use human readable type for responses

DiSSCo · Nov 29, 2024 · 298cc68 · 298cc68
1 parent 439fc29
commit 298cc68
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Showing 20 changed files with 119 additions and 98 deletions.
diff --git a/src/main/java/eu/dissco/backend/component/FdoRecordComponent.java b/src/main/java/eu/dissco/backend/component/FdoRecordComponent.java
@@ -2,7 +2,7 @@
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dissco.backend.domain.OdsType;
+import eu.dissco.backend.domain.FdoType;
 import lombok.Getter;
 import org.springframework.stereotype.Component;
 
@@ -15,7 +15,7 @@ public class FdoRecordComponent {
   public FdoRecordComponent(ObjectMapper mapper) {
     this.postRequest = mapper.createObjectNode()
         .set("data", mapper.createObjectNode()
-            .put("type", OdsType.MJR.getPid())
+            .put("type", FdoType.MJR.getPid())
             .set("attributes", mapper.createObjectNode()));
   }
 }
diff --git a/src/main/java/eu/dissco/backend/controller/AnnotationController.java b/src/main/java/eu/dissco/backend/controller/AnnotationController.java
@@ -1,5 +1,6 @@
 package eu.dissco.backend.controller;
 
+import static eu.dissco.backend.domain.FdoType.ANNOTATION;
 import static eu.dissco.backend.repository.RepositoryUtils.HANDLE_STRING;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -56,7 +57,6 @@
 @RequestMapping("/api/v1/annotation")
 public class AnnotationController extends BaseController {
 
-  public static final String ANNOTATION_TYPE = "ods:Annotation";
   private final AnnotationService service;
   private final SchemaValidatorComponent schemaValidator;
 
@@ -330,19 +330,19 @@ public ResponseEntity<Void> tombstoneAnnotation(Authentication authentication,
   }
 
   private AnnotationProcessingRequest getAnnotationFromRequest(AnnotationRequest requestBody) {
-    if (!requestBody.data().type().equals(ANNOTATION_TYPE)) {
+    if (!requestBody.data().type().equals(ANNOTATION)) {
       throw new IllegalArgumentException(
-          "Invalid type. Type must be " + ANNOTATION_TYPE + " but was " + requestBody.data()
-              .type());
+          "Invalid type. Type must be " + ANNOTATION.getPid() + " or " + ANNOTATION.getName()
+              + " but was " + requestBody.data().type());
     }
     return requestBody.data().attributes();
   }
 
   private AnnotationEventRequest getAnnotationFromRequestEvent(BatchAnnotationRequest requestBody) {
-    if (!requestBody.data().type().equals(ANNOTATION_TYPE)) {
+    if (!requestBody.data().type().equals(ANNOTATION)) {
       throw new IllegalArgumentException(
-          "Invalid type. Type must be " + ANNOTATION_TYPE + " but was " + requestBody.data()
-              .type());
+          "Invalid type. Type must be " + ANNOTATION.getPid() + " or " + ANNOTATION.getName()
+              + " but was " + requestBody.data().type());
     }
     return requestBody.data().attributes();
   }

