Merge pull request #1258 from alliance-genome/dynamic_view

oblodgett · web-flow · commit c5a0fc7f3c18 · 2025-03-06T13:36:38.000-05:00
Fixed all interfaces
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AGMDiseaseAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AGMDiseaseAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/agm-disease-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface AGMDiseaseAnnotationInterface extends ForPublicFindInterface<AGMDiseaseAnnotation> {
-	@Override
+public interface AGMDiseaseAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({View.ForPublic.class})
-	SearchResponse<AGMDiseaseAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<AGMDiseaseAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AGMPhenotypeAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AGMPhenotypeAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/agm-phenotype-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface AGMPhenotypeAnnotationInterface extends ForPublicFindInterface<AGMPhenotypeAnnotation> {
-	@Override
+public interface AGMPhenotypeAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({ View.PhenotypeAnnotationView.class })
-	SearchResponse<AGMPhenotypeAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<AGMPhenotypeAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AlleleDiseaseAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AlleleDiseaseAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/allele-disease-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface AlleleDiseaseAnnotationInterface extends ForPublicFindInterface<AlleleDiseaseAnnotation> {
-	@Override
+public interface AlleleDiseaseAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
 	@JsonView({ View.ForPublic.class })
-	SearchResponse<AlleleDiseaseAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	SearchResponse<AlleleDiseaseAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AllelePhenotypeAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/AllelePhenotypeAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/allele-phenotype-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface AllelePhenotypeAnnotationInterface extends ForPublicFindInterface<AllelePhenotypeAnnotation> {
-	@Override
+public interface AllelePhenotypeAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({ View.PhenotypeAnnotationView.class })
-	SearchResponse<AllelePhenotypeAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<AllelePhenotypeAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/EcoTermRESTInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/EcoTermRESTInterface.java
@@ -1,16 +1,24 @@
 package org.alliancegenome.indexer.indexers.curation.interfaces;
 
-import org.alliancegenome.curation_api.interfaces.base.crud.BaseReadCurieControllerInterface;
 import org.alliancegenome.curation_api.model.entities.ontology.ECOTerm;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.view.View;
+
+import com.fasterxml.jackson.annotation.JsonView;
 
 import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.GET;
 import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
 import jakarta.ws.rs.Produces;
 import jakarta.ws.rs.core.MediaType;
 
 @Path("/ecoterm")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface EcoTermRESTInterface extends BaseReadCurieControllerInterface<ECOTerm> {
-
+public interface EcoTermRESTInterface {
+	@GET
+	@Path("/{curie}")
+	@JsonView(View.FieldsOnly.class)
+	ObjectResponse<ECOTerm> getByCurie(@PathParam("curie") String curie);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneDiseaseAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneDiseaseAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/gene-disease-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneDiseaseAnnotationInterface extends ForPublicFindInterface<GeneDiseaseAnnotation> {
-	@Override
+public interface GeneDiseaseAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
 	@JsonView({ View.ForPublic.class })
-	SearchResponse<GeneDiseaseAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	SearchResponse<GeneDiseaseAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneExpressionAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneExpressionAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/gene-expression-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneExpressionAnnotationInterface extends ForPublicFindInterface<GeneExpressionAnnotation> {
-	@Override
+public interface GeneExpressionAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
 	@JsonView({ View.ForPublic.class })
-	SearchResponse<GeneExpressionAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	SearchResponse<GeneExpressionAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneGeneticInteractionInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneGeneticInteractionInterface.java
@@ -19,10 +19,12 @@
 @Path("/gene-genetic-interaction")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneGeneticInteractionInterface extends ForPublicFindInterface<GeneGeneticInteraction> {
-	@Override
+public interface GeneGeneticInteractionInterface {
 	@POST
 	@Path("/findForPublic")
 	@JsonView({ View.ForPublic.class })
-	SearchResponse<GeneGeneticInteraction> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	SearchResponse<GeneGeneticInteraction> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneMolecularInteractionInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneMolecularInteractionInterface.java
@@ -19,10 +19,12 @@
 @Path("/gene-molecular-interaction")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneMolecularInteractionInterface extends ForPublicFindInterface<GeneMolecularInteraction> {
-	@Override
+public interface GeneMolecularInteractionInterface {
 	@POST
 	@Path("/findForPublic")
 	@JsonView({ View.ForPublic.class })
-	SearchResponse<GeneMolecularInteraction> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	SearchResponse<GeneMolecularInteraction> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GenePhenotypeAnnotationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GenePhenotypeAnnotationInterface.java
@@ -19,10 +19,12 @@
 @Path("/gene-phenotype-annotation")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GenePhenotypeAnnotationInterface extends ForPublicFindInterface<GenePhenotypeAnnotation> {
-	@Override
+public interface GenePhenotypeAnnotationInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({ View.PhenotypeAnnotationView.class })
-	SearchResponse<GenePhenotypeAnnotation> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<GenePhenotypeAnnotation> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneOrthologyGeneratedInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneOrthologyGeneratedInterface.java
@@ -19,12 +19,12 @@
 @Path("/orthologygenerated")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneToGeneOrthologyGeneratedInterface extends ForPublicFindInterface<GeneToGeneOrthologyGenerated> {
-
-	@Override
+public interface GeneToGeneOrthologyGeneratedInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({View.ForPublic.class})
-	SearchResponse<GeneToGeneOrthologyGenerated> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
-
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<GeneToGeneOrthologyGenerated> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneParalogyInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneParalogyInterface.java
@@ -19,11 +19,12 @@
 @Path("/paralogy")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface GeneToGeneParalogyInterface extends ForPublicFindInterface<GeneToGeneParalogy> {
-	@Override
+public interface GeneToGeneParalogyInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({View.ForPublic.class})
-	SearchResponse<GeneToGeneParalogy> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
-
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<GeneToGeneParalogy> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/OrganizationInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/OrganizationInterface.java
@@ -1,15 +1,30 @@
 package org.alliancegenome.indexer.indexers.curation.interfaces;
 
