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Merge branch 'release-2.4.x' of github.com:opencb/opencga into releas…
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…e-2.4.x
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@imedina
imedina committed Aug 19, 2022
2 parents 54eb3eb + 9bc860f commit fb9fd4c
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Showing 3 changed files with 114 additions and 105 deletions.
172 changes: 83 additions & 89 deletions ...s/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@
import java.util.*;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.function.Supplier;
import java.util.stream.Collectors;

import static org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance.*;
Expand Down Expand Up @@ -593,75 +594,10 @@ public Query parseQuery(Query query, QueryOptions queryOptions, CellBaseUtils ce
individualToSample.put(entry.getKey(), samplesUidToId.get(entry.getValue()));
}

String gtFilter = buildMoIGenotypeFilter(pedigree, disorder, segregationMode, individualToSample);
if (gtFilter == null) {
throw VariantQueryException.malformedParam(FAMILY_SEGREGATION, segregationMode.toString(),
"Invalid segregation mode for the family '" + family.getId() + "'");
}
switch (segregationMode) {
case X_LINKED_DOMINANT:
case X_LINKED_RECESSIVE:
segregationChromosome = new Region("X");
break;
case Y_LINKED:
segregationChromosome = new Region("Y");
break;
case MITOCHONDRIAL:
segregationChromosome = new Region("MT");
break;
default:
break;
}
if (segregationChromosome != null) {
boolean mightAddRegionFilter = true;
if (isValidParam(query, REGION.key())) {
mightAddRegionFilter = false;
List<Region> invalidRegions = new ArrayList<>();
for (Region region : Region.parseRegions(query.getString(REGION.key()))) {
if (VariantQueryUtils.intersectRegions(segregationChromosome, region) == null) {
invalidRegions.add(region);
}
}
if (!invalidRegions.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
REGION, invalidRegions.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (!xrefs.getVariants().isEmpty()) {
mightAddRegionFilter = false;
List<Variant> invalidVariants = new ArrayList<>();
for (Variant variant : xrefs.getVariants()) {
if (!variant.getChromosome().equals(segregationChromosome.getChromosome())) {
invalidVariants.add(variant);
}
}
if (!invalidVariants.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
ID, invalidVariants.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (!xrefs.getGenes().isEmpty()) {
mightAddRegionFilter = false;
List<String> invalidGenes = new ArrayList<>();
Map<String, Region> geneRegionMap = cellBaseUtils.getGeneRegionMap(xrefs.getGenes(), false);
for (Map.Entry<String, Region> entry : geneRegionMap.entrySet()) {
if (VariantQueryUtils.intersectRegions(segregationChromosome, entry.getValue()) == null) {
invalidGenes.add(entry.getKey());
}
}
if (!invalidGenes.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
GENE, invalidGenes.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (mightAddRegionFilter) {
query.put(REGION.key(), segregationChromosome);
}
}
query.put(GENOTYPE.key(), gtFilter);
segregationChromosome = processSegregationFilter(query, cellBaseUtils, xrefs,
pedigree, segregationMode, disorder, individualToSample,
() -> VariantQueryException.malformedParam(FAMILY_SEGREGATION, segregationMode.toString(),
"Invalid segregation mode for the family '" + family.getId() + "'"));
}
} else {
if (isValidParam(query, FAMILY_DISORDER)) {
Expand Down Expand Up @@ -703,7 +639,7 @@ public Query parseQuery(Query query, QueryOptions queryOptions, CellBaseUtils ce
}

if (isValidParam(query, SAMPLE)) {
processSampleFilter(query, defaultStudyStr, token);
segregationChromosome = processSampleFilter(query, defaultStudyStr, cellBaseUtils, xrefs, token);
}

if (isValidParam(query, PANEL)) {
Expand Down Expand Up @@ -1005,7 +941,9 @@ private String toIndividualId(String study, String individuaOrSample, String tok
return individuaOrSample;
}

private void processSampleFilter(Query query, String defaultStudyStr, String token) throws CatalogException {
private Region processSampleFilter(Query query, String defaultStudyStr, CellBaseUtils cellBaseUtils,
ParsedVariantQuery.VariantQueryXref xrefs, String token) throws CatalogException {
Region segregationChromosome = null;
String sampleFilterValue = query.getString(SAMPLE.key());
if (sampleFilterValue.contains(IS)) {
ClinicalProperty.ModeOfInheritance moi = null;
Expand Down Expand Up @@ -1122,17 +1060,15 @@ private void processSampleFilter(Query query, String defaultStudyStr, String tok
throw VariantQueryException.malformedParam(SAMPLE, sampleFilterValue,
"Found multiple disorders for sample '" + sampleId + "'");
}
String genotypeFilter = buildMoIGenotypeFilter(pedigree, individual.getDisorders().get(0), moi);
if (genotypeFilter == null) {
throw VariantQueryException.malformedParam(SAMPLE, sampleFilterValue,
"Invalid segregation mode for the sample '" + sampleId + "'");
}
query.put(GENOTYPE.key(), genotypeFilter);
segregationChromosome = processSegregationFilter(query, cellBaseUtils, xrefs,
pedigree, moi, individual.getDisorders().get(0), null,
() -> VariantQueryException.malformedParam(SAMPLE, sampleFilterValue,
"Invalid segregation mode for the sample '" + sampleId + "'"));
query.remove(SAMPLE.key());
}
}

