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8 changes: 6 additions & 2 deletions
8
src/main/cliapp/src/components/Actions/EntityDetailsAction.js
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44 changes: 44 additions & 0 deletions
44
...ud/associations/agmAssociations/AgmSequenceTargetingReagentAssociationCrudController.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,44 @@ | ||
| package org.alliancegenome.curation_api.controllers.crud.associations.agmAssociations; | ||
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| import java.util.List; | ||
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| import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController; | ||
| import org.alliancegenome.curation_api.dao.associations.agmAssociations.AgmSequenceTargetingReagentAssociationDAO; | ||
| import org.alliancegenome.curation_api.interfaces.crud.associations.agmAssociations.AgmSequenceTargetingReagentAssociationCrudInterface; | ||
| import org.alliancegenome.curation_api.jobs.executors.associations.agmAssociations.AgmStrAssociationExecutor; | ||
| import org.alliancegenome.curation_api.model.entities.associations.agmAssociations.AgmSequenceTargetingReagentAssociation; | ||
| import org.alliancegenome.curation_api.model.ingest.dto.associations.agmAssociations.AgmSequenceTargetingReagentAssociationDTO; | ||
| import org.alliancegenome.curation_api.response.APIResponse; | ||
| import org.alliancegenome.curation_api.response.ObjectResponse; | ||
| import org.alliancegenome.curation_api.services.associations.agmAssociations.AgmStrAssociationService; | ||
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| import jakarta.annotation.PostConstruct; | ||
| import jakarta.enterprise.context.RequestScoped; | ||
| import jakarta.inject.Inject; | ||
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| @RequestScoped | ||
| public class AgmSequenceTargetingReagentAssociationCrudController extends | ||
| BaseEntityCrudController<AgmStrAssociationService, AgmSequenceTargetingReagentAssociation, AgmSequenceTargetingReagentAssociationDAO> | ||
| implements AgmSequenceTargetingReagentAssociationCrudInterface { | ||
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| @Inject | ||
| AgmStrAssociationService agmStrAssociationService; | ||
| @Inject | ||
| AgmStrAssociationExecutor agmStrAssociationExecutor; | ||
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| @Override | ||
| @PostConstruct | ||
| protected void init() { | ||
| setService(agmStrAssociationService); | ||
| } | ||
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| public ObjectResponse<AgmSequenceTargetingReagentAssociation> getAssociation(Long alleleId, String relationName, Long geneId) { | ||
| return agmStrAssociationService.getAssociation(alleleId, relationName, geneId); | ||
| } | ||
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| @Override | ||
| public APIResponse updateAgmStrAssociations(String dataProvider, List<AgmSequenceTargetingReagentAssociationDTO> associationData) { | ||
| return agmStrAssociationExecutor.runLoadApi(agmStrAssociationService, dataProvider, associationData); | ||
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| } | ||
| } |
15 changes: 15 additions & 0 deletions
15
...ation_api/dao/associations/agmAssociations/AgmSequenceTargetingReagentAssociationDAO.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,15 @@ | ||
| package org.alliancegenome.curation_api.dao.associations.agmAssociations; | ||
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| import org.alliancegenome.curation_api.dao.base.BaseSQLDAO; | ||
| import org.alliancegenome.curation_api.model.entities.associations.agmAssociations.AgmSequenceTargetingReagentAssociation; | ||
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| import jakarta.enterprise.context.ApplicationScoped; | ||
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| @ApplicationScoped | ||
| public class AgmSequenceTargetingReagentAssociationDAO extends BaseSQLDAO<AgmSequenceTargetingReagentAssociation> { | ||
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| protected AgmSequenceTargetingReagentAssociationDAO() { | ||
| super(AgmSequenceTargetingReagentAssociation.class); | ||
| } | ||
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| } |
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39 changes: 39 additions & 0 deletions
39
...rud/associations/agmAssociations/AgmSequenceTargetingReagentAssociationCrudInterface.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,39 @@ | ||
| package org.alliancegenome.curation_api.interfaces.crud.associations.agmAssociations; | ||
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| import java.util.List; | ||
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| import org.alliancegenome.curation_api.interfaces.base.BaseIdCrudInterface; | ||
| import org.alliancegenome.curation_api.model.entities.associations.agmAssociations.AgmSequenceTargetingReagentAssociation; | ||
| import org.alliancegenome.curation_api.model.ingest.dto.associations.agmAssociations.AgmSequenceTargetingReagentAssociationDTO; | ||
| import org.alliancegenome.curation_api.response.APIResponse; | ||
| import org.alliancegenome.curation_api.response.ObjectResponse; | ||
| import org.alliancegenome.curation_api.view.View; | ||
| import org.eclipse.microprofile.openapi.annotations.tags.Tag; | ||
