Merge branch 'develop' - version 0.4.0

molbiodiv · Nov 22, 2016 · 4a1e725 · 4a1e725
2 parents ff0a844 + a53c2e5
commit 4a1e725
Show file tree

Hide file tree

Showing 49 changed files with 508 additions and 577 deletions.
diff --git a/README.md b/README.md
@@ -35,6 +35,11 @@ gulp sassLint
 gulp sass
 ```
 ## Changes
+### 0.4.0 <2016-11-22>
+ - Rename organism_id to fennec_id
+ - Update webservices for db schema 0.4.0
+ - Fix frontend for new data schema
+ - Fix bugs (related to biom json export)
 ### 0.3.2 <2016-11-04>
  - Add organism_id mapping to project details page
  - Export project as biom (v1)

diff --git a/app/Resources/client/jsx/project/details/details.jsx b/app/Resources/client/jsx/project/details/details.jsx
@@ -28,7 +28,11 @@ $('document').ready(function () {
     });
 
     $('#project-export-as-biom-v1').click(() => {
-        exportProjectAsBiom();
+        exportProjectAsBiom(false);
+    });
+
+    $('#project-export-as-biom-v2').click(() => {
+        exportProjectAsBiom(true);
     });
 
 });
@@ -55,11 +59,17 @@ function saveBiomToDB() {
     });
 }
 
-function exportProjectAsBiom() {
-    biom.write().then(function (biomJson) {
-        var blob = new Blob([biomJson], {type: "text/plain"});
-        saveAs(blob, biom.id+".json");
+/**
+ * Opens a file download dialog of the current project in biom format
+ * @param {boolean} asHdf5
+ */
+function exportProjectAsBiom(asHdf5) {
+    let conversionServerURL = Routing.generate('biomcs_convert');
+    let contentType = asHdf5 ? "application/octet-stream" : "text/plain";
+    biom.write({conversionServer: conversionServerURL, asHdf5: asHdf5}).then(function (biomContent) {
+        var blob = new Blob([biomContent], {type: contentType});
+        saveAs(blob, biom.id+".biom");
     }, function (failure) {
-        console.log(failure);
+        showMessageDialog(failure+"", 'danger');
     });
 }
diff --git a/app/Resources/client/jsx/project/details/mapping.jsx b/app/Resources/client/jsx/project/details/mapping.jsx
@@ -3,8 +3,8 @@
 /* global _ */
 $('document').ready(() => {
     // Calculate values for mapping overview table
-    let sampleOrganismIDs = biom.getMetadata({dimension: 'columns', attribute: ['fennec', dbversion, 'organism_id']}).filter(element => element !== null);
-    let otuOrganismIDs = biom.getMetadata({dimension: 'rows', attribute: ['fennec', dbversion, 'organism_id']}).filter(element => element !== null);
+    let sampleOrganismIDs = biom.getMetadata({dimension: 'columns', attribute: ['fennec', dbversion, 'fennec_id']}).filter(element => element !== null);
+    let otuOrganismIDs = biom.getMetadata({dimension: 'rows', attribute: ['fennec', dbversion, 'fennec_id']}).filter(element => element !== null);
     var mappedSamples = sampleOrganismIDs.length;
     var percentageMappedSamples = 100 * mappedSamples / biom.shape[1];
     var mappedOTUs = otuOrganismIDs.length;
@@ -97,28 +97,28 @@ $('document').ready(() => {
      * Create the results component from the returned mapping and store result in global biom object
      * @param {string} dimension
      * @param {Array} idsFromBiom those are the ids used for mapping in the order they appear in the biom file
-     * @param {Array} mapping from ids to organism_ids as returned by webservice
+     * @param {Array} mapping from ids to fennec_ids as returned by webservice
      * @param {string} method of mapping
      */
