Merge pull request #384 from medizininformatik-initiative/feature/382…

…-change-display-and-translations-structure-for-criteria-and-concepts

#382 - Change display and translations structure for criteria and concepts

.github/scripts/post-elastic-test-queries.sh

@@ -2,39 +2,6 @@
 
 curl "$ELASTIC_HOST/_cat/indices"
 
-response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/ontology/_doc/9c2328b0-ac4e-3d69-8f2f-d8b905875348")
-http_code="${response: -3}"
-json_body=$(cat response_body)
-
-if [ "$http_code" -eq 200 ]; then
-    if echo "$json_body" | jq '.found == true' | grep -q true; then
-        echo "Ontology Document found in elastic search"
-    else
-        echo "Empty or nonexistent response from elastic search"
-        exit 1
-    fi
-else
-    echo "Response code $http_code"
-    exit 1
-fi
-
-
-response=$(curl -s -w "%{http_code}" -o response_body "$ELASTIC_HOST/codeable_concept/_doc/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc")
-http_code="${response: -3}"
-json_body=$(cat response_body)
-
-if [ "$http_code" -eq 200 ]; then
-    if echo "$json_body" | jq '.found == true' | grep -q true; then
-        echo "Codeable Concept Document found in elastic search"
-    else
-        echo "Empty or nonexistent response from elastic search"
-        exit 1
-    fi
-else
-    echo "Response code $http_code"
-    exit 1
-fi
-
 access_token="$(curl -s --request POST \
   --url http://localhost:8083/auth/realms/dataportal/protocol/openid-connect/token \
   --header 'Content-Type: application/x-www-form-urlencoded' \
@@ -76,21 +43,5 @@ else
     exit 1
 fi
 
-response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/d676be36-7f34-3ea6-9838-c0c9e1ca3dcc")
-http_code="${response: -3}"
-json_body=$(cat response_body)
-
-if [ "$http_code" -eq 200 ]; then
-    if echo "$json_body" | jq -e '.code and .code != ""' | grep -q true; then
-        echo "OK response with non-empty array"
-    else
-        echo "Empty or nonexistent response"
-        exit 1
-    fi
-else
-    echo "Response code $http_code"
-    exit 1
-fi
-
 echo "All elastic search tests completed"
 exit 0

.github/workflows/ci.yml

@@ -148,7 +148,7 @@ jobs:
     needs: tests
     runs-on: ubuntu-latest
     env:
-      ONTOLOGY_GIT_TAG: v3.0.1
+      ONTOLOGY_GIT_TAG: v3.0.2-alpha
       ELASTIC_HOST: http://localhost:9200
       ELASTIC_FILEPATH: https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download/TAGPLACEHOLDER/
       ELASTIC_FILENAME: elastic.zip

docker-compose.yml

@@ -139,7 +139,7 @@ services:
     environment:
       ES_HOST: http://dataportal-elastic
       ES_PORT: 9200
-      ONTO_GIT_TAG: v3.0.1
+      ONTO_GIT_TAG: v3.0.2-alpha
       ONTO_REPO: https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download
       DOWNLOAD_FILENAME: elastic.zip
       EXIT_ON_EXISTING_INDICES: false

src/main/java/de/numcodex/feasibility_gui_backend/common/api/DisplayEntry.java

@@ -0,0 +1,33 @@
+package de.numcodex.feasibility_gui_backend.common.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.dse.api.LocalizedValue;
+import de.numcodex.feasibility_gui_backend.terminology.es.model.Display;
+import lombok.Builder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@Builder
+public record DisplayEntry(
+    @JsonProperty String original,
+    @JsonProperty List<LocalizedValue> translations
+    ) {
+
+    public static DisplayEntry of(Display display) {
+        return DisplayEntry.builder()
+            .original(display.original())
+            .translations(List.of(
+                LocalizedValue.builder()
+                    .language("de-DE")
+                    .value(display.deDe())
+                    .build(),
+                LocalizedValue.builder()
+                    .language("en-US")
+                    .value(display.enUs())
+                    .build()
+            ))
+            .build();
+    }
+}

src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfile.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
 import lombok.Builder;
 
 import java.util.List;

src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfileTreeNode.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
 import lombok.Builder;
 
 import java.util.List;

src/main/java/de/numcodex/feasibility_gui_backend/dse/api/Field.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
 import lombok.Builder;
 
 import java.util.List;

src/main/java/de/numcodex/feasibility_gui_backend/terminology/TerminologyService.java

