#318 - Add endpoints for profile data

- remove profile_tree.json and terminology_systems.json from resources and move to filesystem (will be loaded with ontology files when this is available) - add tests
medizininformatik-initiative · Aug 16, 2024 · 527e944 · 527e944
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diff --git a/.github/integration-test/docker-compose.yml b/.github/integration-test/docker-compose.yml
@@ -67,6 +67,8 @@ services:
       - ./ontology/ui_profiles:/opt/codex-feasibility-backend/ontology/ui_profiles
       - ./ontology/codex-code-tree.json:/opt/codex-feasibility-backend/ontology/codex-code-tree.json
       - ./ontology/codex-term-code-mapping.json:/opt/codex-feasibility-backend/ontology/codex-term-code-mapping.json
+      - ./ontology/terminology_systems.json:/opt/codex-feasibility-backend/ontology/terminology_systems.json
+      - ./ontology/dse/profile_tree.json:/opt/codex-feasibility-backend/ontology/dse/profile_tree.json
       - ./ontology/migration/R__Load_latest_ui_profile.sql:/opt/codex-feasibility-backend/ontology/migration/R__Load_latest_ui_profile.sql
       - ./secrets:/opt/codex-feasibility-security
   feasibility-gui-backend-db:

diff --git a/.github/integration-test/ontology/dse/profile_tree.json b/.github/integration-test/ontology/dse/profile_tree.json
@@ -0,0 +1,63 @@
+{
+    "name": "Root",
+    "module": "no-module",
+    "url": "no-url",
+    "children": [
+        {
+            "id": "de5c2903-00aa-4d64-92e5-2161d56e3daf",
+            "children": [
+                {
+                    "id": "69f4718f-1767-4517-90f8-6c079f627eed",
+                    "name": "MII_PR_Medikation_MedicationStatement",
+                    "display": "MII PR Medikation MedicationStatement",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "83b4d6be-b3e1-451a-adf2-c307477e7b97",
+                    "name": "MII_PR_Medikation_Medikationsliste",
+                    "display": "MII PR Medikation Medikationsliste",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/medikationsliste",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "fd375ed9-b3cd-414f-8a56-c70e10bb9609",
+                    "name": "MII_PR_Medikation_MedicationRequest",
+                    "display": "MII PR Medikation MedicationRequest",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationRequest",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "323a3ad1-1c10-45f5-848a-2dc5fb100c47",
+                    "name": "MII_PR_Medikation_Medication",
+                    "display": "MII PR Medikation Medication",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication",
+                    "leaf": true,
+                    "selectable": true
+                },
+                {
+                    "id": "81ed0f03-1d77-49c9-8391-d4c25702652c",
+                    "name": "MII_PR_Medikation_MedicationAdministration",
+                    "display": "MII PR Medikation MedicationAdministration",
+                    "module": "modul-medikation",
+                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationAdministration",
+                    "leaf": true,
+                    "selectable": true
+                }
+            ],
+            "name": "modul-medikation",
+            "display": "Medikation",
+            "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
+            "module": "modul-medikation",
+            "selectable": true,
+            "leaf": false
+        }
+    ]
+}
diff --git a/...kend/terminology/terminology-systems.json → ...on-test/ontology/terminology_systems.json b/...kend/terminology/terminology-systems.json → ...on-test/ontology/terminology_systems.json
diff --git a/...ibility_gui_backend/dse/profile_tree.json → ontology/dse/profile_tree.json b/...ibility_gui_backend/dse/profile_tree.json → ontology/dse/profile_tree.json
diff --git a/ontology/terminology_systems.json b/ontology/terminology_systems.json
@@ -0,0 +1,18 @@
+[
+  {
+    "url": "http://loinc.org",
+    "name": "loinc"
+  },
+  {
+    "url": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+    "name": "ICD-10"
+  },
+  {
+    "url": "http://fhir.de/CodeSystem/bfarm/ops",
+    "name": "OPS"
+  },
+  {
+    "url": "TBD",
+    "name": "obviously this is just an example"
+  }
+]
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/DseProfileException.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/DseProfileException.java
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/DseService.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/DseService.java
@@ -5,39 +5,38 @@
 import de.numcodex.feasibility_gui_backend.dse.api.DseProfile;
 import de.numcodex.feasibility_gui_backend.dse.api.DseProfileTreeNode;
 import de.numcodex.feasibility_gui_backend.dse.persistence.DseProfileRepository;
+import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.io.Resource;
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 
 @Service
 @Slf4j
 public class DseService {
 