     function handleMappingResult(dimension, idsFromBiom, mapping, method) {
-        let organism_ids = new Array(idsFromBiom.length).fill(null);
+        let fennec_ids = new Array(idsFromBiom.length).fill(null);
         var idsFromBiomNotNullCount = 0;
         var idsFromBiomMappedCount = 0;
         for (let i = 0; i < idsFromBiom.length; i++) {
             if (idsFromBiom[i] !== null) {
                 idsFromBiomNotNullCount++;
                 if (idsFromBiom[i] in mapping && mapping[idsFromBiom[i]] !== null) {
                     idsFromBiomMappedCount++;
-                    organism_ids[i] = mapping[idsFromBiom[i]];
+                    fennec_ids[i] = mapping[idsFromBiom[i]];
                 }
             }
         }
-        biom.addMetadata({dimension: dimension, attribute: ['fennec', dbversion, 'organism_id'], values: organism_ids});
+        biom.addMetadata({dimension: dimension, attribute: ['fennec', dbversion, 'fennec_id'], values: fennec_ids});
         biom.addMetadata({dimension: dimension, attribute: ['fennec', dbversion, 'assignment_method'], defaultValue: method});
         var idString = getIdStringForMethod(method);
         $('#mapping-action-busy-indicator').hide();
         $('#mapping-results-section').show();
-        $('#mapping-results').text(`From a total of ${idsFromBiom.length} organisms:  ${idsFromBiomNotNullCount} have a ${idString}, of which ${idsFromBiomMappedCount} could be mapped to organism_ids.`);
+        $('#mapping-results').text(`From a total of ${idsFromBiom.length} organisms:  ${idsFromBiomNotNullCount} have a ${idString}, of which ${idsFromBiomMappedCount} could be mapped to fennec_ids.`);
     }
 
     // Set action for click on mapping "Save to database" button
@@ -128,16 +128,16 @@ $('document').ready(() => {
 
     // Set action for click on mapping "Download as csv" button
     $('#mapping-download-csv-button').on('click', function () {
-        var ids = biom[dimension].map(function (element) {
+        let ids = biom[dimension].map(function (element) {
             return element.id;
         });
-        var ids = getIdsForMethod(method, dimension);
-        var fennec_id = biom.getMetadata({dimension: dimension, attribute: ['fennec', dbversion, 'organism_id']});
-        var id_header = dimension === 'rows' ? 'OTU_ID' : 'Sample_ID';
+        let mappingIds = getIdsForMethod(method, dimension);
+        let fennecIds = biom.getMetadata({dimension: dimension, attribute: ['fennec', dbversion, 'fennec_id']});
+        let idHeader = dimension === 'rows' ? 'OTU_ID' : 'Sample_ID';
         let idString = getIdStringForMethod(method);
-        var csv = `${id_header}\t${idString}\tFennec_ID\n`;
+        var csv = `${idHeader}\t${idString}\tFennec_ID\n`;
         for(var i=0; i<ids.length; i++){
-            csv += ids[i]+"\t"+ids[i]+"\t"+fennec_id[i]+"\n";
+            csv += ids[i]+"\t"+mappingIds[i]+"\t"+fennecIds[i]+"\n";
         }
         var blob = new Blob([csv], {type: "text/plain;charset=utf-8"});
         saveAs(blob, "mapping.csv");

diff --git a/app/Resources/client/jsx/project/details/trait.jsx b/app/Resources/client/jsx/project/details/trait.jsx
@@ -5,15 +5,15 @@ $('document').ready(() => {
     var traits = [];
     var webserviceUrl = Routing.generate('api', {'namespace': 'details', 'classname': 'traitsOfOrganisms'});
 
-    // Extract row organism_ids from biom
-    var organism_ids = biom.getMetadata({dimension: 'rows', attribute: ['fennec', dbversion, 'organism_id']})