diff --git a/src/main/java/eu/dissco/backend/domain/FdoType.java b/src/main/java/eu/dissco/backend/domain/FdoType.java
@@ -0,0 +1,39 @@
+package eu.dissco.backend.domain;
+
+import com.fasterxml.jackson.annotation.JsonAlias;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Getter;
+
+@Getter
+public enum FdoType {
+  @JsonProperty("https://doi.org/21.T11148/894b1e6cad57e921764e")
+  @JsonAlias("ods:DigitalSpecimen")
+  DIGITAL_SPECIMEN("https://doi.org/21.T11148/894b1e6cad57e921764e", "ods:DigitalSpecimen"),
+  @JsonProperty("https://doi.org/21.T11148/bbad8c4e101e8af01115")
+  @JsonAlias("ods:DigitalMedia")
+  DIGITAL_MEDIA("https://doi.org/21.T11148/bbad8c4e101e8af01115", "ods:DigitalMedia"),
+  @JsonProperty("https://doi.org/21.T11148/cf458ca9ee1d44a5608f")
+  @JsonAlias("ods:Annotation")
+  ANNOTATION("https://doi.org/21.T11148/cf458ca9ee1d44a5608f", "ods:Annotation"),
+  @JsonProperty("https://doi.org/21.T11148/417a4f472f60f7974c12")
+  @JsonAlias("ods:SourceSystem")
+  SOURCE_SYSTEM("https://doi.org/21.T11148/417a4f472f60f7974c12", "ods:SourceSystem"),
+  @JsonProperty("https://doi.org/21.T11148/ce794a6f4df42eb7e77e")
+  @JsonAlias("ods:DataMapping")
+  DATA_MAPPING("https://doi.org/21.T11148/ce794a6f4df42eb7e77e", "ods:DataMapping"),
+  @JsonProperty("https://doi.org/21.T11148/22e71a0015cbcfba8ffa")
+  @JsonAlias("ods:MachineAnnotationService")
+  MAS("https://doi.org/21.T11148/22e71a0015cbcfba8ffa", "ods:MachineAnnotationService"),
+  @JsonProperty("https://doi.org/21.T11148/532ce6796e2828dd2be6")
+  @JsonAlias("MachineAnnotationServiceJobRecord")
+  MJR("https://doi.org/21.T11148/532ce6796e2828dd2be6", "MachineAnnotationServiceJobRecord");
+
+  private final String pid;
+  private final String name;
+
+
+  FdoType(String pid, String name){
+    this.pid = pid;
+    this.name = name;
+  }
+}
diff --git a/src/main/java/eu/dissco/backend/domain/OdsType.java b/src/main/java/eu/dissco/backend/domain/OdsType.java
diff --git a/src/main/java/eu/dissco/backend/domain/openapi/annotation/AnnotationRequest.java b/src/main/java/eu/dissco/backend/domain/openapi/annotation/AnnotationRequest.java
@@ -1,5 +1,6 @@
 package eu.dissco.backend.domain.openapi.annotation;
 
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.schema.AnnotationProcessingRequest;
 import io.swagger.v3.oas.annotations.media.Schema;
 
@@ -9,7 +10,7 @@ public record AnnotationRequest(
 
   @Schema
   public record AnnotationRequestData(
-      @Schema(description = "Type of request. For annotations, must be \"ods:Annotation\"") String type,
+      @Schema(description = "Type of request. For annotations, must be \"ods:Annotation\"") FdoType type,
       @Schema(description = "Desired annotation") AnnotationProcessingRequest attributes) {
 
   }

diff --git a/src/main/java/eu/dissco/backend/domain/openapi/annotation/BatchAnnotationRequest.java b/src/main/java/eu/dissco/backend/domain/openapi/annotation/BatchAnnotationRequest.java
@@ -1,5 +1,6 @@
 package eu.dissco.backend.domain.openapi.annotation;
 
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.domain.annotation.batch.AnnotationEventRequest;
 import io.swagger.v3.oas.annotations.media.Schema;
 
@@ -9,7 +10,7 @@ public record BatchAnnotationRequest(
 
   @Schema
   public record BatchAnnotationRequestData(
-      @Schema(description = "Type of request, in this case \"ods:Annotation\"") String type,
+      @Schema(description = "Type of request, in this case \"ods:Annotation\"") FdoType type,
       AnnotationEventRequest attributes) {
 
   }

diff --git a/src/main/java/eu/dissco/backend/repository/DigitalSpecimenRepository.java b/src/main/java/eu/dissco/backend/repository/DigitalSpecimenRepository.java
@@ -6,6 +6,7 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.exceptions.DisscoJsonBMappingException;
 import eu.dissco.backend.schema.DigitalSpecimen;
 import java.util.Date;
@@ -41,7 +42,7 @@ private DigitalSpecimen mapToDigitalSpecimen(Record dbRecord) {
     try {
       return mapper.readValue(dbRecord.get(DIGITAL_SPECIMEN.DATA).data(), DigitalSpecimen.class)
           .withId("https://doi.org/" + dbRecord.get(DIGITAL_SPECIMEN.ID))
-          .withType("ods:DigitalSpecimen")
+          .withType(FdoType.DIGITAL_SPECIMEN.getName())
           .withDctermsIdentifier("https://doi.org/" + dbRecord.get(DIGITAL_SPECIMEN.ID))
           .withOdsFdoType(dbRecord.get(DIGITAL_SPECIMEN.TYPE))
           .withOdsMidsLevel(dbRecord.get(DIGITAL_SPECIMEN.MIDSLEVEL).intValue())

diff --git a/src/main/java/eu/dissco/backend/service/AnnotationService.java b/src/main/java/eu/dissco/backend/service/AnnotationService.java
@@ -1,11 +1,13 @@
 package eu.dissco.backend.service;
 
