Skip to content

update curation library #1252

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
adamgibs merged 3 commits into from
Mar 4, 2025
Merged

update curation library #1252

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e849b1e
update curation library
adamgibs Mar 4, 2025
f8d635a
Fix for API
oblodgett Mar 4, 2025
5cda7c3
Fix find lookup
oblodgett Mar 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion ...rg/alliancegenome/indexer/indexers/curation/interfaces/AGMDiseaseAnnotationInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
@Consumes({"application/json"})
public interface AGMDiseaseAnnotationInterface extends BaseIdCrudInterface<AGMDiseaseAnnotation> {

@Override
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
Expand Down
1 change: 0 additions & 1 deletion ...alliancegenome/indexer/indexers/curation/interfaces/AlleleDiseaseAnnotationInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
@Consumes({"application/json"})
public interface AlleleDiseaseAnnotationInterface extends BaseIdCrudInterface<AlleleDiseaseAnnotation> {

@Override
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
Expand Down
1 change: 0 additions & 1 deletion ...g/alliancegenome/indexer/indexers/curation/interfaces/GeneDiseaseAnnotationInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
@Consumes({"application/json"})
public interface GeneDiseaseAnnotationInterface extends BaseIdCrudInterface<GeneDiseaseAnnotation> {

@Override
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
Expand Down
15 changes: 11 additions & 4 deletions ...lliancegenome/indexer/indexers/curation/interfaces/GeneExpressionAnnotationInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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"})
Expand All @@ -16,7 +23,7 @@ public interface GeneExpressionAnnotationInterface extends BaseIdCrudInterface<G
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
SearchResponse<GeneExpressionAnnotation> find(
SearchResponse<GeneExpressionAnnotation> findForPublic(
@DefaultValue("0") @QueryParam("page") Integer page,
@DefaultValue("10") @QueryParam("limit") Integer limit,
HashMap<String, Object> params
Expand Down
1 change: 0 additions & 1 deletion .../alliancegenome/indexer/indexers/curation/interfaces/GeneGeneticInteractionInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
@Consumes({"application/json"})
public interface GeneGeneticInteractionInterface extends BaseIdCrudInterface<GeneGeneticInteraction> {

@Override
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
Expand Down
1 change: 0 additions & 1 deletion ...lliancegenome/indexer/indexers/curation/interfaces/GeneMolecularInteractionInterface.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
@Consumes({"application/json"})
public interface GeneMolecularInteractionInterface extends BaseIdCrudInterface<GeneMolecularInteraction> {

@Override
@POST
@Path("/findForPublic")
@JsonView({View.ForPublic.class})
Expand Down
7 changes: 4 additions & 3 deletions ...org/alliancegenome/indexer/indexers/curation/service/GeneExpressionAnnotationService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 {

Expand All @@ -17,6 +18,6 @@ public SearchResponse<GeneExpressionAnnotation> getGeneExpressionAnnotations(Int
HashMap<String, Object> params = new HashMap<>();
params.put("internal", false);
params.put("obsolete", false);
return geneExpressionAnnotationClient.find(page, limit, params);
return geneExpressionAnnotationClient.findForPublic(page, limit, params);
}
}
2 changes: 1 addition & 1 deletion pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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>v0.36.5</curation.version>
<curation.version>v0.36.7</curation.version>
<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
</properties>
<dependencyManagement>
Expand Down
Loading