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TASK-7170 - Fix addIndividual function in VariantMetadataManager #283

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TASK-7170 - Fix addIndividual function in VariantMetadataManager #283

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15 changes: 8 additions & 7 deletions ...tools/src/main/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,6 @@
import org.opencb.biodata.models.variant.metadata.VariantFileMetadata;
import org.opencb.biodata.models.variant.metadata.VariantMetadata;
import org.opencb.biodata.models.variant.metadata.VariantStudyMetadata;
import org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileHeaderConverter;
import org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileMetadataConverter;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.utils.FileUtils;
Expand All @@ -59,6 +58,7 @@
public class VariantMetadataManager {

private VariantMetadata variantMetadata;
private Set<String> individualSet = new HashSet<>();

private ObjectMapper mapper;
private Logger logger;
Expand Down Expand Up @@ -109,6 +109,7 @@ public void load(Path path) throws IOException {
for (VariantStudyMetadata variantStudyMetadata: variantMetadata.getStudies()) {
if (variantStudyMetadata.getIndividuals() != null) {
for (Individual individual : variantStudyMetadata.getIndividuals()) {
individualSet.add(individual.getId());
for (Sample sample : individual.getSamples()) {
sample.getAnnotations().put(INDIVIDUAL_ID, individual.getId());
sample.getAnnotations().put(INDIVIDUAL_FAMILY, individual.getFamily());
Expand Down Expand Up @@ -272,6 +273,7 @@ public void addFile(VariantFileMetadata fileMetadata, String studyId) {
individual.setSamples(samples);

variantStudyMetadata.getIndividuals().add(individual);
individualSet.add(individual.getId());
}


Expand Down Expand Up @@ -383,14 +385,12 @@ public void addIndividual(Individual individual, String studyId) {
if (variantStudyMetadata.getIndividuals() == null) {
variantStudyMetadata.setIndividuals(new ArrayList<>());
}
for (Individual indi: variantStudyMetadata.getIndividuals()) {
if (indi.getId() != null && indi.getId().equals(individual.getId())) {
logger.error("Individual with id '{}' already exists in study '{}'", individual.getId(),
studyId);
return;
}
if (individualSet.contains(individual.getId())) {
logger.error("Individual with id '{}' already exists in study '{}'", individual.getId(), studyId);
return;
}
variantStudyMetadata.getIndividuals().add(individual);
individualSet.add(individual.getId());
}

/**
Expand Down Expand Up @@ -430,6 +430,7 @@ public void removeIndividual(String individualId, String studyId) {
for (int i = 0; i < variantStudyMetadata.getIndividuals().size(); i++) {
if (individualId.equals(variantStudyMetadata.getIndividuals().get(i).getId())) {
variantStudyMetadata.getIndividuals().remove(i);
individualSet.remove(individualId);
return;
}
}
Expand Down
36 changes: 35 additions & 1 deletion ...s/src/test/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataManagerTest.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
package org.opencb.biodata.tools.variant.metadata;

import org.apache.commons.collections4.map.HashedMap;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.opencb.biodata.models.metadata.Individual;
import org.opencb.biodata.models.metadata.Sample;
import org.opencb.biodata.models.variant.metadata.VariantMetadata;
import org.opencb.biodata.models.variant.metadata.VariantStudyMetadata;
import org.opencb.biodata.tools.variant.metadata.VariantMetadataManager;
import org.opencb.commons.datastore.core.Query;

import java.io.IOException;
Expand Down Expand Up @@ -184,4 +184,38 @@ public void load() {
}
}

@Test
public void testAddIndividual() {
try {
Path path = Paths.get("/tmp/ds.meta.json");
if (path.toFile().exists()) {
path.toFile().delete();
}
manager.save(path, true);

manager = new VariantMetadataManager();
manager.load(path);

String studyId = variantMetadata.getStudies().get(0).getId();
Assert.assertEquals(3, manager.getVariantStudyMetadata(studyId).getIndividuals().size());

manager.addIndividual("Person_0", "Sample_0_0", studyId);

String newIndividualId = "Person_100";
manager.addIndividual(newIndividualId, "Sample_100_0", studyId);
Assert.assertEquals(4, manager.getVariantStudyMetadata(studyId).getIndividuals().size());

manager.addIndividual(newIndividualId, "Sample_100_0", studyId);
Assert.assertEquals(4, manager.getVariantStudyMetadata(studyId).getIndividuals().size());

manager.removeIndividual(newIndividualId, studyId);
Assert.assertEquals(3, manager.getVariantStudyMetadata(studyId).getIndividuals().size());

manager.addIndividual(newIndividualId, "Sample_100_0", studyId);
Assert.assertEquals(4, manager.getVariantStudyMetadata(studyId).getIndividuals().size());
} catch (IOException e) {
e.printStackTrace();
fail();
}
}
}
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