;
+ }
+
+}
+
+.disabled-link{
+ pointer-events: none;
+ color: #888888 !important;
+ span{
+ opacity: 0.6;
+ }
+ a {
+ color: #888888 !important;
+ }
+ svg path{
+ fill: #888888 !important;
+ }
+}
+.text-truncate-scroll{
+ overflow: scroll;
+ white-space: nowrap;
+}
+
+
+.bg-warning-light{
+ background-color: var(--bg-warning-light-color) !important;
+}
+
+.bg-danger-light{
+ background-color: var(--bg-danger-light-color) !important;
+}
+
+@keyframes gradient {
+ 0% {
+ background-position: 0% 50%;
+ }
+ 50% {
+ background-position: 100% 50%;
+ }
+ 100% {
+ background-position: 0% 50%;
+ }
+}
+
#hd {
background: image-url('layout/header_bg.png') repeat-x;
width: 100%;
@@ -474,11 +556,15 @@ tr.mainresource td {
margin-bottom: 1em;
}
-.feedback ul li, .enable-lists ul li {
+.enable-lists ul li {
list-style-position: outside;
list-style-type: square;
margin-left: 1.5em;
}
+.feedback ul li{
+ list-style-position: outside;
+ margin-left: 1.5em;
+}
.enable-lists ul {
margin-bottom: 15px;
@@ -498,7 +584,7 @@ tr.mainresource td {
}
.obsolete_class {
- color: rgb(100,100,100);
+ color: rgb(100,100,100)!important;
cursor: help;
font-style: oblique;
}
@@ -568,7 +654,8 @@ div.tree_error {
}
#bd ul.simpleTree li{
- margin-left:-10px;
+ margin-left: 0px;
+ padding: 5px 0 0 10px;
}
#bd ul.simpleTree{
@@ -586,6 +673,26 @@ div.tree_error {
overflow:auto;
border: 1px solid #444444;
*/
+ a.tree-link {
+ display: inline-block;
+ padding: 5px;
+ word-break: break-all;
+ text-wrap: wrap;
+ color: var(--primary-color) !important;
+ }
+
+ a.tree-link.active {
+ cursor: default;
+ background-color: var(--light-color);
+ font-weight: bold;
+ border-radius: 3px;
+ padding: 7px 5px;
+ }
+
+ .tree-border-left{
+ border-left: 2px dotted #eee;
+ margin-left: 2px;
+ }
}
.simpleTree li {
list-style: none;
@@ -958,27 +1065,6 @@ button.fg-button-menu, button.fg-button {
border: none;
}
-#ontology_picker_container div.chzn-container {
- width: 432px !important;
-}
-
-#ontology_picker_container div.chzn-container-active ul.chzn-choices li.search-field input {
- font-style: normal !important;
-}
-
-#ontology_picker_container div.chzn-container ul.chzn-choices {
- max-height: 110px;
- overflow: auto !important;
-}
-
-#ontology_picker_container div.chzn-container li.search-field input {
- font-style: oblique;
-}
-
-#ontology_picker_container div.chzn-drop {
- display: none;
-}
-
.no_right_border {
border-right: none !important;
}
@@ -1137,6 +1223,9 @@ a.truncated_less, a.truncated_more {
.highlighted .search_ontology_acronym {
color: white;
}
+.hide {
+ display: none !important;
+}
.empty-state {
display: none;
@@ -1158,3 +1247,7 @@ turbo-frame[busy] .hide-if-loading, .show-if-loading {
turbo-frame[busy] ~ .show-if-loading {
display: inline-block;
}
+
+.hide{
+ display:none;
+}
\ No newline at end of file
diff --git a/app/assets/stylesheets/browse.scss b/app/assets/stylesheets/browse.scss
new file mode 100644
index 000000000..2dc96db26
--- /dev/null
+++ b/app/assets/stylesheets/browse.scss
@@ -0,0 +1,656 @@
+
+.browse-container p {
+ margin: unset;
+}
+
+.browse-container h2 {
+ margin: unset;
+ line-height: unset;
+}
+
+.browse-container hr {
+ margin: unset;
+}
+
+.browse-center {
+ display: flex;
+ justify-content: center;
+ margin: 20px 50px 50px;
+}
+
+.browse-title {
+ font-size: 22px;
+ font-weight: 700;
+}
+
+.browse-submit-new-ontology-and-you-are-admin-container {
+ display: flex;
+ justify-content: center;
+ margin-bottom: 20px;
+ padding: 20px;
+ & > div {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ border-radius: 5px;
+ border: 1px solid #DFDFDF;
+ }
+
+}
+
+.browse-desc-text {
+ font-size: 16px;
+ color: #666666;
+ font-weight: 400;
+ margin: 5px 0 !important;
+ overflow: hidden;
+ display: -webkit-box;
+ -webkit-box-orient: vertical;
+ -webkit-line-clamp: var(--read-more-line-clamp, 2);
+}
+
+
+.browse-you-are-admin {
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ padding: 20px;
+ div {
+ display: flex;
+ align-items: center;
+ }
+}
+
+.browse-you-are-admin h3 {
+ font-size: 20px;
+ font-weight: 600;
+
+}
+
+.browse-you-are-admin div p {
+ margin-left: 20px;
+}
+
+.browse-upload-ontology-button {
+ margin: 20px 0;
+ display: flex;
+ justify-content: space-between;
+ align-items: center;
+ font-size: 15px;
+ font-weight: 500;
+ color: var(--primary-color);
+ width: 226px;
+ padding: 15px 25px;
+ border: 1px solid var(--primary-color);
+ border-radius: 40px;
+}
+
+.browse-show-more-button {
+ cursor: pointer;
+ font-size: 14px;
+ color: gray;
+ margin-bottom: 10px;
+}
+
+.browse-ontology-container {
+ border: 1px solid #DFDFDF;
+ border-radius: 5px;
+ padding: 15px 20px;
+ margin-bottom: 20px;
+ position: relative;
+ box-shadow: rgba(100, 100, 111, 0.08) 0 7px 29px 0;
+}
+
+.browse-ontology-description {
+ width: 540px;
+}
+
+.browse-ontology-title {
+ color: var(--primary-color) !important;
+ font-weight: 600;
+ font-size: 18px;
+}
+
+.browse-fair {
+ display: flex;
+ align-items: center;
+ justify-content: space-between;
+ width: 400px;
+}
+
+.browse-sub-container {
+ display: flex;
+}
+
+.browse-first-row {
+ width: 300px;
+ margin-right: 35px;
+
+ .pill-button {
+ width: 100%;
+ justify-content: center;
+ }
+}
+
+.browse-second-row {
+ width: 828px;
+
+ .browse-ontologies {
+ margin-top: 90px;
+ }
+
+}
+
+#browse-title-line {
+ width: 55px;
+ margin-top: 3px;
+ border: 0.5px solid var(--primary-color);
+ border-radius: 5px;
+}
+
+.browse-fair-title {
+ font-size: 16px;
+ color: #666666;
+ font-weight: 400;
+}
+
+.browse-progress-bar {
+ width: 154px;
+ height: 10px;
+ border-radius: 20px;
+ background-color: #E7E7E7;
+
+}
+
+.browse-faire-progress {
+ width: 100%;
+ height: 10px;
+ background-color: var(--primary-color);
+ border-radius: 20px 0px 0px 20px;
+}
+
+.browse-fair-score {
+ font-size: 14px;
+ font-weight: 500;
+ color: #666666;
+}
+
+.browse-fair-details {
+ font-size: 14px;
+ font-weight: 400;
+ color: var(--primary-color) !important;
+}
+
+.browse-uploaded {
+ font-size: 13px;
+ height: 37px;
+ max-width: 400px;
+ background-color: var(--light-color);
+ border-radius: 5px;
+ display: flex;
+ padding: 2px 15px;
+ justify-content: space-between;
+ align-items: center;
+ color: var(--primary-color);
+ margin-top: 15px;
+}
+
+.browse-uploaded-date {
+ white-space: nowrap;
+}
+
+.browse-ontology-cards {
+ display: grid;
+ grid-template-columns: 113px 113px;
+ grid-template-rows: min-content;
+ grid-column-gap: 15px;
+ grid-row-gap: 15px;
+ direction: rtl;
+}
+
+.browse-onology-card {
+ border: 0.5px solid var(--primary-color);
+ border-radius: 5px;
+ height: 70px;
+ width: 100px;
+ display: flex;
+ flex-direction: column;
+ align-items: center;
+ justify-content: center;
+ color: var(--primary-color) !important;
+}
+
+.browse-card-number {
+ font: 17px;
+ font-weight: 700;
+}
+
+.browse-card-text {
+ font-size: 15px;
+ font-weight: 500;
+}
+
+#browse-sub-title-line {
+ width: 20px;
+ margin-top: 3px;
+ border: 0.5px solid var(--primary-color);
+ border-radius: 5px;
+ margin-bottom: 15px;
+}
+
+.browse-filters-title {
+ font-weight: 600;
+ font-size: 16px;
+ text-decoration: underline;
+ text-underline-offset: 12px;
+ text-decoration-color: var(--primary-color);
+ text-decoration-thickness: 2px;
+ margin-bottom: 13px !important;
+}
+
+.browse-search-bar {
+ display: flex;
+
+}
+
+.browse-search-bar input {
+ border-radius: 14px;
+ box-shadow: rgba(100, 100, 111, 0.08) 0 7px 29px 0;
+ border: none;
+ // border: 1px solid #dee2e6;
+ padding: 20px 20px;
+ margin-bottom: 20px;
+ font-size: 16px;
+ position: absolute;
+ width: 828px;
+ z-index: 1;
+
+}
+
+.browse-search-bar input:focus {
+ box-shadow: rgba(100, 100, 111, 0.2) 0px 7px 29px 0px;
+ outline: none;
+}
+
+.browse-search-bar select {
+ border: none;
+ background-color: white;
+ padding: 20px 20px;
+ margin: 1px;
+ font-size: 16px;
+ background-image: url("data:image/svg+xml;utf8,#{selected} ".html_safe if obsolete
+ selected
+ end
+
+ def ontology_name_acronym(ontologies, selected_acronym)
+ ontology = ontologies.select { |x| x.acronym.eql?(selected_acronym.split('/').last) }.first
+ "#{ontology.name} (#{ontology.acronym})"
+ end
+
+ def aggregate_by_ontology(results)
+ ontologies = {}
+
+ results.each do |res|
+ ont = res.links['ontology']
+ unless ontologies[ont]
+ ontologies[ont] = {
+ # classes with same URI
+ same_cls: [],
+ # other classes from the same ontology
+ same_ont: [],
+ # subordinate ontologies
+ sub_ont: []
+ }
+ end
+ ontologies[ont][:same_ont] << res
+ end
+ ontologies.values
+ end
+
+ def add_subordinate_ontologies(query, ontologies)
+ # get for each concept his main ontology parent
+ concepts_ontology_owner = extract_concepts_owners(ontologies, query)
+
+ # aggregate the subordinate results below the owner ontology results
+ subordinate_ontologies = []
+ ontologies.each_with_index do |ont, i|
+ cls_id = ont[:same_ont].first["@id"]
+
+ if concepts_ontology_owner.has_key?(cls_id)
+ # get the ontology that owns this class (if any)
+ ont_owner = concepts_ontology_owner[cls_id]
+ if ont_owner[:index].eql?(i)
+ # the current ontology is the owner of this primary result
+ subordinate_ontologies.push(ont)
+ else
+ # There is an owner, so put this ont result set into the sub_ont array of the owner
+ real_owner = ontologies[ont_owner[:index]]
+ real_owner[:sub_ont].push(ont)
+ end
+ else
+ # There is no ontology that owns this primary class result, just
+ # display this at the top level (it's not a subordinate)
+ subordinate_ontologies.push(ont)
+ end
+ end
+ subordinate_ontologies
+ end
+
+ def extract_concepts_owners(ontologies, query)
+ cls_ont_owner_tracker = {}
+ ontologies.each do |ont|
+ ont[:sub_ont] = [] # array for any subordinate ontology results regrouping the concept reuses
+
+ cls_id = ont[:same_ont].first["@id"]
+ next if cls_ont_owner_tracker.has_key?(cls_id)
+
+ # find the best match for the ontology owner (must iterate over all acronyms)
+ ont_owner = ontology_owner_of_class(cls_id, ontologies, query)
+
+ # This primary class result is owned by an ontology
+ cls_ont_owner_tracker[cls_id] = ont_owner if ont_owner[:index]
+ end
+ cls_ont_owner_tracker
+ end
+
+ def extract_back_list_words(acronyms, query)
+ blacklist_words = []
+ query.split(/\s+/).each_with_index do |search_word, i|
+ # Convert blacklist_search_words_arr to regex constructs so they are removed
+ # with case-insensitive matches in blacklist_cls_id_components
+ blacklist_words.push(Regexp.new(search_word, Regexp::IGNORECASE))
+
+ # Check for any substring matches against ontology acronyms, where the
+ # acronyms are assumed to be upper case strings.
+ # Note: We cannot use the ont_acronyms array .index method because it doesn't search for substring matches.
+ search_token = search_word
+ match = false
+
+ acronyms.each do |acronym|
+ match = acronym.include?(search_token)
+ break if match
+ end
+
+ # Remove this blacklisted search token because it matches or partially matches an ontology acronym.
+ blacklist_words.delete_at(i) if match
+ end
+ blacklist_words
+ end
+
+ def ontology_owner_of_class(cls_id, ontologies, query)
+ acronyms = ontologies.map { |ont| ont[:same_ont].first.links['ontology'].split('/').last }
+
+ # Remove any items in blacklistSearchWordsArr that match ontology acronyms.
+ # TODO make sure this is really useful
+ blacklist_words = extract_back_list_words(acronyms, query)
+
+ ont_owner = {
+ acronym: "",
+ index: nil,
+ weight: 0
+ }
+
+ acronyms.each_with_index do |acronym, i|
+ if ontology_own_class?(cls_id, acronym, blacklist_words)
+ weight = acronym.size * (cls_id.upcase.rindex(acronym) + 1)
+ if weight > ont_owner[:weight]
+ ont_owner = {
+ acronym: acronym,
+ index: i,
+ weight: weight
+ }
+ # Cannot break here, in case another acronym has greater weight.
+ end
+ end
+ end
+
+ ont_owner
+ end
+
+ def ontology_own_class?(cls_id, acronym, blacklist_words)
+ cls_id = blacklist_cls_id_components(cls_id.dup, blacklist_words)
+
+ cls_id.upcase.include?(acronym)
+ end
+
+ def blacklist_cls_id_components(cls_id, blacklist_words)
+
+ stripped_id = cls_id
+
+ # Remove fixed strings first
+ BLACKLIST_FIX_STR.each do |fixed_str|
+ stripped_id.gsub!(fixed_str, "")
+ end
+
+ # Cleanup with regex replacements
+ BLACKLIST_REGEX.each do |regex|
+ stripped_id.gsub!(regex, "")
+ end
+
+ # Remove search keywords (see perform_search and aggregate_results_with_subordinate_ontologies)
+ blacklist_words.each do |search_word_regex|
+ stripped_id.gsub!(search_word_regex, "")
+ end
+
+ stripped_id
+ end
+end
+
diff --git a/app/controllers/concerns/search_content.rb b/app/controllers/concerns/search_content.rb
new file mode 100644
index 000000000..e8fd48a59
--- /dev/null
+++ b/app/controllers/concerns/search_content.rb
@@ -0,0 +1,181 @@
+module SearchContent
+ extend ActiveSupport::Concern
+
+ def search_ontologies(query: '*', groups: [], categories: [], languages: [], private_only: false, formats: [],
+ is_of_type: [], formality_level: [],
+ show_views: false, status: 'alpha,beta,production',
+ page: 1, page_size: 10)
+
+ visibility = private_only ? "private" : 'public'
+ qf = [
+ "ontology_acronymSuggestEdge^25 ontology_nameSuggestEdge^15 descriptionSuggestEdge^10 ", # start of the word first
+ "ontology_acronym_text^15 ontology_name_text^10 description_text^5 "
+ ]
+ submissions = LinkedData::Client::HTTP.get('search/ontologies',
+ { query: query.blank? ? "*" : query,
+ groups: groups,
+ hasDomain: categories,
+ hasOntologyLanguage: formats,
+ status: status,
+ page: page, pagesize: page_size,
+ visibility: visibility,
+ isOfType: is_of_type,
+ hasFormat: formality_level,
+ show_views: show_views,
+ qf: qf, # custom ranking
+ languages: languages }
+ .reject { |k, v| v.blank? })
+
+ submissions = submissions.collection
+
+ submissions.map do |os|
+ transformed_os = OpenStruct.new
+ ontology = OpenStruct.new
+ metrics = OpenStruct.new
+ os.each_pair do |key, value|
+ if key.to_s.start_with?("ontology_")
+ ontology[key.to_s.sub("ontology_", "").gsub(/_.*\z/, "")] = value
+ elsif key.to_s.start_with?("metrics_")
+ metrics[key.to_s.sub("metrics_", "").gsub(/_.*\z/, "")] = value
+ elsif key != :links && key != :context
+ new_key = key.to_s.gsub(/_.*\z/, "")
+ transformed_os[new_key] = value
+ end
+ end
+ transformed_os[:ontology] = ontology unless ontology.to_h.empty?
+ transformed_os[:metrics] = metrics unless metrics.to_h.empty?
+ transformed_os
+ end
+ end
+
+ def search_ontologies_content(query:, page: 1, page_size: 10, filter_by_ontologies: [], filter_by_types: [])
+ acronyms = filter_by_ontologies
+ original_query = query
+ types = filter_by_types
+ query = query.gsub(':', '\:').gsub('/', '\/') if page.eql?(1)
+
+ qf = [
+ "ontology_t^100 resource_id^10",
+ "http___www.w3.org_2004_02_skos_core_prefLabel_txt^30",
+ "http___www.w3.org_2004_02_skos_core_prefLabel_t^30",
+ "http___www.w3.org_2000_01_rdf-schema_label_txt^30",
+ "http___www.w3.org_2000_01_rdf-schema_label_t^30",
+ ]
+ ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name,viewOf', also_include_views: true)
+ selected_onto = []
+
+ q = query.split(' ').first || ''
+ selected_onto += ontologies.select { |x| (acronyms.empty? && x.acronym.downcase.eql?(q.downcase)) || acronyms.include?(x.acronym) }
+
+ selected_onto.uniq!
+ [selected_onto.first].compact.each do |o|
+ acr = o.acronym
+ acronyms << acr
+ query.gsub!(/\b#{acr}\b/, "")
+ query.gsub!(/\b#{acr.downcase}\b/, "")
+ query.gsub!('-', " ")
+ end
+
+ query = query
+ if query.blank?
+ query = "*"
+ elsif query.split(' ').size > 1
+ query = "^#{query}*"
+ else
+ query = "*#{query}*"
+ end
+
+ results = search_content( q: query, qf: qf.join(' '), page: page, pagesize: page_size, ontologies: acronyms.first, types: types.join(','))
+ [search_content_result_to_json(original_query, query, results, ontologies, selected_onto), results.page,results.nextPage, results.totalCount]
+ end
+
+
+
+ def search_content(params)
+ LinkedData::Client::HTTP.get('search/ontologies/content', params)
+ end
+
+ private
+
+ def search_content_result_to_json(query, changed_query, results, ontologies, selected_onto = [])
+ json = []
+ selected_onto = selected_onto.empty? ? ontologies.select { |x| x.name.downcase.include?(query.downcase) || x.acronym.downcase.include?(query.downcase) } : selected_onto
+
+ json += selected_onto.map do |x|
+ {
+ id: ontology_path(id: x.acronym, p: 'summary'),
+ name: x.name,
+ acronym: x.acronym,
+ type: x.viewOf.blank? ? 'Ontology' : 'Ontology View',
+ label: nil
+ }
+ end
+
+ changed_query.gsub!('*', '')
+
+ json += results.collection.map do |x|
+ acronym = x.ontology_t || x.submission_id_t.split('/')[-3]
+ next nil unless acronym
+
+ label = nil
+ [
+ "http___www.w3.org_2000_01_rdf-schema_label_t",
+ "http___www.w3.org_2000_01_rdf-schema_label_txt",
+ "http___www.w3.org_2004_02_skos_core_prefLabel_t",
+ "http___www.w3.org_2004_02_skos_core_prefLabel_txt",
+ ].each do |v|
+ v = Array(x[v])
+ selected_label = v&.select { |p| p.downcase[changed_query.strip.downcase] || changed_query.downcase[p.strip.downcase] }&.first
+ label = selected_label if selected_label
+ label ||= v&.first
+ end
+
+
+ type = id_type(x.type_t, x.type_txt)
+ {
+ id: link_by_type(x.resource_id, acronym, type),
+ name: x.resource_id,
+ acronym: acronym,
+ type: type || '',
+ label: label
+ }
+ end.compact
+
+ json
+ end
+
+ def supported_types
+ %w[Concept Class Ontology ConceptScheme Collection NamedIndividual AnnotationProperty ObjectProperty DatatypeProperty]
+ end
+
+ def id_type(type_t, type_txt)
+
+ type = (Array(type_t) + Array(type_txt)).map { |x| helpers.link_last_part(x) }
+ .select{|x| supported_types.include?(x)}
+
+ type = Array(type).reject { |x| x.eql?("NamedIndividual") } if (Array(type).size > 1)
+
+ type.first
+ end
+
+ def link_by_type(id, ontology, type)
+ case type
+ when 'Concept', 'Class'
+ ontology_path(id: ontology, p: 'classes', conceptid: id)
+ when 'Ontology'
+ ontology_path(id: ontology, p: 'summary')
+ when 'ConceptScheme'
+ ontology_path(id: ontology, p: 'schemes', schemeid: id)
+ when 'Collection'
+ ontology_path(id: ontology, p: 'collections', collectionid: id)
+ when 'NamedIndividual'
+ ontology_path(id: ontology, p: 'instances', instanceid: id)
+ when 'AnnotationProperty', 'ObjectProperty', 'DatatypeProperty'
+ ontology_path(id: ontology, p: 'properties', propertyid: id)
+ else
+ "/content_finder?acronym=#{ontology}&uri=#{helpers.escape(id)}&output_format=html"
+ end
+ end
+
+end
+
diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
new file mode 100644
index 000000000..44d4f6e52
--- /dev/null
+++ b/app/controllers/concerns/submission_filter.rb
@@ -0,0 +1,383 @@
+module SubmissionFilter
+ extend ActiveSupport::Concern
+
+ include SearchContent
+
+ BROWSE_ATTRIBUTES = ['ontology', 'submissionStatus', 'description', 'pullLocation', 'creationDate',
+ 'contact', 'released', 'naturalLanguage', 'hasOntologyLanguage',
+ 'hasFormalityLevel', 'isOfType', 'deprecated', 'status', 'metrics']
+
+ def init_filters(params)
+ @show_views = params[:show_views]&.eql?('true')
+ @show_private_only = params[:private_only]&.eql?('true')
+ @show_retired = params[:show_retired]&.eql?('true')
+ @selected_format = params[:format]
+ @sort_by = params[:sort_by].blank? ? 'visits' : params[:sort_by]
+ @search = params[:search]
+ end
+
+ def submissions_paginate_filter(params)
+ request_params = filters_params(params, page: params[:page], pagesize: 10)
+ filter_params = params.permit(@filters.keys).to_h
+ init_filters(params)
+
+ @analytics = Rails.cache.fetch("ontologies_analytics-#{Time.now.year}-#{Time.now.month}") do
+ helpers.ontologies_analytics
+ end
+
+ @ontologies = LinkedData::Client::Models::Ontology.all(include: 'all', also_include_views: true, display_links: false, display_context: false)
+
+ # get fair scores of all ontologies
+ @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil
+
+ @total_ontologies = @ontologies.size
+ search_backend = params[:search_backend]
+ params = { query: @search,
+ status: request_params[:status],
+ show_views: @show_views,
+ private_only: @show_private_only,
+ languages: request_params[:naturalLanguage],
+ page_size: @total_ontologies,
+ formality_level: request_params[:hasFormalityLevel],
+ is_of_type: request_params[:isOfType],
+ groups: request_params[:group], categories: request_params[:hasDomain],
+ formats: request_params[:hasOntologyLanguage] }
+
+
+ if search_backend.eql?('index')
+ submissions = filter_using_index(**params)
+ submissions = @ontologies.map{ |ont| ontology_hash(ont, submissions) }
+ else
+ submissions = filter_using_data(@ontologies, **params)
+ end
+
+ submissions = sort_submission_by(submissions, @sort_by, @search)
+
+
+ @page = paginate_submissions(submissions, request_params[:page].to_i, request_params[:pagesize].to_i)
+
+ count = @page.page.eql?(1) ? count_objects(submissions) : {}
+
+ [@page.collection, @page.totalCount, count, filter_params]
+ end
+
+ def ontologies_filter_url(filters, page: 1, count: false)
+ helpers.ontologies_filter_url(filters, page: page, count: count)
+ end
+
+ private
+
+ def filter_using_index(query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
+ search_ontologies(
+ query: query,
+ status: status,
+ show_views: show_views,
+ private_only: private_only,
+ languages: languages,
+ page_size: page_size,
+ formality_level: formality_level,
+ is_of_type: is_of_type,
+ groups: groups, categories: categories,
+ formats: formats
+ )
+
+ end
+
+ def filter_using_data(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
+ submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
+ submissions = ontologies.map { |ont| ontology_hash(ont, submissions) }
+
+ submissions.map do |s|
+ out = ((s.ontology.viewingRestriction.eql?('public') && !private_only) || private_only && s.ontology.viewingRestriction.eql?('private'))
+ out = out && (groups.blank? || (s.ontology.group.map { |x| helpers.link_last_part(x) } & groups.split(',')).any?)
+ out = out && (categories.blank? || (s.ontology.hasDomain.map { |x| helpers.link_last_part(x) } & categories.split(',')).any?)
+ out = out && (status.blank? || status.eql?('alpha,beta,production,retired') || status.split(',').include?(s.status))
+ out = out && (formats.blank? || formats.split(',').any? { |f| s.hasOntologyLanguage.eql?(f) })
+ out = out && (is_of_type.blank? || is_of_type.split(',').any? { |f| helpers.link_last_part(s.isOfType).eql?(f) })
+ out = out && (formality_level.blank? || formality_level.split(',').any? { |f| helpers.link_last_part(s.hasFormalityLevel).eql?(f) })
+ out = out && (languages.blank? || languages.split(',').any? { |f| s.naturalLanguage.any? { |n| helpers.link_last_part(n).eql?(f) } })
+ out = out && (s.ontology.viewOf.blank? || (show_views && !s.ontology.viewOf.blank?))
+
+ out = out && (query.blank? || [s.description, s.ontology.name, s.ontology.acronym].any? { |x| (x|| '').downcase.include?(query.downcase) })
+
+ if out
+ s[:rank] = 0
+
+ next s if query.blank?
+
+ s[:rank] += 3 if s.ontology.acronym && s.ontology.acronym.downcase.include?(query.downcase)
+
+ s[:rank] += 2 if s.ontology.name && s.ontology.name.downcase.include?(query.downcase)
+
+ s[:rank] += 1 if s.description && s.description.downcase.include?(query.downcase)
+
+ s
+ else
+ nil
+ end
+
+ end.compact
+ end
+
+ def paginate_submissions(all_submissions, page, size)
+ current_page = page
+ page_size = size
+
+ start_index = (current_page - 1) * page_size
+ end_index = start_index + page_size - 1
+ next_page = current_page * page_size < all_submissions.size ? current_page + 1 : nil
+ OpenStruct.new(page: current_page, nextPage: next_page, totalCount: all_submissions.size,
+ collection: all_submissions[start_index..end_index])
+ end
+
+ def sort_submission_by(submissions, sort_by, query = nil)
+ return submissions.sort_by { |x| x[:rank] ? -x[:rank] : 0} unless query.blank?
+
+ if sort_by.eql?('visits')
+ submissions = submissions.sort_by { |x| -(x[:popularity] || 0) }
+ elsif sort_by.eql?('fair')
+ submissions = submissions.sort_by { |x| -x[:fairScore] }
+ elsif sort_by.eql?('notes')
+ submissions = submissions.sort_by { |x| -x[:note_count] }
+ elsif sort_by.eql?('projects')
+ submissions = submissions.sort_by { |x| -x[:project_count] }
+ elsif sort_by.eql?('metrics_classes')
+ submissions = submissions.sort_by { |x| -x[:class_count] }
+ elsif sort_by.eql?('metrics_individuals')
+ submissions = submissions.sort_by { |x| -x[:individual_count] }
+ elsif sort_by.eql?('creationDate')
+ submissions = submissions.sort_by { |x| x[:creationDate] || '' }.reverse
+ elsif sort_by.eql?('released')
+ submissions = submissions.sort_by { |x| x[:released] || '' }.reverse
+ elsif sort_by.eql?('ontology_name')
+ submissions = submissions.sort_by { |x| -x[:name] }
+ end
+ submissions
+ end
+
+ def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pagesize: 5)
+ request_params = { display_links: false, display_context: false,
+ include: includes, include_status: 'RDF' }
+ request_params.merge!(page: page.to_i, pagesize: pagesize.to_i) if page
+ filters_values_map = {
+ categories: :hasDomain,
+ groups: :group,
+ naturalLanguage: :naturalLanguage,
+ isOfType: :isOfType,
+ format: :hasOntologyLanguage,
+ hasFormalityLevel: :hasFormalityLevel,
+ search: %i[name acronym description],
+ sort_by: :order_by
+ }
+
+ filters_boolean_map = {
+ show_views: { api_key: :also_include_views, default: 'true' },
+ private_only: { api_key: :viewingRestriction, default: 'private' },
+ show_retired: { api_key: :status, default: 'retired' }
+ }
+ @filters = {}
+
+ filters_boolean_map.each do |k, v|
+ next unless params[k].eql?('true') || params[k].eql?(v[:default])
+
+ @filters.merge!(k => v[:default])
+ request_params.merge!(v[:api_key] => v[:default])
+ end
+
+ if params[:show_retired].blank?
+ @filters[:show_retired] = ''
+ request_params[:status] = 'alpha,beta,production'
+ else
+ request_params[:status] = 'alpha,beta,production,retired'
+ @filters[:show_retired] = 'true'
+ end
+
+ filters_values_map.each do |filter, api_key|
+ next if params[filter].nil? || params[filter].empty?
+
+ @filters.merge!(filter => params[filter])
+ Array(api_key).each do |key|
+ request_params.merge!(key => params[filter])
+ end
+ end
+
+ unless params[:sort_by].blank?
+ @filters[:sort_by] = params[:sort_by]
+ end
+
+ unless params[:search].blank?
+ @filters[:search] = params[:search]
+ end
+
+ request_params.delete(:order_by) if %w[visits fair].include?(request_params[:sort_by].to_s)
+ request_params
+ end
+
+ def ontology_hash(ont, submissions)
+ o = {}
+ sub = submissions.select{|x| x.ontology&.id.eql?(ont.id)}.first
+
+ o[:ontology] = ont
+
+ add_ontology_attributes(o, ont)
+ add_submission_attributes(o, sub)
+ add_fair_score_metrics(o, ont)
+
+ o[:hasOntologyLanguage] = sub&.hasOntologyLanguage
+
+ if sub&.metrics
+ o[:class_count] = sub.metrics.classes
+ o[:individual_count] = sub.metrics.individuals
+ else
+ o[:class_count] = 0
+ o[:individual_count] = 0
+ end
+ o[:class_count_formatted] = number_with_delimiter(o[:class_count], delimiter: ',')
+ o[:individual_count_formatted] = number_with_delimiter(o[:individual_count], delimiter: ',')
+
+ o[:note_count] = ont.notes&.length || 0
+ o[:project_count] = ont.projects&.length || 0
+ o[:popularity] = @analytics[ont.acronym] || 0
+ o[:rank] = sub&[:rank] || 0
+
+ OpenStruct.new(o)
+ end
+
+ def add_submission_attributes(ont_hash, sub)
+ return if sub.nil?
+
+ ont_hash[:submissionStatus] = sub.submissionStatus
+ ont_hash[:deprecated] = sub.deprecated
+ ont_hash[:status] = sub.status
+ ont_hash[:submission] = true
+ ont_hash[:pullLocation] = sub.pullLocation
+ ont_hash[:description] = sub.description
+ ont_hash[:creationDate] = sub.creationDate
+ ont_hash[:released] = sub.released
+ ont_hash[:naturalLanguage] = sub.naturalLanguage
+ ont_hash[:hasFormalityLevel] = sub.hasFormalityLevel
+ ont_hash[:isOfType] = sub.isOfType
+ ont_hash[:submissionStatusFormatted] = submission_status2string(sub).gsub(/\(|\)/, '')
+ ont_hash[:format] = sub.hasOntologyLanguage&.split('/').last
+ ont_hash[:contact] = sub.contact.map { |c| c.is_a?(String) ? c.split('|').first : c.name }.first unless sub.contact.nil?
+ end
+
+ def add_ontology_attributes(ont_hash, ont)
+ return if ont.nil?
+
+ ont_hash[:id] = ont.id
+ ont_hash[:type] = ont.viewOf.nil? ? 'ontology' : 'ontology_view'
+ ont_hash[:show] = ont.viewOf.nil? ? true : false # show ontologies only by default
+ ont_hash[:groups] = ont.group || []
+ ont_hash[:categories] = ont.hasDomain || []
+ ont_hash[:private] = ont.private?
+ ont_hash[:submissionStatus] = []
+ ont_hash[:administeredBy] = ont.administeredBy
+ ont_hash[:name] = ont.name
+ ont_hash[:acronym] = ont.acronym
+ ont_hash[:projects] = ont.projects
+ ont_hash[:notes] = ont.notes
+ ont_hash[:viewOfOnt] = ont.viewOf
+ end
+
+ def add_fair_score_metrics(ont_hash, ont)
+ if !@fair_scores.nil? && !@fair_scores[ont.acronym].nil?
+ ont_hash[:fairScore] = @fair_scores[ont.acronym]['score']
+ ont_hash[:normalizedFairScore] = @fair_scores[ont.acronym]['normalizedScore']
+ else
+ ont_hash[:fairScore] = 0
+ ont_hash[:normalizedFairScore] = 0
+ end
+ end
+
+ def ontology_filters_init(categories, groups)
+ @languages = submission_metadata.select { |x| x['@id']['naturalLanguage'] }.first['enforcedValues'].map do |id, name|
+ { 'id' => id, 'name' => name, 'value' => id.split('/').last, 'acronym' => name }
+ end
+
+ @formalityLevel = submission_metadata.select { |x| x['@id']['hasFormalityLevel'] }.first['enforcedValues'].map do |id, name|
+ { 'id' => id, 'name' => helpers.link_last_part(id), 'acronym' => name, 'value' => helpers.link_last_part(id) }
+ end
+
+ @isOfType = submission_metadata.select { |x| x['@id']['isOfType'] }.first['enforcedValues'].map do |id, name|
+ { 'id' => id, 'name' => helpers.link_last_part(id), 'acronym' => name, 'value' => helpers.link_last_part(id) }
+ end
+
+ @formats = [[t("submissions.filter.all_formats"), ''], 'OBO', 'OWL', 'SKOS', 'UMLS']
+ @sorts_options = [
+ [t("submissions.filter.sort_by_name"), 'ontology_name'],
+ [t("submissions.filter.sort_by_classes"), 'metrics_classes'],
+ [t("submissions.filter.sort_by_instances_concepts"), 'metrics_individuals'],
+ [t("submissions.filter.sort_by_submitted_date"), 'creationDate'],
+ [t("submissions.filter.sort_by_creation_date"), 'released'],
+ [t("submissions.filter.sort_by_fair_score"), 'fair'],
+ [t("submissions.filter.sort_by_popularity"), 'visits'],
+ [t("submissions.filter.sort_by_notes"), 'notes'],
+ [t("submissions.filter.sort_by_projects"), 'projects'],
+ ]
+
+ init_filters(params)
+ # @missingStatus = [
+ # {'id' => 'RDF', 'name' => 'RDF', 'acronym' => 'RDF'},
+ # {'id' => 'ABSOLETE', 'name' => 'ABSOLETE', 'acronym' => 'ABSOLETE'},
+ # {'id' => 'METRICS', 'name' => 'METRICS', 'acronym' => 'METRICS'},
+ # {'id' => 'RDF_LABELS', 'name' => 'RDF LABELS', 'acronym' => 'RDFLABELS'},
+ # {'id' => 'UPLOADED', 'name' => 'UPLOADED', 'acronym' => 'UPLOADED'},
+ # {'id' => 'INDEXED_PROPERTIES', 'name' => 'INDEXED PROPERTIES', 'acronym' => 'INDEXED_PROPERTIES'},
+ # {'id' => 'ANNOTATOR', 'name' => 'ANNOTATOR', 'acronym' => 'ANNOTATOR'},
+ # {'id' => 'DIFF', 'name' => 'DIFF', 'acronym' => 'DIFF'}
+ # ]
+
+ {
+ categories: object_filter(categories, :categories),
+ groups: object_filter(groups, :groups),
+ naturalLanguage: object_filter(@languages, :naturalLanguage, "value"),
+ hasFormalityLevel: object_filter(@formalityLevel, :hasFormalityLevel),
+ isOfType: object_filter(@isOfType, :isOfType, "value"),
+ # missingStatus: object_filter(@missingStatus, :missingStatus)
+ }
+ end
+
+ def check_id(name_value, objects, name_key)
+ selected_category = objects.select { |x| x[name_key].parameterize.underscore.eql?(name_value.parameterize.underscore) }
+ selected_category.first && selected_category.first['id']
+ end
+
+
+ def object_filter(objects, object_name, name_key = 'acronym')
+ checks = params[object_name]&.split(',') || []
+ checks = checks.map { |x| check_id(x, objects, name_key) }.compact
+
+ ids = objects.map { |x| x['id'] }
+ count = ids.count { |x| checks.include?(x) }
+ [objects, checks, count]
+ end
+
+ def count_objects(ontologies)
+ objects_count = {}
+ @categories = LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
+ @groups = LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
+
+ @filters = ontology_filters_init(@categories, @groups)
+ object_names = @filters.keys
+
+ @filters.each do |filter, values|
+ objects = values.first
+ objects_count[filter] = objects.map { |v| [v['id'], 0] }.to_h
+ end
+
+ ontologies.each do |ontology|
+ object_names.each do |name|
+ values = Array(ontology[name])
+ values.each do |v|
+ v.gsub!('http://data.bioontology.org', rest_url)
+
+ objects_count[name] = {} unless objects_count[name]
+ objects_count[name][v] = (objects_count[name][v] || 0) + 1
+ end
+ end
+ end
+ objects_count
+ end
+
+end
diff --git a/app/controllers/concerns/submission_updater.rb b/app/controllers/concerns/submission_updater.rb
index 4f330ad95..0120ef33e 100644
--- a/app/controllers/concerns/submission_updater.rb
+++ b/app/controllers/concerns/submission_updater.rb
@@ -1,24 +1,27 @@
module SubmissionUpdater
extend ActiveSupport::Concern
- def save_submission(new_submission_hash)
+ def submission_from_params(new_submission_hash)
convert_values_to_types(new_submission_hash)
-
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(new_submission_hash[:ontology]).first
- @submission = LinkedData::Client::Models::OntologySubmission.new(values: submission_params(new_submission_hash))
+ LinkedData::Client::Models::OntologySubmission.new(values: submission_params(new_submission_hash))
+ end
+ def save_submission(new_submission_hash)
+ @submission = submission_from_params(new_submission_hash)
update_ontology_summary_only
@submission.save(cache_refresh_all: false)
end
- def update_submission(new_submission_hash)
+ def update_submission(new_submission_hash, submission_id , ontology = nil)
convert_values_to_types(new_submission_hash)
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(new_submission_hash[:ontology]).first
- @submission = @ontology.explore.submissions({ display: 'all' }, new_submission_hash[:id])
+ @ontology = ontology || LinkedData::Client::Models::Ontology.find_by_acronym(new_submission_hash[:ontology]).first
+ new_submission_hash.delete(:ontology)
+
+ @submission = @ontology.explore.submissions({ include: 'all' }, submission_id)
- new_values = submission_params(new_submission_hash)
+ new_values = new_submission_hash
new_values.each do |key, values|
@submission.send("#{key}=", values)
rescue StandardError
@@ -26,25 +29,53 @@ def update_submission(new_submission_hash)
end
update_ontology_summary_only
- @submission.update(values: new_values, cache_refresh_all: false)
+ [@submission, @submission.update(values: new_values, cache_refresh_all: false)]
+ end
+
+ def add_ontologies_to_object(ontologies,object)
+ ontologies.each do |ont|
+ next if object.ontologies.include?(ont)
+ ontology = LinkedData::Client::Models::Ontology.find(ont)
+ if object.type.match(/\/([^\/]+)$/)[1] == 'Group'
+ ontology.group.push(object.id)
+ else
+ ontology.hasDomain.push(object.id)
+ end
+ ontology.update
+ end
+ end
+
+ def delete_ontologies_from_object(new_ontologies,old_ontologies,object)
+ new_ontologies = [] if new_ontologies.nil?
+ ontologies = old_ontologies - new_ontologies
+ ontologies.each do |ont|
+ ontology = LinkedData::Client::Models::Ontology.find(ont)
+ if object.type.match(/\/([^\/]+)$/)[1] == 'Group'
+ ontology.group.delete(object.id)
+ else
+ ontology.hasDomain.delete(object.id)
+ end
+ ontology.update
+ end
end
private
def update_ontology_summary_only(is_remote = @submission.isRemote)
- @ontology.summaryOnly = is_remote&.eql?('3')
- @ontology.update
+ if is_remote && @ontology.summaryOnly != is_remote.eql?('3')
+ @ontology.update(values: {summaryOnly: is_remote.eql?('3')}, cache_refresh_all: false)
+ end
end
def convert_values_to_types(new_submission_hash)
unless new_submission_hash[:contact].nil?
- new_submission_hash[:contact] = new_submission_hash[:contact].values
+ new_submission_hash[:contact] = new_submission_hash[:contact].values unless new_submission_hash[:contact].is_a?(Array)
new_submission_hash[:contact].delete_if { |c| c[:name].empty? || c[:email].empty? }
end
# Convert metadata that needs to be integer to int
- @metadata.map do |hash|
+ submission_metadata.map do |hash|
if hash["enforce"].include?("integer")
if !new_submission_hash[hash["attribute"]].nil? && !new_submission_hash[hash["attribute"]].eql?("")
new_submission_hash[hash["attribute"].to_s.to_sym] = Integer(new_submission_hash[hash["attribute"].to_s.to_sym])
@@ -83,22 +114,19 @@ def submission_params(params)
{ contact: %i[name email] },
:homepage,
:documentation,
- :publication,
+ {copyrightHolder: {}} # TODO add automatically no list Agents
:identifier,
:is_doi_requested,
]
- @metadata.each do |m|
-
+ submission_metadata.each do |m|
m_attr = m["attribute"].to_sym
-
- attributes << if m["enforce"].include?("list")
- [{ m_attr => {} }, { m_attr => []}]
- else
- m_attr
- end
+ m_attr = Array(m["enforce"]).include?("list") ? [{ m_attr => {} }, { m_attr => []}] : m_attr
+ attributes << m_attr
end
p = params.permit(attributes.uniq)
+ p['pullLocation'] = '' if p['isRemote']&.eql?('3')
+
p = p.to_h.transform_values do |v|
if v.is_a? Hash
v.values.reject(&:empty?)
@@ -109,7 +137,14 @@ def submission_params(params)
end
end
- @metadata.each do |m|
+ if p["copyrightHolder"]&.first&.include?("id") # TODO automatize
+ p["copyrightHolder"] = p["copyrightHolder"].first["id"]
+ elsif p["copyrightHolder"]
+ p["copyrightHolder"] = ''
+ end
+
+
+ submission_metadata.each do |m|
m_attr = m['attribute'].to_sym
if p[m_attr] && m['enforce'].include?('list')
p[m_attr] = Array(p[m_attr]) unless p[m_attr].is_a?(Array)
diff --git a/app/controllers/concerns/uri_redirection.rb b/app/controllers/concerns/uri_redirection.rb
new file mode 100644
index 000000000..9ef86fcd4
--- /dev/null
+++ b/app/controllers/concerns/uri_redirection.rb
@@ -0,0 +1,96 @@
+# frozen_string_literal: true
+
+module UriRedirection
+ extend ActiveSupport::Concern
+
+ include SearchContent
+
+ def find_type_by_id(id, acronym)
+ type, resource_id = find_type_by_search(id, acronym)
+ return type, resource_id if type
+
+ type, resource_id = find_type_by_metadata(id, acronym)
+ return type, resource_id if type
+
+ return nil, nil
+ end
+
+
+ def redirect_to_file?
+ accept_header.nil? || (accept_header != "text/html" && params[:p].nil?)
+ end
+
+ def redirect_to_file
+ # when dont have the specified format in the accept header
+ return not_acceptable("Invalid requested format, valid format are: JSON, XML, HTML and CSV\nto download the original file you can get it from: #{rest_url}/ontologies/#{params[:id]}/download\n") if accept_header.nil?
+
+ # when the format is different than text/html
+ redirect_to_download_file if (accept_header != "text/html" && params[:p].nil?)
+ end
+
+ private
+
+ def find_type_by_search(id, acronym)
+ # search for URIs that ends with "/id" or "#id"
+ result = search_content(q: "*##{id} || *\/#{id}", qf: "resource_id", page: 1, pagesize: 10, ontologies: acronym)
+
+ find_exact_resource = result[:collection].select { |x| helpers.link_last_part(x[:resource_id]).eql?(id) }.first
+
+ if !find_exact_resource
+ type = nil
+ resource_id = nil
+ else
+ type = id_type(find_exact_resource[:type_t], find_exact_resource[:type_txt])
+ resource_id = find_exact_resource[:resource_id]
+ end
+
+ [type, resource_id]
+ end
+
+ def find_type_by_metadata(id, acronym)
+ return nil, nil # TODO maybe implemented if needed
+ end
+
+
+ def not_acceptable(message = nil)
+ render plain: message, status: 406
+ end
+
+ def redirect_to_download_file
+ redirect_to("/ontologies/#{params[:id]}/download?format=#{helpers.escape(accept_header)}", allow_other_host: true)
+ end
+
+
+ def accept_header
+ header = request.env["HTTP_ACCEPT"]
+ entries = header.to_s.split(',')
+ parsed_entries = entries.map { |e| accept_entry(e) }
+ sorted_entries = parsed_entries.sort_by(&:last)
+ content_types = sorted_entries.map(&:first)
+ filtered_content_types = content_types.map { |e| find_content_type_for_media_range(e) }
+ filtered_content_types.flatten.compact.first
+ end
+
+ def accept_entry(entry)
+ type, *options = entry.split(';').map(&:strip)
+ quality = 0
+ options.delete_if { |e| quality = 1 - e[2..-1].to_f if e.start_with? 'q=' }
+ [options.unshift(type).join(';'), [quality, type.count('*'), 1 - options.size]]
+ end
+
+ def find_content_type_for_media_range(media_range)
+ case media_range.to_s
+ when '*/*', 'text/html', 'text/*'
+ 'text/html'
+ when 'application/json', 'application/ld+json', 'application/*'
+ 'application/ld+json'
+ when 'text/xml', 'text/rdf+xml', 'application/rdf+xml', 'application/xml'
+ 'application/rdf+xml'
+ when 'text/csv'
+ 'text/csv'
+ else
+ nil
+ end
+ end
+
+end
\ No newline at end of file
diff --git a/app/controllers/content_finder_controller.rb b/app/controllers/content_finder_controller.rb
new file mode 100644
index 000000000..c387efcf7
--- /dev/null
+++ b/app/controllers/content_finder_controller.rb
@@ -0,0 +1,12 @@
+require 'faraday'
+
+class ContentFinderController < ApplicationController
+ include OntologyContentSerializer
+
+ def index
+ @result, _ = serialize_content(ontology_acronym: params[:acronym],
+ concept_id: params[:uri],
+ format: params[:output_format])
+ render 'content_finder/index', layout: 'tool'
+ end
+end
\ No newline at end of file
diff --git a/app/controllers/errors_controller.rb b/app/controllers/errors_controller.rb
index b5ffb1eec..8b55c7903 100644
--- a/app/controllers/errors_controller.rb
+++ b/app/controllers/errors_controller.rb
@@ -3,10 +3,12 @@ class ErrorsController < ApplicationController
layout :determine_layout
def not_found
+ @referer_url = request.referer
render status: 404
end
def internal_server_error
+ @referer_url = request.referer
render status: 500
end
diff --git a/app/controllers/fair_score_controller.rb b/app/controllers/fair_score_controller.rb
index 9564a5875..8f62995b3 100644
--- a/app/controllers/fair_score_controller.rb
+++ b/app/controllers/fair_score_controller.rb
@@ -28,7 +28,7 @@ def get_fair
@fair_scores_data = create_fair_scores_data(get_fair_score(@ontologies).values.first, 1)
end
rescue NameError
- raise StandardError, 'Error: load failed'
+ #raise StandardError, 'Error: load failed'
end
end
end
\ No newline at end of file
diff --git a/app/controllers/history_controller.rb b/app/controllers/history_controller.rb
deleted file mode 100644
index 687839df5..000000000
--- a/app/controllers/history_controller.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-class HistoryController < ApplicationController
-
- def remove # removes a 'history' tab
- remove_tab(undo_param(params[:ontology]))
- render :text =>"success"
- end
-
- def update # updates the 'history' tab to point to the new node
- ontology = DataAccess.getOntology(params[:ontology])
- update_tab(ontology,params[:concept])
- render :text =>"success"
- end
-
-
-end
diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index 3e6952386..87f9e6e2c 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -7,71 +7,62 @@ class HomeController < ApplicationController
include FairScoreHelper
def index
- @ontologies_views = LinkedData::Client::Models::Ontology.all(include_views: true)
- @ontologies = @ontologies_views.select {|o| !o.viewOf}
- @ontologies_hash = Hash[@ontologies_views.map {|o| [o.acronym, o]}]
- @groups = LinkedData::Client::Models::Group.all
- @notes = LinkedData::Client::Models::Note.all
- @last_notes = []
- unless @notes.empty?
- @notes.sort! {|a,b| b.created <=> a.created }
- @notes[0..20].each do |n|
- ont_uri = n.relatedOntology.first
- ont = LinkedData::Client::Models::Ontology.find(ont_uri)
- next if ont.nil?
- username = n.creator.split("/").last
- note = {
- :uri => n.links['ui'],
- :id => n.id,
- :subject => n.subject,
- :body => n.body,
- :created => n.created,
- :author => username,
- :ont_name => ont.name
- }
- @last_notes.push note
- break if @last_notes.length >= [$HOME_LATEST_NOTES_COUNT.to_i, 5].max
- end
- end
- # Get the latest manual mappings
- # All mapping classes are bidirectional.
- # Each class in the list maps to all other classes in the list.
- if $DISPLAY_RECENT.nil? || $DISPLAY_RECENT == true
- @recent_mappings = get_recent_mappings # application_controller
+ @analytics = helpers.ontologies_analytics
+ # Calculate BioPortal summary statistics
+ @ont_count = @analytics.keys.size
+ metrics = LinkedData::Client::Models::Metrics.all
+ metrics = metrics.each_with_object(Hash.new(0)) do |h, sum|
+ h.to_hash.slice(:classes, :properties, :individuals).each { |k, v| sum[k] += v }
end
-
- organize_groups
- # Calculate BioPortal summary statistics
- @ont_count = @ontologies.length
- @cls_count = LinkedData::Client::Models::Metrics.all.map { |m| m.classes.to_i }.sum
- @individuals_count = LinkedData::Client::Models::Metrics.all.map {|m| m.individuals.to_i}.sum
- @prop_count = 36286
+ @cls_count = metrics[:classes]
+ @individuals_count = metrics[:individuals]
+ @prop_count = metrics[:properties]
@map_count = total_mapping_count
- #@analytics = LinkedData::Client::Analytics.last_month
-
- @ontology_names = @ontologies.map { |ont| ["#{ont.name} (#{ont.acronym})", ont.acronym] }
-
- @anal_ont_names = {}
+ @projects_count = LinkedData::Client::Models::Project.all.length
+ @users_count = LinkedData::Client::Models::User.all.length
+
+ @upload_benefits = [
+ t('home.benefit1'),
+ t('home.benefit2'),
+ t('home.benefit3'),
+ t('home.benefit4'),
+ t('home.benefit5')
+ ]
+
+ @anal_ont_names = []
@anal_ont_numbers = []
- # @analytics.onts[0..4].each do |visits|
- # ont = @ontologies_hash[visits[:ont].to_s]
- # @anal_ont_names[ont.acronym] = ont.name
- # @anal_ont_numbers << visits[:views]
- # end
-
-
- end
+ @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
+ @anal_ont_names << ont
+ @anal_ont_numbers << count
+ end
- def render_layout_partial
- partial = params[:partial]
- render partial: "layouts/#{partial}"
end
- def help
- # Show the header/footer or not
- layout = params[:pop].eql?('true') ? 'popup' : 'ontology'
- render layout: layout
+ def tools
+ @tools = {
+ search: {
+ link: "search/ontologies/content",
+ icon: "icons/search.svg",
+ title: t('tools.search.title'),
+ description: t('tools.search.description'),
+ },
+ converter: {
+ link: "/content_finder",
+ icon: "icons/settings.svg",
+ title: t('tools.converter.title'),
+ description: t('tools.converter.description'),
+ },
+ url_checker: {
+ link: check_resolvability_path,
+ icon: "check.svg",
+ title: t('tools.url_checker.title'),
+ description: t('tools.url_checker.description')
+ }
+ }
+
+ @title = "#{helpers.portal_name} #{t('layout.footer.tools')}"
+ render 'tools', layout: 'tool'
end
def all_resources
@@ -95,37 +86,37 @@ def feedback
@tags = []
unless params[:bug].nil? || params[:bug].empty?
- @tags << "Bug"
+ @tags << t('home.bug')
end
unless params[:proposition].nil? || params[:proposition].empty?
- @tags << "Proposition"
+ @tags << t('home.proposition')
end
unless params[:question].nil? || params[:question].empty?
- @tags << "Question"
+ @tags << t('home.question')
end
- unless params[:ontology_submissions_request].nil? || params[:bug].empty?
- @tags << "Ontology submissions request"
+ unless params[:ontology_submissions_request].nil? || params[:ontology_submissions_request].empty?
+ @tags << t('home.ontology_submissions_request')
end
@errors = []
if params[:name].nil? || params[:name].empty?
- @errors << 'Please include your name'
+ @errors << t('home.include_name')
end
if params[:email].nil? || params[:email].length < 1 || !params[:email].match(/^[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}$/i)
- @errors << 'Please include your email'
+ @errors << t('home.include_email')
end
if params[:comment].nil? || params[:comment].empty?
- @errors << 'Please include your comment'
+ @errors << t('home.include_comment')
end
if using_captcha? && !session[:user]
unless verify_recaptcha
- @errors << 'Please fill in the proper text from the supplied image'
+ @errors << t('home.fill_text')
end
end
unless @errors.empty?
- render 'home/feedback/feedback', layout: feedback_layout
+ render 'home/feedback/feedback', layout: feedback_layout
return
end
@@ -134,21 +125,18 @@ def feedback
if params[:pop].eql?('true')
render 'home/feedback/feedback_complete', layout: 'popup'
else
- flash[:notice] = 'Feedback has been sent'
+ flash[:notice] = t('home.notice_feedback')
redirect_to_home
end
end
- def user_intention_survey
- render partial: 'user_intention_survey', layout: false
- end
def site_config
render json: bp_config_json
end
def account
- @title = 'Account Information'
+ @title = t('home.account_title')
if session[:user].nil?
redirect_to controller: 'login', action: 'index', redirect: '/account'
return
@@ -159,7 +147,7 @@ def account
@user_ontologies = @user.customOntology
@user_ontologies ||= []
- onts = LinkedData::Client::Models::Ontology.all
+ onts = LinkedData::Client::Models::Ontology.all(include_views: true);
@admin_ontologies = onts.select { |o| o.administeredBy.include? @user.id }
projects = LinkedData::Client::Models::Project.all
@@ -170,11 +158,12 @@ def account
def feedback_complete; end
- def validate_ontology_file_show; end
-
- def validate_ontology_file
- response = LinkedData::Client::HTTP.post('/validate_ontology_file', ontology_file: params[:ontology_file])
- @process_id = response.process_id
+ def annotator_recommender_form
+ if params[:submit_button] == "annotator"
+ redirect_to "/annotator?text=#{helpers.escape(params[:text])}"
+ elsif params[:submit_button] == "recommender"
+ redirect_to "/recommender?input=#{helpers.escape(params[:input])}"
+ end
end
private
diff --git a/app/controllers/instances_controller.rb b/app/controllers/instances_controller.rb
index 5d346ef3b..a980ccc61 100644
--- a/app/controllers/instances_controller.rb
+++ b/app/controllers/instances_controller.rb
@@ -1,53 +1,53 @@
class InstancesController < ApplicationController
- include InstancesHelper
- def index_by_ontology
- get_ontology(params)
- custom_render get_instances_by_ontology_json(@ontology, get_query_parameters)
- end
+ include InstancesHelper, SearchContent
+
+ def index
+ if params[:type].blank?
