Merge pull request #1534 from alliance-genome/api_refactor

refactor: remove unused API endpoints not consumed by the UI

Author: oblodgett

agr_api/src/main/java/org/alliancegenome/api/controller/EntityController.java

@@ -3,32 +3,19 @@
 import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Objects;
 
 import org.alliancegenome.api.dto.RibbonSummary;
 import org.alliancegenome.api.rest.interfaces.ExpressionRESTInterface;
 import org.alliancegenome.api.service.EntityType;
 import org.alliancegenome.api.service.ExpressionESService;
 import org.alliancegenome.api.service.ExpressionRibbonESService;
-import org.alliancegenome.api.service.ExpressionService;
-import org.alliancegenome.api.service.GeneService;
 import org.alliancegenome.api.service.helper.APIServiceHelper;
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
-import org.alliancegenome.core.ExpressionDetail;
 import org.alliancegenome.core.exceptions.RestErrorException;
 import org.alliancegenome.core.exceptions.RestErrorMessage;
 import org.alliancegenome.core.translators.tdf.ExpressionToTdfTranslator;
 import org.alliancegenome.curation_api.model.document.es.GeneExpressionDocument;
-import org.alliancegenome.es.model.query.FieldFilter;
 import org.alliancegenome.es.model.query.Pagination;
-import org.alliancegenome.neo4j.entity.SpeciesType;
-import org.alliancegenome.neo4j.entity.node.BioEntityGeneExpressionJoin;
-import org.alliancegenome.neo4j.view.BaseFilter;
-import org.alliancegenome.neo4j.view.PublicView;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.MapperFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
 
 import io.quarkus.logging.Log;
 import jakarta.enterprise.context.RequestScoped;
@@ -38,15 +25,9 @@
 @RequestScoped
 public class ExpressionController implements ExpressionRESTInterface {
 
-	//@Context
-	//private HttpRequest request;
-
-	@Inject ExpressionService expressionService;
 	@Inject ExpressionESService expressionESService;
 	@Inject ExpressionRibbonESService expressionRibbonESService;
 
-	@Inject GeneService geneService;
-	
 	private static final ExpressionToTdfTranslator expressionTranslator = new ExpressionToTdfTranslator();
 
 	@Override
@@ -111,33 +92,6 @@ private JsonResultResponse<GeneExpressionDocument> getExpressionDetailJsonResult
 
 	}
 
-	@Override
-	public String getExpressionAnnotationsByTaxon(String species, String termID, Integer limit, Integer page) throws JsonProcessingException {
-		Pagination pagination = new Pagination(page, limit, null, null);
-		BaseFilter filterMap = new BaseFilter();
-		filterMap.put(FieldFilter.TERM_NAME, termID);
-		filterMap.values().removeIf(Objects::isNull);
-		pagination.setFieldFilterValueMap(filterMap);
-
-		LocalDateTime startDate = LocalDateTime.now();
-		JsonResultResponse<ExpressionDetail> response = new JsonResultResponse<>();
-		response.setHttpServletRequest(null);
-
-		ObjectMapper mapper = new ObjectMapper();
-		mapper.disable(MapperFeature.DEFAULT_VIEW_INCLUSION);
-
-		// check if valid taxon identifier
-		String taxon = SpeciesType.getTaxonId(species);
-
-		List<BioEntityGeneExpressionJoin> joins = geneService.getExpressionAnnotationsByTaxon(taxon, termID, pagination);
-
-		JsonResultResponse<ExpressionDetail> result = expressionService.getExpressionDetails(joins, pagination);
-		response.setResults(result.getResults());
-		response.setTotal(result.getTotal());
-		response.calculateRequestDuration(startDate);
-		return mapper.writerWithView(PublicView.Expression.class).writeValueAsString(response);
-	}
-
 	@Override
 	public RibbonSummary getExpressionSummary(List<String> geneIDs) {
 		List<String> ids = new ArrayList<>();

agr_api/src/main/java/org/alliancegenome/api/controller/ExpressionController.java

@@ -4,7 +4,6 @@
 import java.util.Arrays;
 import java.util.List;
 
-import org.alliancegenome.api.dto.ExpressionSummary;
 import org.alliancegenome.api.entity.DiseaseRibbonSummary;
 import org.alliancegenome.api.entity.GeneGeneticInteractionDocument;
 import org.alliancegenome.api.entity.GeneMolecularInteractionDocument;
@@ -18,7 +17,6 @@
 
 import org.alliancegenome.api.service.DiseaseESService;
 import org.alliancegenome.api.service.EntityType;
-import org.alliancegenome.api.service.ExpressionService;
 import org.alliancegenome.api.service.GeneESService;
 import org.alliancegenome.api.service.GeneService;
 import org.alliancegenome.api.service.GeneToGeneParalogyESService;
@@ -42,7 +40,6 @@
 import org.alliancegenome.curation_api.model.document.es.SequenceSummaryDocument;
 import org.alliancegenome.es.model.query.FieldFilter;
 import org.alliancegenome.es.model.query.Pagination;
-import org.alliancegenome.neo4j.entity.EntitySummary;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 
@@ -72,9 +69,6 @@ public class GeneController implements GeneRESTInterface {
 	@Inject
 	DiseaseService diseaseService;
 
