Merge branch 'OHDSI:master' into master

.editorconfig

@@ -0,0 +1,13 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 2
+end_of_line = crlf
+charset = utf-8
+trim_trailing_whitespace = false
+insert_final_newline = false
+quote_type = single

Dockerfile

@@ -26,7 +26,7 @@ RUN find . -type f "(" \
       | xargs -0 -n 1 gzip -kf
 
 # Production Nginx image
-FROM docker.io/nginxinc/nginx-unprivileged:1.23.3-alpine@sha256:c748ba587e7436aaa8729b64d4e0412410a486f0c592f0eec100fb3804ff9afd
+FROM docker.io/nginxinc/nginx-unprivileged:1.27.2-alpine
 
 LABEL org.opencontainers.image.title="OHDSI-Atlas"
 LABEL org.opencontainers.image.authors="Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com, Shaun Turner<[email protected]>"

js/components/atlas-state.js

@@ -13,23 +13,28 @@ define(['knockout', 'lscache', 'services/job/jobDetail', 'assets/ohdsi.util', 'c
 	state.vocabularyUrl = ko.observable(sessionStorage.vocabularyUrl);
 	state.evidenceUrl = ko.observable(sessionStorage.evidenceUrl);
 	state.resultsUrl = ko.observable(sessionStorage.resultsUrl);
+	state.currentVocabularyVersion = ko.observable(sessionStorage.currentVocabularyVersion);
 	state.vocabularyUrl.subscribe(value => updateKey('vocabularyUrl', value));
 	state.evidenceUrl.subscribe(value => updateKey('evidenceUrl', value));
 	state.resultsUrl.subscribe(value => updateKey('resultsUrl', value));
+	state.currentVocabularyVersion.subscribe(value => updateKey('currentVocabularyVersion', value));
 
 	// This default values are stored during initialization
 	// and used to reset after session finished
 	state.defaultVocabularyUrl = ko.observable();
 	state.defaultEvidenceUrl = ko.observable();
 	state.defaultResultsUrl = ko.observable();
+	state.defaultVocabularyVersion = ko.observable();
 	state.defaultVocabularyUrl.subscribe((value) => state.vocabularyUrl(value));
 	state.defaultEvidenceUrl.subscribe((value) => state.evidenceUrl(value));
 	state.defaultResultsUrl.subscribe((value) => state.resultsUrl(value));
+	state.defaultVocabularyVersion.subscribe((value) => state.currentVocabularyVersion(value));
 
 	state.resetCurrentDataSourceScope = function() {
 		state.vocabularyUrl(state.defaultVocabularyUrl());
 		state.evidenceUrl(state.defaultEvidenceUrl());
 		state.resultsUrl(state.defaultResultsUrl());
+		state.currentVocabularyVersion(state.defaultVocabularyVersion());
 	}
 
 	state.sourceKeyOfVocabUrl = ko.computed(() => {

js/components/conceptAddBox/concept-add-box.js

@@ -157,6 +157,20 @@ define([
 
       sharedState.activeConceptSet(conceptSet);
 
+      const filterSource = localStorage?.getItem('filter-source') || null;
+      const filterData = JSON.parse(localStorage?.getItem('filter-data') || null);
+      const datasAdded = JSON.parse(localStorage?.getItem('data-add-selected-concept') || null) || [];
+      const dataSearch = { filterData, filterSource }
+      const payloadAdd = this.conceptsToAdd().map(item => {
+        return {
+          "searchData": dataSearch,
+          "vocabularyVersion": sharedState.currentVocabularyVersion(),
+          "conceptId": item.CONCEPT_ID
+        }
+      })
+
+      localStorage.setItem('data-add-selected-concept', JSON.stringify([...datasAdded, ...payloadAdd]))
+
       // if concepts were previewed, then they already built and can have individual option flags!
       if (this.previewConcepts().length > 0) {
         if (!conceptSet.current()) {

js/components/conceptset/const.js

@@ -14,6 +14,7 @@ define([
 		RECOMMEND: 'recommend',
 		EXPORT: 'conceptset-export',
 		IMPORT: 'conceptset-import',
+		ANNOTATION: 'annotation'
 	};
 
 	const ConceptSetSources = {

js/components/faceted-datatable.js

@@ -68,7 +68,52 @@ define(['knockout', 'text!./faceted-datatable.html', 'crossfilter', 'utils/Commo
 
 		self.outsideFilters = (params.outsideFilters || ko.observable()).extend({notify: 'always'});
 
