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Merged
oblodgett merged 1 commit into from
Mar 6, 2025
Merged

Fixed all interfaces #1258

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10 changes: 6 additions & 4 deletions ...rg/alliancegenome/indexer/indexers/curation/interfaces/AGMDiseaseAnnotationInterface.java
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@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);
}
10 changes: 6 additions & 4 deletions .../alliancegenome/indexer/indexers/curation/interfaces/AGMPhenotypeAnnotationInterface.java
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@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);
}
8 changes: 5 additions & 3 deletions ...alliancegenome/indexer/indexers/curation/interfaces/AlleleDiseaseAnnotationInterface.java
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@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);
}
10 changes: 6 additions & 4 deletions ...liancegenome/indexer/indexers/curation/interfaces/AllelePhenotypeAnnotationInterface.java
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@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);
}
14 changes: 11 additions & 3 deletions ...in/java/org/alliancegenome/indexer/indexers/curation/interfaces/EcoTermRESTInterface.java
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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);
}
8 changes: 5 additions & 3 deletions ...g/alliancegenome/indexer/indexers/curation/interfaces/GeneDiseaseAnnotationInterface.java
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@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);
}
8 changes: 5 additions & 3 deletions ...lliancegenome/indexer/indexers/curation/interfaces/GeneExpressionAnnotationInterface.java
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@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);
}
8 changes: 5 additions & 3 deletions .../alliancegenome/indexer/indexers/curation/interfaces/GeneGeneticInteractionInterface.java
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@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);
}
8 changes: 5 additions & 3 deletions ...lliancegenome/indexer/indexers/curation/interfaces/GeneMolecularInteractionInterface.java
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@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);
}
10 changes: 6 additions & 4 deletions ...alliancegenome/indexer/indexers/curation/interfaces/GenePhenotypeAnnotationInterface.java
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@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);
}
12 changes: 6 additions & 6 deletions ...ncegenome/indexer/indexers/curation/interfaces/GeneToGeneOrthologyGeneratedInterface.java
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@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);
}
11 changes: 6 additions & 5 deletions .../org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneParalogyInterface.java
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@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);
}
19 changes: 17 additions & 2 deletions ...n/java/org/alliancegenome/indexer/indexers/curation/interfaces/OrganizationInterface.java
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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);
}
14 changes: 11 additions & 3 deletions ...main/java/org/alliancegenome/indexer/indexers/curation/interfaces/ReferenceInterface.java
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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);
}
12 changes: 6 additions & 6 deletions .../org/alliancegenome/indexer/indexers/curation/interfaces/VocabularyTermRESTInterface.java
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@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);
}
2 changes: 1 addition & 1 deletion .../org/alliancegenome/indexer/indexers/curation/service/GenePhenotypeAnnotationService.java
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Expand Up @@ -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());
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2 changes: 1 addition & 1 deletion pom.xml
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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>v0.36.12</curation.version>
<curation.version>v0.36.14</curation.version>
<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
</properties>
<dependencyManagement>
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