+ concept_type = 'NamedIndividual'
+ else
+ is_concept_instance = true
+ concept_type = params[:type]
+ end
- def index_by_class
get_ontology(params)
- get_class(params)
- custom_render get_instances_by_class_json(@concept, get_query_parameters)
+
+ query, page, page_size = helpers.search_content_params
+
+ results, _, next_page, total_count = search_ontologies_content(query: query,
+ page: page,
+ page_size: page_size,
+ filter_by_ontologies: [@ontology.acronym],
+ filter_by_types: Array(concept_type))
+
+ view = helpers.render_search_paginated_list(container_id: (is_concept_instance ? 'concept_' : '') + 'instances_sorted_list',
+ next_page_url: "/ontologies/#{@ontology.acronym}/instances?type=#{helpers.escape(params[:type])}",
+ child_url: "/ontologies/#{@ontology.acronym}/instances/show?modal=#{is_concept_instance.to_s}",
+ child_turbo_frame: 'instance_show',
+ child_param: :instanceid,
+ show_count: is_concept_instance,
+ auto_click: params[:instanceid].blank? && page.eql?(1),
+ results: results, next_page: next_page, total_count: total_count)
+
+ if is_concept_instance && page.eql?(1)
+ render turbo_stream: view
+ else
+ render inline: view
+ end
end
def show
- @instance = get_instance_details_json(params[:ontology_id], params[:instance_id], {include: 'all'})
- render partial: 'instances/instance_details'
+ get_ontology(params)
+ @instance = get_instance_details_json(params[:ontology], params[:id] || params[:instanceid], {include: 'all'})
+
+ redirect_to(ontology_path(id: params[:ontology], p: 'instances', instanceid: params[:id] || params[:instanceid], lang: request_lang)) and return unless turbo_frame_request?
+
+ render partial: 'instances/details', layout: nil
end
private
def get_ontology(params)
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology] || params[:acronym] || params[:ontology_id]).first
ontology_not_found(params[:ontology]) if @ontology.nil?
end
- # json render + adding next and prev pages links
- def custom_render(instances)
- instances[:collection].map! { |i| add_labels_to_print(i, @ontology.acronym)}
- if (instances.respond_to? :links) && (!instances.respond_to? :errors)
- instances.links = {
- nextPage: get_page_link(instances.nextPage),
- prevPage: get_page_link(instances.prevPage)
- }
- end
-
- render json: instances
- end
-
- def get_page_link(page_number)
- return nil if page_number.nil?
-
- if request.query_parameters.has_key?(:page)
- request.original_url.gsub(/page=\d+/, "page=#{page_number}")
- elsif request.query_parameters.empty?
- request.original_url + "?" + "page=#{page_number}"
- else
- request.original_url + "&" + "page=#{page_number}"
- end
- end
-
- def get_query_parameters
- request.query_parameters.slice(:include, :display, :page, :pagesize, :search , :sortby , :order) || {}
- end
end
\ No newline at end of file
diff --git a/app/controllers/label_xl_controller.rb b/app/controllers/label_xl_controller.rb
index e5543aa6d..521d35fb7 100644
--- a/app/controllers/label_xl_controller.rb
+++ b/app/controllers/label_xl_controller.rb
@@ -10,7 +10,7 @@ def show_label
label_xl_label = label_xl ? label_xl['literalForm'] : nil
label_xl_label = params[:id] if label_xl_label.nil? || label_xl_label.empty?
- render LabelLinkComponent.inline(params[:id], label_xl_label)
+ render LabelLinkComponent.inline(params[:id], helpers.main_language_label(label_xl_label))
end
private
@@ -19,7 +19,7 @@ def get_request_label_xl
params[:id] = params[:id] ? params[:id] : params[:label_xl_id]
params[:ontology_id] = params[:ontology_id] ? params[:ontology_id] : params[:ontology]
if params[:id].nil? || params[:id].empty?
- render text: 'Error: You must provide a valid label_xl id'
+ render text: t('label_xl.error_valid_label_xl')
return
end
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
diff --git a/app/controllers/landscape_controller.rb b/app/controllers/landscape_controller.rb
index 2ddc5b1eb..6909b2cf3 100644
--- a/app/controllers/landscape_controller.rb
+++ b/app/controllers/landscape_controller.rb
@@ -43,16 +43,16 @@ def index
ontologyFormatsCount = {"OWL" => 0, "SKOS" => 0, "UMLS" => 0, "OBO" => 0}
- @metrics_average = [{attr: "numberOfClasses", label: "Number of classes", array: []},
- {attr: "numberOfIndividuals", label: "Number of individuals", array: []},
- {attr: "numberOfProperties", label: "Number of properties", array: []},
- {attr: "maxDepth", label: "Max depth", array: []},
- {attr: "maxChildCount", label: "Max child count", array: []},
- {attr: "averageChildCount", label: "Average child count", array: []},
- {attr: "classesWithOneChild", label: "Classes with one child", array: []},
- {attr: "classesWithMoreThan25Children", label: "Classes with more than 25 children", array: []},
- {attr: "classesWithNoDefinition", label: "Classes with no definition ", array: []},
- {attr: "numberOfAxioms", label: "Number of axioms (triples)", array: []}]
+ @metrics_average = [{attr: "classes", label: t('landscape.classes'), array: []},
+ {attr: "individuals", label: t('landscape.individuals'), array: []},
+ {attr: "properties", label: t('landscape.properties'), array: []},
+ {attr: "maxDepth", label: t('landscape.max_depth'), array: []},
+ {attr: "maxChildCount", label: t('landscape.max_child_count'), array: []},
+ {attr: "averageChildCount", label: t('landscape.average_child_count'), array: []},
+ {attr: "classesWithOneChild", label: t('landscape.classes_with_one_child'), array: []},
+ {attr: "classesWithMoreThan25Children", label: t('landscape.classes_with_more_than_25_children'), array: []},
+ {attr: "classesWithNoDefinition", label: t('landscape.classes_with_no_definition'), array: []},
+ {attr: "numberOfAxioms", label: t('landscape.number_of_xioms_triples'), array: []}]
# Attributes to include. To avoid to get everything and make it faster
# They are also used to get the value of each property later in the controller
@@ -73,16 +73,18 @@ def index
# We need prefixes to display them, we remove them to call them in the include
relations_attributes = @relations_array.map {|r| r.to_s.split(":")[1]}
+
metrics_attributes = @metrics_average.map {|m| m[:attr]}
# Concat all attributes array and generate a string separated with comma for include param
all_attributes = sub_attributes.concat(contributors_attr_list).concat(org_attr_list)
- .concat(relations_attributes).concat(metrics_attributes).concat(pref_properties_attributes).join(",")
+ .concat(relations_attributes).concat([:metrics]).concat(pref_properties_attributes).join(",")
# Special treatment for includedInDataCatalog: arrays with a lot of different values, so it trigger the SPARQL default
# when we retrieve multiple attr with multiple values in the array, and make the request slower
- data_catalog_submissions = LinkedData::Client::Models::OntologySubmission.all(include_status: "any", include_views: true, display_links: false, display_context: false, include: "includedInDataCatalog")
+ @submissions = LinkedData::Client::Models::OntologySubmission.all(include_status: "any", include_views: true, display_links: false, display_context: false, include: 'all')
+ data_catalog_submissions = @submissions
dataCatalog_count_hash = {}
# Add our Portal to the dataCatalog list
@@ -99,9 +101,6 @@ def index
end
end
- # Get all latest submissions with the needed attributes (this request can be slow)
- @submissions = LinkedData::Client::Models::OntologySubmission.all(include_status: "any", include_views: true, display_links: false, display_context: false, include: all_attributes)
-
# Iterate ontologies to get the submissions with all metadata
@submissions.each do |sub|
ont = sub.ontology
@@ -147,9 +146,9 @@ def index
# Count the number of classes (individuals for skos by ontologies) to get number of ontologies by slice of size
if sub.hasOntologyLanguage.eql?("SKOS")
- ontology_size = sub.numberOfIndividuals
+ ontology_size = sub.metrics&.individuals || 0
else
- ontology_size = sub.numberOfClasses
+ ontology_size = sub.metrics&.classes || 0
end
if (!ontology_size.nil?)
if (ontology_size >= 100000)
@@ -188,36 +187,36 @@ def index
end
# Get the count for usedOntologyEngineeringTool (to create a tag cloud)
- if (engineering_tool_count.has_key?(sub.usedOntologyEngineeringTool))
- engineering_tool_count[sub.usedOntologyEngineeringTool] += 1
- else
- engineering_tool_count[sub.usedOntologyEngineeringTool] = 1
+ Array(sub.usedOntologyEngineeringTool).each do |tool|
+ if engineering_tool_count.key?(tool)
+ engineering_tool_count[tool] += 1
+ else
+ engineering_tool_count[tool] = 1
+ end
end
# Get people that are mentioned as ontology actors (contact, contributors, creators, curator) to create a tag cloud
# hasContributor hasCreator contact(explore,name) curatedBy
contributors_attr_list.each do |contributor_attr|
- contributor_label = sub.send(contributor_attr.to_s).to_s
- if !contributor_label.nil?
- contributors_split = contributor_label.split(",")
- contributors_split.each do |contrib|
- if people_count_hash.has_key?(contrib)
- people_count_hash[contrib][contributor_attr] += 1
- else
- # Create the contributor entry in the Hash and create the attr entries that will be incremented
- people_count_hash[contrib] = {}
- people_count_hash[contrib][:contact] = 0
- contributors_attr_list.each do |create_contributor_attr|
- people_count_hash[contrib][create_contributor_attr] = 0
- end
- people_count_hash[contrib][contributor_attr] += 1
+ contributors = sub.send(contributor_attr.to_s)
+ Array(contributors).each do |contributor|
+ contrib = contributor.name || contributor.to_s
+ if people_count_hash.has_key?(contrib)
+ people_count_hash[contrib][contributor_attr] += 1
+ else
+ # Create the contributor entry in the Hash and create the attr entries that will be incremented
+ people_count_hash[contrib] = {}
+ people_count_hash[contrib][:contact] = 0
+ contributors_attr_list.each do |create_contributor_attr|
+ people_count_hash[contrib][create_contributor_attr] = 0
end
+ people_count_hash[contrib][contributor_attr] += 1
end
end
end
sub.contact.each do |contact|
contributor_label = contact.name
- if !contributor_label.nil?
+ unless contributor_label.nil?
if people_count_hash.has_key?(contributor_label)
people_count_hash[contributor_label][:contact] += 1
else
@@ -229,44 +228,35 @@ def index
end
people_count_hash[contributor_label][:contact] += 1
end
- people_count_emails[contributor_label] = contact.email if !contact.email.nil?
+ people_count_emails[contributor_label] = contact.email unless contact.email.nil?
end
end
org_attr_list.each do |org_attr|
# If the attribute object is not a list we make it a list of the single object we get
- orgs_list = sub.send(org_attr.to_s)
- if !orgs_list.kind_of?(Array)
- orgs_list = [orgs_list]
- end
+ organizations_list = Array(sub.send(org_attr.to_s))
+
+ organizations_list.each do |org|
+ org_str = org.name || org.to_s rescue org.to_s
+ org_uri = nil
+ # Check if the organization is actually an URL
+ if org_str =~ /\A#{URI::regexp}\z/
+ org_uri = org_str
+ # Remove http, www and last / from URI
+ org_str = org_str.sub("http://", "").sub("https://", "").sub("www.", "")
+ org_str = org_str[0..-2] if org_str.last.eql?("/")
+ end
- orgs_list.each do |orgs_comma_list|
- if !orgs_comma_list.nil? &&
- orgs_comma_split = orgs_comma_list.split(",")
- orgs_comma_split.each do |org_str|
- # TODO: handle badly formatted strings and URI
- org_uri = nil
- # Check if the organization is actually an URL
- if org_str =~ /\A#{URI::regexp}\z/
- org_uri = org_str
- # Remove http, www and last / from URI
- org_str = org_str.sub("http://", "").sub("https://", "").sub("www.", "")
- org_str = org_str[0..-2] if org_str.last.eql?("/")
-
- end
-
- if org_count_hash.has_key?(org_str)
- org_count_hash[org_str][org_attr] += 1
- else
- # Create the contrinutor entry in the Hash and create the attr entries that will be incremented
- org_count_hash[org_str] = {}
- org_attr_list.each do |create_org_attr|
- org_count_hash[org_str][create_org_attr] = 0
- end
- org_count_hash[org_str][:uri] = org_uri if !org_uri.nil?
- org_count_hash[org_str][org_attr] += 1
- end
+ if org_count_hash.has_key?(org_str)
+ org_count_hash[org_str][org_attr] += 1
+ else
+ # Create the contrinutor entry in the Hash and create the attr entries that will be incremented
+ org_count_hash[org_str] = {}
+ org_attr_list.each do |create_org_attr|
+ org_count_hash[org_str][create_org_attr] = 0
end
+ org_count_hash[org_str][:uri] = org_uri unless org_uri.nil?
+ org_count_hash[org_str][org_attr] += 1
end
end
end
@@ -281,17 +271,19 @@ def index
relation_values.each do |relation_value|
target_id = relation_value
target_in_portal = false
+ target_ont = nil
# if we find our portal URL in the ontology URL, then we just keep the ACRONYM to try to get the ontology.
- if relation_value.include?($UI_URL)
+ if relation_value.include?(helpers.portal_name)
relation_value = relation_value.split('/').last
+ target_ont = LinkedData::Client::Models::Ontology.find_by_acronym(relation_value).first
end
+
# Use acronym to get ontology from the portal
- target_ont = LinkedData::Client::Models::Ontology.find_by_acronym(relation_value).first
if target_ont
target_id = target_ont.acronym
target_in_portal = true
end
- ontology_relations_array.push({source: ont.acronym, target: target_id, relation: relation_attr.to_s, targetInPortal: target_in_portal})
+ ontology_relations_array.push({ source: ont.acronym, target: target_id, relation: relation_attr.to_s, targetInPortal: target_in_portal })
end
end
end
@@ -342,15 +334,15 @@ def index
title_array = []
total_count = 0
if hash_counts.has_key?(:projects)
- title_array.push("#{hash_counts[:projects]} projects")
+ title_array.push(t('landscape.projects_count', count: hash_counts[:projects]))
total_count += hash_counts[:projects]
end
if hash_counts.has_key?(:notes)
- title_array.push("#{hash_counts[:notes]} notes")
+ title_array.push(t('landscape.notes_count', count: hash_counts[:notes]))
total_count += hash_counts[:notes]
end
if hash_counts.has_key?(:reviews)
- title_array.push("#{hash_counts[:reviews]} reviews")
+ title_array.push(t('landscape.reviews_count', count: hash_counts[:reviews]))
total_count += hash_counts[:reviews]
end
if total_count > 0
@@ -364,15 +356,15 @@ def index
title_array = []
total_count = 0
if hash_counts.has_key?(:projects)
- title_array.push("#{hash_counts[:projects]} projects")
+ title_array.push(t('landscape.projects_count', count: hash_counts[:projects]))
total_count += hash_counts[:projects]
end
if hash_counts.has_key?(:notes)
- title_array.push("#{hash_counts[:notes]} notes")
+ title_array.push(t('landscape.notes_count', count: hash_counts[:notes]))
total_count += hash_counts[:notes]
end
if hash_counts.has_key?(:reviews)
- title_array.push("#{hash_counts[:reviews]} reviews")
+ title_array.push(t('landscape.reviews_count', count: hash_counts[:reviews]))
total_count += hash_counts[:reviews]
end
if total_count > 0
@@ -397,22 +389,22 @@ def index
title_array = []
total_count = 0
if hash_count[:contact] > 0
- title_array.push("#{hash_count[:contact]} as contact")
+ title_array.push(t('landscape.as_contact_count', count: hash_count[:contact]))
total_count += hash_count[:contact]
end
if hash_count[:hasContributor] > 0
- title_array.push("#{hash_count[:hasContributor]} as contributor")
+ title_array.push(t('landscape.as_contributor_count', count: hash_count[:hasContributor]))
total_count += hash_count[:hasContributor]
end
if hash_count[:hasCreator] > 0
- title_array.push("#{hash_count[:hasCreator]} as creator")
+ title_array.push(t('landscape.as_creator_count', count: hash_count[:hasCreator]))
total_count += hash_count[:hasCreator]
end
if hash_count[:curatedBy] > 0
- title_array.push("#{hash_count[:curatedBy]} as curator")
+ title_array.push(t('landscape.as_curator_count', count: hash_count[:curatedBy]))
total_count += hash_count[:curatedBy]
end
- title_str = "Contributions: #{title_array.join(", ")}"
+ title_str = t('landscape.contributions', title: title_array.join(", "))
if total_count > 1
if people_count_emails[people.to_s].nil?
@@ -430,18 +422,18 @@ def index
title_array = []
total_count = 0
if hash_count[:publisher] > 0
- title_array.push("published #{hash_count[:publisher]} ontologies")
+ title_array.push(t('landscape.published_ontologies', count: hash_count[:publisher]))
total_count += hash_count[:publisher]
end
if hash_count[:fundedBy] > 0
- title_array.push("funded #{hash_count[:fundedBy]} ontologies")
+ title_array.push( t('landscape.funded_ontologies', count: hash_count[:fundedBy]))
total_count += hash_count[:fundedBy]
end
if hash_count[:endorsedBy] > 0
- title_array.push("endorsed #{hash_count[:endorsedBy]} ontologies")
+ title_array.push( t('landscape.endorsed_ontologies', count: hash_count[:endorsedBy]))
total_count += hash_count[:endorsedBy]
end
- title_str = "Contributions: #{title_array.join(", ")}"
+ title_str = t('landscape.contributions', title: title_array.join(", "))
if total_count > 1
if hash_count.has_key?(:uri)
@@ -506,36 +498,36 @@ def index
# Format the ontologyFormatsCount hash as the JSON needed to generate the chart
ontologyFormatsChartJson = { labels: ontologyFormatsCount.keys,
- datasets: [{ label: "Number of ontologies using this format",
+ datasets: [{ label: t('landscape.number_of_ontologies_using_format'),
data: ontologyFormatsCount.values,
backgroundColor: pie_colors_array[3]}] }
isOfTypeChartJson = { labels: isOfTypeCount.keys,
- datasets: [{ label: "Number of ontologies of this ontology type",
+ datasets: [{ label: t('landscape.number_of_ontologies_of_type'),
data: isOfTypeCount.values,
backgroundColor: pie_colors_array[0]}] }
formalityLevelChartJson = { labels: formalityLevelCount.keys,
- datasets: [{ label: "Number of ontologies of this formality level",
+ datasets: [{ label: t('landscape.number_of_ontologies_of_formality_level'),
data: formalityLevelCount.values,
backgroundColor: pie_colors_array[2]}] }
dataCatalogChartJson = { labels: dataCatalog_count_hash.keys,
- datasets: [{ label: "Number of ontologies in this catalog", data: dataCatalog_count_hash.values,
+ datasets: [{ label: t('landscape.number_of_ontologies_in_catalog'), data: dataCatalog_count_hash.values,
backgroundColor: pie_colors_array[5]}] }
# Format the groupOntologiesCount hash as the JSON needed to generate the chart
groupCountChartJson = { labels: groups_count_hash.keys,
- datasets: [{ label: "Number of ontologies", data: groups_count_hash.values,
+ datasets: [{ label: t('landscape.number_of_ontologies'), data: groups_count_hash.values,
backgroundColor: pie_colors_array[3]}] }
domainCountChartJson = { labels: domains_count_hash.keys,
- datasets: [{ label: "Number of ontologies", data: domains_count_hash.values,
+ datasets: [{ label: t('landscape.number_of_ontologies'), data: domains_count_hash.values,
backgroundColor: pie_colors_array[4]}] }
# Format the groupOntologiesCount hash as the JSON needed to generate the chart
sizeSlicesChartJson = { labels: size_slices_hash.keys,
- datasets: [{ label: "Number of ontologies with a class count in this range",
+ datasets: [{ label: t('landscape.number_of_ontologies_with_class_count_in_range'),
data: size_slices_hash.values,
backgroundColor: pie_colors_array[2]}] }
@@ -550,7 +542,7 @@ def index
groups_info_hash[group.acronym][:name] = group.name
groups_info_hash[group.acronym][:description] = []
# Slice the description in 6 words string to avoid too long sentence in the bar chart tooltip in js
- group.description.split(" ").each_slice(6) {|slice| groups_info_hash[group.acronym][:description].push(slice.join(" ")) }
+ group.description.split(" ").each_slice(6) {|slice| groups_info_hash[group.acronym][:description].push(slice.join(" ")) } if group.description
end
domains_info_hash = {}
@@ -560,31 +552,31 @@ def index
domains_info_hash[domain.acronym][:name] = domain.name
domains_info_hash[domain.acronym][:description] = []
# Slice the description in 6 words string to avoid too long sentence in the bar chart tooltip in js
- domain.description.split(" ").each_slice(6) {|slice| domains_info_hash[domain.acronym][:description].push(slice.join(" ")) }
+ domain.description.split(" ").each_slice(6) {|slice| domains_info_hash[domain.acronym][:description].push(slice.join(" ")) } if domain.description
end
@landscape_data = {
- people_count_json_cloud: people_count_json_cloud,
- org_count_json_cloud: org_count_json_cloud,
- engineering_tool_cloud_json: engineering_tool_cloud_json,
- notes_ontologies_json_cloud: notes_ontologies_json_cloud,
- notes_people_json_cloud: notes_people_json_cloud,
- natural_language_json_pie: natural_language_json_pie,
- licenseProperty_json_pie: licenseProperty_json_pie,
- ontology_relations_array: ontology_relations_array,
- prefLabelProperty_json_pie: prefLabelProperty_json_pie,
- synonymProperty_json_pie: synonymProperty_json_pie,
- definitionProperty_json_pie: definitionProperty_json_pie,
- authorProperty_json_pie: authorProperty_json_pie,
- ontologyFormatsChartJson: ontologyFormatsChartJson,
- isOfTypeChartJson: isOfTypeChartJson,
- formalityLevelChartJson: formalityLevelChartJson,
- dataCatalogChartJson: dataCatalogChartJson,
- groupCountChartJson: groupCountChartJson,
- groupsInfoHash: groups_info_hash,
- domainCountChartJson: domainCountChartJson,
- domainsInfoHash: domains_info_hash,
- sizeSlicesChartJson: sizeSlicesChartJson
+ people_count_json_cloud: people_count_json_cloud,
+ org_count_json_cloud: org_count_json_cloud,
+ engineering_tool_cloud_json: engineering_tool_cloud_json,
+ notes_ontologies_json_cloud: notes_ontologies_json_cloud,
+ notes_people_json_cloud: notes_people_json_cloud,
+ natural_language_json_pie: natural_language_json_pie,
+ licenseProperty_json_pie: licenseProperty_json_pie,
+ ontology_relations_array: ontology_relations_array,
+ prefLabelProperty_json_pie: prefLabelProperty_json_pie,
+ synonymProperty_json_pie: synonymProperty_json_pie,
+ definitionProperty_json_pie: definitionProperty_json_pie,
+ authorProperty_json_pie: authorProperty_json_pie,
+ ontologyFormatsChartJson: ontologyFormatsChartJson,
+ isOfTypeChartJson: isOfTypeChartJson,
+ formalityLevelChartJson: formalityLevelChartJson,
+ dataCatalogChartJson: dataCatalogChartJson,
+ groupCountChartJson: groupCountChartJson,
+ groupsInfoHash: groups_info_hash,
+ domainCountChartJson: domainCountChartJson,
+ domainsInfoHash: domains_info_hash,
+ sizeSlicesChartJson: sizeSlicesChartJson
}.to_json.html_safe
end
@@ -610,11 +602,14 @@ def notes_create_hash_entry(uri_id, notes_type, hash)
# Add metrics metadata from the param sub to the @metrics_average var to get the average for each metrics
def get_metrics_for_average(sub)
# Adding metrics to their arrays
-
- @metrics_average.each do |metrics|
- if !sub.send(metrics[:attr]).nil?
- metrics[:array].push(sub.metrics.send(metrics[:attr]))
+ metrics = sub.send(:metrics)
+ @metrics_average.each do |m|
+ if metrics.nil? || metrics.send(m[:attr]).nil?
+ m[:array].push(0)
+ else
+ m[:array].push(metrics.send(m[:attr]))
end
+
end
end
diff --git a/app/controllers/language_controller.rb b/app/controllers/language_controller.rb
new file mode 100644
index 000000000..0ccf6b59c
--- /dev/null
+++ b/app/controllers/language_controller.rb
@@ -0,0 +1,21 @@
+class LanguageController < ApplicationController
+
+ # set locale to the language selected by the user
+ def set_locale_language
+ language = params[:language].strip.downcase.to_sym
+ supported_languages = I18n.available_locales
+
+ if language
+ if supported_languages.include?(language)
+ cookies.permanent[:locale] = language
+ else
+ # in case we want to show a message if the language is not available
+ flash.now[:notice] = t('language.translation_not_available', language: language)
+ logger.error flash.now[:notice]
+ end
+ end
+
+ redirect_to request.referer || root_path
+ end
+
+end
diff --git a/app/controllers/login_controller.rb b/app/controllers/login_controller.rb
index bae176851..11b113b17 100755
--- a/app/controllers/login_controller.rb
+++ b/app/controllers/login_controller.rb
@@ -16,9 +16,14 @@ def index
# logs in a user
def create
+ if is_email(params[:user][:username])
+ username = LinkedData::Client::Models::User.find_by_email(params[:user][:username]).first.username
+ else
+ username = params[:user][:username]
+ end
@errors = validate(params[:user])
if @errors.size < 1
- logged_in_user = LinkedData::Client::Models::User.authenticate(params[:user][:username], params[:user][:password])
+ logged_in_user = LinkedData::Client::Models::User.authenticate(username, params[:user][:password])
if logged_in_user && !logged_in_user.errors
login(logged_in_user)
redirect = "/"
@@ -27,10 +32,9 @@ def create
redirect = CGI.unescape(session[:redirect])
end
-
- redirect_to redirect
+ redirect_to redirect, allow_other_host: true
else
- @errors << "Invalid account name/password combination"
+ @errors << t('login.invalid_account_combination')
render :action => 'index'
end
else
@@ -38,6 +42,28 @@ def create
end
end
+
+ def create_omniauth
+ auth_data = request.env['omniauth.auth']
+ auth_code = auth_data.credentials.token
+ token_provider = helpers.omniauth_token_provider(params[:provider])
+
+ logged_in_user = LinkedData::Client::HTTP.post("#{LinkedData::Client.settings.rest_url}/users/authenticate", { access_token: auth_code , token_provider: token_provider})
+ if logged_in_user && !logged_in_user.errors
+ login(logged_in_user)
+ redirect = "/"
+
+ if session[:redirect]
+ redirect = CGI.unescape(session[:redirect])
+ end
+
+ redirect_to redirect
+ else
+ @errors = [t('login.authentication_failed', provider: params[:provider])]
+ render :action => 'index'
+ end
+ end
+
# Login as the provided username (only for admin users)
def login_as
unless session[:user] && session[:user].admin?
@@ -64,10 +90,10 @@ def destroy
old_user = session[:user]
session[:user] = session[:admin_user]
session.delete(:admin_user)
- flash[:success] = "Logged out #{old_user.username} , returned to #{session[:user].username} ".html_safe
+ flash[:success] = t('login.admin_logged_out', old_user: old_user.username, user: session[:user].username).html_safe
else
session[:user] = nil
- flash[:success] = "You have successfully logged out"
+ flash[:success] = t('login.user_logged_out')
end
redirect_to request.referer || "/"
end
@@ -88,7 +114,7 @@ def send_pass
if resp.nil?
redirect_to "/lost_pass_success"
else
- flash[:notice] = resp.errors.first + ". Please try again."
+ flash[:notice] = resp.errors.first + t('login.try_again_notice')
redirect_to "/lost_pass"
end
end
@@ -99,11 +125,12 @@ def reset_password
token = params[:tk]
@user = LinkedData::Client::HTTP.post("/users/reset_password", {username: username, email: email, token: token})
if @user.is_a?(LinkedData::Client::Models::User)
- @user.validate_password = true
login(@user)
+ @user = LinkedData::Client::Models::User.find(@user.id, include: 'all')
+ @user.validate_password = true
render "users/edit"
else
- flash[:notice] = @user.errors.first + ". Please reset your password again."
+ flash[:notice] = @user.errors.first + t('login.reset_password_again')
redirect_to "/lost_pass"
end
end
@@ -113,8 +140,8 @@ def reset_password
def login(user)
return unless user
session[:user] = user
- custom_ontologies_text = session[:user].customOntology && !session[:user].customOntology.empty? ? "The display is now based on your Custom Ontology Set ." : ""
- notice = "Welcome " + user.username.to_s + " ! " + custom_ontologies_text
+ custom_ontologies_text = session[:user].customOntology && !session[:user].customOntology.empty? ? t('login.custom_ontology_set') : ""
+ notice = t('login.welcome') + user.username.to_s + "! " + custom_ontologies_text
flash[:success] = notice.html_safe
end
@@ -122,14 +149,18 @@ def validate(params)
errors=[]
if params[:username].nil? || params[:username].length <1
- errors << "Please enter an account name"
+ errors << t('login.error_account_name')
end
if params[:password].nil? || params[:password].length <1
- errors << "Please enter a password"
+ errors << t('login.error_password')
end
return errors
end
+ def is_email(email)
+ email =~ /\A[^@\s]+@[^@\s]+\z/
+ end
+
end
diff --git a/app/controllers/mappings_controller.rb b/app/controllers/mappings_controller.rb
index e35ef3a15..e6c9fabd4 100644
--- a/app/controllers/mappings_controller.rb
+++ b/app/controllers/mappings_controller.rb
@@ -15,32 +15,26 @@ class MappingsController < ApplicationController
INTERPORTAL_HASH = $INTERPORTAL_HASH ||= {}
def index
+ @ontologies_mapping_count = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}/statistics/ontologies")
ontology_list = LinkedData::Client::Models::Ontology.all.select { |o| !o.summaryOnly }
- ontologies_mapping_count = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}/statistics/ontologies")
ontologies_hash = {}
ontology_list.each do |ontology|
ontologies_hash[ontology.acronym] = ontology
end
- # TODO_REV: Views support for mappings
- # views_list.each do |view|
- # ontologies_hash[view.ontologyId] = view
- # end
-
@options = {}
- ontologies_mapping_count&.members&.each do |ontology_acronym|
- # Adding external and interportal mappings to the dropdown list
+ @ontologies_mapping_count&.members&.each do |ontology_acronym|
if ontology_acronym.to_s == EXTERNAL_MAPPINGS_GRAPH
- mapping_count = ontologies_mapping_count[ontology_acronym.to_s] || 0
- select_text = "External Mappings (#{number_with_delimiter(mapping_count, delimiter: ',')})" if mapping_count >= 0
+ mapping_count = @ontologies_mapping_count[ontology_acronym.to_s] || 0
+ select_text = t('mappings.external_mappings', number_with_delimiter: number_with_delimiter(mapping_count, delimiter: ',')) if mapping_count >= 0
ontology_acronym = EXTERNAL_URL_PARAM_STR
elsif ontology_acronym.to_s.start_with?(INTERPORTAL_MAPPINGS_GRAPH)
- mapping_count = ontologies_mapping_count[ontology_acronym.to_s] || 0
- select_text = "Interportal Mappings - #{ontology_acronym.to_s.split("/")[-1].upcase} (#{number_with_delimiter(mapping_count, delimiter: ',')})" if mapping_count >= 0
+ mapping_count = @ontologies_mapping_count[ontology_acronym.to_s] || 0
+ select_text = t('mappings.interportal_mappings', acronym: ontology_acronym.to_s.split("/")[-1].upcase, number_with_delimiter: number_with_delimiter(mapping_count, delimiter: ',')) if mapping_count >= 0
ontology_acronym = INTERPORTAL_URL_PARAM_STR + ontology_acronym.to_s.split("/")[-1]
else
ontology = ontologies_hash[ontology_acronym.to_s]
- mapping_count = ontologies_mapping_count[ontology_acronym] || 0
+ mapping_count = @ontologies_mapping_count[ontology_acronym] || 0
next unless ontology && mapping_count > 0
select_text = "#{ontology.name} - #{ontology.acronym} (#{number_with_delimiter(mapping_count, delimiter: ',')})"
end
@@ -48,21 +42,13 @@ def index
end
@options = @options.sort
- end
-
- def count
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
- @ontology_acronym = @ontology&.acronym || params[:id]
- @mapping_counts = mapping_counts(@ontology_acronym)
- render partial: 'count'
- end
+ @options.unshift([])
- def loader
@example_code = [{
"classes": ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Image_Algorithm",
"http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000202"],
- "name": 'This is the mappings produced to test the bulk load',
+ "name": t('mappings.test_bulk_load'),
"source": 'https://w3id.org/semapv/LexicalMatching',
"comment": 'mock data',
"relation": [
@@ -74,9 +60,20 @@ def loader
"source_contact_info": 'orcid:1234,orcid:5678',
"date": '2020-05-30'
}]
- render partial: 'mappings/bulk_loader/loader'
end
+
+ def count
+ @ontology_acronym = params[:ontology] || params[:id]
+ @mapping_counts = mapping_counts(@ontology_acronym)
+
+ respond_to do |format|
+ format.html { render partial: 'mappings/count' }
+ format.json { render json: @mapping_counts }
+ end
+ end
+
+
def loader_process
response = LinkedData::Client::HTTP.post('/mappings/load', file: params[:file])
errors = response.errors
@@ -85,6 +82,7 @@ def loader_process
created = response.created
respond_to do |format|
format.turbo_stream do
+ # TO test
render turbo_stream: turbo_stream.replace('file_loader_result',
partial: 'mappings/bulk_loader/loaded_mappings',
locals: { errors: errors, created: created })
@@ -105,36 +103,37 @@ def show
def show_mappings
page = params[:page] || 1
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
- @target_ontology = LinkedData::Client::Models::Ontology.find(params[:target])
+ @target_ontology = LinkedData::Client::Models::Ontology.find(params[:target].split('/').last)
# Cases if ontology or target are interportal or external
if @ontology.nil?
ontology_acronym = params[:id]
if params[:id] == EXTERNAL_URL_PARAM_STR
- @ontology_name = "External Mappings"
+ @ontology_name = t('mappings.external_mappings')
elsif params[:id].start_with?(INTERPORTAL_URL_PARAM_STR)
@ontology_name = params[:id].sub(":", " - ")
end
else
ontology_acronym = @ontology.acronym
- @ontology_name = @ontology.name
+ @ontology_name = ontology_acronym
end
if @target_ontology.nil?
if params[:target] == EXTERNAL_MAPPINGS_GRAPH
target_acronym = EXTERNAL_URL_PARAM_STR
- @target_ontology_name = "External Mappings"
+ @target_ontology_name = t('mappings.external_mappings')
elsif params[:target].start_with?(INTERPORTAL_MAPPINGS_GRAPH)
target_acronym = "#{INTERPORTAL_URL_PARAM_STR}:#{params[:target].split("/")[-1]}"
- @target_ontology_name = "Interportal - #{params[:target].split("/")[-1].upcase}"
+ @target_ontology_name = t('mappings.interportal_mappings', params: params[:target].split("/")[-1].upcase)
end
else
target_acronym = @target_ontology.acronym
- @target_ontology_name = @target_ontology.name
+ @target_ontology_name = target_acronym
end
ontologies = [ontology_acronym, target_acronym]
@mapping_pages = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}", { page: page, ontologies: ontologies.join(',') })
+ not_found(@mapping_pages.errors) if @mapping_pages.respond_to?(:errors)
@mappings = @mapping_pages.collection
@delete_mapping_permission = check_delete_mapping_permission(@mappings)
@@ -160,13 +159,9 @@ def get_concept_table
@concept = @ontology.explore.single_class({ full: true }, params[:conceptid])
@mappings = @concept.explore.mappings
-
+ @type = params[:type]
@delete_mapping_permission = check_delete_mapping_permission(@mappings)
- render turbo_stream: [
- replace('mapping_count') { "#{@mappings.size}" },
- replace('concept_mappings', partial: 'mappings/concept_mappings')
- ]
-
+ render partial: 'mappings/concept_mappings', layout: false
end
def new
@@ -195,7 +190,7 @@ def create
@delete_mapping_permission = check_delete_mapping_permission(@mapping_saved)
mapping = LinkedData::Client::Models::Mapping.find(@mapping_saved.id)
render turbo_stream: [
- alert(type: 'success') { 'Mapping created' },
+ alert(type: 'success') {t('mappings.mapping_created')},
prepend('concept_mappings_table_content', partial: 'show_line', locals: { map: mapping, concept: @concept })
]
end
@@ -219,7 +214,7 @@ def update
render_turbo_stream(alert_error { JSON.pretty_generate errors })
else
render_turbo_stream(
- alert_success { 'Mapping updated' },
+ alert_success { t('mappings.mapping_updated') },
replace(@mapping.id.split('/').last, partial: 'show_line', locals: { map: request_mapping, concept: @concept })
)
end
@@ -235,7 +230,7 @@ def destroy
map_uri = "#{MAPPINGS_URL}/#{CGI.escape(map_id)}"
result = LinkedData::Client::HTTP.delete(map_uri)
if result.status == 204
- success_text = "#{map_id} deleted successfully"
+ success_text = t('mappings.mapping_deleted', map_id: map_id)
else
error = result.body
end
@@ -248,7 +243,7 @@ def destroy
]
else
- render alert(type: 'danger') { error }
+ render_turbo_stream alert(type: 'danger') { error }
end
end
format.html { render json: { success: success_text, error: error } }
@@ -279,8 +274,8 @@ def mapping_form(mapping: nil)
end
else
mapping = LinkedData::Client::Models::Mapping.new
- @ontology_from = LinkedData::Client::Models::Ontology.find(params[:ontology_from])
- @ontology_to = LinkedData::Client::Models::Ontology.find(params[:ontology_to])
+ @ontology_from = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_from].split('/').last).first
+ @ontology_to = params[:ontology_to].present? ? LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_to].split('/').last).first : nil
@concept_from = @ontology_from.explore.single_class({ full: true }, params[:conceptid_from]) if @ontology_from
if @ontology_to
@concept_to = @ontology_to.explore.single_class({ full: true }, params[:conceptid_to])
@@ -335,15 +330,15 @@ def mapping_form_values
def request_mapping
mapping = LinkedData::Client::Models::Mapping.find(params[:id])
- not_found("Mapping #{params[:id]} not found") if mapping.nil? || mapping.errors
+ not_found( t('mappings.mapping_not_found', id: params[:id]) ) if mapping.nil? || mapping.errors
mapping
end
def valid_values?(values)
errors = []
if values[:classes].reject(&:blank?).size != 2
- errors << 'Source and target concepts need to be specified'
+ errors << t('mappings.error_of_source_and_target')
end
errors
end
-end
+end
\ No newline at end of file
diff --git a/app/controllers/metadata_export_controller.rb b/app/controllers/metadata_export_controller.rb
new file mode 100644
index 000000000..46a56cc2c
--- /dev/null
+++ b/app/controllers/metadata_export_controller.rb
@@ -0,0 +1,32 @@
+class MetadataExportController < ApplicationController
+ include MetadataHelper
+
+ def index
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
+ ontology_not_found(params[:ontology]) if @ontology.nil?
+
+ @submission_latest = @ontology.explore.latest_submission(include: 'all')
+ @ontology_metadata = {}
+ @ontology.to_hash.each do |k, v|
+ @ontology_metadata[k] = v
+ end
+
+ content_metadata_attributes.each do |attr, label|
+ value = @submission_latest.send(attr)
+
+ if attr.to_s.eql?('contact') || agent?(attr)
+ new_values = Array(value).map do |x|
+ next x if x.is_a?(String)
+
+ x = x.to_h || x.to_hash
+ x.delete(:context)
+ x.delete(:links)
+ x.delete(:id)
+ x[:email] || x[:name]
+ end
+ value = value.is_a?(Array) ? new_values : new_values.first
+ end
+ @ontology_metadata[attr] = value
+ end
+ end
+end
diff --git a/app/controllers/ncbo_annotatorplus_controller.rb b/app/controllers/ncbo_annotatorplus_controller.rb
deleted file mode 100644
index d6a418a30..000000000
--- a/app/controllers/ncbo_annotatorplus_controller.rb
+++ /dev/null
@@ -1,224 +0,0 @@
-class NcboAnnotatorplusController < ApplicationController
- layout :determine_layout
-
- before_action :check_ncbo_annotatorplus_enabled
-
- NCBO_ANNOTATOR_URI = $NCBO_ANNOTATOR_URL
- NCBO_API_KEY = $NCBO_API_KEY
-
- def index
- @semantic_types_for_select = []
- @semantic_groups_for_select = []
- @semantic_types ||= get_semantic_types
- @sem_type_ont = LinkedData::Client::Models::Ontology.find_by_acronym('STY').first
- @semantic_groups ||= {"ACTI" => "Activities & Behaviors", "ANAT" => "Anatomy", "CHEM" => "Chemicals & Drugs","CONC" => "Concepts & Ideas",
- "DEVI" => "Devices", "DISO" => "Disorders", "GENE" => "Genes & Molecular Sequences", "GEOG" => "Geographic Areas", "LIVB" => "Living Beings",
- "OBJC" => "Objects", "OCCU" => "Occupations", "ORGA" => "Organizations", "PHEN" => "Phenomena", "PHYS" => "Physiology","PROC" => "Procedures"}
- @semantic_types.each_pair do |code, label|
- @semantic_types_for_select << ["#{label} (#{code})", code]
- end
- @semantic_groups.each_pair do |group, label|
- @semantic_groups_for_select << ["#{label} (#{group})", group]
- end
- @semantic_types_for_select.sort! {|a,b| a[0] <=> b[0]}
- @semantic_groups_for_select.sort! {|a,b| a[0] <=> b[0]}
- @recognizers = parse_json(REST_URI + "/annotator/recognizers")
- @annotator_ontologies = LinkedData::Client::Models::Ontology.all
- @ontologies_for_select = get_ontologies_for_select
- end
-
-
- def create
- params[:mappings] ||= []
- params[:max_level] ||= 0
- params[:ontologies] ||= []
- params[:semantic_types] ||= []
- params[:semantic_groups] ||= []
- text_to_annotate = params[:text].strip.gsub("\r\n", " ").gsub("\n", " ")
-
- options = { :ontologies => params[:ontologies],
- :class_hierarchy_max_level => params[:class_hierarchy_max_level].to_i,
- :expand_class_hierarchy => params[:class_hierarchy_max_level].to_i > 0,
- :semantic_types => params[:semantic_types],
- :semantic_groups => params[:semantic_groups],
- :mappings => params[:mappings],
- :longest_only => params[:longest_only],
- :exclude_numbers => params[:exclude_numbers] ||= "false", # service default is false
- :whole_word_only => params[:whole_word_only] ||= "true", # service default is true
- :exclude_synonyms => params[:exclude_synonyms] ||= "false", # service default is false
- :fast_context => params[:fast_context] ||= "false", # service default is false
- :score => params[:score],
- :score_threshold => params[:score_threshold] ||=-1,
- :confidence_threshold => params[:confidence_threshold] ||=-1,
- :ncbo_slice => params[:ncbo_slice] || ''
- }
-
- start = Time.now
- query = NCBO_ANNOTATOR_URI
- query += "?text=" + CGI.escape(text_to_annotate)
- query += "&apikey=" + NCBO_API_KEY
- query += "&include=prefLabel"
- query += "&expand_class_hierarchy=true" if options[:class_hierarchy_max_level] > 0
- query += "&class_hierarchy_max_level=" + options[:class_hierarchy_max_level].to_s if options[:class_hierarchy_max_level] > 0
- query += "&score=" + options[:score] unless options[:score] == ""
- query += "&score_threshold=" + options[:score_threshold] unless options[:score] == "" or options[:score_threshold]==-1
- query += "&confidence_threshold=" + options[:confidence_threshold] unless options[:score] == "" or options[:confidence_threshold]==-1
- query += "&fast_context=" + options[:fast_context] unless options[:fast_context].empty?
- query += "&ontologies=" + CGI.escape(options[:ontologies].join(',')) unless options[:ontologies].empty?
- query += "&semantic_types=" + options[:semantic_types].join(',') unless options[:semantic_types].empty?
- query += "&semantic_groups=" + options[:semantic_groups].join(',') unless options[:semantic_groups].empty?
- query += "&mappings=" + options[:mappings].join(',') unless options[:mappings].empty?
- query += "&longest_only=#{options[:longest_only]}"
- query += "&recognizer=#{params[:recognizer]}"
- query += "&exclude_numbers=" + options[:exclude_numbers].to_s unless options[:exclude_numbers].empty?
- query += "&whole_word_only=" + options[:whole_word_only].to_s unless options[:whole_word_only].empty?
- query += "&exclude_synonyms=" + options[:exclude_synonyms].to_s unless options[:exclude_synonyms].empty?
- query += "&ncbo_slice=" + options[:ncbo_slice].to_s unless options[:ncbo_slice].empty?
-
- annotations = parse_json(query) # See application_controller.rb
- #annotations = LinkedData::Client::HTTP.get(query)
- LOG.add :debug, "Query: #{query}"
- LOG.add :debug, "Retrieved #{annotations.length} annotations: #{Time.now - start}s"
- if annotations.empty? || params[:raw] == "true"
- # TODO: if params contains select ontologies and/or semantic types, only return those selected.
- response = {
- annotations: annotations,
- ontologies: get_simplified_ontologies_hash, # application_controller
- semantic_types: get_semantic_types # application_controller
- }
- else
- massage_annotated_classes(annotations, options)
- response = {
- annotations: annotations,
- ontologies: {}, # ontology data are in annotations already.
- semantic_types: {} # semantic types are in annotations already.
- }
- end
-
- render :json => response
- end
-
- private
-
- def get_semantic_types
- semantic_types = {}
- sty_ont = LinkedData::Client::Models::Ontology.find_by_acronym('STY').first
- return semantic_types if sty_ont.nil?
- # The first 500 items should be more than sufficient to get all semantic types.
- sty_classes = sty_ont.explore.classes({'pagesize'=>500, include: 'prefLabel'})
- sty_classes.collection.each do |cls|
- code = cls.id.split("/").last
- semantic_types[ code ] = cls.prefLabel
- end
- semantic_types
- end
-
- def massage_annotated_classes(annotations, options)
- # Get the class details required for display, assume this is necessary
- # for every element of the annotations array because the API returns a set.
- # Use the batch REST API to get all the annotated class prefLabels.
- start = Time.now
- semantic_types = options[:semantic_types] || []
- class_details = get_annotated_classes(annotations, semantic_types)
- simplify_annotated_classes(annotations, class_details)
- # repeat the simplification for any annotation hierarchy or mappings.
- hierarchy = annotations.map {|a| a if a.keys.include? 'hierarchy' }.compact
- hierarchy.each do |a|
- simplify_annotated_classes(a['hierarchy'], class_details) if not a['hierarchy'].empty?
- end
- mappings = annotations.map {|a| a if a.keys.include? 'mappings' }.compact
- mappings.each do |a|
- simplify_annotated_classes(a['mappings'], class_details) if not a['mappings'].empty?
- end
- LOG.add :debug, "Completed massage for annotated classes: #{Time.now - start}s"
- end
-
- def simplify_annotated_classes(annotations, class_details)
- annotations2delete = []
- annotations.each do |a|
- cls_id = a['annotatedClass']['@id']
- details = class_details[cls_id]
- if details.nil?
- LOG.add :debug, "Failed to get class details for: #{a['annotatedClass']['links']['self']}"
- annotations2delete.push(cls_id)
- else
- # Replace the annotated class with simplified details.
- a['annotatedClass'] = details
- end
- end
- # Remove any annotations that fail to resolve details.
- annotations.delete_if { |a| annotations2delete.include? a['annotatedClass']['@id'] }
- end
-
- def get_annotated_class_hash(a)
- return {
- :class => a['annotatedClass']['@id'],
- :ontology => a['annotatedClass']['links']['ontology']
- }
- end
-
- def get_annotated_classes(annotations, semantic_types=[])
- # Use batch service to get class prefLabels
- class_list = []
- annotations.each {|a| class_list << get_annotated_class_hash(a) }
- hierarchy = annotations.map {|a| a if a.keys.include? 'hierarchy' }.compact
- hierarchy.each do |a|
- a['hierarchy'].each {|h| class_list << get_annotated_class_hash(h) }
- end
- mappings = annotations.map {|a| a if a.keys.include? 'mappings' }.compact
- mappings.each do |a|
- a['mappings'].each {|m| class_list << get_annotated_class_hash(m) }
- end
- classes_simple = {}
- return classes_simple if class_list.empty?
- # remove duplicates
- class_set = class_list.to_set # get unique class:ontology set
- class_list = class_set.to_a # collection requires a list in batch call
- # make the batch call
- properties = 'prefLabel'
- properties = 'prefLabel,semanticType' if not semantic_types.empty?
- call_params = {'http://www.w3.org/2002/07/owl#Class'=>{'collection'=>class_list, 'include'=>properties}}
- classes_json = get_batch_results(call_params)
- # Simplify the response data for the UI
- @ontologies_hash ||= get_simplified_ontologies_hash # application_controller
- classes_data = JSON.parse(classes_json)
- classes_data["http://www.w3.org/2002/07/owl#Class"].each do |cls|
- c = simplify_class_model(cls)
- ont_details = @ontologies_hash[ c[:ontology] ]
- next if ont_details.nil? # NO DISPLAY FOR ANNOTATIONS ON ANY CLASS OUTSIDE THE BIOPORTAL ONTOLOGY SET.
- c[:ontology] = ont_details
- unless semantic_types.empty? || cls['semanticType'].nil?
- @semantic_types ||= get_semantic_types # application_controller
- # Extract the semantic type descriptions that are requested.
- semanticTypeURI = 'http://bioportal.bioontology.org/ontologies/umls/sty/'
- semanticCodes = cls['semanticType'].map {|t| t.sub( semanticTypeURI, '') }
- requestedCodes = semanticCodes.map {|code| (semantic_types.include? code and code) || nil }.compact
- requestedDescriptions = requestedCodes.map {|code| @semantic_types[code] }.compact
- c[:semantic_types] = requestedDescriptions
- else
- c[:semantic_types] = []
- end
- classes_simple[c[:id]] = c
- end
- return classes_simple
- end
-
- # Get the ontologies from NCBO to populate select onto for the Annotator plus
- def get_ontologies_for_select
- ontologies_json = JSON.parse(Net::HTTP.get(URI.parse("http://data.bioontology.org/ontologies?apikey=#{NCBO_API_KEY}")))
- ontologies_array = []
-
- ontologies_json.each do |onto|
- ontologies_array.push(["#{onto['name']} (#{onto['acronym']})", onto['acronym']])
- end
-
- return ontologies_array
- end
-
- protected
-
- def check_ncbo_annotatorplus_enabled
- raise ActionController::RoutingError.new('Not Found') unless $NCBO_ANNOTATORPLUS_ENABLED == true
- end
-
-end
diff --git a/app/controllers/notes_controller.rb b/app/controllers/notes_controller.rb
index 83051c4e1..e08836392 100644
--- a/app/controllers/notes_controller.rb
+++ b/app/controllers/notes_controller.rb
@@ -1,17 +1,19 @@
class NotesController < ApplicationController
include TurboHelper
layout 'ontology'
+
NOTES_PROPOSAL_TYPES = {
- ProposalNewClass: "New Class Proposal",
- ProposalChangeHierarchy: "New Relationship Proposal",
- ProposalChangeProperty: "Change Property Value Proposal"
+ ProposalNewClass: t('notes.new_class_proposal'),
+ ProposalChangeHierarchy: t('notes.new_relationship_proposal'),
+ ProposalChangeProperty: t('notes.change_property_value_proposal')
}
def show
id = clean_note_id(params[:id])
@note = LinkedData::Client::Models::Note.get(id, include_threads: true)
- @ontology = (@notes.explore.relatedOntology || []).first
+ @note_decorator = NoteDecorator.new(@note, view_context)
+ @ontology = (@note.explore.relatedOntology || []).first
if request.xhr?
