SCRUM-4513

src/main/java/org/alliancegenome/curation_api/controllers/crud/BiogridOrcCrudController.java

@@ -0,0 +1,35 @@
+package org.alliancegenome.curation_api.controllers.crud;
+
+import org.alliancegenome.curation_api.controllers.base.BaseEntityCrudController;
+import org.alliancegenome.curation_api.dao.CrossReferenceDAO;
+import org.alliancegenome.curation_api.interfaces.crud.BiogridOrcCrudInterface;
+import org.alliancegenome.curation_api.jobs.executors.BiogridOrcExecutor;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.services.CrossReferenceService;
+
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+
+@RequestScoped
+public class BiogridOrcCrudController extends BaseEntityCrudController<CrossReferenceService, CrossReference, CrossReferenceDAO> implements BiogridOrcCrudInterface {
+
+	@Inject
+	CrossReferenceService crossReferenceService;
+
+	@Inject
+	BiogridOrcExecutor biogridOrcExecutor;
+
+	@Override
+	@PostConstruct
+	protected void init() {
+		setService(crossReferenceService);
+	}
+
+	@Override
+	public APIResponse updateBiogridOrc(String dataProvider, BiogridOrcIngestFmsDTO biogridOrcData) {
+		return biogridOrcExecutor.runLoadApi(dataProvider, biogridOrcData.getData());
+	}
+}

src/main/java/org/alliancegenome/curation_api/dao/CrossReferenceDAO.java

@@ -9,6 +9,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 @ApplicationScoped
 public class CrossReferenceDAO extends BaseSQLDAO<CrossReference> {
@@ -32,6 +33,22 @@ public Map<String, Long> getGenesWithCrossRefs(ResourceDescriptorPage page) {
 		return ensemblGeneMap;
 	}
 
+	public Map<String, Long> getGenesWithCrossRefs(Set<String> referencedCuries) {
+		String sql = """
+			select gc.genomicentity_id, cr.referencedcurie from genomicentity_crossreference as gc, crossreference as cr
+				where gc.crossreferences_id = cr.id AND cr.referencedCurie IN (:referencedCuries)
+			""";
+		Query query = entityManager.createNativeQuery(sql);
+		query.setParameter("referencedCuries", referencedCuries);
+		List<Object[]> objects = query.getResultList();
+		Map<String, Long> idCurieMap = new HashMap<>();
+		objects.forEach(object -> {
+			idCurieMap.put((String) object[1], (Long) object[0]);
+		});
+		return idCurieMap;
+
+	}
+
 	public Integer persistAccessionGeneAssociated(Long crossReferenceID, Long geneID) {
 		String sql = """
 			insert into genomicentity_crossreference (crossreferences_id,genomicentity_id)

src/main/java/org/alliancegenome/curation_api/interfaces/crud/BiogridOrcCrudInterface.java

@@ -0,0 +1,26 @@
+package org.alliancegenome.curation_api.interfaces.crud;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.MediaType;
+import org.alliancegenome.curation_api.interfaces.base.crud.BaseCreateControllerInterface;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcIngestFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+
+
+@Path("/biogrid-orc")
+@Tag(name = "CRUD - Biogrid Orc")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface BiogridOrcCrudInterface extends BaseCreateControllerInterface<CrossReference> {
+
+
+	@POST
+	@Path("/bulk/{dataProvider}/biogridfile")
+	@JsonView(View.FieldsAndLists.class)
+	APIResponse updateBiogridOrc(@PathParam("dataProvider") String dataProvider, BiogridOrcIngestFmsDTO biogridOrcData);
+
+}

src/main/java/org/alliancegenome/curation_api/jobs/executors/BiogridOrcExecutor.java

@@ -1,17 +1,32 @@
 package org.alliancegenome.curation_api.jobs.executors;
 
 import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.zip.GZIPInputStream;
 
-import org.alliancegenome.curation_api.exceptions.ObjectUpdateException.ObjectUpdateExceptionData;
+import org.alliancegenome.curation_api.dao.CrossReferenceDAO;
+import org.alliancegenome.curation_api.dao.GeneDAO;
+import org.alliancegenome.curation_api.dao.ResourceDescriptorPageDAO;
 import org.alliancegenome.curation_api.jobs.util.CsvSchemaBuilder;
+import org.alliancegenome.curation_api.model.entities.CrossReference;
+import org.alliancegenome.curation_api.model.entities.DataProvider;
+import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.model.entities.ResourceDescriptorPage;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
 import org.alliancegenome.curation_api.model.ingest.dto.fms.BiogridOrcFmsDTO;
+import org.alliancegenome.curation_api.response.APIResponse;
+import org.alliancegenome.curation_api.response.LoadHistoryResponce;
+import org.alliancegenome.curation_api.services.CrossReferenceService;
+import org.alliancegenome.curation_api.services.DataProviderService;
+import org.alliancegenome.curation_api.services.OrganizationService;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
@@ -23,16 +38,54 @@
 import com.fasterxml.jackson.dataformat.csv.CsvSchema;
 
 import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
 
 @ApplicationScoped
 public class BiogridOrcExecutor extends LoadFileExecutor {
 
+	@Inject
+	ResourceDescriptorPageDAO resourceDescriptorPageDAO;
+
+	@Inject
+	GeneDAO geneDAO;
+
+	@Inject
+	CrossReferenceDAO crossRefDAO;
+
+	@Inject
+	CrossReferenceService crossReferenceService;
+
+	@Inject
+	OrganizationService organizationService;
+
+	@Inject
+	DataProviderService dataProviderService;
+
 	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 		try (TarArchiveInputStream tarInputStream = new TarArchiveInputStream(
-			new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())))) {
+				new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath())))) {
 			TarArchiveEntry tarEntry;
 
