Release 47

idc/urls.py

@@ -53,7 +53,6 @@
     re_path(r'^studymp/', views.studymp, name='studymp'),
     re_path(r'^warning/', views.warn_page, name='warn'),
     re_path(r'^about/', views.about_page, name='about_page'),
-    re_path(r'^test(.*)/', views.test_page, name='test_page'),
     re_path(r'^dashboard/', views.dashboard_page, name='dashboard'),
     re_path(r'^extended_login/$', views.extended_login_view, name='extended_login'),
     re_path(r'^privacy/', views.privacy_policy, name='privacy'),
@@ -62,6 +61,8 @@
     re_path(r'^explore/cart/$', views.cart_page, name='get_explore_cart'),
     re_path(r'^cart_data/$', views.cart_data, name='get_cart_data'),
     re_path(r'^cart_data_stats/$', views.cart_data_stats, name='get_cart_data_stats'),
+    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/$', views.get_series, name='get_series_by_case'),
+    re_path(r'^series_ids/(?P<patient_id>[A-Za-z0-9\.\-_]+)/(?P<study_uid>[0-9\.]+)/$', views.get_series, name='get_series'),
     re_path(r'^collaborators/', views.collaborators, name='collaborators'),
     re_path(r'^collections/', include('idc_collections.urls')),
     # re_path(r'^share/', include('sharing.urls')),

static/css/search.css

@@ -395,24 +395,22 @@ tr {
     background-color: #b7cfe5;
 }
 
-.export-button:hover, .btnGroupDropViewers:hover {
+.export-button:hover, .citations-button:hover, .btnGroupDropViewers:hover {
     cursor: pointer;
 }
 
 #projects_table td.cartnumholder, #projects_table_head th.cartnumholder,
 #cases_table td.cartnumholder, #cases_table_head th.cartnumholder,
-#studies_table td.cartnumholder, #studies_table_head th.cartnumholder
-{
+#studies_table td.cartnumholder, #studies_table_head th.cartnumholder {
     width: 10%;
-
 }
 
 #projects_table td.ckbx:not(.cartnumholder), #projects_table_head th.ckbx:not(.cartnumholder),
 #cases_table_head th.ckbx:not(.cartnumholder), #cases_table td.ckbx:not(.cartnumholder),
 #studies_table_head th.ckbx:not(.cartnumholder), #studies_table td.ckbx:not(.cartnumholder),
 #series_table_head th.ckbx, #series_table td.ckbx {
     width: 5%;
-     }
+}
 
 #search_def_stats {
     padding-top: 8px; }
@@ -455,6 +453,11 @@ tr {
 #studies_table_head th.open-viewer,
 #studies_table td.open-viewer {
     width:4%;
+    /* This is necessary to make sure the 2 icons remain together, lined up. */
+    min-width: 80px;
+}
+
+#studies_table td.open-viewer {
     /* This is necessary to make sure the 2 icons remain together, lined up. */
     min-width: 70px;
 }

static/css/style.css

@@ -1786,7 +1786,7 @@ a.skip-nav {
     background-color: #F8F8F8;
     border-color: #76b876; }
   .alert.alert-info {
-    color: #2d81c4;
+    color: #1c5c8d;
     background-color: #F8F8F8;
     border-color: #1976D2; }
   .alert.alert-warning {
@@ -1795,6 +1795,10 @@ a.skip-nav {
   .alert.alert-error {
     background-color: #F8F8F8;
     border-color: #D32F2F; }
+  .alert.alert-message {
+    background-color: #F8F8F8;
+    border-color: #47435b;
+  }
 
 .alert a {
   font-weight: 600;
@@ -2539,10 +2543,18 @@ section .min-max {
   border-radius: 4px;
 }
 
+.modal pre {
+    margin-top: 10px;
+}
+
 pre.bq-string {
   max-height: 600px;
   width: 570px;
-  margin-top: 10px;
+}
+
+pre.citations-list {
+  white-space: pre-wrap;
+  word-break: break-word;
 }
 
 .bq-string-display img {
@@ -4506,11 +4518,19 @@ d-topics-list iframe {
   font-size: smaller;
 }
 
-.collapse-all, .open-all {
+.collapse-all, .open-all, .download-all-instances {
   cursor: pointer;
 }
 
+#floating-message {
+  position: fixed;
+  bottom: 50px;
+  width: 500px;
+  right: 40px;
+  z-index: 9999;
+}
+
 .special-announcement {
   margin-bottom: 0px;
   text-align: center;
-}
+}

static/js/base.js

@@ -214,6 +214,8 @@ require([
         sessionStorage.removeItem("user-manifest");
     });
 