render :partial => 'thread'
@@ -100,10 +102,10 @@ def create
new_note = note.save
parent_type = params[:type].eql?("ontology") ? 'ontology' : 'class'
ontology_acronym = new_note.relatedOntology.first.split('/').last
- success_message = 'New comment added successfully'
+ success_message = t('notes.new_comment_added')
locals = { note: new_note, ontology_acronym: ontology_acronym, parent_type: parent_type }
partial = 'notes/note_line'
- container_id = "#{parent_type}_notes_table_content"
+ container_id = "#{parent_type}_notes_table_body"
alerts_container_id = nil
end
@@ -128,10 +130,10 @@ def destroy
if note.errors
response[:errors] = note.errors
else
- response[:success] = "Note #{note_id} was deleted successfully"
+ response[:success] = t('notes.note_deleted_successfully', note_id: note_id)
end
else
- response[:errors] = "Note #{note_id} was not found in the system"
+ response[:errors] = t('notes.note_not_found', note_id: note_id)
end
parent_type = params[:parent_type]
alerts_container_id = "notes_#{parent_type}_list_table_alerts"
diff --git a/app/controllers/ontolobridge_controller.rb b/app/controllers/ontolobridge_controller.rb
index 476f3efa5..89d3d62b6 100644
--- a/app/controllers/ontolobridge_controller.rb
+++ b/app/controllers/ontolobridge_controller.rb
@@ -36,7 +36,7 @@ def request_term
response["error"] = e.message
rescue Exception => e
code = 500
- response["error"] = "Problem creating a new term #{endpoint}: #{e.class} - #{e.message}"
+ response["error"] = t('ontolobridge.problem_of_creating_new_term', endpoint: endpoint, class: e.class, message: e.message)
end
render json: [response, code], status: code
@@ -45,7 +45,7 @@ def request_term
def save_new_term_instructions
code = 200
response = {error: '', success: ''}
- response[:success] = "New term request instructions for #{params['acronym']} saved"
+ response[:success] = t('ontolobridge.new_term_instructions_saved', acronym: params['acronym'])
ont_data = Ontology.find_by(acronym: params['acronym'])
ont_data ||= Ontology.new
ont_data.acronym = params['acronym']
@@ -55,7 +55,7 @@ def save_new_term_instructions
ont_data.save
rescue Exception => e
code = 500
- response[:error] = "Unable to save new term instructions for #{params['acronym']} due to a server error"
+ response[:error] = t('ontolobridge.error_saving_new_term_instructions', acronym: params['acronym'])
end
sleep(1)
render json: [response, code], status: code
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index f84c34a09..caec35f99 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -4,9 +4,16 @@ class OntologiesController < ApplicationController
include InstancesHelper
include ActionView::Helpers::NumberHelper
include OntologiesHelper
+ include ConceptsHelper
include SchemesHelper
include CollectionsHelper
include MappingStatistics
+ include OntologyUpdater
+ include TurboHelper
+ include SparqlHelper
+ include SubmissionFilter
+ include OntologyContentSerializer
+ include UriRedirection
require 'multi_json'
require 'cgi'
@@ -14,143 +21,45 @@ class OntologiesController < ApplicationController
helper :concepts
helper :fair_score
- layout :determine_layout
+ layout 'ontology'
- before_action :authorize_and_redirect, :only=>[:edit,:update,:create,:new]
+ before_action :authorize_and_redirect, :only => [:edit, :update, :create, :new]
before_action :submission_metadata, only: [:show]
- KNOWN_PAGES = Set.new(["terms", "classes", "mappings", "notes", "widgets", "summary", "properties" ,"instances", "schemes", "collections"])
+ KNOWN_PAGES = Set.new(["terms", "classes", "mappings", "notes", "widgets", "summary", "properties", "instances", "schemes", "collections", "sparql"])
EXTERNAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/ExternalMappings"
INTERPORTAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/InterportalMappings"
- $LEXVO_TO_FLAG = { 'http://lexvo.org/id/iso639-3/aar' => 'aa', 'http://lexvo.org/id/iso639-3/abk' => 'ab',
- 'http://lexvo.org/id/iso639-3/ave' => 'ae', 'http://lexvo.org/id/iso639-3/afr' => 'af',
- 'http://lexvo.org/id/iso639-3/aka' => 'ak', 'http://lexvo.org/id/iso639-3/amh' => 'am',
- 'http://lexvo.org/id/iso639-3/arg' => 'an', 'http://lexvo.org/id/iso639-3/ara' => 'ar', 'http://lexvo.org/id/iso639-3/asm' => 'as', 'http://lexvo.org/id/iso639-3/ava' => 'av', 'http://lexvo.org/id/iso639-3/aym' => 'ay', 'http://lexvo.org/id/iso639-3/aze' => 'az', 'http://lexvo.org/id/iso639-3/bak' => 'ba', 'http://lexvo.org/id/iso639-3/bel' => 'be', 'http://lexvo.org/id/iso639-3/bul' => 'bg', 'http://lexvo.org/id/iso639-3/bis' => 'bi', 'http://lexvo.org/id/iso639-3/bam' => 'bm', 'http://lexvo.org/id/iso639-3/ben' => 'bn', 'http://lexvo.org/id/iso639-3/bod' => 'bo', 'http://lexvo.org/id/iso639-3/bre' => 'br', 'http://lexvo.org/id/iso639-3/bos' => 'bs', 'http://lexvo.org/id/iso639-3/cat' => 'ca', 'http://lexvo.org/id/iso639-3/che' => 'ce', 'http://lexvo.org/id/iso639-3/cha' => 'ch', 'http://lexvo.org/id/iso639-3/cos' => 'co', 'http://lexvo.org/id/iso639-3/cre' => 'cr', 'http://lexvo.org/id/iso639-3/ces' => 'cs', 'http://lexvo.org/id/iso639-3/chu' => 'cu', 'http://lexvo.org/id/iso639-3/chv' => 'cv', 'http://lexvo.org/id/iso639-3/cym' => 'cy', 'http://lexvo.org/id/iso639-3/dan' => 'da', 'http://lexvo.org/id/iso639-3/deu' => 'de', 'http://lexvo.org/id/iso639-3/div' => 'dv', 'http://lexvo.org/id/iso639-3/dzo' => 'dz', 'http://lexvo.org/id/iso639-3/ewe' => 'ee', 'http://lexvo.org/id/iso639-3/ell' => 'el', 'http://lexvo.org/id/iso639-3/eng' => 'en', 'http://lexvo.org/id/iso639-3/epo' => 'eo', 'http://lexvo.org/id/iso639-3/spa' => 'es', 'http://lexvo.org/id/iso639-3/est' => 'et', 'http://lexvo.org/id/iso639-3/eus' => 'eu', 'http://lexvo.org/id/iso639-3/fas' => 'fa', 'http://lexvo.org/id/iso639-3/ful' => 'ff', 'http://lexvo.org/id/iso639-3/fin' => 'fi', 'http://lexvo.org/id/iso639-3/fij' => 'fj', 'http://lexvo.org/id/iso639-3/fao' => 'fo', 'http://lexvo.org/id/iso639-3/fra' => 'fr', 'http://lexvo.org/id/iso639-3/fry' => 'fy', 'http://lexvo.org/id/iso639-3/gle' => 'ga', 'http://lexvo.org/id/iso639-3/gla' => 'gd', 'http://lexvo.org/id/iso639-3/glg' => 'gl', 'http://lexvo.org/id/iso639-3/grn' => 'gn', 'http://lexvo.org/id/iso639-3/guj' => 'gu', 'http://lexvo.org/id/iso639-3/glv' => 'gv', 'http://lexvo.org/id/iso639-3/hau' => 'ha', 'http://lexvo.org/id/iso639-3/heb' => 'he', 'http://lexvo.org/id/iso639-3/hin' => 'hi', 'http://lexvo.org/id/iso639-3/hmo' => 'ho', 'http://lexvo.org/id/iso639-3/hrv' => 'hr', 'http://lexvo.org/id/iso639-3/hat' => 'ht', 'http://lexvo.org/id/iso639-3/hun' => 'hu', 'http://lexvo.org/id/iso639-3/hye' => 'hy', 'http://lexvo.org/id/iso639-3/her' => 'hz', 'http://lexvo.org/id/iso639-3/ina' => 'ia', 'http://lexvo.org/id/iso639-3/ind' => 'id', 'http://lexvo.org/id/iso639-3/ile' => 'ie', 'http://lexvo.org/id/iso639-3/ibo' => 'ig', 'http://lexvo.org/id/iso639-3/iii' => 'ii', 'http://lexvo.org/id/iso639-3/ipk' => 'ik', 'http://lexvo.org/id/iso639-3/ido' => 'io', 'http://lexvo.org/id/iso639-3/isl' => 'is', 'http://lexvo.org/id/iso639-3/ita' => 'it', 'http://lexvo.org/id/iso639-3/iku' => 'iu', 'http://lexvo.org/id/iso639-3/jpn' => 'ja', 'http://lexvo.org/id/iso639-3/jav' => 'jv', 'http://lexvo.org/id/iso639-3/kat' => 'ka', 'http://lexvo.org/id/iso639-3/kon' => 'kg', 'http://lexvo.org/id/iso639-3/kik' => 'ki', 'http://lexvo.org/id/iso639-3/kua' => 'kj', 'http://lexvo.org/id/iso639-3/kaz' => 'kk', 'http://lexvo.org/id/iso639-3/kal' => 'kl', 'http://lexvo.org/id/iso639-3/khm' => 'km', 'http://lexvo.org/id/iso639-3/kan' => 'kn', 'http://lexvo.org/id/iso639-3/kor' => 'ko', 'http://lexvo.org/id/iso639-3/kau' => 'kr', 'http://lexvo.org/id/iso639-3/kas' => 'ks', 'http://lexvo.org/id/iso639-3/kur' => 'ku', 'http://lexvo.org/id/iso639-3/kom' => 'kv', 'http://lexvo.org/id/iso639-3/cor' => 'kw', 'http://lexvo.org/id/iso639-3/kir' => 'ky', 'http://lexvo.org/id/iso639-3/lat' => 'la', 'http://lexvo.org/id/iso639-3/ltz' => 'lb', 'http://lexvo.org/id/iso639-3/lug' => 'lg', 'http://lexvo.org/id/iso639-3/lim' => 'li', 'http://lexvo.org/id/iso639-3/lin' => 'ln', 'http://lexvo.org/id/iso639-3/lao' => 'lo', 'http://lexvo.org/id/iso639-3/lit' => 'lt', 'http://lexvo.org/id/iso639-3/lub' => 'lu', 'http://lexvo.org/id/iso639-3/lav' => 'lv', 'http://lexvo.org/id/iso639-3/mlg' => 'mg', 'http://lexvo.org/id/iso639-3/mah' => 'mh', 'http://lexvo.org/id/iso639-3/mri' => 'mi', 'http://lexvo.org/id/iso639-3/mkd' => 'mk', 'http://lexvo.org/id/iso639-3/mal' => 'ml', 'http://lexvo.org/id/iso639-3/mon' => 'mn', 'http://lexvo.org/id/iso639-3/mar' => 'mr', 'http://lexvo.org/id/iso639-3/msa' => 'ms', 'http://lexvo.org/id/iso639-3/mlt' => 'mt', 'http://lexvo.org/id/iso639-3/mya' => 'my', 'http://lexvo.org/id/iso639-3/nau' => 'na', 'http://lexvo.org/id/iso639-3/nob' => 'nb', 'http://lexvo.org/id/iso639-3/nde' => 'nd', 'http://lexvo.org/id/iso639-3/nep' => 'ne', 'http://lexvo.org/id/iso639-3/ndo' => 'ng', 'http://lexvo.org/id/iso639-3/nld' => 'nl', 'http://lexvo.org/id/iso639-3/nno' => 'nn', 'http://lexvo.org/id/iso639-3/nor' => 'no', 'http://lexvo.org/id/iso639-3/nbl' => 'nr', 'http://lexvo.org/id/iso639-3/nav' => 'nv', 'http://lexvo.org/id/iso639-3/nya' => 'ny', 'http://lexvo.org/id/iso639-3/oci' => 'oc', 'http://lexvo.org/id/iso639-3/oji' => 'oj', 'http://lexvo.org/id/iso639-3/orm' => 'om', 'http://lexvo.org/id/iso639-3/ori' => 'or', 'http://lexvo.org/id/iso639-3/oss' => 'os', 'http://lexvo.org/id/iso639-3/pan' => 'pa', 'http://lexvo.org/id/iso639-3/pli' => 'pi', 'http://lexvo.org/id/iso639-3/pol' => 'pl', 'http://lexvo.org/id/iso639-3/pus' => 'ps', 'http://lexvo.org/id/iso639-3/por' => 'pt', 'http://lexvo.org/id/iso639-3/que' => 'qu', 'http://lexvo.org/id/iso639-3/roh' => 'rm', 'http://lexvo.org/id/iso639-3/run' => 'rn', 'http://lexvo.org/id/iso639-3/ron' => 'ro', 'http://lexvo.org/id/iso639-3/rus' => 'ru', 'http://lexvo.org/id/iso639-3/kin' => 'rw', 'http://lexvo.org/id/iso639-3/san' => 'sa', 'http://lexvo.org/id/iso639-3/srd' => 'sc', 'http://lexvo.org/id/iso639-3/snd' => 'sd', 'http://lexvo.org/id/iso639-3/sme' => 'se', 'http://lexvo.org/id/iso639-3/sag' => 'sg', 'http://lexvo.org/id/iso639-3/hbs' => 'sh', 'http://lexvo.org/id/iso639-3/sin' => 'si', 'http://lexvo.org/id/iso639-3/slk' => 'sk', 'http://lexvo.org/id/iso639-3/slv' => 'sl', 'http://lexvo.org/id/iso639-3/smo' => 'sm', 'http://lexvo.org/id/iso639-3/sna' => 'sn', 'http://lexvo.org/id/iso639-3/som' => 'so', 'http://lexvo.org/id/iso639-3/sqi' => 'sq', 'http://lexvo.org/id/iso639-3/srp' => 'sr', 'http://lexvo.org/id/iso639-3/ssw' => 'ss', 'http://lexvo.org/id/iso639-3/sot' => 'st', 'http://lexvo.org/id/iso639-3/sun' => 'su', 'http://lexvo.org/id/iso639-3/swe' => 'sv', 'http://lexvo.org/id/iso639-3/swa' => 'sw', 'http://lexvo.org/id/iso639-3/tam' => 'ta', 'http://lexvo.org/id/iso639-3/tel' => 'te', 'http://lexvo.org/id/iso639-3/tgk' => 'tg', 'http://lexvo.org/id/iso639-3/tha' => 'th', 'http://lexvo.org/id/iso639-3/tir' => 'ti', 'http://lexvo.org/id/iso639-3/tuk' => 'tk', 'http://lexvo.org/id/iso639-3/tgl' => 'tl', 'http://lexvo.org/id/iso639-3/tsn' => 'tn', 'http://lexvo.org/id/iso639-3/ton' => 'to', 'http://lexvo.org/id/iso639-3/tur' => 'tr', 'http://lexvo.org/id/iso639-3/tso' => 'ts', 'http://lexvo.org/id/iso639-3/tat' => 'tt', 'http://lexvo.org/id/iso639-3/twi' => 'tw', 'http://lexvo.org/id/iso639-3/tah' => 'ty', 'http://lexvo.org/id/iso639-3/uig' => 'ug', 'http://lexvo.org/id/iso639-3/ukr' => 'uk', 'http://lexvo.org/id/iso639-3/urd' => 'ur', 'http://lexvo.org/id/iso639-3/uzb' => 'uz', 'http://lexvo.org/id/iso639-3/ven' => 've', 'http://lexvo.org/id/iso639-3/vie' => 'vi', 'http://lexvo.org/id/iso639-3/vol' => 'vo', 'http://lexvo.org/id/iso639-3/wln' => 'wa', 'http://lexvo.org/id/iso639-3/wol' => 'wo', 'http://lexvo.org/id/iso639-3/xho' => 'xh', 'http://lexvo.org/id/iso639-3/yid' => 'yi', 'http://lexvo.org/id/iso639-3/yor' => 'yo', 'http://lexvo.org/id/iso639-3/zha' => 'za', 'http://lexvo.org/id/iso639-3/zho' => 'zh', 'http://lexvo.org/id/iso639-3/zul' => 'zu' }
-
-
# GET /ontologies
def index
- @app_name = 'FacetedBrowsing'
- @app_dir = '/browse'
- @base_path = @app_dir
- ontologies = LinkedData::Client::Models::Ontology.all(
-include: LinkedData::Client::Models::Ontology.include_params + ',viewOf', include_views: true, display_context: false)
- ontologies_hash = Hash[ontologies.map {|o| [o.id, o] }]
- @admin = session[:user] ? session[:user].admin? : false
- @development = Rails.env.development?
-
- # We could get naturalLanguages, isOfType and formalityLevels from the API, but for performance we are storing it in config/bioportal_config_production.rb
- #@metadata = submission_metadata
-
- # The attributes used when retrieving the submission. We are not retrieving all attributes to be faster
- browse_attributes = 'ontology,acronym,submissionStatus,description,pullLocation,creationDate,released,name,naturalLanguage,hasOntologyLanguage,hasFormalityLevel,isOfType,contact'
- submissions = LinkedData::Client::Models::OntologySubmission.all(include_views: true, display_links: false,
-display_context: false, include: browse_attributes)
- submissions_map = Hash[submissions.map {|sub| [sub.ontology.acronym, sub] }]
-
@categories = LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
- @categories_hash = Hash[@categories.map {|c| [c.id, c] }]
-
@groups = LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
- @groups_hash = Hash[@groups.map {|g| [g.id, g] }]
- #analytics = LinkedData::Client::Analytics.last_month
- #@analytics = Hash[analytics.onts.map {|o| [o[:ont].to_s, o[:views]]}]
+ @filters = ontology_filters_init(@categories, @groups)
+ init_filters(params)
+ render 'ontologies/browser/browse'
+ end
- reviews = {}
- LinkedData::Client::Models::Review.all(display_links: false, display_context: false).each do |r|
- reviews[r.reviewedOntology] ||= []
- reviews[r.reviewedOntology] << r
+ def ontologies_filter
+ @time = Benchmark.realtime do
+ @ontologies, @count, @count_objects, @request_params = submissions_paginate_filter(params)
end
- metrics_hash = get_metrics_hash
-
- @formats = Set.new
- #get fairscores of all ontologies
- @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil;
-
- @ontologies = []
- ontologies.each do |ont|
- o = {}
-
- if metrics_hash[ont.id]
- o[:class_count] = metrics_hash[ont.id].classes
- o[:individual_count] = metrics_hash[ont.id].individuals
- else
- o[:class_count] = 0
- o[:individual_count] = 0
- end
- o[:class_count_formatted] = number_with_delimiter(o[:class_count], delimiter: ',')
- o[:individual_count_formatted] = number_with_delimiter(o[:individual_count], delimiter: ',')
-
- o[:id] = ont.id
- o[:type] = ont.viewOf.nil? ? 'ontology' : 'ontology_view'
- o[:show] = ont.viewOf.nil? ? true : false # show ontologies only by default
- o[:reviews] = reviews[ont.id] || []
- o[:groups] = ont.group || []
- o[:categories] = ont.hasDomain || []
- o[:note_count] = ont.notes.length
- o[:review_count] = ont.reviews.length
- o[:project_count] = ont.projects.length
- o[:private] = ont.private?
- #o[:popularity] = @analytics[ont.acronym] || 0
- o[:submissionStatus] = []
- o[:administeredBy] = ont.administeredBy
- o[:name] = ont.name
- o[:acronym] = ont.acronym
- o[:projects] = ont.projects
- o[:notes] = ont.notes
-
- if !@fair_scores.nil? && !@fair_scores[ont.acronym].nil?
- o[:fairScore] = @fair_scores[ont.acronym]['score']
- o[:normalizedFairScore] = @fair_scores[ont.acronym]['normalizedScore']
- else
- o[:fairScore] = nil
- o[:normalizedFairScore] = 0
- end
-
- if o[:type].eql?('ontology_view')
- unless ontologies_hash[ont.viewOf].blank?
- o[:viewOfOnt] = {
- name: ontologies_hash[ont.viewOf].name,
- acronym: ontologies_hash[ont.viewOf].acronym
- }
+ if @page.page.eql?(1)
+ streams = [prepend("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
+ streams += @count_objects.map do |section, values_count|
+ values_count.map do |value, count|
+ replace("count_#{section}_#{value}") do
+ helpers.turbo_frame_tag("count_#{section}_#{value}") do
+ helpers.content_tag(:span, count.to_s, class: "hide-if-loading #{count.zero? ? 'disabled' : ''}")
+ end
+ end
end
- end
-
- o[:artifacts] = []
- o[:artifacts] << 'notes' if ont.notes.length > 0
- o[:artifacts] << 'reviews' if ont.reviews.length > 0
- o[:artifacts] << 'projects' if ont.projects.length > 0
- o[:artifacts] << 'summary_only' if ont.summaryOnly
-
- sub = submissions_map[ont.acronym]
- if sub
- o[:submissionStatus] = sub.submissionStatus
- o[:submission] = true
- o[:pullLocation] = sub.pullLocation
- o[:description] = sub.description
- o[:creationDate] = sub.creationDate
- o[:released] = sub.released
- o[:naturalLanguage] = sub.naturalLanguage
- o[:hasFormalityLevel] = sub.hasFormalityLevel
- o[:isOfType] = sub.isOfType
- o[:submissionStatusFormatted] = submission_status2string(sub).gsub(/\(|\)/, '')
-
- o[:format] = sub.hasOntologyLanguage
- @formats << sub.hasOntologyLanguage
- else
- # Used to sort ontologies without submissions to the end when sorting on upload date
- o[:creationDate] = DateTime.parse('19900601')
- end
-
- @ontologies << o
+ end.flatten
+ else
+ streams = [replace("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
end
- @ontologies.sort! {|a,b| b[:popularity] <=> a[:popularity]}
-
-
- render 'browse'
+ render turbo_stream: streams
end
def classes
@@ -158,7 +67,7 @@ def classes
get_class(params)
if @submission.hasOntologyLanguage == 'SKOS'
- @schemes = get_schemes(@ontology)
+ @schemes = get_schemes(@ontology)
@collections = get_collections(@ontology, add_colors: true)
else
@instance_details, type = get_instance_and_type(params[:instanceid])
@@ -168,19 +77,16 @@ def classes
@instances_concept_id = get_concept_id(params, @concept, @root)
end
-
if ['application/ld+json', 'application/json'].include?(request.accept)
render plain: @concept.to_jsonld, content_type: request.accept and return
end
@current_purl = @concept.purl if $PURL_ENABLED
- unless @concept.id == 'bp_fake_root'
+ unless @concept.nil? || @concept.id == 'bp_fake_root'
@notes = @concept.explore.notes
end
- update_tab(@ontology, @concept.id)
-
if request.xhr?
render 'ontologies/sections/visualize', layout: false
else
@@ -189,6 +95,9 @@ def classes
end
def properties
+ @acronym = @ontology.acronym
+ @properties = LinkedData::Client::HTTP.get("/ontologies/#{@acronym}/properties/roots", { lang: request_lang })
+
if request.xhr?
return render 'ontologies/sections/properties', layout: false
else
@@ -197,41 +106,40 @@ def properties
end
def create
- if params[:commit].eql? 'Cancel'
- redirect_to ontologies_path and return
+ @is_update_ontology = false
+ @ontology = ontology_from_params.save
+
+ if response_error?(@ontology)
+ show_new_errors(@ontology)
+ return
end
- @ontology = LinkedData::Client::Models::Ontology.new(values: ontology_params)
- @ontology_saved = @ontology.save
- if response_error?(@ontology_saved)
- @categories = LinkedData::Client::Models::Category.all
- @groups = LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
- @user_select_list = LinkedData::Client::Models::User.all.map { |u| [u.username, u.id] }
- @user_select_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
- @errors = response_errors(@ontology_saved)
- render 'new'
+ @submission = save_submission(new_submission_hash(@ontology))
+
+ if response_error?(@submission)
+ @ontology.delete
+ show_new_errors(@submission)
else
- if @ontology_saved.summaryOnly
- redirect_to "/ontologies/success/#{@ontology.acronym}"
- else
- redirect_to new_ontology_submission_path(@ontology.acronym)
- end
+ redirect_to "/ontologies/success/#{@ontology.acronym}"
end
end
def edit
- # Note: find_by_acronym includes ontology views
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
redirect_to_home unless session[:user] && @ontology.administeredBy.include?(session[:user].id) || session[:user].admin?
- @categories = LinkedData::Client::Models::Category.all
- @groups = LinkedData::Client::Models::Group.all
- @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
- @user_select_list.sort! {|a,b| a[1].downcase <=> b[1].downcase}
+
+ submission = @ontology.explore.latest_submission(include: 'submissionId')
+ if submission
+ redirect_to edit_ontology_submission_path(@ontology.acronym, submission.submissionId)
+ else
+ redirect_to new_ontology_submission_path(@ontology.acronym)
+ end
end
def mappings
@ontology_acronym = @ontology.acronym || params[:id]
@mapping_counts = mapping_counts(@ontology_acronym)
+ @ontologies_mapping_count = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}/statistics/ontologies")
if request.xhr?
render partial: 'ontologies/sections/mappings', layout: false
else
@@ -241,12 +149,14 @@ def mappings
def new
@ontology = LinkedData::Client::Models::Ontology.new
- @ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym', include_views: true,
-display_links: false, display_context: false)
+ @ontology.viewOf = params.dig(:ontology, :viewOf)
+ @submission = LinkedData::Client::Models::OntologySubmission.new
+ @submission.hasOntologyLanguage = 'OWL'
+ @ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym', include_views: true, display_links: false, display_context: false)
@categories = LinkedData::Client::Models::Category.all
@groups = LinkedData::Client::Models::Group.all
- @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
- @user_select_list.sort! {|a,b| a[1].downcase <=> b[1].downcase}
+ @user_select_list = LinkedData::Client::Models::User.all.map { |u| [u.username, u.id] }
+ @user_select_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
end
def notes
@@ -263,40 +173,50 @@ def notes
end
def instances
- if request.xhr?
- render partial: 'instances/instances', locals: { id: 'instances-data-table'}, layout: false
- else
- render partial: 'instances/instances', locals: { id: 'instances-data-table'}, layout: 'ontology_viewer'
+
+ if params[:instanceid]
+ @instance = helpers.get_instance_details_json(@ontology.acronym, params[:instanceid], {include: 'all'})
end
+
+ render partial: 'instances/instances', locals: { id: 'instances-data-table' }, layout: 'ontology_viewer'
end
def schemes
@schemes = get_schemes(@ontology)
- scheme_id = params[:scheme_id] || @submission_latest.URI || nil
+ scheme_id = params[:schemeid] || @submission_latest.URI || nil
@scheme = get_scheme(@ontology, scheme_id) if scheme_id
- if request.xhr?
- render partial: 'ontologies/sections/schemes', layout: false
- else
- render partial: 'ontologies/sections/schemes', layout: 'ontology_viewer'
- end
+ render partial: 'ontologies/sections/schemes', layout: 'ontology_viewer'
end
def collections
@collections = get_collections(@ontology)
- collection_id = params[:collection_id]
- @collection = get_collection(@ontology, collection_id) if collection_id
+ collection_id = params[:collectionid]
+ @collection = collection_id ? get_collection(@ontology, collection_id) : @collections.first
+
+ render partial: 'ontologies/sections/collections', layout: 'ontology_viewer'
+ end
+ def sparql
if request.xhr?
- render partial: 'ontologies/sections/collections', layout: false
+ render partial: 'ontologies/sections/sparql', layout: false
else
- render partial: 'ontologies/sections/collections', layout: 'ontology_viewer'
+ render partial: 'ontologies/sections/sparql', layout: 'ontology_viewer'
end
end
+ def content_serializer
+ @result, _ = serialize_content(ontology_acronym: params[:acronym],
+ concept_id: params[:id],
+ format: params[:output_format])
+
+ render 'ontologies/content_serializer', layout: nil
+ end
+
# GET /ontologies/ACRONYM
# GET /ontologies/1.xml
def show
+ return redirect_to_file if redirect_to_file?
# Hack to make ontologyid and conceptid work in addition to id and ontology params
params[:id] = params[:id].nil? ? params[:ontologyid] : params[:id]
@@ -326,21 +246,30 @@ def show
# Note: find_by_acronym includes ontology views
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
- ontology_not_found(params[:ontology]) if @ontology.nil?
+ ontology_not_found(params[:ontology]) if @ontology.nil? || @ontology.errors
# Handle the case where an ontology is converted to summary only.
# See: https://github.com/ncbo/bioportal_web_ui/issues/133.
- if @ontology.summaryOnly && params[:p].present?
- pages = KNOWN_PAGES - ['summary', 'notes']
- if pages.include?(params[:p])
- redirect_to(ontology_path(params[:ontology]), status: :temporary_redirect) and return
- end
+ data_pages = KNOWN_PAGES - %w[summary notes]
+ if @ontology.summaryOnly && params[:p].present? && data_pages.include?(params[:p].to_s)
+ params[:p] = "summary"
end
#@ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
# Get the latest submission (not necessarily the latest 'ready' submission)
- @submission_latest = @ontology.explore.latest_submission(include: 'all') rescue @ontology.explore.latest_submission(include: '')
+
+ @submission_latest = @ontology.explore.latest_submission(include: 'all', invalidate_cache: invalidate_cache?) rescue @ontology.explore.latest_submission(include: '')
+
+
+ unless helpers.submission_ready?(@submission_latest)
+ submissions = @ontology.explore.submissions(include: 'submissionId,submissionStatus')
+ if submissions.any?{|x| helpers.submission_ready?(x)}
+ @old_submission_ready = true
+ elsif !params[:p].blank?
+ params[:p] = "summary"
+ end
+ end
# Is the ontology downloadable?
@ont_restricted = ontology_restricted?(@ontology.acronym)
@@ -354,15 +283,15 @@ def show
params[:p] = 'classes'
redirect_to "/ontologies/#{params[:ontology]}#{params_string_for_redirect(params)}", status: :moved_permanently
when 'classes'
- self.classes #rescue self.summary
+ self.classes # rescue self.summary
when 'mappings'
- self.mappings #rescue self.summary
+ self.mappings # rescue self.summary
when 'notes'
- self.notes #rescue self.summary
+ self.notes # rescue self.summary
when 'widgets'
- self.widgets #rescue self.summary
+ self.widgets # rescue self.summary
when 'properties'
- self.properties #rescue self.summary
+ self.properties # rescue self.summary
when 'summary'
self.summary
when 'instances'
@@ -371,10 +300,11 @@ def show
self.schemes
when 'collections'
self.collections
+ when 'sparql'
+ self.sparql
else
self.summary
end
-
end
def submit_success
@@ -382,31 +312,50 @@ def submit_success
render 'submit_success'
end
+
# Main ontology description page (with metadata): /ontologies/ACRONYM
def summary
- # Note: find_by_acronym includes ontology views
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first if @ontology.nil?
- ontology_not_found(params[:id]) if @ontology.nil?
- # Check to see if user is requesting json-ld, return the file from REST service if so
-
- if request.accept.to_s.eql?('application/ld+json') || request.accept.to_s.eql?('application/json')
- headers['Content-Type'] = request.accept.to_s
- render plain: @ontology.to_jsonld
- return
- end
@metrics = @ontology.explore.metrics rescue []
#@reviews = @ontology.explore.reviews.sort {|a,b| b.created <=> a.created} || []
- @projects = @ontology.explore.projects.sort {|a,b| a.name.downcase <=> b.name.downcase } || []
+ @projects = @ontology.explore.projects.sort { |a, b| a.name.downcase <=> b.name.downcase } || []
@analytics = LinkedData::Client::HTTP.get(@ontology.links['analytics'])
- #Call to fairness assessment service
+ # Call to fairness assessment service
tmp = fairness_service_enabled? ? get_fair_score(@ontology.acronym) : nil
@fair_scores_data = create_fair_scores_data(tmp.values.first) unless tmp.nil?
@views = get_views(@ontology)
- @view_decorators = @views.map{ |view| ViewDecorator.new(view, view_context) }
-
+ @view_decorators = @views.map { |view| ViewDecorator.new(view, view_context) }
+ @ontology_relations_data = ontology_relations_data
+
+ category_attributes = submission_metadata.group_by { |x| x['category'] }.transform_values { |x| x.map { |attr| attr['attribute'] } }
+ @relations_array_display = @relations_array.map do |relation|
+ attr = relation.split(':').last
+ ["#{helpers.attr_label(attr, attr_metadata: helpers.attr_metadata(attr), show_tooltip: false)}(#{relation})",
+ relation]
+ end
+ @config_properties = properties_hash_values(category_attributes["object description properties"])
+ @methodology_properties = properties_hash_values(category_attributes["methodology"])
+ @agents_properties = properties_hash_values(category_attributes["persons and organizations"])
+ @dates_properties = properties_hash_values(category_attributes["dates"])
+ @links_properties = properties_hash_values([:isFormatOf, :hasFormat, :source, :includedInDataCatalog])
+ @content_properties = properties_hash_values(category_attributes["content"])
+ @community_properties = properties_hash_values(category_attributes["community"] + [:notes])
+ @identifiers = properties_hash_values([:URI, :versionIRI, :identifier])
+ @identifiers["ontology_portal_uri"] = ["#{$UI_URL}/ontologies/#{@ontology.acronym}", "#{portal_name} URI"]
+ @projects_properties = properties_hash_values(category_attributes["usage"])
+ @ontology_icon_links = [%w[summary/download dataDump],
+ %w[summary/homepage homepage],
+ %w[summary/documentation documentation],
+ %w[icons/github repository],
+ %w[summary/sparql endpoint],
+ %w[icons/publication publication],
+ %w[icons/searching_database openSearchDescription]
+ ]
+ @ontology_icon_links.each do |icon|
+ icon << helpers.attr_label(icon[1], attr_metadata: helpers.attr_metadata(icon[1]), show_tooltip: false)
+ end
if request.xhr?
render partial: 'ontologies/sections/metadata', layout: false
else
@@ -414,31 +363,27 @@ def summary
end
end
- def update
- if params['commit'] == 'Cancel'
- acronym = params['id']
- redirect_to "/ontologies/#{acronym}"
- return
- end
- # Note: find_by_acronym includes ontology views
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology][:acronym] || params[:id]).first
- @ontology.update_from_params(ontology_params)
- error_response = @ontology.update
- if response_error?(error_response)
- @categories = LinkedData::Client::Models::Category.all
- @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
- @user_select_list.sort! {|a,b| a[1].downcase <=> b[1].downcase}
- @errors = response_errors(error_response)
- @errors = { acronym: 'Acronym already exists, please use another' } if error_response.status == 409
- flash[:error] = @errors
- redirect_to "/ontologies/#{@ontology.acronym}/edit"
+ def subscriptions
+ ontology_id = params[:ontology_id]
+ return not_found if ontology_id.nil?
+
+ ontology_acronym = ontology_id.split('/').last
+
+ if session[:user].nil?
+ link = "/login?redirect=#{request.url}"
+ subscribed = false
+ user_id = nil
else
- # TODO_REV: Enable subscriptions
- # if params["ontology"]["subscribe_notifications"].eql?("1")
- # DataAccess.createUserSubscriptions(@ontology.administeredBy, @ontology.ontologyId, NOTIFICATION_TYPES[:all])
- # end
- redirect_to "/ontologies/#{@ontology.acronym}"
+ user = LinkedData::Client::Models::User.find(session[:user].id)
+ subscribed = helpers.subscribed_to_ontology?(ontology_acronym, user)
+ link = "javascript:void(0);"
+ user_id = user.id
end
+
+ count = helpers.count_subscriptions(params[:ontology_id])
+ render inline: helpers.turbo_frame_tag('subscribe_button') {
+ render_to_string(OntologySubscribeButtonComponent.new(id: '', ontology_id: ontology_id, subscribed: subscribed, user_id: user_id, count: count, link: link), layout: nil)
+ }
end
def virtual
@@ -457,20 +402,152 @@ def widgets
end
end
+ def show_licenses
+
+ @metadata = submission_metadata
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
+ @licenses = %w[hasLicense morePermissions copyrightHolder useGuidelines]
+ @submission_latest = @ontology.explore.latest_submission(include: @licenses.join(","))
+ render partial: 'ontologies/sections/licenses'
+ end
+
+ def ajax_ontologies
+
+ render json: LinkedData::Client::Models::Ontology.all(include_views: true,
+ display: 'acronym,name', display_links: false, display_context: false)
+ end
+
+ def metrics
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
+ @metrics = @ontology.explore.metrics(display_context: false, display_links: false)
+ render partial: 'ontologies/sections/metrics'
+ end
+
+ def metrics_evolution
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
+ key = params[:metrics_key]
+ ontology_not_found(params[:ontology_id]) if @ontology.nil?
+
+ # Retrieve submissions in descending submissionId order (should be reverse chronological order)
+ @submissions = @ontology.explore.submissions({ include: "metrics" })
+ .sort { |a, b| a.submissionId.to_i <=> b.submissionId.to_i }.reverse || []
+
+ metrics = @submissions.map { |s| s.metrics }
+
+ data = {
+ key => metrics.map { |m| m.nil? ? 0 : m[key] }
+ }
+
+ render partial: 'ontologies/sections/metadata/metrics_evolution_graph', locals: { data: data }
+ end
+
+ def ontologies_selector
+ @categories = LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
+ @groups = LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
+ @filters = ontology_filters_init(@categories, @groups)
+ @select_id = params[:id]
+ render 'ontologies/ontologies_selector/ontologies_selector', layout: false
+ end
+
+ def ontologies_selector_results
+ @ontologies = LinkedData::Client::Models::Ontology.all(include_views: params[:showOntologyViews])
+ @total_ontologies_number = @ontologies.length
+ @input = params[:input] || ''
+ @ontologies = @ontologies.select { |ontology| ontology.name.downcase.include?(@input.downcase) || ontology.acronym.downcase.include?(@input.downcase) }
+
+ if params[:groups]
+ @ontologies = @ontologies.select do |ontology|
+ (ontology.group & params[:groups]).any?
+ end
+ end
+
+ if params[:categories]
+ @ontologies = @ontologies.select do |ontology|
+ (ontology.hasDomain & params[:categories]).any?
+ end
+ end
+
+ if params[:formats] || params[:naturalLanguage] || params[:formalityLevel] || params[:isOfType] || params[:showRetiredOntologies]
+ submissions = LinkedData::Client::Models::OntologySubmission.all({ also_include_views: 'true' })
+ if params[:formats]
+ submissions = submissions.select { |submission| params[:formats].include?(submission.hasOntologyLanguage) }
+ end
+ if params[:naturalLanguage]
+ submissions = submissions.select do |submission|
+ (submission.naturalLanguage & params[:naturalLanguage]).any?
+ end
+ end
+ if params[:formalityLevel]
+ submissions = submissions.select { |submission| params[:formalityLevel].include?(submission.hasFormalityLevel) }
+ end
+ if params[:isOfType]
+ submissions = submissions.select { |submission| params[:isOfType].include?(submission.isOfType) }
+ end
+ if params[:showRetiredOntologies]
+ submissions = submissions.reject { |submission| submission.status.eql?('retired') }
+ end
+ @ontologies = @ontologies.select do |ontology|
+ submissions.any? { |submission| submission.ontology.id == ontology.id }
+ end
+ end
+ render 'ontologies/ontologies_selector/ontologies_selector_results'
+ end
private
- def ontology_params
- p = params.require(:ontology).permit(:name, :acronym, { administeredBy:[] }, :viewingRestriction, { acl:[] },
- { hasDomain:[] }, :isView, :viewOf, :subscribe_notifications, {group:[]})
+ def get_views(ontology)
+ views = ontology.explore.views || []
+ views.select! { |view| view.access?(session[:user]) }
+ views.sort { |a, b| a.acronym.downcase <=> b.acronym.downcase }
+ end
+
+ def ontology_relations_data(sub = @submission_latest)
+ ontology_relations_array = []
+ @relations_array = ["omv:useImports", "door:isAlignedTo", "door:ontologyRelatedTo", "omv:isBackwardCompatibleWith", "omv:isIncompatibleWith", "door:comesFromTheSameDomain", "door:similarTo",
+ "door:explanationEvolution", "voaf:generalizes", "door:hasDisparateModelling", "dct:hasPart", "voaf:usedBy", "schema:workTranslation", "schema:translationOfWork"]
+
+ return if sub.nil?
+
+ ont = sub.ontology
+ # Get ontology relations between each other (ex: STY isAlignedTo GO)
+ @relations_array.each do |relation_attr|
+ relation_values = sub.send(relation_attr.to_s.split(':')[1])
+ next if relation_values.nil? || relation_values.empty?
+
+ relation_values = [relation_values] unless relation_values.kind_of?(Array)
- p[:administeredBy].reject!(&:blank?)
- p[:acl].reject!(&:blank?)
- p[:hasDomain].reject!(&:blank?)
- p[:group].reject!(&:blank?)
- p.to_h
+ relation_values.each do |relation_value|
+ next if relation_value.eql?(ont.acronym)
+
+ target_id = relation_value
+ target_in_portal = false
+ target_ont = nil
+ # if we find our portal URL in the ontology URL, then we just keep the ACRONYM to try to get the ontology.
+ if relation_value.include?(helpers.portal_name.downcase)
+ relation_value = relation_value.split('/').last
+ target_ont = LinkedData::Client::Models::Ontology.find_by_acronym(relation_value).first
+ end
+
+ # Use acronym to get ontology from the portal
+ if target_ont
+ target_id = target_ont.acronym
+ target_in_portal = true
+ end
+
+ ontology_relations_array.push({ source: ont.acronym, target: target_id, relation: relation_attr.to_s, targetInPortal: target_in_portal })
+ end
+ end
+
+ ontology_relations_array
end
+ def properties_hash_values(properties, sub: @submission_latest, custom_labels: {})
+ return {} if sub.nil?
+
+ properties.map { |x| [x.to_s, [sub.send(x.to_s), custom_labels[x.to_sym]]] }.to_h
+ end
+
+
def determine_layout
case action_name
when 'index'
@@ -480,10 +557,5 @@ def determine_layout
end
end
- def get_views(ontology)
- views = ontology.explore.views || []
- views.select!{ |view| view.access?(session[:user]) }
- views.sort{ |a,b| a.acronym.downcase <=> b.acronym.downcase }
- end
end
diff --git a/app/controllers/ontologies_metadata_curator_controller.rb b/app/controllers/ontologies_metadata_curator_controller.rb
index 7b9c95cfb..b66c5df32 100644
--- a/app/controllers/ontologies_metadata_curator_controller.rb
+++ b/app/controllers/ontologies_metadata_curator_controller.rb
@@ -5,40 +5,46 @@ class OntologiesMetadataCuratorController < ApplicationController
before_action :submission_metadata, only: [:result, :edit, :update, :show_metadata_by_ontology]
def result
- @ontologies_ids = params[:ontology][:ontologyId].drop(1)
- @metadata_sel = params[:search][:metadata].drop(1)
+ @ontologies_ids = params[:ontology] ? Array(params[:ontology][:ontologyId]) : []
+ @metadata_sel = params[:search] ? params[:search][:metadata] : []
@show_submissions = !params[:show_submissions].nil?
- @ontologies = []
@submissions = []
- if @ontologies_ids.nil? || @ontologies_ids.empty?
- @ontologies = LinkedData::Client::Models::Ontology.all
- else
- @ontologies_ids.each do |data|
- @ontologies << LinkedData::Client::Models::Ontology.find_by_acronym(data).first
- end
- end
-
+ @ontologies = []
display_attribute = equivalent_properties(@metadata_sel) + %w[submissionId]
- @ontologies.each do |ont|
- if @show_submissions
- submissions = ont.explore.submissions({ include: display_attribute.join(',') })
+
+ if @show_submissions
+ if @ontologies_ids.nil? || @ontologies_ids.empty?
+ @ontologies = LinkedData::Client::Models::Ontology.all
else
- submissions = [ont.explore.latest_submission({ include: display_attribute.join(',') })]
+ @ontologies_ids.each do |data|
+ @ontologies << LinkedData::Client::Models::Ontology.find_by_acronym(data).first
+ end
+ end
+ @ontologies.each do |ont|
+ submissions = ont.explore.submissions({ include: display_attribute.join(',') })
+ submissions.each { |sub| append_submission(ont, sub) }
end
- submissions.each { |sub| append_submission(ont, sub) }
+ else
+ @submissions = LinkedData::Client::Models::OntologySubmission.all(acronym: @ontologies_ids.join('|'), display_links: false, display_context: false, include: display_attribute.join(','))
+ @submissions.reject! { |x| !@ontologies_ids.include?(x.id.split('/')[-3]) } unless @ontologies_ids.empty?
+ @submissions.sort_by! { |x| x.id }
end
+
+
+
respond_to do |format|
format.html { redirect_to admin_index_path }
format.turbo_stream { render turbo_stream: [
- replace("selection_metadata_form", partial: "ontologies_metadata_curator/metadata_table"),
- replace('edit_metadata_btn') do
- "
- #{helpers.button_tag("Start bulk edit", onclick: 'showEditForm(event)', class: "btn btn-outline-primary mx-1 w-100")}
- #{raw helpers.help_tooltip('To use the bulk edit select in the table submissions (the rows) and metadata properties (the columns) for which you want to edit')}
- ".html_safe
- end
- ]}
+ replace("selection_metadata_form", partial: "ontologies_metadata_curator/metadata_table")
+ # TODO put again when bulk edit fixed
+ # replace('edit_metadata_btn') do
+ # "
+ # #{helpers.button_tag(t('ontologies_metadata_curator.bulk_edit'), onclick: 'showEditForm(event)', class: "btn btn-outline-primary mx-1 w-100")}
+ # #{raw helpers.help_tooltip(t('ontologies_metadata_curator.use_the_bulk_edit'))}
+ # ".html_safe
+ # end
+ ] }
end
end
@@ -46,8 +52,7 @@ def show_metadata_by_ontology
@acronym = params[:ontology]
inline_save = params[:inline_save] && params[:inline_save].eql?('true')
display_submission_attributes(@acronym, params[:properties]&.split(','),
- submissionId: params[:submission_id],
- show_sections: false, inline_save: inline_save)
+ submissionId: params[:submission_id], inline_save: inline_save)
render partial: 'submissions/form_content', locals: { id: params[:form_id] || '', acronym: @acronym, submissionId: params[:submission_id] }
end
@@ -57,14 +62,15 @@ def show_metadata_value
submission_id = params[:submission_id]
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
@submission = @ontology.explore.submissions({ display: "#{attribute},submissionId" }, submission_id)
-
- render_submission_attribute(attribute)
+ id = attribute_input_frame_id(acronym, submission_id, attribute)
+ render_turbo_stream replace(id, partial: 'ontologies_metadata_curator/attribute', locals: { id: id, attribute: attribute,
+ submission: @submission, ontology: @ontology })
end
def edit
if params[:selected_acronyms].nil? || params[:selected_metadata].nil?
- render_turbo_stream alert_error(id: 'application_modal_content') {'Select in the table submissions (rows) and metadata properties (columns) to start the bulk edit'}
+ render_turbo_stream alert_error(id: 'application_modal_content') { t('ontologies_metadata_curator.start_the_bulk_edit') }
return
end
@@ -79,14 +85,14 @@ def update
@active_ontology = ontology_and_submission_id(params[:active_ontology])
@all_metadata = params[:all_metadata]&.split
error_responses = []
- @submissions = []
+ @submissions = []
active_submission_data = params['submission']["#{@active_ontology[0]}_#{@active_ontology[1]}"]
@selected_ontologies.each do |onto, sub_i|
new_data = active_submission_data
new_data[:ontology] = onto
new_data[:id] = sub_i
- error_responses << update_submission(new_data) if new_data
+ error_responses << update_submission(new_data, sub_i).last if new_data
@submissions << @submission
end
@@ -99,10 +105,10 @@ def update
if errors
render_turbo_stream(alert_error { errors.map { |e| e[:error] }.join(',') })
else
- streams = [alert_success { 'Submissions were successfully updated' }]
+ streams = [alert_success { t('ontologies_metadata_curator.alert_success_submissions') }]
@submissions.each do |submission|
- submission.ontology = OpenStruct.new({acronym: submission.ontology})
- streams << replace("#{ontology_submission_id_label(submission.ontology.acronym, submission.submissionId)}_row", partial: 'ontologies_metadata_curator/metadata_table_row', locals: {submission: submission, attributes: @all_metadata })
+ submission.ontology = OpenStruct.new({ acronym: submission.ontology })
+ streams << replace("#{ontology_submission_id_label(submission.ontology.acronym, submission.submissionId)}_row", partial: 'ontologies_metadata_curator/submission', locals: { submission: submission, attributes: @all_metadata })
end
render_turbo_stream(*streams)
end
@@ -121,45 +127,4 @@ def append_submission(ontology, submission)
@submissions << sub
end
- def metadata_params
- attributes = [
- :ontology,
- :description,
- :hasOntologyLanguage,
- :prefLabelProperty,
- :synonymProperty,
- :definitionProperty,
- :authorProperty,
- :obsoleteProperty,
- :obsoleteParent,
- :version,
- :status,
- :released,
- :isRemote,
- :pullLocation,
- :filePath,
- { contact: [:name, :email] },
- :homepage,
- :documentation,
- :publication
- ]
-
- @metadata.each do |m|
-
- m_attr = m["attribute"].to_sym
-
- attributes << if m["enforce"].include?("list")
- { m_attr => [] }
- else
- m_attr
- end
- end
- out = []
- params.require(:submission).permit!.tap do |x|
- x.keys.each do |y|
- out << x.require(y).permit(attributes.uniq)
- end
- end
- out
- end
end
diff --git a/app/controllers/ontologies_redirection_controller.rb b/app/controllers/ontologies_redirection_controller.rb
new file mode 100644
index 000000000..43269e788
--- /dev/null
+++ b/app/controllers/ontologies_redirection_controller.rb
@@ -0,0 +1,93 @@
+class OntologiesRedirectionController < ApplicationController
+ include UriRedirection
+ include OntologyContentSerializer
+
+ # GET /ontologies/:acronym/:id
+ def redirect
+ return not_found unless params[:acronym] && params[:id]
+
+ request_accept_header = request.env["HTTP_ACCEPT"].split(",")[0]
+ type, resource_id = find_type_by_id(params[:id], params[:acronym])
+
+ if resource_id.nil?
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:acronym]).first
+ @submission_latest = @ontology.explore.latest_submission(include: "URI")
+ resource_id = @submission_latest.URI
+ end
+
+ if request_accept_header == "text/html"
+ if type.nil? || resource_id.blank?
+ redirect_to ontology_path(id: params[:acronym], p: 'summary')
+ else
+ redirect_to link_by_type(resource_id, params[:acronym], type)
+ end
+ else
+ content, serializer_content_type = serialize_content(ontology_acronym: params[:acronym], concept_id: resource_id, format: request_accept_header)
+ render plain: content, content_type: serializer_content_type
+ end
+ end
+
+ # GET /ontologies/:acronym/htaccess
+ def generate_htaccess
+ ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:acronym]).first
+ ontology_uri = ontology.explore.latest_submission(include: 'URI').URI
+ ontology_portal_url = "#{$UI_URL}/ontologies/#{params[:acronym]}"
+
+ @htaccess_content = generate_htaccess_content(ontology_portal_url, ontology_uri)
+ @nginx_content = generate_nginx_content(ontology_portal_url, ontology_uri)
+
+ render 'ontologies/htaccess', layout: nil
+ end
+
+ # GET /ontologies/ACRONYM/download?format=FORMAT
+ def redirect_ontology
+ redirect_url = "#{rest_url}/ontologies/#{params[:acronym]}"
+ download_url = "#{redirect_url}/download?apikey=#{get_apikey}"
+ case params[:format]
+ when 'text/csv', 'csv'
+ redirect_to("#{download_url}&download_format=csv", allow_other_host: true)
+ when 'text/xml', 'text/rdf+xml', 'application/rdf+xml', 'application/xml', 'xml'
+ redirect_to("#{download_url}&download_format=rdf", allow_other_host: true)
+ when 'application/json', 'application/ld+json', 'application/*', 'json'
+ # redirect to the api
+ redirect_to("#{redirect_url}?apikey=#{get_apikey}", allow_other_host: true)
+ else
+ # redirect to download the original file
+ redirect_to("#{download_url}", allow_other_host: true)
+ end
+ end
+
+
+ private
+
+ def generate_htaccess_content(ontology_portal_url, ontology_uri)
+ ontology_rule = nil
+ if ontology_uri
+ ontology_uri += '/' unless ontology_uri.end_with?('/')
+ ontology_rule = "RewriteRule ^#{URI.parse(ontology_uri).path[1..-1]}?$ #{ontology_portal_url} [R=301,L]"
+ end
+
+ <<-HTACCESS.strip_heredoc
+ RewriteEngine On
+ #{ontology_rule if ontology_rule}
+ RewriteRule ^.*/([^/#]+)$ #{ontology_portal_url}/$1 [R=301,L]
+ HTACCESS
+ end
+
+ def generate_nginx_content(ontology_portal_url, ontology_uri)
+ ontology_rule = nil
+ if ontology_uri
+ ontology_uri += '/' unless ontology_uri.end_with?('/')
+ ontology_rule = "rewrite ^#{URI.parse(ontology_uri).path[1..-1]}?$ #{ontology_portal_url} permanent"
+ end
+
+ <<-NGINX.strip_heredoc
+ location / {
+ #{ontology_rule if ontology_rule}
+ if ($request_uri ~ ^.*/([^/]+)$){
+ return 301 #{ontology_portal_url}/$1;
+ }
+ }
+ NGINX
+ end
+end
\ No newline at end of file
diff --git a/app/controllers/precache_controller.rb b/app/controllers/precache_controller.rb
deleted file mode 100644
index 54f229074..000000000
--- a/app/controllers/precache_controller.rb
+++ /dev/null
@@ -1,96 +0,0 @@
-require 'uri'
-
-class PrecacheController < ApplicationController
-
- $UI_PORT = "80"
- # $UI_PORT = "3000"
-
-
- def self.precache_all(delete_cache = false)
- if delete_cache
- p "Deleting general cache info"
- CACHE.delete("act_ont_list")
- CACHE.delete("ont_list")
- CACHE.delete("ontology_acronyms")
- CACHE.delete("classes_all_ontologies")
- end
-
- get_url("http://localhost:#{$UI_PORT}")
- get_url("http://localhost:#{$UI_PORT}/ontologies")
- get_url("http://localhost:#{$UI_PORT}/mappings")
- precache_ontology_summary(delete_cache)
- precache_ontology_notes(delete_cache)
- precache_ontology_mappings(delete_cache)
- precache_ontology_classes(delete_cache)
- end
-
- def self.precache_ontology_classes(delete_cache = false)
- ontologies = DataAccess.getOntologyList
- ontologies.each do |ont|
- if delete_cache
- # remove relevant cache data
- end
-
- get_url("http://localhost:#{$UI_PORT}/ontologies/#{ont.ontologyId}?p=classes")
- end
- end
-
- def self.precache_ontology_summary(delete_cache = false)
- ontologies = DataAccess.getOntologyList
- ontologies.each do |ont|
- if delete_cache
- p "Deleting cache for #{ont.displayLabel}"
- CACHE.delete("#{ont.ontologyId}::_latest")
- CACHE.delete("#{ont.ontologyId}::_versions")
- CACHE.delete("#{ont.ontologyId}::_details")
- CACHE.delete("#{ont.ontologyId}::_metrics")
- end
-
- get_url("http://localhost:#{$UI_PORT}/ontologies/#{ont.ontologyId}")
- end
- end
-
- def self.precache_ontology_mappings(delete_cache = false)
- ontologies = DataAccess.getOntologyList
- ontologies.each do |ont|
- if delete_cache
- CACHE.delete("between_ontologies::map_count::#{ont.ontologyId}")
- end
-
- get_url("http://localhost:#{$UI_PORT}/ontologies/#{ont.ontologyId}?p=mappings")
- end
- end
-
- def self.precache_ontology_notes(delete_cache = false)
- ontologies = DataAccess.getOntologyList
- ontologies.each do |ont|
- if delete_cache
- # remove relevant cache data
- end
-
- get_url("http://localhost:#{$UI_PORT}/ontologies/#{ont.ontologyId}?p=notes")
- end
- end
-
- def self.get_url(url)
- p url
- uri = URI.parse(url)
-
- http = Net::HTTP.new(uri.host, uri.port)
- http.read_timeout = 360
-
- begin
- timer = Time.now
- res = http.start { |con|
- path = uri.path.empty? ? "/" : uri.path
- con.get(path)
- }
- p "Retrieved in #{(Time.now - timer).to_f.round(2)}s"
- rescue Exception => e
- p "Failed to get #{url}: #{e.message}"
- end
-
- res.body
- end
-
-end
diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index eb9f35297..490072b4b 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -22,7 +22,7 @@ def index
def show
projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
if projects.nil? || projects.empty?
- flash[:notice] = flash_error("Project not found: #{params[:id]}")
+ flash[:notice] = flash_error(t('projects.project_not_found', id: params[:id]))
redirect_to projects_path
return
end
@@ -55,7 +55,7 @@ def new
def edit
projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
if projects.nil? || projects.empty?
- flash[:notice] = flash_error("Project not found: #{params[:id]}")
+ flash[:notice] = flash_error(t('projects.project_not_found', id: params[:id]))
redirect_to projects_path
return
end
@@ -79,14 +79,14 @@ def create
# Project successfully created.
if response_success?(@project_saved)
- flash[:notice] = 'Project successfully created'
+ flash[:notice] = t('projects.project_successfully_created')
redirect_to project_path(@project.acronym)
return
end
# Errors creating project.
if @project_saved.status == 409
- error = OpenStruct.new existence: "Project with acronym #{params[:project][:acronym]} already exists. Please enter a unique acronym."
+ error = OpenStruct.new existence: t('projects.error_unique_acronym', acronym: params[:project][:acronym])
@errors = Hash[:error, OpenStruct.new(acronym: error)]
else
@errors = response_errors(@project_saved)
@@ -107,7 +107,7 @@ def update
end
projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
if projects.nil? || projects.empty?
- flash[:notice] = flash_error("Project not found: #{params[:id]}")
+ flash[:notice] = flash_error(t('projects.project_not_found', id: params[:id]))
redirect_to projects_path
return
end
@@ -122,7 +122,7 @@ def update
@errors = response_errors(error_response)
render :edit
else
- flash[:notice] = 'Project successfully updated'
+ flash[:notice] = t('projects.project_successfully_updated')
redirect_to project_path(@project.acronym)
end
end
@@ -132,7 +132,7 @@ def update
def destroy
projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
if projects.nil? || projects.empty?
- flash[:notice] = flash_error("Project not found: #{params[:id]}")
+ flash[:notice] = flash_error(t('projects.project_not_found', id: params[:id]))
redirect_to projects_path
return
end
@@ -140,13 +140,13 @@ def destroy
error_response = @project.delete
if response_error?(error_response)
@errors = response_errors(error_response)
- flash[:notice] = "Project delete failed: #{@errors}"
+ flash[:notice] = t('projects.error_delete_project', errors: @errors)
respond_to do |format|
format.html { redirect_to projects_path }
format.xml { head :internal_server_error }
end
else
- flash[:notice] = 'Project successfully deleted'
+ flash[:notice] = t('projects.project_successfully_deleted')
respond_to do |format|
format.html { redirect_to projects_path }
format.xml { head :ok }
@@ -160,8 +160,9 @@ def destroy
def project_params
p = params.require(:project).permit(:name, :acronym, :institution, :contacts, { creator:[] }, :homePage,
:description, { ontologyUsed:[] })
- p[:creator].reject!(&:blank?)
- p[:ontologyUsed].reject!(&:blank?)
+
+ p[:creator]&.reject!(&:blank?)
+ p[:ontologyUsed]&.reject!(&:blank?)
p.to_h
end
diff --git a/app/controllers/properties_controller.rb b/app/controllers/properties_controller.rb
new file mode 100644
index 000000000..0ff2a3167
--- /dev/null
+++ b/app/controllers/properties_controller.rb
@@ -0,0 +1,94 @@
+class PropertiesController < ApplicationController
+ include TurboHelper, SearchContent
+
+ def index
+ acronym = params[:ontology]
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
+ ontology_not_found(acronym) if @ontology.nil?
+
+ if params[:search].blank?
+ index_tree('properties_sorted_list_view-page-1')
+ else
+ query, page, page_size = helpers.search_content_params
+
+ results, _, next_page, total_count = search_ontologies_content(query: query,
+ page: page,
+ page_size: page_size,
+ filter_by_ontologies: [acronym],
+ filter_by_types: %w[AnnotationProperty ObjectProperty DatatypeProperty])
+
+
+ render inline: helpers.render_search_paginated_list(container_id: 'properties_sorted_list',
+ next_page_url: "/ontologies/#{@ontology.acronym}/properties",
+ child_url: "/ontologies/#{@ontology.acronym}/properties/show",
+ child_turbo_frame: 'property_show',
+ child_param: :propertyid,
+ results: results, next_page: next_page, total_count: total_count)
+ end
+ end
+
+
+ def show
+ @acronym = params[:ontology]
+ @property = get_property(params[:id], @acronym, include: 'all')
+
+ redirect_to(ontology_path(id: params[:ontology], p: 'properties', propertyid: params[:id], lang: request_lang)) and return unless turbo_frame_request?
+
+ render partial: 'show'
+ end
+
+
+ def show_children
+ acronym = params[:ontology]
+ id = params[:propertyid]
+ @property = get_property(id, acronym)
+ @property.children = property_children(id, acronym)
+
+ render turbo_stream: [
+ replace(helpers.child_id(@property) + '_open_link') { TreeLinkComponent.tree_close_icon },
+ replace(helpers.child_id(@property) + '_childs') do
+ helpers.property_tree_component(@property, @property, acronym, request_lang, sub_tree: true)
+ end
+ ]
+ end
+
+ private
+
+ def get_property(id, acronym = params[:acronym], lang = request_lang, include: nil)
+ LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}", { lang: lang , include: include})
+ end
+
+ def property_tree(id, acronym = params[:acronym], lang = request_lang)
+ LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}/tree", { lang: lang })
+ end
+
+ def property_roots(acronym = params[:acronym], lang = request_lang)
+ LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/roots", { lang: lang })
+ end
+
+ def property_children(id, acronym = params[:acronym], lang = request_lang)
+ LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}/children", { lang: lang })
+ end
+
+
+ private
+
+ def index_tree(container_id)
+ if !params[:propertyid].blank?
+ @root = OpenStruct.new({ children: property_tree(params[:propertyid], params[:ontology]) })
+ not_found(@root.children.errors.join) if @root.children.respond_to?(:errors)
+
+ @property = get_property(params[:propertyid], params[:ontology])
+ else
+ @root = OpenStruct.new({ children: property_roots(params[:ontology]) })
+ not_found(@root.children.errors.join) if @root.children.respond_to?(:errors)
+
+ @property ||= @root.children.first
+ end
+
+ render inline: helpers.property_tree_component(@root, @property,
+ @ontology.acronym, request_lang,
+ id: container_id, auto_click: true)
+ end
+
+end
diff --git a/app/controllers/recommender_controller.rb b/app/controllers/recommender_controller.rb
index 591ffc326..64759cd50 100644
--- a/app/controllers/recommender_controller.rb
+++ b/app/controllers/recommender_controller.rb
@@ -1,49 +1,57 @@
class RecommenderController < ApplicationController
layout :determine_layout
+ include ApplicationHelper
# REST_URI is defined in application_controller.rb
RECOMMENDER_URI = "/recommender"
def index
+ @text = params[:text]
+ @results_table_header = [t('recommender.results_table.ontology'), t('recommender.results_table.final_score'),
+ t('recommender.results_table.coverage_score'), t('recommender.results_table.acceptance_score'),
+ t('recommender.results_table.detail_score'), t('recommender.results_table.specialization_score'),
+ t('recommender.results_table.annotations')
+ ]
+ @advanced_options_open = false
+ if params[:max_elements_set]
+ @not_valid_max_num_set = (params[:max_elements_set] < '2') || (params[:max_elements_set] > '4')
+ end
+ unless params[:input].nil? || params[:input].empty? || @not_valid_max_num_set
+ recommendations = LinkedData::Client::HTTP.post(RECOMMENDER_URI, params)
+ @advanced_options_open = !recommender_params_empty?