-			Set<String> biogridIds = new HashSet<>();
+			List<BiogridOrcFmsDTO> biogridData = new ArrayList<>();
+			String name = bulkLoadFileHistory.getBulkLoad().getName();
+			String dataProviderName = name.substring(0, name.indexOf(" "));
+
+			Organization organization = organizationService.getByAbbr(dataProviderName).getEntity();
+
+			HashMap<String, Object> rdpParams = new HashMap<>();
+			rdpParams.put("name", "biogrid/orcs");
+			ResourceDescriptorPage resourceDescriptorPage = resourceDescriptorPageDAO.findByParams(rdpParams).getSingleResult();
+
+			List<Long> dataProviderIdsBefore = new ArrayList<>(
+					dataProviderService.getDataProviderMap(organization, resourceDescriptorPage)
+							.values()
+							.stream()
+							.map(DataProvider::getId)
+							.toList());
+
+			dataProviderIdsBefore.removeIf(Objects::isNull);
+
+			List<Long> dataProviderIdsLoaded = new ArrayList<>();
 
 			while ((tarEntry = tarInputStream.getNextEntry()) != null) {
 
@@ -53,40 +106,61 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) {
 						.with(biogridOrcFmsSchema)
 						.readValues(tarInputStream.readAllBytes());
 
-				List<BiogridOrcFmsDTO> biogridData = it.readAll();
-				runLoad(bulkLoadFileHistory, biogridData, biogridIds);
+				biogridData.addAll(it.readAll());
 
 			}
+			runLoad(bulkLoadFileHistory, biogridData, resourceDescriptorPage, organization, dataProviderService,
+					dataProviderIdsLoaded);
+
+			runCleanup(dataProviderService, bulkLoadFileHistory, dataProviderName, dataProviderIdsBefore,
+					dataProviderIdsLoaded, "Biogrid Orc Load Type");
 		} catch (Exception e) {
 			failLoad(bulkLoadFileHistory, e);
 			e.printStackTrace();
 		}
 	}
 
-	private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biogridList, Set<String> biogridIds) {
+	private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biogridList,
+			ResourceDescriptorPage resourceDescriptorPage, Organization organization,
+			DataProviderService dataProviderService, List<Long> dataProviderIdsLoaded) {
 		ProcessDisplayHelper ph = new ProcessDisplayHelper();
 		ph.addDisplayHandler(loadProcessDisplayService);
 		if (CollectionUtils.isNotEmpty(biogridList)) {
-			String loadMessage = biogridList.get(0).getClass().getSimpleName() + " update";
-			ph.startProcess(loadMessage, biogridList.size());
+			try {
+				String loadMessage = "BioGrid update";
+				Set<String> referencedCuries = populateEntrezIdsFromFiles(biogridList, history);
+				ph.startProcess(loadMessage, referencedCuries.size());
+				updateHistory(history);
 
-			updateHistory(history);
-			for (BiogridOrcFmsDTO biogridOrcFmsDTO : biogridList) {
-				try {
-					if (biogridOrcFmsDTO.getIdentifierType().equals("ENTREZ_GENE")) {
-						String identifier = "NCBI_Gene:" + biogridOrcFmsDTO.getIdentifierId();
-						biogridIds.add(identifier);
+				Map<String, Long> genomicEntityCrossRefMap = crossReferenceService
+						.getGenomicEntityCrossRefMap(referencedCuries);
+
+				for (String referencedCurie : referencedCuries) {
+
+					CrossReference newCrossRef = new CrossReference();
+					newCrossRef.setReferencedCurie(referencedCurie);
+					newCrossRef.setDisplayName("BioGRID CRISPR Screen Cell Line Phenotypes");
+					newCrossRef.setResourceDescriptorPage(resourceDescriptorPage);
+
+					DataProvider provider = new DataProvider();
+					provider.setSourceOrganization(organization);
+					provider.setCrossReference(newCrossRef);
+
+					DataProvider entity = dataProviderService
+							.insertBioGridOrcDataProvider(provider, genomicEntityCrossRefMap.get(referencedCurie))
+							.getEntity();
+
+					if (entity != null) {
+						dataProviderIdsLoaded.add(entity.getId());
 						history.incrementCompleted();
 					} else {
 						history.incrementSkipped();
-
 					}
-				} catch (Exception e) {
-					e.printStackTrace();
-					history.incrementFailed();
-					addException(history,
-							new ObjectUpdateExceptionData(biogridOrcFmsDTO, e.getMessage(), e.getStackTrace()));
+
 				}
+			} catch (Exception e) {
+				e.printStackTrace();
+				history.incrementFailed();
 				ph.progressProcess();
 			}
 			updateHistory(history);
@@ -96,4 +170,42 @@ private boolean runLoad(BulkLoadFileHistory history, List<BiogridOrcFmsDTO> biog
 
