Merge pull request #232 from AAFC-BICoE/34325_use_vocabulary_methods_…

…from_dina-base

34325 use vocabulary methods from dina base

pom.xml

@@ -34,7 +34,7 @@
     <checkstyle.version>10.17.0</checkstyle.version>
 
     <asciidoctor-maven-plugin.version>2.1.0</asciidoctor-maven-plugin.version>
-    <dina-base-api.version>0.125</dina-base-api.version>
+    <dina-base-api.version>0.127</dina-base-api.version>
 
     <postgresql.version>42.4.4</postgresql.version>
     <snakeyaml.version>1.33</snakeyaml.version>    

src/main/java/ca/gc/aafc/seqdb/api/dto/VocabularyDto.java

@@ -2,17 +2,21 @@
 
 import ca.gc.aafc.dina.vocabulary.VocabularyElementConfiguration;
 
-import io.crnk.core.resource.annotations.JsonApiId;
-import io.crnk.core.resource.annotations.JsonApiResource;
 import lombok.AllArgsConstructor;
 import lombok.Getter;
 
 import java.util.List;
 
+import com.toedter.spring.hateoas.jsonapi.JsonApiId;
+import com.toedter.spring.hateoas.jsonapi.JsonApiTypeForClass;
+
 @AllArgsConstructor
 @Getter
-@JsonApiResource(type = "vocabulary")
+@JsonApiTypeForClass(VocabularyDto.TYPE)
 public class VocabularyDto {
+
+  public static final String TYPE = "vocabulary";
+
   @JsonApiId
   private final String id;
 

src/main/java/ca/gc/aafc/seqdb/api/repository/VocabularyRepository.java

@@ -1,34 +1,63 @@
 package ca.gc.aafc.seqdb.api.repository;
 
-import ca.gc.aafc.seqdb.api.SequenceVocabularyConfiguration;
+import org.springframework.hateoas.CollectionModel;
+import org.springframework.hateoas.RepresentationModel;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.toedter.spring.hateoas.jsonapi.JsonApiModelBuilder;
+
+import ca.gc.aafc.dina.repository.ReadOnlyDinaRepositoryV2;
 import ca.gc.aafc.seqdb.api.dto.VocabularyDto;
-import io.crnk.core.queryspec.QuerySpec;
-import io.crnk.core.repository.ReadOnlyResourceRepositoryBase;
-import io.crnk.core.resource.list.ResourceList;
-import lombok.NonNull;
-import org.springframework.stereotype.Repository;
+import ca.gc.aafc.seqdb.api.service.VocabularyService;
+
+import static com.toedter.spring.hateoas.jsonapi.JsonApiModelBuilder.jsonApiModel;
+import static com.toedter.spring.hateoas.jsonapi.MediaTypes.JSON_API_VALUE;
 
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.util.List;
-import java.util.stream.Collectors;
+import javax.servlet.http.HttpServletRequest;
+
+@RestController
+@RequestMapping(value = "/api", produces = JSON_API_VALUE)
+public class VocabularyRepository extends ReadOnlyDinaRepositoryV2<String, VocabularyDto> {
+
+  protected VocabularyRepository(VocabularyService vocabularyService) {
+    super(vocabularyService);
+  }
 
-@Repository
-public class VocabularyRepository extends ReadOnlyResourceRepositoryBase<VocabularyDto, String> {
+  @GetMapping("vocabulary/{id}")
+  public ResponseEntity<RepresentationModel<?>> handleFindOne(@PathVariable String id) {
 
-  private final List<VocabularyDto> vocabulary;
+    VocabularyDto dto = findOne(id);
 
-  protected VocabularyRepository(
-          @NonNull SequenceVocabularyConfiguration collectionVocabularyConfiguration) {
-    super(VocabularyDto.class);
+    if (dto == null) {
+      return ResponseEntity.notFound().build();
+    }
 
