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Merge branch 'master' into rails51-with-asset-pipeline-and-jquery-in-gems
2 parents 871ad4c + c7f98a8 commit 7a4b07e

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-251
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Diff for: ‎.yardopts

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--markup 'markdown'
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--private
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--protected
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--tag postconditions:"Postconditions"
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--type-name-tag constant:"Constants this method uses"
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--type-name-tag used_instance_variable:"Instance variables this method uses before setting"
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--type-name-tag changed_instance_variable:"Instance variables set by this method"
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--type-name-tag changed_instance_variable:"Instance variables set (or altered) by this method"
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--tag calls:"Calls"
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--tag callers:"Called by"
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--tag side_effect:"Side effects"

Diff for: ‎.zenodo.json

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{
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"metadata": {
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"access_right": "open",
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"creators": [{
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"affiliation": "University of Illinois",
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"name": "Scott Rohde"
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},
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{
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"name": "Carl Crott"
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},
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{
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"affiliation": "University of Illinois",
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"name": "David LeBauer"
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},
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{
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"name": "Patrick Mulrooney"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Rob Kooper"
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},
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{
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"name": "Jeremy Kemball"
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},
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{
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"name": "Jimmy Chen"
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},
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{
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"name": "Andrew Shirk"
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},
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{
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"name": "Zhengqi Yang"
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},
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{
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"affiliation": "National Center for Supercomputing Applications",
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"name": "Max Burnette"
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},
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{
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"name": "Haotian Jiang"
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},
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{
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"name": "Yilin Dong"
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},
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{
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"name": "Uday Saraf"
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},
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{
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"affiliation": "Boston University",
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"name": "Michael Dietze"
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},
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{
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"name": "Chris Black"
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}
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],
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"language": "eng",
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"license": {
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"id": "NCSA"
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},
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"references": [
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"LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second\u2010generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71",
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"LeBauer, David, Michael Dietze, Rob Kooper, Steven Long, Patrick Mulrooney, Gareth Scott Rohde, Dan Wang (2010). Biofuel Ecophysiological Traits and Yields Database (BETYdb), Energy Biosciences Institute, University of Illinois at Urbana-Champaign. doi:10.13012/J8H41PB9"
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],
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"notes": "Development of BETYdb is supported by the National Science Foundation (ABI #1062547, ABI #1458021), the Department of Energy (ARPA-E awards #DE-AR0000594 and DE-AR0000598), and the Energy Biosciences Institute.",
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"resource_type": {
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"title": "Software",
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"type": "software"
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}
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}
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}

Diff for: ‎Gemfile

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@@ -11,7 +11,7 @@ gem "json"
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gem "rgeo", "~> 0.5.0"
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gem "multi_json"
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gem "railroad", "0.5.0"
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gem "recaptcha", "0.3.4", :require => "recaptcha/rails"
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gem "recaptcha", "4.8.0", :require => "recaptcha/rails"
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gem "ruby-graphviz", "1.0.8"
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gem "safe_attributes"
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gem "seer", "0.10.0"

Diff for: ‎Gemfile.lock

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rb-fsevent (0.10.3)
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rb-inotify (0.9.10)
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ffi (>= 0.5.0, < 2)
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recaptcha (0.3.4)
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rgeo (0.5.0)
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recaptcha (4.8.0)
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json
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rgeo (0.5.3)
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rgeo-activerecord (5.1.1)
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activerecord (~> 5.0)
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rgeo (~> 0.3)
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rails (= 5.1.5)
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rails-controller-testing
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rails3-restful-authentication (~> 3.0.1)
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recaptcha (= 0.3.4)
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recaptcha (= 4.8.0)
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rgeo (~> 0.5.0)
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rspec-rails (~> 3.0)
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rspec_api_documentation

Diff for: ‎README.md

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[![DOI](https://zenodo.org/badge/4469/PecanProject/bety.svg)](https://zenodo.org/badge/latestdoi/4469/PecanProject/bety)
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[![Build Status](https://travis-ci.org/PecanProject/bety.svg?branch=master)](https://travis-ci.org/PecanProject/bety)[![Join the chat at https://gitter.im/PecanProject/bety](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/PecanProject/bety?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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[![Build Status](https://travis-ci.org/PecanProject/bety.svg?branch=master)](https://travis-ci.org/PecanProject/bety)
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[![Slack](https://img.shields.io/badge/slack-login-brightgreen.svg)](https://pecanproject.slack.com/)
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[![Slack](https://img.shields.io/badge/slack-join_chat-brightgreen.svg)](https://publicslack.com/slacks/pecanproject/invites/new)
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This is the source code for the [Biofuel Ecophysiological Traits and Yields database (BETYdb)](http://www.betydb.org)
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Diff for: ‎app/assets/javascripts/lazy/bulk_upload.js