}
return segregationChromosome;
}

private Set<Long> fetchIndexedSampleUIds(String token, String defaultStudyStr) throws CatalogException {
Expand All @@ -1146,15 +1082,13 @@ private Set<Long> fetchIndexedSampleUIds(String token, String defaultStudyStr) t
.map(Sample::getUid).collect(Collectors.toSet());
}


private String buildMoIGenotypeFilter(Pedigree pedigree, Disorder disorder, ClinicalProperty.ModeOfInheritance moi) {
return buildMoIGenotypeFilter(pedigree, disorder, moi, null);
}

private String buildMoIGenotypeFilter(Pedigree pedigree, Disorder disorder, ClinicalProperty.ModeOfInheritance moi,
Map<String, String> pedigreeMemberToSampleId) {
private Region processSegregationFilter(Query query, CellBaseUtils cellBaseUtils, ParsedVariantQuery.VariantQueryXref xrefs,
Pedigree pedigree,
ClinicalProperty.ModeOfInheritance segregationMode, Disorder disorder,
Map<String, String> pedigreeMemberToSampleId, Supplier<VariantQueryException> onError) {
Region segregationChromosome = null;
Map<String, List<String>> genotypes;
switch (moi) {
switch (segregationMode) {
case AUTOSOMAL_DOMINANT:
genotypes = ModeOfInheritance.dominant(pedigree, disorder, ClinicalProperty.Penetrance.COMPLETE);
break;
Expand All @@ -1168,22 +1102,28 @@ private String buildMoIGenotypeFilter(Pedigree pedigree, Disorder disorder, Clin
// genotypes = ModeOfInheritance.recessive(pedigree, disorder, ClinicalProperty.Penetrance.INCOMPLETE);
// break;
case X_LINKED_DOMINANT:
segregationChromosome = new Region("X");
genotypes = ModeOfInheritance.xLinked(pedigree, disorder, true, ClinicalProperty.Penetrance.COMPLETE);
break;
case X_LINKED_RECESSIVE:
segregationChromosome = new Region("X");
genotypes = ModeOfInheritance.xLinked(pedigree, disorder, false, ClinicalProperty.Penetrance.COMPLETE);
break;
case Y_LINKED:

segregationChromosome = new Region("Y");
genotypes = ModeOfInheritance.yLinked(pedigree, disorder, ClinicalProperty.Penetrance.COMPLETE);
break;
case MITOCHONDRIAL:

segregationChromosome = new Region("MT");
genotypes = ModeOfInheritance.mitochondrial(pedigree, disorder, ClinicalProperty.Penetrance.COMPLETE);
break;
default:
throw new IllegalArgumentException("Unexpected segregation mode " + moi);
throw new IllegalArgumentException("Unexpected segregation mode " + segregationMode);
}
if (ModeOfInheritance.isEmptyMapOfGenotypes(genotypes)) {
return null;
throw onError.get();
}

StringBuilder sb = new StringBuilder();
Expand Down Expand Up @@ -1215,7 +1155,61 @@ private String buildMoIGenotypeFilter(Pedigree pedigree, Disorder disorder, Clin
sb.append(gt);
}
}
return sb.toString();
String gtFilter = sb.toString();


