Merge remote-tracking branch 'remotes/origin/master' into tools-module

.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

.github/workflows/ci.yaml

@@ -23,7 +23,7 @@ jobs:
       - uses: actions/checkout@v2
 
       # Caches NPM dependencies, as long as the package-lock.json is not modified
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -50,7 +50,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}

.github/workflows/release.yaml

@@ -23,7 +23,7 @@ jobs:
           node-version: 12
 
       - name: NPM cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}

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/authorship.html

@@ -1,14 +1,12 @@
 <!-- ko if: createdBy && createdDate -->
 <div data-bind="css: classes('container')">
-	<span data-bind="text: createdText"></span>
-	<span data-bind="visible: createdBy, text: ko.i18nformat('components.authorship.byCreated', 'by <%=createdBy%>', {createdBy: createdBy})"></span>
-	<span data-bind="text: ko.i18n('components.authorship.on', 'on')"></span>
-	<span data-bind="text: createdDate"></span><span data-bind="visible: modifiedDate">,</span>
-	<span data-bind="visible: modifiedDate">
-		<span data-bind="text: ko.i18n('components.authorship.modified', 'modified')"></span>
-		<span data-bind="visible: createdBy, text: ko.i18nformat('components.authorship.byModified', 'by <%=modifiedBy%>', {modifiedBy: modifiedBy})"></span>
-		<span data-bind="text: ko.i18n('components.authorship.on', 'on')"></span>
-		<span data-bind="text: modifiedDate"></span>
-	</span>
+	<span data-bind="visible: createdBy,
+	    text: ko.i18nformat('components.authorship.createdLabel',
+						'created by <%=createdBy%> on <%=cratedDate%>',
+						{createdBy: createdBy, createdDate: createdDate})"></span><span data-bind="visible: modifiedDate">,</span>
+    <span data-bind="visible: modifiedDate,
+	    text: ko.i18nformat('components.authorship.modifiedLabel',
+						'modified by <%=modifiedBy%> on <%=modifiedDate%>',
+						{modifiedBy: modifiedBy, modifiedDate: modifiedDate})"></span>
 </div>
-<!-- /ko -->
+<!-- /ko -->

js/components/cohortbuilder/CriteriaGroup.js

@@ -25,7 +25,7 @@ define(function (require, exports, module) {
 
 		if (data.DemographicCriteriaList && data.DemographicCriteriaList.length > 0) {
 			data.DemographicCriteriaList.forEach(function (d) {
-				self.DemographicCriteriaList.push(new DemographicCriteria(d));
+				self.DemographicCriteriaList.push(new DemographicCriteria(d, conceptSets));
 			});
 		}
 

js/components/cohortbuilder/CriteriaTypes/ConditionEra.js

@@ -1,4 +1,4 @@
-define(['knockout', './Criteria', '../InputTypes/Range', 'conceptpicker/InputTypes/Concept'], function (ko, Criteria, Range, Concept) {
+define(['knockout', './Criteria', '../InputTypes/Range', 'conceptpicker/InputTypes/Concept', '../InputTypes/ConceptSetSelection'], function (ko, Criteria, Range, Concept, ConceptSetSelection) {
 
 	function ConditionEra(data, conceptSets) {
 		var self = this;
@@ -35,6 +35,8 @@ define(['knockout', './Criteria', '../InputTypes/Range', 'conceptpicker/InputTyp
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
+
 	}
 
 	ConditionEra.prototype = new Criteria();

js/components/cohortbuilder/CriteriaTypes/ConditionOccurrence.js

@@ -1,4 +1,5 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text'], function (ko, Criteria, Range, Concept, Text) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text', '../InputTypes/ConceptSetSelection'
+], function (ko, Criteria, Range, Concept, Text,ConceptSetSelection) {
 
 	function ConditionOccurrence(data, conceptSets) {
 		var self = this;
@@ -29,11 +30,14 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 			return new Concept(d);
 		})));
 		self.ConditionTypeExclude = ko.observable(data.ConditionTypeExclude || null);
+		self.ConditionTypeCS = ko.observable(data.ConditionTypeCS && new ConceptSetSelection(data.ConditionTypeCS, conceptSets));
+
 		self.StopReason = ko.observable(data.StopReason && new Text(data.StopReason));
 		self.ConditionSourceConcept = ko.observable(data.ConditionSourceConcept != null ? ko.observable(data.ConditionSourceConcept) : null);
 		self.ConditionStatus = ko.observable(data.ConditionStatus && ko.observableArray(data.ConditionStatus.map(function (d) {
 			return new Concept(d);
 		})));
+		self.ConditionStatusCS = ko.observable(data.ConditionStatusCS && new ConceptSetSelection(data.ConditionStatusCS, conceptSets));
 
