adding source and sourceId filter to existing api (#566)

* adding filter to existing api #564 * updated gbif-api version * adding filter to existing api #564 * gbif/pipelines#957 Add extra logging to track step changes * gbif/pipelines#957 Add type to extra logging to track step changes * adding filter to existing api #564 * adding filter to existing api #564 * adding filter to existing api #564 * adding filter to existing api #564 * adding filter to existing api #564 --------- Co-authored-by: Marcos Lopez Gonzalez <[email protected]> Co-authored-by: Nikolay Volik <[email protected]>
gbif · Apr 24, 2024 · 20fe72d · 20fe72d
1 parent 83ddbf1
commit 20fe72d
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Showing 16 changed files with 161 additions and 23 deletions.
diff --git a/pom.xml b/pom.xml
@@ -92,7 +92,7 @@
     <gbif-doi.version>2.17</gbif-doi.version>
     <gbif-download-query-tools.version>1.51.0</gbif-download-query-tools.version>
     <gbif-httputils.version>0.10</gbif-httputils.version>
-    <gbif-metadata-profile.version>2.1</gbif-metadata-profile.version>
+    <gbif-metadata-profile.version>2.2-SNAPSHOT</gbif-metadata-profile.version>
     <gbif-parsers.version>0.60</gbif-parsers.version>
     <gbif-postal-service.version>1.8.0</gbif-postal-service.version>
     <xoai.version>4.1.0-gbif-4</xoai.version>

diff --git a/...ests/src/test/java/org/gbif/registry/ws/it/collections/resource/CollectionResourceIT.java b/...ests/src/test/java/org/gbif/registry/ws/it/collections/resource/CollectionResourceIT.java
@@ -101,6 +101,7 @@ public void listTest() {
     req.setAccessionStatus(AccessionStatus.INSTITUTIONAL);
     req.setPreservationTypes(
         Arrays.asList(PreservationType.SAMPLE_CRYOPRESERVED, PreservationType.SAMPLE_DRIED));
+
     PagingResponse<CollectionView> result = getClient().list(req);
     assertEquals(views.size(), result.getResults().size());
   }

diff --git a/...-tests/src/test/java/org/gbif/registry/ws/it/collections/service/CollectionServiceIT.java b/...-tests/src/test/java/org/gbif/registry/ws/it/collections/service/CollectionServiceIT.java
@@ -144,17 +144,31 @@ public void listTest() {
     collection2.setAddress(address2);
     UUID key2 = collectionService.create(collection2);
 
+    Collection collection3 = testData.newEntity();
+    collection3.setCode("c3");
+    collection3.setName("n3");
+    MasterSourceMetadata sourceMetadata = new MasterSourceMetadata();
+    sourceMetadata.setCreatedBy("test");
+    sourceMetadata.setSourceId("test-123");
+    sourceMetadata.setSource(Source.IH_IRN);
+    collection3.setMasterSourceMetadata(sourceMetadata);
+    UUID key3 = collectionService.create(collection3);
+    collectionService.addMasterSourceMetadata(key3,sourceMetadata);
+
     // query param
     PagingResponse<CollectionView> response =
         collectionService.list(
             CollectionSearchRequest.builder().query("dummy").page(DEFAULT_PAGE).build());
-    assertEquals(2, response.getResults().size());
+    assertEquals(3, response.getResults().size());
+
+    response = collectionService.list(CollectionSearchRequest.builder().source(Source.IH_IRN).sourceId("test-123").build());
+    assertEquals(1,response.getResults().size());
 
     // empty queries are ignored and return all elements
     response =
         collectionService.list(
             CollectionSearchRequest.builder().query("").page(DEFAULT_PAGE).build());
-    assertEquals(2, response.getResults().size());
+    assertEquals(3, response.getResults().size());
 
     response =
         collectionService.list(
@@ -169,7 +183,7 @@ public void listTest() {
     assertEquals(key2, response.getResults().get(0).getCollection().getKey());
 
     assertEquals(
-        2,
+        3,
         collectionService
             .list(CollectionSearchRequest.builder().query("c").page(DEFAULT_PAGE).build())
             .getResults()
@@ -193,13 +207,13 @@ public void listTest() {
             .getResults()
             .size());
     assertEquals(
-        2,
+        3,
         collectionService
             .list(CollectionSearchRequest.builder().page(DEFAULT_PAGE).build())
             .getResults()
             .size());
     assertEquals(
-        2,
+        3,
         collectionService
             .list(CollectionSearchRequest.builder().query("  ").page(DEFAULT_PAGE).build())
             .getResults()
@@ -233,13 +247,13 @@ public void listTest() {
             .getResults()
             .size());
     assertEquals(
-        1,
+        2,
         collectionService
             .list(CollectionSearchRequest.builder().active(true).page(DEFAULT_PAGE).build())
             .getResults()
             .size());
     assertEquals(
-        1,
+        2,
         collectionService
             .list(
                 CollectionSearchRequest.builder()
@@ -399,7 +413,7 @@ public void listTest() {
             .size());
 