+		self.setDataLocalStorage = (data, nameItem) => {
+			const filterArrayString = localStorage.getItem(nameItem)
+			let filterArrayObj = filterArrayString? JSON.parse(filterArrayString): []
+
+			if(!data?.selected()){
+				filterArrayObj.push({title:data.facet.caption(), value:`${data.key} (${data.value})`,key:data.key})
+			}else{
+				filterArrayObj = filterArrayObj.filter((item)=> item.key !== data.key)
+			}
+			localStorage.setItem(nameItem, JSON.stringify(filterArrayObj))
+		}
+
+		self.setDataObjectLocalStorage = (data, nameItem) => {
+			const filterObjString = localStorage.getItem(nameItem)
+			let filterObj = filterObjString ? JSON.parse(filterObjString): {}
+			let newFilterObj = {}
+
+			if(!data?.selected()){
+				const dataPush = { title: data.facet.caption(), value: `${data.key} (${data.value})`, key: data.key };
+				newFilterObj.filterColumns = filterObj['filterColumns'] ? [...filterObj['filterColumns'], dataPush] : [dataPush]
+				newFilterObj = { ...filterObj, filterColumns : newFilterObj.filterColumns };
+			}else{
+				newFilterObj.filterColumns = filterObj['filterColumns'].filter((item)=> item.key !== data.key);
+				newFilterObj = { ...filterObj, filterColumns : newFilterObj.filterColumns };
+			}
+			localStorage.setItem(nameItem, JSON.stringify(newFilterObj))
+		}
+
 		self.updateFilters = function (data, event) {
+			const currentPath = window.location?.href;
+			if (currentPath?.includes('/conceptset/')) {
+				if (currentPath?.includes('/included-sourcecodes')) {
+					localStorage.setItem('filter-source', 'Included Source Codes');
+				} else if (currentPath?.includes('/included')) {
+					localStorage.setItem('filter-source', 'Included Concepts');
+				}
+				self.setDataLocalStorage(data, 'filter-data');
+			}
+			const isAddConcept = currentPath?.split('?').reduce((prev, curr) => prev || curr.includes('search'), false) &&
+				currentPath?.split('?').reduce((prev, curr) => prev || curr.includes('query'), false) ||
+				currentPath?.includes('/concept/')
+
+			if (isAddConcept) {
+				localStorage.setItem('filter-source', 'Search');
+				self.setDataObjectLocalStorage(data, 'filter-data')
+			}
 			var facet = data.facet;
 			data.selected(!data.selected());
 			if (data.selected()) {

js/components/multi-select.html

@@ -1,8 +1,8 @@
 <div class="multi-select" data-bind="eventListener: [{event: 'hide.bs.dropdown', selector: 'div.dropdown.bootstrap-select', callback: onSelectionComplete}]">
     <!-- ko if: multiple == true -->
-        <select data-bind="selectedOptions: selectedValues, options: optionVals, optionsText: optionsText, multiSelect: { liveSearch: true, selectedTextFormat: selectedTextFormat, noneSelectedText: ko.unwrap(noneSelectedText), noneResultsText: ko.unwrap(noneResultsText), countSelectedText: ko.unwrap(countSelectedText) }" multiple></select>
+        <select data-bind="attr: disabled, selectedOptions: selectedValues, options: optionVals, optionsText: optionsText, multiSelect: { liveSearch: true, selectedTextFormat: selectedTextFormat, noneSelectedText: ko.unwrap(noneSelectedText), noneResultsText: ko.unwrap(noneResultsText), countSelectedText: ko.unwrap(countSelectedText) }" multiple></select>
     <!-- /ko -->
     <!-- ko if: multiple == false -->
-        <select data-bind="options: options, value: selectedValue, optionsText: 'label', optionsValue: 'value', multiSelect: { liveSearch: true, selectedTextFormat: 'count > 2', noneSelectedText: ko.unwrap(noneSelectedText), noneResultsText: ko.unwrap(noneResultsText) }"></select>
+        <select data-bind="attr: disabled, options: options, value: selectedValue, optionsText: 'label', optionsValue: 'value', multiSelect: { liveSearch: true, selectedTextFormat: 'count > 2', noneSelectedText: ko.unwrap(noneSelectedText), noneResultsText: ko.unwrap(noneResultsText) }"></select>
     <!-- /ko -->
 </div>