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jQuery('#global_values_citation_id').val(ui.item.value);
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});
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jQuery("form").submit(function(event, ui) {
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var allowSubmission = true;
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for (autocompletion_widget_id in bu_completion_fields) {
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allowSubmission = allowSubmission && bu_completion_fields[autocompletion_widget_id]["valid"];
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}
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return allowSubmission;
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});
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for (autocompletion_widget_id in bu_completion_fields) {
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jQuery('#' + autocompletion_widget_id).autocomplete({
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minLength: 0,
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source: ROOT_URL + "/methods/bu_autocomplete.json",
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select: create_select_function(autocompletion_widget_id),
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focus: function(event, ui) {
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// Prevent the value (the id number) of an item selected from
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// displaying when using the arrow keys:
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event.preventDefault();
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},
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change: create_change_function(autocompletion_widget_id)
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});
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jQuery('#' + autocompletion_widget_id).click(create_click_function(autocompletion_widget_id));
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}
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});
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function create_select_function(autocompletion_widget_id) {
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return function(event, ui) {
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// Prevent the value (the id number) of the item selected from
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// displaying after a selection has been made ...
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event.preventDefault();
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// ... and display the *label* of the item selected instead ...
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var display = ui.item.label;
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// ... unless it's "[no value]"; then just display the placeholder.
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if (ui.item.label == "[no value]") {
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display = "";
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}
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jQuery(this).val(display);
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// Clear the error message if present:
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jQuery('label[for = "' + autocompletion_widget_id + '"] span.error').hide();
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// Save the selected values in the session, both for making
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// values "sticky" and for use by subsequent pages of the
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// wizard:
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jQuery.post(ROOT_URL + "/bulk_upload/store_trait_method_mapping_in_session",
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{
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"trait_name": event.target.id,
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"method_info": {
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"label": display,
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"value": ui.item.value
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}
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});
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}
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}
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function create_change_function(autocompletion_widget_id) {
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return function(event, ui) {
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var validValue = (ui.item != null && ui.item.label != null);
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if (validValue) {
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jQuery('label[for = "' + autocompletion_widget_id + '"] span.error').hide();
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}
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else {
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jQuery('label[for = "' + autocompletion_widget_id + '"] span.error').show();
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jQuery(this).select();
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}
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bu_completion_fields[autocompletion_widget_id]["valid"] = validValue;
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}
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}
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function create_click_function(autocompletion_widget_id) {
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return function(event, ui) {
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jQuery('#' + autocompletion_widget_id).select();
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jQuery('#' + autocompletion_widget_id).autocomplete("search");
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}
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}

Diff for: ‎app/controllers/application_controller.rb

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redirect_back(fallback_location: root_path)
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end
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# Given a model class, a list of columns (attributes) of the model, and a
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# search term, search the database table corresponding to the model and return
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# objects for all rows that contain the text of the search term in any of the
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# text of any of the given columns.
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# Given a model class, a list of columns (attributes) of the model,
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# and a search term, search the database table corresponding to the
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# model and return objects for all rows that contain the text of the
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# search term in the text of at least one of the given columns. If
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# the search string has fewer than two characters and no matches are
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# found, or if +column_list+ is empty, return objects for _all_
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# rows.
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#
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# @param model_class [#where, #scoped] Typically this will be either a
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# subclass of {ActiveRecord::Base} (e.g. {Citation}) or and instance of
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# {ActiveRecord::Relation} (e.g. {Citation.order('author')}).
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# @param column_list [Array<String>] An array of names of columns in the table
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# corresponding to `model_class`.
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# @param search_term [String]
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#
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# @return [ActiveRecord::Relation] This acts like an Array whose members are
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# instances of the model associated with `model_class`.
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def search_model(model_class, column_list, search_term)
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where_clause = clauses.join(" OR ")
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# If the user has only typed one letter, just return everything so the
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# user can at least see some possible options.
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result_set = model_class.scoped
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else
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# Otherwise, let the user know there were no matches.
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result_set = [ { label: "No matches", value: "" }]
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end
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end
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return result_set

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