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| import com.fasterxml.jackson.annotation.JsonView; | ||
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| import jakarta.ws.rs.Consumes; | ||
| import jakarta.ws.rs.GET; | ||
| import jakarta.ws.rs.POST; | ||
| import jakarta.ws.rs.Path; | ||
| import jakarta.ws.rs.PathParam; | ||
| import jakarta.ws.rs.Produces; | ||
| import jakarta.ws.rs.QueryParam; | ||
| import jakarta.ws.rs.core.MediaType; | ||
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| @Path("/agmstrassociation") | ||
| @Tag(name = "CRUD - AGM Sequence Targeting Reagent Associations") | ||
| @Produces(MediaType.APPLICATION_JSON) | ||
| @Consumes(MediaType.APPLICATION_JSON) | ||
| public interface AgmSequenceTargetingReagentAssociationCrudInterface extends BaseIdCrudInterface<AgmSequenceTargetingReagentAssociation> { | ||
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| @GET | ||
| @Path("/findBy") | ||
| @JsonView(View.FieldsAndLists.class) | ||
| ObjectResponse<AgmSequenceTargetingReagentAssociation> getAssociation(@QueryParam("agmId") Long agmId, @QueryParam("relationName") String relationName, @QueryParam("strId") Long strId); | ||
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| @POST | ||
| @Path("/bulk/{dataProvider}/associationFile") | ||
| @JsonView(View.FieldsAndLists.class) | ||
| APIResponse updateAgmStrAssociations(@PathParam("dataProvider") String dataProvider, List<AgmSequenceTargetingReagentAssociationDTO> associationData); | ||
| } |
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63 changes: 63 additions & 0 deletions
63
...e/curation_api/jobs/executors/associations/agmAssociations/AgmStrAssociationExecutor.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,63 @@ | ||
| package org.alliancegenome.curation_api.jobs.executors.associations.agmAssociations; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
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| import org.alliancegenome.curation_api.enums.BackendBulkDataProvider; | ||
| import org.alliancegenome.curation_api.jobs.executors.LoadFileExecutor; | ||
| import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory; | ||
| import org.alliancegenome.curation_api.model.entities.bulkloads.BulkManualLoad; | ||
| import org.alliancegenome.curation_api.model.ingest.dto.IngestDTO; | ||
| import org.alliancegenome.curation_api.model.ingest.dto.associations.agmAssociations.AgmSequenceTargetingReagentAssociationDTO; | ||
| import org.alliancegenome.curation_api.services.associations.agmAssociations.AgmStrAssociationService; | ||
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| import jakarta.enterprise.context.ApplicationScoped; | ||
| import jakarta.inject.Inject; | ||
| import lombok.extern.jbosslog.JBossLog; | ||
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| @JBossLog | ||
| @ApplicationScoped | ||
| public class AgmStrAssociationExecutor extends LoadFileExecutor { | ||
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| @Inject AgmStrAssociationService agmStrAssociationService; | ||
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| public void execLoad(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) { | ||
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| BulkManualLoad manual = (BulkManualLoad) bulkLoadFileHistory.getBulkLoad(); | ||
| BackendBulkDataProvider dataProvider = manual.getDataProvider(); | ||
| log.info("Running with dataProvider: " + dataProvider.name()); | ||
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| IngestDTO ingestDto = readIngestFile(bulkLoadFileHistory, AgmSequenceTargetingReagentAssociationDTO.class); | ||
| if (ingestDto == null) { | ||
| return; | ||
| } | ||
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| List<AgmSequenceTargetingReagentAssociationDTO> associations = ingestDto.getAgmStrAssociationIngestSet(); | ||
| if (associations == null) { | ||
| associations = new ArrayList<>(); | ||
| } | ||
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| List<Long> associationIdsLoaded = new ArrayList<>(); | ||
| List<Long> associationIdsBefore = new ArrayList<>(); | ||
| if (cleanUp) { | ||
| associationIdsBefore.addAll(agmStrAssociationService.getAssociationsByDataProvider(dataProvider)); | ||
| associationIdsBefore.removeIf(Objects::isNull); | ||
| } | ||
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| bulkLoadFileHistory.getBulkLoadFile().setRecordCount(associations.size() + bulkLoadFileHistory.getBulkLoadFile().getRecordCount()); | ||
| bulkLoadFileDAO.merge(bulkLoadFileHistory.getBulkLoadFile()); | ||
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| bulkLoadFileHistory.setCount(associations.size()); | ||
| updateHistory(bulkLoadFileHistory); | ||
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| boolean success = runLoad(agmStrAssociationService, bulkLoadFileHistory, dataProvider, associations, associationIdsLoaded); | ||
| if (success && cleanUp) { | ||
| runCleanup(agmStrAssociationService, bulkLoadFileHistory, dataProvider.name(), associationIdsBefore, associationIdsLoaded, "agm str association"); | ||
| } | ||
| bulkLoadFileHistory.finishLoad(); | ||
| updateHistory(bulkLoadFileHistory); | ||
| updateExceptions(bulkLoadFileHistory); | ||
| } | ||
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| } |
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