js/components/multi-select.js

@@ -14,6 +14,7 @@ define(
 
       self.multiple = params.multiple;
       self.options = params.options;
+	  self.disable = (params.disable || false);
       self.selectedValues = ko.observableArray(params.selectedValues && params.selectedValues());
       self.selectedValue = params.selectedValue;
       self.selectedTextFormat = params.selectedTextFormat || 'count > 2';

js/components/reports/classes/Treemap.js

@@ -146,10 +146,10 @@ define([
 			data
 		}) {
 			const normalizedData = atlascharts.chart.normalizeDataframe(ChartUtils.normalizeArray(data, true));
+			let tableData = [];
 
 			if (!normalizedData.empty) {
 				let distinctConceptIds = new Set([]);
-				let tableData = [];
 				// Make the values unique per https://github.com/OHDSI/Atlas/issues/913
 				normalizedData.conceptPath.forEach((d, i) => {
 					if (!distinctConceptIds.has(normalizedData.conceptId[i])) {
@@ -165,14 +165,13 @@ define([
 						});
 					}
 				});
-				this.tableData(tableData); 
 				this.treeData(normalizedData);
-
-				return {
-					data
-				};
 			}
+			this.tableData(tableData);
 
+			return {
+				data
+			};
 		}
 
 		getData() {

js/components/reports/reportDrilldown.js

@@ -234,7 +234,7 @@ define([
 					this.chartFormats.frequencyDistribution.yMax = yScaleMax;
 					this.chartFormats.frequencyDistribution.xLabel = ko.pureComputed(function () {
 						return ko.i18n('dataSources.drilldown.chartFormat.frequencyDistribution.xLabel1', 'Count ("x" or more ')() +
-							report() +
+							report +
 							ko.i18n('dataSources.drilldown.chartFormat.frequencyDistribution.xLabel2', 's)')();
 					});
 					this.chartFormats.frequencyDistribution.ticks = Math.min(5, frequencyHistogram.INTERVALS);

js/pages/characterizations/components/feature-analyses/fa-view-edit/fa-design.html

@@ -16,13 +16,13 @@
             <!-- /ko -->
             <textarea data-bind="
                     css: classes({ element: 'descr', extra: 'form-control' }),
-                    attr: { disabled: $component.canEdit() ? null : true },
+					attr: { disabled: $component.canEdit() ? null : true }
                     textInput: $component.data().descr
                 "></textarea>
         </div>
     </div>
 
