Merge pull request #443 from medizininformatik-initiative/425-update-ui-profile-model-to-allow-support-of-multiple-value-sets

425 update UI profile model to allow support of multiple value sets

Author: Shayan1375

.github/scripts/setup-ontology.sh

@@ -1,8 +1,8 @@
 #!/bin/bash -e
 
-ONTOLOGY_GIT_TAG=${ONTOLOGY_GIT_TAG:-v3.8.1}
+ONTOLOGY_GIT_TAG=${ONTOLOGY_GIT_TAG:-v3.9.0-experimental.0}
 
-BASE_DIR="cypress/docker/ontology"
+BASE_DIR="../../cypress/docker/ontology"
 DSE_DIR="$BASE_DIR/dse"
 MIGRATION_DIR="$BASE_DIR/migration"
 
@@ -13,7 +13,7 @@ curl -fsSL -o "$BASE_DIR/backend.zip" \
   "https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download/${ONTOLOGY_GIT_TAG}/backend.zip"
 
 echo "Unzipping all files to ontology folder..."
-unzip -oj "$BASE_DIR/backend.zip" -d "$BASE_DIR"
+unzip -oj -o "$BASE_DIR/backend.zip" -d "$BASE_DIR"
 
 echo "Moving profile_tree.json to ontology/dse/ folder..."
 mv "$BASE_DIR/profile_tree.json" "$DSE_DIR/" 2>/dev/null || true
@@ -26,7 +26,11 @@ curl -fsSL -o "$BASE_DIR/elastic.zip" \
   "https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download/${ONTOLOGY_GIT_TAG}/elastic.zip"
 
 echo "Cleaning up zip..."
-rm "$BASE_DIR/backend.zip"
+#rm "$BASE_DIR/backend.zip"
+
+chmod 644 "$BASE_DIR"/*.zip
+chmod 644 "$DSE_DIR"/* || true
+chmod 644 "$MIGRATION_DIR"/* || true
 
 echo "Final files:"
 ls -l "$BASE_DIR"

.github/workflows/e2e.yml

@@ -11,7 +11,7 @@ jobs:
   cypress-run:
     runs-on: ubuntu-24.04
     env:
-      ONTOLOGY_GIT_TAG: v3.8.1 # Or dynamically set it
+      ONTOLOGY_GIT_TAG: v3.9.0-experimental.0 # Or dynamically set it
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
@@ -65,9 +65,6 @@ jobs:
         run: .github/scripts/create-keycloak-user.sh
 
 
-      - name: Checkout
-        uses: actions/checkout@v4
-
       - name: Cypress install
         uses: cypress-io/github-action@v6
         with:

angular.json

@@ -74,7 +74,7 @@
                 {
                   "type": "anyComponentStyle",
                   "maximumWarning": "6kb",
-                  "maximumError": "10kb"
+                  "maximumError": "20kb"
                 }
               ]
             },
@@ -94,7 +94,7 @@
                 {
                   "type": "anyComponentStyle",
                   "maximumWarning": "6kb",
-                  "maximumError": "10kb"
+                  "maximumError": "20kb"
                 }
               ]
             }

cypress/docker/docker-compose.yml

@@ -3,7 +3,7 @@
 services:
   dataportal-backend:
     container_name: dataportal-backend
-    image:  ghcr.io/medizininformatik-initiative/feasibility-backend:latest
+    image:  ghcr.io/medizininformatik-initiative/feasibility-backend:pr-600
     ports:
       - "8090:8090"
     depends_on:
@@ -27,6 +27,9 @@ services:
       DATABASE_USER: "dataportaluser"
       DATABASE_PASSWORD: "dataportalpw"
       DATABASE_DBNAME: "dataportal"
+      ONTOLOGY_DB_MIGRATION_FOLDER: "/opt/dataportal-backend/ontology/migration"
+      DSE_PROFILE_TREE_FILE: "/opt/dataportal-backend/ontology/dse/profile_tree.json"
+      TERMINOLOGY_SYSTEMS_FILE: "/opt/dataportal-backend/ontology/terminology_systems.json"
       # ---- auth
       KEYCLOAK_ENABLED: "true"
       KEYCLOAK_ALLOWED_ROLE: "DataportalUser"
@@ -63,6 +66,7 @@ services:
     restart: unless-stopped
     volumes:
       - ./secrets:/opt/dataportal-security
+      - ./ontology:/opt/ontology:ro
 