     assertEquals(
-        1,
+        2,
         collectionService
             .list(
                 CollectionSearchRequest.builder()

diff --git a/...tests/src/test/java/org/gbif/registry/ws/it/collections/service/InstitutionServiceIT.java b/...tests/src/test/java/org/gbif/registry/ws/it/collections/service/InstitutionServiceIT.java
@@ -124,16 +124,31 @@ public void listTest() {
     institution2.setAddress(address2);
     UUID key2 = institutionService.create(institution2);
 
+    Institution institution3 = testData.newEntity();
+    institution3.setCode("c3");
+    institution3.setName("n3");
+    institution3.setActive(true);
+
+    MasterSourceMetadata sourceMetadata = new MasterSourceMetadata();
+    sourceMetadata.setCreatedBy("test");
+    sourceMetadata.setSourceId("test-123");
+    sourceMetadata.setSource(Source.IH_IRN);
+    institution3.setMasterSourceMetadata(sourceMetadata);
+    UUID key3 = institutionService.create(institution3);
+    institutionService.addMasterSourceMetadata(key3,sourceMetadata);
+
     PagingResponse<Institution> response =
         institutionService.list(
             InstitutionSearchRequest.builder().query("dummy").page(DEFAULT_PAGE).build());
-    assertEquals(2, response.getResults().size());
+    assertEquals(3, response.getResults().size());
 
+    response = institutionService.list(InstitutionSearchRequest.builder().source(Source.IH_IRN).sourceId("test-123").build());
+    assertEquals(1,response.getResults().size());
     // empty queries are ignored and return all elements
     response =
         institutionService.list(
             InstitutionSearchRequest.builder().query("").page(DEFAULT_PAGE).build());
-    assertEquals(2, response.getResults().size());
+    assertEquals(3, response.getResults().size());
 
     response =
         institutionService.list(
@@ -201,7 +216,7 @@ public void listTest() {
 
     // query param
     assertEquals(
-        2,
+        3,
         institutionService
             .list(InstitutionSearchRequest.builder().query("c").page(DEFAULT_PAGE).build())
             .getResults()
@@ -225,19 +240,19 @@ public void listTest() {
             .getResults()
             .size());
     assertEquals(
-        2,
+        3,
         institutionService
             .list(InstitutionSearchRequest.builder().page(DEFAULT_PAGE).build())
             .getResults()
             .size());
     assertEquals(
-        2,
+        3,
         institutionService
             .list(InstitutionSearchRequest.builder().query("  ").page(DEFAULT_PAGE).build())
             .getResults()
             .size());
     assertEquals(
-        1,
+        2,
         institutionService
             .list(InstitutionSearchRequest.builder().active(true).page(DEFAULT_PAGE).build())
             .getResults()
@@ -362,7 +377,7 @@ public void listTest() {
             .size());
 
     assertEquals(
-        1,
+        2,
         institutionService
             .list(
                 InstitutionSearchRequest.builder()

diff --git a/...on-tests/src/test/java/org/gbif/registry/ws/it/persistence/mapper/CollectionMapperIT.java b/...on-tests/src/test/java/org/gbif/registry/ws/it/persistence/mapper/CollectionMapperIT.java
@@ -17,6 +17,7 @@
 import org.gbif.api.model.collections.AlternativeCode;
 import org.gbif.api.model.collections.Collection;
 import org.gbif.api.model.collections.Contact;
+import org.gbif.api.model.collections.MasterSourceMetadata;
 import org.gbif.api.model.collections.UserId;
 import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.registry.Identifier;
@@ -27,12 +28,14 @@
 import org.gbif.api.vocabulary.collections.IdType;
 import org.gbif.api.vocabulary.collections.MasterSourceType;
 import org.gbif.api.vocabulary.collections.PreservationType;
+import org.gbif.api.vocabulary.collections.Source;
 import org.gbif.registry.database.TestCaseDatabaseInitializer;
 import org.gbif.registry.persistence.mapper.IdentifierMapper;
 import org.gbif.registry.persistence.mapper.MachineTagMapper;
 import org.gbif.registry.persistence.mapper.collections.AddressMapper;
 import org.gbif.registry.persistence.mapper.collections.CollectionContactMapper;
 import org.gbif.registry.persistence.mapper.collections.CollectionMapper;
+import org.gbif.registry.persistence.mapper.collections.MasterSourceSyncMetadataMapper;
 import org.gbif.registry.persistence.mapper.collections.dto.CollectionDto;
 import org.gbif.registry.persistence.mapper.collections.params.CollectionSearchParams;
 import org.gbif.registry.search.test.EsManageServer;
@@ -66,6 +69,7 @@ public class CollectionMapperIT extends BaseItTest {
   private MachineTagMapper machineTagMapper;
   private IdentifierMapper identifierMapper;
   private CollectionContactMapper contactMapper;
+  private MasterSourceSyncMetadataMapper metadataMapper;
 