-    <div data-bind="css: classes({ element: 'design-panel', extra: 'panel panel-primary' })">
+    <div data-bind="css: classes({ element: 'design-panel', extra: 'panel panel-primary'})">
         <div class="panel-heading" data-bind="text: ko.i18n('cc.fa.design', 'Design')"></div>
         <div data-bind="css: classes({ element: 'design-panel-body' })">
             <div data-bind="css: classes('type-selector')">
@@ -32,6 +32,7 @@
                         data-bind="
                             if: $component.canEdit() || $component.data().type() === $component.featureTypes.PRESET,
                             css: classes({ element: 'nav-pill', extra: $component.data().type() === $component.featureTypes.PRESET ? 'active' : null }),
+							attr: { disabled: $component.canEdit() ? null : true },
                             click: setType.bind(null, $component.featureTypes.PRESET)
                         ">
                         <a data-bind="text: ko.i18n('cc.fa.preset', 'Preset')"></a>
@@ -44,6 +45,7 @@
                         data-bind="
                             if: ($component.canEdit() && !$component.featureId()) || $component.data().type() === $component.featureTypes.CRITERIA_SET,
                             css: classes({ element: 'nav-pill', extra: $component.data().type() === $component.featureTypes.CRITERIA_SET ? 'active' : null }),
+							attr: { disabled: $component.canEdit() ? null : true },
                             click: setType.bind(null, $component.featureTypes.CRITERIA_SET)
                         ">
                         <a data-bind="text: ko.i18n('cc.fa.criteria', 'Criteria')"></a>
@@ -52,6 +54,7 @@
                         data-bind="
                             if: ($component.canEdit() && !$component.featureId()) || $component.data().type() === $component.featureTypes.CUSTOM_FE,
                             css: classes({ element: 'nav-pill', extra: $component.data().type() === $component.featureTypes.CUSTOM_FE ? 'active' : null }),
+							attr: { disabled: $component.canEdit() ? null : true },
                             click: setType.bind(null, $component.featureTypes.CUSTOM_FE)
                         ">
                         <a data-bind="text: ko.i18n('cc.fa.custom', 'Custom')"></a>
@@ -63,27 +66,27 @@
                 <span data-bind="css: classes('criteria-descr'), text: ko.i18n('cc.fa.featureExtractionPresetName', 'FeatureExtraction preset name:')"></span>
                 <input data-bind="
                         css: classes({ element: 'preset-input', extra: 'form-control' }),
-                        attr: { disabled: $component.canEdit() ? null : true },
                         textInput: $component.data().design
                     " />
             </div>
             <!-- /ko -->
             <div data-bind="
-                    if: $component.data().type() === $component.featureTypes.CRITERIA_SET, css: classes('design')
+                    if: $component.data().type() === $component.featureTypes.CRITERIA_SET, 
+					css: classes('design')
                 ">
                 <div data-bind="css: classes({extra: 'panel panel-primary'})">
                     <div data-bind="css: classes({ extra: 'panel-heading' }), text: ko.i18n('cc.fa.analysisType', 'Analysis type:')"></div>
                     <div data-bind="css: classes('stat-type-selector')">
                         <multi-select
                                 data-bind="css: classes()"
-                                params="options: $component.statTypeOptions,
+                                params="options: $component.statTypeOptions,  disable: !$component.canEdit(),
                                 selectedValue: $component.data().statType, multiple: false"></multi-select>
                     </div>
                 </div>
                 <span data-bind="if: data().statType() === 'PREVALENCE'">
-                        <button data-bind="css: classes({ element: 'add-criteria-group', extra: 'btn btn-success' }), click: addCriteria, text: ko.i18n('cc.fa.addCriteriaFeature', 'Add Criteria feature')"></button>
+                        <button data-bind="css: classes({ element: 'add-criteria-group', extra: 'btn btn-success' }), attr: { disabled: $component.canEdit() ? null : true }, click: addCriteria, text: ko.i18n('cc.fa.addCriteriaFeature', 'Add Criteria feature')"></button>
                     </span>
-                <span data-bind="if: data().statType() === 'DISTRIBUTION', css: classes('add-criteria-windowed')">
+                <span data-bind="if: data().statType() === 'DISTRIBUTION', css: classes('add-criteria-windowed'), attr: { disabled: $component.canEdit() ? null : true }">
                         <div>
                             <div class="btn-group">
                                 <button type="button" class="btn btn-primary btn-sm dropdown-toggle" data-toggle="dropdown"><i class="fa fa-plus"></i>
@@ -100,35 +103,37 @@
                         </div>
                     </span>
                 <!-- ko foreach: $component.data().design -->
-                <div data-bind="
-                            css: $component.classes('criteria'),
-                            eventListener: [
-                                { event: 'click', selector: '.conceptset_import', callback: $component.handleConceptSetImport},