if (segregationChromosome != null) {
boolean mightAddRegionFilter = true;
if (isValidParam(query, REGION.key())) {
mightAddRegionFilter = false;
List<Region> invalidRegions = new ArrayList<>();
for (Region region : Region.parseRegions(query.getString(REGION.key()))) {
if (VariantQueryUtils.intersectRegions(segregationChromosome, region) == null) {
invalidRegions.add(region);
}
}
if (!invalidRegions.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
REGION, invalidRegions.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (!xrefs.getVariants().isEmpty()) {
mightAddRegionFilter = false;
List<Variant> invalidVariants = new ArrayList<>();
for (Variant variant : xrefs.getVariants()) {
if (!variant.getChromosome().equals(segregationChromosome.getChromosome())) {
invalidVariants.add(variant);
}
}
if (!invalidVariants.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
ID, invalidVariants.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (!xrefs.getGenes().isEmpty()) {
mightAddRegionFilter = false;
List<String> invalidGenes = new ArrayList<>();
Map<String, Region> geneRegionMap = cellBaseUtils.getGeneRegionMap(xrefs.getGenes(), false);
for (Map.Entry<String, Region> entry : geneRegionMap.entrySet()) {
if (VariantQueryUtils.intersectRegions(segregationChromosome, entry.getValue()) == null) {
invalidGenes.add(entry.getKey());
}
}
if (!invalidGenes.isEmpty()) {
throw VariantQueryException.unsupportedParamsCombination(
GENE, invalidGenes.toString(),
FAMILY_SEGREGATION, query.getString(FAMILY_SEGREGATION.key()));
}
}
if (mightAddRegionFilter) {
query.put(REGION.key(), segregationChromosome);
query.put(PANEL_INTERSECTION.key(), true);
}
}
query.put(GENOTYPE.key(), gtFilter);
return segregationChromosome;
}

/**
Expand Down
35 changes: 19 additions & 16 deletions ...c/test/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtilsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -412,38 +412,41 @@ public void queryByFamilySegregation() throws Exception {

@Test
public void queryByFamilySegregationChromosomal() throws Exception {
Query query = queryUtils.parseQuery(new VariantQuery()
queryBySegregationChromosomal(new Query()
.append(FAMILY.key(), "f1")
.append(FAMILY_SEGREGATION.key(), "X_LINKED_RECESSIVE"));
}

@Test
public void queryBySampleSegregationChromosomal() throws Exception {
queryBySegregationChromosomal(new Query(SAMPLE.key(), "sample3:X_LINKED_RECESSIVE"));
}

public void queryBySegregationChromosomal(Query baseQuery) throws Exception {
Query query = queryUtils.parseQuery(new VariantQuery(baseQuery)
.study("s1")
.region("X:1-1000")
.id("X:1:C:T")
.gene("BEX2")
.append(FAMILY.key(), "f1")
.append(FAMILY_SEGREGATION.key(), "X_LINKED_RECESSIVE"), null, cellBaseUtils, sessionId);
.gene("BEX2"), null, cellBaseUtils, sessionId);
// Region untouched
assertEquals("X:1-1000", query.getString(REGION.key()));

query = queryUtils.parseQuery(new VariantQuery()
query = queryUtils.parseQuery(new VariantQuery(baseQuery)
.study("s1")
.id("X:1:C:T")
.append(FAMILY.key(), "f1")
.append(FAMILY_SEGREGATION.key(), "X_LINKED_RECESSIVE"), null, cellBaseUtils, sessionId);
.id("X:1:C:T"), null, cellBaseUtils, sessionId);
// Region untouched, as filtering by variant IDs
assertEquals(null, query.get(REGION.key()));

query = queryUtils.parseQuery(new VariantQuery()
query = queryUtils.parseQuery(new VariantQuery(baseQuery)
.study("s1")
.append(PANEL.key(), myPanel.getId())
.append(FAMILY.key(), "f1")
.append(FAMILY_SEGREGATION.key(), "X_LINKED_RECESSIVE"), null, cellBaseUtils, sessionId);
.append(PANEL.key(), myPanel.getId()), null, cellBaseUtils, sessionId);
// Region untouched, as filtering by gene
assertEquals(null, query.get(REGION.key()));
assertEquals("BEX2", query.getString(GENE.key()));

query = queryUtils.parseQuery(new VariantQuery()
query = queryUtils.parseQuery(new VariantQuery(baseQuery)
.study("s1")
.append(PANEL.key(), myPanelWithRegions.getId())
.append(FAMILY.key(), "f1")
.append(FAMILY_SEGREGATION.key(), "X_LINKED_RECESSIVE"), null, cellBaseUtils, sessionId);
.append(PANEL.key(), myPanelWithRegions.getId()), null, cellBaseUtils, sessionId);
// Region untouched, as filtering by gene
System.out.println("query = " + query.toJson());
assertEquals("X:1-1000", query.getString(REGION.key()));
Expand Down
12 changes: 12 additions & 0 deletions ...age-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQuery.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,15 @@

import java.util.Arrays;
import java.util.List;
import java.util.Map;

public class VariantQuery extends Query {
public VariantQuery() {
}

public VariantQuery(Map<String, Object> map) {
super(map);
}

public VariantQuery id(String value) {
put(VariantQueryParam.ID.key(), value);
Expand Down Expand Up @@ -558,4 +565,9 @@ public String release() {
public VariantQuery append(String key, Object value) {
return (VariantQuery) super.append(key, value);
}

@Override
public VariantQuery appendAll(Map<String, ?> m) {
return (VariantQuery) super.appendAll(m);
}
}

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