+    // Extract row fennec_ids from biom
+    var fennec_ids = biom.getMetadata({dimension: 'rows', attribute: ['fennec', dbversion, 'fennec_id']})
         .filter( element => element !== null );
 
     // Get traits for rows
     $.ajax(webserviceUrl, {
         data: {
             "dbversion": dbversion,
-            "organism_ids": organism_ids
+            "fennec_ids": fennec_ids
         },
         method: "POST",
         success: function (data) {
@@ -22,7 +22,7 @@ $('document').ready(() => {
                     id: key,
                     trait: value['trait_type'],
                     count: value['trait_entry_ids'].length,
-                    range: 100 * value['organism_ids'].length / organism_ids.length
+                    range: 100 * value['fennec_ids'].length / fennec_ids.length
                 };
                 traits.push(thisTrait);
             });

diff --git a/app/Resources/views/components/searchForm.quickSearch.html.twig b/app/Resources/views/components/searchForm.quickSearch.html.twig
@@ -21,7 +21,7 @@
 
         $("#search_{{ type }}").data("ui-autocomplete")._renderItem = function (ul, item) {
             {% if type == 'organism' %}
-                var details = Routing.generate('{{ type }}_details', {'dbversion': '{{ dbversion }}', 'organism_id': item.organism_id});
+                var details = Routing.generate('{{ type }}_details', {'dbversion': '{{ dbversion }}', 'fennec_id': item.fennec_id});
                 var link = "<a href='"+details+"'><span style='display:inline-block; width: 100%; font-style: italic;'>" + item.scientific_name + "</span><span style='color: #338C8C'>" + item.rank + "</span></a>";
             {% elseif type == 'trait' %}
                 var details = Routing.generate('{{ type }}_details', {'dbversion': '{{ dbversion }}', 'trait_type_id': item.trait_type_id});

diff --git a/app/Resources/views/organism/details.html.twig b/app/Resources/views/organism/details.html.twig
@@ -2,10 +2,10 @@
 
 {% block javascripts %}
     {{ parent() }}
-    {% if organism.eol_accession is defined %}
+    {% if organism.eol_identifier is defined %}
         <script type="text/javascript">
             $('document').ready(function(){
-                var eol_id = {{ organism.eol_accession }};
+                var eol_id = {{ organism.eol_identifier }};
                 var img_template = '<a class="thumbnail" href="<%= href %>"><img src="<%= src %>"/></a><a href="<%= source %>"><div>(c) <%= rightsHolder %> <%= license %></div></a>';
                 $.ajax({
                     method: "GET",
@@ -104,7 +104,7 @@
                         <button type="button" class="close" data-dismiss="alert" aria-label="Close">
                             <span aria-hidden="true">&times;</span>
                         </button>
-                        Content on this page is dynamically included from <a href="http://eol.org">EOL</a> via its <a href="http://eol.org/api">API</a>. <a href="http://eol.org/pages/{{ organism.eol_accession }}">Visit full page at EOL for this organism (id {{ organism.eol_accession }})</a>.
+                        Content on this page is dynamically included from <a href="http://eol.org">EOL</a> via its <a href="http://eol.org/api">API</a>. <a href="http://eol.org/pages/{{ organism.eol_identifier }}">Visit full page at EOL for this organism (id {{ organism.eol_identifier }})</a>.
