Merge pull request #369 from ImagingDataCommons/idc-test-sp

s-paquette · web-flow · commit 2df4f85efb68 · 2020-10-07T10:36:17.000-07:00
MVP
diff --git a/scripts/database_bootstrap.py b/scripts/database_bootstrap.py
@@ -58,7 +58,22 @@
     'year_of_diagnosis': 'year',
     'days_to_birth': 'by_negative_3k',
     'year_of_initial_pathologic_diagnosis': 'year',
-    'age_at_diagnosis': None
+    'age_at_diagnosis': None,
+    'SUVbw': 'SUVbw',
+    'Volume': 'Volume',
+    'Diameter': 'Diameter',
+    'Surface_area_of_mesh': 'Surface_area_of_mesh',
+    'Total_Lesion_Glycolysis': 'Total_Lesion_Glycolysis',
+    'Standardized_Added_Metabolic_Activity': 'Standardized_Added_Metabolic_Activity',
+    'Percent_Within_First_Quarter_of_Intensity_Range': 'Percent_Within_First_Quarter_of_Intensity_Range',
+    'Percent_Within_Third_Quarter_of_Intensity_Range': 'Percent_Within_Third_Quarter_of_Intensity_Range',
+    'Percent_Within_Fourth_Quarter_of_Intensity_Range': 'Percent_Within_Fourth_Quarter_of_Intensity_Range',
+    'Percent_Within_Second_Quarter_of_Intensity_Range': 'Percent_Within_Second_Quarter_of_Intensity_Range',
+    'Standardized_Added_Metabolic_Activity_Background': 'Standardized_Added_Metabolic_Activity_Background',
+    'Glycolysis_Within_First_Quarter_of_Intensity_Range': 'Glycolysis_Within_First_Quarter_of_Intensity_Range',
+    'Glycolysis_Within_Third_Quarter_of_Intensity_Range': 'Glycolysis_Within_Third_Quarter_of_Intensity_Range',
+    'Glycolysis_Within_Fourth_Quarter_of_Intensity_Range': 'Glycolysis_Within_Fourth_Quarter_of_Intensity_Range',
+    'Glycolysis_Within_Second_Quarter_of_Intensity_Range': 'Glycolysis_Within_Second_Quarter_of_Intensity_Range'
 }
 
 ranges = {
@@ -69,7 +84,22 @@
     'by_500': [{'first': "500", "last": "6000", "gap": "500", "include_lower": False, "unbounded": True,
                              "include_upper": True, 'type': 'I'}],
     'year': [{'first': "1976", "last": "2015", "gap": "5", "include_lower": True, "unbounded": False,
-                             "include_upper": False, 'type': 'I'}]
+                             "include_upper": False, 'type': 'I'}],
+    'SUVbw': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '3', 'last': '12', 'gap': '1'}],
+    'Volume': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '10', 'last': '28000', 'gap': '2800'}],
+    'Diameter': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '6', 'last': '55', 'gap': '6'}],
+    'Surface_area_of_mesh': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '150', 'last': '4500', 'gap': '435'}],
+    'Total_Lesion_Glycolysis': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '78', 'last': '698', 'gap': '78'}],
+    'Standardized_Added_Metabolic_Activity': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '56', 'last': '502', 'gap': '56'}],
+    'Percent_Within_First_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '10', 'last': '90', 'gap': '10'}],
+    'Percent_Within_Third_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '10', 'last': '90', 'gap': '10'}],
+    'Percent_Within_Fourth_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '10', 'last': '90', 'gap': '10'}],
+    'Percent_Within_Second_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '10', 'last': '90', 'gap': '10'}],
+    'Standardized_Added_Metabolic_Activity_Background': [{'type': 'F', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '0.5', 'last': '5', 'gap': '0.5'}],
+    'Glycolysis_Within_First_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '28', 'last': '251', 'gap': '28'}],
+    'Glycolysis_Within_Third_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '25', 'last': '225', 'gap': '25'}],
+    'Glycolysis_Within_Fourth_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '19', 'last': '170', 'gap': '19'}],
+    'Glycolysis_Within_Second_Quarter_of_Intensity_Range': [{'type': 'I', 'include_lower': '1', 'include_upper': '0', 'unbounded': '1', 'first': '25', 'last': '227', 'gap': '25'}]
 }
 
