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George
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merge
2 parents a408ba1 + 6aab017 commit 326ce4b

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5 files changed

+70
-9
lines changed

5 files changed

+70
-9
lines changed

‎shell/index.sh‎

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

‎shell/install-deps.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -135,5 +135,5 @@ if [ -n "${CI}" ]; then
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TIER=${DEPLOYMENT_TIER,,}
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fi
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SHA=$(git rev-list -1 HEAD)
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echo "APP_VERSION=${TIER}.$(date '+%Y%m%d%H%M').${SHA: -6}" > ${HOMEROOT}/version.env
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echo "APP_VERSION=${TIER}.$(date '+%Y%m%d%H%M').${SHA:0:7}" > ${HOMEROOT}/version.env
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fi

‎static/js/image_search.js‎

Lines changed: 26 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2504,7 +2504,7 @@ require([
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checkBox.indeterminate = false;
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}
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2507-
if ( (checked) && (filtnm ==='tcga_clinical')){
2507+
if ( (checked) && (filtnm ==='tcga_clinical') && !is_cohort){
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checkTcga();
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}
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@@ -2797,9 +2797,9 @@ require([
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_.each(filters, function(group){
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_.each(group['filters'], function(filter){
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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']+'"]';
2800+
$(selector).parents('.collection-list').collapse('show');
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$(selector).collapse('show');
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$(selector).find('.show-more').triggerHandler('click');
2802-
$(selector).parents('.collection-list').collapse('show');
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$(selector).parents('.tab-pane.search-set').length > 0 && $('a[href="#'+$(selector).parents('.tab-pane.search-set')[0].id + '"]').tab('show');
28042804
if($(selector).children('.ui-slider').length > 0) {
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sliders.push({
@@ -2818,7 +2818,6 @@ require([
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if(sliders.length > 0) {
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load_sliders(sliders, false);
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}
2821-
console.debug("Making filter text...");
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mkFiltText();
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return updateFacetsData(true).promise();
28242823
};
@@ -2844,6 +2843,30 @@ require([
28442843

28452844
// Get all checked filters
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var filters = [];
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// For collection list
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$('.collection-list').each(function() {
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var $group = $(this);
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var checkboxes = $group.find("input:checked");
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if (checkboxes.length > 0)
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{
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var values = [];
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var my_id = "";
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checkboxes.each(function() {
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var $checkbox = $(this);
2858+
var my_value = $checkbox[0].value;
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my_id = $checkbox.data('filter-attr-id');
2860+
values.push(my_value);
2861+
});
2862+
filters.push({
2863+
'id': my_id,
2864+
'values': values,
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});
2866+
}
2867+
});
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// For other list item groups
28472870
$('.list-group-item__body').each(function() {
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var $group = $(this);
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var my_id = $group.data('filter-attr-id');

‎templates/idc/explore_data_core.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@ <h4 class="panel-title">Search Scope</h4>
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<div id="Program_heading" class="list-group-item__heading">
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<a role="button" data-toggle="collapse" href="#Program" aria-expanded="false" aria-controls="Program">
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<i class="fa fa-caret-right"></i> <i class="fa fa-caret-down"></i>COLLECTION
39-
</a>
39+
</a>
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</div>
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<div id="Program" class="collapse filter-panel collection-list">
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<ul id="Program_list" class="search-checkbox-list" style="list-style: none;">

‎templates/idc/landing.html‎

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Original file line numberDiff line numberDiff line change
@@ -114,10 +114,10 @@
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</div>
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<div class="summary col-lg-8 col-md-12 col-sm-12">
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<div class="summary-contents panel-body">
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/collex_icon_2.png' %}" alt="" /></div> <div>27<br/> Collections</div></div>
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/cases_icon.png' %}" alt="" /></div> <div>3,230<br/> Cases</div></div>
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/volume_icon.png' %}" alt="" /></div> <div>1.03 TB<br/> Data Volume</div></div>
120-
<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/img_series_icon.png' %}" alt="" /></div> <div>49,818<br/> Image Series</div></div>
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/collex_icon_2.png' %}" alt="" /></div> <div>28<br/> Collections</div></div>
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/cases_icon.png' %}" alt="" /></div> <div>3,652<br/> Cases</div></div>
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<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/volume_icon.png' %}" alt="" /></div> <div>1.04 TB<br/> Data Volume</div></div>
120+
<div class="summary-block col-lg-3 col-md-3 col-sm-3"><div class="img-container"><img src="{% static 'img/img_series_icon.png' %}" alt="" /></div> <div>51,247<br/> Image Series</div></div>
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</div>
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</div>
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</div>

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