+ @results = []
+ @json_link = "#{$REST_URL}/recommender?input=#{params[:input]}&apikey=#{$API_KEY}&ontologies=#{params[:ontologies]}&max_elements_set=#{params[:max_elements_set]}&input_type=#{params[:input_type]}&output_type=#{params[:output_type]}&wc=#{params[:wc]}&wa=#{params[:wa]}&wd=#{params[:wd]}&ws=#{params[:ws]}"
+ recommendations.each do |recommendation|
+ row = {
+ ontologies: recommendation_ontologies(recommendation),
+ final_score: percentage(recommendation.evaluationScore),
+ coverage_score: percentage(recommendation.coverageResult.normalizedScore),
+ acceptance_score: percentage(recommendation.acceptanceResult.normalizedScore),
+ details_score: percentage(recommendation.detailResult.normalizedScore),
+ specialization_score: percentage(recommendation.specializationResult.normalizedScore),
+ annotations: recommendation_annotations(recommendation),
+ highlighted: false,
+ }
+ @results.push(row)
+ @results.max_by { |element| element[:final_score] }[:highlighted] = true
+ end
+ end
end
- # def create
- # # Parse params (default values are set at the service level)
- # input = params[:input].strip.gsub("\r\n", " ").gsub("\n", " ")
- # start = Time.now
- # query = RECOMMENDER_URI
- # query += "?input=" + CGI.escape(input)
- # query += "&ontologies=" + CGI.escape(params[:ontologies].join(',')) unless params[:ontologies].nil?
- # query += "&input_type=" + params[:input_type] unless params[:input_type].nil?
- # query += "&output_type=" + params[:output_type] unless params[:output_type].nil?
- # query += "&max_elements_set=" + params[:max_elements_set] unless params[:output_type].nil?
- # query += "&wc=" + params[:wc].to_s unless params[:wc].nil?
- # query += "&ws=" + params[:ws].to_s unless params[:ws].nil?
- # query += "&wa=" + params[:wa].to_s unless params[:wa].nil?
- # query += "&wd=" + params[:wd].to_s unless params[:wd].nil?
- # recommendations = parse_json(query) # See application_controller.rb
- # LOG.add :debug, "Retrieved #{recommendations.length} recommendations: #{Time.now - start}s"
- # render :json => recommendations
- # end
+ def recommendation_ontologies(recommendation)
+ recommendation.ontologies.map { |ont| { acronym: ont.acronym, link: ont.id } }
+ end
+
+ def recommendation_annotations(recommendation)
+ recommendation.coverageResult.annotations.map{|annotation| {text: annotation.text, link: url_to_endpoint(annotation.annotatedClass.links['self'])}}
+ end
- # NOTE: this call (POST) works at a local environment but not in staging
- def create
- start = Time.now
- input = params[:input].strip.gsub("\r\n", " ").gsub("\n", " ")
- # Default values are set at the service level)
- form_data = Hash.new
- form_data['input'] = input
- form_data['ontologies'] = params[:ontologies].join(',') unless params[:ontologies].nil?
- form_data['input_type'] = params[:input_type] unless params[:input_type].nil?
- form_data['output_type'] = params[:output_type] unless params[:output_type].nil?
- form_data['max_elements_set'] = params[:max_elements_set] unless params[:output_type].nil?
- form_data['wc'] = params[:wc].to_s unless params[:wc].nil?
- form_data['ws'] = params[:ws].to_s unless params[:ws].nil?
- form_data['wa'] = params[:wa].to_s unless params[:wa].nil?
- form_data['wd'] = params[:wd].to_s unless params[:wd].nil?
- recommendations = LinkedData::Client::HTTP.post(RECOMMENDER_URI, form_data, raw: true)
- LOG.add :debug, "Retrieved #{recommendations.length} recommendations: #{Time.now - start}s"
- render json: recommendations
+ def percentage(string)
+ result = string.to_f * 100
+ result.round(1).to_s
end
+ def recommender_params_empty?
+ (params[:wc].eql?('0.55') && params[:wa].eql?('0.15') && params[:wd].eql?('0.15') && params[:ws].eql?('0.15') && params[:max_elements_set].eql?('3') && params[:ontologies].nil?)
+ end
end
diff --git a/app/controllers/reviews_controller.rb b/app/controllers/reviews_controller.rb
deleted file mode 100644
index c36ef5b7b..000000000
--- a/app/controllers/reviews_controller.rb
+++ /dev/null
@@ -1,90 +0,0 @@
-class ReviewsController < ApplicationController
-
- layout 'ontology_viewer'
-
- RATING_TYPES = [
- :usabilityRating,
- :coverageRating,
- :qualityRating,
- :formalityRating,
- :correctnessRating,
- :documentationRating
- ].freeze
-
- def new
- @rating_types = RATING_TYPES
- @ontology = LinkedData::Client::Models::Ontology.find(params[:ontology])
- @review = LinkedData::Client::Models::Review.new(values: {ontologyReviewed: @ontology.id, creator: session[:user].id})
-
- if request.xhr?
- render layout: false
- end
- end
-
- # GET /reviews/1/edit
- def edit
- @review = Review.find(params[:id])
- @rating_types = RatingType.all
-
- if request.xhr?
- render layout: false
- end
- end
-
- def create
- @review = LinkedData::Client::Models::Review.new(values: params[:review])
- @ontology = LinkedData::Client::Models::Ontology.find(@review.ontologyReviewed)
- @review_saved = @review.save
- if response_error?(@review_saved)
- @errors = response_errors(@review_saved)
- render :action => "new"
- else
- respond_to do |format|
- format.html do
- flash[:notice] = 'Review was successfully created'
- redirect_to "/ontologies/#{@ontology.acronym}?p=summary"
- end
- format.js do
- render json: {}
- end
- end
- end
- end
-
- # PUT /reviews/1
- # PUT /reviews/1.xml
- def update
- @review = Review.find(params[:id])
- ratings = Hash[*(@review.ratings.map{|rate| [rate.id.to_i, rate] }.flatten)]
- #puts ratings.inspect
- for rating_key in params.keys
- if rating_key.include?("star")
- #puts rating_key.split("_")[1].to_i
- ratings[rating_key.split("_")[1].to_i].value=params[rating_key].to_i
- ratings[rating_key.split("_")[1].to_i].save
- end
- end
- if @review.update_attributes(params[:review])
- @review.reload
- if request.xhr?
- render :action=>'show', :layout=>false
- else
- redirect_to reviews(:ontology=>review.ontology_id)
- end
- else
- render :action => "edit"
- end
- end
-
- # DELETE /reviews/1
- # DELETE /reviews/1.xml
- def destroy
- @review = Review.find(params[:id])
- @review.destroy
-
- respond_to do |format|
- format.html { redirect_to(reviews_url) }
- format.xml { head :ok }
- end
- end
-end
diff --git a/app/controllers/schemes_controller.rb b/app/controllers/schemes_controller.rb
index 661bda5ab..bea96a89d 100644
--- a/app/controllers/schemes_controller.rb
+++ b/app/controllers/schemes_controller.rb
@@ -1,7 +1,39 @@
class SchemesController < ApplicationController
- include SchemesHelper
+ include SchemesHelper, SearchContent
+
+
+ def index
+ acronym = params[:ontology]
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
+ ontology_not_found(acronym) if @ontology.nil?
+
+ if params[:search].blank?
+ @submission_latest = @ontology.explore.latest_submission(include: 'all', invalidate_cache: invalidate_cache?) rescue @ontology.explore.latest_submission(include: '')
+ @schemes = get_schemes(@ontology)
+
+ render partial: 'schemes/tree_view'
+ else
+ query, page, page_size = helpers.search_content_params
+
+ results, _, next_page, total_count = search_ontologies_content(query: query,
+ page: page,
+ page_size: page_size,
+ filter_by_ontologies: [acronym],
+ filter_by_types: ['ConceptScheme'])
+
+
+ render inline: helpers.render_search_paginated_list(container_id: 'schemes_sorted_list',
+ next_page_url: "/ontologies/#{@ontology.acronym}/schemes",
+ child_url: "/ontologies/#{@ontology.acronym}/schemes/show", child_turbo_frame: 'scheme',
+ child_param: :schemeid,
+ results: results, next_page: next_page, total_count: total_count
+ )
+ end
+ end
def show
+ redirect_to(ontology_path(id: params[:ontology_id], p: 'schemes', schemeid: params[:id],lang: request_lang)) and return unless turbo_frame_request?
+
@scheme = get_request_scheme
end
@@ -10,17 +42,17 @@ def show_label
scheme_label = scheme ? scheme['prefLabel'] : params[:id]
scheme_label = scheme_label.nil? || scheme_label.empty? ? params[:id] : scheme_label
- render LabelLinkComponent.inline(params[:id], scheme_label)
+ render LabelLinkComponent.inline(params[:id], helpers.main_language_label(scheme_label))
end
private
def get_request_scheme
- params[:id] = params[:id] ? params[:id] : params[:scheme_id]
+ params[:id] = params[:id] ? params[:id] : params[:schemeid]
params[:ontology_id] = params[:ontology_id] ? params[:ontology_id] : params[:ontology]
if params[:id].nil? || params[:id].empty?
- render :text => "Error: You must provide a valid scheme id"
+ render :text => t('schemes.error_valid_scheme_id')
return
end
@ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index b5d052583..eeb510ca3 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -1,52 +1,72 @@
require 'uri'
class SearchController < ApplicationController
+ include SearchAggregator, SearchContent
skip_before_action :verify_authenticity_token
layout :determine_layout
def index
- @search_query = params[:query].nil? ? params[:q] : params[:query]
- @search_query ||= ""
+ @search_query = params[:query] || params[:q] || ''
+ params[:query] = nil
+ @advanced_options_open = false
+ @search_results = []
+ @json_url = json_link("#{rest_url}/search", {})
+
+ return if @search_query.empty?
+
+ params[:pagesize] = "150"
+ results = LinkedData::Client::Models::Class.search(@search_query, params).collection
+
+ @advanced_options_open = !search_params_empty?
+ @search_results = aggregate_results(@search_query, results)
+ @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
end
def json_search
if params[:q].nil?
- render :text => "No search class provided"
+ render :text => t('search.no_search_class_provided')
return
end
check_params_query(params)
check_params_ontologies(params) # Filter on ontology_id
+ if params["id"]&.eql?('All')
+ params.delete("id")
+ params.delete("ontologies")
+ end
search_page = LinkedData::Client::Models::Class.search(params[:q], params)
@results = search_page.collection
response = ""
obsolete_response = ""
separator = (params[:separator].nil?) ? "~!~" : params[:separator]
- for result in @results
+
+ for result in Array(@results)
# TODO_REV: Format the response with type information, target information
# record_type = format_record_type(result[:recordType], result[:obsolete])
record_type = ""
- target_value = result.prefLabel
+ target_value = result.prefLabel.select{|x| x.include?( params[:q].delete('*'))}.first || result.prefLabel.first
+
case params[:target]
- when "name"
- target_value = result.prefLabel
- when "shortid"
- target_value = result.id
- when "uri"
- target_value = result.id
+ when "name"
+ target_value = result.prefLabel
+ when "shortid"
+ target_value = result.id
+ when "uri"
+ target_value = result.id
end
+ acronym = result.links["ontology"].split('/').last
json = []
json << "#{target_value}"
json << " [obsolete]" if result.obsolete? # used by JS in ontologies/visualize to markup obsolete classes
json << "|#{result.id}"
json << "|#{record_type}"
- json << "|#{result.explore.ontology.acronym}"
+ json << "|#{acronym}"
json << "|#{result.id}" # Duplicated because we used to have shortId and fullId
- json << "|#{result.prefLabel}"
+ json << "|#{target_value}"
# This is nasty, but hard to workaround unless we rewrite everything (form_autocomplete, jump_to, crossdomain_autocomplete)
# to use JSON from the bottom up. To avoid this, we pass a tab separated column list
# Columns: synonym
@@ -54,8 +74,8 @@ def json_search
if params[:id] && params[:id].split(",").length == 1
json << "|#{CGI.escape((result.definition || []).join(". "))}#{separator}"
else
- json << "|#{result.explore.ontology.name}"
- json << "|#{result.explore.ontology.acronym}"
+ json << "|#{acronym}"
+ json << "|#{acronym}"
json << "|#{CGI.escape((result.definition || []).join(". "))}#{separator}"
end
@@ -80,6 +100,22 @@ def json_search
render plain: response, content_type: content_type
end
+ def json_ontology_content_search
+ query = params[:search] || '*'
+ page = (params[:page] || 1).to_i
+ acronyms = params[:ontologies]&.split(',') || []
+ page_size = (params[:page_size] || 10).to_i
+ type = params[:types]&.split(',') || []
+
+
+ results, page, next_page, total_count = search_ontologies_content(query: query,
+ page: page,
+ page_size: page_size,
+ filter_by_ontologies: acronyms,
+ filter_by_types: type)
+
+ render json: results
+ end
private
@@ -103,21 +139,17 @@ def check_params_ontologies(params)
end
end
- def format_record_type(record_type, obsolete = false)
- case record_type
- when "apreferredname"
- record_text = "Preferred Name"
- when "bconceptid"
- record_text = "Class ID"
- when "csynonym"
- record_text = "Synonym"
- when "dproperty"
- record_text = "Property"
- else
- record_text = ""
- end
- record_text = "Obsolete Class" if obsolete
- record_text
+ def search_params
+ [
+ :ontologies, :categories,
+ :also_search_properties, :also_search_obsolete, :also_search_views,
+ :require_exact_match, :require_definition
+ ]
+ end
+
+ def search_params_empty?
+ (params[:lang].nil? || params[:lang].eql?('all')) &&
+ search_params.all?{|key| params[key].nil? || params[key].empty?}
end
end
diff --git a/app/controllers/statistics_controller.rb b/app/controllers/statistics_controller.rb
new file mode 100644
index 000000000..ac3828f02
--- /dev/null
+++ b/app/controllers/statistics_controller.rb
@@ -0,0 +1,14 @@
+class StatisticsController < ApplicationController
+ include StatisticsHelper, ComponentsHelper
+
+ layout :determine_layout
+
+ def index
+ projects = LinkedData::Client::Models::Project.all({include: 'created'})
+ users = LinkedData::Client::Models::User.all({include: 'created'})
+ year_month_count, @year_month_visits = ontologies_by_year_month
+ @merged_data = merge_time_evolution_data([group_by_year_month(users),
+ group_by_year_month(projects),
+ year_month_count])
+ end
+end
diff --git a/app/controllers/submissions_controller.rb b/app/controllers/submissions_controller.rb
index 5bb8b3501..d08a99055 100644
--- a/app/controllers/submissions_controller.rb
+++ b/app/controllers/submissions_controller.rb
@@ -1,5 +1,5 @@
class SubmissionsController < ApplicationController
- include SubmissionsHelper, SubmissionUpdater
+ include SubmissionsHelper, SubmissionUpdater, OntologyUpdater
include DoiRequest
layout :determine_layout
before_action :authorize_and_redirect, :only => [:edit, :update, :create, :new]
@@ -14,41 +14,44 @@ def index
@ont_restricted = ontology_restricted?(@ontology.acronym)
# Retrieve submissions in descending submissionId order (should be reverse chronological order)
- @submissions = @ontology.explore.submissions({include: "submissionId,creationDate,released,modificationDate,submissionStatus,hasOntologyLanguage,version,diffFilePath,ontology"})
+ @submissions = @ontology.explore.submissions({include: "submissionId,creationDate,released,modificationDate,submissionStatus,hasOntologyLanguage,version,diffFilePath,ontology", invalidate_cache: invalidate_cache?})
.sort {|a,b| b.submissionId.to_i <=> a.submissionId.to_i } || []
- LOG.add :error, "No submissions for ontology: #{@ontology.id}" if @submissions.empty?
-
+ LOG.add :error, t('submissions.no_submissions_for_ontology', ontology: @ontology.id) if @submissions.empty?
+ render :index, layout: nil
end
# When getting "Add submission" form to display
def new
- @required_only = params[:required].nil? || !params[:required]&.eql?('false')
- @ontology = LinkedData::Client::Models::Ontology.get(CGI.unescape(params[:ontology_id])) rescue nil
- @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first unless @ontology
- @submission = @ontology.explore.latest_submission
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
+ @submission = @ontology.explore.latest_submission || LinkedData::Client::Models::OntologySubmission.new
@identifier_request = first_pending_doi_request
- @submission ||= LinkedData::Client::Models::OntologySubmission.new
@submission.id = nil
+ @categories = LinkedData::Client::Models::Category.all
+ @groups = LinkedData::Client::Models::Group.all
+ @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
+ @user_select_list.sort! {|a,b| a[1].downcase <=> b[1].downcase}
+ @is_update_ontology = true
+ render "ontologies/new"
end
# Called when form to "Add submission" is submitted
def create
- # Make the contacts an array
- _, submission_params = params[:submission].each.first
- @required_only = !params['required-only'].nil?
- @filters_disabled = true
- @submission_saved = save_submission(submission_params)
- if response_error?(@submission_saved)
- @errors = response_errors(@submission_saved) # see application_controller::response_errors
- if @errors && @errors[:uploadFilePath]
- @errors = ["Please specify the location of your ontology"]
- elsif @errors && @errors[:contact]
- @errors = ["Please enter a contact"]
+ @is_update_ontology = true
+
+ if params[:ontology]
+ @ontology, response = update_existent_ontology(params[:ontology_id])
+
+ if response.nil? || response_error?(response)
+ show_new_errors(response)
+ return
end
+ end
+ @submission = @ontology.explore.latest_submission({ display: 'all' })
+ @submission = save_submission(new_submission_hash(@ontology, @submission))
- reset_agent_attributes
- render 'new', status: 422
+ if response_error?(@submission)
+ show_new_errors(@submission)
else
cancel_pending_doi_requests
submit_new_doi_request if doi_requested?
@@ -57,51 +60,70 @@ def create
end
# Called when form to "Edit submission" is submitted
- def edit
- display_submission_attributes params[:ontology_id], params[:properties]&.split(','), submissionId: params[:id],
- required: params[:required]&.eql?('true'),
- show_sections: params[:show_sections].nil? || params[:show_sections].eql?('true'),
+ def edit_properties
+ display_submission_attributes params[:ontology_id], params[:properties]&.split(','), submissionId: params[:submission_id],
inline_save: params[:inline_save]&.eql?('true')
@identifier_request = first_pending_doi_request
+
+ attribute_template_output = render_to_string(inline: helpers.render_submission_inputs(params[:container_id] || 'metadata_by_ontology', @submission))
+
+ render inline: attribute_template_output
+
+ end
+
+ def edit
+ @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
+ ontology_not_found(params[:ontology_id]) unless @ontology
+ category_attributes = submission_metadata.group_by{|x| x['category']}.transform_values{|x| x.map{|attr| attr['attribute']} }
+ category_attributes = category_attributes.reject{|key| ['no'].include?(key.to_s)}
+ category_attributes['general'] << %w[acronym name groups administeredBy categories]
+ category_attributes['licensing'] << 'viewingRestriction'
+ category_attributes['relations'] << 'viewOf'
+ @selected_attributes = Array(params[:properties])
+ if @selected_attributes.empty?
+ @categories_order = ['general', 'description', 'dates', 'licensing', 'persons and organizations', 'links', 'media', 'community', 'usage' ,'relations', 'content','methodology', 'object description properties']
+ @category_attributes = category_attributes
+ end
+ render 'submissions/edit', layout: params[:container_id] ? nil : 'ontology'
end
# When editing a submission (called when submit "Edit submission information" form)
def update
- error_responses = []
- _, submission_params = params[:submission].each.first
-
- error_responses << update_submission(submission_params)
+ @is_update_ontology = true
+ acronym = params[:ontology_id]
+ submission_id = params[:id]
+ if params[:ontology]
+ @ontology, response = update_existent_ontology(acronym)
+
+ if response.nil? || response_error?(response)
+ show_new_errors(response, partial: 'submissions/form_content', id: 'test')
+ return
+ end
+ end
- if error_responses.compact.any? { |x| x.status != 204 }
- @errors = error_responses.map { |error_response| response_errors(error_response) }
+ if params[:submission].nil?
+ return redirect_to "/ontologies/#{acronym}",
+ notice: t('submissions.submission_updated_successfully')
end
- if @errors && !params[:attribute]
- @required_only = !params['required-only'].nil?
- @filters_disabled = true
- reset_agent_attributes
- render 'edit', status: 422
- elsif params[:attribute]
+ @submission, response = update_submission(update_submission_hash(acronym), submission_id, @ontology)
+ if params[:attribute].nil?
+ if response_error?(response)
+ show_new_errors(response, partial: 'submissions/form_content', id: 'test')
+ else
+ redirect_to "/ontologies/#{acronym}",
+ notice: t('submissions.submission_updated_successfully'), status: :see_other
+ end
+ else
+ @errors = response_errors(response) if response_error?(response)
+ @submission = submission_from_params(params[:submission])
+ @submission.submissionId = submission_id
reset_agent_attributes
render_submission_attribute(params[:attribute])
- else
submit_new_doi_request if doi_requested?
- redirect_to "/ontologies/#{@ontology.acronym}"
end
end
- private
-
- def reset_agent_attributes
- helpers.agent_attributes.each do |attr|
- current_val = @submission.send(attr)
- new_values = Array(current_val).map { |x| LinkedData::Client::Models::Agent.find(x) }
-
- new_values = new_values.first unless current_val.is_a?(Array)
-
- @submission.send("#{attr}=", new_values)
- end
- end
end
diff --git a/app/controllers/subscriptions_controller.rb b/app/controllers/subscriptions_controller.rb
index 54040a415..54d262c56 100644
--- a/app/controllers/subscriptions_controller.rb
+++ b/app/controllers/subscriptions_controller.rb
@@ -3,7 +3,7 @@ class SubscriptionsController < ApplicationController
def create
# Try to get the user linked data instance
user_id = params[:user_id]
- u = LinkedData::Client::Models::User.find(user_id)
+ u = LinkedData::Client::Models::User.get(helpers.escape(user_id), include: 'all')
raise Exception if u.nil?
# Try to get the ontology linked data instance
@@ -25,6 +25,8 @@ def create
# So here we re-generate a new subscription Array (instead of directly updating it, which causes error)
all_subs = []
u.subscription.each do |subs|
+ next if subs.ontology.nil?
+
# Add all subscription to the array, but not the one to be deleted
if !subs.ontology.split('/').last.eql?(ont.acronym)
all_subs.push({ontology: subs.ontology, notification_type: subs.notification_type})
@@ -42,6 +44,7 @@ def create
already_subscribed = false
all_subs = []
u.subscription.each do |subs|
+ next if subs.ontology.nil?
# add all existing subscriptions
all_subs.push({ontology: subs.ontology, notification_type: subs.notification_type})
if subs.ontology.split("/").last == ont.acronym && subs.notification_type == "NOTES"
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index 288b352f3..f487637be 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -1,25 +1,36 @@
class UsersController < ApplicationController
- before_action :unescape_id, only: [:edit, :show, :update]
before_action :verify_owner, only: [:edit, :show, :subscribe, :un_subscribe]
before_action :authorize_admin, only: [:index,:subscribe, :un_subscribe]
layout :determine_layout
+ include TurboHelper
+
+
+ def index
+
+ onts = LinkedData::Client::Models::Ontology.all(include: 'administeredBy')
+ projects = LinkedData::Client::Models::Project.all(include: 'creator')
+
+ @users = LinkedData::Client::Models::User.all(include: 'all')
+ @users.each do |user|
+ user.ontologies = onts.select {|o| o.administeredBy.include? user.id }
+ user.project = projects.select {|p| p.creator.include? user.id }
+ end
+
+ end
# GET /users/1
# GET /users/1.xml
def show
@user = if session[:user].admin? && params.has_key?(:id)
- LinkedData::Client::Models::User.find_by_username(params[:id]).first
+ find_user(params[:id])
else
- LinkedData::Client::Models::User.find(session[:user].id)
+ find_user(session[:user].id)
end
@all_ontologies = LinkedData::Client::Models::Ontology.all(ignore_custom_ontologies: true)
- logger.info 'user show'
- logger.info @user.bring_remaining
- logger.info @user
@user_ontologies = @user.customOntology
## Copied from home controller , account action
@@ -37,10 +48,9 @@ def new
# GET /users/1;edit
def edit
- @user = LinkedData::Client::Models::User.find(params[:id])
- @user ||= LinkedData::Client::Models::User.find_by_username(params[:id]).first
+ @user = find_user
- if (params[:password].eql?("true"))
+ if params[:password].eql?("true")
@user.validate_password = true
end
end
@@ -63,7 +73,7 @@ def create
SubscribeMailer.register_for_announce_list(@user.email,@user.firstName,@user.lastName).deliver rescue nil
end
- flash[:notice] = 'Account was successfully created'
+ flash[:notice] = t('users.account_successfully_created')
session[:user] = LinkedData::Client::Models::User.authenticate(@user.username, @user.password)
redirect_to_browse
end
@@ -75,8 +85,7 @@ def create
# PUT /users/1
# PUT /users/1.xml
def update
- @user = LinkedData::Client::Models::User.find(params[:id])
- @user = LinkedData::Client::Models::User.find_by_username(params[:id]).first if @user.nil?
+ @user = find_user
@errors = validate_update(user_params)
if @errors.size < 1
@@ -98,7 +107,7 @@ def update
# @errors = {acronym: "Username already exists, please use another"} if error_response.status == 409
render action: "edit"
else
- flash[:notice] = 'Account was successfully updated'
+ flash[:notice] = t('users.account_successfully_updated')
if session[:user].username == @user.username
session[:user].update_from_params(user_params)
@@ -112,23 +121,33 @@ def update
# DELETE /users/1
def destroy
- response = {errors: '', success: ''}
- @user = LinkedData::Client::Models::User.find(params[:id])
- @user = LinkedData::Client::Models::User.find_by_username(params[:id]).first if @user.nil?
- if(session[:user].admin?)
+ response = {errors: nil, success: ''}
+ @user = find_user
+
+ if session[:user].admin?
@user.delete
- response[:success] << 'User deleted successfully '
+ response[:success] << t('users.user_deleted_successfully')
else
- response[:errors] << 'Not permitted '
+ response[:errors] << t('users.not_permitted')
end
- render json: response
+ respond_to do |format|
+ format.turbo_stream do
+ if response[:errors]
+ render_turbo_stream alert(type: 'danger') { response[:errors].to_s }
+ else
+ render turbo_stream: [
+ alert(type: 'success') { response[:success] },
+ turbo_stream.remove(params[:id])
+ ]
+ end
+ end
+ end
end
def custom_ontologies
- @user = LinkedData::Client::Models::User.find(params[:id])
- @user = LinkedData::Client::Models::User.find_by_username(params[:id]).first if @user.nil?
+ @user = find_user
custom_ontologies = params[:ontology] ? params[:ontology][:ontologyId] : []
custom_ontologies.reject!(&:blank?)
@@ -136,14 +155,14 @@ def custom_ontologies
error_response = !@user.update
if error_response
- flash[:notice] = 'Error saving Custom Ontologies, please try again'
+ flash[:notice] = t('users.error_saving_custom_ontologies')
else
updated_user = LinkedData::Client::Models::User.find(@user.id)
session[:user].update_from_params(customOntology: updated_user.customOntology)
flash[:notice] = if updated_user.customOntology.empty?
- 'Custom Ontologies were cleared'
+ t('users.custom_ontologies_cleared')
else
- 'Custom Ontologies were saved'
+ t('users.custom_ontologies_saved')
end
end
redirect_to user_path(@user.username)
@@ -151,10 +170,11 @@ def custom_ontologies
def subscribe
- @user = LinkedData::Client::Models::User.find_by_username(params[:username]).first
+ @user = find_user
deliver "subscribe", SubscribeMailer.register_for_announce_list(@user.email,@user.firstName,@user.lastName)
end
+
def un_subscribe
@email = params[:email]
deliver "unsubscribe", SubscribeMailer.unregister_for_announce_list(@email)
@@ -163,13 +183,23 @@ def un_subscribe
private
+ def find_user(id = params[:id])
+ id = helpers.unescape(id)
+ @user = LinkedData::Client::Models::User.find(helpers.escape(id), include: 'all')
+ @user ||= LinkedData::Client::Models::User.find_by_username(helpers.escape(id), include: 'all').first
+
+ not_found("User with id #{id} not found") if @user.nil?
+
+ @user
+ end
+
def deliver(action,job)
begin
job.deliver
to_or_from = action.eql?("subscribe") ? "to" : "from"
- flash[:success] = "You have successfully #{action} #{to_or_from} our user mailing list: #{$ANNOUNCE_LIST}"
+ flash[:success] = t('users.subscribe_flash_message', action: action, to_or_from: to_or_from, list: $ANNOUNCE_LIST)
rescue => exception
- flash[:error] = "Something went wrong ..."
+ flash[:error] = t('users.error_subscribe')
end
redirect_to '/account'
end
@@ -178,7 +208,7 @@ def user_params
params[:user]["orcidId"] = extract_id_from_url(params[:user]["orcidId"], 'orcid.org')
params[:user]["githubId"] = extract_id_from_url(params[:user]["githubId"], 'github.com')
p = params.require(:user).permit(:firstName, :lastName, :username, :orcidId, :githubId, :email, :email_confirmation, :password,
- :password_confirmation, :register_mail_list, :admin)
+ :password_confirmation, :register_mail_list, :admin, :terms_and_conditions)
p.to_h
end
@@ -213,25 +243,31 @@ def get_ontology_list(ont_hash)
def validate(params)
errors = []
if params[:email].nil? || params[:email].length < 1 || !params[:email].match(/^[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,}$/i)
- errors << "Please enter an email address"
+ errors << t('users.validate_email_address')
end
if params[:password].nil? || params[:password].length < 1
- errors << "Please enter a password"
+ errors << t('users.validate_password')
end
if !params[:password].eql?(params[:password_confirmation])
- errors << "Your Password and Password Confirmation do not match"
+ errors << t('users.validate_password_confirmation')
end
if using_captcha?
if !verify_recaptcha
- errors << "Please fill in the proper text from the supplied image"
+ errors << t('users.recaptcha_validation')
end
end
+
+
if ((!params[:orcidId].match(/^\d{4}+(-\d{4})+$/)) || (params[:orcidId].length != 19)) && !(params[:orcidId].nil? || params[:orcidId].length < 1)
- errors << "Please enter a valide orcid id"
+ errors << t('users.validate_orcid')
end
if params[:username].nil? || params[:username].length < 1 || !params[:username].match(/^[a-zA-Z0-9]([._-](?![._-])|[a-zA-Z0-9]){3,18}[a-zA-Z0-9]$/)
- errors << "please enter a valid username"
+ errors << t('users.validate_username')
+ end
+
+ unless params[:terms_and_conditions]
+ errors << t('users.validate_terms_and_conditions')
end
return errors
end
@@ -239,22 +275,22 @@ def validate(params)
def validate_update(params)
errors = []
if params[:email].nil? || params[:email].length < 1 || !params[:email].match(/^[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}$/i)
- errors << "Please enter a valid email adresse"
+ errors << t('users.valid_email_adresse')
end
if params[:firstName].nil? || params[:firstName].length < 1
- errors << "First name field is required"
+ errors << t('users.first_name_required')
end
if params[:lastName].nil? || params[:lastName].length < 1
- errors << "Last name field is required"
+ errors << t('users.last_name_required')
end
if params[:username].nil? || params[:username].length < 1
- errors << "Last name field is required"
+ errors << t('users.last_name_required')
end
if params[:orcidId].present? && ((!params[:orcidId].match(/^\d{4}-\d{4}-\d{4}-\d{4}$/)) || (params[:orcidId].length != 19))
- errors << "Please enter a valide orcide id"
+ errors << t('users.validate_orcid')
end
if !params[:password].eql?(params[:password_confirmation])
- errors << "Your Password and Password Confirmation do not match"
+ errors << t('users.validate_password_confirmation')
end
return errors
diff --git a/app/controllers/virtual_appliance_controller.rb b/app/controllers/virtual_appliance_controller.rb
index 5b3701711..c78b6603f 100644
--- a/app/controllers/virtual_appliance_controller.rb
+++ b/app/controllers/virtual_appliance_controller.rb
@@ -19,7 +19,7 @@ def create
user = LinkedData::Client::Models::User.find_by_username(params[:appliance_user][:user_id]).first
if user.nil?
- flash[:error] = "Problem adding account #{params[:appliance_user][:user_id]} : account does not exist".html_safe
+ flash[:error] = t('ontoportal_virtual_appliance.problem_adding_account', id: params[:appliance_user][:user_id]).html_safe
redirect_to action: 'index' and return
end
@@ -38,7 +38,7 @@ def create
def require_login
return if session[:user]
- flash[:error] = 'You must be logged in to access this section'
+ flash[:error] = t('ontoportal_virtual_appliance.require_login')
redirect_to login_index_path(redirect: virtual_appliance_index_path)
end
end
diff --git a/app/helpers/admin/licenses_helper.rb b/app/helpers/admin/licenses_helper.rb
index 4d11f0b1f..90fa67bbf 100644
--- a/app/helpers/admin/licenses_helper.rb
+++ b/app/helpers/admin/licenses_helper.rb
@@ -2,12 +2,11 @@ module Admin::LicensesHelper
def license_notification(license)
days = license.days_remaining
-
if (days == 0)
- msg = (t(".license_expired") << " " << t(".license_contact")).html_safe
+ msg = (t("admin.licenses.license_notification.license_expired") << " " << t("admin.licenses.license_notification.license_contact")).html_safe
notification = tag.div msg, class: "alert alert-danger mt-3", role: "alert"
elsif license.is_trial?
- msg = (t(".license_trial", count: days) << " " << t(".license_obtain") << " " << t(".license_contact")).html_safe
+ msg = (t("admin.licenses.license_notification.license_trial", count: days) << " " << t("admin.licenses.license_notification.license_obtain") << " " << t("admin.licenses.license_notification.license_contact")).html_safe
notification = tag.div msg, class: "alert alert-info mt-3", role: "alert"
end
diff --git a/app/helpers/admin_helper.rb b/app/helpers/admin_helper.rb
index 7553a567d..b7814bef3 100644
--- a/app/helpers/admin_helper.rb
+++ b/app/helpers/admin_helper.rb
@@ -3,4 +3,23 @@ def selected_admin_section?(section_title)
current_section = params[:section] || 'site'
current_section.eql?(section_title)
end
+
+
+ def new_ontologies_created_title
+ content_tag(:div,
+ t('admin.new_ontologies_created_title', count: @new_ontologies_count.join(', ')),
+ style: 'width: 400px; max-height: 300px')
+ end
+
+ def visits_evolution
+ return 0 if @users_visits[:visits].empty?
+
+ @users_visits[:visits].last - @users_visits[:visits][-2]
+ end
+
+ def action_button(name, link, method: :post, class_style: 'btn btn-link')
+ button_to name, link, method: method, class: class_style,
+ form: {data: { turbo: true, turbo_confirm: t('admin.turbo_confirm', name: name), turbo_frame: '_top'}}
+
+ end
end
diff --git a/app/helpers/agent_helper.rb b/app/helpers/agent_helper.rb
index 1b3630a55..00caebe47 100644
--- a/app/helpers/agent_helper.rb
+++ b/app/helpers/agent_helper.rb
@@ -41,17 +41,34 @@ def agent_id(agent)
def link_to_agent_edit_modal(agent, parent_id = nil)
- link_to_modal(nil, edit_agent_path(agent_id(agent), parent_id: parent_id, show_affiliations: parent_id.nil? || parent_id.empty?), class: 'btn btn-sm btn-light', data: { show_modal_title_value: "Edit agent #{agent.id}" }) do
+ link_to_modal(nil, edit_agent_path(agent_id(agent), parent_id: parent_id, show_affiliations: parent_id.nil? || parent_id.empty?), class: 'btn btn-sm btn-light', data: { show_modal_title_value: "Edit agent #{agent.name}" }) do
content_tag(:i, '', class: 'far fa-edit')
end
end
- def link_to_agent_edit(agent, parent_id = nil)
- link_to(edit_agent_path(agent_id(agent), parent_id: parent_id, show_affiliations: parent_id.nil? || parent_id.empty?), class: 'btn btn-sm btn-light') do
+ def link_to_agent_edit(agent, parent_id, name_prefix, deletable: false, show_affiliations: true)
+ link_to(edit_agent_path(agent_id(agent), name_prefix: name_prefix, deletable: deletable, parent_id: parent_id, show_affiliations: show_affiliations), class: 'btn btn-sm btn-light') do
content_tag(:i, '', class: 'far fa-edit')
end
end
+
+ def link_to_search_agent(id, parent_id , name_prefix, agent_type, deletable)
+ link_to("/agents/show_search?id=#{id}&parent_id=#{parent_id}&agent_type=#{agent_type}&deletable=#{deletable}&name_prefix=#{name_prefix}", class: 'btn btn-sm btn-light') do
+ inline_svg_tag "x.svg", width: "25", height: "25"
+ end
+ end
+
+ def agent_search_input(id, agent_type, parent_id: , name_prefix:, deletable: false)
+ render TurboFrameComponent.new(id: agent_id_frame_id(id, parent_id)) do
+ render AgentSearchInputComponent.new(id: id, agent_type: agent_type,
+ name_prefix: name_prefix,
+ parent_id: parent_id, deletable: deletable,
+ edit_on_modal: false)
+ end
+ end
+
+
def affiliation?(agent)
agent.agentType.eql?('organization')
end
@@ -78,15 +95,6 @@ def display_identifiers(identifiers, link: true)
end.join(', ')
end
- def display_agent(agent, link: true)
- out = agent.name.to_s.titleize
- identifiers = display_identifiers(agent.identifiers, link: link)
- out = "#{out} (#{identifiers})" unless identifiers.empty?
- affiliations = agent.affiliations.map { |a| display_agent(a, link: link) }.join(', ')
- out = "#{out} (affiliations: #{affiliations})" unless affiliations.empty?
- out
- end
-
def agent_field_name(name, name_prefix = '')
name_prefix&.empty? ? name : "#{name_prefix}[#{name}]"
end
@@ -101,4 +109,132 @@ def new_affiliation_obj
a.creator = session[:user].id
a
end
+
+ def agent_usages(agent = @agent)
+ usages = agent.usages.to_h
+ usages.delete(:links)
+ usages.delete(:context)
+ usages
+ end
+
+ def agent_usages_count(agent = @agent)
+ usages = agent_usages(agent)
+ usages.values.flatten.size
+ end
+
+ def agents_metadata
+ submission_metadata.select { |x| x["enforce"]&.include?('Agent') }.map do |x|
+ SubmissionInputsHelper::SubmissionMetadataInput.new(attribute_key: x["attribute"], attr_metadata: x)
+ end
+ end
+ def agents_metadata_attributes
+ agents_metadata.map { |x| [x.attr, x.label] }
+ end
+
+ def agents_used_properties(agent)
+ usages = agent_usages(agent)
+ attributes = agents_metadata_attributes
+
+ attributes.map do |attr, label|
+ [attr, usages.select { |x, v| v.any? { |uri| uri[attr] } }.keys.map { |x| x.to_s.split('/')[-3] }]
+ end.to_h
+ end
+
+ def agent_usage_errors_display(errors)
+ content_tag(:div) do
+ errors.map do |ont, message|
+ content_tag(:p) do
+ (content_tag(:strong, ont) + t('agents.ontology_not_valid') + agent_usage_error_display(message[:error])).html_safe
+ end
+ end.join.html_safe
+ end
+ end
+
+ def agent_usage_error_display(error)
+ error.map do |attr, details|
+ details.values.join(', ').html_safe
+ end.join('. ').html_safe
+ end
+
+ def display_agent(agent, link: true)
+ agent_chip_component(agent)
+ end
+
+ def agent_tooltip(agent)
+ name = agent.name
+ email = agent.email
+ type = agent.agentType
+ identifiers = display_identifiers(agent.identifiers, link: false)
+ identifiers = orcid_number(identifiers)
+ if agent.affiliations && agent.affiliations != []
+ affiliations = ""
+ agent.affiliations.each do |affiliation|
+ affiliations = affiliations + affiliation.acronym + " "
+ end
+ end
+ person_icon = inline_svg_tag 'icons/person.svg' , class: 'agent-type-icon'
+ organization_icon = inline_svg_tag 'icons/organization.svg', class: 'agent-type-icon'
+ ror_icon = inline_svg_tag 'icons/ror.svg', class: 'agent-dependency-icon ror'
+ orcid_icon = inline_svg_tag 'icons/orcid.svg', class: 'agent-dependency-icon'
+ agent_icon = type == "organization" ? organization_icon : person_icon
+ identifiers_icon = type == "organization" ? ror_icon : orcid_icon
+ tooltip_html = generate_agent_tooltip(agent_icon, name, email, identifiers, affiliations, identifiers_icon)
+ return tooltip_html
+ end
+
+ def generate_agent_tooltip(agent_icon, name, email = nil, identifiers = nil, affiliations = nil, identifiers_icon = nil)
+ content_tag(:div, class: 'agent-container') do
+ content_tag(:div, agent_icon, class: 'agent-circle') +
+ content_tag(:div) do
+ content_tag(:div, name, class: 'agent-name') +
+ content_tag(:div, email || '', class: 'agent-dependency') +
+ unless identifiers.to_s.empty?
+ content_tag(:div, class: 'agent-dependency') do
+ identifiers_icon +
+ identifiers || ''
+ end
+ end +
+ unless affiliations.to_s.empty?
+ content_tag(:div, class: 'agent-dependency') do
+ inline_svg_tag('icons/organization.svg', class: 'agent-dependency-icon') +
+ affiliations || ''
+ end
+ end
+ end
+ end
+ end
+
+
+ def agent_chip_component(agent)
+ person_icon = inline_svg_tag 'icons/person.svg' , class: 'agent-type-icon'
+ organization_icon = inline_svg_tag 'icons/organization.svg', class: 'agent-type-icon'
+ agent_icon = person_icon
+
+ if agent.is_a?(String)
+ name = agent
+ title = nil
+ else
+ name = agent.name
+ agent_icon = agent.agentType.eql?("organization") ? organization_icon : person_icon
+ title = agent_tooltip(agent)
+ end
+ render_chip_component(title, agent_icon, name)
+ end
+
+
+ def render_chip_component(title,agent_icon,name)
+ render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: title , class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do
+ content_tag(:div, class: 'agent-chip') do
+ content_tag(:div, agent_icon, class: 'agent-chip-circle') +
+ content_tag(:div, name, class: 'agent-chip-name text-truncate')
+ end
+ end
+ end
+
+ def orcid_number(orcid)
+ return orcid.split("/").last
+ end
+
+
+
end
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index ddff53082..e768f3b95 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -6,6 +6,41 @@
require 'pry' # used in a rescue
module ApplicationHelper
+ REST_URI = $REST_URL
+ API_KEY = $API_KEY
+
+ include ModalHelper, MultiLanguagesHelper, UrlsHelper
+
+ RESOLVE_NAMESPACE = {:omv => "http://omv.ontoware.org/2005/05/ontology#", :skos => "http://www.w3.org/2004/02/skos/core#", :owl => "http://www.w3.org/2002/07/owl#",
+ :rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#", :rdfs => "http://www.w3.org/2000/01/rdf-schema#", :metadata => "http://data.bioontology.org/metadata/",
+ :metadata_def => "http://data.bioontology.org/metadata/def/", :dc => "http://purl.org/dc/elements/1.1/", :xsd => "http://www.w3.org/2001/XMLSchema#",
+ :oboinowl_gen => "http://www.geneontology.org/formats/oboInOwl#", :obo_purl => "http://purl.obolibrary.org/obo/",
+ :umls => "http://bioportal.bioontology.org/ontologies/umls/", :door => "http://kannel.open.ac.uk/ontology#", :dct => "http://purl.org/dc/terms/",
+ :void => "http://rdfs.org/ns/void#", :foaf => "http://xmlns.com/foaf/0.1/", :vann => "http://purl.org/vocab/vann/", :adms => "http://www.w3.org/ns/adms#",
+ :voaf => "http://purl.org/vocommons/voaf#", :dcat => "http://www.w3.org/ns/dcat#", :mod => "http://www.isibang.ac.in/ns/mod#", :prov => "http://www.w3.org/ns/prov#",
+ :cc => "http://creativecommons.org/ns#", :schema => "http://schema.org/", :doap => "http://usefulinc.com/ns/doap#", :bibo => "http://purl.org/ontology/bibo/",
+ :wdrs => "http://www.w3.org/2007/05/powder-s#", :cito => "http://purl.org/spar/cito/", :pav => "http://purl.org/pav/", :nkos => "http://w3id.org/nkos/nkostype#",
+ :oboInOwl => "http://www.geneontology.org/formats/oboInOwl#", :idot => "http://identifiers.org/idot/", :sd => "http://www.w3.org/ns/sparql-service-description#",
+ :cclicense => "http://creativecommons.org/licenses/",
+ 'skos-xl' => "http://www.w3.org/2008/05/skos-xl#"}
+ def url_to_endpoint(url)
+ uri = URI.parse(url)
+ endpoint = uri.path.sub(/^\//, '')
+ endpoint
+ end
+
+ def search_json_link(link = @json_url, style: '')
+ custom_style = "font-size: 50px; line-height: 0.5; margin-left: 6px; #{style}".strip
+ render IconWithTooltipComponent.new(icon: "json.svg",link: link, target: '_blank', title: t('fair_score.go_to_api'), size:'small', style: custom_style)
+ end
+
+ def resolve_namespaces
+ RESOLVE_NAMESPACE
+ end
+ def ontologies_analytics
+ data = LinkedData::Client::Analytics.last_month.onts
+ data.map{|x| [x[:ont].to_s, x[:views]]}.to_h
+ end
def get_apikey
unless session[:user].nil?
@@ -15,6 +50,31 @@ def get_apikey
end
end
+ def rest_hostname
+ extract_hostname(REST_URI)
+ end
+
+ def extract_hostname(url)
+ begin
+ uri = URI.parse(url)
+ uri.hostname
+ rescue URI::InvalidURIError
+ url
+ end
+ end
+
+ def omniauth_providers_info
+ $OMNIAUTH_PROVIDERS
+ end
+
+ def omniauth_provider_info(strategy)
+ omniauth_providers_info.select {|k,v| v[:strategy].eql?(strategy.to_sym) || k.eql?(strategy)}
+ end
+
+ def omniauth_token_provider(strategy)
+ omniauth_provider_info(strategy.to_sym).keys.first
+ end
+
def isOwner?(id)
unless session[:user].nil?
if session[:user].admin?
@@ -27,16 +87,10 @@ def isOwner?(id)
end
end
- def encode_param(string)
- CGI.escape(string)
- end
- def escape(string)
- CGI.escape(string)
- end
- def unescape(string)
- CGI.unescape(string)
+ def encode_param(string)
+ CGI.escape(string)
end
def clean(string)
@@ -67,151 +121,13 @@ def current_user_admin?
session[:user] && session[:user].admin?
end
- def remove_owl_notation(string)
- # TODO_REV: No OWL notation, but should we modify the IRI?
- return string
-
- unless string.nil?
- strings = string.split(":")
- if strings.size<2
- #return string.titleize
- return string
- else
- #return strings[1].titleize
- return strings[1]
- end
- end
- end
-
- def draw_note_tree(notes,key)
- output = ""
- draw_note_tree_leaves(notes,0,output,key)
- return output
- end
-
- def draw_note_tree_leaves(notes,level,output,key)
- for note in notes
- name="Anonymous"
- unless note.user.nil?
- name=note.user.username
- end
- headertext=""
- notetext=""
- if note.note_type.eql?(5)
- headertext<< "
-%footer.footer.pt-4.mt-5
- %div.container-fluid
- %div.row
- %div.col
- = link_to(image_tag('logos/logoLW_eric_outline_white-01.svg', alt: "LifeWatch logo", class: "logo"), 'https://www.lifewatch.eu/', target: '_blank')
- .col.col-md
- %h6 Products
- %ul.list-unstyled
- %li
- %a{href: "#{$REST_URL.chomp('/') + "/documentation"}", target: "_blank"} EcoPortal REST API
- .col.footer-support
- %h6 Support
- %ul.list-unstyled
- %li
- %a.pop_window{href: "/feedback?location=http%253A%252F%252Fecoportal.lifewatchitaly.eu%252F"} Contact Us
- %li
- = link_to("Help", Rails.configuration.settings.links[:help], target: "_blank")
- %li
- %a{href: Rails.configuration.settings.links[:wiki], target: "_blank"} EcoPortal Wiki Documentation
- .col.col-md
- %h6 Disclaimers & Agreements
- %ul.list-unstyled
- %li
- = link_to('Terms & Conditions', Rails.configuration.settings.links[:terms], target: '_blank')
- %li
- = link_to('Privacy Policy', Rails.configuration.settings.links[:privacy_policy], target: '_blank')
- %li
- = link_to('Cite Us', Rails.configuration.settings.links[:cite], target: '_blank')
- .col.col-md
- %h6 About
- %ul.list-unstyled
- %li
- -# %a{href: "#", target: "_blank"} About Us
- = link_to("About Us", Rails.configuration.settings.links[:about])
- %li
- -# %a{href: "#", target: "_blank"} Team
- = link_to("Team", Rails.configuration.settings.links[:team])
- %li
- %a{href: "/projects"} Projects
- .col.col-md
- %ul.list-inline.social-icons
- %li.list-inline-item
- %a{href: Rails.configuration.settings.links[:twitter], target: "_blank"}
- %i.fab.fa-twitter
- %li.list-inline-item
- %a{href: Rails.configuration.settings.links[:facebook], target: "_blank"}
- %i.fab.fa-facebook
- %li.list-inline-item
- %a{href: Rails.configuration.settings.links[:youtube], target: "_blank"}
- %i.fab.fa-youtube
- %li.list-inline-item
- %a{href: Rails.configuration.settings.links[:linkedin], target: "_blank"}
- %i.fab.fa-linkedin-in
- %li.list-inline-item
- %a{href: Rails.configuration.settings.links[:github], target: "_blank"}
- %i.fab.fa-github
- .row
- .col-sm-12{:style => "text-align:center;clear:both;"}
- %a{:href => "http://ontoportal.org/", :title => "Powered by Ontoportal", target: "_blank"} Powered by Ontoportal
+%br
+%br/
+.footer-container
+ %footer
+ .footer-header
+ .footer-logo
+ %img{:src => "#{asset_path("logos/ontoportal.svg")}"}
+ %p
+ = portal_name
+ .footer-social-media-links
+ - $FOOTER_LINKS[:social].each do |link|
+ %a{:href => link[:link], :target => "_blank"}
+ = inline_svg(link[:logo], width: "32px", height: "32px")
+ .footer-nav-links
+ - $FOOTER_LINKS[:sections].each do |key, section_links|
+ %div
+ %h2
+ = t("layout.footer."+key.to_s)
+ %div
+ - section_links.each do |section , link|
+ %a{:href => link, :target => "_blank"}
+ = t("layout.footer."+section.to_s)
+
+
+
= javascript_include_tag "application"
-= render partial: "ga_tracking"
diff --git a/app/views/layouts/_header.html.erb b/app/views/layouts/_header.html.erb
index be11c10a1..7e23fd5f5 100644
--- a/app/views/layouts/_header.html.erb
+++ b/app/views/layouts/_header.html.erb
@@ -1,6 +1,7 @@
-
+ lang="<%=I18n.locale%>">
+ <%= render partial: 'ga_tracking' %>
<%if @title.nil?%><%=$ORG_SITE%><%else%><%="#{@title} | #{$ORG_SITE}"%><%end%>
- <%=render partial: 'layouts/notices'%>
-
-
-
-
- <%=yield%>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- <%= render partial: 'layouts/footer' %>
-
-
-
\ No newline at end of file
diff --git a/app/views/layouts/appliance.html.haml b/app/views/layouts/appliance.html.haml
index 20f13cb35..2497fd07e 100644
--- a/app/views/layouts/appliance.html.haml
+++ b/app/views/layouts/appliance.html.haml
@@ -1,6 +1,7 @@
!!! Strict
%html
%head
+ = render partial: 'ga_tracking'
Component Preview
+
+ <%= yield %>
+ <%= javascript_include_tag "application" %>
+
+
+
+
+
\ No newline at end of file
diff --git a/app/views/layouts/component_preview_not_centred.html.erb b/app/views/layouts/component_preview_not_centred.html.erb
new file mode 100644
index 000000000..81b1c2964
--- /dev/null
+++ b/app/views/layouts/component_preview_not_centred.html.erb
@@ -0,0 +1,56 @@
+
+
+ Component Preview
+ <%if @title.nil?%><%=$ORG_SITE%><%else%><%="#{@title} | #{$ORG_SITE}"%><%end%>
-
-
- <%if flash[:notice] %>
-
-
- <%=flash[:notice] %>
-
-
- <% message_name = "" %>
- <% unless $SITE_NOTICE.nil? || $SITE_NOTICE.empty? %>
- <% $SITE_NOTICE.each_key { |k| message_name = k } %>
- <% unless cookies[message_name.to_sym].eql?("true") %>
-
-
- <%=$SITE_NOTICE[message_name.to_sym]%>
[close]
-
- <% end %>
- <% end %>
-
- <%=yield%>
-
- <%= render TurboModalComponent.new(id: 'application_modal')%>
+ <%= modal_frame_container%>
<%=yield%>
<%=render partial: 'layouts/footer'%>
diff --git a/app/views/layouts/ontology_viewer/_header.html.haml b/app/views/layouts/ontology_viewer/_header.html.haml
new file mode 100644
index 000000000..877e8c408
--- /dev/null
+++ b/app/views/layouts/ontology_viewer/_header.html.haml
@@ -0,0 +1,46 @@
+- sub = @submission_latest
+
+
+-# A header of sorts to display ontology name and subset of details.
+.ontology-details-header-container
+ .ontology-details-path
+ %a{href: "/ontologies"} ontologies
+ - if @ontology.viewOf
+ = inline_svg_tag 'arrow-right-outlined.svg'
+ %div
+ = @ontology.viewOf.split('/').last
+ = inline_svg_tag 'arrow-right-outlined.svg'
+ %div
+ = @ontology.acronym
+ .ontology-details-header-sub-container
+ .ontology-details-header-left-container{style:'width: 70%'}
+ .ontology-details-name-bar
+ %div
+ = @ontology.name
+ %span{data: { controller: 'tooltip'}, title: ontology_alternative_names}
+ = "("+ @ontology.acronym+")"
+ - if @ontology.viewOf
+ = render ChipButtonComponent.new(class: 'chip_button_small mr-1', text: 'view', type: 'clickable', clickable: false)
+ - if @ontology.private?
+ = render ChipButtonComponent.new(class: 'chip_button_small mr-1') do
+ = private_ontology_icon(@ontology.private?)
+ - if @submission_latest&.hasOntologyLanguage
+ = render ChipButtonComponent.new(class: 'chip_button_small mr-1', text: @submission_latest.hasOntologyLanguage)
+ = ontology_retired_badge(@submission_latest, small: true, clickable: false)
+ = ontology_license_badge(@ontology.acronym, @submission_latest)
+
+ - unless sub.nil? || sub.creationDate.nil?
+ .ontology-details-last-update
+ %img{src: asset_path("update.svg")}/
+ %div
+ = t('ontology_details.header.last_submission_date')
+ = render DateTimeFieldComponent.new(value: sub.creationDate)
+ .ontology-details-header-right-container.justify-content-end{style: 'min-width: 20%;'}
+ %span.mx-1
+ = new_submission_button
+ - if @submission_latest
+ %span.mx-1
+ = ontology_edit_button
+ %span
+ = submission_json_button
+ = subscribe_button(@ontology.id)
diff --git a/app/views/layouts/popup.html.erb b/app/views/layouts/popup.html.erb
index d78ac254d..fda7af554 100644
--- a/app/views/layouts/popup.html.erb
+++ b/app/views/layouts/popup.html.erb
@@ -1,6 +1,7 @@
+ <%= render partial: "ga_tracking" %>
<%= @ontology.contactEmail%> if you have questions regarding the license.<%=flash[:error] unless flash[:error].nil?%>
-
This ontology is private
- <% ontology_authors = @ontology.contactName.nil? || @ontology.contactName.empty? ? "the authors" : @ontology.contactName%>
-
- This ontology is private and only those who have been granted access by the ontology author may browse its classes.
- Please contact <%= ontology_authors%> at <%= @ontology.contactEmail%> if you would like access.
-
- <%if session[:user].nil?%>If you have already been granted access then please log in and you will be taken to the class browser.<%end%>
-
-
-
Semantic resources loading
-
please wait...