+import static eu.dissco.backend.domain.FdoType.ANNOTATION;
 import static eu.dissco.backend.service.DigitalServiceUtils.createVersionNode;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dissco.backend.client.AnnotationClient;
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.domain.annotation.AnnotationTombstoneWrapper;
 import eu.dissco.backend.domain.annotation.batch.AnnotationEvent;
 import eu.dissco.backend.domain.annotation.batch.AnnotationEventRequest;
@@ -41,7 +43,6 @@
 @RequiredArgsConstructor
 public class AnnotationService {
 
-  private static final String ANNOTATION = "ods:Annotation";
   private static final String ATTRIBUTES = "attributes";
   private static final String DATA = "data";
   private final AnnotationRepository repository;
@@ -53,7 +54,7 @@ public class AnnotationService {
 
   public JsonApiWrapper getAnnotation(String id, String path) {
     var annotation = repository.getAnnotation(id);
-    var dataNode = new JsonApiData(id, ANNOTATION, mapper.valueToTree(annotation));
+    var dataNode = new JsonApiData(id, FdoType.ANNOTATION.getName(), mapper.valueToTree(annotation));
     return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
   }
 
@@ -67,8 +68,7 @@ public JsonApiWrapper getAnnotationByVersion(String id, int version, String path
       throws NotFoundException, JsonProcessingException {
     var eventNode = mongoRepository.getByVersion(id, version, "annotation_provenance");
     validateAnnotationNode(eventNode);
-    var type = eventNode.get("@type").asText();
-    var dataNode = new JsonApiData(id, type, eventNode);
+    var dataNode = new JsonApiData(id, ANNOTATION.getName(), eventNode);
     return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
   }
 
@@ -104,7 +104,7 @@ public JsonApiWrapper formatResponse(JsonNode response, String path)
       throws JsonProcessingException {
     if (response != null) {
       var annotationResponse = parseToAnnotation(response);
-      var dataNode = new JsonApiData(annotationResponse.getId(), ANNOTATION,
+      var dataNode = new JsonApiData(annotationResponse.getId(), ANNOTATION.getName(),
           response);
       return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
     }
@@ -224,14 +224,14 @@ private String getFullId(String id) {
 
   // Response Constructors
   private void validateAnnotationNode(JsonNode annotationNode) throws JsonProcessingException {
-    mapper.treeToValue(annotationNode.get(ANNOTATION), Annotation.class);
+    mapper.treeToValue(annotationNode.get(ANNOTATION.getName()), Annotation.class);
   }
 
   private JsonApiListResponseWrapper wrapListResponse(List<Annotation> annotationsPlusOne,
       int pageNumber, int pageSize, String path) {
     List<JsonApiData> dataNodePlusOne = new ArrayList<>();
     annotationsPlusOne.forEach(annotation -> dataNodePlusOne.add(
-        new JsonApiData(annotation.getId(), ANNOTATION,
+        new JsonApiData(annotation.getId(), FdoType.ANNOTATION.getName(),
             mapper.valueToTree(annotation))));
     return new JsonApiListResponseWrapper(dataNodePlusOne, pageNumber, pageSize, path);
   }
@@ -242,7 +242,7 @@ private JsonApiListResponseWrapper wrapListResponseElasticSearchResults(
     List<JsonApiData> dataNodePlusOne = new ArrayList<>();
     var annotationsPlusOne = elasticSearchResults.getRight();
     annotationsPlusOne.forEach(annotation -> dataNodePlusOne.add(
-        new JsonApiData(annotation.getId(), ANNOTATION,
+        new JsonApiData(annotation.getId(), FdoType.ANNOTATION.getName(),
             mapper.valueToTree(annotation))));
     return new JsonApiListResponseWrapper(dataNodePlusOne, pageNumber, pageSize, path,
         new JsonApiMeta(elasticSearchResults.getLeft()));
@@ -252,7 +252,7 @@ private JsonApiListResponseWrapper wrapListResponse(List<Annotation> annotations
       String path) {
     List<JsonApiData> dataNode = new ArrayList<>();
     annotations.forEach(annotation -> dataNode.add(
-        new JsonApiData(annotation.getId(), ANNOTATION,
+        new JsonApiData(annotation.getId(), ANNOTATION.getName(),
             mapper.valueToTree(annotation))));
     return new JsonApiListResponseWrapper(dataNode, new JsonApiLinksFull(path));
   }

