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add unit tests
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@onursumer @alisman
onursumer authored and alisman committed Nov 25, 2024
1 parent 17a5dad commit c97fc06
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Showing 3 changed files with 123 additions and 7 deletions.
112 changes: 112 additions & 0 deletions src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringRunner;

import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
Expand All @@ -32,6 +33,7 @@ public class FilteredSamplesTest extends AbstractTestcontainers {

private static final String STUDY_TCGA_PUB = "study_tcga_pub";
private static final String STUDY_ACC_TCGA = "acc_tcga";
private static final String STUDY_GENIE_PUB = "study_genie_pub";

@Autowired
private StudyViewMapper studyViewMapper;
Expand All @@ -57,4 +59,114 @@ public void getFilteredSamples() {
var filteredSamples2 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, Arrays.asList(customSampleIdentifier)));
assertEquals(1, filteredSamples2.size());
}

@Test
public void getSamplesFilteredByClinicalData() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(Arrays.asList(STUDY_GENIE_PUB, STUDY_ACC_TCGA));

// samples of patients with AGE <= 20.0
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, 20.0, null)
)
)
)
);
var filteredSamples1 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
assertEquals(4, filteredSamples1.size());

// samples of patients with AGE <= 20.0 or (80.0, 82.0]
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, 20.0, null),
newDataFilterValue(80.0, 82.0, null)
)
)
)
);
var filteredSamples2 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
assertEquals(6, filteredSamples2.size());

// samples of patients with UNKNOWN AGE
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, null, "Unknown")
)
)
)
);
var filteredSamples3 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
assertEquals(1, filteredSamples3.size());

// samples of patients with AGE <= 20.0 or (80.0, 82.0] or UNKNOWN
// this is a mixed list of filters of both numerical and non-numerical values
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, 20.0, null),
newDataFilterValue(80.0, 82.0, null),
newDataFilterValue(null, null, "unknown")
)
)
)
);
var filteredSamples4 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
assertEquals(7, filteredSamples4.size());

// NA filter
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, null, "NA")
)
)
)
);
var filteredSamples5 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
// 4 acc_tcga + 4 study_genie_pub samples with "NA" AGE data or no AGE data
assertEquals(8, filteredSamples5.size());

// NA + UNKNOWN
studyViewFilter.setClinicalDataFilters(
List.of(
newClinicalDataFilter(
"age", List.of(
newDataFilterValue(null, null, "NA"),
newDataFilterValue(null, null, "UNKNOWN")
)
)
)
);
var filteredSamples6 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
// 8 NA + 1 UNKNOWN
assertEquals(9, filteredSamples6.size());
}

private DataFilterValue newDataFilterValue(Double start, Double end, String value) {
DataFilterValue dataFilterValue = new DataFilterValue();

dataFilterValue.setStart(start == null ? null : new BigDecimal(start));
dataFilterValue.setEnd(end == null ? null: new BigDecimal(end));
dataFilterValue.setValue(value);

return dataFilterValue;
}

private ClinicalDataFilter newClinicalDataFilter(String attributeId, List<DataFilterValue> values) {
ClinicalDataFilter clinicalDataFilter = new ClinicalDataFilter();

clinicalDataFilter.setAttributeId(attributeId);
clinicalDataFilter.setValues(values);

return clinicalDataFilter;
}
}
15 changes: 8 additions & 7 deletions ...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,8 @@ public void getMutationCounts() {
assertEquals(2, findClinicaDataCount(mutationsCounts, "4"));
assertEquals(4, findClinicaDataCount(mutationsCounts, "2"));
assertEquals(2, findClinicaDataCount(mutationsCounts, "1"));
// 1 empty string + 1 'NAN' + 11 samples with no data
assertEquals(13, findClinicaDataCount(mutationsCounts, "NA"));
// 1 empty string + 1 'NAN' + 12 samples with no data
assertEquals(14, findClinicaDataCount(mutationsCounts, "NA"));
}

@Test
Expand All @@ -87,8 +87,8 @@ public void getCenterCounts() {
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "MDA"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "OHSU"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UCSF"));
// 1 empty string + 1 'NA' + 11 samples with no data
assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
// 1 empty string + 1 'NA' + 12 samples with no data
assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
}

@Test
Expand All @@ -114,8 +114,8 @@ public void getDeadCounts() {
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT RELEASED"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT COLLECTED"));
assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UNKNOWN"));
// 1 empty string + 1 'N/A' + 11 samples with no data
assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
// 1 empty string + 1 'N/A' + 12 samples with no data
assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
}

@Test
Expand Down Expand Up @@ -181,7 +181,7 @@ public void getAgeCountsForMultipleStudies() {
}

private void assertAgeCounts(List<ClinicalDataCount> ageCounts) {
assertEquals(14, ageCounts.size());
assertEquals(15, ageCounts.size());

assertEquals(3, findClinicaDataCount(ageCounts, "<18"));
assertEquals(1, findClinicaDataCount(ageCounts, "18"));
Expand All @@ -197,6 +197,7 @@ private void assertAgeCounts(List<ClinicalDataCount> ageCounts) {
assertEquals(2, findClinicaDataCount(ageCounts, "82"));
assertEquals(1, findClinicaDataCount(ageCounts, "89"));
assertEquals(2, findClinicaDataCount(ageCounts, ">89"));
assertEquals(1, findClinicaDataCount(ageCounts, "UNKNOWN"));
}

@Test
Expand Down
3 changes: 3 additions & 0 deletions src/test/resources/clickhouse_data.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,7 @@ insert into patient (internal_id,stable_id,cancer_study_id) values (320,'GENIE-T
insert into patient (internal_id,stable_id,cancer_study_id) values (321,'GENIE-TEST-321',3);
insert into patient (internal_id,stable_id,cancer_study_id) values (322,'GENIE-TEST-322',3);
insert into patient (internal_id,stable_id,cancer_study_id) values (323,'GENIE-TEST-323',3);
insert into patient (internal_id,stable_id,cancer_study_id) values (324,'GENIE-TEST-324',3);

insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values(10,'1,2,3,4,5,6,7,8,9,10,11,');

Expand Down Expand Up @@ -178,6 +179,7 @@ insert into sample (internal_id,stable_id,sample_type,patient_id) values (320,'G
insert into sample (internal_id,stable_id,sample_type,patient_id) values (321,'GENIE-TEST-321-01','primary solid tumor',321);
insert into sample (internal_id,stable_id,sample_type,patient_id) values (322,'GENIE-TEST-322-01','primary solid tumor',322);
insert into sample (internal_id,stable_id,sample_type,patient_id) values (323,'GENIE-TEST-323-01','primary solid tumor',323);
insert into sample (internal_id,stable_id,sample_type,patient_id) values (324,'GENIE-TEST-324-01','primary solid tumor',324);


insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2038,672,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'BRCA1 truncating');
Expand Down Expand Up @@ -457,6 +459,7 @@ insert into clinical_patient (internal_id,attr_id,attr_value) values (319,'age',
insert into clinical_patient (internal_id,attr_id,attr_value) values (320,'age','N/A');
insert into clinical_patient (internal_id,attr_id,attr_value) values (321,'age','');
insert into clinical_patient (internal_id,attr_id,attr_value) values (322,'age','NAN');
insert into clinical_patient (internal_id,attr_id,attr_value) values (324,'age','UNKNOWN');

insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'other_sample_id','5c631ce8-f96a-4c35-a459-556fc4ab21e1');
insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'days_to_collection','276');
Expand Down

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