-
- Browser
-
- <%= t('ontologies.intro').html_safe %>
- <%= link_to(Rails.configuration.settings.links[:help_ontology_browse], target: '_blank') do %>
-
-
-
-
- Welcome admin
-
-
-
Debug Info
- types: {{facets.types.active}}
-
-
- <%if session[:user].nil?%>
-
Submit New Semantic Resource
- <%else%>
-
Submit New Semantic Resource
- <%end%>
-
-
-
-
Entry Type
-
-
-
- {{type.id | idToTitle}}
- ({{facet_counts["types"][type.id] || 0}})
-
-
-
-
-
-
-
Uploaded in the Last
-
-
-
- {{day | idToTitle}}
-
-
-
-
-
-
-
Category
-
-
- {{category.name}}
- ({{facet_counts["categories"][category.id] || 0}})
-
-
-
-
-
-
Group
-
-
- {{group.acronym}}
- ({{facet_counts["groups"][group.id] || 0}})
-
-
-
-
-
-
-
-
Ontology Content
-
-
- {{artifact | idToTitle}}
- ({{facet_counts["artifacts"][artifact] || 0}})
-
-
-
-
-
-
Natural Language
-
-
- {{language_label}}
- ({{facet_counts["natural_languages"][language_uri] || 0}})
-
-
-
-
-
-
-
-
Is of Type
-
-
- {{is_of_type_label}}
- ({{facet_counts["is_of_type"][is_of_type_uri] || 0}})
-
-
-
-
-
-
Missing Status
-
-
-
- {{status | idToTitle}}
-
-
-
-
-
-
-
-
-
-
-
-
-
- Showing {{visible_ont_count}} of {{ontologies.length}}
- Sort:
-
- Popular
- Name
- Classes count
- Instances/Concepts count
- Projects
- Notes
-
- Upload Date
- Release Date
- FAIR score
- Search Rank
-
-
-
-
-
-
-
-
-
VIEW
-
-
-
{{ontology.description | descriptionToText}}
-
- Uploaded : {{ontology.creationDate | date:'shortDate'}}
-
-
- Format : {{ontology.format}}
-
-
- View of : {{ontology.viewOfOnt.acronym}}
-
-
- Summary Only
-
-
- Groups : {{groupAcronyms(ontology.groups).join(', ')}}
-
-
- Categories : {{categoryNames(ontology.categories).join(', ')}}
-
-
-
- Admins : {{adminUsernames(ontology.administeredBy).join(', ')}}
-
-
- Pull URL
-
- Status : {{ontology.submissionStatusFormatted}}
-
-
-
-
-
No submissions available
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/app/views/ontologies/browser/_ontologies.html.haml b/app/views/ontologies/browser/_ontologies.html.haml
new file mode 100644
index 000000000..8e3d8bd30
--- /dev/null
+++ b/app/views/ontologies/browser/_ontologies.html.haml
@@ -0,0 +1,17 @@
+= render InfiniteScrollComponent.new(id: 'ontologies_list',
+ collection: @ontologies,
+ next_url: ontologies_filter_url(@request_params, page: @page.nextPage),
+ current_page: @page.page, next_page: @page.nextPage) do |c|
+
+ - if @page.page.eql?(1)
+ = content_tag(:p, class: "browse-desc-text", style: "margin-bottom: 12px !important;") { "#{t("ontologies.showing_ontologies_size", ontologies_size: @count, analytics_size: @total_ontologies)} (#{sprintf("%.2f", @time)}s)" }
+
+ - ontologies = c.collection
+ - ontologies.each do |ontology|
+ = render OntologyBrowseCardComponent.new(ontology: ontology)
+ - c.loader do
+ - ontologies_browse_skeleton
+ - c.error do
+ .browse-empty-illustration
+ %img{:src => "#{asset_path("empty-box.svg")}"}
+ %p No result was found
\ No newline at end of file
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
new file mode 100644
index 000000000..83da56b6c
--- /dev/null
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -0,0 +1,85 @@
+.browse-center
+ .browse-container
+ .container.align-alert
+ - if session[:user]&.admin?
+ %div{style:'width: 70%;'}
+ = render Display::AlertComponent.new(type: 'info') do
+ %span.d-flex.align-items-center
+ %svg{:fill => "none", :height => "11", :viewbox => "0 0 11 11", :width => "11", :xmlns => "http://www.w3.org/2000/svg"}
+ %circle{:cx => "5.5", :cy => "5.5", :fill => 'var(--admin-color)', :r => "5.5"}
+ %p{style: "margin: 10px"}= t("ontologies.browser.admin_welcome")
+ .browse-submit-new-ontology-and-you-are-admin-container
+ %a#back_top_btn.btn.btn-primary.btn-floating.btn-lg
+ %i.fas.fa-arrow-up.text-white
+
+ :javascript
+ const btn = document.getElementById("back_top_btn");
+ window.addEventListener("scroll", function() {
+ if (window.scrollY > 300) {
+ btn.classList.add("show");
+ } else {
+ btn.classList.remove("show");
+ }
+ });
+
+ btn.addEventListener("click", function(e) {
+ e.preventDefault();
+ window.scrollTo({
+ top: 0,
+ behavior: "smooth"
+ });
+ });
+
+ %div{data: { controller: "turbo-frame history browse-filters" , "turbo-frame-url-value": "/ontologies_filter?page=1&#{request.original_url.split('?').last}", action: "change->browse-filters#dispatchFilterEvent changed->history#updateURL changed->turbo-frame#updateFrame"}}
+
+ .browse-sub-container
+ .browse-first-row{data:{controller: "browse-filters", action: "change->browse-filters#dispatchFilterEvent changed->history#updateURL"}}
+ %div.pt-1
+ = upload_ontology_button
+ %div{style:'margin-top: 30px'}
+ %p.browse-filters-title= t("ontologies.filters")
+ - if session[:user]&.admin?
+ %div.browse-filter.admin-border
+ = render SwitchInputComponent.new(id:'filter-private', name:'private_only', checked: @show_private_only) do
+ = t("ontologies.browser.show_private_ontology")
+ %div.browse-filter
+ = render SwitchInputComponent.new(id:'filter-views', name:'views', checked: @show_views) do
+ = t("ontologies.browser.show_ontology_views")
+ = render SwitchInputComponent.new(id:'filter-retired', name:'retired',checked: @show_retired) do
+ = t("ontologies.browser.show_retired_ontologies")
+
+ - @filters.each do |key, values|
+ - if session[:user]&.admin? || key != :missingStatus
+ .browse-filter{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "#{key}_filter_container", style: "#{"border-color: var(--admin-color);" if key == :missingStatus}"}
+ .browse-filter-title-bar{"data-target" => "#browse-#{key}-filter", "data-toggle" => "collapse"}
+ %p
+ = browse_filter_section_label(key)
+ %span.badge.badge-primary{"data-show-filter-count-target":"countSpan", style: "#{values[2] && values[2].positive? ? '' : 'display: none;'}"}
+ = values[2]
+ = inline_svg_tag 'arrow-down.svg'
+ .collapse{id: "browse-#{key}-filter", class: "#{values[2].positive? ? 'show': ''}"}
+ .browse-filter-checks-container
+ - values.first.each do |object|
+ - title = (key.eql?(:categories) || key.eql?(:groups)) ? nil : ''
+ = group_chip_component(name: key, object: object, checked: values[1]&.include?(object["id"]) || values[1]&.include?(object["value"]) , title: title) do |c|
+ - c.count do
+ %span.badge.badge-light.ml-1
+ = turbo_frame_tag "count_#{key}_#{object["id"]}", busy: true
+ %span.show-if-loading
+ = render LoaderComponent.new(small:true)
+
+ .browse-second-row
+ .browse-search-bar
+ .browse-search-container
+ %input{:name => "search", :placeholder => t("ontologies.browser.search_placeholder"), :type => "text", :value => @search, data: {action: "input->browse-filters#dispatchInputEvent"}}
+ .browse-search-filters
+ %select#format.browse-format-filter{:name => "format"}
+ = options_for_select(@formats, @selected_format)
+ %select#Sort_by.browse-sort-by-filter{:name => "Sort_by"}
+ = options_for_select(@sorts_options, @sort_by)
+ .browse-ontologies
+ = render TurboFrameComponent.new(id: "ontologies_list_view-page-1" , src: "/ontologies_filter?page=1&#{request.original_url.split('?').last}", data:{"turbo-frame-target":"frame", "turbo-frame-url-value": "/ontologies_filter"}) do |list|
+ - list.loader do
+ = browser_counter_loader
+ - ontologies_browse_skeleton
+
diff --git a/app/views/ontologies/concepts_browsers/_collections_picker.html.haml b/app/views/ontologies/concepts_browsers/_collections_picker.html.haml
index 098d547b7..1191df3ac 100644
--- a/app/views/ontologies/concepts_browsers/_collections_picker.html.haml
+++ b/app/views/ontologies/concepts_browsers/_collections_picker.html.haml
@@ -7,6 +7,6 @@
.form-group
%label{:for => id} Collections
%div
- = select_tag(:collections,options_for_select(collections_labels.map{|s| [s["prefLabel"], s["@id"], {'data-color': s['color']}]}, selected_collection.map{|x| x["@id"]}),
+ = select_tag(:collections,options_for_select(collections_labels.map{|s| [s["prefLabel"].last, s["@id"], {'data-color': s['color']}]}, selected_collection.map{|x| x["@id"]}),
{ multiple: multiple, id: id, class:"form-control", include_blank: true,
- data:{controller:'chosen', 'chosen-name-value': :collection_id}.merge(data)})
\ No newline at end of file
+ data:{controller:'chosen', 'chosen-name-value': :collectionid}.merge(data)})
\ No newline at end of file
diff --git a/app/views/ontologies/concepts_browsers/_concepts_browser.html.haml b/app/views/ontologies/concepts_browsers/_concepts_browser.html.haml
index 4537606ab..98aad66d7 100644
--- a/app/views/ontologies/concepts_browsers/_concepts_browser.html.haml
+++ b/app/views/ontologies/concepts_browsers/_concepts_browser.html.haml
@@ -1,18 +1,25 @@
-%nav
- .nav.nav-tabs.text-center{:role => "tablist", style:"background-color: rgba(0, 0, 0, 0.03);"}
+%div#concept_browser.tree-container
+ = render TabsContainerComponent.new(type:'outline') do |c|
+ - c.item(id: 'tree-tab', selected: default_sub_menu?) do
+ %span{title: 'Hierarchy view', 'data-controller': "tooltip"}
+ = inline_svg('icons/list-tree.svg', style:'width: 18px; height: 18px')
- %a#concepts-tree-tab.nav-item.nav-link.active.flex-grow-1.border-radius-0{"data-toggle" => "tab", :href => "#concepts-tree-container", title: 'Hierarchy view', 'data-controller': "tooltip"}
- = inline_svg('list-tree.svg',style:'width: 25px; height: 25px')
- if skos?
- %a#concepts-list-tab.nav-item.nav-link.flex-grow-1.border-radius-0{"data-toggle" => "tab", :href => "#concepts-list-container", title: 'Collection view', 'data-controller': "tooltip"}
- %i.fas.fa-list{style:'font-size: 25px; color: var(--primary-color)'}
- %a#concepts-date-sort-tab.nav-item.nav-link.flex-grow-1.border-radius-0{"data-toggle" => "tab", :href => "#concepts-date-sort-container", title: 'Date view', 'data-controller': "tooltip"}
- %i.far.fa-calendar-alt{style:'font-size: 25px'}
-.tab-content.px-1.py-2
- #concepts-tree-container.tab-pane.fade.show.active
- = render partial: 'ontologies/concepts_browsers/concepts_tree'
- - if skos?
- #concepts-list-container.tab-pane.fade
- = render partial: 'ontologies/concepts_browsers/concepts_list'
- #concepts-date-sort-container.tab-pane.fade
- = render partial: 'ontologies/concepts_browsers/concepts_date_sort'
\ No newline at end of file
+ - c.item(id: 'list-tab', selected: sub_menu_active?('list')) do
+ %span{title: 'Collection view', 'data-controller': "tooltip"}
+ = inline_svg('icons/list.svg', style:'width: 18px; height: 18px')
+
+ - c.item(id: 'date-tab', selected: sub_menu_active?('date')) do
+ %span{title: 'Date view', 'data-controller': "tooltip"}
+ = inline_svg('icons/calendar.svg', style:'width: 18px; height: 18px')
+
+ - c.item_content do
+ %div.p-1
+ = render partial: 'ontologies/concepts_browsers/concepts_tree'
+ - if skos?
+ - c.item_content do
+ %div.p-1
+ = render partial: 'ontologies/concepts_browsers/concepts_list'
+ - c.item_content do
+ %div.p-1
+ = render partial: 'ontologies/concepts_browsers/concepts_date_sort'
diff --git a/app/views/ontologies/concepts_browsers/_concepts_list.html.haml b/app/views/ontologies/concepts_browsers/_concepts_list.html.haml
index 07d48f680..c293620e9 100644
--- a/app/views/ontologies/concepts_browsers/_concepts_list.html.haml
+++ b/app/views/ontologies/concepts_browsers/_concepts_list.html.haml
@@ -1,7 +1,7 @@
%div{data:{controller: 'turbo-frame',
'turbo-frame': {
- 'url-value': "/ajax/classes/list?ontology_id=#{@ontology.acronym}",
- 'place-holder-value': "Please select a collection to display"
+ 'url-value': "/ajax/classes/list?ontology_id=#{@ontology.acronym}&language=#{request_lang}",
+ 'place-holder-value': t("ontologies.concepts_browsers.select_collection")
}}}
%div.pb-2
%div.mb-1
@@ -12,6 +12,12 @@
locals: {multiple: false, id: 'collections_select',
data: {action: 'changed->turbo-frame#updateFrame'}}
- %div#sd_content.card.p-1{style: 'overflow-y: scroll; height: 60vh;'}
- = render TurboFrameComponent.new(id: 'concepts_list_view-page-1', data: {'turbo-frame-target': 'frame'}) do
- Please select a collection to display
\ No newline at end of file
+ - unless no_collections?
+ %div#sd_content.card.p-1{style: 'overflow-y: auto; height: 60vh;'}
+ = render TurboFrameComponent.new(id: 'concepts_list_view-page-1', data: {'turbo-frame-target': 'frame'}, src:params[:concept_collections] ? "/ajax/classes/list?ontology_id=#{@ontology.acronym}&collectionid=#{params[:concept_collections]}" : '') do
+ .select-collection-placeholder
+ = t("ontologies.concepts_browsers.select_collection")
+
+
+
+
\ No newline at end of file
diff --git a/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml b/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml
index 9e0460185..d4affe93f 100644
--- a/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml
+++ b/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml
@@ -1,8 +1,8 @@
-%div{data:{controller: 'skos-collection-colors turbo-frame history',
+%div{data:{controller: 'skos-collection-colors turbo-frame',
'skos-collection-colors': {'collections-color-select-target-value': 'collection-color-filter'},
'turbo-frame': {
'url-value': "/ajax/classes/treeview?ontology=#{@ontology.acronym}&conceptid=root",
- 'place-holder-value': "Please select a scheme to display"
+ 'place-holder-value': t("ontologies.concepts_browsers.select_scheme")
}}}
%div.pb-2
%div.mb-1
@@ -15,7 +15,13 @@
data: {action: 'changed->skos-collection-colors#updateCollectionTags' ,
'chosen-enable-colors-value': 'true'}}
-# Class tree
- %div#sd_content.card.p-1.py-3{style: 'overflow-y: scroll; height: 60vh;'}
- = render TurboFrameComponent.new(id: 'concepts_tree_view',
- src: "/ajax/classes/treeview?ontology=#{@ontology.acronym}&conceptid=#{escape(@concept.id)}&concept_schemes=#{params[:concept_schemes]}&auto_click=false",
+ %div#sd_content.px-1{style: 'overflow-y: scroll; height: 60vh;'}
+ - if skos? && @roots&.empty?
+ %div.text-wrap
+ = render Display::AlertComponent.new do
+ = t("ontologies.concepts_browsers.missing_roots", acronym: @ontology.acronym)
+ - else
+ - concept_schemes = skos? ? "&concept_schemes=#{params[:concept_schemes]}" : ''
+ = render TurboFrameComponent.new(id: 'concepts_tree_view',
+ src: "/ajax/classes/treeview?ontology=#{@ontology.acronym}&conceptid=#{escape(@concept.id)}#{concept_schemes}&auto_click=false&language=#{request_lang}",
data: {'turbo-frame-target': 'frame'})
\ No newline at end of file
diff --git a/app/views/ontologies/concepts_browsers/_jump_to.html.haml b/app/views/ontologies/concepts_browsers/_jump_to.html.haml
index f597488ed..5fa4248e5 100644
--- a/app/views/ontologies/concepts_browsers/_jump_to.html.haml
+++ b/app/views/ontologies/concepts_browsers/_jump_to.html.haml
@@ -2,7 +2,7 @@
%div.input-group-prepend
%span.input-group-text
%i.fas.fa-search
- = text_field_tag("search_box", nil, class: "form-control rounded-right", placeholder: "Jump to", aria: {label: "Jump to:"},
+ = text_field_tag("search_box", nil, class: "form-control rounded-right", placeholder: t("ontologies.concepts_browsers.placeholder_jump"), aria: {label: t("ontologies.concepts_browsers.label_jump")},
data: {controller: 'class-search-auto-complete',
'class-search-auto-complete-ontology-acronym-value': @ontology.acronym,
'class-search-auto-complete-spinner-src-value': asset_path("jquery.simple.tree/spinner.gif")})
@@ -11,4 +11,4 @@
%div.input-group-append
%button.btn.btn-outline-primary.dropdown-toggle{ "data-toggle": "collapse", href: id}
%i.fas.fa-sliders-h.mx-1
- Filter
\ No newline at end of file
+ = t("ontologies.concepts_browsers.filter")
\ No newline at end of file
diff --git a/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml b/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml
index ca3131e1b..958807977 100644
--- a/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml
+++ b/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml
@@ -10,7 +10,7 @@
%label{:for => "schemes_select"} Schemes
%div
= select_tag(:concept_schemes,
- options_for_select(schemes_labels.map{|s| [s["prefLabel"], s["@id"]]}, selected_scheme.compact.map{|x| x["@id"]} ),
+ options_for_select(schemes_labels.map{|s| [s["prefLabel"].last, s["@id"]]}, selected_scheme.compact.map{|x| x["@id"]} ),
{multiple: true, id: "schemes_select",
data:{controller:'chosen', 'chosen-name-value': :concept_schemes,
action: 'changed->history#updateURL changed->turbo-frame#updateFrame'}})
diff --git a/app/views/ontologies/content_serializer.html.haml b/app/views/ontologies/content_serializer.html.haml
new file mode 100644
index 000000000..beda31695
--- /dev/null
+++ b/app/views/ontologies/content_serializer.html.haml
@@ -0,0 +1,2 @@
+= render_in_modal do
+ = rdf_highlighter_container(@format, @result) if @result
diff --git a/app/views/ontologies/edit.html.haml b/app/views/ontologies/edit.html.haml
deleted file mode 100644
index fbbc47baf..000000000
--- a/app/views/ontologies/edit.html.haml
+++ /dev/null
@@ -1,5 +0,0 @@
-- @title = "Edit a Semantic Resource Information"
-
-%div{:style => "margin:10px;"}
- = form_for :ontology, url: ontology_path(@ontology.acronym), html: {method: :put, id: "ontologyForm"} do |f|
- = render partial: "form", locals: {f: f, button_text: "Save semantic resource", title_text: "Edit Semantic Resource Information"}
diff --git a/app/views/ontologies/htaccess.html.haml b/app/views/ontologies/htaccess.html.haml
new file mode 100644
index 000000000..bd59fcbe1
--- /dev/null
+++ b/app/views/ontologies/htaccess.html.haml
@@ -0,0 +1,68 @@
+= render_in_modal do
+ %p
+ = t("ontologies.htaccess_redirection_description")
+
+ %h5
+ %strong
+ = t("ontologies.instructions_servers", server: "Apache")
+ %ol
+ %li
+ %strong
+ = t("ontologies.htaccess_redirection.instruction_1")
+ = t("ontologies.htaccess_redirection.instruction_1_content")
+ %li
+ %strong
+ = t("ontologies.htaccess_redirection.instruction_2")
+ = t("ontologies.htaccess_redirection.instruction_2_content")
+ %li
+ %strong
+ = t("ontologies.htaccess_redirection.instruction_3")
+ = t("ontologies.htaccess_redirection.instruction_3_content")
+
+ .htacess-code-container
+ .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'}
+ = render ClipboardComponent.new(message: @htaccess_content, show_content: false)
+ %pre.mb-0
+ %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'}
+ = @htaccess_content
+
+ %hr
+
+ %h5
+ %strong
+ = t("ontologies.instructions_servers", server: "Nginx")
+ %ol
+ %li
+ %strong
+ = t("ontologies.nginx_redirection.instruction_1")
+ = t("ontologies.nginx_redirection.instruction_1_content")
+ %li
+ %strong
+ = t("ontologies.nginx_redirection.instruction_2")
+ = t("ontologies.nginx_redirection.instruction_2_content")
+ %li
+ %strong
+ = t("ontologies.nginx_redirection.instruction_3")
+ = t("ontologies.nginx_redirection.instruction_3_content")
+ %li
+ %strong
+ = t("ontologies.nginx_redirection.instruction_4")
+ = t("ontologies.nginx_redirection.instruction_4_content")
+ %li
+ %strong
+ = t("ontologies.nginx_redirection.instruction_5")
+ = t("ontologies.nginx_redirection.instruction_5_content")
+
+ .htacess-code-container
+ .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'}
+ = render ClipboardComponent.new(message: @nginx_content, show_content: false)
+ %pre.mb-0
+ %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'}
+ = @nginx_content
+
+ %h5
+ %strong Note
+ = render Display::AlertComponent.new(message: t("ontologies.redirection_note"), closable: false, type: "warning")
+
+ .contact-support{style: "width: 100%; display: flex; justify-content: end;"}
+ = render Buttons::RegularButtonComponent.new(id:'regular-button', value: t("ontologies.contact_support"), variant: "primary", href: "/feedback", target: "_blank", state: "regular")
\ No newline at end of file
diff --git a/app/views/ontologies/new.html.haml b/app/views/ontologies/new.html.haml
index 63165a10c..92f88fc21 100644
--- a/app/views/ontologies/new.html.haml
+++ b/app/views/ontologies/new.html.haml
@@ -1,5 +1,52 @@
-- @title = "Submit a New Semantic Resource"
+- @title = t("ontologies.submit_new_ontology")
%div{:style => "margin:10px;"}
- = form_for :ontology, url: {action: "create"}, html: {id: "ontologyForm"} do |f|
- = render partial: "form", locals: {f: f}
+ = form_for :ontology, url: {action: "create"}, html: {id: "ontologyForm", multipart: true} do
+ .upload-ontology-container
+ %div{style: 'width: 589px'}
+ = error_message_alert
+ .upload-ontology-card
+ .upload-ontology-center
+ .d-flex.justify-content-between
+ %a{:href => "javascript:javascript:history.go(-1)"}
+ %img.lost-password-arrowback{:src => "#{asset_path("arrow-back.svg")}"}
+ .register-title-container
+ %h2.register-title
+ = @is_update_ontology ? t("ontologies.add_new_submission", acronym: @ontology.acronym) : t("ontologies.submit_new_ontology")
+ %hr#register-title-line/
+ %div
+ .upload-ontology-progress
+ = render Layout::ProgressPagesComponent.new(pages_title: [t("ontologies.details"), t("ontologies.general_information"), t("ontologies.dates_and_contacts")]) do |c|
+ - c.page do
+ = render partial: 'ontologies/form'
+ - c.page do
+ .upload-ontology-desc
+ = metadata_help_link
+ .upload-ontology-input-field-container
+ = attribute_input('URI', label: t("ontologies.uri"))
+ .upload-ontology-input-field-container
+ = attribute_input('description', long_text: true)
+ - if @is_update_ontology
+ .upload-ontology-input-field-container{id: "submissionnotes_from_group_input"}
+ = attribute_input("notes", label: t("ontologies.change_notes"), long_text: true)
+ .upload-ontology-field-container
+ = has_ontology_language_input
+ .upload-ontology-field-container.mt-3
+ = render Layout::RevealComponent.new(selected: @submission.status, possible_values: ['retired']) do |c|
+ - c.button do
+ = attribute_input("status")
+ - c.container do
+ .upload-ontology-field-container
+ - @submission.valid = nil unless @submission.status&.eql?('retired')
+ = attribute_input("valid")
+ .upload-ontology-field-container
+ = render partial: 'ontologies/submission_location_form'
+
+ - c.page do
+ .upload-ontology-input-field-container
+ - if @is_update_ontology
+ = attribute_input('modificationDate', label: t("ontologies.modification_date"), max_date: Date.today)
+ - else
+ = attribute_input('released', label: t("ontologies.date_of_original_creation"), max_date: Date.today)
+ .upload-ontology-contact{id: "submissioncontact_from_group_input"}
+ = contact_input(show_help: false)
diff --git a/app/views/ontologies/ontologies_selector/ontologies_selector.html.haml b/app/views/ontologies/ontologies_selector/ontologies_selector.html.haml
new file mode 100644
index 000000000..932a061cd
--- /dev/null
+++ b/app/views/ontologies/ontologies_selector/ontologies_selector.html.haml
@@ -0,0 +1,73 @@
+= render_in_modal do
+ = form_tag('/ontologies_selector/results', method: :get, novalidate: true, data: {turbo_frame: 'selector_results_frame'}) do
+ .d-flex.align-items-center.justify-content-center{'data-controller': 'ontologies-selector', 'data-ontologies-selector-id-value': @select_id, 'data-ontologies-selector-select-all-value': t('ontologies_selector.select_all'), 'data-ontologies-selector-unselect-all-value': t('ontologies_selector.unselect_all')}
+ .ontologies-selector-container
+ .ontologies-selector-input
+ = text_input(label: '', placeholder: t('ontologies_selector.search_hint'), name: 'input', data: {action: 'input->ontologies-selector#input'})
+ = inline_svg_tag 'icons/search.svg'
+ .ontologies-selector-options{'data-action': 'change->ontologies-selector#change'}
+ .switch-filters
+ .show-ontology-views
+ .text
+ = t('ontologies_selector.show_ontology_view')
+ = render SwitchInputComponent.new(id: 'show-ontology-views', name: 'showOntologyViews')
+ .show-retired-ontologies
+ .text
+ = t('ontologies_selector.hide_retired_ontologies')
+ = render SwitchInputComponent.new(id: 'show-retired-ontologies', name: 'showRetiredOntologies')
+ - formats = @formats.drop(1)
+ %div{'data-ontologies-selector-target': 'table'}
+ = render TabsContainerComponent.new do |c|
+ = c.item(title: t('ontologies_selector.tabs_title.categories'), selected: true)
+ = c.item_content do
+ .chips.categories
+ - @filters[:categories][0].each do |item|
+ = chips_component(label: item.acronym, id: item.acronym, value: item.id, name: 'categories[]', tooltip: item.name)
+ = c.item(title: t('ontologies_selector.tabs_title.groups'))
+ = c.item_content do
+ .chips.groups
+ - @filters[:groups][0].each do |item|
+
+ = chips_component(label: item.acronym, id: item.acronym, value: item.id, name: 'groups[]', tooltip: item.name)
+
+ = c.item(title: t('ontologies_selector.tabs_title.format'))
+ = c.item_content do
+ .chips.format
+ - formats.each do |item|
+ = chips_component(label: item, id: item, name: 'formats[]', value: item)
+
+ = c.item(title: t('ontologies_selector.tabs_title.natural_languages'))
+ = c.item_content do
+ .chips.natural-language
+ - @filters[:naturalLanguage][0].each do |item|
+ = chips_component(label: item["acronym"], id: item["acronym"], name: 'naturalLanguage[]', value: item['id'])
+
+ = c.item(title: t('ontologies_selector.tabs_title.formality_levels'))
+ = c.item_content do
+ .chips
+ - @filters[:hasFormalityLevel][0].each do |item|
+ = chips_component(label: item["name"],id: item["acronym"], name: 'formalityLevel[]', value: item["id"])
+
+ = c.item(title: t('ontologies_selector.tabs_title.ontology_types'))
+ = c.item_content do
+ .chips
+ - @filters[:isOfType][0].each do |item|
+ = chips_component(label: item["name"],id: item["acronym"], name: 'isOfType[]', value: item["id"])
+ %input.d-none{type: 'submit', 'data-ontologies-selector-target': 'submit'}
+ = render TurboFrameComponent.new(id: 'selector_results_frame', src: '/ontologies_selector/results') do |container|
+ - container.loader do
+ = render LoaderComponent.new(type: 'pulsing')
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml b/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml
new file mode 100644
index 000000000..2aeafa23d
--- /dev/null
+++ b/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml
@@ -0,0 +1,19 @@
+= render TurboFrameComponent.new(id:'selector_results_frame') do |container|
+ .ontologies-selector-results
+ .horizontal-line
+ .results-number
+ = t("ontologies.showing_ontologies_size", ontologies_size: @ontologies.length, analytics_size: @total_ontologies_number)
+ %span.select-all{'data-action': 'click->ontologies-selector#selectall'}
+ = t('ontologies_selector.select_all')
+ .ontologies
+ - @ontologies.each do |ontology|
+ .ontology{'data-ontologies-selector-target': 'ontology'}
+ = chips_component(id: "selector[#{ontology.acronym}]",value: ontology.acronym, label: "#{ontology.name} (#{ontology.acronym})", name: ontology.acronym)
+ .horizontal-line
+ .save-cancel-buttons
+ = cancel_button_component(class_name: 'button', id:'cancel-selector', value: t('ontologies_selector.cancel'), data: {action: "click->turbo-modal#hide", 'ontologies-selector-target': 'exit'})
+ = save_button_component(class_name: 'button', id:'apply-selector', value: t('ontologies_selector.apply'), data: {action: "click->ontologies-selector#apply"})
+
+
+ - container.loader do
+ = render LoaderComponent.new(type: 'pulsing')
\ No newline at end of file
diff --git a/app/views/ontologies/sections/_additional_metadata.html.haml b/app/views/ontologies/sections/_additional_metadata.html.haml
new file mode 100644
index 000000000..345656a7e
--- /dev/null
+++ b/app/views/ontologies/sections/_additional_metadata.html.haml
@@ -0,0 +1,8 @@
+= turbo_frame_tag 'application_modal_content' do
+ %div.card.overflow-hidden{style: 'border-radius: 20px;'}
+ %section{style:'height: 70vh; overflow-y: scroll'}
+ = render SubmissionMetadataComponent.new(submission: @submission_latest, submission_metadata: submission_metadata) unless @submission_latest.nil?
+ %div.scroll-message.text-center.py-3.bg-light.text-primary
+ %p.scroll-text.mb-0
+ = t("ontologies.sections.scroll_down_to_see_more")
+ %i.scroll-icon.fa.fa-chevron-down
\ No newline at end of file
diff --git a/app/views/ontologies/sections/_collections.html.haml b/app/views/ontologies/sections/_collections.html.haml
index 3ddd1d27d..280c64760 100644
--- a/app/views/ontologies/sections/_collections.html.haml
+++ b/app/views/ontologies/sections/_collections.html.haml
@@ -1,11 +1,15 @@
-= turbo_frame_tag 'collections' do
+= render TurboFrameComponent.new(id: "collections", data: {"turbo-frame-target": "frame"} ) do
- if no_collections?
= no_collections_alert
- else
%div.ont-collections{data:{controller: 'container-splitter'}}
- %div#collectionsTree{data:{'container-splitter-target': 'container'}}
- = render partial: 'collections/list_view'
- %div#collection_contents.pl-3{data:{'container-splitter-target': 'container'}}
+ %div#collectionsTree.card.sidebar{data:{'container-splitter-target': 'container'}}
+ = tree_container_component(id: "collections_sorted_list_view-page-1",
+ placeholder: t('ontologies.sections.collections_search_placeholder', acronym: @ontology.acronym),
+ frame_url: "/ontologies/#{@ontology.acronym}/collections",
+ tree_url: "/ontologies/#{@ontology.acronym}/collections?#{request.original_url.split('?')[1]}")
+
+ %div#collection_contents{data:{'container-splitter-target': 'container'}}
= render TurboFrameComponent.new(id: 'collection') do
- if @collection
= render partial: 'collections/collection', locals: {collection: @collection}
diff --git a/app/views/ontologies/sections/_licenses.html.haml b/app/views/ontologies/sections/_licenses.html.haml
new file mode 100644
index 000000000..3b5a15403
--- /dev/null
+++ b/app/views/ontologies/sections/_licenses.html.haml
@@ -0,0 +1,8 @@
+= render_in_modal do
+ = render Layout::ListComponent.new do |l|
+ - attrs = @licenses.reject{|x| x.to_s.eql?('copyrightHolder')}
+ - properties_list_component(l, attrs.map { |x| [x, @submission_latest.send(x.to_s)] }.to_h)
+ - properties_list_component(l, {copyrightHolder: [@submission_latest.copyrightHolder]}) do |values|
+ = horizontal_list_container(values) do |v|
+ = render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: '', class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do
+ = display_agent(v, link: false)
diff --git a/app/views/ontologies/sections/_metadata.html.haml b/app/views/ontologies/sections/_metadata.html.haml
old mode 100644
new mode 100755
index 71931d60a..9dd1a07df
--- a/app/views/ontologies/sections/_metadata.html.haml
+++ b/app/views/ontologies/sections/_metadata.html.haml
@@ -1,202 +1,76 @@
= turbo_frame_tag 'summary', target:"_top" do
- %div.ont-metadata
- -# Details pane
- %section.ont-metadata-card.ont-details-card
- %header.pb-2.font-weight-bold Details
- %table.table.table-sm
- %tr
- %td Acronym
- %td= @ontology.acronym
- %tr
- %td Visibility
- %td= strip_links(visibility_link(@ontology))
- - if @ontology.viewing_restricted?
- %tr
- %td Viewing restriction
- %td= @ontology.viewingRestriction.capitalize
- - unless @ontology.viewOf.nil?
- %tr
- %td View of ontology
- %td
- - ont_parent_acronym = @ontology.viewOf.split('/').last
- - if $PURL_ENABLED
- - ont_url = @ontology.purl.sub(@ontology.acronym, ont_parent_acronym)
- - else
- - ont_url = @ontology.links['ui'].sub(@ontology.acronym, ont_parent_acronym)
- = link_to(ont_parent_acronym, ont_url)
- - unless @submission_latest.nil?
- %tr
- %td Description
- %td= sanitize(@submission_latest.description)
- %tr
- %td Status
- %td= @submission_latest.status.capitalize unless @submission_latest.status.nil?
- %tr
- %td Format
- %td= @submission_latest.hasOntologyLanguage
- %tr
- %td Contact
- %td= raw @submission_latest.contact.map {|c| [c.name, c.email].join(", ") if c.member?(:name) && c.member?(:email)}.join("
-
-
+ :javascript
+ var BP_SEARCH_SERVER = "#{$UI_URL}";
+ var BP_SITE = "#{$SITE}";
+ var BP_ORG = "#{$ORG}";
+ var BP_ontology_id = "#{@ontology.acronym}";
+ = javascript_include_tag "/javascripts/widgets/quick_jump.js"
+ - c.help_text do
+ .enable-lists
+ %ul
+ %li
+ = t("ontologies.sections.download")
+ %a.external.free{:href => "/javascripts/widgets/quick_jump.js", :rel => "nofollow", :title => "/javascripts/widgets/quick_jump.js"}
+ %b quick_jump.js file
+ = t("ontologies.sections.put_on_server")
+ %li
+ = t("ontologies.sections.copy_and_paste")
+ %li
+ %b= t("ontologies.sections.note")
+ = t("ontologies.sections.use_quick_jump")
+ %ul
+ %li
+ = t("ontologies.sections.enter_list_of_ontologies")
+ %br/
+ var BP_ontology_id = "NCIt,SNOMEDCT";
+ %li
+ = t("ontologies.sections.set_the_variable", site: "#{$SITE}")
+ %br/
+ var BP_ontology_id = "all";
+ %li
+ = t("ontologies.sections.include_definitions")
+ %br/
+ %pre var BP_include_definitions = true;
+ %li
+ = t("ontologies.sections.info_pasted_code")
+ %ul
+ %li
+ = t("ontologies.sections.example_to_use_code")
+ %pre
+ = preserve do
+ :escaped
+
+
+
%p
- For more help visit
- %a{:href => "http://bioontology.org/wiki/index.php/NCBO_Widgets#How_to_use_NCBO_Widgets", :target => "_blank"} NCBO Widget Wiki
- %tr
- %td
- %div.card
- %div.card-body
- %h5.card-title Form Autocomplete
- %p.card-text Fill your form fields with classes from #{@ontology.acronym}
- %a.btn.btn-info.thickbox{href: "#{get_code_prefix}&inlineId=form".html_safe} Get code
- %td
- = javascript_include_tag "/javascripts/widgets/form_complete.js"
- Example 1 (start typing the class name to get its full URI)
- %br/
- %input{:class => "bp_form_complete-#{CGI.escape(@ontology.acronym).sub('-', '%2d')}-uri", :name => "a", :size => "100", :type => "text"}/
- %br/
- Example 2 (get the ID for a class)
- %br/
- %input{:class => "bp_form_complete-#{CGI.escape(@ontology.acronym).sub('-', '%2d')}-shortid", :name => "b", :size => "100", :type => "text"}/
- %br/
- Example 3 (get the preferred name for a class)
- %br/
- %input{:class => "bp_form_complete-#{CGI.escape(@ontology.acronym).sub('-', '%2d')}-name", :name => "c", :size => "100", :type => "text"}/
- #form{:style => "display:none;"}
- .enable-lists
- %h2 Step 2: Follow the Instructions
- %hr/
- %ul
- %li
- Download the
- %a.external.free{:href => "/javascripts/widgets/form_complete.js", :rel => "nofollow", :title => "/javascripts/widgets/form_complete.js"}
- %b form_complete.js file
- and put it on your server.
- %li
- In the header for the page where you want the form field, include the
- %b form_complete.js
- file.
- %li
- On your form, for the fields where you want to use the class-selection widget, specify the field's class in the following format:
- %code bp_form_complete-{ontology_id_list}-{value}
- %ul
- %li
- For example,
- %code bp_form_complete-NCIT-uri
- will use NCI Thesaurus (ontology id is NCIT) and will put the class URI in the field after the user selects the class from the pull-down list.
- %ul
- %li
- %b Note:
- In addition to single ontology ids, you can use a list:
- %br/
- %code bp_form_complete-NCIT,NCBITAXON-uri
- %li
- %b OR
- use 'all' to search across all #{$SITE} ontologies:
- %br/
- %code bp_form_complete-all-uri
- %li The autocomplete widget accesses ontology content from the latest version of the ontology.
- %li
- You can use the following parameters to select which value will be placed into the user-visible input field:
- %ul
- %li
- %code uri
- put the complete URI of the class (e.g.,
- = succeed ")" do
- %a.external.free{:href => @ontology.explore.classes["collection"].first.id, :rel => "nofollow", :title => "/visualize/39478/Common_Neoplasm"}
- = @ontology.explore.classes["collection"].first.id
- %li
- %code shortid
- put the short id of the class, as used in #{$SITE} (e.g., "Common_Neoplasm");
- %li
- %code name
- put the preferred name of the class (e.g., "Common Neoplasm");
- %li
- In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a class from the list. For example, if you create a field with this code:
- %ul
- %pre= h '
@@ -236,9 +197,12 @@
ontology: "#{@ontology.acronym}"
});
- %p
- You can also view a
- %a{href: "/widgets/ncbo_tree.html"} detailed demonstration
- %p
- For more help visit
- %a{:href => "http://bioontology.org/wiki/index.php/NCBO_Widgets#How_to_use_NCBO_Widgets", :target => "_blank"} NCBO Widget Wiki
+ %p
+ = t("ontologies.sections.can_also_view")
+ %a{href: "/widgets/ncbo_tree.html", target: '_blank'}
+ = t("ontologies.sections.detailed_demonstration")
+ %p
+ = t("ontologies.sections.more_help_visit")
+ %a{:href => "http://bioontology.org/wiki/index.php/NCBO_Widgets#How_to_use_NCBO_Widgets", :target => "_blank"}
+ = t("ontologies.sections.ncbo_widget_wiki")
+
diff --git a/app/views/ontologies/sections/metadata/_metrics_evolution_graph.html.haml b/app/views/ontologies/sections/metadata/_metrics_evolution_graph.html.haml
new file mode 100644
index 000000000..918c5275a
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_metrics_evolution_graph.html.haml
@@ -0,0 +1,6 @@
+= turbo_frame_tag 'application_modal_content' do
+ - data = data.values.first.each_with_index.map{|x, i| ["Submission #{i + 1}", x]}.reject{|_, count| count.zero?}.to_h
+
+ = chart_component(title: '', type: 'line',
+ labels: data.keys,
+ datasets: visits_chart_dataset_array({ count: data.to_a}, fill: false))
diff --git a/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml b/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml
new file mode 100644
index 000000000..dc0c5221f
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml
@@ -0,0 +1,73 @@
+= render Layout::CardComponent.new do |c|
+ - c.header(text: t("ontologies.sections.metadata.general_information"))
+ = render Layout::ListComponent.new do |l|
+ - l.row do
+ %div
+ - if @submission_latest&.abstract.blank?
+ .creation_text.d-flex.align-items-center
+ = render TextAreaFieldComponent.new(value: @submission_latest&.description)
+ - unless @submission_latest&.logo.nil? || !link?(@submission_latest&.logo)
+ = image_tag(@submission_latest&.logo, class: 'description_img ml-2', width: '145px')
+ - else
+ .d-flex.align-items-center
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.abstract")) do
+ .creation_text
+ = render TextAreaFieldComponent.new(value: @submission_latest&.abstract)
+ - unless @submission_latest&.logo.nil? || !link?(@submission_latest&.logo)
+ = image_tag(@submission_latest&.logo, class: 'description_img ml-2', width: '145px')
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.description")) do
+ .creation_text
+ = render TextAreaFieldComponent.new(value: @submission_latest&.description)
+
+
+
+
+ - l.row do
+ %div.creation_text
+ - if @submission_latest&.released
+ = t("ontologies.sections.metadata.initial_created_on")
+ %span.date_creation_text= l(Date.parse(@submission_latest.released), format: :monthfull_day_year) + '.'
+ - if @submission_latest&.contact
+ = t("ontologies.sections.metadata.additional_information")
+ %span
+ #{display_contact(@submission_latest.contact).html_safe}.
+
+ - unless Array(@submission_latest&.naturalLanguage).empty?
+ - l.row do
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.languages")) do
+ = horizontal_list_container(Array(@submission_latest&.naturalLanguage)) do |v|
+ = render LanguageFieldComponent.new(value: v)
+
+
+ - unless Array(@submission_latest&.keywords).empty? && Array(@submission_latest&.keyClasses).empty?
+ - l.row do
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.keywords_and_classes")) do
+ - values = (Array(@submission_latest&.keywords) + Array(@submission_latest&.keyClasses))
+ - values = values.map{|x| x.split(',')}.flatten
+ = horizontal_list_container(values) do |v|
+ - if link?(v)
+ = raw get_link_for_cls_ajax(v, @ontology.acronym, '_blank')
+ - else
+ = render ChipButtonComponent.new(text: v, type: "static")
+ - domains = Array(@ontology&.hasDomain) + Array(@submission_latest&.hasDomain)
+ - unless domains.empty?
+ - l.row do
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.categories_and_subjects")) do
+ = horizontal_list_container(show_ontology_domains(domains).uniq) do |v|
+ = render ChipButtonComponent.new(text: show_category_name(v), type: "static")
+
+ - if @submission_latest&.pullLocation
+ - l.row do
+ = admin_block(class_css: '') do
+ = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.pull_location") ) do
+ = horizontal_list_container([@submission_latest&.pullLocation]) do |v|
+ %span.admin-background
+ = render LinkFieldComponent.new(value: v)
+ %hr.w-100.my-3
+ .icons_container
+ = ontology_icon_links(@ontology_icon_links, @submission_latest)
+ %hr.w-100.my-3
+ %div.text-center.pb-3
+ = link_to_modal(nil, metadata_export_index_path(ontology: @ontology.acronym), {data: {show_modal_title_value: metadata_filled_count, show_modal_size_value: 'modal-xl' }}) do
+ = t("ontologies.sections.metadata.export_metadata")
+
diff --git a/app/views/ontologies/sections/metadata/_ontology_fairness_section.html.haml b/app/views/ontologies/sections/metadata/_ontology_fairness_section.html.haml
new file mode 100644
index 000000000..87c9bb5c1
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_ontology_fairness_section.html.haml
@@ -0,0 +1,15 @@
+- if fairness_service_enabled? && @ontology.acronym != 'AGROVOC' && @fair_scores_data
+ = render SummarySectionComponent.new(title: t("ontologies.sections.metadata.fair_score_title")) do |s|
+ - s.action_link do
+ = render partial: "fair_score/fair_service_header"
+
+ %div.p-2
+ %section.ont-metadata-card.ont-fair-score-card#fair-summary
+ %div.ont-section-toolbar.justify-content-between.flex-row-reverse
+ %div.align-items-start
+ .btn.btn-primary.rounded-pill.right-button
+ .span{ style: 'cursor: default;' }= t("ontologies.sections.metadata.total_score", score: @fair_scores_data[:score], normalized_score: @fair_scores_data[:normalizedScore])
+
+ %div#fair-score-charts-container
+ = render partial: "fairs_score"
+ .account-page-card-sub-container
\ No newline at end of file
diff --git a/app/views/ontologies/sections/metadata/_ontology_metrics_section.html.haml b/app/views/ontologies/sections/metadata/_ontology_metrics_section.html.haml
new file mode 100644
index 000000000..130dbefa5
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_ontology_metrics_section.html.haml
@@ -0,0 +1,20 @@
+= render SummarySectionComponent.new(title: t("ontologies.sections.metadata.metrics") , link: Rails.configuration.settings.links[:metrics], link_title: t("ontologies.sections.metadata.metrics_link_title"), show_card: false, service_link: "#{@ontology.id}/metrics?display=all") do |s|
+ - s.action_link do
+ = link_to_modal '', ontology_path(@ontology.acronym) + "/metrics",
+ class: "metrics-item", title: t("ontologies.sections.metadata.see_all_metrics", acronym: @ontology.acronym),
+ data: { controller: "tooltip", show_modal_size_value: 'modal-md' , show_modal_title_value: t("ontologies.sections.metadata.show_modal_title_1", acronym: @ontology.acronym)}
+
+ - if @metrics.nil? || (@metrics.is_a?(Array) && @metrics.empty?) || (@metrics.respond_to?(:status) && @metrics.status == 404)
+ = empty_state_message(t("ontologies.sections.metadata.not_calculated_metrics", acronym: @ontology.acronym))
+ - else
+ .metrics-container.metrics
+ - %w[classes individuals properties].each do |metric|
+ = link_to_modal nil, ontology_path(@ontology.acronym) + "/metrics_evolution?metrics_key=#{metric}",
+ class: "metrics-item", data: { show_modal_title_value: t("ontologies.sections.metadata.show_modal_title_2", metric: metric, acronym: @ontology.acronym) } do
+ %hr
+ %div
+ %h4
+ = @metrics.send(metric)
+ %p
+ = render PopupLinkTextComponent.new(text: t("ontologies.sections.#{metric}"))
+
diff --git a/app/views/ontologies/sections/metadata/_ontology_relations_network.html.haml b/app/views/ontologies/sections/metadata/_ontology_relations_network.html.haml
new file mode 100644
index 000000000..13d3f1a64
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_ontology_relations_network.html.haml
@@ -0,0 +1,14 @@
+- unless @ontology_relations_data.nil? || @ontology_relations_data.empty?
+ = render SummarySectionComponent.new(title: t("ontologies.sections.metadata.relations_network"), link: "", link_title: generate_link_title) do
+ %div.d-flex.flex-column.justify-content-center{data: {controller: "ontology-relations-network", "ontology-relations-network-data-value": @ontology_relations_data.to_json.html_safe }}
+ %button.btn.btn-link.m-2{'data-toggle': "collapse",'data-target': "#ontologyRelations"}
+ %span= t("landscape.filter_network")
+ %i.fas.fa-chevron-down
+ %div#ontologyRelations.collapse.flex-row.flex-wrap.px-2.my-1.fade{'data-action': "change->ontology-relations-network#build"}
+ - values = @relations_array_display
+ = render SelectInputComponent.new(id:'relation-network', name: 'selectedRelations[]', values: values, selected:@relations_array , multiple: true)
+
+ %div{:style => "width: 100%;"}
+ %div#networkContainer{:style => "height: 465px; width: 100%;", "data-ontology-relations-network-target": "container" }
+ %div#ontologyNetwork
+ %button#fullscreen-button
\ No newline at end of file
diff --git a/app/views/ontologies/sections/metadata/_ontology_submissions_section.html.haml b/app/views/ontologies/sections/metadata/_ontology_submissions_section.html.haml
new file mode 100644
index 000000000..d7375b8bb
--- /dev/null
+++ b/app/views/ontologies/sections/metadata/_ontology_submissions_section.html.haml
@@ -0,0 +1,2 @@
+= render SummarySectionComponent.new(title: t("ontologies.sections.metadata.submissions") , link: "", link_title: t("ontologies.sections.metadata.submissions_link_title", site: portal_name), service_link: "#{@ontology.id}/submissions?display=all") do |s|
+ = render TurboFrameComponent.new(id: 'ontology_submissions', src: ontology_submissions_path(@ontology.acronym, invalidate_cache: params[:invalidate_cache]))
\ No newline at end of file
diff --git a/app/views/ontologies/sections/properties.html.haml b/app/views/ontologies/sections/properties.html.haml
index dc3f796fa..99fb1873a 100644
--- a/app/views/ontologies/sections/properties.html.haml
+++ b/app/views/ontologies/sections/properties.html.haml
@@ -1,84 +1,13 @@
-= turbo_frame_tag 'properties' do
- %div.ont-properties{data:{controller: 'container-splitter'}}
- %div#propTree{data:{'container-splitter-target': 'container'}}
- %div#prop_contents.pl-3{data:{'container-splitter-target': 'container'}}
-
- :plain
-
-
- :javascript
- $(document).ready(function(){
- jQuery(document).data().bp.ontPropertiesTab = {};
-
- jQuery(document).data().bp.ontPropertiesTab.init = function() {
- var source = jQuery("#property-details").html();
- var propDetailsTemp = Handlebars.compile(source);
-
- $("#propTree").NCBOPropertyTree({
- ontology: "#{@ontology.acronym}",
- ncboUIURL: jQuery(document).data().bp.config.ui_url,
- width: "100%",
- onInit: function() {
- var ontPropTree = $("#propTree").data().NCBOPropertyTree;
- var data = $("#propTree").find("a:first").data();
- if (data) {
- ontPropTree.selectClass(data.id);
- data.id = decodeURIComponent(data.id);
- jQuery("#prop_contents").html(propDetailsTemp(data));
- }
- }
- }).on("afterSelect", function (e, classId, label, node) {
- var data = node.data();
- data.id = decodeURIComponent(data.id);
- jQuery("#prop_contents").html(propDetailsTemp(data));
- });
- }
-
- jQuery(document).data().bp.ontPropertiesTab.init();
-
- })
+= render TurboFrameComponent.new(id: "properties", data: {"turbo-frame-target": "frame"} ) do
+ - if no_properties?
+ = no_properties_alert
+ - else
+ %div.ont-properties{data: {controller: 'container-splitter turbo-frame', 'turbo-frame-url-value': "/ontologies/#{@ontology.acronym}/properties/show"}}
+ %div.sidebar.position-relative.card{data: {'container-splitter-target': 'container', action: 'change->turbo-frame#updateFrame'}}
+ = tree_container_component(id: 'properties_sorted_list_view-page-1',
+ placeholder: t('ontologies.sections.properties_search_placeholder', acronym: @ontology.acronym),
+ frame_url: "/ontologies/#{@ontology.acronym}/properties",
+ tree_url: "/ontologies/#{@ontology.acronym}/properties?propertyid=#{escape(params[:propertyid])}&ontology=#{@ontology.acronym}&auto_click=false&language=#{request_lang}")
+
+ %div#prop_contents{data: {'container-splitter-target': 'container'}}
+ = render partial: 'properties/show'
diff --git a/app/views/ontologies/sections/visualize.html.haml b/app/views/ontologies/sections/visualize.html.haml
index 14dee3422..121b57daa 100644
--- a/app/views/ontologies/sections/visualize.html.haml
+++ b/app/views/ontologies/sections/visualize.html.haml
@@ -1,31 +1,21 @@
-= turbo_frame_tag 'classes' do
- - unless @error
- - @title = "#{@ontology.name} - #{@concept.prefLabel}"
+= render TurboFrameComponent.new(id: "classes", data: {"turbo-frame-target": "frame"} ) do
+ - unless @error || @concept.nil?
+ - @title = "#{@ontology.acronym} - #{@concept.prefLabel}"
- @new_term_request_ontologies
- @enable_ontolobridge = !$NEW_TERM_REQUEST_ONTOLOGIES.nil? && $NEW_TERM_REQUEST_ONTOLOGIES.include?(@ontology.acronym)
%div.tooltip
%div#bd_content.bd_content.explore{data:{controller: 'container-splitter'}}
- %div.sidebar.d-flex.flex-column.mr-2.card{data:{'container-splitter-target': 'container'}}
+ %div.sidebar{data:{'container-splitter-target': 'container'}}
= render partial: 'ontologies/concepts_browsers/concepts_browser'
- %div#concept_content.d-flex.flex-column.card.p-1.ml-2{data:{'container-splitter-target': 'container'}}
+ %div#concept_content.d-flex.flex-column{data:{'container-splitter-target': 'container'}}
= render partial: 'concepts/show'
- form_for(:search, :url => {:controller =>'search',:action=>'fetch_results'},:html=>{:id=>'search_form'}) do |f|
%input{:name => "search[ontologies][]", :type => "hidden", :value => @ontology.acronym}/
= hidden_field :search, :search_type, :value=>"contains"
= hidden_field :search, :keyword, :value=>"",:id=>"search_keyword"
- - else # found an error
- = "
#{@error} "
-
- :javascript
- $(document).ready(function() {
- const ontology_acronym = "#{@ontology.acronym}"
- let data = #{raw @instance_details.to_json} || null
-
- if(data && Object.keys(data).length !== 0){
- $.facebox({ajax: `/ontologies/${ontology_acronym}/instances/${encodeURIComponent(data["@id"])}`})
- }
- })
-
+ - else
+ = render Display::AlertComponent.new(type: 'danger') do
+ = @concept.nil? ? t("ontologies.sections.no_class_concept_found") : @error
diff --git a/app/views/ontologies/submit_success.html.haml b/app/views/ontologies/submit_success.html.haml
index b77274868..5836a272f 100644
--- a/app/views/ontologies/submit_success.html.haml
+++ b/app/views/ontologies/submit_success.html.haml
@@ -1,24 +1,22 @@
%div.p-4
- %h2.pb-3 Ontology submitted successfully!
+ %h2.pb-3= t("ontologies.ontology_submitted")
-if @ontology.summaryOnly
- %p Thank you for submitting your metadata-only ontology to #{$SITE}.
+ %p= t("ontologies.ontology_submitted", site: "#{$SITE}")
%p
- Users can now see
- = link_to "your ontology", ontology_path(@ontology.acronym)
- in our ontology list but they cannot explore or search it. To enable exploring and searching,
- please upload a full version of your ontology.
+ = t("ontologies.users_can_see")
+ = link_to t("ontologies.your_ontology"), ontology_path(@ontology.acronym)
+ = t("ontologies.exploring_and_searching")
-else
-if @ontology.viewOf
- %p Thank you for submitting your ontology view to #{$SITE}.
+ %p= t("ontologies.submitting_ontology_view", site: "#{$SITE}")
-else
- %p Thank you for submitting your ontology to #{$SITE}.
+ %p= t("ontologies.submitting_ontology", site: "#{$SITE}")
%p
- We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several
- hours before #{$SITE} users will be able to explore and search your ontology.