-  @Value("classpath:de/numcodex/feasibility_gui_backend/dse/profile_tree.json")
-  private Resource profileTreeResource;
+  @Getter
+  private final DseProfileTreeNode profileTree;
 
   private final DseProfileRepository dseProfileRepository;
 
   private final ObjectMapper objectMapper;
 
-  public DseService(DseProfileRepository dseProfileRepository, ObjectMapper objectMapper) {
+  public DseService(@Value("${app.dseProfileTreeFile}") String dseProfileTreeFilename,
+                    DseProfileRepository dseProfileRepository,
+                    ObjectMapper objectMapper) throws IOException {
     this.dseProfileRepository = dseProfileRepository;
     this.objectMapper = objectMapper;
+    this.profileTree = readProfileTree(dseProfileTreeFilename);
   }
 
-  public DseProfileTreeNode getProfileTree() {
-    try {
-      var profileTreeString = profileTreeResource.getContentAsString(StandardCharsets.UTF_8);
-      return objectMapper.readValue(profileTreeString, DseProfileTreeNode.class);
-    } catch (IOException e) {
-      throw new DseProfileException("Could not read profile tree: " + e.getMessage());
-    }
+  public DseProfileTreeNode readProfileTree(String dseProfileTreeFilename) throws IOException {
+    return objectMapper.readValue(
+        new URL("file:" + dseProfileTreeFilename), DseProfileTreeNode.class);
   }
 
   public List<DseProfile> getProfileData(List<String> profileIds) {

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/v3/DseRestController.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/v3/DseRestController.java
@@ -3,9 +3,12 @@
 import de.numcodex.feasibility_gui_backend.dse.DseService;
 import de.numcodex.feasibility_gui_backend.dse.api.DseProfile;
 import de.numcodex.feasibility_gui_backend.dse.api.DseProfileTreeNode;
+import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.*;
+import org.springframework.web.server.ResponseStatusException;
 
+import java.io.FileNotFoundException;
 import java.util.List;
 
 @RequestMapping("api/v3/dse")
@@ -20,8 +23,13 @@ public DseRestController(DseService dseService) {
   }
 
   @GetMapping(value = "profile-tree", produces = MediaType.APPLICATION_JSON_VALUE)
-  public DseProfileTreeNode getProfileTree() {
-    return dseService.getProfileTree();
+  public DseProfileTreeNode getProfileTree() throws FileNotFoundException {
+    DseProfileTreeNode profileTree = dseService.getProfileTree();
+    if (profileTree == null) {
+      throw new ResponseStatusException(HttpStatus.NOT_FOUND, "DSE profile tree not found");
+    } else {
+      return profileTree;
+    }
   }
 
   @GetMapping(value = "profile-data", produces = MediaType.APPLICATION_JSON_VALUE)

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/terminology/TerminologyService.java b/src/main/java/de/numcodex/feasibility_gui_backend/terminology/TerminologyService.java
@@ -1,22 +1,21 @@
 package de.numcodex.feasibility_gui_backend.terminology;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import de.numcodex.feasibility_gui_backend.terminology.api.CategoryEntry;
-import de.numcodex.feasibility_gui_backend.terminology.api.CriteriaProfileData;
-import de.numcodex.feasibility_gui_backend.terminology.api.TerminologyEntry;
+import de.numcodex.feasibility_gui_backend.terminology.api.*;
 import de.numcodex.feasibility_gui_backend.terminology.persistence.*;
+import de.numcodex.feasibility_gui_backend.terminology.persistence.UiProfile;
+import lombok.Getter;
 import lombok.NonNull;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.io.Resource;
 import org.springframework.stereotype.Service;
 
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
-import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -33,7 +32,10 @@ public class TerminologyService {
 
   private final MappingRepository mappingRepository;
 
-  private String uiProfilePath;
+  private final String uiProfilePath;
+
+  @Getter
+  private final List<TerminologySystemEntry> terminologySystems;
 
