Merge branch 'master' of https://github.com/ImagingDataCommons/IDC-WebApp into idc-test-sp

Author: s-paquette

shell/index.sh

@@ -0,0 +1,38 @@
+CORE=${1:-test_core}
+SKIP_DOWNLOAD=${2:-true}
+
+echo ""
+echo "Beginning index run for core ${CORE}"
+echo "-------------------------------------------------------"
+echo ""
+
+if [[ "$SKIP_DOWNLOAD" = false ]]; then
+        echo "Deleting current CSV files."
+        rm dicom_derived_all_*.csv
+
+        echo "Downloading new index data."
+        gsutil cp gs://idc-dev-files/dicom_derived_all_*.csv ./
+else
+	echo "Skipping download. Files are assumed to be present in the directory."
+fi
+
+echo ""
+echo "Deleting and re-creating the core."
+sudo -u solr /opt/bitnami/apache-solr/bin/solr delete -c $CORE
+sudo -u solr /opt/bitnami/apache-solr/bin/solr create -c $CORE -s 2 -rf 2
+
+echo ""
+echo "Creating the core schema."
+echo '{"add-field":['$(cat core_schema.json)']}' | curl -u idc:$SOLR_PASSWORD -X POST -H 'Content-type:application/json' --data-binary @-  https://localhost:8983/solr/$CORE/schema --cacert solr-ssl.pem
+
+echo ""
+echo "Indexing the following files:"
+ls -l dicom_derived_all_*.csv
+
+echo ""
+for CSV in $(ls dicom_derived_all_*.csv)
+do
+        echo "Indexing file ${CSV}..."
+        curl -u idc:$SOLR_PASSWORD -X POST https://localhost:8983/solr/$CORE/update?commit=yes --data-binary @$CSV -H 'Content-type:application/csv' --cacert solr-ssl.pem
+        echo "...done."
+done

shell/install-deps.sh

@@ -135,5 +135,5 @@ if [ -n "${CI}" ]; then
         TIER=${DEPLOYMENT_TIER,,}
     fi
     SHA=$(git rev-list -1 HEAD)
-    echo "APP_VERSION=${TIER}.$(date '+%Y%m%d%H%M').${SHA: -6}" > ${HOMEROOT}/version.env
+    echo "APP_VERSION=${TIER}.$(date '+%Y%m%d%H%M').${SHA:0:6}" > ${HOMEROOT}/version.env
 fi

static/js/image_search.js

@@ -2258,7 +2258,7 @@ require([
                     checkBox.indeterminate = false;
                 }
 
-                if ( (checked) && (filtnm ==='tcga_clinical')){
+                if ( (checked) && (filtnm ==='tcga_clinical') && !is_cohort){
                     checkTcga();
                 }
 
@@ -2551,9 +2551,9 @@ require([
         _.each(filters, function(group){
             _.each(group['filters'], function(filter){
                 let selector = 'div.list-group-item__body[data-filter-attr-id="'+filter['id']+'"], '+'div.list-group-sub-item__body[data-filter-attr-id="'+filter['id']+'"]';
+                $(selector).parents('.collection-list').collapse('show');
                 $(selector).collapse('show');
                 $(selector).find('.show-more').triggerHandler('click');
-                $(selector).parents('.collection-list').collapse('show');
                 $(selector).parents('.tab-pane.search-set').length > 0 && $('a[href="#'+$(selector).parents('.tab-pane.search-set')[0].id + '"]').tab('show');
                 if($(selector).children('.ui-slider').length > 0) {
                     sliders.push({
@@ -2572,7 +2572,6 @@ require([
         if(sliders.length > 0) {
             load_sliders(sliders, false);
         }
-        console.debug("Making filter text...");
         mkFiltText();
         return updateFacetsData(true).promise();
      };
@@ -2598,6 +2597,30 @@ require([
 
         // Get all checked filters
         var filters = [];
+
+        // For collection list
+        $('.collection-list').each(function() {
+            var $group = $(this);
+
+            var checkboxes = $group.find("input:checked");
+            if (checkboxes.length > 0)
+            {
+                var values = [];
+                var my_id = "";
+                checkboxes.each(function() {
+                    var $checkbox = $(this);
+                    var my_value = $checkbox[0].value;
+                    my_id = $checkbox.data('filter-attr-id');
+                    values.push(my_value);
+                });
+                filters.push({
+                    'id': my_id,
+                    'values': values,
+                });
+            }
+        });
+
+        // For other list item groups
         $('.list-group-item__body').each(function() {
             var $group = $(this);
             var my_id = $group.data('filter-attr-id');

templates/idc/explore_data_core.html

@@ -36,7 +36,7 @@ <h4 class="panel-title">Search Scope</h4>
                                      <div id="Program_heading" class="list-group-item__heading">
                                          <a role="button" data-toggle="collapse" href="#Program" aria-expanded="false" aria-controls="Program">
                                              <i class="fa fa-caret-right"></i> <i class="fa fa-caret-down"></i>COLLECTION
-                                         </a>
+                                         </a> 
                                      </div>
                                      <div id="Program" class="collapse filter-panel collection-list">
                                          <ul id="Program_list" class="search-checkbox-list" style="list-style: none;">