diff --git a/src/main/java/eu/dissco/backend/service/DigitalMediaService.java b/src/main/java/eu/dissco/backend/service/DigitalMediaService.java
@@ -11,7 +11,7 @@
 import eu.dissco.backend.database.jooq.enums.MjrTargetType;
 import eu.dissco.backend.domain.DigitalMediaFull;
 import eu.dissco.backend.domain.MasJobRequest;
-import eu.dissco.backend.domain.OdsType;
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.domain.jsonapi.JsonApiData;
 import eu.dissco.backend.domain.jsonapi.JsonApiLinks;
 import eu.dissco.backend.domain.jsonapi.JsonApiLinksFull;
@@ -30,7 +30,6 @@
 import java.util.Map;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.security.core.parameters.P;
 import org.springframework.stereotype.Service;
 
 @Slf4j
@@ -51,15 +50,15 @@ public JsonApiListResponseWrapper getDigitalMediaObjects(int pageNumber, int pag
       String path) {
     var mediaPlusOne = repository.getDigitalMediaObjects(pageNumber, pageSize);
     var dataNodePlusOne = mediaPlusOne.stream().map(media ->
-        new JsonApiData(media.getDctermsIdentifier(), media.getOdsFdoType(),
+        new JsonApiData(media.getDctermsIdentifier(), FdoType.DIGITAL_MEDIA.getName(),
             mapper.valueToTree(media))).toList();
     return wrapResponse(dataNodePlusOne, pageNumber, pageSize, path);
   }
 
   public JsonApiWrapper getDigitalMediaById(String id, String path) {
     var mediaObject = repository.getLatestDigitalMediaObjectById(id);
     var dataNode = new JsonApiData(mediaObject.getDctermsIdentifier(),
-        mediaObject.getOdsFdoType(), mediaObject, mapper);
+        FdoType.DIGITAL_MEDIA.getName(), mediaObject, mapper);
     var linksNode = new JsonApiLinks(path);
     return new JsonApiWrapper(dataNode, linksNode);
   }
@@ -79,7 +78,7 @@ public JsonApiWrapper getDigitalMediaObjectByVersion(String id, int version, Str
       throws JsonProcessingException, NotFoundException {
     var digitalMediaNode = mongoRepository.getByVersion(id, version, "digital_media_provenance");
     var digitalMedia = mapResultToDigitalMedia(digitalMediaNode);
-    var dataNode = new JsonApiData(digitalMedia.getDctermsIdentifier(), digitalMedia.getOdsFdoType(), digitalMedia,
+    var dataNode = new JsonApiData(digitalMedia.getDctermsIdentifier(), FdoType.DIGITAL_MEDIA.getName(), digitalMedia,
         mapper);
     return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
   }
@@ -112,7 +111,7 @@ public List<JsonApiData> getDigitalMediaForSpecimen(String id) {
     var mediaList = repository.getDigitalMediaForSpecimen(id);
     List<JsonApiData> dataNode = new ArrayList<>();
     mediaList.forEach(media -> dataNode.add(
-        new JsonApiData(media.getDctermsIdentifier(), media.getOdsFdoType(), mapper.valueToTree(media))));
+        new JsonApiData(media.getDctermsIdentifier(), FdoType.DIGITAL_MEDIA.getName(), mapper.valueToTree(media))));
     return dataNode;
   }
 
@@ -136,7 +135,7 @@ public JsonApiListResponseWrapper getMass(String id, String path) {
   public JsonApiWrapper getOriginalDataForMedia(String targetId, String path) {
     var originalData = repository.getMediaOriginalData(targetId);
     return new JsonApiWrapper(
-        new JsonApiData(targetId, OdsType.DIGITAL_MEDIA.getPid(), originalData),
+        new JsonApiData(targetId, FdoType.DIGITAL_MEDIA.getName(), originalData),
         new JsonApiLinks(path));
   }
 