+ = t("ontologies.processing_message", site: "#{$SITE}")
%p
- When your ontology is ready for viewing, it will be available here:
+ = t("ontologies.notification_message")
= link_to ontology_url(@ontology.acronym), ontology_path(@ontology.acronym)
%p
- If you have any questions or problems, please email the #{$SITE} support team at:
+ = t("ontologies.contact_support_at", site: "#{$SITE}")
= mail_to "#{$SUPPORT_EMAIL}", "#{$SUPPORT_EMAIL}"
diff --git a/app/views/ontologies_metadata_curator/_attribute.html.haml b/app/views/ontologies_metadata_curator/_attribute.html.haml
new file mode 100644
index 000000000..135be1b01
--- /dev/null
+++ b/app/views/ontologies_metadata_curator/_attribute.html.haml
@@ -0,0 +1,36 @@
+- acronym = ontology ? ontology.acronym : submission.id.split('/')[-3]
+= render TurboFrameComponent.new(id: id) do
+ %div.d-flex.justify-content-between.align-items-center
+ %div.d-flex.justify-content-between
+ %div
+ - equivalents = equivalent_properties(attribute)
+ - equivalents.each do |attr|
+ %div.d-flex
+ - if equivalents.size > 1
+ %span= "#{attr}: "
+ %div
+ %div
+ = error_message_alert
+ %div
+ - if attribute == "contact"
+ = raw submission.contact.map {|c| [c["name"], c["email"]].join(", ") if c.member?(:name) && c.member?(:email)}.join("
- Review For <%=@review.ontology.displayLabel%>
-
-
-
- <%=submit_tag "Submit Reviews",:class=>"blueButton"%>
-
-<%end%>
-
-
-
diff --git a/app/views/reviews/index.html.erb b/app/views/reviews/index.html.erb
deleted file mode 100644
index 4f42e1faa..000000000
--- a/app/views/reviews/index.html.erb
+++ /dev/null
@@ -1,56 +0,0 @@
-<%@title = "Reviews of the #{@ontology.displayLabel}"%>
-
-<%=link_to "Review Ontology",new_review_path(:ontology=>@ontology.ontologyId)%>
-<%end%>
-
-
-Reviews for <%=@ontology.displayLabel%>
-
-
-
-
-
diff --git a/app/views/reviews/new.html.haml b/app/views/reviews/new.html.haml
deleted file mode 100644
index a71e4b267..000000000
--- a/app/views/reviews/new.html.haml
+++ /dev/null
@@ -1,24 +0,0 @@
-= form_for(:review, :url => reviews_path, :remote => true, :id => "new_review_form") do |f|
- = f.hidden_field :ontologyReviewed, value: @review.ontologyReviewed
- = f.hidden_field :creator, value: @review.creator
- %fieldset
- %legend
- %b
- Review For #{@ontology.name}
- %table
- %tr
- %td
- Ratings
- %br/
- - for rating in @rating_types
- %div{:style => "padding:2px;border-top:1px solid gray;"}
- - (1..5).each do |i|
- = f.radio_button rating, i, class: "star"
- #{rating.to_s.chomp("Rating").capitalize}
- %tr
- %td= f.text_area :body, value: @review.body, cols: 80, rows: 5
- = submit_tag "Submit Review", class: "blueButton"
-
-:javascript
- // Do this after the HTML above loads
- jQuery('input.star').rating();
diff --git a/app/views/reviews/show.html.erb b/app/views/reviews/show.html.erb
deleted file mode 100644
index fee6e546d..000000000
--- a/app/views/reviews/show.html.erb
+++ /dev/null
@@ -1,37 +0,0 @@
-
-
-
-
-
- Review By <%=@review.user.username %><%unless @review.project.nil? %> From Project <%=link_to @review.project.name,project_path(@review.project) %><%end %><%if isOwner?(@review.user_id) %> <%=link_to "Edit Review", edit_review_path(@review) + "?height=500&width=600", :class => "thickbox" %><%end %>
-
-
-
-
-
-
-
-
- <%=@review.review%>
-
-
-
-
-
-Preview of <%=link_to "#{@concept.label_html},#{@concept.id}",uri_url(:ontology=>@ontology,:conceptid=>@concept.id),:target=>"_new"%>
-
-
-
-<%@concept.properties.each_pair{|key,value| %>
-
-
- <%="#{remove_owl_notation(key)}:"%> <%="#{value}"%>
-
-
-<% } %>
-
-
-
-
\ No newline at end of file
diff --git a/app/views/search/_concepts.html.erb b/app/views/search/_concepts.html.erb
deleted file mode 100644
index b0593ccee..000000000
--- a/app/views/search/_concepts.html.erb
+++ /dev/null
@@ -1,22 +0,0 @@
-<%if @concepts.size > 0%>
-
-
-
- <%for option in @concepts%>
- <%=option[:preferredName]%>
- <%end%>
-
-
-
-
-
-
Comment
-
- <%= select("mapping", "directionality", { "Bidirectional" => "bidirectional", "Unidirectional" => "unidirectional" })%>
-<%else%>
- No Results Found
-<%end%>
\ No newline at end of file
diff --git a/app/views/search/_results.html.erb b/app/views/search/_results.html.erb
deleted file mode 100644
index 314707ad3..000000000
--- a/app/views/search/_results.html.erb
+++ /dev/null
@@ -1,69 +0,0 @@
-
-<%if @results.size > 0%>
-
- <%if params[:page].to_i > 1 %>
- << Previous Page
-
- <%end%>
- Page <%=params[:page] || 1%> of <%=@pages%>
- <%if !params[:page].to_i.eql?(@pages.to_i)%>
- Next Page >>
-
- <%end%>
-
-
-
-
-
- <%if params[:page].to_i >1 %> << Previous Page <%end%> Page <%=params[:page] || 1%> of <%=@pages%> <%if !params[:page].to_i.eql?(@pages.to_i)%> Next Page >> <%end%>
-
-
-
-
- Class Name
- Found In
- Ontology
-
-
- <%for result in @results%>
- <%begin
- #catch exceptions and dont draw row
- row = "
- #{link_to highlight(result[:contents],@keyword), uri_url(:ontology => result[:ontologyVersionId], :conceptid => result[:conceptIdShort]), :onclick => "YAHOO.tabwait.container.wait.show();"}
- #{result[:recordType].titleize.gsub("Record Type","")}
- #{link_to result[:ontologyDisplayLabel], ontology_path(:id=>result[:ontologyVersionId])}
- "%>
- <%=row%>
- <%rescue
- end
- %>
- <%end%>
-
-
-
- <%if params[:page].to_i >1 %> << Previous Page <%end%> Page <%=params[:page] || 1%> of <%=@pages%> <%if !params[:page].to_i.eql?(@pages.to_i)%> Next Page >> <%end%>
-
-
-
-
-<%else%>
- No Results Found
-<%end%>
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 6b8246641..28ecbf2ee 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -1,67 +1,72 @@
-- @title = "Search"
+.search-page-container
+ .search-page-subcontainer{'data-controller': 'reveal-component'}
+ = form_tag(search_path, method: :get,data:{turbo: true, controller: 'form-url', action: 'submit->form-url#submit'}) do
+ = search_page_input_component(placeholder: t('search.search_place_holder'), name: "q", value: @search_query) do
+ .search-page-advanced{'data-reveal-component-target': 'item', class: "#{@advanced_options_open ? '' : 'd-none'}"}
+ .left
+ .filter-container
+ .title
+ = t('search.advanced_options.search_language')
+ .field
+ = search_language_selector(name: 'lang', selected: params[:lang])
-%div.container.mt-5
- %h1
- Class Search
+ .filter-container
+ .title
+ = t("search.advanced_options.ontologies")
+ .field
+ = ontologies_selector(id:'search_page_ontologies' ,name: 'ontologies[]', selected: params[:ontologies]&.split(','))
- = form_tag("/search", method: "post") do
- %div.form-group
- = text_field_tag("search_keywords", nil, class: "form-control", aria: {describedby: "classSearchHelpBlock"})
- %small#classSearchHelpBlock.form-text.text-muted
- = t(".search_keywords_placeholder")
- = link_to("help", Rails.configuration.settings.links[:help_search], target: '_blank',
- aria: {label: "View search documentation"}, class: "float-right")
- %div.form-group
- = link_to("Show advanced options", "javascript:void(0)", id: "advanced_options", data: {text_swap: "Hide advanced options"}, class: "form-text")
+ .right
+ .filter-container
+ .title
+ = t("search.advanced_options.include_in_search_title")
+ .d-flex
+ = render(ChipsComponent.new(name: 'also_search_properties', label: t("search.advanced_options.include_in_search_values.property_values"), checked: params[:also_search_properties]))
+ = render(ChipsComponent.new(name: 'also_search_obsolete', label: t("search.advanced_options.include_in_search_values.obolete_classses"), checked: params[:also_search_obsolete]))
+ = render(ChipsComponent.new(name: 'also_search_views', label: t("search.advanced_options.include_in_search_values.ontology_views"), checked: params[:also_search_views]))
- -# Advanced search options
- %div#search_options{style: "display: none;"}
- %div.form-group.row
- %div.col-sm-2 Include in search:
- %div.col-sm-10
- %div.form-check
- = check_box(:search, :include_properties, class: "form-check-input")
- = label(:search, :include_properties, "Property values", class: "form-check-label definition", title: t(".property_definition"))
- %div.form-check
- = check_box(:search, :include_obsolete, class: "form-check-input")
- = label(:search, :include_obsolete, "Obsolete classes", class: "form-check-label definition", title: t(".obsolete_definition"))
- %div.form-check
- = check_box(:search, :include_views, class: "form-check-input")
- = label(:search, :include_views, "Ontology views", class: "form-check-label")
- %div.form-group.row
- %div.col-sm-2 Narrow search to:
- %div.col-sm-10
- %div.form-check
- = check_box(:search, :exact_match, class: "form-check-input")
- = label(:search, :exact_match, "Exact matches", class: "form-check-label")
- %div.form-check
- = check_box(:search, :require_definition, class: "form-check-input")
- = label(:search, :require_definition, "Classes with definitions", class: "form-check-label")
- %div.form-group
- %h2{style: "font-size: 10pt !important"} Categories
- = select(:search, :categories, options_for_select(categories_for_select), {}, style: "width: 432px", multiple: "true", data: {placeholder: t(".categories_placeholder")})
- %div.form-group.mb-5{style: "width:432px"}
- = render :partial => "shared/ontology_picker", locals: {sel_text: "Ontologies"}
+ .filter-container
+ .title
+ =t('search.advanced_options.show_only_title')
+ .d-flex
+ = render(ChipsComponent.new(name: 'require_exact_match', label: t('search.advanced_options.show_only_values.exact_matches'), checked: params[:require_exact_match]))
+ = render(ChipsComponent.new(name: 'require_definition', label: t('search.advanced_options.show_only_values.classes_with_definitions'), checked: params[:require_definition]))
- = button_tag("Search", id: "search_button", class: "btn btn-primary")
- = content_tag(:span, id: "search_spinner") do
- %img{src: asset_path('spinners/spinner_000000_16px.gif'), style: "vertical-align: middle;"}
+ .search-page-options{class: @search_results.empty? ? 'justify-content-end': ''}
+ - unless @search_results.empty?
+ .search-page-number-of-results
+ = "#{t('search.match_in')} #{@search_results.length} #{t('search.ontologies')}"
+ %div.d-flex
+ .search-page-json.mx-4.mt-1
+ = search_json_link
+ .search-page-advanced-button.show-options{class: "#{@advanced_options_open ? 'd-none' : ''}",'data': {'action': 'click->reveal-component#show', 'reveal-component-target': 'showButton'}}
+ .icon
+ =inline_svg_tag 'icons/settings.svg'
+ .text
+ = t('search.show_advanced_options')
+ .search-page-advanced-button.hide-options{class: "#{@advanced_options_open ? '' : 'd-none'}", 'data': {'action': 'click->reveal-component#hide', 'reveal-component-target': 'hideButton'}}
+ .icon
+ =inline_svg_tag 'icons/hide.svg'
+ .text
+ = t('search.hide_advanced_options')
+ - if @search_results
+ .search-page-results-container
+ - number = 0
+ - @search_results.each do |result|
+ .search-page-result-element
+ - number = number + 1
+ - descendants = result[:descendants]
+ - reuses = result[:reuses]
+ - result[:root][:number] = number
+ = render Display::SearchResultComponent.new(result[:root]) do |c|
+ - descendants.each { |d| c.subresult(d.merge(is_sub_component: true))}
+ - reuses.each do |r|
+ - number = number + 1
+ - c.reuse(r[:root].merge(is_sub_component: true, number: number)) do |b|
+ - r[:descendants].each { |dd| b.subresult(dd.merge(is_sub_component: true))}
- -# Search results
- %div.row.mt-4#search_results_container
- %div.col
- #result_stats
- #search_messages
- #search_results
-
-%div#biomixer{style: "display: none;"}
-
-:javascript
- // Hash of ontology id => name, acronym for lookup use via JS
- jQuery(document).ready(function() {
- jQuery(document).data().bp.ontologies = #{Hash[LinkedData::Client::Models::Ontology.all(include_views: true).map {|o| [o.id, {name: o.name, acronym: o.acronym}]}].to_json.html_safe}
-
- if (jQuery("#search_keywords").val() !== "") {
- performSearch();
- }
- });
+ - if @search_results.empty? && !@search_query.empty?
+ .browse-empty-illustration
+ %img{:src => "#{asset_path("empty-box.svg")}"}
+ %p No result was found
+
\ No newline at end of file
diff --git a/app/views/search/search.html.erb b/app/views/search/search.html.erb
deleted file mode 100644
index 3eb433b1c..000000000
--- a/app/views/search/search.html.erb
+++ /dev/null
@@ -1,6 +0,0 @@
-
-<%for result in @results%>
- <%=result.name%>
-
-<%end%>
-
\ No newline at end of file
diff --git a/app/views/shared/_concept_picker.html.haml b/app/views/shared/_concept_picker.html.haml
index d1b32729a..a3b61e816 100644
--- a/app/views/shared/_concept_picker.html.haml
+++ b/app/views/shared/_concept_picker.html.haml
@@ -1,5 +1,5 @@
= text_field_tag(name, concept_label, class: "search_autocomplete form-control",
- placeholder: "Start typing to select a class",
+ placeholder: 'Start typing to select a class/concept',
data: {controller: "form-auto-complete",
"form-auto-complete-ontology_id-value": ontology_acronym ,
"form-auto-complete-target_property-value": 'name',
diff --git a/app/views/shared/_not_browsable.html.erb b/app/views/shared/_not_browsable.html.erb
deleted file mode 100644
index 17a5d9dbf..000000000
--- a/app/views/shared/_not_browsable.html.erb
+++ /dev/null
@@ -1,21 +0,0 @@
-
-
-
-
Not Browsable
-
- <%= ErrorHelpers::not_browsable_text(@concept) %>
-
- Go back to your previous pageView <%=link_to @ontology.displayLabel, visualize_url(:ontology => @ontology.id)%>, which contains <%=@concept.name%>
-
-
-
-
-
-
- <%=sel_text%>
-
-
-
- <%=select form_object, form_attribute, options_for_select(@onts_for_select, selected_ontologies), { }, :multiple => 'true', "data-placeholder".to_sym => "Start typing to select ontologies or leave blank to use all", :style => "width: 432px;" %>
-
-
-
-
- <%=render_advanced_picker(custom_ontologies, selected_ontologies)%>
-
-
-
Select Multiple Ontologies close
-
-
-
-
-
-
-
-
-
Filtered Groups and Categories:
-
-
-
-
-
- <%= check_box_tag "ont_select_all_filtered" %>
- <%= label_tag "ont_select_all_filtered", "Select all filtered ontologies", :style => "color: var(--primary-color); font-weight: bold;" %> (show all )
-
-
- <% @onts_for_select.each do |ont| %>
-
- <%= check_box_tag "ont_select_adv_check", ont[1], false, :id => "ont_select_adv_check#{ont[1]}" %>
- <%= label_tag "ont_select_adv_check#{ont[1]}", ont[0] %>
-
- <% end %>
-
-
-
-
- <%= select object_name, field_name, @onts_for_select, { :include_blank => true, :selected => selected }, :id => picker_id, :class => "ontology_picker_single form-control", "data-placeholder".to_sym => placeholder, disabled: disabled %>
-
-
diff --git a/app/views/statistics/index.html.haml b/app/views/statistics/index.html.haml
new file mode 100644
index 000000000..e42fac412
--- /dev/null
+++ b/app/views/statistics/index.html.haml
@@ -0,0 +1,33 @@
+%div.px-3.py-3.pt-md-5.pb-md-4.text-center
+ %h1.display-4
+ = t('statistics.title', portal: portal_name)
+ %p.lead
+ = t('statistics.lead', last_years: Date.today.year - Date.parse(@merged_data[:labels].first).year)
+%div.container
+ %div
+ = chart_component(title: nil, type: 'line', show_legend: true,
+ labels: @merged_data[:labels], datasets: visits_chart_dataset_array({ t('statistics.ontologies') => @merged_data[:visits][2],
+ t('statistics.users') => @merged_data[:visits][0], t('statistics.projects') => @merged_data[:visits][1] }, fill: false))
+
+ %div.pb-3.pb-md-4
+ - size = @merged_data[:labels].size - 1
+ - visits = @year_month_visits
+ = render TableComponent.new(id: 'statistics_table') do |t|
+ - t.header do |h|
+ - h.th {t('statistics.date')}
+ - h.th {t('statistics.ontologies')}
+ - h.th {t('statistics.users')}
+ - h.th {t('statistics.projects')}
+ - h.th {t('statistics.ontology_visits')}
+
+ - @merged_data[:labels].reverse.each_with_index do |year_month, i|
+ - t.row do |r|
+ - r.td {year_month}
+ - r.td {@merged_data[:visits][2][size - i].to_s}
+ - r.td {@merged_data[:visits][0][size - i].to_s}
+ - r.td {@merged_data[:visits][1][size - i].to_s}
+ - r.td do
+ - year = Date.parse(year_month).year
+ - month = Date.parse(year_month).month
+ = visits[[year, month]] || 0
+
diff --git a/app/views/submissions/_form.html.haml b/app/views/submissions/_form.html.haml
deleted file mode 100644
index 04410cfbe..000000000
--- a/app/views/submissions/_form.html.haml
+++ /dev/null
@@ -1,25 +0,0 @@
-:javascript
- $(document).ready(function() {
- jQuery("#ontology_submission_form").validate();
- });
-
-
- function onMetadataChange(){
- let frame = document.getElementById('metadata_by_ontology')
- let properties = document.getElementById('search_metadata')
- let required = document.getElementById('filter-required-only')
- let selectedProperties = "all"
- if(properties){
- selectedProperties = Array.from(properties.selectedOptions).map(({ value }) => value).join(',')
- }
- frame.src = "?properties=" + selectedProperties + "&required=" + required.checked + "&show_sections=true"
- }
-
-
-= render partial: 'form_content', locals: {id: 'metadata_by_ontology', acronym: @ontology.acronym, submissionId: @submission.submissionId}
-
-%div.d-flex.justify-content-end.mt-1
- %div
- = link_to "Cancel", :back, class: "btn btn-secondary"
- %div.ml-1
- = submit_tag button_text, class: "btn btn-primary"
diff --git a/app/views/submissions/_form_content.html.haml b/app/views/submissions/_form_content.html.haml
index 68de9b3bf..f7d97aed5 100644
--- a/app/views/submissions/_form_content.html.haml
+++ b/app/views/submissions/_form_content.html.haml
@@ -1,178 +1,12 @@
-= render TurboFrameComponent.new(id:id) do
- %div#editMetadataDiv
- %div
- %p
- To understand the ontologies metadata:
- %a{:href => "https://github.com/agroportal/documentation/wiki/Ontology-metadata", :target => "_blank"} see the Wiki
- %div.d-flex.align-items-center.justify-content-between{onchange: "onMetadataChange()", style: "visibility: #{@filters_disabled ? 'hidden' : 'visible'}"}
- %div.w-75.mt-3
- - if @submission.id
- = render MetadataSelectorComponent.new(label: 'Filter properties to show', values: submission_editable_properties , selected: nil, inline: true)
- %div
- = render SwitchInputComponent.new(id:"filter-required-only", name: "required-only", label: "Required only", checked: @required_only)
+- unless @errors.nil?
+ = turbo_frame_tag 'test', target: '_top' do
+ = error_message_alert
+ = form_for :submission, url: ontology_submission_path(params["ontology_id"], params["id"]), html: { id: "ontology_submission_form", method: :put, multipart: true, 'data-turbo': true, novalidate: 'true'} do
+ = render_submission_inputs('', @submission)
+ %hr#edit-ontology-actions-devider
+ .edit-ontology-actions
+ .save-button
+ = render Buttons::RegularButtonComponent.new(id:'save-button', value: t('submissions.save_button'), variant: "primary", size: "slim", type: "submit") do |btn|
+ - btn.icon_left do
+ - inline_svg_tag "check.svg"
-
- - unless @errors.nil?
- %div
- %div.enable-lists{style: "color:red;"}
- %strong Errors On Form
- %ul
- - Array(@errors).each do |error|
- - error = error[:error] if error.is_a?(Hash) && error[:error]
- - if error.is_a?(String)
- = error
- - else
- - error.each do |key, value|
- %li
- - value = value.values if value.is_a?(Hash)
- #{key}: #{Array(value).join(', ')}
-
- = hidden_field object_name, :ontology, value: acronym
- = hidden_field object_name, :id, value: submissionId
- %div#general-card.mt-4
- = metadata_section('general', 'General', collapsed: false) do
- = attribute_container('format', required: true) do
- = turbo_frame_tag "#{object_name(acronym, submissionId)}Format_from_group_input" do
- = render partial: 'submissions/submission_format_form'
- = attribute_text_field_container('version', required: true)
-
- = attribute_form_group_container('status', required: true) do |c|
- - selected_status = c.value ? c.value : "alpha"
- - status_options = %w[alpha beta production retired]
- = select c.name, c.method_name, status_options, {selected: selected_status, required: true}, class: "form-control"
-
- = attribute_form_group_container('location', required: true) do
- = render partial: 'submissions/submission_location_form'
-
-
- %div#key-properties-card.mt-4
- = metadata_section('key-properties', 'Key properties', collapsed: false) do
- = form_group_attribute("URI", required: true)
- = render partial: 'submissions/submission_identifier_form'
-
- = form_group_attribute('hasCreator', label: 'Creator(s)', required: true)
- = form_group_attribute('publisher', required: true)
-
- = attribute_form_group_container('description', required: true) do |c|
- = text_area c.name, c.method_name, rows: 5, value: @submission.description, required: true, class: "form-control"
-
- = form_group_attribute('alternative', required: true)
-
- -# Publications page
- = form_group_attribute('publication', label: 'Publication(s)', required: true) do
- %p
- Enter a URL for a page that lists publications about your ontology.
-
- = form_group_attribute("released", default: Date.today, required: true)
-
- = form_group_attribute("hasFormalityLevel", required: true)
-
- %div#description-card.mt-4
- = metadata_section('more-description-details', 'More description details', parent_id: "description-card") do
- = form_group_attribute("deprecated")
- = form_group_attribute("isOfType")
- = form_group_attribute("hasOntologySyntax") do
- %p
- Properties taken from
- = link_to "W3C URIs for file format", "https://www.w3.org/ns/formats/", target: "_blank"
-
- = form_group_attribute("naturalLanguage") do
- %p
- Consider using a
- = link_to "Lexvo URI", "http://www.lexvo.org", target: "_blank"
- with ISO639-3 code
- %br
- e.g.: http://lexvo.org/id/iso639-3/eng
-
- -# Home page
- = form_group_attribute('homepage') do
- Enter a URL for the main page of your ontology.
-
- -# Documentation page
- = form_group_attribute('documentation') do
- Enter a URL for a page that provides ontology documentation.
-
-
- -# Used ontology engineering tool
- = form_group_attribute("usedOntologyEngineeringTool")
-
- - for attr_name in %w[abstract notes keywords]
- = form_group_attribute(attr_name)
-
- - data = sections
-
- - data.each do |d|
- = metadata_section(d[0], d[1], parent_id: "description-card") do
- - for attr in @metadata.select { |m| m['category'] == d[2] }
- = form_group_attribute(attr["attribute"])
-
- %div#ontology-dates-card.mt-4
- = metadata_section('more-dates', 'More dates', parent_id: "ontology-dates-card") do
- = form_group_attribute("modificationDate")
- - for attr in @metadata.select { |m| m['category'] == 'dates' }
- = form_group_attribute(attr["attribute"])
-
- %div#licenses-card.mt-4
- = metadata_section('licenses', 'Licenses') do
- = form_group_attribute("hasLicense") do
- %p
- Consider using a
- = link_to "URI to describe your License", "http://rdflicense.appspot.com", target: "_blank"
- %p
- Consider using
- = link_to "INRIA licentia", "http://licentia.inria.fr/", target: "_blank"
- to choose your license
-
- = metadata_section('more-licensing-info', 'More licensing information', parent_id: "licenses-card") do
- = form_group_attribute("morePermissions")
- = form_group_attribute("copyrightHolder")
-
- %div#community.mt-4
- = metadata_section('contacts-panel', 'Contacts', parent_id: "community", collapsed: !@required_only || !@submission.id.nil?) do
- -# Contact(s)
- = attribute_form_group_container('contact' ,required: true) do |c|
- - @submission.contact = [] unless @submission.contact && @submission.contact.size > 0
- = render NestedFormInputsComponent.new do |c|
- - c.template do
- = render partial: "submissions/submission_contact_form", locals: {contact: nil, index: 'NEW_RECORD'}
- - c.empty_state do
- = hidden_field_tag object_name+"[contact][#{@submission.contact.size}][email]"
- = hidden_field_tag object_name+"[contact][#{@submission.contact.size}][name]"
- - @submission.contact.each_with_index do |contact, i|
- - c.row do
- = render partial: "submissions/submission_contact_form", locals: {contact: contact, index: i}
-
- = form_group_attribute("hasContributor")
-
- = metadata_section('more-community-info', 'More community information', parent_id: "community") do
- - for attr in @metadata.select { |m| m['category'] == 'community' }
- = form_group_attribute(attr["attribute"])
-
- = metadata_section('more-people-info', 'More people information', parent_id: "community") do
- - for attr in @metadata.select { |m| m['category'] == 'people' }
- = form_group_attribute(attr["attribute"])
-
- %div#ontology-relations-more.mt-4
- = metadata_section('ontology-relations', 'Ontology relations', parent_id: "ontology-relations-more") do
- = form_group_attribute("useImports")
- = form_group_attribute("hasPriorVersion")
- = form_group_attribute("isAlignedTo")
- = form_group_attribute("ontologyRelatedTo")
-
- = metadata_section('more-relations', 'More relations', parent_id: "ontology-relations-more") do
- - for attr in @metadata
- - if attr["category"].eql?("relations")
- = form_group_attribute(attr["attribute"])
-
- %div#ontology-content-metrics.mt-4
- = metadata_section('ontology-content', 'Ontology content', parent_id: "ontology-content-metrics") do
- = form_group_attribute("preferredNamespacePrefix")
- = form_group_attribute("preferredNamespaceUri")
-
- = metadata_section('more-informations', 'More content informations', parent_id: "ontology-content-metrics") do
- - for attr in @metadata.select { |m| m['category'] == 'content' }
- = form_group_attribute(attr["attribute"])
-
- = metadata_section('more-metrics-informations', 'More metrics informations', parent_id: "ontology-content-metrics") do
- - for attr in @metadata.select { |m| m['category'] == 'metrics' }
- = form_group_attribute(attr["attribute"])
\ No newline at end of file
diff --git a/app/views/submissions/_submission_contact_form.html.haml b/app/views/submissions/_submission_contact_form.html.haml
deleted file mode 100644
index 55248fe65..000000000
--- a/app/views/submissions/_submission_contact_form.html.haml
+++ /dev/null
@@ -1,5 +0,0 @@
-%div.d-flex
- %div.w-50.mx-1
- = text_field object_name, "contact[#{index.to_s.upcase}][name]", placeholder: 'Name', value: contact ? contact["name"] : '' , class: "form-control flex-grow-1 mx-2"
- %div.w-50.mx-1
- = text_field object_name, "contact[#{index.to_s.upcase}][email]", placeholder: 'Email', value: contact ? contact["email"] : '', class: "form-control flex-grow-1 mx-2"
diff --git a/app/views/submissions/_submission_format_form.html.haml b/app/views/submissions/_submission_format_form.html.haml
deleted file mode 100644
index d47d9284f..000000000
--- a/app/views/submissions/_submission_format_form.html.haml
+++ /dev/null
@@ -1,26 +0,0 @@
-:javascript
-
- function ontologyFormatChange(event){
- let selected = event.target.selectedOptions.item(0)
- let options = document.querySelectorAll('.format_options')
- Array.from(options).forEach( x => $(x).hide())
- switch(selected.value){
- case 'OWL':
- jQuery("#owl_options").show()
- break
- case 'SKOS':
- jQuery("#skos_options").show()
- break
- }
- }
-
-= attribute_form_group_container('hasOntologyLanguage', label: 'Format', required: true) do |c|
- - ont_formats = %w[OBO OWL UMLS SKOS].sort
- - selected = @submission.hasOntologyLanguage ? @submission.hasOntologyLanguage : "OWL"
- = select c.name, c.method_name, options_for_select(ont_formats, selected), {required: true}, {class: "form-control", onchange: 'ontologyFormatChange(event)'}
- - c.help do
- %div#skos_options.format_options{style: "display:#{skos? ? 'block': 'none'}"}
- SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion.
- Please refer to the NCBO wiki for a more #{link_to 'detailed explanation', 'https://www.bioontology.org/wiki/index.php/SKOSSupport', target: "_blank" }
- with examples.
-
\ No newline at end of file
diff --git a/app/views/submissions/_submission_location_form.html.haml b/app/views/submissions/_submission_location_form.html.haml
deleted file mode 100644
index 07faedf61..000000000
--- a/app/views/submissions/_submission_location_form.html.haml
+++ /dev/null
@@ -1,61 +0,0 @@
-:javascript
- $(document).ready(function() {
-
- // Properly display the information for 'File Location' based on radio button
- if (jQuery("#submission_isRemote_0").is(":checked")) {
- location_toggle("upload");
- }
- if (jQuery("#submission_isRemote_1").is(":checked")) {
- location_toggle("remote");
- }
-
- // Select default 'File Location' radio button
- if (!jQuery("#submission_isRemote_0").is(":checked") && !jQuery("#submission_isRemote_1").is(":checked") && !jQuery("#submission_isRemote_2").is(":checked")) {
- jQuery("#submission_isRemote_0").attr("checked", "checked")
- }
- });
-
- // Show/hide location inputs
- function location_toggle(input_div) {
- jQuery('.hidden_field').hide();
- jQuery('.hidden_field input').attr("disabled", true);
- jQuery('#' + input_div + " input").removeAttr("disabled");
- jQuery('#' + input_div).show();
- }
-
-
-- if !@masterFileOptions
- %div.form-check
- - checked = @ontology.summaryOnly
- = radio_button(object_name, :isRemote, 3, :onclick=>"$('.hidden_field').hide();", checked: checked, aria: {describedBy: "metadataHelpBlock"}, class: "form-check-input")
- %label.form-check-label{for: "submission_isRemote_3"}
- Metadata only
- %small.form-text.text-muted#metadataHelpBlock Allow users to view and search your ontology metadata, but not its classes and properties.
- %div.form-check
- - checked = !(@submission.pullLocation.nil? || @submission.pullLocation.empty?)
- = radio_button(object_name, :isRemote, 1, :onclick=>"location_toggle('remote');", checked: checked, aria: {describedBy: "loadFromURLHelpBlock"}, class: "form-check-input")
- %label.form-check-label{for: "submission_isRemote_1"}
- Load from URL
- %small.form-text.text-muted#loadFromURLHelpBlock New versions loaded on a nightly basis.
- - display = (checked and "" or "display:none;")
- %div.hidden_field#remote{style: display}
- = text_field(object_name, :pullLocation, value: @submission.pullLocation, aria: {describedBy: "enterURLHelpBlock"}, class: "form-control")
- %small.form-text.text-muted#enterURLHelpBlock Enter a URL, including the name of your ontology source file, e.g., http://www.example.com/my_ontology.owl.
- %div.form-check
- - checked = (!@ontology.summaryOnly) && @submission.pullLocation.nil?
- = radio_button(object_name, :isRemote, 0, :onclick=>"location_toggle('upload');", checked: checked, class: "form-check-input")
- %label.form-check-label{for: "submission_isRemote_0"}
- Upload local file
- - display = (checked and "" or "display:none;")
- %div.hidden_field#upload{style: display}
- = file_field(object_name, :filePath, class: "mt-2")
-- else
- -# TODO: Has this section of code actually been tested?
- = radio_button object_name, :isRemote, 0, :onclick=>"location_toggle('upload');", checked: true
- Upload Local File
- %br/
- %span{:style => "font-size:11px;"} (choose a file on your local file system to upload)
- - display = (checked and "" or "display:none;")
- %div#upload{style: display}
- = file_field object_name, :filePath, required: true
- = select(object_name, "masterFileName", @masterFileOptions, { include_blank: "Select primary file from zip contents", required: true}, {style: "border-color: red;"})
diff --git a/app/views/submissions/_submissions.html.haml b/app/views/submissions/_submissions.html.haml
index 827862902..49ab54333 100644
--- a/app/views/submissions/_submissions.html.haml
+++ b/app/views/submissions/_submissions.html.haml
@@ -4,59 +4,64 @@
- more_colspan = 7
- more_colspan = 6 if @ont_restricted
- %div.click_versions_collapse
+ %div.click_versions_collapse.p-1
= render_alerts_container(AdminController)
- %table#ontology_versions.table.table-sm.table-striped
- %thead
- %tr
- - if @ontology.admin?(session[:user])
- %th.align-middle ID
- %th.align-middle Version
- %th
- = generate_attribute_text("released", "Released")
- %th
- = generate_attribute_text("modificationDate", "Modified")
- %th
- = generate_attribute_text("creationDate", "Uploaded")
- - unless @ont_restricted
- %th.align-middle Downloads
- - if @ontology.admin?(session[:user])
- %th.align-middle Actions
+ = render TableComponent.new(id: 'ontology_versions', stripped: false, borderless: true) do |t|
+ - t.header do |header|
+ - if @ontology.admin?(session[:user])
+ - header.th do
+ %div.align-middle
+ = t('submissions.id')
+ - header.th do
+ %div.align-middle
+ = t('submissions.version')
+ - header.th do
+ = attr_label("modificationDate", t('submissions.modified'), show_tooltip: false)
+ - header.th do
+ = attr_label("creationDate", t('submissions.submitted'), show_tooltip: false)
+ - unless @ont_restricted
+ - header.th do
+ %div.align-middle{style: 'text-align: center; margin-right: 33px;'}
+ = t('submissions.actions')
- - begin
- - submission_ready = @ontology.explore.latest_submission({:include_status => 'ready', display: 'submissionId'})
- - submission_readyId = submission_ready.submissionId unless submission_ready.nil?
- - rescue
- - submission_readyId = -1
- @submissions.each_with_index do |sub, index|
- hidden_row_class = index >= 5 ? "hidden_ont hidden_select" : ""
- %tr{class: "#{hidden_row_class}", id: "submission_#{sub.submissionId}"}
+ - t.row(id:"submission_#{sub.submissionId}" , class_css: hidden_row_class) do |r|
- if @ontology.admin?(session[:user])
- %td
- = sub.submissionId
- %td
- = raw status_link(sub, sub.submissionId==submission_readyId)
- %td
- = xmldatetime_to_date(sub.released) unless sub.released.nil?
- %td
- = xmldatetime_to_date(sub.modificationDate) unless sub.modificationDate.nil?
- %td
- = xmldatetime_to_date(sub.creationDate) unless sub.creationDate.nil?
+ - r.td { raw sub.submissionId }
+ - r.td do
+ = render SubmissionStatusComponent.new(sub, sub.submissionId==submission_ready?(sub))
+ - r.td { render DateTimeFieldComponent.new(value: sub.modificationDate) unless sub.modificationDate.nil? }
+ - r.td { render DateTimeFieldComponent.new(value: sub.creationDate) unless sub.creationDate.nil? }
+
+
- unless @ont_restricted
- %td
- = raw download_link(sub, @ontology)
- - if @ontology.admin?(session[:user])
- %td
+ - r.td do
%div.d-flex
- -#%a.btn.btn-sm.btn-link{:href => "/ontologies/#{@ontology.acronym}/submissions/#{sub.submissionId}/edit", 'data-turbo-frame':"_top"}
- -# %span Edit
- - unless sub.submissionId.eql?(submission_readyId)
- - alert_text = "Are you sure you want to delete submission " + sub.submissionId.to_s + " for ontology " + @ontology.acronym + " ?This action CAN NOT be undone!!! "
- = button_to "Delete", "/admin/ontologies/#{@ontology.acronym}/submissions/#{sub.submissionId}?turbo_stream=true", method: :delete, class:'btn btn-sm btn-link', form: {data: { turbo: true, turbo_confirm: alert_text, turbo_frame: '_top'}}
+ %div.dropdown
+ %button.btn.btn-outline-primary.rounded-pill.dropdown-toggle{type:"button", 'data-toggle':"dropdown", 'aria-expanded': "false", style:'white-space: nowrap; width: 94%;font-size: small;'}
+ = t('submissions.download')
+ %span.sr-only= t('submissions.toggle_dropdown')
+ .dropdown-menu
+ - links = download_link(sub,@ontology)
+ - links.each do |value|
+ - link,label = value.values
+ %a.dropdown-item{ href: link }= label
+
+ -# = raw download_link(sub, @ontology)
+ - if @ontology.admin?(session[:user])
+ %div.d-flex
+ %div{style: 'margin-right: 10px;'}
+ = service_button(link: "#{@ontology.id}/submissions/#{sub.submissionId}?display=all", title: t('submissions.go_to_api'))
+ = edit_button(link: "/ontologies/#{@ontology.acronym}/submissions/#{sub.submissionId}/edit", title: t('submissions.edit_button'))
+ - unless index.zero?
+ - alert_text = t('submissions.delete_submission_alert.content_1') + sub.submissionId.to_s + t('submissions.delete_submission_alert.content_2') + @ontology.acronym + t('submissions.delete_submission_alert.content_3')
+ = button_to "/admin/ontologies/#{@ontology.acronym}/submissions/#{sub.submissionId}?turbo_stream=true", method: :delete, class: 'btn btn-sm btn-link', form: {data: { turbo: true, turbo_confirm: alert_text, turbo_frame: '_top'}} do
+ = inline_svg_tag('icons/delete.svg')
- if @submissions.length > 5
- %tr
- %td{colspan: more_colspan, class: "show_more_subs"}
+ - t.row(class_css: "show_more_subs") do |r|
+ - r.td(colspan: more_colspan) do
%a#version_toggle{:href => ""} more...
:javascript
diff --git a/app/views/submissions/edit.html.haml b/app/views/submissions/edit.html.haml
index 1977ef4b1..848e3da82 100644
--- a/app/views/submissions/edit.html.haml
+++ b/app/views/submissions/edit.html.haml
@@ -1,6 +1,59 @@
-%div.container.py-4.py-md-5
- %h1
- Edit submission information
- %small.text-muted for #{@ontology.acronym}
- = form_for :submission, url: ontology_submission_path(@ontology.acronym, @submission.submissionId), html: { id: "ontology_submission_form", method: :put, multipart: true, 'data-turbo': true } do |f|
- = render partial: "form", locals: {f: f, button_text: "Save submission"}
+- section = params[:section] || 'general'
+.center
+ .edit-ontology-container
+ = turbo_frame_tag(params[:container_id] || 'test') do
+ = form_for :submission, url: ontology_submission_path(@ontology.acronym, params["id"]), html: { id: "ontology_submission_form", method: :put, multipart: true, 'data-turbo': true, 'data-turbo-frame': '_top', novalidate: 'true'} do
+ .edit-ontology-title
+ %div
+ = t('submission_inputs.edit_ontology_title')
+ %hr
+ .edit-ontology-sub-container
+ - if @selected_attributes.empty?
+ .edit-ontology-left-column{:role => "tablist",onchange:"onMetadataChange()"}
+ .edit-ontology-desc
+ = submission_metadata_selector
+ %div.nav.nav-pills.flex-column#categories-tabs
+ - @categories_order.each_with_index do |key, index|
+ %a.edit-ontology-tab-item.d-block{href: "##{key.parameterize}-tab", "data-toggle" => "pill", class: section.eql?(key.parameterize) ? 'active show' : ''}
+ = key.humanize
+
+ #myTabContent.edit-ontology-right-column.w-100
+ = render TurboFrameComponent.new(id:"metadata_by_ontology") do
+ = metadata_help_link
+ %div.tab-content
+ - if @selected_attributes.empty?
+ - @categories_order.each_with_index do |key, index|
+ - properties = @category_attributes[key]
+ .edit-ontology-tab.tab-pane.fade{id: key.parameterize+'-tab', class: section.eql?(key.parameterize) ? 'active show' : ''}
+ = render TurboFrameComponent.new(id: "ontology-content-#{index}", loading:"lazy", src: "edit_properties?properties=#{properties.join(',')}&container_id=ontology-content-#{index}")
+ - else
+ - link = ontology_submission_edit_properties_path(@ontology.acronym, params[:id], properties: @selected_attributes.join(','), container_id: 'ontology-content-0')
+ = render TurboFrameComponent.new(id: "ontology-content-0", loading:"lazy", src: link)
+
+ %hr#edit-ontology-actions-devider
+ .edit-ontology-actions
+ - unless params[:container_id]
+ .cancel-button.mx-2{onClick: 'window.history.back();'}
+ = form_cancel_button
+ .save-button
+ = form_save_button
+
+
+ :javascript
+ function onMetadataChange(){
+ document.querySelector('.edit-ontology-tab-item.d-block.active.show')?.classList.remove('active', 'show')
+ document.querySelector('.edit-ontology-tab.tab-pane.fade.active.show')?.classList.remove('active', 'show')
+ document.getElementById('categories-tabs')?.classList.add('disabled')
+
+ let frame = document.getElementById('metadata_by_ontology')
+ let properties = document.getElementById('select_search_metadata')
+
+ let selectedProperties = "all"
+ if(properties && properties.selectedOptions.length > 0){
+ selectedProperties = Array.from(properties.selectedOptions).map(({ value }) => value).join(',')
+ frame.src = "./edit_properties?properties=" + selectedProperties
+ } else {
+ Turbo.visit(location.href)
+ }
+
+ }
diff --git a/app/views/submissions/index.html.haml b/app/views/submissions/index.html.haml
index d31fd94d2..df4cbe078 100644
--- a/app/views/submissions/index.html.haml
+++ b/app/views/submissions/index.html.haml
@@ -1 +1 @@
-= render partial: "submissions", locals: {id: 'ontology_submissions'}
\ No newline at end of file
+= render partial: "submissions", locals: {id: params['container_id'] || 'ontology_submissions'}
\ No newline at end of file
diff --git a/app/views/submissions/new.html.haml b/app/views/submissions/new.html.haml
deleted file mode 100644
index c4871177c..000000000
--- a/app/views/submissions/new.html.haml
+++ /dev/null
@@ -1,9 +0,0 @@
-- @title = "Add new ontology submission"
-
-%div.container.py-4.py-md-5
- %h1
- Add new submission
- - if !(@submission.ontology.nil? || (@submission.ontology.is_a? String))
- %small.text-muted for #{@submission.ontology.acronym}
- = form_for :submission, url: {action: "create"}, html: {id: "ontology_submission_form", multipart: true, 'data-turbo': true} do |f|
- = render partial: "form", locals: {f: f, button_text: "Add submission"}
diff --git a/app/views/users/_form.html.haml b/app/views/users/_form.html.haml
index 2b1e13d4c..3a2f38b52 100644
--- a/app/views/users/_form.html.haml
+++ b/app/views/users/_form.html.haml
@@ -5,49 +5,60 @@
%img.lost-password-arrowback{:src => "#{asset_path("arrow-back.svg")}"}
.register-title-container
%h2.register-title
- Create a new account
+ = t('register.create_account')
%hr#register-title-line/
%div
.register-double-input
.register-first-input
%p.register-input-title
- First name
+ = t('register.first_name')
%font{:color => "red"} *
- = text_field :user, :firstName, value: @user.firstname, class: "register-input-short"
+ = text_field :user, :firstName, value: @user.firstName, class: "register-input-short"
%div
%p.register-input-title
- Last name
+ = t('register.last_name')
%font{:color => "red"} *
- = text_field :user, :lastName, value: @user.lastname, class: "register-input-short"
+ = text_field :user, :lastName, value: @user.lastName, class: "register-input-short"
%p.register-input-title
- Username
+ = t('register.username')
%font{:color => "red"} *
= text_field :user, :username, value: @user.username, class: "register-input-long"
%p.register-input-title
ORCID ID
- %font.register-optional (optional)
+ %font.register-optional
+ = t('register.optional')
%img.register-input-icon{:src => "#{asset_path("orcid.svg")}"}/
= text_field :user, :orcidId, value: @user.orcidId, class: "register-input-long register-input-with-icon"
%p.register-input-title
Github ID
- %font.register-optional (optional)
+ %font.register-optional
+ = t('register.optional')
%img.register-input-icon{:src => "#{asset_path("github-icon.svg")}"}/
= text_field :user, :githubId, value: @user.githubId, class: "register-input-long register-input-with-icon"
%p.register-input-title
- Email
+ = t('register.email')
%font{:color => "red"} *
= text_field :user, :email, value: @user.email, class: "register-input-long"
%p.register-input-title
- Password
+ = t('register.password')
%font{:color => "red"} *
= password_field :user, :password, class: "register-input-long"
%p.register-input-title
- Confirm password
+ = t('register.confirm_password')
%font{:color => "red"} *
= password_field :user, :password_confirmation, class: "register-input-long"
- if using_captcha?
= recaptcha_tags
.d-flex
- %input#user_register_mail_list{:checked => "checked", :name => "user[register_mail_list]", :type => "checkbox", :value => "1"}/
- %p#register-check-text Register for the Ecoportal's mailing list
- %input.register-button{:type => "submit", :value => "Register"}/
+ %input.user_register_checkbox{:checked => "checked", :name => "user[register_mail_list]", :type => "checkbox", :value => "1"}/
+ %p#register-check-text
+ = t('register.mailing_list', site: portal_name)
+ .d-flex
+ %input.user_register_checkbox{:name => "user[terms_and_conditions]", :type => "checkbox"}/
+ %p#register-check-text
+ = t('register.accept_terms_and_conditions')
+ %a{href: $TERMS_AND_CONDITIONS_LINK, target: '_blank'}
+ = t('register.terms_and_conditions', site: portal_name)
+ %font{:color => "red"} *
+ .register-button-container
+ = render Buttons::RegularButtonComponent.new(id: 'register-button', value: "Register", type:'submit')
diff --git a/app/views/users/edit.html.haml b/app/views/users/edit.html.haml
index da8327ff0..d00e8c61b 100644
--- a/app/views/users/edit.html.haml
+++ b/app/views/users/edit.html.haml
@@ -7,7 +7,7 @@
event.preventDefault()
let admin_checkbox = jQuery('input[id=user_admin]')
if(admin_checkbox.attr('checked') && !admin_checkbox.hasClass('admin')){
- alertify.confirm('Are you sure you want to make this user an admin?', (e) => {
+ alertify.confirm(t('users.edit.user_to_admin'), (e) => {
if(e){
this.submit()
}else {
@@ -15,7 +15,7 @@
}
})
} else if (!admin_checkbox.attr('checked') && admin_checkbox.hasClass('admin')){
- alertify.confirm('Are you sure you want to revoke admin privileges for this user?', (e) => {
+ alertify.confirm(t('users.edit.admin_privileges'), (e) => {
if(e){
this.submit()
}else {
@@ -62,7 +62,7 @@
= form_for(:user, :url => user_path(@user.username), :html => { :id => "user_info", :method => :put }) do |f|
- unless @errors.nil?
.enable-lists{:style => "color: red; padding: 1em;"}
- Errors creating your account:
+ = t('users.edit.errors_creating_account')
%ul
- for error in @errors
%li= error
@@ -73,36 +73,36 @@
%img.lost-password-arrowback{:src => "#{asset_path("arrow-back.svg")}"}
.register-title-container
%h2.register-title
- Edit personal information
+ = t('users.edit.edit_information')
%hr#register-title-line/
%div
- if @user.validate_password.nil?
.register-double-input
.register-first-input
%p.register-input-title
- First name
+ = t('users.edit.first_name')
%font{:color => "red"} *
= text_field :user, :firstName, value: @user.firstName, class: "register-input-short"
%div
%p.register-input-title
- Last name
+ = t('users.edit.last_name')
%font{:color => "red"} *
= text_field :user, :lastName, value: @user.lastName, class: "register-input-short"
%p.register-input-title
- Username
+ = t('users.edit.username')
%font{:color => "red"} *
= text_field :user, :username, value: @user.username, class: "register-input-long"
%p.register-input-title
- Email
+ = t('users.edit.email')
%font{:color => "red"} *
= text_field :user, :email, value: @user.email, class: "register-input-long"
%p.register-input-title
- ORCID ID
+ = t('users.edit.orcid_id')
%font.register-optional (optional)
%img.register-input-icon{:src => "#{asset_path("orcid.svg")}"}/
= text_field :user, :orcidId, value: @user.orcidId, class: "register-input-long register-input-with-icon"
%p.register-input-title
- Github ID
+ = t('users.edit.github_id')
%font.register-optional (optional)
%img.register-input-icon{:src => "#{asset_path("github-icon.svg")}"}/
= text_field :user, :githubId, value: @user.githubId, class: "register-input-long register-input-with-icon no-margin"
@@ -116,17 +116,17 @@
= hidden_field :user, :lastName, value: @user.lastName
= hidden_field :user, :email, value: @user.email
%p.register-input-title
- New password
+ = t('users.edit.new_password')
%font{:color => "red"} *
= password_field :user, :password, class: "register-input-long"
%p.register-input-title
- Confirm password
+ = t('users.edit.confirm_password')
%font{:color => "red"} *
= password_field :user, :password_confirmation, class: "register-input-long"
%br
- %input.register-button{:type => "submit", :value => "Save", :name => "Update"}/
+ = render Buttons::RegularButtonComponent.new(id: 'update-button', value: "Save", type:'submit')
- unless params[:password].eql?("true")
.change-password
%a{:href => edit_user_path(@user.username, password: true)}
- Change password
\ No newline at end of file
+ = t('users.edit.change_password')
\ No newline at end of file
diff --git a/app/views/users/index.html.haml b/app/views/users/index.html.haml
new file mode 100644
index 000000000..20a3c0bdb
--- /dev/null
+++ b/app/views/users/index.html.haml
@@ -0,0 +1,40 @@
+= turbo_frame_tag 'users-list' do
+ %div.my-1
+ = render_alerts_container
+ .d-flex.justify-content-end.my-1
+ = rounded_button_component("#{$REST_URL}/users?display=all&apikey=#{get_apikey}")
+
+ = render TableComponent.new(id: 'admin_users', custom_class: 'border rounded p-1', searching: true, paging: true, sort_column: '7') do |t|
+ - t.header do |h|
+ - h.th {t('users.index.first_name')}
+ - h.th {t('users.index.last_name')}
+ - h.th {t('users.index.username')}
+ - h.th {t('users.index.email')}
+ - h.th {t('users.index.roles')}
+ - h.th {t('users.index.ontologies')}
+ - h.th {t('users.index.project')}
+ - h.th {t('users.index.created')}
+ - h.th {t('users.index.actions')}
+ - @users.each do |user|
+ - t.row(id: user.id.split('/').last) do |r|
+ - r.td {user.firstName}
+ - r.td {user.lastName}
+ - r.td {user.username}
+ - r.td {user.email}
+ - r.td {user.role.join(', ')}
+ - r.td {(user.ontologies&.size || 0).to_s}
+ - r.td {(user.projects&.size || 0).to_s}
+ - r.td {Date.parse(user.created).to_s}
+ - r.td do
+ - count = (user.ontologies&.size || 0) + (user.projects&.size || 0)
+ %div.d-flex.align-items-center{style: 'min-width: 200px'}
+ %span
+ = link_to t('users.index.detail'), user_path(user.id.split('/').last), {data: {turbo_frame: '_top'}}
+ %span
+ - if count.zero?
+ = button_to t('users.index.delete'), user_path(user.id.split('/').last), method: :delete, class: 'btn btn-link', form: {data: { turbo: true, turbo_confirm: t('users.index.turbo_confirm'), turbo_frame: '_top'}}
+ - else
+ %span{data: { controller: 'tooltip' }, title:t('users.index.error_delete_message')}
+ = link_to t('users.index.delete'), "", class: 'btn btn-link disabled'
+ %span
+ = link_to t('users.index.login_as'), "login_as/#{user.username}", {data: {turbo_frame: '_top'}}
\ No newline at end of file
diff --git a/app/views/users/new.html.haml b/app/views/users/new.html.haml
index 95b41374e..cb42a4ac0 100644
--- a/app/views/users/new.html.haml
+++ b/app/views/users/new.html.haml
@@ -1,9 +1,10 @@
-- @title = "Register"
+- @title = t('register.title')
= form_for(:user, :url => users_path) do |f|
- unless @errors.nil?
- .enable-lists{:style => "color: red; padding: 1em;"}
- Errors creating your account:
- %ul
- - for error in @errors
- %li= error
+ .d-flex.justify-content-center.mt-4
+ = render Display::AlertComponent.new(type: "danger", closable: false) do
+ = t('register.account_errors')
+ %ul.mb-0
+ - for error in @errors
+ %li= error.is_a?(Array) ? error.last : error
= render :partial => 'form', :locals => {:f => f}
diff --git a/app/views/users/show.html.haml b/app/views/users/show.html.haml
index 96e462eb1..3c4f28597 100644
--- a/app/views/users/show.html.haml
+++ b/app/views/users/show.html.haml
@@ -1,78 +1,76 @@
.account-page-center
.account-page-container
- %h3.account-page-title My account
+ %h3.account-page-title= t('users.show.my_account')
%hr#account-page-title-line/
.account-page-sub-container
.account-page-first-row
.account-page-card
.account-page-personal-informations-title-bar
- %h4.account-page-card-title Personal information
+ %h4.account-page-card-title Personal Information
%a.account-page-rounded-button{:href => edit_user_path(url_encode(@user.username))}
= render partial: "shared/svgs/edit_icon"
.account-page-info-column
- %p.title First name:
+ %p.title= t('users.show.first_name')
%p.info
= @user.firstName
.account-page-info-column
- %p.title Last name:
+ %p.title= t('users.show.last_name')
%p.info
= @user.lastName
.account-page-info-column
- %p.title Email address:
+ %p.title= t('users.show.email')
%p.info
= @user.email
.account-page-info-column
- %p.title Username:
+ %p.title= t('users.show.username')
%p.info
= @user.username
.account-page-info-column
- %p.title ORCID ID:
+ %p.title= t('users.show.orcid_id')
%p.info
=@user.orcidId
.account-page-info-column
- %p.title Github ID:
+ %p.title= t('users.show.github_id')
%p.info
=@user.githubId
.account-page-card
.account-page-card-container
.account-page-card-sub-container
- %h4.account-page-card-title Mailing list subscription
- %p.account-page-card-desc #{$SITE} announcements email list
+ %h4.account-page-card-title= t('users.show.mailing_list_subscription')
+ %p.account-page-card-desc= t('users.show.mailing_list_description', portal: portal_name)
- subscribed = false
- - if subscribed
- %a.btn.btn-primary{:href =>"mailto:#{$ANNOUNCE_SERVICE_HOST}?Subject=unsubscribe%20#{$ANNOUNCE_LIST}"}
- Unsubscribe
+ - if subscribed
+ %a.account-page-subscribe-button{:href =>"mailto:#{$ANNOUNCE_SERVICE_HOST}?subject=unsubscribe%20#{$ANNOUNCE_LIST}"}
+ = t('users.show.unsubscribe')
- else
- %a.btn.btn-primary{:href => "mailto:#{$ANNOUNCE_SERVICE_HOST}?Subject=subscribe%20#{$ANNOUNCE_LIST}%20#{@user.firstName}%20#{@user.lastName}"}
- Subscribe
+ %a.account-page-subscribe-button{:href => "mailto:#{$ANNOUNCE_SERVICE_HOST}?subject=subscribe%20#{$ANNOUNCE_LIST}%20#{@user.firstName}%20#{@user.lastName}"}
+ = t('users.show.subscribe')
.account-page-card
.account-page-card-container
.account-page-card-sub-container
%h4.account-page-card-title API Key
- %p.account-page-card-desc Your API Key can be used to access the NCBO API (REST) Services
- %p.apikey
- = session[:user].apikey
- %a{:href => "javascript:navigator.clipboard.writeText('"+session[:user].apikey+"');"}
- = render partial: "shared/svgs/copy_icon"
+ %p.account-page-card-desc
+ = t('users.show.api_key_description', portal: portal_name)
+ %div.apikey
+ = render ClipboardComponent.new(message: session[:user].apikey)
.account-page-api-documentation-link
- %a{href: "#{$REST_URL.chomp('/')}/documentation", target: "_blank"}
- API documentation
+ %a{href: "#{$REST_URL}/documentation", target: "_blank"}
+ = t('users.show.api_documentation')
= render partial: "shared/svgs/external_link_icon"
.account-page-card
%h4.account-page-card-title
- Custom semantic resource set
+ = t('users.show.custom_semantic_resource')
#custom_ontologies.enable-lists
- if at_slice?
%p{style: "padding-left: 7px; font-size: 10pt; margin: -3px 0 7px;"}
- Please
- %a{href: "#{$UI_URL}/account"} visit the main site
- to modify your Custom semantic resource set.
+ = t('users.show.please')
+ %a{href: "#{$UI_URL}/account"}= t('users.show.modify_custom_semantic_resource')
- else
%p.account-page-card-desc
- Customize your #{$SITE} display: pick the semantic resources that you want to see on #{$SITE}. Pay attention: this will hide all other Semantic Resources.
+ = t('users.show.customize_portal_display', portal: portal_name)
%p
%span{style: "font-weight: normal; font-size: 9pt; padding-left: 7px;"}
- %a#edit_custom_ontologies{href: "javascript:void(0);"} Select semantic resources
+ %a#edit_custom_ontologies{href: "javascript:void(0);"}= t('users.show.select_semantic_resources')
- if @user_ontologies && !@user_ontologies.empty?
%ul
- @user_ontologies.each do |ont|
@@ -80,17 +78,19 @@
%li
#{ont.name} (#{ont.acronym})
- else
- %p{style: "padding-left: 7px;"} You haven't picked any Semantic Resources yet.
+ %p{style: "padding-left: 7px;"}= t('users.show.no_semantic_resources')
+ %p.account-page-card-desc= t('users.show.note_feature_logged_in')
#custom_ontologies_picker{style: "left: -9999px; position: absolute;"}
= form_tag custom_ontologies_path(url_encode(@user.username)) do
- selected = @user.customOntology.map {|o| LinkedData::Client::Models::Ontology.get(o).acronym}
- - locals = { custom_ontologies: @all_ontologies, selected_ontologies: selected, sel_text: "Select Custom Semantic Resources" }
- = render partial: "shared/ontology_picker", locals: locals
- = submit_tag "Save custom semantic resources", class: "bnt btn-primary"
+ = ontologies_selector(id:'account_page_ontologies_selector' ,name: 'ontologies', selected: selected)
+ = submit_tag t('users.show.save_custom_semantic_resources'), class: "link_button"
.account-page-second-row
- - unless @user.subscription.nil? || @user.subscription.empty?
- .account-page-card
- %h4.account-page-card-title Subscriptions
+ .account-page-card
+ %h4.account-page-card-title= t('users.show.subscriptions')
+ - if @user.subscription.nil? || @user.subscription.empty?
+ = t('users.show.not_subscribed')
+ - else
- @user.subscription.each do |subscription|
- ont_id = subscription[:ontology]
- ont = (!subscription[:ontology].nil? ? subscription[:ontology].split('/').last: nil) # ensure we get the acronym
@@ -99,33 +99,37 @@
%a{:href => "/ontologies/#{ont}?p=notes"}= ont
%div
- if type == "notes"
- %a.notes{:href => "/ontologies/#{ont}?p=notes"} Notes
+ %a.notes{:href => "/ontologies/#{ont}?p=notes"}= t('users.show.notes')
- else
= type
= subscribe_button(ont_id)
- - no_ontologies = true
- - unless @admin_ontologies.nil? || @admin_ontologies.empty?
- - no_ontologies = false
- .account-page-card
- %h4.account-page-card-title Submitted semantic resources
- .account-page-small-cards-container
+ .account-page-card
+ %h4.account-page-card-title= t('users.show.submitted_semantic_resources')
+ .account-page-small-cards-container
+ - if @admin_ontologies.nil? || @admin_ontologies.empty?
+ .account-page-no-ontology.w-100
+ %img{:src => "#{asset_path("empty-box.svg")}"}/
+ %p= t('users.show.no_uploaded_resources')
+ %a.account-page-upload-ontology-button{href: "/ontologies/new"}= t('users.show.upload_semantic_resources')
+ - else
- @admin_ontologies.each do |ont|
- .account-page-submitted-ontology
- %a{href: "/ontologies/#{ont.acronym}"}= ont.name
- - unless @user_projects.nil? || @user_projects.empty?
- - no_ontologies = false
- .account-page-card
- %h4.account-page-card-title Projects Created
- .account-page-small-cards-container
+ .account-page-submitted-ontology{data: {controller: 'tooltip'}, title: ont.name}
+ %a{href: "/ontologies/#{ont.acronym}"}= ont.acronym
+ - unless ont.views.nil? || ont.views.empty?