   @NonNull
   private ObjectMapper jsonUtil;
@@ -45,10 +47,8 @@ public class TerminologyService {
   private Map<UUID, TerminologyEntry> terminologyEntriesWithOnlyDirectChildren = new HashMap<>();
   private Map<UUID, Set<TerminologyEntry>> selectableEntriesByCategory = new HashMap<>();
 
-  @Value("classpath:de/numcodex/feasibility_gui_backend/terminology/terminology-systems.json")
-  private Resource terminologySystemsResource;
-
   public TerminologyService(@Value("${app.ontologyFolder}") String uiProfilePath,
+                            @Value("${app.terminologySystemsFile}") String terminologySystemsFilename,
                             UiProfileRepository uiProfileRepository,
                             TermCodeRepository termCodeRepository,
                             ContextualizedTermCodeRepository contextualizedTermCodeRepository,
@@ -63,6 +63,7 @@ public TerminologyService(@Value("${app.ontologyFolder}") String uiProfilePath,
     this.contextualizedTermCodeRepository = contextualizedTermCodeRepository;
     this.mappingRepository = mappingRepository;
     this.jsonUtil = jsonUtil;
+    this.terminologySystems = jsonUtil.readValue(new URL("file:" + terminologySystemsFilename), new TypeReference<>() {});
   }
 
   private void readInTerminologyEntries() throws IOException {
@@ -263,12 +264,4 @@ public List<CriteriaProfileData> getCriteriaProfileData(List<String> criteriaIds
 
     return results;
   }
-
-  public String getTerminologySystems() {
-    try {
-      return terminologySystemsResource.getContentAsString(StandardCharsets.UTF_8);
-    } catch (IOException e) {
-      throw new MappingNotFoundException();
-    }
-  }
 }
diff --git a/...main/java/de/numcodex/feasibility_gui_backend/terminology/api/TerminologySystemEntry.java b/...main/java/de/numcodex/feasibility_gui_backend/terminology/api/TerminologySystemEntry.java
@@ -0,0 +1,13 @@
+package de.numcodex.feasibility_gui_backend.terminology.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Builder;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@Builder
+public record TerminologySystemEntry(
+    @JsonProperty String url,
+    @JsonProperty String name
+) {
+}
diff --git a/...in/java/de/numcodex/feasibility_gui_backend/terminology/v3/TerminologyRestController.java b/...in/java/de/numcodex/feasibility_gui_backend/terminology/v3/TerminologyRestController.java
@@ -2,9 +2,7 @@
 
 
 import de.numcodex.feasibility_gui_backend.terminology.TerminologyService;
-import de.numcodex.feasibility_gui_backend.terminology.api.CategoryEntry;
-import de.numcodex.feasibility_gui_backend.terminology.api.CriteriaProfileData;
-import de.numcodex.feasibility_gui_backend.terminology.api.TerminologyEntry;
+import de.numcodex.feasibility_gui_backend.terminology.api.*;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.*;
@@ -71,7 +69,7 @@ public List<String> getIntersection(
     }
 
     @GetMapping(value = "systems", produces = MediaType.APPLICATION_JSON_VALUE)
-    public String getTerminologySystems() {
+    public List<TerminologySystemEntry> getTerminologySystems() {
         return terminologyService.getTerminologySystems();
     }
 }
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -41,7 +41,8 @@ management:
       enabled: ${ELASTIC_SEARCH_ENABLED:true}
 
 app:
-  # AKTIN or DSF or MOCK or DIRECT
+  dseProfileTreeFile: ${DSE_PROFILE_TREE_FILE:ontology/dse/profile_tree.json}
+  terminologySystemsFile: ${TERMINOLOGY_SYSTEMS_FILE:ontology/terminology_systems.json}
   ontologyFolder: ${ONTOLOGY_FILES_FOLDER_UI:ontology/ui_trees}
   ontologyOrder: ${ONTOLOGY_ORDER:Diagnose, Prozedur, Person, Laboruntersuchung, Medikamentenverabreichung, Bioprobe, Einwilligung}
   mappingsFile: ${MAPPINGS_FILE:ontology/mapping_cql.json}