@@ -108,4 +108,14 @@ public List<CriteriaProfileData> getCriteriaProfileData(List<String> criteriaIds
 
     return results;
   }
+
+  public List<CriteriaProfileData> addDisplayDataToCriteriaProfileData(List<CriteriaProfileData> criteriaProfileData, List<EsSearchResultEntry> displayData) {
+    var result = new ArrayList<CriteriaProfileData>();
+    for (CriteriaProfileData cpd : criteriaProfileData) {
+      var searchResultEntry = displayData.stream().filter(dd -> cpd.getId().equals(dd.id())).findFirst().orElse(null);
+      cpd.setDisplay(searchResultEntry ==  null ? null : searchResultEntry.display());
+      result.add(cpd);
+    }
+    return result;
+  }
 }

src/main/java/de/numcodex/feasibility_gui_backend/terminology/api/CcSearchResult.java

@@ -10,5 +10,5 @@
 @Builder
 public class CcSearchResult {
   private long totalHits;
-  private List<TermCode> results;
+  private List<CodeableConceptEntry> results;
 }

src/main/java/de/numcodex/feasibility_gui_backend/terminology/api/CodeableConceptEntry.java

@@ -0,0 +1,35 @@
+package de.numcodex.feasibility_gui_backend.terminology.api;
+
+import de.numcodex.feasibility_gui_backend.common.api.TermCode;
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
+import de.numcodex.feasibility_gui_backend.dse.api.LocalizedValue;
+import de.numcodex.feasibility_gui_backend.terminology.es.model.CodeableConceptDocument;
+import lombok.Builder;
+
+import java.util.List;
+
+@Builder
+public record CodeableConceptEntry(
+    TermCode termCode,
+    DisplayEntry display
+) {
+  public static CodeableConceptEntry of(CodeableConceptDocument document) {
+    return CodeableConceptEntry.builder()
+        .termCode(document.termCode())
+        .display(DisplayEntry.builder()
+            .original(document.display().original())
+            .translations(List.of(
+                LocalizedValue.builder()
+                    .language("de-DE")
+                    .value(document.display().deDe())
+                    .build(),
+                LocalizedValue.builder()
+                    .language("en-US")
+                    .value(document.display().enUs())
+                    .build()
+            ))
+            .build()
+        )
+        .build();
+  }
+}

src/main/java/de/numcodex/feasibility_gui_backend/terminology/api/CriteriaProfileData.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
 import de.numcodex.feasibility_gui_backend.common.api.TermCode;
 import lombok.Builder;
 import lombok.Data;
@@ -17,6 +18,8 @@
 public class CriteriaProfileData {
     @JsonProperty("id")
     private String id;
+    @JsonProperty("display")
+    private DisplayEntry display;
     @JsonProperty("context")
     private TermCode context;
     @JsonProperty("termCodes")

src/main/java/de/numcodex/feasibility_gui_backend/terminology/api/EsSearchResultEntry.java

@@ -1,12 +1,13 @@
 package de.numcodex.feasibility_gui_backend.terminology.api;
 
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
 import de.numcodex.feasibility_gui_backend.terminology.es.model.OntologyListItemDocument;
 import lombok.Builder;
 