 		// Derived Fields
 		self.First = ko.observable(data.First || null);
@@ -43,14 +47,17 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 
 		self.ProviderSpecialty = ko.observable(data.ProviderSpecialty && ko.observableArray(data.ProviderSpecialty.map(function (d) {
 			return new Concept(d);
 		})));
+		self.ProviderSpecialtyCS = ko.observable(data.ProviderSpecialtyCS && new ConceptSetSelection(data.ProviderSpecialtyCS, conceptSets));
 
 		self.VisitType = ko.observable(data.VisitType && ko.observableArray(data.VisitType.map(function (d) {
 			return new Concept(d);
 		})));
+		self.VisitTypeCS = ko.observable(data.VisitTypeCS && new ConceptSetSelection(data.VisitTypeCS, conceptSets));
 
 	}
 

js/components/cohortbuilder/CriteriaTypes/Death.js

@@ -1,4 +1,5 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text'], function (ko, Criteria, Range, Concept, Text) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/ConceptSetSelection'], 
+	function (ko, Criteria, Range, Concept, ConceptSetSelection) {
 
 	function Death(data, conceptSets) {
 		var self = this;
@@ -28,6 +29,8 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 			return new Concept(d);
 		})));
 		self.DeathTypeExclude = ko.observable(data.DeathTypeExclude || null);
+		self.DeathTypeCS = ko.observable(data.DeathTypeCS && new ConceptSetSelection(data.DeathTypeCS, conceptSets));
+
 		self.DeathSourceConcept = ko.observable(data.DeathSourceConcept != null ? ko.observable(data.DeathSourceConcept) : null);
 		// Derived Fields
 		self.Age = ko.observable(data.Age && new Range(data.Age));
@@ -36,11 +39,8 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 
-	  /* Do we still need prior enroll days inside the individual criteria?
-		self.PriorEnrollDays = ko.observable((typeof data.PriorEnrollDays == "number") ? data.PriorEnrollDays : null);
-		self.AfterEnrollDays = ko.observable((typeof data.AfterEnrollDays == "number") ? data.AfterEnrollDays : null);
-		*/
 	}
 
 	Death.prototype = new Criteria();

js/components/cohortbuilder/CriteriaTypes/DemographicCriteria.js

@@ -1,4 +1,4 @@
-define(['knockout', '../InputTypes/Range', 'conceptpicker/InputTypes/Concept'], function (ko, Range, Concept) {
+define(['knockout', '../InputTypes/Range', 'conceptpicker/InputTypes/Concept', '../InputTypes/ConceptSetSelection'], function (ko, Range, Concept, ConceptSetSelection) {
 
 	function DemographicCriteria(data, conceptSets) {
 		var self = this;
@@ -9,14 +9,17 @@ define(['knockout', '../InputTypes/Range', 'conceptpicker/InputTypes/Concept'],
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 
 		self.Race = ko.observable(data.Race && ko.observableArray(data.Race.map(function (d) {
 			return new Concept(d);
 		})));
+		self.RaceCS = ko.observable(data.RaceCS && new ConceptSetSelection(data.RaceCS, conceptSets));
 
 		self.Ethnicity = ko.observable(data.Ethnicity && ko.observableArray(data.Ethnicity.map(function (d) {
 			return new Concept(d);
 		})));
+		self.EthnicityCS = ko.observable(data.EthnicityCS && new ConceptSetSelection(data.EthnicityCS, conceptSets));
 
 
 		self.OccurrenceStartDate = ko.observable(data.OccurrenceStartDate && new Range(data.OccurrenceStartDate));

js/components/cohortbuilder/CriteriaTypes/DeviceExposure.js

@@ -1,4 +1,4 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text'], function (ko, Criteria, Range, Concept, Text) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text', '../InputTypes/ConceptSetSelection'], function (ko, Criteria, Range, Concept, Text, ConceptSetSelection) {
 
 	function DeviceOccurence(data, conceptSets) {
 		var self = this;
@@ -29,6 +29,8 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 			return new Concept(d);
 		})));
 		self.DeviceTypeExclude = ko.observable(data.DeviceTypeExclude || null);
+		self.DeviceTypeCS = ko.observable(data.DeviceTypeCS && new ConceptSetSelection(data.DeviceTypeCS, conceptSets));
+
 		self.UniqueDeviceId = ko.observable(data.UniqueDeviceId && new Text(data.StopReason));
 		self.Quantity = ko.observable(data.Quantity && new Range(data.Quantity));
 		self.DeviceSourceConcept = ko.observable(data.DeviceSourceConcept != null ? ko.observable(data.DeviceSourceConcept) : null);
@@ -41,18 +43,17 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 
-	  /* Do we still need prior enroll days inside the individual criteria?
-		self.PriorEnrollDays = ko.observable((typeof data.PriorEnrollDays == "number") ? data.PriorEnrollDays : null);
-		self.AfterEnrollDays = ko.observable((typeof data.AfterEnrollDays == "number") ? data.AfterEnrollDays : null);
-		*/
-
 		self.ProviderSpecialty = ko.observable(data.ProviderSpecialty && ko.observableArray(data.ProviderSpecialty.map(function (d) {
 			return new Concept(d);
 		})));
+		self.ProviderSpecialtyCS = ko.observable(data.ProviderSpecialtyCS && new ConceptSetSelection(data.ProviderSpecialtyCS, conceptSets));
+
 		self.VisitType = ko.observable(data.VisitType && ko.observableArray(data.VisitType.map(function (d) {
 			return new Concept(d);
 		})));
+		self.VisitTypeCS = ko.observable(data.VisitTypeCS && new ConceptSetSelection(data.VisitTypeCS, conceptSets));
 