+ - ont.views.each do |view|
+ .account-page-submitted-ontology{data: {controller: 'tooltip'}, title: ont.name}
+ %a{href: "/ontologies/#{view.match(/\/([^\/]+)$/)[1]}"}= view.match(/\/([^\/]+)$/)[1]
+
+ .account-page-card
+ %h4.account-page-card-title= t('users.show.projects_created')
+ .account-page-small-cards-container
+ - if @user_projects.nil? || @user_projects.empty?
+ = t('users.show.no_project_created')
+ - else
- @user_projects.each do |project|
.account-page-submitted-ontology
%a{href: "/projects/#{project.acronym}"}= project.name
- - if no_ontologies
- .account-page-card
- .account-page-no-ontology
- %img{:src => "#{asset_path("empty-box.svg")}"}/
- %p You didn't upload any semantic resources yet
- %a.account-page-upload-ontology-button{href: "/ontologies/new"} Upload Semantic Resource
+
:javascript
jQuery(document).ready(function(){
jQuery("#edit_custom_ontologies").click(editCustomOntologies);
diff --git a/app/views/virtual_appliance/index.html.haml b/app/views/virtual_appliance/index.html.haml
index 7e13ec310..867d25c02 100644
--- a/app/views/virtual_appliance/index.html.haml
+++ b/app/views/virtual_appliance/index.html.haml
@@ -1,23 +1,19 @@
--@title = "OntoPortal Virtual Appliance Download"
+-@title = t("ontoportal_virtual_appliance.title")
%div{:style => "padding: 13px; max-width: 800px;", :class => "enable-lists"}
- %h1 OntoPortal Virtual Appliance Download
- %p
- OntoPortal Virtual Appliance distribution contains a pre-installed,
- pre-configured version of commonly-used open source NCBO software running
- on a Linux operating system.
- %p The following software is included on the image:
+ %h1= t("ontoportal_virtual_appliance.title")
+ %p= t("ontoportal_virtual_appliance.intro_paragraph.main")
+ %p= t("ontoportal_virtual_appliance.included_software")
%ul
- %li Ontologies API (REST service)
- %li Annotator
- %li Recommender
- %li BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI)
+ %li= t("ontoportal_virtual_appliance.ontologies_api")
+ %li= t("ontoportal_virtual_appliance.annotator")
+ %li= t("ontoportal_virtual_appliance.recommender")
+ %li= t("ontoportal_virtual_appliance.web_user_interface")
%p
- Please see our
+ = t("ontoportal_virtual_appliance.see_documentation")
=link_to 'documentation', 'https://ontoportal.github.io/administration/steps/getting_started/', target: '_blank'
- for more information on working with the Appliance.
- %h2 Download Latest OntoPortal
- %ul
+ = t("ontoportal_virtual_appliance.more_information")
+ %h2= t("ontoportal_virtual_appliance.download_button_text")
%li
Version 3.1.1
OVA
@@ -55,33 +51,30 @@
Amazon EC2
-if @virtual_appliance_access
- %h3 Archives
- %p
- The OntoPortal 2.5 Virtual Appliance is not longer offered for new
- users. This archival distribution is available only as a backup for
- those who registered for the Appliance before June 2020
+ %h3= t("ontoportal_virtual_appliance.archives.title")
+ %p= t("ontoportal_virtual_appliance.archives.archival_distribution")
%ul
%li
- Version 2.5
+ = t("ontoportal_virtual_appliance.archives.version")
=link_to 'OVF', 'https://www.bioontology.org/ontoportal-appliance/ontoportal-2.5.zip'
-if @user.admin?
%div{:style => "margin: 2em 0 0; padding: 1em 1em; border: solid thin gray; background-color: lightGray;"}
- %h1{:style => "margin-bottom: 15px;"} Admin: Add Users
+ %h1{:style => "margin-bottom: 15px;"}= t("ontoportal_virtual_appliance.admin_add_users.title")
=form_for :appliance_user do |f|
- = f.label :user_id, "Account Name: "
+ = f.label :user_id, t("ontoportal_virtual_appliance.admin_add_users.label_account_name")
= f.text_field :user_id
- = f.submit "Add User"
+ = f.submit t("ontoportal_virtual_appliance.admin_add_users.add_user_button")
%h2{:style => "margin-top: 1em;"}
- Accounts with access
+ = t("ontoportal_virtual_appliance.admin_add_users.accounts_with_access")
%a#export{href: "#", style: "margin-left: 2em; margin-top: -1em; font-size: 11px;"}
- Export Appliance Users As CSV
+ = t("ontoportal_virtual_appliance.admin_add_users.export_users_link")
%table#user_table.zebra{style: "border: thin lightGray solid; background-color: white;"}
%thead
%tr
- %th BioPortal User ID
+ %th= t("ontoportal_virtual_appliance.admin_add_users.bioportal_user")
%tbody
-@va_users.each do |u|
%tr
diff --git a/app/views/visits/index.html.haml b/app/views/visits/index.html.haml
index ee7e1cee1..57da2545c 100644
--- a/app/views/visits/index.html.haml
+++ b/app/views/visits/index.html.haml
@@ -1,16 +1,15 @@
-%div.container.pb-3.pb-md-4
-
- %h1.mt-5
- Ontology Visits
- %small.text-muted (#{@analytics.date.strftime("%B %Y")})
+%div.px-3.py-3.pt-md-5.pb-md-4.text-center
+ %h1.display-4
+ = t('visits.ontology_visits')
+ %p.lead (#{@analytics.date.strftime("%B %Y")})
%div.table-responsive
%table.table.table-hover
%thead.thead-light
%tr
%th #
- %th name
- %th # visits
+ %th= t('visits.name')
+ %th= t('visits.visits')
%tbody
- count = 0
- @analytics.onts.each do |visits|
diff --git a/config/bioportal_config_test.rb b/config/bioportal_config_test.rb
new file mode 100644
index 000000000..44169096b
--- /dev/null
+++ b/config/bioportal_config_test.rb
@@ -0,0 +1,224 @@
+# frozen_string_literal: true
+
+$SITE = 'Testportal'
+$HOSTNAME = 'testportal'
+$UI_HOSTNAME = 'localhost'
+$UI_URL = "http://#{$UI_HOSTNAME}:3000"
+
+$API_KEY = ENV['API_KEY']
+$REST_URL = ENV['API_URL']
+$BIOMIXER_URL = ENV['BIOMIXER_URL']
+$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL']
+$FAIRNESS_URL = ENV['FAIRNESS_URL']
+
+# Resource term
+$RESOURCE_TERM = ENV['RESOURCE_TERM'] || 'ontology'
+
+# config/initializers/omniauth_providers.rb
+$OMNIAUTH_PROVIDERS = {
+ github: {
+ client_id: 'CLIENT_ID',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'github.svg',
+ enable: true
+ },
+ google: {
+ strategy: :google_oauth2,
+ client_id: 'CLIENT_ID',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'google.svg',
+ enable: true
+ },
+ orcid: {
+ client_id: 'CLIENT_SECRET',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'orcid.svg',
+ enable: false
+ },
+ keycloak: {
+ strategy: :keycloak_openid,
+ client_id: 'YOUR_KEYCLOAK_CLIENT_ID',
+ client_secret: 'YOUR_KEYCLOAK_CLIENT_SECRET',
+ client_options: { site: 'KEYCLOAK_SITE', realm: 'KEYCLOAK_REALM' },
+ name: 'keycloak',
+ icon: 'keycloak.svg',
+ enable: false
+ }
+}.freeze
+
+$INTERPORTAL_HASH = {}
+
+# If your BioPortal installation includes Fairness score set this to true
+$FAIRNESS_DISABLED = false
+
+# Pairing a name with an array of ontology virtual ids will allow you to filter ontologies based on a subdomain.
+# If your main UI is hosted at example.org and you add custom.example.org pointing to the same Rails installation
+# you could filter the ontologies visible at custom.example.org by adding this to the hash: "custom" => { :name => "Custom Slice", :ontologies => [1032, 1054, 1099] }
+# Any number of slices can be added. Groups are added automatically using the group acronym as the subdomain.
+$ENABLE_SLICES = false
+$ONTOLOGY_SLICES = {}
+
+# Cube metrics reporting
+$ENABLE_CUBE = false
+
+$NOT_DOWNLOADABLE = {}
+# Enable client request caching
+$CLIENT_REQUEST_CACHING = true
+
+# If you don't use Airbrake you can have exceptions emailed to the $ERROR_EMAIL address by setting this to 'true'
+$EMAIL_EXCEPTIONS = false
+
+# Announcements mailman mailing list REQUEST address, EX: list-request@lists.example.org
+# NOTE: You must use the REQUEST address for the mailing list. ONLY WORKS WITH MAILMAN LISTS.
+$ANNOUNCE_LIST ||= 'appliance-users-request@localhost'
+
+# Email addresses used for sending notifications (errors, feedback, support)
+$SUPPORT_EMAIL ||= 'support@localhost'
+$ADMIN_EMAIL ||= 'admin@localhost'
+$ERROR_EMAIL ||= 'errors@localhost'
+
+# Custom BioPortal logging
+require 'log'
+$REMOTE_LOGGING = false
+
+##
+# Custom Ontology Details
+# Custom details can be added on a per ontology basis using a key/value pair as columns of the details table
+#
+# Example:
+# $ADDITIONAL_ONTOLOGY_DETAILS = { 1000 => { "Additional Detail" => "Text to be shown in the right-hand column." } }
+##
+$ADDITIONAL_ONTOLOGY_DETAILS = {}
+
+# Site notice appears on all pages and remains closed indefinitely. Stored below as a hash with a unique key and a
+# EX: $SITE_NOTICE = { :unique_key => 'Put your message here (can include html if you use
+$SITE_NOTICE = {}
+################################
+## AUTO-GENERATED DO NOT MODIFY
+#################################
+
+# Full string for site, EX: "NCBO BioPortal"
+$ORG_SITE = $ORG.nil? || $ORG.empty? ? $SITE : "#{$ORG} #{$SITE}"
+
+$HOME_PAGE_LOGOS = [
+ {
+ img_src: 'logos/supports/numev.png',
+ url: 'http://www.lirmm.fr/numev',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/supports/anr.png',
+ url: 'https://anr.fr/en',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/supports/eu.png',
+ url: 'https://commission.europa.eu/research-and-innovation_en',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/d2kab.png',
+ url: 'http://d2kab.mystrikingly.com',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/lirmm.png',
+ url: 'http://www.lirmm.fr',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/inrae.png',
+ url: 'https://www.inrae.fr/enm',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/stanford.png',
+ url: 'https://www.stanford.edu',
+ target: '_blank'
+ }
+]
+
+$FOOTER_LINKS = {
+ social: [
+ { logo: 'social/people.svg', link: 'https://github.com/orgs/agroportal/people' },
+ { logo: 'social/github.svg', link: 'https://github.com/agroportal' },
+ { logo: 'social/twitter.svg', link: 'https://twitter.com/lagroportal' }
+ ],
+ sections: {
+ products: {
+ ontoportal: 'https://ontoportal.org/',
+ release_notes: 'https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/release-notes-btKjZk5tU2',
+ api: 'https://data.agroportal.lirmm.fr/',
+ sparql: 'https://sparql.agroportal.lirmm.fr/test/'
+ },
+ support: {
+ contact_us: 'https://agroportal.lirmm.fr/feedback',
+ wiki: 'https://www.bioontology.org/wiki/',
+ documentation: 'https://ontoportal.github.io/documentation/'
+ },
+ agreements: {
+ terms: '',
+ privacy_policy: '',
+ cite_us: '',
+ acknowledgments: ''
+ },
+ about: {
+ about_us: 'https://github.com/agroportal/project-management',
+ projects: 'https://d2kab.mystrikingly.com/',
+ team: 'https://github.com/orgs/agroportal/people'
+ }
+ }
+}
+
+$PORTALS_INSTANCES = [
+ {
+ color: '#31b403',
+ portal: 'AgroPortal',
+ link: 'https://agroportal.lirmm.fr/'
+ },
+ {
+ color: '#234979',
+ portal: 'BioPortal',
+ link: 'https://bioportal.bioontology.org/'
+ },
+ {
+ color: '#74a9cb',
+ portal: 'SIFR BioPortal',
+ link: 'https://bioportal.lirmm.fr/'
+ },
+ {
+ color: '#0d508a',
+ portal: 'EcoPortal',
+ link: 'https://ecoportal.lifewatch.eu/'
+ },
+ {
+ color: '#234979',
+ portal: 'MedPortal',
+ link: 'http://medportal.bmicc.cn/'
+ },
+ {
+ color: '#009574',
+ portal: 'MatPortal',
+ link: 'https://matportal.org/'
+ },
+ {
+ color: '#1c0f5d',
+ portal: 'IndustryPortal',
+ link: 'http://industryportal.enit.fr'
+ },
+ {
+ color: '#1e2251',
+ portal: 'EarthPortal',
+ link: 'https://earthportal.eu/'
+ },
+ {
+ color: '#33691B',
+ portal: 'BiodivPortal',
+ link: 'https://biodivportal.gfbio.org/'
+ }
+]
+
+$UI_THEME = :stageportal
+if File.exist?('config/bioportal_config_development_testportal.lirmm.fr.rb')
+ require_relative 'bioportal_config_development_testportal.lirmm.fr' # local credentials
+end
\ No newline at end of file
diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb
new file mode 100644
index 000000000..47b158aec
--- /dev/null
+++ b/config/deploy/staging.rb
@@ -0,0 +1,17 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+role :app, %w{stageportal.lirmm.fr}
+role :db, %w{stageportal.lirmm.fr} # sufficient to run db:migrate only on one system
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'stage'
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+set :log_level, :error
diff --git a/config/deploy/test.rb b/config/deploy/test.rb
new file mode 100644
index 000000000..fcbe1efce
--- /dev/null
+++ b/config/deploy/test.rb
@@ -0,0 +1,17 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+role :app, %w{testportal.lirmm.fr}
+role :db, %w{testportal.lirmm.fr} # sufficient to run db:migrate only on one system
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+set :log_level, :error
+set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'test'
diff --git a/package.json b/package.json
index d112843e7..392e650aa 100644
--- a/package.json
+++ b/package.json
@@ -4,11 +4,25 @@
"dependencies": {
"@hotwired/stimulus": "^3.0.1",
"@hotwired/turbo-rails": "^7.1.1",
+ "@triply/yasgui": "^4.2.28",
+ "chart.js": "^4.4.1",
+ "d3": "^7.8.5",
+ "datatables.net-dt": "^1.13.8",
+ "debounce": "^1.2.1",
"esbuild": "^0.14.41",
"flatpickr": "^4.6.13",
+ "highlight.js": "^11.9.0",
+ "jsonld": "^8.3.2",
"split.js": "^1.6.5",
"stimulus-flatpickr": "^3.0.0-0",
- "stimulus-rails-nested-form": "^4.0.0"
+ "stimulus-rails-nested-form": "^4.0.0",
+ "stimulus-read-more": "^4.1.0",
+ "stimulus-timeago": "^4.1.0",
+ "tippy.js": "^6.3.7",
+ "tom-select": "^2.2.2",
+ "vis-data": "^7.1.6",
+ "vis-network": "^9.1.6",
+ "vis-util": "^5.0.3"
},
"scripts": {
"build": "esbuild app/javascript/*.* --bundle --sourcemap --outdir=app/assets/builds"
diff --git a/vendor/assets/javascripts/ajax-chosen.js b/vendor/assets/javascripts/ajax-chosen.js
deleted file mode 100644
index 8d9b4ae5b..000000000
--- a/vendor/assets/javascripts/ajax-chosen.js
+++ /dev/null
@@ -1,164 +0,0 @@
-
-/*
-ajax-chosen
-A complement to the jQuery library Chosen that adds ajax autocomplete
-Contributors:
-https://github.com/jobvite/ajax-chosen
-https://github.com/bicouy0/ajax-chosen
-*/
-
-(function() {
-
- (function($) {
- return $.fn.ajaxChosen = function(options, callback) {
- var clickSelector, container, defaultedOptions, field, inputSelector, multiple, search, select, currentSearchId,
- _this = this;
- defaultedOptions = {
- minLength: 3,
- queryLimit: 10,
- delay: 100,
- chosenOptions: {},
- searchingText: "Searching...",
- noresultsText: "No results.",
- initialQuery: false
- };
- $.extend(defaultedOptions, options);
- defaultedOptions.chosenOptions.no_results_text = defaultedOptions.searchingText;
- select = this;
- multiple = select.attr('multiple') != null;
- if (multiple) {
- inputSelector = ".search-field > input";
- clickSelector = ".chzn-choices";
- } else {
- inputSelector = ".chzn-search > input";
- clickSelector = ".chzn-single";
- }
- select.chosen(defaultedOptions.chosenOptions);
- select.data('chosen').winnow_results = function(){};
- container = select.next('.chzn-container');
- field = container.find(inputSelector);
- if (defaultedOptions.initialQuery) {
- field.bind('focus', function(evt) {
- if (this.previousSearch || !container.hasClass('chzn-container-active')) {
- return;
- }
- return search(evt);
- });
- }
- field.bind('keyup', function(evt) {
- if (this.previousSearch) clearTimeout(this.previousSearch);
- return this.previousSearch = setTimeout((function() {
- return search(evt);
- }), defaultedOptions.delay);
- });
- return search = function(evt) {
- var clearSearchingLabel, currentOptions, prevVal, response, val, _ref, thisSearchId;
- val = $.trim(field.attr('value'));
- prevVal = (_ref = field.data('prevVal')) != null ? _ref : false;
- field.data('prevVal', val);
- thisSearchId = new Date().getTime() + val;
- currentSearchId = thisSearchId;
- var resultsDiv;
- if (multiple) {
- resultsDiv = field.parent().parent().siblings();
- } else {
- resultsDiv = field.parent().parent();
- }
- clearSearchingLabel = function(val) {
- if (typeof val === "undefined" || val === null || val === "") val = $(_this).attr('value');
- return resultsDiv.find('.no-results').html(defaultedOptions.noresultsText + " '" + val + "'");
- };
- if (val === prevVal || (val.length < defaultedOptions.minLength && evt.type === 'keyup')) {
- clearSearchingLabel(val);
- return false;
- }
- if (resultsDiv.find(".no-results").length < 1) {
- resultsDiv.find(".no-results").remove();
- resultsDiv.find(".chzn-results").prepend($("');
- newOpt.attr('value', value).html(text);
- return newOptions.push($(newOpt));
- });
- _fn = function(currentOpt) {
- var $currentOpt, newOption, presenceInNewOptions;
- $currentOpt = $(currentOpt);
- if ($currentOpt.attr('selected') && multiple) return;
- if ($currentOpt.attr('value') === '' && $currentOpt.html() === '' && !multiple) {
- return;
- }
- presenceInNewOptions = (function() {
- var _j, _len2, _results;
- _results = [];
- for (_j = 0, _len2 = newOptions.length; _j < _len2; _j++) {
- newOption = newOptions[_j];
- if (newOption.attr('value') === $currentOpt.attr('value')) {
- _results.push(newOption);
- }
- }
- return _results;
- })();
- if (presenceInNewOptions.length === 0) return $currentOpt.remove();
- };
- for (_i = 0, _len = currentOptions.length; _i < _len; _i++) {
- currentOpt = currentOptions[_i];
- _fn(currentOpt);
- }
- select.html(select.find("option:selected"));
- currentOptions = select.find('option');
- _fn2 = function(newOpt) {
- var currentOption, presenceInCurrentOptions, _fn3, _k, _len3;
- presenceInCurrentOptions = false;
- _fn3 = function(currentOption) {
- if ($(currentOption).attr('value') === newOpt.attr('value')) {
- return presenceInCurrentOptions = true;
- }
- };
- for (_k = 0, _len3 = currentOptions.length; _k < _len3; _k++) {
- currentOption = currentOptions[_k];
- _fn3(currentOption);
- }
- if (!presenceInCurrentOptions) return select.append(newOpt);
- };
- for (_j = 0, _len2 = newOptions.length; _j < _len2; _j++) {
- newOpt = newOptions[_j];
- _fn2(newOpt);
- }
- latestVal = field.val();
- if ($.isEmptyObject(items)) {
- noResult = $(' ');
- noResult.addClass('no-results');
- noResult.html(defaultedOptions.noresultsText + " '" + latestVal + "'").attr('value', '');
- select.find('.no-results').remove();
- select.append(noResult);
- } else {
- select.change();
- }
- select.trigger("liszt:updated");
- $('.no-results').removeClass('active-result');
- field.val(latestVal);
- field.trigger($.Event("keydown"))
- if (!$.isEmptyObject(items)) {
- keydownEvent = $.Event('keydown');
- keydownEvent.which = 40;
- field.trigger(keydownEvent);
- }
- if (success) return success(items);
- };
- return callback(defaultedOptions, response, evt);
- };
- };
- })(jQuery);
-
-}).call(this);
diff --git a/vendor/assets/javascripts/dataTables.fixedHeader.js b/vendor/assets/javascripts/dataTables.fixedHeader.js
deleted file mode 100644
index 90df87867..000000000
--- a/vendor/assets/javascripts/dataTables.fixedHeader.js
+++ /dev/null
@@ -1,1028 +0,0 @@
-/*! FixedHeader 2.1.2
- * ©2010-2014 SpryMedia Ltd - datatables.net/license
- */
-
-/**
- * @summary FixedHeader
- * @description Fix a table's header or footer, so it is always visible while
- * Scrolling
- * @version 2.1.2
- * @file dataTables.fixedHeader.js
- * @author SpryMedia Ltd (www.sprymedia.co.uk)
- * @contact www.sprymedia.co.uk/contact
- * @copyright Copyright 2009-2014 SpryMedia Ltd.
- *
- * This source file is free software, available under the following license:
- * MIT license - http://datatables.net/license/mit
- *
- * This source file is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
- * or FITNESS FOR A PARTICULAR PURPOSE. See the license files for details.
- *
- * For details please refer to: http://www.datatables.net
- */
-
-/* Global scope for FixedColumns for backwards compatibility - will be removed
- * in future. Not documented in 1.1.x.
- */
-
-/* Global scope for FixedColumns */
-var FixedHeader;
-
-(function(window, document, undefined) {
-
-
-var factory = function( $, DataTable ) {
-"use strict";
-
-/*
- * Function: FixedHeader
- * Purpose: Provide 'fixed' header, footer and columns for a DataTable
- * Returns: object:FixedHeader - must be called with 'new'
- * Inputs: mixed:mTable - target table
- * @param {object} dt DataTables instance or HTML table node. With DataTables
- * 1.10 this can also be a jQuery collection (with just a single table in its
- * result set), a jQuery selector, DataTables API instance or settings
- * object.
- * @param {object} [oInit] initialisation settings, with the following
- * properties (each optional)
- * * bool:top - fix the header (default true)
- * * bool:bottom - fix the footer (default false)
- * * int:left - fix the left column(s) (default 0)
- * * int:right - fix the right column(s) (default 0)
- * * int:zTop - fixed header zIndex
- * * int:zBottom - fixed footer zIndex
- * * int:zLeft - fixed left zIndex
- * * int:zRight - fixed right zIndex
- */
-FixedHeader = function ( mTable, oInit ) {
- /* Sanity check - you just know it will happen */
- if ( ! this instanceof FixedHeader )
- {
- alert( "FixedHeader warning: FixedHeader must be initialised with the 'new' keyword." );
- return;
- }
-
- var that = this;
- var oSettings = {
- "aoCache": [],
- "oSides": {
- "top": true,
- "bottom": false,
- "left": 0,
- "right": 0
- },
- "oZIndexes": {
- "top": 104,
- "bottom": 103,
- "left": 102,
- "right": 101
- },
- "oCloneOnDraw": {
- "top": false,
- "bottom": false,
- "left": true,
- "right": true
- },
- "oMes": {
- "iTableWidth": 0,
- "iTableHeight": 0,
- "iTableLeft": 0,
- "iTableRight": 0, /* note this is left+width, not actually "right" */
- "iTableTop": 0,
- "iTableBottom": 0 /* note this is top+height, not actually "bottom" */
- },
- "oOffset": {
- "top": 0
- },
- "nTable": null,
- "bFooter": false,
- "bInitComplete": false
- };
-
- /*
- * Function: fnGetSettings
- * Purpose: Get the settings for this object
- * Returns: object: - settings object
- * Inputs: -
- */
- this.fnGetSettings = function () {
- return oSettings;
- };
-
- /*
- * Function: fnUpdate
- * Purpose: Update the positioning and copies of the fixed elements
- * Returns: -
- * Inputs: -
- */
- this.fnUpdate = function () {
- this._fnUpdateClones();
- this._fnUpdatePositions();
- };
-
- /*
- * Function: fnPosition
- * Purpose: Update the positioning of the fixed elements
- * Returns: -
- * Inputs: -
- */
- this.fnPosition = function () {
- this._fnUpdatePositions();
- };
-
-
- var dt = $.fn.dataTable.Api ?
- new $.fn.dataTable.Api( mTable ).settings()[0] :
- mTable.fnSettings();
-
- dt._oPluginFixedHeader = this;
-
- /* Let's do it */
- this.fnInit( dt, oInit );
-
-};
-
-
-/*
- * Variable: FixedHeader
- * Purpose: Prototype for FixedHeader
- * Scope: global
- */
-FixedHeader.prototype = {
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Initialisation
- */
-
- /*
- * Function: fnInit
- * Purpose: The "constructor"
- * Returns: -
- * Inputs: {as FixedHeader function}
- */
- fnInit: function ( oDtSettings, oInit )
- {
- var s = this.fnGetSettings();
- var that = this;
-
- /* Record the user definable settings */
- this.fnInitSettings( s, oInit );
-
- if ( oDtSettings.oScroll.sX !== "" || oDtSettings.oScroll.sY !== "" )
- {
- alert( "FixedHeader 2 is not supported with DataTables' scrolling mode at this time" );
- return;
- }
-
- s.nTable = oDtSettings.nTable;
- oDtSettings.aoDrawCallback.unshift( {
- "fn": function () {
- FixedHeader.fnMeasure();
- that._fnUpdateClones.call(that);
- that._fnUpdatePositions.call(that);
- },
- "sName": "FixedHeader"
- } );
-
- s.bFooter = ($('>tfoot', s.nTable).length > 0) ? true : false;
-
- /* Add the 'sides' that are fixed */
- if ( s.oSides.top )
- {
- s.aoCache.push( that._fnCloneTable( "fixedHeader", "FixedHeader_Header", that._fnCloneThead ) );
- }
- if ( s.oSides.bottom )
- {
- s.aoCache.push( that._fnCloneTable( "fixedFooter", "FixedHeader_Footer", that._fnCloneTfoot ) );
- }
- if ( s.oSides.left )
- {
- s.aoCache.push( that._fnCloneTable( "fixedLeft", "FixedHeader_Left", that._fnCloneTLeft, s.oSides.left ) );
- }
- if ( s.oSides.right )
- {
- s.aoCache.push( that._fnCloneTable( "fixedRight", "FixedHeader_Right", that._fnCloneTRight, s.oSides.right ) );
- }
-
- /* Event listeners for window movement */
- FixedHeader.afnScroll.push( function () {
- that._fnUpdatePositions.call(that);
- } );
-
- $(window).resize( function () {
- FixedHeader.fnMeasure();
- that._fnUpdateClones.call(that);
- that._fnUpdatePositions.call(that);
- } );
-
- $(s.nTable)
- .on('column-reorder.dt', function () {
- FixedHeader.fnMeasure();
- that._fnUpdateClones( true );
- that._fnUpdatePositions();
- } )
- .on('column-visibility.dt', function () {
- FixedHeader.fnMeasure();
- that._fnUpdateClones( true );
- that._fnUpdatePositions();
- } );
-
- /* Get things right to start with */
- FixedHeader.fnMeasure();
- that._fnUpdateClones();
- that._fnUpdatePositions();
-
- s.bInitComplete = true;
- },
-
-
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Support functions
- */
-
- /*
- * Function: fnInitSettings
- * Purpose: Take the user's settings and copy them to our local store
- * Returns: -
- * Inputs: object:s - the local settings object
- * object:oInit - the user's settings object
- */
- fnInitSettings: function ( s, oInit )
- {
- if ( oInit !== undefined )
- {
- if ( oInit.top !== undefined ) {
- s.oSides.top = oInit.top;
- }
- if ( oInit.bottom !== undefined ) {
- s.oSides.bottom = oInit.bottom;
- }
- if ( typeof oInit.left == 'boolean' ) {
- s.oSides.left = oInit.left ? 1 : 0;
- }
- else if ( oInit.left !== undefined ) {
- s.oSides.left = oInit.left;
- }
- if ( typeof oInit.right == 'boolean' ) {
- s.oSides.right = oInit.right ? 1 : 0;
- }
- else if ( oInit.right !== undefined ) {
- s.oSides.right = oInit.right;
- }
-
- if ( oInit.zTop !== undefined ) {
- s.oZIndexes.top = oInit.zTop;
- }
- if ( oInit.zBottom !== undefined ) {
- s.oZIndexes.bottom = oInit.zBottom;
- }
- if ( oInit.zLeft !== undefined ) {
- s.oZIndexes.left = oInit.zLeft;
- }
- if ( oInit.zRight !== undefined ) {
- s.oZIndexes.right = oInit.zRight;
- }
-
- if ( oInit.offsetTop !== undefined ) {
- s.oOffset.top = oInit.offsetTop;
- }
- if ( oInit.alwaysCloneTop !== undefined ) {
- s.oCloneOnDraw.top = oInit.alwaysCloneTop;
- }
- if ( oInit.alwaysCloneBottom !== undefined ) {
- s.oCloneOnDraw.bottom = oInit.alwaysCloneBottom;
- }
- if ( oInit.alwaysCloneLeft !== undefined ) {
- s.oCloneOnDraw.left = oInit.alwaysCloneLeft;
- }
- if ( oInit.alwaysCloneRight !== undefined ) {
- s.oCloneOnDraw.right = oInit.alwaysCloneRight;
- }
- }
- },
-
- /*
- * Function: _fnCloneTable
- * Purpose: Clone the table node and do basic initialisation
- * Returns: -
- * Inputs: -
- */
- _fnCloneTable: function ( sType, sClass, fnClone, iCells )
- {
- var s = this.fnGetSettings();
- var nCTable;
-
- /* We know that the table _MUST_ has a DIV wrapped around it, because this is simply how
- * DataTables works. Therefore, we can set this to be relatively position (if it is not
- * alreadu absolute, and use this as the base point for the cloned header
- */
- if ( $(s.nTable.parentNode).css('position') != "absolute" )
- {
- s.nTable.parentNode.style.position = "relative";
- }
-
- /* Just a shallow clone will do - we only want the table node */
- nCTable = s.nTable.cloneNode( false );
- nCTable.removeAttribute( 'id' );
-
- var nDiv = document.createElement( 'div' );
- nDiv.style.position = "absolute";
- nDiv.style.top = "0px";
- nDiv.style.left = "0px";
- nDiv.className += " FixedHeader_Cloned "+sType+" "+sClass;
-
- /* Set the zIndexes */
- if ( sType == "fixedHeader" )
- {
- nDiv.style.zIndex = s.oZIndexes.top;
- }
- if ( sType == "fixedFooter" )
- {
- nDiv.style.zIndex = s.oZIndexes.bottom;
- }
- if ( sType == "fixedLeft" )
- {
- nDiv.style.zIndex = s.oZIndexes.left;
- }
- else if ( sType == "fixedRight" )
- {
- nDiv.style.zIndex = s.oZIndexes.right;
- }
-
- /* remove margins since we are going to position it absolutely */
- nCTable.style.margin = "0";
-
- /* Insert the newly cloned table into the DOM, on top of the "real" header */
- nDiv.appendChild( nCTable );
- document.body.appendChild( nDiv );
-
- return {
- "nNode": nCTable,
- "nWrapper": nDiv,
- "sType": sType,
- "sPosition": "",
- "sTop": "",
- "sLeft": "",
- "fnClone": fnClone,
- "iCells": iCells
- };
- },
-
- /*
- * Function: _fnMeasure
- * Purpose: Get the current positioning of the table in the DOM
- * Returns: -
- * Inputs: -
- */
- _fnMeasure: function ()
- {
- var
- s = this.fnGetSettings(),
- m = s.oMes,
- jqTable = $(s.nTable),
- oOffset = jqTable.offset(),
- iParentScrollTop = this._fnSumScroll( s.nTable.parentNode, 'scrollTop' ),
- iParentScrollLeft = this._fnSumScroll( s.nTable.parentNode, 'scrollLeft' );
-
- m.iTableWidth = jqTable.outerWidth();
- m.iTableHeight = jqTable.outerHeight();
- m.iTableLeft = oOffset.left + s.nTable.parentNode.scrollLeft;
- m.iTableTop = oOffset.top + iParentScrollTop;
- m.iTableRight = m.iTableLeft + m.iTableWidth;
- m.iTableRight = FixedHeader.oDoc.iWidth - m.iTableLeft - m.iTableWidth;
- m.iTableBottom = FixedHeader.oDoc.iHeight - m.iTableTop - m.iTableHeight;
- },
-
- /*
- * Function: _fnSumScroll
- * Purpose: Sum node parameters all the way to the top
- * Returns: int: sum
- * Inputs: node:n - node to consider
- * string:side - scrollTop or scrollLeft
- */
- _fnSumScroll: function ( n, side )
- {
- var i = n[side];
- while ( n = n.parentNode )
- {
- if ( n.nodeName == 'HTML' || n.nodeName == 'BODY' )
- {
- break;
- }
- i = n[side];
- }
- return i;
- },
-
- /*
- * Function: _fnUpdatePositions
- * Purpose: Loop over the fixed elements for this table and update their positions
- * Returns: -
- * Inputs: -
- */
- _fnUpdatePositions: function ()
- {
- var s = this.fnGetSettings();
- this._fnMeasure();
-
- for ( var i=0, iLen=s.aoCache.length ; i oWin.iScrollTop + s.oOffset.top )
- {
- /* Above the table */
- this._fnUpdateCache( oCache, 'sPosition', "absolute", 'position', nTable.style );
- this._fnUpdateCache( oCache, 'sTop', oMes.iTableTop+"px", 'top', nTable.style );
- this._fnUpdateCache( oCache, 'sLeft', oMes.iTableLeft+"px", 'left', nTable.style );
- }
- else if ( oWin.iScrollTop + s.oOffset.top > oMes.iTableTop+iTbodyHeight )
- {
- /* At the bottom of the table */
- this._fnUpdateCache( oCache, 'sPosition', "absolute", 'position', nTable.style );
- this._fnUpdateCache( oCache, 'sTop', (oMes.iTableTop+iTbodyHeight)+"px", 'top', nTable.style );
- this._fnUpdateCache( oCache, 'sLeft', oMes.iTableLeft+"px", 'left', nTable.style );
- }
- else
- {
- /* In the middle of the table */
- this._fnUpdateCache( oCache, 'sPosition', 'fixed', 'position', nTable.style );
- this._fnUpdateCache( oCache, 'sTop', s.oOffset.top+"px", 'top', nTable.style );
- this._fnUpdateCache( oCache, 'sLeft', (oMes.iTableLeft-oWin.iScrollLeft)+"px", 'left', nTable.style );
- }
- },
-
- /*
- * Function: _fnUpdateCache
- * Purpose: Check the cache and update cache and value if needed
- * Returns: -
- * Inputs: object:oCache - local cache object
- * string:sCache - cache property
- * string:sSet - value to set
- * string:sProperty - object property to set
- * object:oObj - object to update
- */
- _fnUpdateCache: function ( oCache, sCache, sSet, sProperty, oObj )
- {
- if ( oCache[sCache] != sSet )
- {
- oObj[sProperty] = sSet;
- oCache[sCache] = sSet;
- }
- },
-
-
-
- /**
- * Copy the classes of all child nodes from one element to another. This implies
- * that the two have identical structure - no error checking is performed to that
- * fact.
- * @param {element} source Node to copy classes from
- * @param {element} dest Node to copy classes too
- */
- _fnClassUpdate: function ( source, dest )
- {
- var that = this;
-
- if ( source.nodeName.toUpperCase() === "TR" || source.nodeName.toUpperCase() === "TH" ||
- source.nodeName.toUpperCase() === "TD" || source.nodeName.toUpperCase() === "SPAN" )
- {
- dest.className = source.className;
- }
-
- $(source).children().each( function (i) {
- that._fnClassUpdate( $(source).children()[i], $(dest).children()[i] );
- } );
- },
-
-
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Cloning functions
- */
-
- /*
- * Function: _fnCloneThead
- * Purpose: Clone the thead element
- * Returns: -
- * Inputs: object:oCache - the cached values for this fixed element
- */
- _fnCloneThead: function ( oCache )
- {
- var s = this.fnGetSettings();
- var nTable = oCache.nNode;
-
- if ( s.bInitComplete && !s.oCloneOnDraw.top )
- {
- this._fnClassUpdate( $('thead', s.nTable)[0], $('thead', nTable)[0] );
- return;
- }
-
- /* Set the wrapper width to match that of the cloned table */
- var iDtWidth = $(s.nTable).outerWidth();
- oCache.nWrapper.style.width = iDtWidth+"px";
- nTable.style.width = iDtWidth+"px";
-
- /* Remove any children the cloned table has */
- while ( nTable.childNodes.length > 0 )
- {
- $('thead th', nTable).unbind( 'click' );
- nTable.removeChild( nTable.childNodes[0] );
- }
-
- /* Clone the DataTables header */
- var nThead = $('thead', s.nTable).clone(true)[0];
- nTable.appendChild( nThead );
-
- /* Copy the widths across - apparently a clone isn't good enough for this */
- var a = [];
- var b = [];
-
- $("thead>tr th", s.nTable).each( function (i) {
- a.push( $(this).width() );
- } );
-
- $("thead>tr td", s.nTable).each( function (i) {
- b.push( $(this).width() );
- } );
-
- $("thead>tr th", s.nTable).each( function (i) {
- $("thead>tr th:eq("+i+")", nTable).width( a[i] );
- $(this).width( a[i] );
- } );
-
- $("thead>tr td", s.nTable).each( function (i) {
- $("thead>tr td:eq("+i+")", nTable).width( b[i] );
- $(this).width( b[i] );
- } );
-
- // Stop DataTables 1.9 from putting a focus ring on the headers when
- // clicked to sort
- $('th.sorting, th.sorting_desc, th.sorting_asc', nTable).bind( 'click', function () {
- this.blur();
- } );
- },
-
- /*
- * Function: _fnCloneTfoot
- * Purpose: Clone the tfoot element
- * Returns: -
- * Inputs: object:oCache - the cached values for this fixed element
- */
- _fnCloneTfoot: function ( oCache )
- {
- var s = this.fnGetSettings();
- var nTable = oCache.nNode;
-
- /* Set the wrapper width to match that of the cloned table */
- oCache.nWrapper.style.width = $(s.nTable).outerWidth()+"px";
-
- /* Remove any children the cloned table has */
- while ( nTable.childNodes.length > 0 )
- {
- nTable.removeChild( nTable.childNodes[0] );
- }
-
- /* Clone the DataTables footer */
- var nTfoot = $('tfoot', s.nTable).clone(true)[0];
- nTable.appendChild( nTfoot );
-
- /* Copy the widths across - apparently a clone isn't good enough for this */
- $("tfoot:eq(0)>tr th", s.nTable).each( function (i) {
- $("tfoot:eq(0)>tr th:eq("+i+")", nTable).width( $(this).width() );
- } );
-
- $("tfoot:eq(0)>tr td", s.nTable).each( function (i) {
- $("tfoot:eq(0)>tr td:eq("+i+")", nTable).width( $(this).width() );
- } );
- },
-
- /*
- * Function: _fnCloneTLeft
- * Purpose: Clone the left column(s)
- * Returns: -
- * Inputs: object:oCache - the cached values for this fixed element
- */
- _fnCloneTLeft: function ( oCache )
- {
- var s = this.fnGetSettings();
- var nTable = oCache.nNode;
- var nBody = $('tbody', s.nTable)[0];
-
- /* Remove any children the cloned table has */
- while ( nTable.childNodes.length > 0 )
- {
- nTable.removeChild( nTable.childNodes[0] );
- }
-
- /* Is this the most efficient way to do this - it looks horrible... */
- nTable.appendChild( $("thead", s.nTable).clone(true)[0] );
- nTable.appendChild( $("tbody", s.nTable).clone(true)[0] );
- if ( s.bFooter )
- {
- nTable.appendChild( $("tfoot", s.nTable).clone(true)[0] );
- }
-
- /* Remove unneeded cells */
- var sSelector = 'gt(' + (oCache.iCells - 1) + ')';
- $('thead tr', nTable).each( function (k) {
- $('th:' + sSelector, this).remove();
- } );
-
- $('tfoot tr', nTable).each( function (k) {
- $('th:' + sSelector, this).remove();
- } );
-
- $('tbody tr', nTable).each( function (k) {
- $('td:' + sSelector, this).remove();
- } );
-
- this.fnEqualiseHeights( 'thead', nBody.parentNode, nTable );
- this.fnEqualiseHeights( 'tbody', nBody.parentNode, nTable );
- this.fnEqualiseHeights( 'tfoot', nBody.parentNode, nTable );
-
- var iWidth = 0;
- for (var i = 0; i < oCache.iCells; i++) {
- iWidth += $('thead tr th:eq(' + i + ')', s.nTable).outerWidth();
- }
- nTable.style.width = iWidth+"px";
- oCache.nWrapper.style.width = iWidth+"px";
- },
-
- /*
- * Function: _fnCloneTRight
- * Purpose: Clone the right most column(s)
- * Returns: -
- * Inputs: object:oCache - the cached values for this fixed element
- */
- _fnCloneTRight: function ( oCache )
- {
- var s = this.fnGetSettings();
- var nBody = $('tbody', s.nTable)[0];
- var nTable = oCache.nNode;
- var iCols = $('tbody tr:eq(0) td', s.nTable).length;
-
- /* Remove any children the cloned table has */
- while ( nTable.childNodes.length > 0 )
- {
- nTable.removeChild( nTable.childNodes[0] );
- }
-
- /* Is this the most efficient way to do this - it looks horrible... */
- nTable.appendChild( $("thead", s.nTable).clone(true)[0] );
- nTable.appendChild( $("tbody", s.nTable).clone(true)[0] );
- if ( s.bFooter )
- {
- nTable.appendChild( $("tfoot", s.nTable).clone(true)[0] );
- }
- $('thead tr th:lt('+(iCols-oCache.iCells)+')', nTable).remove();
- $('tfoot tr th:lt('+(iCols-oCache.iCells)+')', nTable).remove();
-
- /* Remove unneeded cells */
- $('tbody tr', nTable).each( function (k) {
- $('td:lt('+(iCols-oCache.iCells)+')', this).remove();
- } );
-
- this.fnEqualiseHeights( 'thead', nBody.parentNode, nTable );
- this.fnEqualiseHeights( 'tbody', nBody.parentNode, nTable );
- this.fnEqualiseHeights( 'tfoot', nBody.parentNode, nTable );
-
- var iWidth = 0;
- for (var i = 0; i < oCache.iCells; i++) {
- iWidth += $('thead tr th:eq('+(iCols-1-i)+')', s.nTable).outerWidth();
- }
- nTable.style.width = iWidth+"px";
- oCache.nWrapper.style.width = iWidth+"px";
- },
-
-
- /**
- * Equalise the heights of the rows in a given table node in a cross browser way. Note that this
- * is more or less lifted as is from FixedColumns
- * @method fnEqualiseHeights
- * @returns void
- * @param {string} parent Node type - thead, tbody or tfoot
- * @param {element} original Original node to take the heights from
- * @param {element} clone Copy the heights to
- * @private
- */
- "fnEqualiseHeights": function ( parent, original, clone )
- {
- var that = this;
- var originals = $(parent +' tr', original);
- var height;
-
- $(parent+' tr', clone).each( function (k) {
- height = originals.eq( k ).css('height');
-
- // This is nasty :-(. IE has a sub-pixel error even when setting
- // the height below (the Firefox fix) which causes the fixed column
- // to go out of alignment. Need to add a pixel before the assignment
- // Can this be feature detected? Not sure how...
- if ( navigator.appName == 'Microsoft Internet Explorer' ) {
- height = parseInt( height, 10 ) + 1;
- }
-
- $(this).css( 'height', height );
-
- // For Firefox to work, we need to also set the height of the
- // original row, to the value that we read from it! Otherwise there
- // is a sub-pixel rounding error
- originals.eq( k ).css( 'height', height );
- } );
- }
-};
-
-
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Static properties and methods
- * We use these for speed! This information is common to all instances of FixedHeader, so no
- * point if having them calculated and stored for each different instance.
- */
-
-/*
- * Variable: oWin
- * Purpose: Store information about the window positioning
- * Scope: FixedHeader
- */
-FixedHeader.oWin = {
- "iScrollTop": 0,
- "iScrollRight": 0,
- "iScrollBottom": 0,
- "iScrollLeft": 0,
- "iHeight": 0,
- "iWidth": 0
-};
-
-/*
- * Variable: oDoc
- * Purpose: Store information about the document size
- * Scope: FixedHeader
- */
-FixedHeader.oDoc = {
- "iHeight": 0,
- "iWidth": 0
-};
-
-/*
- * Variable: afnScroll
- * Purpose: Array of functions that are to be used for the scrolling components
- * Scope: FixedHeader
- */
-FixedHeader.afnScroll = [];
-
-/*
- * Function: fnMeasure
- * Purpose: Update the measurements for the window and document
- * Returns: -
- * Inputs: -
- */
-FixedHeader.fnMeasure = function ()
-{
- var
- jqWin = $(window),
- jqDoc = $(document),
- oWin = FixedHeader.oWin,
- oDoc = FixedHeader.oDoc;
-
- oDoc.iHeight = jqDoc.height();
- oDoc.iWidth = jqDoc.width();
-
- oWin.iHeight = jqWin.height();
- oWin.iWidth = jqWin.width();
- oWin.iScrollTop = jqWin.scrollTop();
- oWin.iScrollLeft = jqWin.scrollLeft();
- oWin.iScrollRight = oDoc.iWidth - oWin.iScrollLeft - oWin.iWidth;
- oWin.iScrollBottom = oDoc.iHeight - oWin.iScrollTop - oWin.iHeight;
-};
-
-
-FixedHeader.version = "2.1.2";
-
-
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Global processing
- */
-
-/*
- * Just one 'scroll' event handler in FixedHeader, which calls the required components. This is
- * done as an optimisation, to reduce calculation and proagation time
- */
-$(window).scroll( function () {
- FixedHeader.fnMeasure();
-
- for ( var i=0, iLen=FixedHeader.afnScroll.length ; iTerms
- * Loads the #terms div in the box
- *
- * Terms
- * Loads the terms.html page in the box
- *
- * Terms
- * Loads the terms.png image in the box
- *
- *
- * You can also use it programmatically:
- *
- * jQuery.facebox('some html')
- * jQuery.facebox('some html', 'my-groovy-style')
- *
- * The above will open a facebox with "some html" as the content.
- *
- * jQuery.facebox(function($) {
- * $.get('blah.html', function(data) { $.facebox(data) })
- * })
- *
- * The above will show a loading screen before the passed function is called,
- * allowing for a better ajaxy experience.
- *
- * The facebox function can also display an ajax page, an image, or the contents of a div:
- *
- * jQuery.facebox({ ajax: 'remote.html' })
- * jQuery.facebox({ ajax: 'remote.html' }, 'my-groovy-style')
- * jQuery.facebox({ image: 'stairs.jpg' })
- * jQuery.facebox({ image: 'stairs.jpg' }, 'my-groovy-style')
- * jQuery.facebox({ div: '#box' })
- * jQuery.facebox({ div: '#box' }, 'my-groovy-style')
- *
- * Want to close the facebox? Trigger the 'close.facebox' document event:
- *
- * jQuery(document).trigger('close.facebox')
- *
- * Facebox also has a bunch of other hooks:
- *
- * loading.facebox
- * beforeReveal.facebox
- * reveal.facebox (aliased as 'afterReveal.facebox')
- * init.facebox
- * afterClose.facebox
- *
- * Simply bind a function to any of these hooks:
- *
- * $(document).bind('reveal.facebox', function() { ...stuff to do after the facebox and contents are revealed... })
- *
- */
-(function($) {
- $.facebox = function(data, klass) {
- $.facebox.loading()
-
- if (data.ajax) fillFaceboxFromAjax(data.ajax, klass)
- else if (data.image) fillFaceboxFromImage(data.image, klass)
- else if (data.div) fillFaceboxFromHref(data.div, klass)
- else if ($.isFunction(data)) data.call($)
- else $.facebox.reveal(data, klass)
- }
-
- /*
- * Public, $.facebox methods
- */
-
- $.extend($.facebox, {
- settings: {
- opacity : 0.2,
- overlay : true,
- loadingImage : '/facebox/loading.gif',
- closeImage : '/facebox/closelabel.png',
- imageTypes : [ 'png', 'jpg', 'jpeg', 'gif' ],
- faceboxHtml : '\
- \
- \
-
'
- },
-
- loading: function() {
- init()
- if ($('#facebox .loading').length == 1) return true
- showOverlay()
-
- $('#facebox .content').empty()
- $('#facebox .body').children().hide().end().
- append('
')
-
- $('#facebox_overlay').hide().addClass("facebox_overlayBG")
- .css('opacity', $.facebox.settings.opacity)
- .click(function() { $(document).trigger('close.facebox') })
- .fadeIn(200)
- return false
- }
-
- function hideOverlay() {
- if (skipOverlay()) return
-
- $('#facebox_overlay').fadeOut(200, function(){
- $("#facebox_overlay").removeClass("facebox_overlayBG")
- $("#facebox_overlay").addClass("facebox_hide")
- $("#facebox_overlay").remove()
- })
-
- return false
- }
-
- /*
- * Bindings
- */
-
- $(document).bind('close.facebox', function() {
- $(document).unbind('keydown.facebox')
- $('#facebox').fadeOut(function() {
- $(document.body).append(jQuery("").hide().append($('#facebox .content').children()))
- $('#facebox .content').removeClass().addClass('content')
- $('#facebox .loading').remove()
- $(document).trigger('afterClose.facebox')
- })
- hideOverlay()
- })
-
-})(jQuery);
diff --git a/vendor/assets/javascripts/fg.menu.js b/vendor/assets/javascripts/fg.menu.js
deleted file mode 100755
index 5d1b92c51..000000000
--- a/vendor/assets/javascripts/fg.menu.js
+++ /dev/null
@@ -1,645 +0,0 @@
-/*--------------------------------------------------------------------
-Scripts for creating and manipulating custom menus based on standard markup
-Version: 3.0, 03.31.2009
-
-By: Maggie Costello Wachs (maggie@filamentgroup.com) and Scott Jehl (scott@filamentgroup.com)
- http://www.filamentgroup.com
- * reference articles: http://www.filamentgroup.com/lab/jquery_ipod_style_drilldown_menu/
-
-Copyright (c) 2009 Filament Group
-Dual licensed under the MIT (filamentgroup.com/examples/mit-license.txt) and GPL (filamentgroup.com/examples/gpl-license.txt) licenses.
