Merge pull request #245 from CBIIT/develop_3.1.3

Develop 3.1.3

Author: fmanuelos

server/components/elasticsearch.js

@@ -209,9 +209,9 @@ const helper_gdc = (fileJson, syns) => {
       });
     }
 
-    if (entry.deprecated_enum) {
-      values = _.differenceWith(values, entry.deprecated_enum, _.isEqual);
-    }
+    // if (entry.deprecated_enum) {
+    //   values = _.differenceWith(values, entry.deprecated_enum, _.isEqual);
+    // }
 
     //generate p.enum
     if(values.length > 0){

server/config/swagger.js

@@ -201,7 +201,7 @@ module.exports = function (protocol, host, basePath) {
             200: {
               description: 'Success.',
               schema: {
-                $ref: '#/definitions/ESDictResults',
+                $ref: '#/definitions/DictResults',
               },
             },
             404: {
@@ -258,7 +258,7 @@ module.exports = function (protocol, host, basePath) {
             200: {
               description: 'Success.',
               schema: {
-                $ref: '#/definitions/ESDictResults',
+                $ref: '#/definitions/DictResults',
               },
             },
             404: {
@@ -322,7 +322,7 @@ module.exports = function (protocol, host, basePath) {
             200: {
               description: 'Success.',
               schema: {
-                $ref: '#/definitions/ESDictPropertiesResults',
+                $ref: '#/definitions/DictPropertiesResults',
               },
             },
             404: {
@@ -575,7 +575,7 @@ module.exports = function (protocol, host, basePath) {
           name: 'ESSearchResults',
         },
       },
-      ESDictResults: {
+      DictResults: {
         type: 'object',
         properties: {
           status: {
@@ -659,10 +659,10 @@ module.exports = function (protocol, host, basePath) {
           },
         },
         xml: {
-          name: 'ESDictResults',
+          name: 'DictResults',
         },
       },
-      ESDictPropertiesResults: {
+      DictPropertiesResults: {
         type: 'object',
         properties: {
           status: {
@@ -701,9 +701,9 @@ module.exports = function (protocol, host, basePath) {
           },
         },
         xml: {
-          name: 'ESDictPropertiesResults',
+          name: 'DictPropertiesResults',
         },
-      }, // end for ESDictPropertiesResults
+      }, // end for DictPropertiesResults
     }, // description:
   } // return
 } // end for the function