 BQ_PROJ_DATASET = 'idc-dev-etl.idc_tcia_views_mvp_wave0'
@@ -576,8 +606,11 @@ def main():
 
             attr = all_attrs[line_split[0]]
 
-            if attr['type'] == Attribute.CONTINUOUS_NUMERIC:
-                attr['range'] = []
+            if attr['type'] == Attribute.CONTINUOUS_NUMERIC and 'range' not in attr:
+                if attr['name'] in ranges_needed:
+                    attr['range'] = ranges.get(ranges_needed.get(attr['name'], ''), [])
+                else:
+                    attr['range'] = []
 
             attr['solr_collex'].append(SOLR_INDEX['dicom_derived'])
             attr['bq_tables'].append(BQ_TABLES['quan'])
diff --git a/static/css/style.css b/static/css/style.css
diff --git a/static/css/vendor.css b/static/css/vendor.css
@@ -2876,7 +2876,6 @@ fieldset[disabled] a.btn {
   fieldset[disabled] .btn-default.focus,
   fieldset[disabled] .btn-default:active,
   fieldset[disabled] .btn-default.active {
-    background-color: transparent;
     border-color: #F7991B; }
   .btn-default .badge {
     color: transparent;
diff --git a/static/js/base.js b/static/js/base.js
@@ -207,6 +207,10 @@ define(['jquery', 'utils'], function($, utils) {
         }
     });
 
+    $.getCookie = utils.getCookie;
+    $.setCookie = utils.setCookie;
+    $.removeCookie = utils.removeCookie;
+
     return {
         blacklist: /<script>|<\/script>|!\[\]|!!\[\]|\[\]\[\".*\"\]|<iframe>|<\/iframe>/ig,
         // From http://www.regular-expressions.info/email.html
@@ -217,6 +221,12 @@ define(['jquery', 'utils'], function($, utils) {
         setReloadMsg: function(type,text) {
             sessionStorage.setItem("reloadMsg",JSON.stringify({type: type, text: text}));
         },
+        setCookie: function(name,val,expires_in,path) {
+            utils.setCookie(name,val,expires_in,path);
+        },
+        removeCookie: function(name, path) {
+            utils.removeCookie(name, path);
+        },
         blockResubmit: utils.blockResubmit
     };
 });
diff --git a/static/js/cohorts/cohort-details.js b/static/js/cohorts/cohort-details.js
@@ -38,12 +38,28 @@ require.config({
 require([
     'jquery',
     'jqueryui',
+    'base',
     'bootstrap',
     'assetscore'
     ,'assetsresponsive',
-    'base'
-], function($, jqueryui, bootstrap) {
+], function($, jqueryui, base, bootstrap) {
     A11y.Core();
 
+    var downloadToken = new Date().getTime();
+    $('#download-manifest').prop("href", $('#download-manifest').prop("href") + "?downloadToken="+downloadToken);
+    $('#download-manifest').data('downloadToken',downloadToken);
+
+    $('#download-manifest').on('click', function() {
+        var self=$(this);
+
+        self.attr('disabled','disabled');
+
+        $('#download-in-progress').modal('show');
+
+        base.blockResubmit(function() {
+            self.removeAttr('disabled');
+            $('#download-in-progress').modal('hide');
+        },downloadToken, 'downloadToken');
+    });
 
