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Merged
markquintontulloch merged 3 commits into from
Mar 6, 2025
Merged

SCRUM-4077 / SCRUM-4078 / SCRUM-4795 / SCRUM-4825 Various interaction fixes #1255

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71fa4e1
Various interaction fixes
markquintontulloch Mar 6, 2025
5d83c16
Merge branch 'stage' into interactions_fixes
markquintontulloch Mar 6, 2025
712713b
Bump curation version
markquintontulloch Mar 6, 2025
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13 changes: 13 additions & 0 deletions agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java
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Expand Up @@ -38,6 +38,7 @@
import org.alliancegenome.neo4j.view.HomologView;
import org.alliancegenome.neo4j.view.OrthologyFilter;
import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang3.StringUtils;

import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -291,6 +292,9 @@ public JsonResultResponse<GeneGeneticInteractionDocument> getGeneticInteractions
@Context UriInfo info) {
long startTime = System.currentTimeMillis();

if (StringUtils.isEmpty(sortBy)) {
sortBy = "geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText.keyword";
}
Pagination pagination = new Pagination(page, limit, sortBy, asc, new InteractionColumnFieldMapping());
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText", interactorGeneSymbol);
pagination.addFilterOption("geneGeneticInteraction.interactionId", source);
Expand Down Expand Up @@ -341,6 +345,9 @@ public Response getGeneticInteractionsDownload(String id, String sortBy, String
String phenotypes,
String interactionType
) {
if (StringUtils.isEmpty(sortBy)) {
sortBy = "geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText.keyword";
}
Pagination pagination = new Pagination(1, 150000, sortBy, asc);
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText", interactorGeneSymbol);
pagination.addFilterOption("geneGeneticInteraction.interactionId", source);
Expand Down Expand Up @@ -378,6 +385,9 @@ public JsonResultResponse<GeneMolecularInteractionDocument> getMolecularInteract
String reference,
@Context UriInfo info) {
long startTime = System.currentTimeMillis();
if (StringUtils.isEmpty(sortBy)) {
sortBy = "geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText.keyword";
}
Pagination pagination = new Pagination(page, limit, sortBy, asc, new InteractionColumnFieldMapping());
pagination.addFilterOption("geneMolecularInteraction.interactorAType.name.keyword", moleculeType);
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText", interactorGeneSymbol);
Expand Down Expand Up @@ -422,6 +432,9 @@ public Response getMolecularInteractionsDownload(String id, String sortBy, Strin
String source,
String reference
) {
if (StringUtils.isEmpty(sortBy)) {
sortBy = "geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText.keyword";
}
Pagination pagination = new Pagination(1, 150000, sortBy, asc);
pagination.addFilterOption("geneMolecularInteraction.interactorAType.name.keyword", moleculeType);
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText", interactorGeneSymbol);
Expand Down
59 changes: 40 additions & 19 deletions agr_api/src/main/java/org/alliancegenome/api/service/GeneService.java
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@@ -1,8 +1,17 @@
package org.alliancegenome.api.service;

import com.fasterxml.jackson.databind.ObjectMapper;
import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;
import static org.alliancegenome.cache.repository.helper.JsonResultResponse.DISTINCT_FIELD_VALUES;
import static org.elasticsearch.index.query.QueryBuilders.boolQuery;

import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

import org.alliancegenome.api.entity.AlleleVariantSequence;
import org.alliancegenome.api.entity.GeneGeneticInteractionDocument;
import org.alliancegenome.api.entity.GeneMolecularInteractionDocument;
Expand All @@ -25,8 +34,6 @@
import org.apache.commons.lang3.StringUtils;
import org.elasticsearch.action.search.SearchResponse;
import org.elasticsearch.index.query.BoolQueryBuilder;
import org.elasticsearch.index.query.MatchQueryBuilder;
import org.elasticsearch.index.query.TermQueryBuilder;
import org.elasticsearch.search.aggregations.AggregationBuilder;
import org.elasticsearch.search.aggregations.AggregationBuilders;
import org.elasticsearch.search.aggregations.bucket.MultiBucketsAggregation;
Expand All @@ -35,12 +42,10 @@
import org.elasticsearch.search.fetch.subphase.highlight.HighlightBuilder;
import org.elasticsearch.search.sort.SortOrder;

import java.time.LocalDateTime;
import java.util.*;
import java.util.stream.Collectors;
import com.fasterxml.jackson.databind.ObjectMapper;

import static org.alliancegenome.cache.repository.helper.JsonResultResponse.DISTINCT_FIELD_VALUES;
import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;

@RequestScoped
public class GeneService {
Expand Down Expand Up @@ -104,10 +109,20 @@ public JsonResultResponse<AlleleVariantSequence> getAllelesAndVariantInfo(String

public JsonResultResponse<GeneGeneticInteractionDocument> getGeneticInteractions(String geneId, Pagination pagination) {
BoolQueryBuilder query = boolQuery();
query.should(new MatchQueryBuilder("geneGeneticInteraction.geneAssociationSubject.curie.keyword", geneId));
query.should(new MatchQueryBuilder("geneGeneticInteraction.geneAssociationSubject.primaryExternalId.keyword", geneId));
query.should(new MatchQueryBuilder("geneGeneticInteraction.geneAssociationSubject.modInternalId.keyword", geneId));

String[] idFields = {
"geneGeneticInteraction.geneAssociationSubject.curie.keyword",
"geneGeneticInteraction.geneAssociationSubject.primaryExternalId.keyword",
"geneGeneticInteraction.geneAssociationSubject.modInternalId.keyword"
};
BoolQueryBuilder idQuery = boolQuery();
Arrays.stream(idFields).forEach(idField -> {
BoolQueryBuilder orClause = elasticSearchHelper.getBooleanAndedQueryBuilder(idField, geneId);
idQuery.should(orClause);
});

query.must(idQuery);