-    vocabulary = collectionVocabularyConfiguration.getVocabulary()
-            .entrySet()
-            .stream()
-            .map(entry -> new VocabularyDto(entry.getKey(), entry.getValue()))
-            .collect(Collectors.toList());
+    JsonApiModelBuilder builder = jsonApiModel().model(RepresentationModel.of(dto));
+
+    return ResponseEntity.ok(builder.build());
   }
 
-  @Override
-  public ResourceList<VocabularyDto> findAll(QuerySpec querySpec) {
-    return querySpec.apply(vocabulary);
+  @GetMapping("vocabulary")
+  public ResponseEntity<RepresentationModel<?>> handleFindAll(HttpServletRequest req) {
+
+    String queryString = URLDecoder.decode(req.getQueryString(), StandardCharsets.UTF_8);
+    List<VocabularyDto> dtos ;
+    try {
+      dtos = findAll(queryString);
+    } catch (IllegalArgumentException iaEx) {
+      return ResponseEntity.badRequest().build();
+    }
+
+    JsonApiModelBuilder builder = jsonApiModel().model(CollectionModel.of(dtos));
+
+    return ResponseEntity.ok(builder.build());
   }
+
 }

src/main/java/ca/gc/aafc/seqdb/api/service/SeqSubmissionService.java

@@ -26,8 +26,4 @@ protected void preCreate(SeqSubmission entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/SequencingFacilityService.java

@@ -10,8 +10,6 @@
 
 import java.util.UUID;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class SequencingFacilityService extends DefaultDinaService<SequencingFacility> {
 
@@ -26,9 +24,4 @@ protected void preCreate(SequencingFacility entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }
-

src/main/java/ca/gc/aafc/seqdb/api/service/ThermocyclerProfileService.java

@@ -10,8 +10,6 @@
 import ca.gc.aafc.seqdb.api.entities.ThermocyclerProfile;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class ThermocyclerProfileService extends DefaultDinaService<ThermocyclerProfile> {
 
@@ -26,8 +24,4 @@ protected void preCreate(ThermocyclerProfile entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/VocabularyService.java

@@ -0,0 +1,21 @@
+package ca.gc.aafc.seqdb.api.service;
+
+import java.util.stream.Collectors;
+
+import org.springframework.stereotype.Service;
+
+import ca.gc.aafc.dina.service.CollectionBackedReadOnlyDinaService;
+import ca.gc.aafc.seqdb.api.SequenceVocabularyConfiguration;
+import ca.gc.aafc.seqdb.api.dto.VocabularyDto;
+
+@Service
+public class VocabularyService extends CollectionBackedReadOnlyDinaService<String, VocabularyDto> {
+
+  public VocabularyService(SequenceVocabularyConfiguration sequenceVocabularyConfiguration) {
+    super(sequenceVocabularyConfiguration.getVocabulary()
+      .entrySet()
+      .stream()
+      .map(entry -> new VocabularyDto(entry.getKey(), entry.getValue()))
+      .collect(Collectors.toList()), VocabularyDto::getId);
+  }
+}

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/IndexSetService.java

@@ -10,8 +10,6 @@
 import ca.gc.aafc.seqdb.api.entities.libraryprep.IndexSet;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class IndexSetService extends DefaultDinaService<IndexSet> {
 
@@ -26,8 +24,4 @@ protected void preCreate(IndexSet entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/LibraryPrepBatchService.java

@@ -26,8 +26,4 @@ protected void preCreate(LibraryPrepBatch entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/LibraryPrepService.java

@@ -15,8 +15,6 @@
 import ca.gc.aafc.seqdb.api.validation.ContainerLocationValidator;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPrepService extends DefaultDinaService<LibraryPrep> {
 
@@ -95,10 +93,4 @@ private void handleOverlap(LibraryPrep libraryPrep) {
       }
     }
   }
-
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
-
 }

src/main/java/ca/gc/aafc/seqdb/api/service/libraryprep/NgsIndexService.java

@@ -10,8 +10,6 @@
 import ca.gc.aafc.seqdb.api.entities.libraryprep.NgsIndex;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class NgsIndexService extends DefaultDinaService<NgsIndex> {
 
