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 index 3c188c932..7c2d5c317 100644 --- 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 { - @Override +public interface AGMDiseaseAnnotationInterface { @POST @Path("/findForPublic") - @JsonView({View.ForPublic.class}) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index d9df14b18..67badf7a1 100644 --- 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 { - @Override +public interface AGMPhenotypeAnnotationInterface { @POST @Path("/findForPublic") - @JsonView({ View.PhenotypeAnnotationView.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 33f2815cc..6fb442ad0 100644 --- 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 { - @Override +public interface AlleleDiseaseAnnotationInterface { @POST @Path("/findForPublic") @JsonView({ View.ForPublic.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 102d36d9b..590050672 100644 --- 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 { - @Override +public interface AllelePhenotypeAnnotationInterface { @POST @Path("/findForPublic") - @JsonView({ View.PhenotypeAnnotationView.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 3eeac43e5..d75c58b7c 100644 --- 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 { - +public interface EcoTermRESTInterface { + @GET + @Path("/{curie}") + @JsonView(View.FieldsOnly.class) + ObjectResponse 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 index 9c99b54da..c654fb87f 100644 --- 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 { - @Override +public interface GeneDiseaseAnnotationInterface { @POST @Path("/findForPublic") @JsonView({ View.ForPublic.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index d934e8175..5bae98d95 100644 --- 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 { - @Override +public interface GeneExpressionAnnotationInterface { @POST @Path("/findForPublic") @JsonView({ View.ForPublic.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index a34cdefdb..5e7551d8f 100644 --- 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 { - @Override +public interface GeneGeneticInteractionInterface { @POST @Path("/findForPublic") @JsonView({ View.ForPublic.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 17316f235..96f470ed1 100644 --- 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 { - @Override +public interface GeneMolecularInteractionInterface { @POST @Path("/findForPublic") @JsonView({ View.ForPublic.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 9174c8aa6..973c4eaa4 100644 --- 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 { - @Override +public interface GenePhenotypeAnnotationInterface { @POST @Path("/findForPublic") - @JsonView({ View.PhenotypeAnnotationView.class }) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 1b79620a8..b4b16cea1 100644 --- 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 { - - @Override +public interface GeneToGeneOrthologyGeneratedInterface { @POST @Path("/findForPublic") - @JsonView({View.ForPublic.class}) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); - + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 1b22a4d02..4479bfc86 100644 --- 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 { - @Override +public interface GeneToGeneParalogyInterface { @POST @Path("/findForPublic") - @JsonView({View.ForPublic.class}) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); - + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index c27aa6989..3a2ef3639 100644 --- 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 { - +public interface OrganizationInterface { + @POST + @Path("/findForPublic") + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 5de917ab6..189ed9742 100644 --- 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 { - +public interface ReferenceInterface { + @GET + @Path("/{curie}") + @JsonView(View.FieldsOnly.class) + ObjectResponse 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 index 2ed3926bd..3920c6802 100644 --- 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 { - - @Override +public interface VocabularyTermRESTInterface { @POST @Path("/findForPublic") - @JsonView({View.ForPublic.class}) - SearchResponse findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, HashMap params); - + @JsonView({ View.ForPublic.class }) + SearchResponse findForPublic( + @DefaultValue("0") @QueryParam("page") Integer page, + @DefaultValue("10") @QueryParam("limit") Integer limit, + HashMap 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 index 6af44c057..a6508595a 100644 --- 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 getFiltered(int threadCount, int bufferSize LinkedBlockingDeque fullList = new LinkedBlockingDeque<>(); SearchResponse 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 index e56c4a321..c6e728f96 100644 --- a/pom.xml +++ b/pom.xml @@ -32,7 +32,7 @@ quarkus-bom io.quarkus.platform ${quarkus.version} - v0.36.12 + v0.36.14