                     </div>
                     <div class='row'>
                         <div class='col-xs-12'>
@@ -136,9 +136,11 @@
                     {% endfor %}
                 </div>
                 <div role="tabpanel" class="tab-pane" id="taxonomy">
-                    <h4 class="page-header">Lineage</h4>
-                    {% for taxon in taxonomy.lineage %}
-                        {{ taxon }}</br>
+                    {% for db, lineage in taxonomy %}
+                        <h4 class="page-header">{{ db }}</h4>
+                        {% for taxon in lineage %}
+                            {{ taxon }}</br>
+                        {% endfor %}
                     {% endfor %}
                 </div>
             </div>

diff --git a/app/Resources/views/organism/grid.html.twig b/app/Resources/views/organism/grid.html.twig
@@ -1,6 +1,6 @@
 {% for organism in organisms %}
 <div class="col-lg-3">
-    <div class="panel grid-organism" organism_id='{{ organism.organism_id }}'>
+    <div class="panel grid-organism" fennec_id='{{ organism.fennec_id }}'>
         <div class="panel-heading" style='height: 60px;'>
             <div class="row">
                 <div class="col-xs-3">
@@ -20,12 +20,9 @@
                     common name: {{ organism.common_name }}
                 </div>
                 {% endif %}
-                <div class="col-xs-10 text-left">
-                    rank: {{ organism.rank }}
-                </div>
                 <a class="grid-details-organism">
                     <div class="col-xs-2 text-right">
-                        <a href="{{ path('organism_details', {'dbversion': dbversion, 'organism_id': organism.organism_id}) }}"><span class="pull-right"><i class="fa fa-arrow-circle-right fa-2x {{ type }}-link"></i></span></a>
+                        <a href="{{ path('organism_details', {'dbversion': dbversion, 'fennec_id': organism.fennec_id}) }}"><span class="pull-right"><i class="fa fa-arrow-circle-right fa-2x {{ type }}-link"></i></span></a>
                     </div>
                 </a>
             </div>

diff --git a/app/Resources/views/project/details.html.twig b/app/Resources/views/project/details.html.twig
@@ -4,12 +4,11 @@
     {{ parent() }}
 
     <script type="text/javascript">
-        var biomString = '{{ project['projects'][internal_project_id]['biom']|raw }}';
         var internalProjectId = '{{ internal_project_id }}';
         var phinchPreviewPath = '{{ asset('assets/Blackbird/preview.html') }}';
         var biom = function(){
             var Biom = require('biojs-io-biom').Biom;
-            var biomObject = JSON.parse(biomString);
+            var biomObject = {{ project['projects'][internal_project_id]['biom']|raw }};
             return new Biom(biomObject);
         }();
     </script>
@@ -45,6 +44,7 @@
                     <tr><th scope="row">Export</th>
                         <td id="project-overview-table-export">
                             <button type="button" class="btn btn-primary" id="project-export-as-biom-v1">BIOM v1</button>
+                            <button type="button" class="btn btn-primary" id="project-export-as-biom-v2">BIOM v2</button>
                         </td></tr>
                 </tbody>
             </table>

diff --git a/app/Resources/views/trait/grid.html.twig b/app/Resources/views/trait/grid.html.twig
@@ -1,5 +1,5 @@
 {% for trait in traits %}
-    {% set traitWithIcon = ['PlantHabit'] %}
+    {% set traitWithIcon = ['Plant Habit'] %}
     <div class="col-xs-12 col-sm-6 col-md-6 col-lg-4">
         <div class="panel panel-trait">
             <div class="panel-heading">

diff --git a/app/config/config.yml b/app/config/config.yml
@@ -37,7 +37,7 @@ twig:
     debug:            "%kernel.debug%"
     strict_variables: "%kernel.debug%"
     globals:
-        fennec_version: 0.3.2
+        fennec_version: 0.4.0
         dbversions: "%dbversions%"
 
 # Doctrine Configuration

diff --git a/bower.json b/bower.json
@@ -23,7 +23,7 @@
     "plotlyjs": "plotly#^1.16.2",
     "datatables": "^1.10.12",
     "bs-confirmation": "^1.0.5",
-    "biojs-io-biom": "^1.0.3",
+    "biojs-io-biom": "^1.0.5",
     "d3": "^4.2.7",
     "react": "^15.3.2",
     "file-saver": "filesaver#^1.3.3",

diff --git a/composer.json b/composer.json
@@ -29,7 +29,8 @@
         "sensio/framework-extra-bundle": "^3.0.2",
         "incenteev/composer-parameter-handler": "^2.0",
         "league/oauth2-github": "^0.2.1",
-        "friendsofsymfony/jsrouting-bundle": "^1.6"
+        "friendsofsymfony/jsrouting-bundle": "^1.6",
+        "iimog/biom-conversion-server": "^1.0"
     },
     "require-dev": {
         "sensio/generator-bundle": "^3.0",

diff --git a/composer.lock b/composer.lock
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "fennec-web",
-  "version": "0.3.2",
+  "version": "0.4.0",
   "description": "Fennec",
   "directories": {
     "test": "test"