+    $('#floating-message').draggable();
+
     $(document).ready(function(){
         if(sessionStorage.getItem("reloadMsg")) {
             var msg = JSON.parse(sessionStorage.getItem("reloadMsg"));
@@ -261,6 +263,7 @@ define(['jquery', 'utils'], function($, utils) {
         // From http://www.regular-expressions.info/email.html
         email: /^[a-z0-9!#$%&'*+/=?^_`{|}~-]+(?:\.[a-z0-9!#$%&'*+/=?^_`{|}~-]+)*@(?:[a-z0-9](?:[a-z0-9-]*[a-z0-9])?\.)+[a-z0-9](?:[a-z0-9-]*[a-z0-9])?$/,
         showJsMessage: utils.showJsMessage,
+        hideFloatingMessage: utils.hideFloatingMessage,
         // Simple method for standardizing storage of a message into sessionStorage so it can be retrieved and reloaded
         // at document load time
         setReloadMsg: function(type,text) {

static/js/citations_modal.js

@@ -0,0 +1,126 @@
+/**
+ *
+ * Copyright 2020-2025, Institute for Systems Biology
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+require.config({
+    baseUrl: STATIC_FILES_URL + 'js/',
+    paths: {
+        jquery: 'libs/jquery-3.7.1.min',
+        bootstrap: 'libs/bootstrap.min',
+        jqueryui: 'libs/jquery-ui.min',
+        underscore: 'libs/underscore-min',
+        tablesorter: 'libs/jquery.tablesorter.min',
+        assetscore: 'libs/assets.core',
+        assetsresponsive: 'libs/assets.responsive',
+        jquerydt: 'libs/jquery.dataTables.min',
+        base: 'base',
+        tippy: 'libs/tippy-bundle.umd.min',
+        '@popperjs/core': 'libs/popper.min',
+        session_security: 'session_security/script'
+
+    },
+    shim: {
+        '@popperjs/core': {
+            exports: "@popperjs/core"
+        },
+        'tippy': {
+            exports: 'tippy',
+            deps: ['@popperjs/core']
+        },
+        'bootstrap': ['jquery'],
+        'jqueryui': ['jquery'],
+        'jquerydt': ['jquery'],
+        'underscore': {exports: '_'},
+        'tablesorter': ['jquery'],
+        'assetscore': ['jquery', 'bootstrap', 'jqueryui'],
+        'session_security': ['jquery'],
+        'assetsresponsive': ['jquery', 'bootstrap', 'jqueryui']
+    }
+});
+
+require([
+    'jquery',
+    'jqueryui',
+    'tippy',
+    'base', // Do not remove
+    'bootstrap',
+    'assetscore',
+    'assetsresponsive',
+], function($, jqueryui, tippy, base) {
+
+    var DOI_CACHE = {};
+
+    A11y.Core();
+
+    var downloadToken = new Date().getTime();
+
+    $('#citations-modal').on('show.bs.modal', async function(event) {
+        let button = $(event.relatedTarget);
+        let dois = button.attr('data-dois').split("||");
+        let cites_list = $("#citations-modal .citations-list");
+        let copy_cites = $("#citations-modal .copy-this");
+        cites_list.html(`
+            Formatting citation(s)... <i class="fa fa-compass fa-spin"></i>
+        `);
+        let citations = [];
+        await Promise.all(dois.map(async function(cite){
+            if(!DOI_CACHE[cite]) {
+                let response = await fetch(`https://doi.org/${cite}`, {
+                    headers: {
+                        "Accept": "text/x-bibliography; style=elsevier-vancouver-no-et-al"
+                    }
+                });
+                if (!response.ok) {
+                    citations.push(`Encountered an error requesting DOI ${cite}`);
+                } else {
+                    DOI_CACHE[cite] = await response.text();
+                }
+            }
+            citations.push(DOI_CACHE[cite]);
+        }));
+        cites_list.html(citations.join("\n\n"));
+        copy_cites.attr('content', citations.join("\n\n"));
+    });
+
+    $('#citations-modal').on('hide.bs.modal', function() {
+
+    });
+
+    $('#export-manifest-modal').on('hidden.bs.modal', function() {
+        $(".citations-list").empty();
+    });
+
+    $('.copy-this').on('click', function(e) {
+        // copy the entire set
+    });
+
+    tippy.delegate('#citations-modal', {
+        content: 'Copied!',
+        theme: 'blue',
+        placement: 'right',
+        arrow: true,
+        interactive: true, // This is required for any table tooltip to show at the appropriate spot!
+        target: '.copy-this',
+        onShow(instance) {
+            setTimeout(function() {
+                instance.hide();
+            }, 1000);
+        },
+        trigger: "click",
+        maxWidth: 85
+    });
+});

static/js/cohorts/export-manifest.js

@@ -394,8 +394,8 @@ require([
                 file_name.attr("name-base", "cohort_" + cohort_ids.join("_") + export_manifest_modal.data('file-timestamp'));
             }
         }
-        let s5cmd_manifest_filename = "<filename>";
-        let idc_index_manifest_filename = "<filename>";
+        let s5cmd_manifest_filename = "<manifest filename>";
+        let idc_index_manifest_filename = "<manifest filename>";
         let s5cmd_endpoint_url = $('input[name="loc_type_s5cmd"]:checked').attr('data-endpoint-url');
 
         let s5cmd_text = `s5cmd --no-sign-request --endpoint-url ${s5cmd_endpoint_url} run ${s5cmd_manifest_filename}`;

static/js/collections_list.js

@@ -18,7 +18,7 @@ require.config({
 require(['jquery', 'datatables.net','jqueryui', 'bootstrap', 'base'],
     function($) {
         var collex_data_table = $('#collections-table').DataTable({
-            "dom": '<"dataTables_controls"i<>lpf>rt<"bottom"><"clear">',
+            "dom": '<"dataTables_controls"i<>lpf>rt<"dataTables_controls"i<>lpf><"bottom"><"clear">',
             "pageLength": 100,
             'order': [[ 2, 'desc' ], [ 1, 'asc' ]]
         });