 	}
 

js/components/cohortbuilder/CriteriaTypes/DoseEra.js

@@ -1,4 +1,4 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept'], function (ko, Criteria, Range, Concept) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/ConceptSetSelection'], function (ko, Criteria, Range, Concept, ConceptSetSelection) {
 
 	function DoseEra(data, conceptSets) {
 		var self = this;
@@ -26,6 +26,8 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Unit = ko.observable(data.Unit && ko.observableArray(data.Unit.map(function (d) {
 			return new Concept(d);
 		}))); 
+		self.UnitCS = ko.observable(data.UnitCS && new ConceptSetSelection(data.UnitCS, conceptSets));
+
 		self.DoseValue = ko.observable(data.DoseValue && new Range(data.DoseValue));
 		self.EraLength = ko.observable(data.EraLength && new Range(data.EraLength));
 
@@ -38,6 +40,8 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
+
 	}
 
 	DoseEra.prototype = new Criteria();

js/components/cohortbuilder/CriteriaTypes/DrugEra.js

@@ -1,4 +1,4 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept'], function (ko, Criteria, Range, Concept) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/ConceptSetSelection'], function (ko, Criteria, Range, Concept, ConceptSetSelection) {
 
 	function DrugEra(data, conceptSets) {
 		var self = this;
@@ -36,6 +36,7 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 	}
 
 	DrugEra.prototype = new Criteria();

js/components/cohortbuilder/CriteriaTypes/DrugExposure.js

@@ -1,4 +1,5 @@
-define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text'], function (ko, Criteria, Range, Concept, Text) {
+define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputTypes/Concept', '../InputTypes/Text','../InputTypes/ConceptSetSelection'
+], function (ko, Criteria, Range, Concept, Text, ConceptSetSelection) {
 
 	function DrugExposure(data, conceptSets) {
 		var self = this;
@@ -29,17 +30,20 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 			return new Concept(d);
 		})));
 		self.DrugTypeExclude = ko.observable(data.DrugTypeExclude || null);		
+		self.DrugTypeCS = ko.observable(data.DrugTypeCS && new ConceptSetSelection(data.DrugTypeCS, conceptSets));
 		self.StopReason = ko.observable(data.StopReason && new Text(data.StopReason));
 		self.Refills = ko.observable(data.Refills && new Range(data.Refills));
 		self.Quantity = ko.observable(data.Quantity && new Range(data.Quantity));
 		self.DaysSupply = ko.observable(data.DaysSupply && new Range(data.DaysSupply));
 		self.RouteConcept = ko.observable(data.RouteConcept && ko.observableArray(data.RouteConcept.map(function (d) {
 			return new Concept(d);
 		})));
+		self.RouteConceptCS = ko.observable(data.RouteConceptCS && new ConceptSetSelection(data.RouteConceptCS, conceptSets));
 		self.EffectiveDrugDose = ko.observable(data.EffectiveDrugDose && new Range(data.EffectiveDrugDose));
 		self.DoseUnit = ko.observable(data.DoseUnit && ko.observableArray(data.DoseUnit.map(function (d) {
 			return new Concept(d);
 		})));
+		self.DoseUnitCS = ko.observable(data.DoseUnitCS && new ConceptSetSelection(data.DoseUnitCS, conceptSets));
 		self.LotNumber = ko.observable(data.LotNumber && new Text(data.LotNumber));
 		self.DrugSourceConcept = ko.observable(data.DrugSourceConcept != null ? ko.observable(data.DrugSourceConcept) : null);
 
@@ -51,18 +55,17 @@ define(['knockout', './Criteria', '../InputTypes/Range','conceptpicker/InputType
 		self.Gender = ko.observable(data.Gender && ko.observableArray(data.Gender.map(function (d) {
 			return new Concept(d);
 		})));
+		self.GenderCS = ko.observable(data.GenderCS && new ConceptSetSelection(data.GenderCS, conceptSets));
 
-	  /* Do we still need prior enroll days inside the individual criteria?
-		self.PriorEnrollDays = ko.observable((typeof data.PriorEnrollDays == "number") ? data.PriorEnrollDays : null);
-		self.AfterEnrollDays = ko.observable((typeof data.AfterEnrollDays == "number") ? data.AfterEnrollDays : null);
-		*/
-
 		self.ProviderSpecialty = ko.observable(data.ProviderSpecialty && ko.observableArray(data.ProviderSpecialty.map(function (d) {
 			return new Concept(d);
 		})));
+		self.ProviderSpecialtyCS = ko.observable(data.ProviderSpecialtyCS && new ConceptSetSelection(data.ProviderSpecialtyCS, conceptSets));
+
 		self.VisitType = ko.observable(data.VisitType && ko.observableArray(data.VisitType.map(function (d) {
 			return new Concept(d);
 		})));
+		self.VisitTypeCS = ko.observable(data.VisitTypeCS && new ConceptSetSelection(data.VisitTypeCS, conceptSets));
 
 	}