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refactor: remove unused API endpoints not consumed by the UI #1534

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Merged
oblodgett merged 4 commits into from
Mar 24, 2026
Merged

refactor: remove unused API endpoints not consumed by the UI #1534

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a934d85
refactor: remove unused API endpoints not consumed by the UI
oblodgett Mar 23, 2026
938c734
Fix NPE
oblodgett Mar 23, 2026
63b3543
Pretty fix
oblodgett Mar 23, 2026
974ebb0
Merge branch 'stage' into api_refactor
oblodgett Mar 24, 2026
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21 changes: 0 additions & 21 deletions agr_api/src/main/java/org/alliancegenome/api/controller/EntityController.java
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46 changes: 0 additions & 46 deletions agr_api/src/main/java/org/alliancegenome/api/controller/ExpressionController.java
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Expand Up @@ -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;
Expand All @@ -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
Expand Down Expand Up @@ -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<>();
Expand Down
16 changes: 0 additions & 16 deletions agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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;

Expand Down Expand Up @@ -72,9 +69,6 @@ public class GeneController implements GeneRESTInterface {
@Inject
DiseaseService diseaseService;

@Inject
ExpressionService service;

@Inject
DiseaseESService diseaseESService;

Expand Down Expand Up @@ -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) {
Expand All @@ -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) {
Expand Down
20 changes: 0 additions & 20 deletions agr_api/src/main/java/org/alliancegenome/api/controller/GoController.java
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65 changes: 0 additions & 65 deletions agr_api/src/main/java/org/alliancegenome/api/controller/VariantController.java
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Expand Up @@ -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);
Expand All @@ -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);
}

}

}
31 changes: 0 additions & 31 deletions agr_api/src/main/java/org/alliancegenome/api/dto/ExpressionSummary.java
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32 changes: 0 additions & 32 deletions agr_api/src/main/java/org/alliancegenome/api/dto/ExpressionSummaryGroup.java
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26 changes: 0 additions & 26 deletions agr_api/src/main/java/org/alliancegenome/api/dto/ExpressionSummaryGroupTerm.java
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30 changes: 0 additions & 30 deletions agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/EntityRESTInterface.java
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