 });
diff --git a/static/js/explore.js b/static/js/explore.js
@@ -170,4 +170,41 @@ require([
         allowHTML: true,
         interactive: true
     });
+
+    tippy('.tooltip_filter_info',{
+        content: 'Each chart below reports the number of cases (or patients) for all attributes within a given attribute '+
+            'category for the cohort constructed by the defined filter. For certain categories (i.e. Modality) some '+
+            'cases may apply to several attributes within the category. Hence some attributes that seem to be excluded '+
+            'in the filter definition may have positive case counts.',
+        theme: 'light',
+        placement: 'right-end',
+        arrow: false
+    });
+
+    tippy('.tooltip_chart_info',{
+        content: 'The panel below reports the number of unique cases (or patients) for each attribute within a cohort '+
+            'constructed by adding the given attribute (when absent) to the defined filter.',
+        theme: 'light',
+        placement: 'right-end',
+        arrow: false
+    });
+
+    tippy('.checkbox-none',{
+        content: 'Filtering on the \'None\' attribute is not currently supported within derived data.',
+        theme: 'light',
+        placement: 'top-start',
+        arrow: false
+    });
+
+    tippy.delegate('.studies-table', {
+        content: function(reference) {
+            return $(reference).data('study-id');
+        },
+        theme: 'dark',
+        placement: 'right',
+        arrow: false,
+        target: '.study-id-col',
+        maxWidth: 300
+    });
+
 });
diff --git a/static/js/image_search.js b/static/js/image_search.js
@@ -893,7 +893,7 @@ require(['jquery', 'underscore', 'jquerydt','jqueryui', 'bootstrap','base'],
                         var studyId = curData.StudyInstanceUID;
                         var ppStudyId = pretty_print_id(studyId);
                         var fetchUrl = DICOM_STORE_PATH + studyId;
-                        var hrefTxt = ppStudyId + '</a><span class="tooltiptext_ex">' + studyId + '</span>';
+                        var hrefTxt = ppStudyId + '</a>';
                         //var hrefTxt =  ppStudyId + '<span class="tooltiptext_ex">' + studyId + '</span>';
                         var pclass = 'project_' + projectId;
                         var newHtml = '';
@@ -911,7 +911,7 @@ require(['jquery', 'underscore', 'jquerydt','jqueryui', 'bootstrap','base'],
                             var seriesTxt = ppSeriesId + '<span class="tooltiptext_ex">' + seriesId + '</span>';
 
                             newHtml = '<tr id="' + rowId + '" class="' + pclass + ' ' + studyClass + ' text_head">' +
-                                '<td class="col1 tooltip_ex study-id">' + hrefTxt + '</td>' +
+                                '<td class="col1 study-id study-id-col" data-study-id="'+studyId+'">' + hrefTxt + '</td>' +
                                 '<td class="series-number">' + seriesNumber + '</td>' +
                                 '<td class="col1 modality">' + modality + '</td>' +
                                 '<td class="col1 body-part-examined">' + bodyPartExamined + '</td>' +
@@ -938,15 +938,15 @@ require(['jquery', 'underscore', 'jquerydt','jqueryui', 'bootstrap','base'],
                                 newHtml = '<tr id="' + rowId + '" class="' + pclass + ' text_head selected_grey" onclick="(toggleStudy(this,\'' + studyId + '\',\'' + projectId + '\'))">' +
                                     '<td class="col1 project-name">' + projectId + '</td>' +
                                     '<td class="col1 case-id">' + patientId +
-                                    '</td><td class="col2 tooltip_ex study-id">' + hrefTxt + '</td>' +
+                                    '</td><td class="col2 study-id study-id-col" data-study-id="'+studyId+'">' + hrefTxt + '</td>' +
                                     '<td class="col1 study-description">' + studyDescription + '</td>' +
                                     '<td class="ohif open-viewer"><a  href="' + fetchUrl + '" target="_blank"><i class="fa fa-eye"></i></a></td></tr>'
 
                             } else {
                                 newHtml = '<tr id="' + rowId + '" class="' + pclass + ' text_head" onclick="(toggleStudy(this,\'' + studyId + '\',\'' + projectId + '\'))">' +
                                     '<td class="col1 project-name">' + projectId + '</td>' +
                                     '<td class="col1 case-id">' + patientId + '</td>' +
-                                    '<td class="col2 tooltip_ex study-id">' + hrefTxt + '</td>' +
+                                    '<td class="col2 study-id study-id-col" data-study-id="'+studyId+'">' + hrefTxt + '</td>' +
                                     '<td class="col1 study-description">' + studyDescription + '</td>' +
                                     '<td class="ohif open-viewer"><a  href="' + fetchUrl + '" target="_blank"><i class="fa fa-eye"></i></a></td></tr>'
                             }
diff --git a/static/js/utils.js b/static/js/utils.js
@@ -1,6 +1,6 @@
 /**
  *
- * Copyright 2017, Institute for Systems Biology
+ * Copyright 2020, 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.
@@ -47,16 +47,45 @@ define(['jquery'], function($) {
     var downloadTimer;
     var attempts = 30;
 