JsonResultResponse<GeneGeneticInteractionDocument> ret = new JsonResultResponse<>();
ret.setSupplementalData(getGeneticInteractionSupplementalData(query));

Expand Down Expand Up @@ -141,13 +156,19 @@ public JsonResultResponse<GeneGeneticInteractionDocument> getGeneticInteractions

public JsonResultResponse<GeneMolecularInteractionDocument> getMolecularInteractions(String geneId, Pagination pagination) {
BoolQueryBuilder query = boolQuery();
BoolQueryBuilder query2 = boolQuery();
query.must(query2);
query2.should(new MatchQueryBuilder("geneMolecularInteraction.geneAssociationSubject.curie.keyword", geneId));
query2.should(new MatchQueryBuilder("geneMolecularInteraction.geneAssociationSubject.primaryExternalId.keyword", geneId));
query2.should(new MatchQueryBuilder("geneMolecularInteraction.geneAssociationSubject.modInternalId.keyword", geneId));
String[] idFields = {
"geneMolecularInteraction.geneAssociationSubject.curie.keyword",
"geneMolecularInteraction.geneAssociationSubject.primaryExternalId.keyword",
"geneMolecularInteraction.geneAssociationSubject.modInternalId.keyword"
};
BoolQueryBuilder idQuery = boolQuery();
Arrays.stream(idFields).forEach(idField -> {
BoolQueryBuilder orClause = elasticSearchHelper.getBooleanAndedQueryBuilder(idField, geneId);
idQuery.should(orClause);
});

query.filter(new TermQueryBuilder("category", "gene_molecular_interaction"));
query.must(idQuery);

JsonResultResponse<GeneMolecularInteractionDocument> ret = new JsonResultResponse<>();
ret.setSupplementalData(getMolecularInteractionSupplementalData(query));

Expand Down
3 changes: 1 addition & 2 deletions agr_api/src/main/java/org/alliancegenome/api/service/helper/ElasticSearchHelper.java
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Expand Up @@ -56,13 +56,12 @@ private void generateFilter(BoolQueryBuilder bool, String filterName, String fil
}
}
}
//Log.info(bool);
}

/*
* split filter values by white spaces and create and ANDed boolean query
*/
private BoolQueryBuilder getBooleanAndedQueryBuilder(String filterName, String filterValue) {
public BoolQueryBuilder getBooleanAndedQueryBuilder(String filterName, String filterValue) {
BoolQueryBuilder andClause = boolQuery();
String[] elements = escapeValue(filterValue).split(" ");
Arrays.stream(elements).forEach(element -> andClause.must(QueryBuilders.queryStringQuery("*" + element + "*").field(filterName)));
Expand Down
7 changes: 6 additions & 1 deletion ...n/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java
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Expand Up @@ -5,6 +5,8 @@

import org.alliancegenome.api.entity.GeneGeneticInteractionDocument;
import org.alliancegenome.core.config.ConfigHelper;
import org.alliancegenome.curation_api.model.entities.InformationContentEntity;
import org.alliancegenome.curation_api.model.entities.Reference;
import org.apache.commons.collections.CollectionUtils;

public class GeneGeneticInteractionToTdfTranslator {
Expand Down Expand Up @@ -81,7 +83,10 @@ public String getAllRows(List<GeneGeneticInteractionDocument> interactions) {
String referenceCuries = "";
if (CollectionUtils.isNotEmpty(interaction.getGeneGeneticInteraction().getEvidence())) {
StringJoiner referenceJoiner = new StringJoiner(",");
interaction.getGeneGeneticInteraction().getEvidence().forEach(reference -> referenceJoiner.add(reference.getCurie()));
for (InformationContentEntity ice : interaction.getGeneGeneticInteraction().getEvidence()) {
Reference reference = (Reference) ice;
referenceJoiner.add(reference.getReferenceID());
}
referenceCuries = referenceJoiner.toString();
}
joiner.add(referenceCuries);
Expand Down
7 changes: 6 additions & 1 deletion ...java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java
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Expand Up @@ -5,6 +5,8 @@

import org.alliancegenome.api.entity.GeneMolecularInteractionDocument;
import org.alliancegenome.core.config.ConfigHelper;
import org.alliancegenome.curation_api.model.entities.InformationContentEntity;
import org.alliancegenome.curation_api.model.entities.Reference;
import org.apache.commons.collections.CollectionUtils;

public class GeneMolecularInteractionToTdfTranslator {
Expand Down Expand Up @@ -100,7 +102,10 @@ public String getAllRows(List<GeneMolecularInteractionDocument> interactions) {
String referenceCuries = "";
if (CollectionUtils.isNotEmpty(interaction.getGeneMolecularInteraction().getEvidence())) {
StringJoiner referenceJoiner = new StringJoiner(",");
interaction.getGeneMolecularInteraction().getEvidence().forEach(reference -> referenceJoiner.add(reference.getCurie()));
for (InformationContentEntity ice : interaction.getGeneMolecularInteraction().getEvidence()) {
Reference reference = (Reference) ice;
referenceJoiner.add(reference.getReferenceID());
}
referenceCuries = referenceJoiner.toString();
}
joiner.add(referenceCuries);
Expand Down
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>v0.36.9</curation.version>
<curation.version>v0.36.12</curation.version>
<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
</properties>
<dependencyManagement>
Expand Down
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