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ALS-6330: Update integration tests to test no-call data
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@ramari16
ramari16 committed Aug 12, 2024
1 parent b034ddc commit e9e418b
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Showing 9 changed files with 197 additions and 227 deletions.
2 changes: 1 addition & 1 deletion service/src/main/resources/application-bdc-auth.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@ SMALL_TASK_THREADS = 1
LARGE_TASK_THREADS = 1
VCF_EXCERPT_ENABLED=true

hpds.genomicProcessor.impl=localDistributed
hpds.genomicProcessor.impl=localPatientDistributed
HPDS_GENOMIC_DATA_DIRECTORY=/opt/local/hpds/all/
3 changes: 2 additions & 1 deletion ...c/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/AbstractProcessorIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@ public void getPatientSubsetForQuery_validRequiredVariant() {
Set<Integer> idList = abstractProcessor.getPatientSubsetForQuery(query);
assertEquals(7, idList.size());
}

@Test
public void getPatientSubsetForQuery_validRequiredVariantOldFormat() {
Query query = new Query();
Expand Down Expand Up @@ -199,7 +200,7 @@ public void getVariantList_validContinuousGenomicFilter() {
query.setVariantInfoFilters(variantInfoFilters);

Collection<String> variantList = abstractProcessor.getVariantList(query);
assertEquals(2, variantList.size());
assertEquals(4, variantList.size());
}

@Test
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219 changes: 46 additions & 173 deletions service/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/test/BucketIndexBySampleTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -117,11 +117,11 @@ public void test_filterVariantSetForPatientSet_VariantsWithoutPatientsLastBucket

assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty());
}

@Test
public void test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket");

variantSet.add(spec6);
variantSet.add(spec6b);

Expand All @@ -130,29 +130,25 @@ public void test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket
patientSet.add(197509);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty());
}

@Test
public void test_filterVariantSetForPatientSet_allValidLastBucket() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_allValidLastBucket");
public void test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucketNoCall() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_PatientsWithNoVariantsFirstBucket");

variantSet.add(spec1);
variantSet.add(spec2);
variantSet.add(spec3);
variantSet.add(spec4);
variantSet.add(spec5);
variantSet.add("chr20,5032061,A,G,LOC102723996,missense_variant");
variantSet.add("chr21,5032061,A,G,ABCDEF123456,synonymous_variant");

patientSet.add(197506);
patientSet.add(197508);
patientSet.add(197509);

patientSet.add(200392);
patientSet.add(200689);
patientSet.add(200972);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);
assertEquals("No variants should be filtered out", (long)2, (long)filteredVariantSet.size());

assertTrue("Patients should not match any variants in the list", filteredVariantSet.isEmpty());
}

@Test
public void test_filterVariantSetForPatientSet_allValidFirstBucket() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_allValidFirstBucket");
Expand All @@ -163,13 +159,29 @@ public void test_filterVariantSetForPatientSet_allValidFirstBucket() throws IOEx
patientSet.add(200392);
patientSet.add(200689);
patientSet.add(200972);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);


assertEquals("No variants should be filtered out", 2, filteredVariantSet.size());
}
@Test
public void test_filterVariantSetForPatientSet_allValidFirstBucketWithNoCall() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_allValidFirstBucket");

variantSet.add("chr20,5032061,A,G,ABC1,missense_variant");
variantSet.add("chr20,5032061,A,G,DEF1,synonymous_variant");

patientSet.add(200392);
patientSet.add(200689);
patientSet.add(200972);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", 2, filteredVariantSet.size());
}

@Test
@Disabled
public void test_filterVariantSetForPatientSet_someValid() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_someValid");

Expand All @@ -185,27 +197,28 @@ public void test_filterVariantSetForPatientSet_someValid() throws IOException {
assertEquals("One variant should be filtered out", 1, filteredVariantSet.size());
assertTrue("Expected variant not found", filteredVariantSet.contains(spec1));
}

@Test
public void test_filterVariantSetForPatientSet_allValidDifferentPatients() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_allValidDifferentPatients");
//specs 1-5 are in the last bucket
variantSet.add(spec1); // only 5
variantSet.add(spec4); // only 6
variantSet.add(spec5); // 5 & 6
variantSet.add(spec7); // only #4

patientSet.add(4);
patientSet.add(5);
patientSet.add(6);

variantSet.add(spec1);
variantSet.add(spec4);
variantSet.add(spec5);
variantSet.add(spec7);

patientSet.add(200194);
patientSet.add(200450);
patientSet.add(200710);
patientSet.add(198206);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", (long)4, (long)filteredVariantSet.size());
}