-	@Inject
-	ExpressionService service;
-
 	@Inject
 	DiseaseESService diseaseESService;
 
@@ -461,11 +455,6 @@ public JsonResultResponse<GeneToGeneParalogyDocument> getGeneParalogy(String id,
 		return response;
 	}
 
-	@Override
-	public ExpressionSummary getExpressionSummary(String id) {
-		return service.getExpressionSummary(id);
-	}
-
 	@Override
 	// the List passed in here is unmodifiable
 	public DiseaseRibbonSummary getDiseaseRibbonSummary(String id, Boolean includeNegation, Boolean debug, List<String> geneIDs) {
@@ -487,11 +476,6 @@ public DiseaseRibbonSummary getDiseaseRibbonSummary(String id, Boolean includeNe
 		}
 	}
 
-	@Override
-	public EntitySummary getPhenotypeSummary(String id) {
-		return geneService.getPhenotypeSummary(id);
-	}
-
 	@Override
 	public JsonResultResponse<GeneTransgenicAlleleSummaryDocument> getTransgenicAlleles(String geneID, Integer limit, Integer page, String sortBy, String alleleSymbol, String constructSymbol, String constructRegulatedGene, String constructTargetedGene, String constructExpressedGene, String species,
 		String hasPhenotype, String hasDisease, UriInfo ui) {

agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

@@ -4,28 +4,18 @@
 
 import org.alliancegenome.api.rest.interfaces.VariantRESTInterface;
 import org.alliancegenome.api.service.VariantService;
-import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.core.exceptions.RestErrorException;
 import org.alliancegenome.core.exceptions.RestErrorMessage;
 import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
-import org.alliancegenome.es.model.query.FieldFilter;
-import org.alliancegenome.es.model.query.Pagination;
-import org.alliancegenome.neo4j.entity.node.Allele;
-import org.alliancegenome.neo4j.entity.node.Transcript;
 
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
-import lombok.extern.slf4j.Slf4j;
 
-@Slf4j
 @RequestScoped
 public class VariantController implements VariantRESTInterface {
 
 	@Inject VariantService variantService;
 
-	//@Inject
-	//private HttpRequest request;
-
 	@Override
 	public VariantSummaryDocument getVariant(String id) {
 		VariantSummaryDocument variant = variantService.getVariantById(id);
@@ -37,59 +27,4 @@ public VariantSummaryDocument getVariant(String id) {
 		return variant;
 	}
 
-	@Override
-	public JsonResultResponse<Transcript> getTranscriptsPerVariant(
-			String id,
-			Integer limit,
-			Integer page,
-			String sortBy,
-			String transcriptType,
-			String molecularConsequence) {
-
-		long startTime = System.currentTimeMillis();
-		Pagination pagination = new Pagination(page, limit, sortBy, null);
-		pagination.addFieldFilter(FieldFilter.VARIANT_TYPE, transcriptType);
-		pagination.addFieldFilter(FieldFilter.MOLECULAR_CONSEQUENCE, molecularConsequence);
-		if (pagination.hasErrors()) {
-			RestErrorMessage message = new RestErrorMessage();
-			message.setErrors(pagination.getErrors());
-			throw new RestErrorException(message);
-		}
-		try {
-			JsonResultResponse<Transcript> alleles = variantService.getTranscriptsByVariant(id, pagination);
-			alleles.setHttpServletRequest(null);
-			alleles.calculateRequestDuration(startTime);
-			return alleles;
-		} catch (Exception e) {
-			log.error("Error while retrieving variant info", e);
-			RestErrorMessage error = new RestErrorMessage();
-			error.addErrorMessage(e.getMessage());
-			throw new RestErrorException(error);
-		}
-	}
-
-	@Override
-	public JsonResultResponse<Allele> getAllelesPerVariant(String id, Integer limit, Integer page) {
-
-		long startTime = System.currentTimeMillis();
-		Pagination pagination = new Pagination(page, limit, null, null);
-		if (pagination.hasErrors()) {
-			RestErrorMessage message = new RestErrorMessage();
-			message.setErrors(pagination.getErrors());
-			throw new RestErrorException(message);
-		}
-		try {
-			JsonResultResponse<Allele> alleles = variantService.getAllelesByVariant(id, pagination);
-			alleles.setHttpServletRequest(null);
-			alleles.calculateRequestDuration(startTime);
-			return alleles;
-		} catch (Exception e) {
-			log.error("Error while retrieving allele info", e);
-			RestErrorMessage error = new RestErrorMessage();
-			error.addErrorMessage(e.getMessage());
-			throw new RestErrorException(error);
-		}
-
-	}
-
 }