   dataportal-postgres:
     image: 'postgres:16-alpine'
@@ -75,7 +79,7 @@ services:
       POSTGRES_DB: "dataportal"
 
   dataportal-elastic:
-    image: docker.elastic.co/elasticsearch/elasticsearch:9.0.2
+    image: docker.elastic.co/elasticsearch/elasticsearch:9.1.3
     container_name: dataportal-elastic
     ports:
       - '9200:9200'
@@ -95,11 +99,14 @@ services:
   elastic-search-init:
     depends_on:
       - dataportal-elastic
-    image: ghcr.io/medizininformatik-initiative/dataportal-es-init:1.2
-    container_name: integration-test_elastic-search-init
+    image: ghcr.io/medizininformatik-initiative/dataportal-es-init:latest
+    container_name: elastic-search-init
     environment:
       ES_HOST: dataportal-elastic
-      LOCAL_PATH: /tmp/mounted_onto.zip
+      ONTO_GIT_TAG: v3.9.0-experimental.0
+      ONTO_REPO: https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download
+      DOWNLOAD_FILENAME: elastic.zip
+      EXIT_ON_EXISTING_INDICES: false
     volumes:
       - type: bind
         source: "./ontology/elastic.zip"

cypress/e2e/CohortSearch/cohort-search.feature

@@ -16,7 +16,7 @@ Feature: Cohort Search
 
     Examples: Search Criteria
       | criterium                       | button1                          | button2                    |
-      | Aktuelles chronologisches Alter | Zur Kohortenselektion hinzufügen | Kohortenselektion anzeigen |
+      | Alter | Zur Kohortenselektion hinzufügen | Kohortenselektion anzeigen |
       | Diabetes                        | Zur Kohortenselektion hinzufügen | Kohortenselektion anzeigen |
 
   Scenario Outline: Select Cohort elements
@@ -30,4 +30,4 @@ Feature: Cohort Search
 
     Examples: Selection Criteria
       | criterium                       | button1                          | button2                    |
-      | Aktuelles chronologisches Alter | Zur Kohortenselektion hinzufügen | Kohortenselektion anzeigen |
+      | Alter | Zur Kohortenselektion hinzufügen | Kohortenselektion anzeigen |

src/app/model/FeasibilityQuery/Criterion/AttributeFilter/AttributeFiltersBuilder.ts

@@ -118,8 +118,8 @@ export class AttributeFiltersBuilder {
     return new QuantityNotSet(allowedUnits, selectedUnit, precision);
   }
 
-  buildConceptFilter(id: string, allowedConceptUri: string, selectedConcepts?: Concept[]) {
-    return new ConceptFilter(id, [allowedConceptUri], selectedConcepts);
+  buildConceptFilter(id: string, allowedConceptUri: string[], selectedConcepts?: Concept[]) {
+    return new ConceptFilter(id, allowedConceptUri, selectedConcepts);
   }
 
   /**
@@ -129,7 +129,7 @@ export class AttributeFiltersBuilder {
    */
   buildReferenceFilter(
     id: string,
-    allowedReferenceUri: string,
+    allowedReferenceUri: string[],
     selectedReference?: ReferenceCriterion[],
     selectedConcepts?: Concept[]
   ): ReferenceFilter {

src/app/model/FeasibilityQuery/Criterion/AttributeFilter/Concept/ReferenceFilter.ts

@@ -1,15 +1,14 @@
 import { AbstractConceptFilter } from './AbstractConceptFilter';
+import { Concept } from './Concept';
 import { FilterTypes } from 'src/app/model/Utilities/FilterTypes';
 import { ReferenceCriterion } from '../../ReferenceCriterion';
-import { TerminologyCode } from 'src/app/model/Terminology/TerminologyCode';
-import { Concept } from './Concept';
 
 /**
  * Class representing a ReferenceFilter.
  */
 export class ReferenceFilter extends AbstractConceptFilter {
+  private allowedReferenceUri: string[];
   private selectedReferences: ReferenceCriterion[] = [];
-  private allowedReferenceUri: string;
   private type: FilterTypes = FilterTypes.REFERENCE;
 