@Test
@Disabled
public void test_filterVariantSetForPatientSet_someValidDifferentPatients() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_allValidDifferentPatients");

Expand All @@ -226,144 +239,4 @@ public void test_filterVariantSetForPatientSet_someValidDifferentPatients() thro
assertFalse("Spec 9 should have been filtered out", filteredVariantSet.contains(spec9));
}

@Test
public void test_filterVariantSetForPatientSet_HeteroPatientA() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroPatientA");

variantSet.add(spec8); //patients 7 and 8 have hetero flags for this variant (1|0 and 0|1)

patientSet.add(7);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", (long)1, (long)filteredVariantSet.size());
}

@Test
public void test_filterVariantSetForPatientSet_HeteroPatientB() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroPatientB");

variantSet.add(spec8); //patients 7 and 8 have hetero flags for this variant (1|0 and 0|1)

patientSet.add(8);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", (long)1, (long)filteredVariantSet.size());
}


@Test
public void test_filterVariantSetForPatientSet_HeteroNoCallPosPatientA() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallPosPatientA");

variantSet.add(spec8); //patients 9 and 10 have hetero No Call flags for this variant (1|. and .|1)

patientSet.add(9);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", (long)1, (long)filteredVariantSet.size());
}

@Test
public void test_filterVariantSetForPatientSet_HeteroNoCallPosPatientB() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallPosPatientB");

variantSet.add(spec8); //patients 9 and 10 have hetero No Call flags for this variant (1|. and .|1)

patientSet.add(10);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("No variants should be filtered out", (long)1, (long)filteredVariantSet.size());
}

@Test
@Disabled
public void test_filterVariantSetForPatientSet_HeteroNoCallNegPatientA() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallNegPatientA");

variantSet.add(spec10); //patients 9 and 10 have hetero No Call flags for this variant (0|. and .|0)

patientSet.add(9);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertTrue("All variants should be filtered out", filteredVariantSet.isEmpty());
}

@Test
@Disabled
public void test_filterVariantSetForPatientSet_HeteroNoCallNegPatientB() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallNegPatientB");

variantSet.add(spec10); //patients 9 and 10 have hetero No Call flags for this variant (0|. and .|0)

patientSet.add(10);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertTrue("All variants should be filtered out", filteredVariantSet.isEmpty());
}

@Test
@Disabled
public void test_filterVariantSetForPatientSet_HomoNoCall() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallNegPatientB");

variantSet.add(spec12);
patientSet.add(7);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertTrue("All variants should be filtered out", filteredVariantSet.isEmpty());
}


@Test
@Disabled
public void test_filterVariantSetForPatientSet_HeteroNoCallMultipleVariantsAndPatientsA() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallMultipleVariantsAndPatientss");

variantSet.add(spec10); //patients 9 and 10 have hetero No Call flags for this variant (0|. and .|0) (#7 has this)
variantSet.add(spec8); //patients 9 and 10 have hetero No Call flags for this variant (1|. and .|1)
variantSet.add(spec4); // 9 and 10 have a spec in this bucket
variantSet.add(spec11); //9 and 10 should not have this spec
variantSet.add(spec12);

patientSet.add(1); //no specs
patientSet.add(9);
patientSet.add(10);
patientSet.add(7);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("Two variant should be filtered out", (long)3, (long)filteredVariantSet.size());
assertFalse("Spec 12 should have been filtered out", filteredVariantSet.contains(spec12));
assertFalse("Spec 11 should have been filtered out", filteredVariantSet.contains(spec11));
}


@Test
@Disabled
public void test_filterVariantSetForPatientSet_HeteroNoCallMultipleVariantsAndPatientsB() throws IOException {
System.out.println("test_filterVariantSetForPatientSet_HeteroNoCallMultipleVariantsAndPatientss");

variantSet.add(spec10); //patients 9 and 10 have hetero No Call flags for this variant (0|. and .|0)
variantSet.add(spec8); //patients 9 and 10 have hetero No Call flags for this variant (1|. and .|1)
variantSet.add(spec4); // 9 and 10 have a spec in this bucket
variantSet.add(spec11); //9 and 10 should not have this spec

patientSet.add(1); //no specs
patientSet.add(9);
patientSet.add(10);

Collection<String> filteredVariantSet = bucketIndexBySample.filterVariantSetForPatientSet(variantSet, patientSet);

assertEquals("Two variant should be filtered out", (long)2, (long)filteredVariantSet.size());
assertFalse("Spec 10 should have been filtered out", filteredVariantSet.contains(spec10));
assertFalse("Spec 11 should have been filtered out", filteredVariantSet.contains(spec11));
}

}
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