feat(catalogue): model update to 5.2 (#4345)

* add internal identifiers table
* add Internal identifiers ontology file and adapt ext identifiers
* add Resources.exclusion criteria and .other exclusion criteria
* add Subpopulations.exclusion criteria .other exclusion criteria
* rename Inclusion Exclusion Criteria table
* edit NetworksStaging profile

apps/nuxt3-ssr/README.md

@@ -78,4 +78,8 @@ Runtime config options can be set via query param to test/debug options:
 - logo: ```logo=[logo-file-name-without-extension]```
 - feature flag cohorts only: ```cohort-only=true``` // defaults to false
 
-for example ```.../catalogue-demo/ssr-catalogue?cohort-only=true&theme=umcg&logo=UMCGkort.woordbeeld```
+for example ```.../catalogue-demo/ssr-catalogue?cohort-only=true&theme=umcg&logo=UMCGkort.woordbeeld```
+
+### generate types
+
+gradle generateTypes --args='catalogue apps/nuxt3-ssr/interfaces/catalogue.ts'

apps/nuxt3-ssr/components/SubpopulationDisplay.vue

@@ -106,9 +106,40 @@ if (subpopulation?.countries) {
 }
 
 if (subpopulation?.inclusionCriteria) {
+  items.push({
+    label: "Inclusion criteria",
+    content: renderList(
+      subpopulation.inclusionCriteria.sort(
+        (a, b) => (b.order ?? 0) - (a.order ?? 0)
+      ),
+      toName
+    ),
+  });
+}
+
+if (subpopulation?.otherInclusionCriteria) {
   items.push({
     label: "Other inclusion criteria",
-    content: subpopulation.inclusionCriteria,
+    content: subpopulation.otherInclusionCriteria,
+  });
+}
+
+if (subpopulation?.exclusionCriteria) {
+  items.push({
+    label: "Exclusion criteria",
+    content: renderList(
+      subpopulation.exclusionCriteria.sort(
+        (a, b) => (b.order ?? 0) - (a.order ?? 0)
+      ),
+      toName
+    ),
+  });
+}
+
+if (subpopulation?.otherExclusionCriteria) {
+  items.push({
+    label: "Other exclusion criteria",
+    content: subpopulation.otherExclusionCriteria,
   });
 }
 

apps/nuxt3-ssr/gql/subpopulation.js

@@ -41,7 +41,16 @@ export default gql`
         name
         order
       }
-      inclusionCriteria
+      inclusionCriteria {
+        name
+        order
+      }
+      otherInclusionCriteria
+      exclusionCriteria {
+        name
+        order
+      }
+      otherExclusionCriteria
       comorbidity {
         name
         code

apps/nuxt3-ssr/interfaces/catalogue.ts

@@ -382,16 +382,16 @@ export interface IICDOTopologies {
   children?: IICDOTopologies[];
 }
 
-export interface IInclusionCriteria {
+export interface IInclusionExclusionCriteria {
   order?: number;
   name: string;
   label?: string;
-  parent?: IInclusionCriteria;
+  parent?: IInclusionExclusionCriteria;
   codesystem?: string;
   code?: string;
   ontologyTermURI?: string;
   definition?: string;
-  children?: IInclusionCriteria[];
+  children?: IInclusionExclusionCriteria[];
 }
 
 export interface IInformedConsentRequired {
@@ -418,6 +418,25 @@ export interface IInformedConsentTypes {
   children?: IInformedConsentTypes[];
 }
 
+export interface IInternalIdentifierTypes {
+  order?: number;
+  name: string;
+  label?: string;
+  parent?: IInternalIdentifierTypes;
+  codesystem?: string;
+  code?: string;
+  ontologyTermURI?: string;
+  definition?: string;
+  children?: IInternalIdentifierTypes[];
+}
+
+export interface IInternalIdentifiers {
+  resource: IResources;
+  identifier: string;
+  internalIdentifierType?: IOntologyNode;
+  internalIdentifierTypeOther?: string;
+}
+
 export interface IKeywords {
   order?: number;
   name: string;
@@ -667,7 +686,8 @@ export interface IResources {
   networkType?: IOntologyNode[];
   website?: string;
   description?: string;
-  keywords?: string;
+  keywords?: string[];
+  internalIdentifiers?: IInternalIdentifiers[];
   externalIdentifiers?: IExternalIdentifiers[];
   startYear?: number;
   endYear?: number;
@@ -698,6 +718,8 @@ export interface IResources {
   populationAgeGroups?: IOntologyNode[];
   inclusionCriteria?: IOntologyNode[];
   otherInclusionCriteria?: string;
+  exclusionCriteria?: IOntologyNode[];
+  otherExclusionCriteria?: string;
   populationEntry?: IOntologyNode[];
   populationEntryOther?: string;
   populationExit?: IOntologyNode[];
@@ -948,6 +970,7 @@ export interface ISubpopulations {
   countries?: IOntologyNode[];
   regions?: IOntologyNode[];
   inclusionCriteria?: string;
+  exclusionCriteria?: string;
 }
 
 export interface ITitles {

apps/nuxt3-ssr/pages/[schema]/ssr-catalogue/[catalogue]/[resourceType]/[resource]/index.vue