   /**
@@ -21,7 +20,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    */
   constructor(
     id: string,
-    allowedReferenceUri: string,
+    allowedReferenceUri: string[],
     selectedReferences: ReferenceCriterion[] = [],
     selectedConcepts: Concept[]
   ) {
@@ -35,7 +34,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @returns An array of selected reference criteria.
    */
-  getSelectedReferences(): ReferenceCriterion[] {
+  public getSelectedReferences(): ReferenceCriterion[] {
     return this.selectedReferences;
   }
 
@@ -44,7 +43,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @param selectedReferences - An array of selected reference criteria.
    */
-  setSelectedReferences(selectedReferences: ReferenceCriterion[]): void {
+  public setSelectedReferences(selectedReferences: ReferenceCriterion[]): void {
     this.selectedReferences = selectedReferences;
   }
 
@@ -53,7 +52,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @returns The allowed reference URI.
    */
-  getAllowedReferenceUri(): string {
+  public getAllowedReferenceUri(): string[] {
     return this.allowedReferenceUri;
   }
 
@@ -62,7 +61,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @param allowedReferenceUri - The allowed reference URI to set.
    */
-  setAllowedReferenceUri(allowedReferenceUri: string): void {
+  public setAllowedReferenceUri(allowedReferenceUri: string[]): void {
     this.allowedReferenceUri = allowedReferenceUri;
   }
 
@@ -71,7 +70,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @returns The filter type.
    */
-  getType(): FilterTypes {
+  public getType(): FilterTypes {
     return this.type;
   }
 
@@ -80,7 +79,7 @@ export class ReferenceFilter extends AbstractConceptFilter {
    *
    * @param type - The new filter type.
    */
-  setType(type: FilterTypes): void {
+  public setType(type: FilterTypes): void {
     this.type = type;
   }
 
@@ -92,16 +91,16 @@ export class ReferenceFilter extends AbstractConceptFilter {
    * @param selectedConcepts - The selected concepts.
    * @returns The created ReferenceFilter instance.
    */
-  static create(
+  public static create(
     id: string,
-    allowedReferenceUri: string,
+    allowedReferenceUri: string[],
     selectedReference: ReferenceCriterion[] = [],
     selectedConcepts: Concept[]
   ): ReferenceFilter {
     return new ReferenceFilter(id, allowedReferenceUri, selectedReference, selectedConcepts);
   }
 
-  isSelectedReferenceSet(): boolean {
+  public isSelectedReferenceSet(): boolean {
     return (
       this.selectedReferences !== undefined &&
       this.selectedReferences !== null &&

src/app/model/Interface/AttributeDefinitionData.ts

@@ -11,8 +11,8 @@ export interface AttributeDefinitionData {
   display: DisplayData
   optional: boolean
   precision: number
-  referencedCriteriaSet?: string
-  referencedValueSet?: string
+  referencedCriteriaSet?: string[]
+  referencedValueSet?: string[]
   selectableConcepts: string[]
   type: FilterTypes
 }

src/app/model/Interface/ValueDefinition.ts

@@ -9,8 +9,8 @@ export interface ValueDefinitionData {
   optional: boolean
   allowedUnits: QuantityUnitData[]
   precision: number
-  referencedCriteriaSet?: string
-  referencedValueSet?: string
+  referencedCriteriaSet?: string[]
+  referencedValueSet?: string[]
   max: number
   min: number
 }

src/app/model/Utilities/AttributeDefinition.ts/AbstractAttributeDefinition.ts

@@ -9,7 +9,7 @@ export abstract class AbstractAttributeDefinition {
   protected optional = false;
   protected precision = 1;
   protected type: FilterTypes;
-  protected referencedValueSet?: string;
+  protected referencedValueSet?: string[];
   protected display: Display;
 
   constructor(
@@ -20,7 +20,7 @@ export abstract class AbstractAttributeDefinition {
     max?: number,
     min?: number,
     precision: number = 1,
-    referencedValueSet?: string
+    referencedValueSet?: string[]
   ) {
     this.display = display;
     this.type = type;
@@ -88,11 +88,11 @@ export abstract class AbstractAttributeDefinition {
     this.precision = precision;
   }
 
-  getReferencedValueSet(): string {
+  getReferencedValueSet(): string[] {
     return this.referencedValueSet;
   }
 
-  setReferencedValueSet(referencedValueSet: string): void {
+  setReferencedValueSet(referencedValueSet: string[]): void {
     this.referencedValueSet = referencedValueSet;
   }
 }