---------------------------------------------------------------------*/
-
-
-var allUIMenus = [];
-
-$.fn.fgmenu = function(options){
- var caller = this;
- var options = options;
- var m = new Menu(caller, options);
- allUIMenus.push(m);
-
- $(this)
- .mousedown(function(){
- if (!m.menuOpen) { m.showLoading(); };
- })
- .click(function(){
- if (m.menuOpen == false) { m.showMenu(); }
- else { m.kill(); };
- return false;
- });
-};
-
-function Menu(caller, options){
- var menu = this;
- var caller = $(caller);
- var container = $('');
-
- this.menuOpen = false;
- this.menuExists = false;
-
- var options = jQuery.extend({
- content: null,
- width: 180, // width of menu container, must be set or passed in to calculate widths of child menus
- maxHeight: 180, // max height of menu (if a drilldown: height does not include breadcrumb)
- positionOpts: {
- posX: 'left',
- posY: 'bottom',
- offsetX: 0,
- offsetY: 0,
- directionH: 'right',
- directionV: 'down',
- detectH: true, // do horizontal collision detection
- detectV: true, // do vertical collision detection
- linkToFront: false
- },
- showSpeed: 200, // show/hide speed in milliseconds
- callerOnState: 'ui-state-active', // class to change the appearance of the link/button when the menu is showing
- loadingState: 'ui-state-loading', // class added to the link/button while the menu is created
- linkHover: 'ui-state-hover', // class for menu option hover state
- linkHoverSecondary: 'li-hover', // alternate class, may be used for multi-level menus
- // ----- multi-level menu defaults -----
- crossSpeed: 200, // cross-fade speed for multi-level menus
- crumbDefaultText: 'Choose an option:',
- backLink: true, // in the ipod-style menu: instead of breadcrumbs, show only a 'back' link
- backLinkText: 'Back',
- flyOut: false, // multi-level menus are ipod-style by default; this parameter overrides to make a flyout instead
- flyOutOnState: 'ui-state-default',
- nextMenuLink: 'ui-icon-triangle-1-e', // class to style the link (specifically, a span within the link) used in the multi-level menu to show the next level
- topLinkText: 'All',
- nextCrumbLink: 'ui-icon-carat-1-e',
- afterItemChosen: function(item){}
-
- }, options);
-
- var killAllMenus = function(){
- $.each(allUIMenus, function(i){
- if (allUIMenus[i].menuOpen) { allUIMenus[i].kill(); };
- });
- };
-
- this.kill = function(){
- caller
- .removeClass(options.loadingState)
- .removeClass('fg-menu-open')
- .removeClass(options.callerOnState);
- container.find('li').removeClass(options.linkHoverSecondary).find('a').removeClass(options.linkHover);
- if (options.flyOutOnState) { container.find('li a').removeClass(options.flyOutOnState); };
- if (options.callerOnState) { caller.removeClass(options.callerOnState); };
- if (container.is('.fg-menu-ipod')) { menu.resetDrilldownMenu(); };
- if (container.is('.fg-menu-flyout')) { menu.resetFlyoutMenu(); };
- container.parent().hide();
- menu.menuOpen = false;
- $(document).unbind('click', killAllMenus);
- $(document).unbind('keydown');
- };
-
- this.showLoading = function(){
- caller.addClass(options.loadingState);
- };
-
- this.showMenu = function(){
- killAllMenus();
- if (!menu.menuExists) { menu.create() };
- caller
- .addClass('fg-menu-open')
- .addClass(options.callerOnState);
- container.parent().show().click(function(){ menu.kill(); return false; });
- container.hide().slideDown(options.showSpeed).find('.fg-menu:eq(0)');
- menu.menuOpen = true;
- caller.removeClass(options.loadingState);
- $(document).click(killAllMenus);
-
- // assign key events
- $(document).keydown(function(event){
- var e;
- if (event.which !="") { e = event.which; }
- else if (event.charCode != "") { e = event.charCode; }
- else if (event.keyCode != "") { e = event.keyCode; }
-
- var menuType = ($(event.target).parents('div').is('.fg-menu-flyout')) ? 'flyout' : 'ipod' ;
-
- switch(e) {
- case 37: // left arrow
- if (menuType == 'flyout') {
- $(event.target).trigger('mouseout');
- if ($('.'+options.flyOutOnState).size() > 0) { $('.'+options.flyOutOnState).trigger('mouseover'); };
- };
-
- if (menuType == 'ipod') {
- $(event.target).trigger('mouseout');
- if ($('.fg-menu-footer').find('a').size() > 0) { $('.fg-menu-footer').find('a').trigger('click'); };
- if ($('.fg-menu-header').find('a').size() > 0) { $('.fg-menu-current-crumb').prev().find('a').trigger('click'); };
- if ($('.fg-menu-current').prev().is('.fg-menu-indicator')) {
- $('.fg-menu-current').prev().trigger('mouseover');
- };
- };
- return false;
- break;
-
- case 38: // up arrow
- if ($(event.target).is('.' + options.linkHover)) {
- var prevLink = $(event.target).parent().prev().find('a:eq(0)');
- if (prevLink.size() > 0) {
- $(event.target).trigger('mouseout');
- prevLink.trigger('mouseover');
- };
- }
- else { container.find('a:eq(0)').trigger('mouseover'); }
- return false;
- break;
-
- case 39: // right arrow
- if ($(event.target).is('.fg-menu-indicator')) {
- if (menuType == 'flyout') {
- $(event.target).next().find('a:eq(0)').trigger('mouseover');
- }
- else if (menuType == 'ipod') {
- $(event.target).trigger('click');
- setTimeout(function(){
- $(event.target).next().find('a:eq(0)').trigger('mouseover');
- }, options.crossSpeed);
- };
- };
- return false;
- break;
-
- case 40: // down arrow
- if ($(event.target).is('.' + options.linkHover)) {
- var nextLink = $(event.target).parent().next().find('a:eq(0)');
- if (nextLink.size() > 0) {
- $(event.target).trigger('mouseout');
- nextLink.trigger('mouseover');
- };
- }
- else { container.find('a:eq(0)').trigger('mouseover'); }
- return false;
- break;
-
- case 27: // escape
- killAllMenus();
- break;
-
- case 13: // enter
- if ($(event.target).is('.fg-menu-indicator') && menuType == 'ipod') {
- $(event.target).trigger('click');
- setTimeout(function(){
- $(event.target).next().find('a:eq(0)').trigger('mouseover');
- }, options.crossSpeed);
- };
- break;
- };
- });
- };
-
- this.create = function(){
- container.css({ width: options.width }).appendTo('body').find('ul:first').not('.fg-menu-breadcrumb').addClass('fg-menu');
- container.find('ul, li a').addClass('ui-corner-all');
-
- // aria roles & attributes
- container.find('ul').attr('role', 'menu').eq(0).attr('aria-activedescendant','active-menuitem').attr('aria-labelledby', caller.attr('id'));
- container.find('li').attr('role', 'menuitem');
- container.find('li:has(ul)').attr('aria-haspopup', 'true').find('ul').attr('aria-expanded', 'false');
- container.find('a').attr('tabindex', '-1');
-
- // when there are multiple levels of hierarchy, create flyout or drilldown menu
- if (container.find('ul').size() > 1) {
- if (options.flyOut) { menu.flyout(container, options); }
- else { menu.drilldown(container, options); }
- }
- else {
- container.find('a').click(function(){
- menu.chooseItem(this);
- return false;
- });
- };
-
- if (options.linkHover) {
- var allLinks = container.find('.fg-menu li a');
- allLinks.hover(
- function(){
- var menuitem = $(this);
- $('.'+options.linkHover).removeClass(options.linkHover).blur().parent().removeAttr('id');
- $(this).addClass(options.linkHover).focus().parent().attr('id','active-menuitem');
- },
- function(){
- $(this).removeClass(options.linkHover).blur().parent().removeAttr('id');
- }
- );
- };
-
- if (options.linkHoverSecondary) {
- container.find('.fg-menu li').hover(
- function(){
- $(this).siblings('li').removeClass(options.linkHoverSecondary);
- if (options.flyOutOnState) { $(this).siblings('li').find('a').removeClass(options.flyOutOnState); }
- $(this).addClass(options.linkHoverSecondary);
- },
- function(){ $(this).removeClass(options.linkHoverSecondary); }
- );
- };
-
- menu.setPosition(container, caller, options);
- menu.menuExists = true;
- };
-
- this.chooseItem = function(item){
- menu.kill();
- options.afterItemChosen(item);
- };
-};
-
-Menu.prototype.flyout = function(container, options) {
- var menu = this;
-
- this.resetFlyoutMenu = function(){
- var allLists = container.find('ul ul');
- allLists.removeClass('ui-widget-content').hide();
- };
-
- container.addClass('fg-menu-flyout').find('li:has(ul)').each(function(){
- var linkWidth = container.width();
- var showTimer, hideTimer;
- var allSubLists = $(this).find('ul');
-
- allSubLists.css({ left: linkWidth, width: linkWidth }).hide();
-
- $(this).find('a:eq(0)').addClass('fg-menu-indicator').html('' + $(this).find('a:eq(0)').text() + ' ').hover(
- function(){
- clearTimeout(hideTimer);
- var subList = $(this).next();
- if (!fitVertical(subList, $(this).offset().top)) { subList.css({ top: 'auto', bottom: 0 }); };
- if (!fitHorizontal(subList, $(this).offset().left + 100)) { subList.css({ left: 'auto', right: linkWidth, 'z-index': 999 }); };
- showTimer = setTimeout(function(){
- subList.addClass('ui-widget-content').show(options.showSpeed).attr('aria-expanded', 'true');
- }, 300);
- },
- function(){
- clearTimeout(showTimer);
- var subList = $(this).next();
- hideTimer = setTimeout(function(){
- subList.removeClass('ui-widget-content').hide(options.showSpeed).attr('aria-expanded', 'false');
- }, 400);
- }
- );
-
- $(this).find('ul a').hover(
- function(){
- clearTimeout(hideTimer);
- if ($(this).parents('ul').prev().is('a.fg-menu-indicator')) {
- $(this).parents('ul').prev().addClass(options.flyOutOnState);
- }
- },
- function(){
- hideTimer = setTimeout(function(){
- allSubLists.hide(options.showSpeed);
- container.find(options.flyOutOnState).removeClass(options.flyOutOnState);
- }, 500);
- }
- );
- });
-
- container.find('a').click(function(){
- menu.chooseItem(this);
- return false;
- });
-};
-
-
-Menu.prototype.drilldown = function(container, options) {
- var menu = this;
- var topList = container.find('.fg-menu');
- var breadcrumb = $('');
- var crumbDefaultHeader = $('');
- var firstCrumbText = (options.backLink) ? options.backLinkText : options.topLinkText;
- var firstCrumbClass = (options.backLink) ? 'fg-menu-prev-list' : 'fg-menu-all-lists';
- var firstCrumbLinkClass = (options.backLink) ? 'ui-state-default ui-corner-all' : '';
- var firstCrumbIcon = (options.backLink) ? ''+firstCrumbIcon+firstCrumbText+' ' + $(this).text() + ' '); })
- .click(function(){ // ----- show the next menu
- var nextList = $(this).next();
- var parentUl = $(this).parents('ul:eq(0)');
- var parentLeft = (parentUl.is('.fg-menu-content')) ? 0 : parseFloat(topList.css('left'));
- var nextLeftVal = Math.round(parentLeft - parseFloat(container.width()));
- var footer = $('.fg-menu-footer');
-
- // show next menu
- resetChildMenu(parentUl);
- checkMenuHeight(nextList);
- topList.animate({ left: nextLeftVal }, options.crossSpeed);
- nextList.show().addClass('fg-menu-current').attr('aria-expanded', 'true');
-
- var setPrevMenu = function(backlink){
- var b = backlink;
- var c = $('.fg-menu-current');
- var prevList = c.parents('ul:eq(0)');
- c.hide().attr('aria-expanded', 'false');
- resetChildMenu(c);
- checkMenuHeight(prevList);
- prevList.addClass('fg-menu-current').attr('aria-expanded', 'true');
- if (prevList.hasClass('fg-menu-content')) { b.remove(); footer.hide(); };
- };
-
- // initialize "back" link
- if (options.backLink) {
- if (footer.find('a').size() == 0) {
- footer.show();
- $('Back
');
- helper.css({ position: 'absolute', left: dims.refX, top: dims.refY, width: dims.refW, height: dims.refH });
- el.wrap(helper);
-
- // get X pos
- switch(options.positionOpts.posX) {
- case 'left': xVal = 0;
- break;
- case 'center': xVal = dims.refW / 2;
- break;
- case 'right': xVal = dims.refW;
- break;
- };
-
- // get Y pos
- switch(options.positionOpts.posY) {
- case 'top': yVal = 0;
- break;
- case 'center': yVal = dims.refH / 2;
- break;
- case 'bottom': yVal = dims.refH;
- break;
- };
-
- // add the offsets (zero by default)
- xVal += options.positionOpts.offsetX;
- yVal += options.positionOpts.offsetY;
-
- // position the object vertically
- if (options.positionOpts.directionV == 'up') {
- el.css({ top: 'auto', bottom: yVal });
- if (options.positionOpts.detectV && !fitVertical(el)) {
- el.css({ bottom: 'auto', top: yVal });
- }
- }
- else {
- el.css({ bottom: 'auto', top: yVal });
- if (options.positionOpts.detectV && !fitVertical(el)) {
- el.css({ top: 'auto', bottom: yVal });
- }
- };
-
- // and horizontally
- if (options.positionOpts.directionH == 'left') {
- el.css({ left: 'auto', right: xVal });
- if (options.positionOpts.detectH && !fitHorizontal(el)) {
- el.css({ right: 'auto', left: xVal });
- }
- }
- else {
- el.css({ right: 'auto', left: xVal });
- if (options.positionOpts.detectH && !fitHorizontal(el)) {
- el.css({ left: 'auto', right: xVal });
- }
- };
-
- // if specified, clone the referring element and position it so that it appears on top of the menu
- if (options.positionOpts.linkToFront) {
- referrer.clone().addClass('linkClone').css({
- position: 'absolute',
- top: 0,
- right: 'auto',
- bottom: 'auto',
- left: 0,
- width: referrer.width(),
- height: referrer.height()
- }).insertAfter(el);
- };
-};
-
-
-/* Utilities to sort and find viewport dimensions */
-
-function sortBigToSmall(a, b) { return b - a; };
-
-jQuery.fn.getTotalWidth = function(){
- return $(this).width() + parseInt($(this).css('paddingRight')) + parseInt($(this).css('paddingLeft')) + parseInt($(this).css('borderRightWidth')) + parseInt($(this).css('borderLeftWidth'));
-};
-
-jQuery.fn.getTotalHeight = function(){
- return $(this).height() + parseInt($(this).css('paddingTop')) + parseInt($(this).css('paddingBottom')) + parseInt($(this).css('borderTopWidth')) + parseInt($(this).css('borderBottomWidth'));
-};
-
-function getScrollTop(){
- return self.pageYOffset || document.documentElement.scrollTop || document.body.scrollTop;
-};
-
-function getScrollLeft(){
- return self.pageXOffset || document.documentElement.scrollLeft || document.body.scrollLeft;
-};
-
-function getWindowHeight(){
- var de = document.documentElement;
- return self.innerHeight || (de && de.clientHeight) || document.body.clientHeight;
-};
-
-function getWindowWidth(){
- var de = document.documentElement;
- return self.innerWidth || (de && de.clientWidth) || document.body.clientWidth;
-};
-
-/* Utilities to test whether an element will fit in the viewport
- Parameters:
- el = element to position, required
- leftOffset / topOffset = optional parameter if the offset cannot be calculated (i.e., if the object is in the DOM but is set to display: 'none') */
-
-function fitHorizontal(el, leftOffset){
- var leftVal = parseInt(leftOffset) || $(el).offset().left;
- return (leftVal + $(el).width() <= getWindowWidth() + getScrollLeft() && leftVal - getScrollLeft() >= 0);
-};
-
-function fitVertical(el, topOffset){
- var topVal = parseInt(topOffset) || $(el).offset().top;
- return (topVal + $(el).height() <= getWindowHeight() + getScrollTop() && topVal - getScrollTop() >= 0);
-};
-
-/*--------------------------------------------------------------------
- * javascript method: "pxToEm"
- * by:
- Scott Jehl (scott@filamentgroup.com)
- Maggie Wachs (maggie@filamentgroup.com)
- http://www.filamentgroup.com
- *
- * Copyright (c) 2008 Filament Group
- * Dual licensed under the MIT (filamentgroup.com/examples/mit-license.txt) and GPL (filamentgroup.com/examples/gpl-license.txt) licenses.
- *
- * Description: Extends the native Number and String objects with pxToEm method. pxToEm converts a pixel value to ems depending on inherited font size.
- * Article: http://www.filamentgroup.com/lab/retaining_scalable_interfaces_with_pixel_to_em_conversion/
- * Demo: http://www.filamentgroup.com/examples/pxToEm/
- *
- * Options:
- scope: string or jQuery selector for font-size scoping
- reverse: Boolean, true reverses the conversion to em-px
- * Dependencies: jQuery library
- * Usage Example: myPixelValue.pxToEm(); or myPixelValue.pxToEm({'scope':'#navigation', reverse: true});
- *
- * Version: 2.0, 08.01.2008
- * Changelog:
- * 08.02.2007 initial Version 1.0
- * 08.01.2008 - fixed font-size calculation for IE
---------------------------------------------------------------------*/
-
-Number.prototype.pxToEm = String.prototype.pxToEm = function(settings){
- //set defaults
- settings = jQuery.extend({
- scope: 'body',
- reverse: false
- }, settings);
-
- var pxVal = (this == '') ? 0 : parseFloat(this);
- var scopeVal;
- var getWindowWidth = function(){
- var de = document.documentElement;
- return self.innerWidth || (de && de.clientWidth) || document.body.clientWidth;
- };
-
- /* When a percentage-based font-size is set on the body, IE returns that percent of the window width as the font-size.
- For example, if the body font-size is 62.5% and the window width is 1000px, IE will return 625px as the font-size.
- When this happens, we calculate the correct body font-size (%) and multiply it by 16 (the standard browser font size)
- to get an accurate em value. */
-
- if (settings.scope == 'body' && $.browser.msie && (parseFloat($('body').css('font-size')) / getWindowWidth()).toFixed(1) > 0.0) {
- var calcFontSize = function(){
- return (parseFloat($('body').css('font-size'))/getWindowWidth()).toFixed(3) * 16;
- };
- scopeVal = calcFontSize();
- }
- else { scopeVal = parseFloat(jQuery(settings.scope).css("font-size")); };
-
- var result = (settings.reverse == true) ? (pxVal * scopeVal).toFixed(2) + 'px' : (pxVal / scopeVal).toFixed(2) + 'em';
- return result;
-};
\ No newline at end of file
diff --git a/vendor/assets/javascripts/history/README.md b/vendor/assets/javascripts/history/README.md
deleted file mode 100644
index 1269bb647..000000000
--- a/vendor/assets/javascripts/history/README.md
+++ /dev/null
@@ -1,4 +0,0 @@
-= Forked version of history.js
-
-This file is being included from a forked version of history.js, specifically a branch that doesn't unencode parameters passed in via URL:
-https://github.com/palexander/history.js/tree/fix_unencoding_of_params
\ No newline at end of file
diff --git a/vendor/assets/javascripts/history/jquery.history.js b/vendor/assets/javascripts/history/jquery.history.js
deleted file mode 100644
index 6bd993b38..000000000
--- a/vendor/assets/javascripts/history/jquery.history.js
+++ /dev/null
@@ -1 +0,0 @@
-window.JSON||(window.JSON={}),function(){"use strict";function f(e){return e<10?"0"+e:e}function quote(e){return escapable.lastIndex=0,escapable.test(e)?'"'+e.replace(escapable,function(e){var t=meta[e];return typeof t=="string"?t:"\\u"+("0000"+e.charCodeAt(0).toString(16)).slice(-4)})+'"':'"'+e+'"'}function str(e,t){var n,r,i,s,o=gap,u,a=t[e];a&&typeof a=="object"&&typeof a.toJSON=="function"&&(a=a.toJSON(e)),typeof rep=="function"&&(a=rep.call(t,e,a));switch(typeof a){case"string":return quote(a);case"number":return isFinite(a)?String(a):"null";case"boolean":case"null":return String(a);case"object":if(!a)return"null";gap+=indent,u=[];if(Object.prototype.toString.apply(a)==="[object Array]"){s=a.length;for(n=0;nFirefox , Safari , Chrome , or Internet Explorer ';
- noticeParagraph.innerHTML=noticeText;
-
- /*------------------------------
- Create and insert hide paragraph
- ------------------------------*/
- hideParagraph = document.createElement('p');
- hideParagraph.id = "ie6-hide-notice";
- noticeDiv.appendChild(hideParagraph);
-
- /*------------------------------
- Create and insert hide link
- ------------------------------*/
- hideLink = document.createElement('a');
- hideLink.setAttribute("href", "#");
- hideParagraph.appendChild(hideLink);
-
- /*------------------------------
- Create and insert hide text
- ------------------------------*/
- hideText = document.createTextNode('Hide this message');
- hideLink.appendChild(hideText);
-
- hideParagraph.onclick = function()
- {
- var today = new Date();
- var expiry = new Date(today.getTime() + 30 * 86400 * 1000);
- document.cookie = name + "=" + "ie6Notice" + "; expires=" + expiry.toGMTString() + "; path=/";
- noticeDiv.style.display="none";
- ie6Css.removeAttribute("href");
- ie6css = null;
- noticeDiv = null;
- return false;
- }
-
-}
-ie6CookieCheck();
diff --git a/vendor/assets/javascripts/jquery.cookie.js b/vendor/assets/javascripts/jquery.cookie.js
deleted file mode 100644
index 927190008..000000000
--- a/vendor/assets/javascripts/jquery.cookie.js
+++ /dev/null
@@ -1,117 +0,0 @@
-/*!
- * jQuery Cookie Plugin v1.4.0
- * https://github.com/carhartl/jquery-cookie
- *
- * Copyright 2013 Klaus Hartl
- * Released under the MIT license
- */
-(function (factory) {
- if (typeof define === 'function' && define.amd) {
- // AMD. Register as anonymous module.
- define(['jquery'], factory);
- } else {
- // Browser globals.
- factory(jQuery);
- }
-}(function ($) {
-
- var pluses = /\+/g;
-
- function encode(s) {
- return config.raw ? s : encodeURIComponent(s);
- }
-
- function decode(s) {
- return config.raw ? s : decodeURIComponent(s);
- }
-
- function stringifyCookieValue(value) {
- return encode(config.json ? JSON.stringify(value) : String(value));
- }
-
- function parseCookieValue(s) {
- if (s.indexOf('"') === 0) {
- // This is a quoted cookie as according to RFC2068, unescape...
- s = s.slice(1, -1).replace(/\\"/g, '"').replace(/\\\\/g, '\\');
- }
-
- try {
- // Replace server-side written pluses with spaces.
- // If we can't decode the cookie, ignore it, it's unusable.
- s = decodeURIComponent(s.replace(pluses, ' '));
- } catch(e) {
- return;
- }
-
- try {
- // If we can't parse the cookie, ignore it, it's unusable.
- return config.json ? JSON.parse(s) : s;
- } catch(e) {}
- }
-
- function read(s, converter) {
- var value = config.raw ? s : parseCookieValue(s);
- return $.isFunction(converter) ? converter(value) : value;
- }
-
- var config = $.cookie = function (key, value, options) {
-
- // Write
- if (value !== undefined && !$.isFunction(value)) {
- options = $.extend({}, config.defaults, options);
-
- if (typeof options.expires === 'number') {
- var days = options.expires, t = options.expires = new Date();
- t.setDate(t.getDate() + days);
- }
-
- return (document.cookie = [
- encode(key), '=', stringifyCookieValue(value),
- options.expires ? '; expires=' + options.expires.toUTCString() : '', // use expires attribute, max-age is not supported by IE
- options.path ? '; path=' + options.path : '',
- options.domain ? '; domain=' + options.domain : '',
- options.secure ? '; secure' : ''
- ].join(''));
- }
-
- // Read
-
- var result = key ? undefined : {};
-
- // To prevent the for loop in the first place assign an empty array
- // in case there are no cookies at all. Also prevents odd result when
- // calling $.cookie().
- var cookies = document.cookie ? document.cookie.split('; ') : [];
-
- for (var i = 0, l = cookies.length; i < l; i++) {
- var parts = cookies[i].split('=');
- var name = decode(parts.shift());
- var cookie = parts.join('=');
-
- if (key && key === name) {
- // If second argument (value) is a function it's a converter...
- result = read(cookie, value);
- break;
- }
-
- // Prevent storing a cookie that we couldn't decode.
- if (!key && (cookie = read(cookie)) !== undefined) {
- result[name] = cookie;
- }
- }
-
- return result;
- };
-
- config.defaults = {};
-
- $.removeCookie = function (key, options) {
- if ($.cookie(key) !== undefined) {
- // Must not alter options, thus extending a fresh object...
- $.cookie(key, '', $.extend({}, options, { expires: -1 }));
- return true;
- }
- return false;
- };
-
-}));
diff --git a/vendor/assets/javascripts/jquery.hoverIntent.js b/vendor/assets/javascripts/jquery.hoverIntent.js
deleted file mode 100644
index e9ebcfc09..000000000
--- a/vendor/assets/javascripts/jquery.hoverIntent.js
+++ /dev/null
@@ -1,107 +0,0 @@
-/**
-* hoverIntent is similar to jQuery's built-in "hover" function except that
-* instead of firing the onMouseOver event immediately, hoverIntent checks
-* to see if the user's mouse has slowed down (beneath the sensitivity
-* threshold) before firing the onMouseOver event.
-*
-* hoverIntent r6 // 2011.02.26 // jQuery 1.5.1+
-*
-*
-* hoverIntent is currently available for use in all personal or commercial
-* projects under both MIT and GPL licenses. This means that you can choose
-* the license that best suits your project, and use it accordingly.
-*
-* // basic usage (just like .hover) receives onMouseOver and onMouseOut functions
-* $("ul li").hoverIntent( showNav , hideNav );
-*
-* // advanced usage receives configuration object only
-* $("ul li").hoverIntent({
-* sensitivity: 7, // number = sensitivity threshold (must be 1 or higher)
-* interval: 100, // number = milliseconds of polling interval
-* over: showNav, // function = onMouseOver callback (required)
-* timeout: 0, // number = milliseconds delay before onMouseOut function call
-* out: hideNav // function = onMouseOut callback (required)
-* });
-*
-* @param f onMouseOver function || An object with configuration options
-* @param g onMouseOut function || Nothing (use configuration options object)
-* @author Brian Cherne
-*/
-(function($) {
- $.fn.hoverIntent = function(f,g) {
- // default configuration options
- var cfg = {
- sensitivity: 7,
- interval: 100,
- timeout: 0
- };
- // override configuration options with user supplied object
- cfg = $.extend(cfg, g ? { over: f, out: g } : f );
-
- // instantiate variables
- // cX, cY = current X and Y position of mouse, updated by mousemove event
- // pX, pY = previous X and Y position of mouse, set by mouseover and polling interval
- var cX, cY, pX, pY;
-
- // A private function for getting mouse position
- var track = function(ev) {
- cX = ev.pageX;
- cY = ev.pageY;
- };
-
- // A private function for comparing current and previous mouse position
- var compare = function(ev,ob) {
- ob.hoverIntent_t = clearTimeout(ob.hoverIntent_t);
- // compare mouse positions to see if they've crossed the threshold
- if ( ( Math.abs(pX-cX) + Math.abs(pY-cY) ) < cfg.sensitivity ) {
- $(ob).unbind("mousemove",track);
- // set hoverIntent state to true (so mouseOut can be called)
- ob.hoverIntent_s = 1;
- return cfg.over.apply(ob,[ev]);
- } else {
- // set previous coordinates for next time
- pX = cX; pY = cY;
- // use self-calling timeout, guarantees intervals are spaced out properly (avoids JavaScript timer bugs)
- ob.hoverIntent_t = setTimeout( function(){compare(ev, ob);} , cfg.interval );
- }
- };
-
- // A private function for delaying the mouseOut function
- var delay = function(ev,ob) {
- ob.hoverIntent_t = clearTimeout(ob.hoverIntent_t);
- ob.hoverIntent_s = 0;
- return cfg.out.apply(ob,[ev]);
- };
-
- // A private function for handling mouse 'hovering'
- var handleHover = function(e) {
- // copy objects to be passed into t (required for event object to be passed in IE)
- var ev = jQuery.extend({},e);
- var ob = this;
-
- // cancel hoverIntent timer if it exists
- if (ob.hoverIntent_t) { ob.hoverIntent_t = clearTimeout(ob.hoverIntent_t); }
-
- // if e.type == "mouseenter"
- if (e.type == "mouseenter") {
- // set "previous" X and Y position based on initial entry point
- pX = ev.pageX; pY = ev.pageY;
- // update "current" X and Y position based on mousemove
- $(ob).bind("mousemove",track);
- // start polling interval (self-calling timeout) to compare mouse coordinates over time
- if (ob.hoverIntent_s != 1) { ob.hoverIntent_t = setTimeout( function(){compare(ev,ob);} , cfg.interval );}
-
- // else e.type == "mouseleave"
- } else {
- // unbind expensive mousemove event
- $(ob).unbind("mousemove",track);
- // if hoverIntent state is true, then call the mouseOut function after the specified delay
- if (ob.hoverIntent_s == 1) { ob.hoverIntent_t = setTimeout( function(){delay(ev,ob);} , cfg.timeout );}
- }
- };
-
- // bind the function to the two event listeners
- return this.bind('mouseenter',handleHover).bind('mouseleave',handleHover);
- };
-})(jQuery);
-
diff --git a/vendor/assets/javascripts/jquery.rating.pack.js b/vendor/assets/javascripts/jquery.rating.pack.js
deleted file mode 100755
index 94c096874..000000000
--- a/vendor/assets/javascripts/jquery.rating.pack.js
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- ### jQuery Star Rating Plugin v3.13 - 2009-03-26 ###
- * Home: http://www.fyneworks.com/jquery/star-rating/
- * Code: http://code.google.com/p/jquery-star-rating-plugin/
- *
- * Dual licensed under the MIT and GPL licenses:
- * http://www.opensource.org/licenses/mit-license.php
- * http://www.gnu.org/licenses/gpl.html
- ###
-*/
-eval(function(p,a,c,k,e,r){e=function(c){return(c35?String.fromCharCode(c+29):c.toString(36))};if(!''.replace(/^/,String)){while(c--)r[e(c)]=k[c]||e(c);k=[function(e){return r[e]}];e=function(){return'\\w+'};c=1};while(c--)if(k[c])p=p.replace(new RegExp('\\b'+e(c)+'\\b','g'),k[c]);return p}(';5(29.1j)(7($){5($.1L.1J)1I{1t.1H("1K",J,H)}1M(e){};$.n.3=7(i){5(4.Q==0)k 4;5(A I[0]==\'1h\'){5(4.Q>1){8 j=I;k 4.W(7(){$.n.3.y($(4),j)})};$.n.3[I[0]].y(4,$.1T(I).1U(1)||[]);k 4};8 i=$.12({},$.n.3.1s,i||{});$.n.3.K++;4.2a(\'.9-3-1f\').o(\'9-3-1f\').W(7(){8 a,l=$(4);8 b=(4.23||\'21-3\').1v(/\\[|\\]/g,\'Z\').1v(/^\\Z+|\\Z+$/g,\'\');8 c=$(4.1X||1t.1W);8 d=c.6(\'3\');5(!d||d.18!=$.n.3.K)d={z:0,18:$.n.3.K};8 e=d[b];5(e)a=e.6(\'3\');5(e&&a)a.z++;x{a=$.12({},i||{},($.1b?l.1b():($.1S?l.6():s))||{},{z:0,F:[],v:[]});a.w=d.z++;e=$(\'<1R V="9-3-1Q"/>\');l.1P(e);e.o(\'3-15-T-17\');5(l.S(\'R\'))a.m=H;e.1c(a.E=$(\'\'+a.1d+\'
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diff --git a/vendor/assets/javascripts/jquery.scrollTo-1.4.0-min.js b/vendor/assets/javascripts/jquery.scrollTo-1.4.0-min.js
deleted file mode 100644
index 453382d24..000000000
--- a/vendor/assets/javascripts/jquery.scrollTo-1.4.0-min.js
+++ /dev/null
@@ -1,11 +0,0 @@
-/**
- * jQuery.ScrollTo - Easy element scrolling using jQuery.
- * Copyright (c) 2007-2008 Ariel Flesler - aflesler(at)gmail(dot)com | http://flesler.blogspot.com
- * Dual licensed under MIT and GPL.
- * Date: 9/11/2008
- * @author Ariel Flesler
- * @version 1.4
- *
- * http://flesler.blogspot.com/2007/10/jqueryscrollto.html
- */
-;(function(h){var m=h.scrollTo=function(b,c,g){h(window).scrollTo(b,c,g)};m.defaults={axis:'y',duration:1};m.window=function(b){return h(window).scrollable()};h.fn.scrollable=function(){return this.map(function(){var b=this.parentWindow||this.defaultView,c=this.nodeName=='#document'?b.frameElement||b:this,g=c.contentDocument||(c.contentWindow||c).document,i=c.setInterval;return c.nodeName=='IFRAME'||i&&h.browser.safari?g.body:i?g.documentElement:this})};h.fn.scrollTo=function(r,j,a){if(typeof j=='object'){a=j;j=0}if(typeof a=='function')a={onAfter:a};a=h.extend({},m.defaults,a);j=j||a.speed||a.duration;a.queue=a.queue&&a.axis.length>1;if(a.queue)j/=2;a.offset=n(a.offset);a.over=n(a.over);return this.scrollable().each(function(){var k=this,o=h(k),d=r,l,e={},p=o.is('html,body');switch(typeof d){case'number':case'string':if(/^([+-]=)?\d+(px)?$/.test(d)){d=n(d);break}d=h(d,this);case'object':if(d.is||d.style)l=(d=h(d)).offset()}h.each(a.axis.split(''),function(b,c){var g=c=='x'?'Left':'Top',i=g.toLowerCase(),f='scroll'+g,s=k[f],t=c=='x'?'Width':'Height',v=t.toLowerCase();if(l){e[f]=l[i]+(p?0:s-o.offset()[i]);if(a.margin){e[f]-=parseInt(d.css('margin'+g))||0;e[f]-=parseInt(d.css('border'+g+'Width'))||0}e[f]+=a.offset[i]||0;if(a.over[i])e[f]+=d[v]()*a.over[i]}else e[f]=d[i];if(/^\d+$/.test(e[f]))e[f]=e[f]<=0?0:Math.min(e[f],u(t));if(!b&&a.queue){if(s!=e[f])q(a.onAfterFirst);delete e[f]}});q(a.onAfter);function q(b){o.animate(e,j,a.easing,b&&function(){b.call(this,r,a)})};function u(b){var c='scroll'+b,g=k.ownerDocument;return p?Math.max(g.documentElement[c],g.body[c]):k[c]}}).end()};function n(b){return typeof b=='object'?b:{top:b,left:b}}})(jQuery);
\ No newline at end of file
diff --git a/vendor/assets/javascripts/jquery.simple.tree.js.erb b/vendor/assets/javascripts/jquery.simple.tree.js.erb
deleted file mode 100755
index 3b134b334..000000000
--- a/vendor/assets/javascripts/jquery.simple.tree.js.erb
+++ /dev/null
@@ -1,468 +0,0 @@
-/*
-* jQuery SimpleTree Drag&Drop plugin
-* Update on 22th May 2008
-* Version 0.3
-*
-* Licensed under BSD
-* Copyright (c) 2008, Peter Panov , IKEEN Group http://www.ikeen.com
-* All rights reserved.
-*
-* Redistribution and use in source and binary forms, with or without
-* modification, are permitted provided that the following conditions are met:
-* * Redistributions of source code must retain the above copyright
-* notice, this list of conditions and the following disclaimer.
-* * Redistributions in binary form must reproduce the above copyright
-* notice, this list of conditions and the following disclaimer in the
-* documentation and/or other materials provided with the distribution.
-* * Neither the name of the Peter Panov, IKEEN Group nor the
-* names of its contributors may be used to endorse or promote products
-* derived from this software without specific prior written permission.
-*
-* THIS SOFTWARE IS PROVIDED BY Peter Panov, IKEEN Group ``AS IS'' AND ANY
-* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-* DISCLAIMED. IN NO EVENT SHALL Peter Panov, IKEEN Group BE LIABLE FOR ANY
-* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-
-$.fn.simpleTree = function(opt){
- return this.each(function(){
- var TREE = this;
- var ROOT = $('.root',this);
- var mousePressed = false;
- var mouseMoved = false;
- var dragMoveType = false;
- var dragNode_destination = false;
- var dragNode_source = false;
- var dragDropTimer = false;
- var ajaxCache = Array();
-
- TREE.option = {
- drag: true,
- animate: false,
- autoclose: false,
- speed: 'fast',
- beforeAjax: false,
- afterAjax: false,
- afterAjaxError: false,
- afterMove: false,
- afterClick: false,
- afterDblClick: false,
- timeout: 999999,
- // added by Erik Dohmen (2BinBusiness.nl) to make context menu cliks available
- afterContextMenu: false,
- docToFolderConvert:false
- };
- TREE.option = $.extend(TREE.option,opt);
- $.extend(this, {getSelected: function(){
- return $('span.active', this).parent();
- }});
- TREE.closeNearby = function(obj)
- {
- $(obj).siblings().filter('.folder-open, .folder-open-last').each(function(){
- var childUl = $('>ul',this);
- var className = this.className;
- this.className = className.replace('open','close');
- if(TREE.option.animate)
- {
- childUl.animate({height:"toggle"},TREE.option.speed);
- }else{
- childUl.hide();
- }
- });
- };
- TREE.nodeToggle = function(obj)
- {
- var childUl = $('>ul',obj);
- if(childUl.is(':visible')){
- obj.className = obj.className.replace('open','close');
-
- if(TREE.option.animate)
- {
- childUl.animate({height:"toggle"},TREE.option.speed);
- }else{
- childUl.hide();
- }
- }else{
- obj.className = obj.className.replace('close','open');
- if(TREE.option.animate)
- {
- childUl.animate({height:"toggle"},TREE.option.speed, function(){
- if(TREE.option.autoclose)TREE.closeNearby(obj);
- if(childUl.is('.ajax'))TREE.setAjaxNodes(childUl, obj.id);
- });
- }else{
- childUl.show();
- if(TREE.option.autoclose)TREE.closeNearby(obj);
- if(childUl.is('.ajax'))TREE.setAjaxNodes(childUl, obj.id);
- }
- }
- };
- TREE.setAjaxNodes = function(node, parentId, successCallback, errorCallback)
- {
- if($.inArray(parentId,ajaxCache) == -1){
- if(typeof TREE.option.beforeAjax == 'function')
- {
- TREE.option.beforeAjax(node);
- }
- var url = $.trim($('a', node).attr("href"));
- if(url)
- {
- $.ajax({
- type: "GET",
- url: url,
- contentType:'text/html',
- cache:false,
- timeout:TREE.option.timeout,
- success: function(response){
- ajaxCache[ajaxCache.length]=parentId;
- node.removeAttr('class');
- node.html(response);
- $.extend(node,{url:url});
- TREE.setTreeNodes(node, true);
- if(typeof TREE.option.afterAjax == 'function')
- {
- TREE.option.afterAjax(node);
- }
- if(typeof successCallback == 'function')
- {
- successCallback(node);
- }
- },
- error: function(response){
- if(typeof TREE.option.afterAjaxError == 'function')
- {
- TREE.option.afterAjaxError(node);
- }
- if(typeof errorCallback == 'function')
- {
- errorCallback(node);
- }
- }
- });
- }
-
- }
- };
- TREE.setTreeNodes = function(obj, useParent){
- obj = useParent? obj.parent():obj;
- $('li>a', obj).addClass('text')
- .bind('selectstart', function() {
- return false;
- }).click(function(){
- $('.active',TREE).attr('class','text');
- if(this.className=='text')
- {
- this.className='active';
- }
- if(typeof TREE.option.afterClick == 'function')
- {
- TREE.option.afterClick($(this).parent());
- }
- return true;
- }).dblclick(function(){
- mousePressed = false;
- TREE.nodeToggle($(this).parent().get(0));
- if(typeof TREE.option.afterDblClick == 'function')
- {
- TREE.option.afterDblClick($(this).parent());
- }
- return false;
- // added by Erik Dohmen (2BinBusiness.nl) to make context menu actions
- // available
- }).bind("contextmenu",function(){
- $('.active',TREE).attr('class','text');
- if(this.className=='text')
- {
- this.className='active';
- }
- if(typeof TREE.option.afterContextMenu == 'function')
- {
- TREE.option.afterContextMenu($(this).parent());
- }
- return false;
- }).mousedown(function(event){
- mousePressed = true;
- cloneNode = $(this).parent().clone();
- var LI = $(this).parent();
- if(TREE.option.drag)
- {
- $('>ul', cloneNode).hide();
- $('body').append('');
- $('#drag_container').hide().css({opacity:'0.8'});
- $('#drag_container >ul').append(cloneNode);
- $(" ')
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-b+'"]';return a}function n(b,a,f){function p(a,b,e){if(f.grouped||!a.length){var g;!1===e||c.isArray(e)?(g=d.messages[b.key||b]||d.messages["*"],g=g[f.lang]||d.messages["*"].en,(b=g.match(/\$\d/g))&&c.isArray(e)&&c.each(b,function(a){g=g.replace(this,e[a])})):g=e[f.lang]||e;a.push(g)}}var e=this,g=a.add(e),b=b.not(":button, :image, :reset, :submit");a.attr("novalidate","novalidate");c.extend(e,{getConf:function(){return f},getForm:function(){return a},getInputs:function(){return b},reflow:function(){b.each(function(){var a=
-c(this),b=a.data("msg.el");b&&(a=i(a,b,f),b.css({top:a.top,left:a.left}))});return e},invalidate:function(a,h){if(!h){var d=[];c.each(a,function(a,f){var c=b.filter("[name='"+a+"']");c.length&&(c.trigger("OI",[f]),d.push({input:c,messages:[f]}))});a=d;h=c.Event()}h.type="onFail";g.trigger(h,[a]);h.isDefaultPrevented()||l[f.effect][0].call(e,a,h);return e},reset:function(a){a=a||b;a.removeClass(f.errorClass).each(function(){var a=c(this).data("msg.el");a&&(a.remove(),c(this).data("msg.el",null))}).off(f.errorInputEvent+
-".v"||"");return e},destroy:function(){a.off(f.formEvent+".V reset.V");b.off(f.inputEvent+".V change.V");return e.reset()},checkValidity:function(a,h){var a=a||b,a=a.not(":disabled"),d={},a=a.filter(function(){var a=c(this).attr("name");if(!d[a])return d[a]=!0,c(this)});if(!a.length)return!0;h=h||c.Event();h.type="onBeforeValidate";g.trigger(h,[a]);if(h.isDefaultPrevented())return h.result;var k=[];a.each(function(){var a=[],b=c(this).data("messages",a),d=m&&b.is(":date")?"onHide.v":f.errorInputEvent+
-".v";b.off(d);c.each(o,function(){var c=this[0];if(b.filter(c).length){var d=this[1].call(e,b,b.val());if(!0!==d){h.type="onBeforeFail";g.trigger(h,[b,c]);if(h.isDefaultPrevented())return!1;var j=b.attr(f.messageAttr);if(j)return a=[j],!1;p(a,c,d)}}});if(a.length&&(k.push({input:b,messages:a}),b.trigger("OI",[a]),f.errorInputEvent))b.on(d,function(a){e.checkValidity(b,a)});if(f.singleError&&k.length)return!1});var i=l[f.effect];if(!i)throw'Validator: cannot find effect "'+f.effect+'"';if(k.length)return e.invalidate(k,
-h),!1;i[1].call(e,a,h);h.type="onSuccess";g.trigger(h,[a]);a.off(f.errorInputEvent+".v");return!0}});c.each(["onBeforeValidate","onBeforeFail","onFail","onSuccess"],function(a,b){if(c.isFunction(f[b]))c(e).on(b,f[b]);e[b]=function(a){if(a)c(e).on(b,a);return e}});if(f.formEvent)a.on(f.formEvent+".V",function(b){if(!e.checkValidity(null,b))return b.preventDefault();b.target=a;b.type=f.formEvent});a.on("reset.V",function(){e.reset()});b[0]&&b[0].validity&&b.each(function(){this.oninvalid=function(){return!1}});
-a[0]&&(a[0].checkValidity=e.checkValidity);if(f.inputEvent)b.on(f.inputEvent+".V",function(a){e.checkValidity(c(this),a)});b.filter(":checkbox, select").filter("[required]").on("change.V",function(a){var b=c(this);(this.checked||b.is("select")&&c(this).val())&&l[f.effect][1].call(e,b,a)});b.filter(":radio[required]").on("change.V",function(a){var b=c("[name='"+c(a.srcElement).attr("name")+"']");b!=null&&b.length!=0&&e.checkValidity(b,a)});c(window).resize(function(){e.reflow()})}c.tools=c.tools||
-{version:"@VERSION"};var r=/\[type=([a-z]+)\]/,s=/^-?[0-9]*(\.[0-9]+)?$/,m=c.tools.dateinput,t=/^([a-z0-9_\.\-\+]+)@([\da-z\.\-]+)\.([a-z\.]{2,6})$/i,u=/^(https?:\/\/)?[\da-z\.\-]+\.[a-z\.]{2,6}[#&+_\?\/\w \.\-=]*$/i,d;d=c.tools.validator={conf:{grouped:!1,effect:"default",errorClass:"invalid",inputEvent:null,errorInputEvent:"keyup",formEvent:"submit",lang:"en",message:"
",messageAttr:"data-message",messageClass:"error",offset:[0,0],position:"center right",singleError:!1,speed:"normal"},messages:{"*":{en:"Please correct this value"}},
-localize:function(b,a){c.each(a,function(a,c){d.messages[a]=d.messages[a]||{};d.messages[a][b]=c})},localizeFn:function(b,a){d.messages[b]=d.messages[b]||{};c.extend(d.messages[b],a)},fn:function(b,a,f){c.isFunction(a)?f=a:("string"==typeof a&&(a={en:a}),this.messages[b.key||b]=a);(a=r.exec(b))&&(b=q(a[1]));o.push([b,f])},addEffect:function(b,a,f){l[b]=[a,f]}};var o=[],l={"default":[function(b){var a=this.getConf();c.each(b,function(b,d){var e=d.input;e.addClass(a.errorClass);var g=e.data("msg.el");
-g||(g=c(a.message).addClass(a.messageClass).appendTo(document.body),e.data("msg.el",g));g.css({visibility:"hidden"}).find("p").remove();c.each(d.messages,function(a,b){c("
").html(b).appendTo(g)});g.outerWidth()==g.parent().width()&&g.add(g.find("p")).css({display:"inline"});e=i(e,g,a);g.css({visibility:"visible",position:"absolute",top:e.top,left:e.left}).fadeIn(a.speed)})},function(b){var a=this.getConf();b.removeClass(a.errorClass).each(function(){var a=c(this).data("msg.el");a&&a.css({visibility:"hidden"})})}]};
-c.each(["email","url","number"],function(b,a){c.expr[":"][a]=function(b){return b.getAttribute("type")===a}});c.fn.oninvalid=function(b){return this[b?"on":"trigger"]("OI",b)};d.fn(":email","Please enter a valid email address",function(b,a){return!a||t.test(a)});d.fn(":url","Please enter a valid URL",function(b,a){return!a||u.test(a)});d.fn(":number","Please enter a numeric value.",function(b,a){return s.test(a)});d.fn("[max]","Please enter a value no larger than $1",function(b,a){if(""===a||m&&b.is(":date"))return!0;
-var c=b.attr("max");return parseFloat(a)<=parseFloat(c)?!0:[c]});d.fn("[min]","Please enter a value of at least $1",function(b,a){if(""===a||m&&b.is(":date"))return!0;var c=b.attr("min");return parseFloat(a)>=parseFloat(c)?!0:[c]});d.fn("[required]","Please complete this mandatory field.",function(b,a){return b.is(":checkbox")?b.is(":checked"):!!a});d.fn("[pattern]",function(b,a){return""===a||RegExp("^"+b.attr("pattern")+"$").test(a)});d.fn(":radio","Please select an option.",function(b){var a=!1;
-c("[name='"+b.attr("name")+"']").each(function(b,d){c(d).is(":checked")&&(a=!0)});return a?!0:!1});c.fn.validator=function(b){var a=this.data("validator");a&&(a.destroy(),this.removeData("validator"));b=c.extend(!0,{},d.conf,b);if(this.is("form"))return this.each(function(){var d=c(this);a=new n(d.find(":input"),d,b);d.data("validator",a)});a=new n(this,this.eq(0).closest("form"),b);return this.data("validator",a)}})(jQuery);
diff --git a/vendor/assets/javascripts/jquery.tooltip.js b/vendor/assets/javascripts/jquery.tooltip.js
deleted file mode 100644
index 63b715f15..000000000
--- a/vendor/assets/javascripts/jquery.tooltip.js
+++ /dev/null
@@ -1,294 +0,0 @@
-/*
- * jQuery Tooltip plugin 1.3
- *
- * http://bassistance.de/jquery-plugins/jquery-plugin-tooltip/
- * http://docs.jquery.com/Plugins/Tooltip
- *
- * Copyright (c) 2006 - 2008 Jörn Zaefferer
- *
- * $Id: jquery.tooltip.js 5741 2008-06-21 15:22:16Z joern.zaefferer $
- *
- * Dual licensed under the MIT and GPL licenses:
- * http://www.opensource.org/licenses/mit-license.php
- * http://www.gnu.org/licenses/gpl.html
- */
-
-;(function($) {
-
- // the tooltip element
- var helper = {},
- // the current tooltipped element
- current,
- // the title of the current element, used for restoring
- title,
- // timeout id for delayed tooltips
- tID,
- // IE 5.5 or 6
- IE = $.browser.msie && /MSIE\s(5\.5|6\.)/.test(navigator.userAgent),
- // flag for mouse tracking
- track = false;
-
- $.tooltip = {
- blocked: false,
- defaults: {
- delay: 200,
- fade: false,
- showURL: true,
- extraClass: "",
- top: 15,
- left: 15,
- id: "tooltip"
- },
- block: function() {
- $.tooltip.blocked = !$.tooltip.blocked;
- }
- };
-
- $.fn.extend({
- tooltip: function(settings) {
- settings = $.extend({}, $.tooltip.defaults, settings);
- createHelper(settings);
- return this.each(function() {
- $.data(this, "tooltip", settings);
- this.tOpacity = helper.parent.css("opacity");
- // copy tooltip into its own expando and remove the title
- this.tooltipText = this.title;
- $(this).removeAttr("title");
- // also remove alt attribute to prevent default tooltip in IE
- this.alt = "";
- })
- .mouseover(save)
- .mouseout(hide)
- .click(hide);
- },
- fixPNG: IE ? function() {
- return this.each(function () {
- var image = $(this).css('backgroundImage');
- if (image.match(/^url\(["']?(.*\.png)["']?\)$/i)) {
- image = RegExp.$1;
- $(this).css({
- 'backgroundImage': 'none',
- 'filter': "progid:DXImageTransform.Microsoft.AlphaImageLoader(enabled=true, sizingMethod=crop, src='" + image + "')"
- }).each(function () {
- var position = $(this).css('position');
- if (position != 'absolute' && position != 'relative')
- $(this).css('position', 'relative');
- });
- }
- });
- } : function() { return this; },
- unfixPNG: IE ? function() {
- return this.each(function () {
- $(this).css({'filter': '', backgroundImage: ''});
- });
- } : function() { return this; },
- hideWhenEmpty: function() {
- return this.each(function() {
- $(this)[ $(this).html() ? "show" : "hide" ]();
- });
- },
- url: function() {
- return this.attr('href') || this.attr('src');
- }
- });
-
- function createHelper(settings) {
- // there can be only one tooltip helper
- if( helper.parent )
- return;
- // create the helper, h3 for title, div for url
- helper.parent = $('')
- // add to document
- .appendTo(document.body)
- // hide it at first
- .hide();
-
- // apply bgiframe if available
- if ( $.fn.bgiframe )
- helper.parent.bgiframe();
-
- // save references to title and url elements
- helper.title = $('h3', helper.parent);
- helper.body = $('div.body', helper.parent);
- helper.url = $('div.url', helper.parent);
- }
-
- function settings(element) {
- return $.data(element, "tooltip");
- }
-
- // main event handler to start showing tooltips
- function handle(event) {
- // show helper, either with timeout or on instant
- if( settings(this).delay )
- tID = setTimeout(show, settings(this).delay);
- else
- show();
-
- // if selected, update the helper position when the mouse moves
- track = !!settings(this).track;
- $(document.body).bind('mousemove', update);
-
- // update at least once
- update(event);
- }
-
- // save elements title before the tooltip is displayed
- function save() {
- // if this is the current source, or it has no title (occurs with click event), stop
- if ( $.tooltip.blocked || this == current || (!this.tooltipText && !settings(this).bodyHandler) )
- return;
-
- // save current
- current = this;
- title = this.tooltipText;
-
- if ( settings(this).bodyHandler ) {
- helper.title.hide();
- var bodyContent = settings(this).bodyHandler.call(this);
- if (bodyContent.nodeType || bodyContent.jquery) {
- helper.body.empty().append(bodyContent)
- } else {
- helper.body.html( bodyContent );
- }
- helper.body.show();
- } else if ( settings(this).showBody ) {
- var parts = title.split(settings(this).showBody);
- helper.title.html(parts.shift()).show();
- helper.body.empty();
- for(var i = 0, part; (part = parts[i]); i++) {
- if(i > 0)
- helper.body.append("
");
- $("#TB_overlay").click(tb_remove);
- }
- }else{//all others
- if(document.getElementById("TB_overlay") === null){
- $("body").append("
");
- $("#TB_overlay").click(tb_remove);
- }
- }
-
- if(tb_detectMacXFF()){
- $("#TB_overlay").addClass("TB_overlayMacFFBGHack");//use png overlay so hide flash
- }else{
- $("#TB_overlay").addClass("TB_overlayBG");//use background and opacity
- }
-
- if(caption===null){caption="";}
- $("body").append("");//add loader to the page
- $('#TB_load').show();//show loader
-
- var baseURL;
- if(url.indexOf("?")!==-1){ //ff there is a query string involved
- baseURL = url.substr(0, url.indexOf("?"));
- }else{
- baseURL = url;
- }
-
- var urlString = /\.jpg$|\.jpeg$|\.png$|\.gif$|\.bmp$/;
- var urlType = baseURL.toLowerCase().match(urlString);
-
- if(urlType == '.jpg' || urlType == '.jpeg' || urlType == '.png' || urlType == '.gif' || urlType == '.bmp'){//code to show images
-
- TB_PrevCaption = "";
- TB_PrevURL = "";
- TB_PrevHTML = "";
- TB_NextCaption = "";
- TB_NextURL = "";
- TB_NextHTML = "";
- TB_imageCount = "";
- TB_FoundURL = false;
- if(imageGroup){
- TB_TempArray = $("a[@rel="+imageGroup+"]").get();
- for (TB_Counter = 0; ((TB_Counter < TB_TempArray.length) && (TB_NextHTML === "")); TB_Counter++) {
- var urlTypeTemp = TB_TempArray[TB_Counter].href.toLowerCase().match(urlString);
- if (!(TB_TempArray[TB_Counter].href == url)) {
- if (TB_FoundURL) {
- TB_NextCaption = TB_TempArray[TB_Counter].title;
- TB_NextURL = TB_TempArray[TB_Counter].href;
- TB_NextHTML = " Next > ";
- } else {
- TB_PrevCaption = TB_TempArray[TB_Counter].title;
- TB_PrevURL = TB_TempArray[TB_Counter].href;
- TB_PrevHTML = " < Prev ";
- }
- } else {
- TB_FoundURL = true;
- TB_imageCount = "Image " + (TB_Counter + 1) +" of "+ (TB_TempArray.length);
- }
- }
- }
-
- imgPreloader = new Image();
- imgPreloader.onload = function(){
- imgPreloader.onload = null;
-
- // Resizing large images - orginal by Christian Montoya edited by me.
- var pagesize = tb_getPageSize();
- var x = pagesize[0] - 150;
- var y = pagesize[1] - 150;
- var imageWidth = imgPreloader.width;
- var imageHeight = imgPreloader.height;
- if (imageWidth > x) {
- imageHeight = imageHeight * (x / imageWidth);
- imageWidth = x;
- if (imageHeight > y) {
- imageWidth = imageWidth * (y / imageHeight);
- imageHeight = y;
- }
- } else if (imageHeight > y) {
- imageWidth = imageWidth * (y / imageHeight);
- imageHeight = y;
- if (imageWidth > x) {
- imageHeight = imageHeight * (x / imageWidth);
- imageWidth = x;
- }
- }
- // End Resizing
-
- TB_WIDTH = imageWidth + 30;
- TB_HEIGHT = imageHeight + 60;
- $("#TB_window").append(""+caption+"
" + TB_imageCount + TB_PrevHTML + TB_NextHTML + "
");
- tb_show(TB_PrevCaption, TB_PrevURL, imageGroup);
- return false;
- }
- $("#TB_prev").click(goPrev);
- }
-
- if (!(TB_NextHTML === "")) {
- function goNext(){
- $("#TB_window").remove();
- $("body").append("
");
- tb_show(TB_NextCaption, TB_NextURL, imageGroup);
- return false;
- }
- $("#TB_next").click(goNext);
-
- }
-
- document.onkeydown = function(e){
- if (e == null) { // ie
- keycode = event.keyCode;
- } else { // mozilla
- keycode = e.which;
- }
- if(keycode == 27){ // close
- tb_remove();
- } else if(keycode == 190){ // display previous image
- if(!(TB_NextHTML == "")){
- document.onkeydown = "";
- goNext();
- }
- } else if(keycode == 188){ // display next image
- if(!(TB_PrevHTML == "")){
- document.onkeydown = "";
- goPrev();
- }
- }
- };
-
- tb_position();
- $("#TB_load").remove();
- $("#TB_ImageOff").click(tb_remove);
- $("#TB_window").css({display:"block"}); //for safari using css instead of show
- };
-
- imgPreloader.src = url;
- }else{//code to show html
-
- var queryString = url.replace(/^[^\?]+\??/,'');
- var params = tb_parseQuery( queryString );
-
- TB_WIDTH = (params['width']*1) + 30 || 630; //defaults to 630 if no paramaters were added to URL
- TB_HEIGHT = (params['height']*1) + 40 || 440; //defaults to 440 if no paramaters were added to URL
- ajaxContentW = TB_WIDTH - 30;
- ajaxContentH = TB_HEIGHT - 45;
-
- if(url.indexOf('TB_iframe') != -1){// either iframe or ajax window
- urlNoQuery = url.split('TB_');
- $("#TB_iframeContent").remove();
- if(params['modal'] != "true"){//iframe no modal
- $("#TB_window").append("");
- }else{//iframe modal
- $("#TB_overlay").unbind();
- $("#TB_window").append("");
- }
- }else{// not an iframe, ajax
- if($("#TB_window").css("display") != "block"){
- if(params['modal'] != "true"){//ajax no modal
- $("#TB_window").append("
");
- }else{//ajax modal
- $("#TB_overlay").unbind();
- $("#TB_window").append("
");
- }
- }else{//this means the window is already up, we are just loading new content via ajax
- $("#TB_ajaxContent")[0].style.width = ajaxContentW +"px";
- $("#TB_ajaxContent")[0].style.height = ajaxContentH +"px";
- $("#TB_ajaxContent")[0].scrollTop = 0;
- $("#TB_ajaxWindowTitle").html(caption);
- }
- }
-
- $("#TB_closeWindowButton").click(tb_remove);
-
- if(url.indexOf('TB_inline') != -1){
- $("#TB_ajaxContent").append($('#' + params['inlineId']).children());
- $("#TB_window").unload(function () {
- $('#' + params['inlineId']).append( $("#TB_ajaxContent").children() ); // move elements back when you're finished
- });
- tb_position();
- $("#TB_load").remove();
- $("#TB_window").css({display:"block"});
- }else if(url.indexOf('TB_iframe') != -1){
- tb_position();
- if($.browser.safari){//safari needs help because it will not fire iframe onload
- $("#TB_load").remove();
- $("#TB_window").css({display:"block"});
- }
- }else{
- $("#TB_ajaxContent").load(url += "&random=" + (new Date().getTime()),function(){//to do a post change this load method
- tb_position();
- $("#TB_load").remove();
- tb_init("#TB_ajaxContent a.thickbox");
- $("#TB_window").css({display:"block"});
- });
- }
-
- }
-
- if(!params['modal']){
- document.onkeyup = function(e){
- if (e == null) { // ie
- keycode = event.keyCode;
- } else { // mozilla
- keycode = e.which;
- }
- if(keycode == 27){ // close
- tb_remove();
- }
- };
- }
-
- } catch(e) {
- //nothing here
- }
-}
-
-//helper functions below
-function tb_showIframe(){
- $("#TB_load").remove();
- $("#TB_window").css({display:"block"});
-}
-
-function tb_remove() {
- $("#TB_imageOff").unbind("click");
- $("#TB_closeWindowButton").unbind("click");
- $("#TB_window").fadeOut("fast",function(){$('#TB_window,#TB_overlay,#TB_HideSelect').trigger("unload").unbind().remove();});
- $("#TB_load").remove();
- if (typeof document.body.style.maxHeight == "undefined") {//if IE 6
- $("body","html").css({height: "auto", width: "auto"});
- $("html").css("overflow","");
- }
- document.onkeydown = "";
- document.onkeyup = "";
- return false;
-}
-
-function tb_position() {
-$("#TB_window").css({marginLeft: '-' + parseInt((TB_WIDTH / 2),10) + 'px', width: TB_WIDTH + 'px'});
- if ( !(jQuery.browser.msie && jQuery.browser.version < 7)) { // take away IE6
- $("#TB_window").css({marginTop: '-' + parseInt((TB_HEIGHT / 2),10) + 'px'});
- }
-}
-
-function tb_parseQuery ( query ) {
- var Params = {};
- if ( ! query ) {return Params;}// return empty object
- var Pairs = query.split(/[;&]/);
- for ( var i = 0; i < Pairs.length; i++ ) {
- var KeyVal = Pairs[i].split('=');
- if ( ! KeyVal || KeyVal.length != 2 ) {continue;}
- var key = unescape( KeyVal[0] );
- var val = unescape( KeyVal[1] );
- val = val.replace(/\+/g, ' ');
- Params[key] = val;
- }
- return Params;
-}
-
-function tb_getPageSize(){
- var de = document.documentElement;
- var w = window.innerWidth || self.innerWidth || (de&&de.clientWidth) || document.body.clientWidth;
- var h = window.innerHeight || self.innerHeight || (de&&de.clientHeight) || document.body.clientHeight;
- arrayPageSize = [w,h];
- return arrayPageSize;
-}
-
-function tb_detectMacXFF() {
- var userAgent = navigator.userAgent.toLowerCase();
- if (userAgent.indexOf('mac') != -1 && userAgent.indexOf('firefox')!=-1) {
- return true;
- }
-}
-
-
');
- YAHOO.tabwait.container.wait.render(document.body);
-
-
-
-}
-
-
-
-function buildSearchWait(){
- YAHOO.namespace("wait.container");
- // Initialize the temporary Panel to display while waiting for external content to load
- YAHOO.wait.container.wait = new YAHOO.widget.Panel("wait",
- { width:"240px",
- fixedcenter:true,
- close:false,
- draggable:false,
- zindex:4,
- modal:true,
- visible:false
- }
- );
-
- YAHOO.wait.container.wait.setHeader("Searching, please wait...");
- YAHOO.wait.container.wait.setBody('
');
- var trigger = $('>.trigger', node);
- trigger.click(function(event){
- obj.nodeToggle(node);
- });
- // TODO: $.browser was removed in jQuery 1.9, check IE compatability
- // if (!$.browser.msie) {
- // trigger.css('float','left');
- // }
- };
-
- this.determineHTTPS = function(url) {
- if (typeof url === 'undefined') { return url; }
- return url.replace("http:", ('https:' == document.location.protocol ? 'https:' : 'http:'));
- }
-
- // Populate roots and init tree
- this.init = function() {
- ROOT.html($("
");
- jQuery.ajax({
- url: jQuery(event.target).attr('href'),
- context: result,
- success: function (data) {
- this.html(data);
- this.simpleTreeCollection.get(0).setTreeNodes(this);
- },
- error: function () {
- this.html("
')
+ jQuery.ajax({
+ url: jQuery(event.target).attr('href'),
+ context: result,
+ success: function (data) {
+ this.html(data)
+ this.simpleTreeCollection.get(0).setTreeNodes(this)
+ },
+ error: function () {
+ this.html('