@@ -87,6 +87,8 @@ const query = gql`
       populationOncologyMorphology ${moduleToString(ontologyFragment)}
       inclusionCriteria ${moduleToString(ontologyFragment)}
       otherInclusionCriteria
+      exclusionCriteria ${moduleToString(ontologyFragment)}
+      otherExclusionCriteria
       publications(orderby: {title:ASC}) {
         doi
         title
@@ -403,6 +405,15 @@ const population: IDefinitionListItem[] = [
     label: "Other inclusion criteria",
     content: resource.value.otherInclusionCriteria,
   },
+  {
+    label: "Exclusion criteria",
+    type: "ONTOLOGY",
+    content: resource.value.exclusionCriteria,
+  },
+  {
+    label: "Other exclusion criteria",
+    content: resource.value.otherExclusionCriteria,
+  },
 ];
 
 if (mainMedicalConditions.value && mainMedicalConditions.value.length > 0) {

apps/nuxt3-ssr/pages/[schema]/ssr-catalogue/[catalogue]/[resourceType]/[resource]/subpopulations/[subpopulation].vue

@@ -101,9 +101,40 @@ if (subpopulation?.countries) {
 }
 
 if (subpopulation?.inclusionCriteria) {
+  items.push({
+    label: "Inclusion criteria",
+    content: renderList(
+      subpopulation.inclusionCriteria.sort(
+        (a, b) => (b.order ?? 0) - (a.order ?? 0)
+      ),
+      toName
+    ),
+  });
+}
+
+if (subpopulation?.otherInclusionCriteria) {
   items.push({
     label: "Other inclusion criteria",
-    content: subpopulation.inclusionCriteria,
+    content: subpopulation.otherInclusionCriteria,
+  });
+}
+
+if (subpopulation?.exclusionCriteria) {
+  items.push({
+    label: "Exclusion criteria",
+    content: renderList(
+      subpopulation.exclusionCriteria.sort(
+        (a, b) => (b.order ?? 0) - (a.order ?? 0)
+      ),
+      toName
+    ),
+  });
+}
+
+if (subpopulation?.otherExclusionCriteria) {
+  items.push({
+    label: "Other exclusion criteria",
+    content: subpopulation.otherExclusionCriteria,
   });
 }
 

backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/io/ImportProfileTask.java

@@ -32,16 +32,21 @@ public ImportProfileTask(Schema schema, String configLocation, boolean includeDe
   @Override
   public void run() {
     this.start();
+    Task commitTask = new Task();
     try {
       schema.tx(
           db -> {
             Schema s = db.getSchema(schema.getName());
             load(s);
+            this.addSubTask(commitTask);
+            commitTask.setDescription("Committing");
           });
     } catch (Exception e) {
+      commitTask.completeWithError("Commit failed: " + e.getMessage());
       this.completeWithError(e.getMessage());
       throw (e);
     }
+    commitTask.complete();
     this.complete();
   }
 

backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java

@@ -71,14 +71,14 @@ public void test01FAIRDataHubLoader() {
   void test06DataCatalogueLoader() {
     Schema dataCatalogue = database.createSchema(DATA_CATALOGUE);
     DataModels.Profile.DATA_CATALOGUE.getImportTask(dataCatalogue, true).run();
-    assertEquals(22, dataCatalogue.getTableNames().size());
+    assertEquals(23, dataCatalogue.getTableNames().size());
   }
 
   @Test
   public void test07DataCatalogueCohortStagingLoader() {
     Schema cohortStaging = database.createSchema(COHORT_STAGING);
     DataModels.Profile.DATA_CATALOGUE_COHORT_STAGING.getImportTask(cohortStaging, true).run();
-    assertEquals(17, cohortStaging.getTableNames().size());
+    assertEquals(18, cohortStaging.getTableNames().size());
   }
 
   @Disabled

backend/molgenis-emx2-typescript/build.gradle

@@ -8,5 +8,6 @@ dependencies {
 task generateTypes(type: JavaExec) {
     group = 'application'
     classpath = sourceSets.main.runtimeClasspath
+    workingDir = rootProject.projectDir
     main = 'org.molgenis.emx2.typescript.AToolToGenerateTypeScriptTypes'
 }