 		return true;
 	}
+
+	public APIResponse runLoadApi(String dataProviderName, List<BiogridOrcFmsDTO> biogridDTOs) {
+		List<Long> dataProviderIdsLoaded = new ArrayList<>();
+		Organization organization = organizationService.getByAbbr(dataProviderName).getEntity();
+
+		HashMap<String, Object> rdpParams = new HashMap<>();
+		rdpParams.put("name", "biogrid/orcs");
+		ResourceDescriptorPage resourceDescriptorPage = resourceDescriptorPageDAO.findByParams(rdpParams).getSingleResult();
+
+		BulkLoadFileHistory history = new BulkLoadFileHistory(biogridDTOs.size());
+		history = bulkLoadFileHistoryDAO.persist(history);
+		runLoad(history, biogridDTOs, resourceDescriptorPage, organization, dataProviderService, dataProviderIdsLoaded);
+		history.finishLoad();
+
+		return new LoadHistoryResponce(history);
+	}
+
+	private Set<String> populateEntrezIdsFromFiles(List<BiogridOrcFmsDTO> biogridList, BulkLoadFileHistory history) {
+		Set<String> biogridIds = new HashSet<>();
+
+		for (BiogridOrcFmsDTO biogridOrcFmsDTO : biogridList) {
+			try {
+				if (!biogridOrcFmsDTO.getIdentifierType().equals("ENTREZ_GENE")) {
+					history.incrementSkipped();
+					continue;
+				}
+
+				String identifier = "NCBI_Gene:" + biogridOrcFmsDTO.getIdentifierId();
+				biogridIds.add(identifier);
+
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+
+		return biogridIds;
+
+	}
 }

src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcFmsDTO.java

@@ -1,8 +1,5 @@
 package org.alliancegenome.curation_api.model.ingest.dto.fms;
 
-import java.util.List;
-
-import org.alliancegenome.curation_api.model.ingest.dto.CrossReferenceDTO;
 import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
 
 import lombok.Data;
@@ -25,5 +22,4 @@ public class BiogridOrcFmsDTO extends BaseDTO {
 	private Double score5;
 	private String hit;
 	private String source;
-	private List<CrossReferenceDTO> crossReferenceDtos;
 }

src/main/java/org/alliancegenome/curation_api/model/ingest/dto/fms/BiogridOrcIngestFmsDTO.java

@@ -0,0 +1,16 @@
+package org.alliancegenome.curation_api.model.ingest.dto.fms;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.ingest.dto.base.BaseDTO;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class BiogridOrcIngestFmsDTO extends BaseDTO {
+
+	private MetaDataFmsDTO metaData;
+	private List<BiogridOrcFmsDTO> data;
+}

src/main/java/org/alliancegenome/curation_api/services/CrossReferenceService.java

@@ -16,6 +16,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 @RequestScoped
 public class CrossReferenceService extends BaseEntityCrudService<CrossReference, CrossReferenceDAO> {
@@ -109,4 +110,8 @@ public String getCrossReferenceUniqueId(CrossReference xref) {
 	public Map<String, Long> getGenomicEntityCrossRefMap(ResourceDescriptorPage page) {
 		return crossReferenceDAO.getGenesWithCrossRefs(page);
 	}
+
+	public Map<String, Long> getGenomicEntityCrossRefMap(Set<String> referencedCuries) {
+		return crossReferenceDAO.getGenesWithCrossRefs(referencedCuries);
+	}
 }

src/main/java/org/alliancegenome/curation_api/services/DataProviderService.java

@@ -92,6 +92,21 @@ public ObjectResponse<DataProvider> insertExpressionAtlasDataProvider(DataProvid
 		return new ObjectResponse<>(dbEntity);
 	}
 
+	@Transactional
+	public ObjectResponse<DataProvider> insertBioGridOrcDataProvider(DataProvider entity, Long geneticEntityId) {
+		String referencedCurie = entity.getCrossReference().getReferencedCurie();
+
+		DataProvider dbEntity = getDataProvider(entity.getSourceOrganization(), referencedCurie, entity.getCrossReference().getResourceDescriptorPage());
+
+		// we only create new records, no updates
+		if (dbEntity == null) {
+			dataProviderDAO.persist(entity);
+			crossReferenceDAO.persistAccessionGeneAssociated(entity.getCrossReference().getId(), geneticEntityId);
+			return new ObjectResponse<>(entity);
+		}
+		return new ObjectResponse<>(dbEntity);
+	}
+
 	@NotNull
 	public static String getFullReferencedCurie(String localReferencedCurie) {
 		return RESOURCE_DESCRIPTOR_PREFIX + ":" + localReferencedCurie;