   @Autowired
   public CollectionMapperIT(
@@ -75,13 +79,15 @@ public CollectionMapperIT(
       IdentifierMapper identifierMapper,
       CollectionContactMapper contactMapper,
       SimplePrincipalProvider principalProvider,
-      EsManageServer esServer) {
+      EsManageServer esServer,
+      MasterSourceSyncMetadataMapper metadataMapper) {
     super(principalProvider, esServer);
     this.collectionMapper = collectionMapper;
     this.addressMapper = addressMapper;
     this.machineTagMapper = machineTagMapper;
     this.identifierMapper = identifierMapper;
     this.contactMapper = contactMapper;
+    this.metadataMapper = metadataMapper;
   }
 
   @Test
@@ -218,13 +224,30 @@ public void listTest() {
     col4.setModifiedBy("test");
     collectionMapper.create(col4);
 
+    Collection col5 = new Collection();
+    col5.setKey(UUID.randomUUID());
+    col5.setCode("c5");
+    col5.setName("name of fifth collection");
+    col5.setCreatedBy("test");
+    col5.setModifiedBy("test");
+    collectionMapper.create(col5);
+
+    MasterSourceMetadata masterSourceMetadata = new MasterSourceMetadata();
+    masterSourceMetadata.setSource(Source.IH_IRN);
+    masterSourceMetadata.setKey(123456);
+    masterSourceMetadata.setSourceId("test-123");
+    masterSourceMetadata.setCreatedBy("test");
+    metadataMapper.create(masterSourceMetadata);
+    collectionMapper.addMasterSourceMetadata(col5.getKey(),masterSourceMetadata.getKey(),MasterSourceType.GRSCICOLL);
+
     Pageable page = PAGE.apply(2, 0L);
     List<CollectionDto> dtos =
         collectionMapper.list(CollectionSearchParams.builder().page(page).build());
     assertEquals(2, dtos.size());
 
     page = PAGE.apply(5, 0L);
-    assertSearch(CollectionSearchParams.builder().page(page).build(), 4);
+    assertSearch(CollectionSearchParams.builder().sourceId("test-123").source(Source.IH_IRN).build(),1,col5.getKey());
+    assertSearch(CollectionSearchParams.builder().page(page).build(), 5);
     assertSearch(CollectionSearchParams.builder().code("c1").page(page).build(), 1);
     assertSearch(CollectionSearchParams.builder().code("C1").page(page).build(), 1);
     assertSearch(CollectionSearchParams.builder().name("n2").page(page).build(), 1);
@@ -340,7 +363,7 @@ public void listTest() {
             .masterSourceType(MasterSourceType.GRSCICOLL)
             .page(page)
             .build(),
-        0);
+        1);
   }
 
   @Test

diff --git a/...n-tests/src/test/java/org/gbif/registry/ws/it/persistence/mapper/InstitutionMapperIT.java b/...n-tests/src/test/java/org/gbif/registry/ws/it/persistence/mapper/InstitutionMapperIT.java
@@ -17,6 +17,7 @@
 import org.gbif.api.model.collections.AlternativeCode;
 import org.gbif.api.model.collections.Contact;
 import org.gbif.api.model.collections.Institution;
+import org.gbif.api.model.collections.MasterSourceMetadata;
 import org.gbif.api.model.collections.UserId;
 import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.registry.Identifier;
@@ -26,12 +27,14 @@
 import org.gbif.api.vocabulary.collections.Discipline;
 import org.gbif.api.vocabulary.collections.IdType;
 import org.gbif.api.vocabulary.collections.MasterSourceType;
+import org.gbif.api.vocabulary.collections.Source;
 import org.gbif.registry.database.TestCaseDatabaseInitializer;
 import org.gbif.registry.persistence.mapper.IdentifierMapper;
 import org.gbif.registry.persistence.mapper.MachineTagMapper;
 import org.gbif.registry.persistence.mapper.collections.AddressMapper;
 import org.gbif.registry.persistence.mapper.collections.CollectionContactMapper;
 import org.gbif.registry.persistence.mapper.collections.InstitutionMapper;
+import org.gbif.registry.persistence.mapper.collections.MasterSourceSyncMetadataMapper;
 import org.gbif.registry.persistence.mapper.collections.params.InstitutionSearchParams;
 import org.gbif.registry.search.test.EsManageServer;
 import org.gbif.registry.ws.it.BaseItTest;
@@ -69,6 +72,7 @@ public class InstitutionMapperIT extends BaseItTest {
   private MachineTagMapper machineTagMapper;
   private IdentifierMapper identifierMapper;
   private CollectionContactMapper contactMapper;
+  private MasterSourceSyncMetadataMapper metadataMapper;
 
