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Updated the code to force qualifiers from sample #177

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Updated the code to force qualifiers from sample #177

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13 changes: 10 additions & 3 deletions src/main/java/uk/ac/ebi/embl/api/validation/helper/SourceFeatureUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,16 +77,23 @@ public void addSourceQualifier(String tag, String value, SourceFeature source) {

if (MASTERSOURCEQUALIFIERS.isNoValueQualifiers(tag)) {
if (!"NO".equalsIgnoreCase(value)) {
source.addQualifier(new QualifierFactory().createQualifier(tag));
enforceQualifierFromSample(source, tag, null);
}
} else {
source.addQualifier(new QualifierFactory().createQualifier(tag, value));
enforceQualifierFromSample(source, tag, value);
}
} else if (isCovidTaxId(source.getTaxId()) && covid19RequiredQuals.contains(tag)) {
source.addQualifier(new QualifierFactory().createQualifier(tag, value));
enforceQualifierFromSample(source, tag, value);
}
}

public void enforceQualifierFromSample(SourceFeature source, String tag, String value) {
if(!source.getQualifiers(tag).isEmpty()){
source.removeQualifier(tag);
}
source.addQualifier(new QualifierFactory().createQualifier(tag, value));
}

public void addExtraSourceQualifiers(
SourceFeature source, TaxonomyClient taxonomyClient, String uniqueName) {
if (addUniqueName(source)
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13 changes: 13 additions & 0 deletions src/test/java/uk/ac/ebi/embl/api/validation/helper/SourceFeatureUtilsTest.java
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Expand Up @@ -15,6 +15,7 @@
import java.util.ArrayList;
import java.util.List;
import org.junit.Test;
import uk.ac.ebi.embl.api.entry.feature.FeatureFactory;
import uk.ac.ebi.embl.api.entry.feature.SourceFeature;
import uk.ac.ebi.embl.api.entry.qualifier.Qualifier;
import uk.ac.ebi.ena.taxonomy.client.TaxonomyClient;
Expand Down Expand Up @@ -225,6 +226,18 @@ public void testAttributesWithNullKeyAndValue() {
assertEquals(1, sourceFeature.getQualifiers().size());
}

@Test
public void testEnforceQualifierFromSample() {

FeatureFactory featureFactory = new FeatureFactory();
SourceFeature sourceFeature = featureFactory.createSourceFeature();
sourceFeature.addQualifier(Qualifier.COLLECTION_DATE_QUALIFIER_NAME,"2025-02-05");
assertEquals( sourceFeature.getSingleQualifier(Qualifier.COLLECTION_DATE_QUALIFIER_NAME).getValue(),"2025-02-05");
//Enforce qualifier value from sample
new SourceFeatureUtils().enforceQualifierFromSample(sourceFeature, Qualifier.COLLECTION_DATE_QUALIFIER_NAME,"2020-02-10");
assertEquals( sourceFeature.getSingleQualifier(Qualifier.COLLECTION_DATE_QUALIFIER_NAME).getValue(),"2020-02-10");
}

private Sample createSampleWithAttributes(List<Attribute> attributes) {
Sample sample = new Sample();
sample.setOrganism("Test Organism");
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