From e849b1ed9a623dc4156c96b9b4dd3ff592f1c37b Mon Sep 17 00:00:00 2001 From: Adam Gibson Date: Tue, 4 Mar 2025 10:54:40 -0600 Subject: [PATCH 1/3] update curation library --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 7ed1fb7d4..755373863 100644 --- a/pom.xml +++ b/pom.xml @@ -32,7 +32,7 @@ quarkus-bom io.quarkus.platform ${quarkus.version} - v0.36.5 + v0.36.7 From f8d635a907ff069c8742aa47e422c91507affb65 Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Tue, 4 Mar 2025 12:08:10 -0500 Subject: [PATCH 2/3] Fix for API --- .../interfaces/AGMDiseaseAnnotationInterface.java | 1 - .../AlleleDiseaseAnnotationInterface.java | 1 - .../GeneDiseaseAnnotationInterface.java | 1 - .../GeneExpressionAnnotationInterface.java | 15 +++++++++++---- .../GeneGeneticInteractionInterface.java | 1 - .../GeneMolecularInteractionInterface.java | 1 - 6 files changed, 11 insertions(+), 9 deletions(-) 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 c3dad3e40..e33ef8011 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 @@ -21,7 +21,6 @@ @Consumes({"application/json"}) public interface AGMDiseaseAnnotationInterface extends BaseIdCrudInterface { - @Override @POST @Path("/findForPublic") @JsonView({View.ForPublic.class}) 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 1fa91e419..a232214e9 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 @@ -21,7 +21,6 @@ @Consumes({"application/json"}) public interface AlleleDiseaseAnnotationInterface extends BaseIdCrudInterface { - @Override @POST @Path("/findForPublic") @JsonView({View.ForPublic.class}) 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 cdf750bde..232a03b68 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 @@ -21,7 +21,6 @@ @Consumes({"application/json"}) public interface GeneDiseaseAnnotationInterface extends BaseIdCrudInterface { - @Override @POST @Path("/findForPublic") @JsonView({View.ForPublic.class}) 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 5b17ba3a9..754a26d22 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 @@ -1,13 +1,20 @@ package org.alliancegenome.indexer.indexers.curation.interfaces; -import com.fasterxml.jackson.annotation.JsonView; -import jakarta.ws.rs.*; +import java.util.HashMap; + import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface; import org.alliancegenome.curation_api.model.entities.GeneExpressionAnnotation; import org.alliancegenome.curation_api.response.SearchResponse; import org.alliancegenome.curation_api.view.View; -import java.util.HashMap; +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; @Path("/gene-expression-annotation") @Produces({"application/json"}) @@ -16,7 +23,7 @@ public interface GeneExpressionAnnotationInterface extends BaseIdCrudInterface find( + 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 cbb31bd1c..7b8b90854 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 @@ -21,7 +21,6 @@ @Consumes({"application/json"}) public interface GeneGeneticInteractionInterface extends BaseIdCrudInterface { - @Override @POST @Path("/findForPublic") @JsonView({View.ForPublic.class}) 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 b8af69753..a2aada415 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 @@ -21,7 +21,6 @@ @Consumes({"application/json"}) public interface GeneMolecularInteractionInterface extends BaseIdCrudInterface { - @Override @POST @Path("/findForPublic") @JsonView({View.ForPublic.class}) From 5cda7c3d9b2cd3146bde080907d5fdae2f74f26f Mon Sep 17 00:00:00 2001 From: Olin Blodgett Date: Tue, 4 Mar 2025 12:09:49 -0500 Subject: [PATCH 3/3] Fix find lookup --- .../curation/service/GeneExpressionAnnotationService.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneExpressionAnnotationService.java b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneExpressionAnnotationService.java index 5746bf010..5b325f723 100644 --- a/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneExpressionAnnotationService.java +++ b/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneExpressionAnnotationService.java @@ -1,13 +1,14 @@ package org.alliancegenome.indexer.indexers.curation.service; +import java.util.HashMap; + import org.alliancegenome.core.config.ConfigHelper; import org.alliancegenome.curation_api.model.entities.GeneExpressionAnnotation; import org.alliancegenome.curation_api.response.SearchResponse; import org.alliancegenome.indexer.RestConfig; import org.alliancegenome.indexer.indexers.curation.interfaces.GeneExpressionAnnotationInterface; -import si.mazi.rescu.RestProxyFactory; -import java.util.HashMap; +import si.mazi.rescu.RestProxyFactory; public class GeneExpressionAnnotationService { @@ -17,6 +18,6 @@ public SearchResponse getGeneExpressionAnnotations(Int HashMap params = new HashMap<>(); params.put("internal", false); params.put("obsolete", false); - return geneExpressionAnnotationClient.find(page, limit, params); + return geneExpressionAnnotationClient.findForPublic(page, limit, params); } }