 @Builder
 public record EsSearchResultEntry(
     String id,
-    String name,
+    DisplayEntry display,
     int availability,
     String context,
     String terminology,
@@ -17,7 +18,7 @@ public record EsSearchResultEntry(
   public static EsSearchResultEntry of(OntologyListItemDocument ontologyListItemDocument) {
     return EsSearchResultEntry.builder()
         .id(ontologyListItemDocument.id())
-        .name(ontologyListItemDocument.name())
+        .display(DisplayEntry.of(ontologyListItemDocument.display()))
         .availability(ontologyListItemDocument.availability())
         .context(ontologyListItemDocument.context().code())
         .terminology(ontologyListItemDocument.terminology())

src/main/java/de/numcodex/feasibility_gui_backend/terminology/api/RelationEntry.java

@@ -0,0 +1,26 @@
+package de.numcodex.feasibility_gui_backend.terminology.api;
+
+import de.numcodex.feasibility_gui_backend.common.api.DisplayEntry;
+import de.numcodex.feasibility_gui_backend.terminology.es.model.OntologyItemRelationsDocument;
+import de.numcodex.feasibility_gui_backend.terminology.es.model.Relative;
+import lombok.Builder;
+
+import java.util.Collection;
+
+@Builder
+public record RelationEntry(
+    DisplayEntry display,
+    Collection<Relative> parents,
+    Collection<Relative> children,
+    Collection<Relative> relatedTerms
+) {
+
+  public static RelationEntry of(OntologyItemRelationsDocument document) {
+    return RelationEntry.builder()
+        .display(DisplayEntry.of(document.display()))
+        .parents(document.parents())
+        .children(document.children())
+        .relatedTerms(document.relatedTerms())
+        .build();
+  }
+}

src/main/java/de/numcodex/feasibility_gui_backend/terminology/es/CodeableConceptService.java

@@ -2,8 +2,8 @@
 
 import co.elastic.clients.elasticsearch._types.FieldValue;
 import co.elastic.clients.elasticsearch._types.query_dsl.*;
-import de.numcodex.feasibility_gui_backend.common.api.TermCode;
 import de.numcodex.feasibility_gui_backend.terminology.api.CcSearchResult;
+import de.numcodex.feasibility_gui_backend.terminology.api.CodeableConceptEntry;
 import de.numcodex.feasibility_gui_backend.terminology.es.model.CodeableConceptDocument;
 import de.numcodex.feasibility_gui_backend.terminology.es.repository.CodeableConceptEsRepository;
 import de.numcodex.feasibility_gui_backend.terminology.es.repository.OntologyItemNotFoundException;
@@ -47,17 +47,18 @@ public CcSearchResult performCodeableConceptSearchWithRepoAndPaging(String keywo
     }
 
     var searchHitPage = findByCodeOrDisplay(keyword, filterList, PageRequest.of(page, pageSize));
-    List<TermCode> codeableConceptEntries = new ArrayList<>();
+    List<CodeableConceptEntry> codeableConceptEntries = new ArrayList<>();
 
-    searchHitPage.getSearchHits().forEach(hit -> codeableConceptEntries.add(hit.getContent().termCode()));
+    searchHitPage.getSearchHits().forEach(hit -> codeableConceptEntries.add(CodeableConceptEntry.of(hit.getContent())));
     return CcSearchResult.builder()
         .totalHits(searchHitPage.getTotalHits())
         .results(codeableConceptEntries)
         .build();
   }
 
-  public TermCode getSearchResultEntryByCode(String code) {
-    return repo.findById(code).orElseThrow(OntologyItemNotFoundException::new).termCode();
+  public CodeableConceptEntry getSearchResultEntryByCode(String code) {
+    var document = repo.findById(code).orElseThrow(OntologyItemNotFoundException::new);
+    return CodeableConceptEntry.of(document);
   }
 
   private SearchHits<CodeableConceptDocument> findByCodeOrDisplay(String keyword,
@@ -88,7 +89,7 @@ private SearchHits<CodeableConceptDocument> findByCodeOrDisplay(String keyword,
     } else {
       var mmQuery = new MultiMatchQuery.Builder()
           .query(keyword)
-          .fields(List.of("termcode.display", "termcode.code^2"))
+          .fields(List.of("display.de", "display.en", "termcode.code^2"))
           .build();
 
       boolQuery = new BoolQuery.Builder()

src/main/java/de/numcodex/feasibility_gui_backend/terminology/es/TerminologyEsService.java