diff --git a/src/main/java/eu/dissco/backend/service/DigitalSpecimenService.java b/src/main/java/eu/dissco/backend/service/DigitalSpecimenService.java
@@ -15,7 +15,7 @@
 import eu.dissco.backend.domain.DigitalSpecimenFull;
 import eu.dissco.backend.domain.MappingTerm;
 import eu.dissco.backend.domain.MasJobRequest;
-import eu.dissco.backend.domain.OdsType;
+import eu.dissco.backend.domain.FdoType;
 import eu.dissco.backend.domain.TaxonMappingTerms;
 import eu.dissco.backend.domain.jsonapi.JsonApiData;
 import eu.dissco.backend.domain.jsonapi.JsonApiLinks;
@@ -93,7 +93,7 @@ public JsonApiListResponseWrapper getLatestSpecimen(int pageNumber, int pageSize
   public JsonApiWrapper getSpecimenById(String id, String path) {
     var digitalSpecimen = repository.getLatestSpecimenById(id);
     var dataNode = new JsonApiData(digitalSpecimen.getDctermsIdentifier(),
-        digitalSpecimen.getOdsFdoType(), digitalSpecimen,
+        FdoType.DIGITAL_SPECIMEN.getName(), digitalSpecimen,
         mapper);
     return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
   }
@@ -118,7 +118,7 @@ public JsonApiListResponseWrapper getMasJobRecordsForSpecimen(String targetId,
   public JsonApiWrapper getOriginalDataForSpecimen(String targetId, String path) {
     var originalData = repository.getSpecimenOriginalData(targetId);
     return new JsonApiWrapper(
-        new JsonApiData(targetId, OdsType.DIGITAL_SPECIMEN.getPid(), originalData),
+        new JsonApiData(targetId, FdoType.DIGITAL_SPECIMEN.getName(), originalData),
         new JsonApiLinks(path));
   }
 
@@ -128,15 +128,15 @@ private JsonApiWrapper mapFullSpecimen(String id, String path, DigitalSpecimen s
     var attributeNode = mapper.valueToTree(
         new DigitalSpecimenFull(specimen, digitalMedia, annotation));
     return new JsonApiWrapper(
-        new JsonApiData(specimen.getDctermsIdentifier(), specimen.getOdsFdoType(), attributeNode),
+        new JsonApiData(specimen.getDctermsIdentifier(), FdoType.DIGITAL_SPECIMEN.getName(), attributeNode),
         new JsonApiLinks(path));
   }
 
   public JsonApiWrapper getSpecimenByVersion(String id, int version, String path)
       throws JsonProcessingException, NotFoundException {
     var specimenNode = mongoRepository.getByVersion(id, version, MONGODB_COLLECTION_NAME);
     var specimen = mapResultToSpecimen(specimenNode);
-    var dataNode = new JsonApiData(specimen.getDctermsIdentifier(), specimen.getOdsFdoType(), specimen, mapper);
+    var dataNode = new JsonApiData(specimen.getDctermsIdentifier(), FdoType.DIGITAL_SPECIMEN.getName(), specimen, mapper);
     return new JsonApiWrapper(dataNode, new JsonApiLinks(path));
   }
 
@@ -167,7 +167,7 @@ private JsonApiListResponseWrapper wrapListResponse(
     var digitalSpecimenList = elasticSearchResults.getRight();
     var dataNodePlusOne = digitalSpecimenList.stream()
         .map(specimen -> new JsonApiData(specimen.getDctermsIdentifier(),
-            specimen.getOdsFdoType(), specimen, mapper))
+            FdoType.DIGITAL_SPECIMEN.getName(), specimen, mapper))
         .toList();
     boolean hasNext = dataNodePlusOne.size() > pageSize;
     var linksNode = new JsonApiLinksFull(pageNumber, pageSize, hasNext, path);
@@ -180,7 +180,7 @@ private JsonApiListResponseWrapper wrapListResponseSearchResults(
       Pair<Long, List<DigitalSpecimen>> digitalSpecimenSearchResult,
       int pageNumber, int pageSize, MultiValueMap<String, String> params, String path) {
     var dataNodePlusOne = digitalSpecimenSearchResult.getRight().stream()
-        .map(specimen -> new JsonApiData(specimen.getDctermsIdentifier(), specimen.getOdsFdoType(), specimen,
+        .map(specimen -> new JsonApiData(specimen.getDctermsIdentifier(), FdoType.DIGITAL_SPECIMEN.getName(), specimen,
             mapper))
         .toList();
     boolean hasNext = dataNodePlusOne.size() > pageSize;