   @Autowired
   public InstitutionMapperIT(
@@ -78,13 +82,15 @@ public InstitutionMapperIT(
       IdentifierMapper identifierMapper,
       CollectionContactMapper contactMapper,
       SimplePrincipalProvider principalProvider,
-      EsManageServer esServer) {
+      EsManageServer esServer,
+      MasterSourceSyncMetadataMapper metadataMapper) {
     super(principalProvider, esServer);
     this.institutionMapper = institutionMapper;
     this.addressMapper = addressMapper;
     this.machineTagMapper = machineTagMapper;
     this.identifierMapper = identifierMapper;
     this.contactMapper = contactMapper;
+    this.metadataMapper = metadataMapper;
   }
 
   @Test
@@ -208,9 +214,26 @@ public void listTest() {
     inst3.setModifiedBy("test");
     institutionMapper.create(inst3);
 
+    Institution inst4 = new Institution();
+    inst4.setKey(UUID.randomUUID());
+    inst4.setCode("i4");
+    inst4.setName("Name of the forth institution");
+    inst4.setCreatedBy("test");
+    inst4.setModifiedBy("test");
+    institutionMapper.create(inst4);
+
+    MasterSourceMetadata masterSourceMetadata = new MasterSourceMetadata();
+    masterSourceMetadata.setSource(Source.IH_IRN);
+    masterSourceMetadata.setKey(123456);
+    masterSourceMetadata.setSourceId("test-123");
+    masterSourceMetadata.setCreatedBy("test");
+    metadataMapper.create(masterSourceMetadata);
+    institutionMapper.addMasterSourceMetadata(inst4.getKey(),masterSourceMetadata.getKey(),MasterSourceType.GRSCICOLL);
+
     Pageable page = PAGE.apply(5, 0L);
 
-    assertSearch(InstitutionSearchParams.builder().page(page).build(), 3);
+    assertSearch(InstitutionSearchParams.builder().sourceId("test-123").source(Source.IH_IRN).build(),1,inst4.getKey());
+    assertSearch(InstitutionSearchParams.builder().page(page).build(), 4);
     assertSearch(InstitutionSearchParams.builder().code("i1").page(page).build(), 1);
     assertSearch(InstitutionSearchParams.builder().code("I1").page(page).build(), 1);
     assertSearch(InstitutionSearchParams.builder().name("n2").page(page).build(), 1);
@@ -326,7 +349,7 @@ public void listTest() {
             .masterSourceType(MasterSourceType.GRSCICOLL)
             .page(page)
             .build(),
-        0);
+        1);
   }
 
   @Test

diff --git a/.../java/org/gbif/registry/persistence/mapper/collections/params/CollectionSearchParams.java b/.../java/org/gbif/registry/persistence/mapper/collections/params/CollectionSearchParams.java
@@ -16,6 +16,7 @@
 import org.gbif.api.vocabulary.collections.AccessionStatus;
 import org.gbif.api.vocabulary.collections.CollectionContentType;
 import org.gbif.api.vocabulary.collections.PreservationType;
+import org.gbif.api.vocabulary.collections.Source;
 
 import java.util.List;
 
@@ -32,4 +33,6 @@ public class CollectionSearchParams extends SearchParams {
   @Nullable List<PreservationType> preservationTypes;
   @Nullable AccessionStatus accessionStatus;
   @Nullable Boolean personalCollection;
+  @Nullable String sourceId;
+  @Nullable Source source;
 }
diff --git a/...java/org/gbif/registry/persistence/mapper/collections/params/InstitutionSearchParams.java b/...java/org/gbif/registry/persistence/mapper/collections/params/InstitutionSearchParams.java
@@ -16,6 +16,7 @@
 import org.gbif.api.vocabulary.collections.Discipline;
 import org.gbif.api.vocabulary.collections.InstitutionGovernance;
 import org.gbif.api.vocabulary.collections.InstitutionType;
+import org.gbif.api.vocabulary.collections.Source;
 
 import java.util.List;
 
@@ -31,4 +32,6 @@ public class InstitutionSearchParams extends SearchParams {
   @Nullable InstitutionType type;
   @Nullable InstitutionGovernance institutionalGovernance;
   @Nullable List<Discipline> disciplines;
+  @Nullable String sourceId;
+  @Nullable Source source;
 }