@@ -7,6 +7,7 @@
 import co.elastic.clients.elasticsearch._types.query_dsl.*;
 import de.numcodex.feasibility_gui_backend.terminology.api.EsSearchResult;
 import de.numcodex.feasibility_gui_backend.terminology.api.EsSearchResultEntry;
+import de.numcodex.feasibility_gui_backend.terminology.api.RelationEntry;
 import de.numcodex.feasibility_gui_backend.terminology.es.model.*;
 import de.numcodex.feasibility_gui_backend.terminology.es.repository.OntologyItemEsRepository;
 import de.numcodex.feasibility_gui_backend.terminology.es.repository.OntologyItemNotFoundException;
@@ -53,6 +54,13 @@ public EsSearchResultEntry getSearchResultEntryByHash(String hash) {
     return EsSearchResultEntry.of(ontologyItem);
   }
 
+  public List<EsSearchResultEntry> getSearchResultEntriesByHash(List<String> hashes) {
+    var ontologyItems = ontologyListItemEsRepository.findAllById(hashes);
+    List<EsSearchResultEntry> results = new ArrayList<>();
+    ontologyItems.forEach(oi  -> results.add(EsSearchResultEntry.of(oi)));
+    return results;
+  }
+
   public List<TermFilter> getAvailableFilters() {
     var filterTerms = List.of(filterFields);
     var list = new ArrayList<TermFilter>();
@@ -150,7 +158,7 @@ private SearchHits<OntologyListItemDocument> findByNameOrTermcode(String keyword
     } else {
       var mmQuery = new MultiMatchQuery.Builder()
           .query(keyword)
-          .fields(List.of("name", "termcode^2"))
+          .fields(List.of("display.de", "display.en", "termcode^2"))
           .build();
 
       boolQuery = new BoolQuery.Builder()
@@ -185,18 +193,21 @@ private SearchHits<OntologyListItemDocument> findByNameOrTermcode(String keyword
         .withPageable(pageRequest)
         .build();
 
+    log.info(finalQuery.getQuery().toString());
+
     return operations.search(finalQuery, OntologyListItemDocument.class);
 
   }
 
-  public OntologyItemRelationsDocument getOntologyItemRelationsByHash(String hash) {
+  public RelationEntry getRelationEntryByHash(String hash) {
     var ontologyItem = ontologyItemEsRepository.findById(hash).orElseThrow(OntologyItemNotFoundException::new);
-    return OntologyItemRelationsDocument.builder()
-        .translations(ontologyItem.translations())
+    var ontologyItemRelationsDocument = OntologyItemRelationsDocument.builder()
+        .display(ontologyItem.display())
         .parents(ontologyItem.parents())
         .children(ontologyItem.children())
         .relatedTerms(ontologyItem.relatedTerms())
         .build();
+    return RelationEntry.of(ontologyItemRelationsDocument);
   }
 
 

src/main/java/de/numcodex/feasibility_gui_backend/terminology/es/model/CodeableConceptDocument.java

@@ -13,9 +13,11 @@
 @Document(indexName = "codeable_concept")
 public record CodeableConceptDocument(
     @Id String id,
-    @Field(type = FieldType.Nested, includeInParent = true, name = "termcode")
+    @Field(name = "termcode")
     TermCode termCode,
-    @Field(type = FieldType.Nested, includeInParent = true, name = "value_sets")
-    List<String> valueSets
+    @Field(name = "value_sets")
+    List<String> valueSets,
+    @Field(name = "display")
+    Display display
 ) {
 }