@@ -26,8 +24,4 @@ protected void preCreate(NgsIndex entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/pooledlibraries/LibraryPoolContentService.java

@@ -17,8 +17,6 @@
 import ca.gc.aafc.seqdb.api.entities.pooledlibraries.LibraryPoolContent;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPoolContentService extends DefaultDinaService<LibraryPoolContent> {
 
@@ -96,9 +94,4 @@ private List<LibraryPrepBatch> getBatches(LibraryPool pool) {
 
     return batchs;
   }
-
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/main/java/ca/gc/aafc/seqdb/api/service/pooledlibraries/LibraryPoolService.java

@@ -10,8 +10,6 @@
 import ca.gc.aafc.seqdb.api.entities.pooledlibraries.LibraryPool;
 import lombok.NonNull;
 
-// CHECKSTYLE:OFF NoFinalizer
-// CHECKSTYLE:OFF SuperFinalize
 @Service
 public class LibraryPoolService extends DefaultDinaService<LibraryPool> {
 
@@ -26,8 +24,4 @@ protected void preCreate(LibraryPool entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
-  // Fixes CT_CONSTRUCTOR_THROW
-  protected final void finalize() {
-    // no-op
-  }
 }

src/test/java/ca/gc/aafc/seqdb/api/repository/VocabularyRepositoryIT.java

@@ -1,17 +1,14 @@
 package ca.gc.aafc.seqdb.api.repository;
 
-import javax.inject.Inject;
+import org.junit.jupiter.api.Test;
+import org.springframework.http.HttpStatus;
 
 import ca.gc.aafc.seqdb.api.dto.VocabularyDto;
-import org.junit.jupiter.api.Test;
 
-import ca.gc.aafc.seqdb.api.entities.PcrPrimer.PrimerType;
-import io.crnk.core.exception.MethodNotAllowedException;
-import io.crnk.core.exception.ResourceNotFoundException;
-import io.crnk.core.queryspec.QuerySpec;
-import io.crnk.core.resource.list.ResourceList;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
-import static org.junit.jupiter.api.Assertions.*;
+import java.util.List;
+import javax.inject.Inject;
 
 public class VocabularyRepositoryIT extends BaseRepositoryTest {
 
@@ -20,25 +17,19 @@ public class VocabularyRepositoryIT extends BaseRepositoryTest {
 
   @Test
   public void findAll_DefaultQuerySpec_AllDtosReturned() {
-    ResourceList<VocabularyDto> resultList = readOnlyRepo.findAll(new QuerySpec(VocabularyDto.class));
+    List<VocabularyDto> resultList = readOnlyRepo.findAll("");
     assertEquals(2, resultList.size());
   }
 
   @Test
   public void findOne_QueryPcrPrimerType_OnePrimerTypeDtoReturned() {
-    VocabularyDto resultDto = readOnlyRepo.findOne("pcrBatchType", new QuerySpec(VocabularyDto.class));
+    VocabularyDto resultDto = readOnlyRepo.findOne("pcrBatchType");
     assertEquals("pcrBatchType", resultDto.getId());
   }
 
   @Test
-  public void findOne_QueryNonExistantID_ThrowResourceNotFoundException() {
-    assertThrows(ResourceNotFoundException.class,
-        () -> readOnlyRepo.findOne("mumbo jumbo", new QuerySpec(VocabularyDto.class)));
-  }
-
-  @Test
-  public void delete_ExistingDtoID_ThrowUnsupportedOperationException() {
-    assertThrows(MethodNotAllowedException.class, () -> readOnlyRepo.delete(PrimerType.class.getSimpleName()));
+  public void findOne_QueryNonExistantID_returnNotFound() {
+    assertEquals(HttpStatus.NOT_FOUND, readOnlyRepo.handleFindOne("mumbo jumbo").getStatusCode());
   }
 
 }