server/data_files/GDC/gdc_props.js

@@ -0,0 +1,258 @@
+id: _definitions
+
+uuid:
+  $ref: "_terms.yaml#/uuid"
+  type: string
+  pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"
+  systemAlias: node_id
+
+parent_uuids:
+  type: array
+  minItems: 1
+  items:
+    $ref: "#/uuid"
+  uniqueItems: true
+
+foreign_key_project:
+  type: object
+  # Allow true here because we can have other unique keys defined on
+  # a target type
+  additionalProperties: True
+  # Can either use 'id' which are GDC IDs (uuid) or 'submitter_id'
+  # which are user defined IDs ("submitter IDs in the backend")
+  properties:
+    id:
+      $ref: "#/uuid"
+    submitter_id:
+      type: string
+
+to_one_project:
+  anyOf:
+    - type: array
+      items:
+        $ref: "#/foreign_key_project"
+        minItems: 1
+        maxItems: 1
+    - $ref: "#/foreign_key_project"
+
+to_many_project:
+  anyOf:
+    - type: array
+      items:
+        $ref: "#/foreign_key_project"
+        minItems: 1
+    - $ref: "#/foreign_key_project"
+
+foreign_key:
+  type: object
+  # Allow true here because we can have other unique keys defined on
+  # a target type
+  additionalProperties: True
+  # Can either use 'id' which are GDC IDs (uuid) or 'submitter_id'
+  # which are user defined IDs ("submitter IDs in the backend")
+  properties:
+    id:
+      $ref: "#/uuid"
+    submitter_id:
+      type: string
+
+to_one:
+  anyOf:
+    - type: array
+      items:
+        $ref: "#/foreign_key"
+        minItems: 1
+        maxItems: 1
+    - $ref: "#/foreign_key"
+
+to_many:
+  anyOf:
+    - type: array
+      items:
+        $ref: "#/foreign_key"
+        minItems: 1
+    - $ref: "#/foreign_key"
+
+datetime:
+  $ref: "_terms.yaml#/datetime"
+  oneOf:
+    - type: string
+      format: date-time
+    - type: 'null'
+
+file_name:
+  $ref: "_terms.yaml#/file_name"
+  type: string
+
+file_size:
+  $ref: "_terms.yaml#/file_size"
+  type: integer
+
+file_format:
+  $ref: "_terms.yaml#/file_format"
+  type: string
+
+md5sum:
+  $ref: "_terms.yaml#/md5sum"
+  type: string
+  pattern: "^[a-f0-9]{32}$"
+
+release_state:
+  description: >-
+    Release state of an entity.
+  default: unreleased
+  enum:
+    - unreleased
+    - released
+    - redacted
+
+data_bundle_state:
+  description:  >-
+    State of a data bundle.
+  default: submitted
+  enum:
+    - submitted
+    - validated
+    - error
+    - released
+    - suppressed
+    - redacted
+
+data_file_error_type:
+  $ref: "_terms.yaml#/data_file_error_type"
+  enum:
+    - file_size
+    - file_format
+    - md5sum
+
+state:
+  $ref: "_terms.yaml#/state"
+  default: validated
+  downloadable:
+    - uploaded
+    - md5summed
+    - validating
+    - validated
+    - error
+    - invalid
+    - released
+  public:
+    - live
+  oneOf:
+    - enum: #This list covers legacy data
+      - uploading
+      - uploaded
+      - md5summing
+      - md5summed
+      - validating
+      - error
+      - invalid
+      - suppressed
+      - redacted
+      - live
+    - enum: #This list covers all future data 1/15/16
+      - validated
+      - submitted
+      - released
+
+file_state:
+  $ref: "_terms.yaml#/file_state"
+  default: registered
+  enum:
+    - registered
+    - uploading
+    - uploaded
+    - validating
+    - validated
+    - submitted
+    - processing
+    - processed
+    - released
+    - error
+    - deleted
+
+qc_metrics_state:
+  $ref: "_terms.yaml#/qc_metric_state"
+  enum:
+    - FAIL
+    - PASS
+    - WARN
+    - Unknown
+    - Not Reported
+
+project_id:
+  $ref: "_terms.yaml#/project_id"
+  type: string
+
+data_file_properties:
+  $ref: "#/ubiquitous_properties"
+
+  file_name:
+    $ref: "#/file_name"
+
+  file_size:
+    $ref: "#/file_size"
+
+  md5sum:
+    $ref: "#/md5sum"
+
+  file_state:
+    $ref: "#/file_state"
+
+  error_type:
+    $ref: "#/data_file_error_type"
+
+  state_comment:
+    description: >-
+      Optional comment about why the file is in the current state, mainly for invalid state.
+    type: string
+
+workflow_properties:
+  $ref: "#/ubiquitous_properties"
+
+  workflow_link:
+    description: >-
+      Link to Github hash for the CWL workflow used.
+    type: string
+
+  workflow_version:
+    description: >-
+      Major version for a GDC workflow.
+    type: string
+
+  workflow_start_datetime:
+    $ref: "#/datetime"
+
+  workflow_end_datetime:
+    $ref: "#/datetime"
+
+ubiquitous_properties:
+  type:
+    type: string
+
+  id:
+    $ref: "#/uuid"
+
+  submitter_id:
+    description: >-
+      A project-specific identifier for a node. This property is the calling card/nickname/alias
+      for a unit of submission. It can be used in place of the uuid for identifying
+      or recalling a node.
+    type: string
+
+  batch_id:
+    description: >-
+      GDC submission batch indicator. It is unique within the context of a project.
+    type: integer
+
+  state:
+    $ref: "#/state"
+
+  project_id:
+    $ref: "#/project_id"
+
+  created_datetime:
+    $ref: "#/datetime"
+
+  updated_datetime:
+    $ref: "#/datetime"