+import java.util.HashMap;
+
 import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.view.View;
+
+import com.fasterxml.jackson.annotation.JsonView;
 
 import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.POST;
 import jakarta.ws.rs.Path;
 import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
 import jakarta.ws.rs.core.MediaType;
 
 @Path("/organization")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface OrganizationInterface extends ForPublicFindInterface<Organization> {
-
+public interface OrganizationInterface {
+	@POST
+	@Path("/findForPublic")
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<Organization> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/ReferenceInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/ReferenceInterface.java
@@ -1,16 +1,24 @@
 package org.alliancegenome.indexer.indexers.curation.interfaces;
 
-import org.alliancegenome.curation_api.interfaces.base.crud.BaseReadCurieControllerInterface;
 import org.alliancegenome.curation_api.model.entities.Reference;
+import org.alliancegenome.curation_api.response.ObjectResponse;
+import org.alliancegenome.curation_api.view.View;
+
+import com.fasterxml.jackson.annotation.JsonView;
 
 import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.GET;
 import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
 import jakarta.ws.rs.Produces;
 import jakarta.ws.rs.core.MediaType;
 
 @Path("/reference")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface ReferenceInterface extends BaseReadCurieControllerInterface<Reference> {
-
+public interface ReferenceInterface {
+	@GET
+	@Path("/{curie}")
+	@JsonView(View.FieldsOnly.class)
+	ObjectResponse<Reference> getByCurie(@PathParam("curie") String curie);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyTermRESTInterface.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyTermRESTInterface.java
@@ -19,12 +19,12 @@
 @Path("/vocabularyterm")
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
-public interface VocabularyTermRESTInterface extends ForPublicFindInterface<VocabularyTerm> {
-	
-	@Override
+public interface VocabularyTermRESTInterface {
 	@POST
 	@Path("/findForPublic")
-	@JsonView({View.ForPublic.class})
-	SearchResponse<VocabularyTerm> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap<String, Object> params);
-
+	@JsonView({ View.ForPublic.class })
+	SearchResponse<VocabularyTerm> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
 }
diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GenePhenotypeAnnotationService.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GenePhenotypeAnnotationService.java
@@ -36,7 +36,7 @@ public List<GenePhenotypeAnnotation> getFiltered(int threadCount, int bufferSize
 		LinkedBlockingDeque<GenePhenotypeAnnotation> fullList = new LinkedBlockingDeque<>();
 
 		SearchResponse<GenePhenotypeAnnotation> response = geneApi.findForPublic(0, 0, null);
-
+		
 		int totalPages = (int) (response.getTotalResults() / bufferSize);
 
 		display.startProcess("Pulling Gene PA's from curation", response.getTotalResults());
diff --git a/pom.xml b/pom.xml
@@ -32,7 +32,7 @@
 		<quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
 		<quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
 		<quarkus.platform.version>${quarkus.version}</quarkus.platform.version>
-		<curation.version>v0.36.12</curation.version>
+		<curation.version>v0.36.14</curation.version>
 		<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
 	</properties>
 	<dependencyManagement>