-    function getCookie(name) {
-        var parts = document.cookie.split(name + "=");
-        if (parts.length == 2) {
-            return parts.pop().split(";").shift();
+    // Adapted from https://docs.djangoproject.com/en/1.9/ref/csrf/
+    function _getCookie(name) {
+        var cookieValue = null;
+        if (document.cookie && document.cookie != '') {
+            var cookies = document.cookie.split(';');
+            for (var i = 0; i < cookies.length; i++) {
+                var cookie = $.trim(cookies[i]);
+                // Does this cookie string begin with the name we want?
+                if (cookie.substring(0, name.length + 1) == (name + '=')) {
+                    cookieValue = decodeURIComponent(cookie.substring(name.length + 1));
+                    break;
+                }
+            }
         }
+        return cookieValue;
+    };
+
+    function _removeCookie(name, path) {
+        path = path || "/";
+        var now = new Date();
+        var time = now.getTime();
+        var expireTime = time-(300*1000);
+        now.setTime(expireTime);
+        document.cookie=encodeURIComponent(name)+"=; expires="+new Date(0).toUTCString()+"; path="+path+";";
+    };
+
+    function _setCookie(name,val,path,expires_in) {
+        var now = new Date();
+        var time = now.getTime();
+        expires_in = expires_in || (300*1000);
+        path = path || '/';
+        var expireTime = time+expires_in;
+        now.setTime(expireTime);
+        document.cookie=encodeURIComponent(name)+"="+val+"; expires="+now.toUTCString()+"; path="+path+";";
     };
 
     // Set the cookie to expire Forever Ago so it dies immediately
     // Optional path parameter for path-specific cookies
-    function expireCookie(name,path) {
+    function _expireCookie(name,path) {
         path = path || "/";
         document.cookie = encodeURIComponent(name) + "=deleted; Path="+path+"; expires=" + new Date(0).toUTCString();
     };
@@ -65,7 +94,7 @@ define(['jquery'], function($) {
     // Callback can be used on a given page to unblock any DOM-based impediments
     function unblockSubmit(callback,cookieName) {
         window.clearInterval(downloadTimer);
-        expireCookie(cookieName);
+        _expireCookie(cookieName);
         attempts = 30;
         callback();
     };
@@ -106,12 +135,15 @@ define(['jquery'], function($) {
         // in its response
         blockResubmit: function(callback,downloadToken,expectedCookie) {
             downloadTimer = window.setInterval( function() {
-                var token = getCookie(expectedCookie);
+                var token = _getCookie(expectedCookie);
                 if((token == downloadToken) || (attempts == 0)) {
                     unblockSubmit(callback,expectedCookie);
                 }
                 attempts--;
             }, 1000 );
-        }
+        },
+        setCookie: _setCookie,
+        getCookie: _getCookie,
+        removeCookie: _removeCookie
     };
 });
diff --git a/templates/base.html b/templates/base.html
@@ -93,7 +93,7 @@
 </main>
 
 <!-- Warning Modal -->
-<div class="modal fade" id="gov_warning" tabindex="-1" role="dialog" aria-labelledby="gov_warning-header" aria-hidden="true">
+<div class="modal fade" id="gov_warning" tabindex="-1" role="dialog" data-backdrop="static" aria-labelledby="gov_warning-header" aria-hidden="true">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header">
diff --git a/templates/cohorts/cohort_details.html b/templates/cohorts/cohort_details.html
@@ -63,6 +63,19 @@ <h3 class="pull-left" role="heading" aria-level="1">Cohort Name: {{ cohort.name
     {% include "idc/explore_data_core.html" %}
 {% endwith %}
 
+    <!-- Download In Progress Modal -->
+<div class="modal fade" id="download-in-progress" tabindex="-1" role="dialog" data-backdrop="static" aria-hidden="true">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header"></div>
+            <div class="modal-body">
+                <p><i class="fa fa-cog fa-spin"></i> Preparing manifest for download...</p>
+            </div>
+            <div class="modal-footer"></div>
+        </div>
+    </div>
+</div>
+
 {% endblock %}
 
 {% block js_file %}
diff --git a/templates/idc/explore_data_core.html b/templates/idc/explore_data_core.html
diff --git a/templates/idc/landing.html b/templates/idc/landing.html