-                                { event: 'click', selector: '.conceptset_edit', callback: $component.handleEditConceptSet }
-                            ]
-                        ">
-                    <div data-bind="css: $component.classes('criteria-heading')">
-                        <input
-                                data-bind="css: $component.classes({ element: 'criteria-name', extra: 'form-control' }), textInput: $data.name, placeholder: ko.i18n('cc.fa.criteriaName', 'Criteria name')"
-                        />
-                        <button
-                                type="button"
-                                data-bind="css: $component.classes({ element: 'criteria-delete', extra: 'btn btn-sm btn-danger' }), click: () => $component.removeCriteria($index())"
-                        ><i class="fa fa-trash-alt"></i></button>
-                    </div>
-                    <!-- Aggregate -->
-                    <div data-bind="if: $parent.data().statType() === 'DISTRIBUTION' && $data.criteriaType !== 'DemographicCriteria'">
-                        <aggregate-select params="aggregates: $component.aggregates, currentAggregate: $data.aggregate, domains: $component.domains, criteria: $data"></aggregate-select>
-                    </div>
-                    <div data-bind="if: $data.criteriaType === 'CriteriaGroup'">
-                        <criteria-group params="{ expression: { ConceptSets: $component.data().conceptSets }, group: $data.expression }"></criteria-group>
-                    </div>
-                    <div data-bind="if: $data.criteriaType === 'DemographicCriteria'">
-                        <demographic-criteria params="{ criteria: $data.expression }"></demographic-criteria>
-                    </div>
-                    <div data-bind="if: $data.criteriaType === 'WindowedCriteria'">
-                        <windowed-criteria params="{ expression: { ConceptSets: $component.data().conceptSets }, criteria: $data.expression, disableObservationPeriod: true, defaultObservationPeriod: true }"></windowed-criteria>
-                    </div>
+				<div data-bind="css: $component.canEdit() ? '' : 'feature-analysis-view-edit__content--disabled'">
+					<div data-bind="
+								css: $component.classes('criteria'),
+								eventListener: [
+									{ event: 'click', selector: '.conceptset_import', callback: $component.handleConceptSetImport},
+									{ event: 'click', selector: '.conceptset_edit', callback: $component.handleEditConceptSet }
+								]
+							">
+						<div data-bind="css: $component.classes('criteria-heading')">
+							<input
+									data-bind="css: $component.classes({ element: 'criteria-name', extra: 'form-control' }), textInput: $data.name, placeholder: ko.i18n('cc.fa.criteriaName', 'Criteria name')"
+							/>
+							<button
+									type="button"
+									data-bind="css: $component.classes({ element: 'criteria-delete', extra: 'btn btn-sm btn-danger' }), attr: { disabled: $component.canEdit() ? null : true }, click: () => $component.removeCriteria($index())"
+							><i class="fa fa-trash-alt"></i></button>
+						</div>
+						<!-- Aggregate -->
+						<div data-bind="if: $parent.data().statType() === 'DISTRIBUTION' && $data.criteriaType !== 'DemographicCriteria'">
+							<aggregate-select params="aggregates: $component.aggregates, currentAggregate: $data.aggregate, domains: $component.domains, criteria: $data"></aggregate-select>
+						</div>
+						<div data-bind="if: $data.criteriaType === 'CriteriaGroup'">
+							<criteria-group params="{ expression: { ConceptSets: $component.data().conceptSets }, group: $data.expression}"></criteria-group>
+						</div>
+						<div data-bind="if: $data.criteriaType === 'DemographicCriteria'">
+							<demographic-criteria params="{ criteria: $data.expression }"></demographic-criteria>
+						</div>
+						<div data-bind="if: $data.criteriaType === 'WindowedCriteria'">
+							<windowed-criteria params="{ expression: { ConceptSets: $component.data().conceptSets }, criteria: $data.expression, disableObservationPeriod: true, defaultObservationPeriod: true }"></windowed-criteria>
+						</div>
+					</div>
                 </div>
                 <!-- /ko -->
             </div>
@@ -146,7 +151,7 @@
                     <span data-bind="css: classes('criteria-sql')">SELECT covariate_id, covariate_name, concept_id, sum_value, average_value FROM (</span>
                     <textarea data-bind="
                             css: classes({ element: 'raw-sql-box', extra: 'form-control' }),
-                            attr: { disabled: $component.canEdit() ? null : true, placeholder: demoCustomSqlAnalysisDesign },
+                            attr: { placeholder: demoCustomSqlAnalysisDesign },
                             textInput: $component.data().design
                         "></textarea>
                     <span data-bind="css: classes('criteria-sql')">)</span>

js/pages/characterizations/components/feature-analyses/feature-analysis-view-edit.html

@@ -38,7 +38,7 @@
     </div>
 
     <!-- ko if: selectedTabKey -->
-    <tabs data-bind="css: editorClasses(), visible: !$component.loading()" params="
+    <tabs data-bind="visible: !$component.loading()" params="
             selectedTabKey: $component.selectedTabKey,
         selectTab: $component.selectTab,
         tabs: $component.tabs">