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Move tests for domain specific Repositories
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@haynescd
haynescd committed Feb 18, 2025
1 parent 7232adb commit 4d51870
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Showing 20 changed files with 874 additions and 1,093 deletions.
4 changes: 2 additions & 2 deletions ...tisclickhouse/AbstractTestcontainers.java → ...ry/clickhouse/AbstractTestcontainers.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package org.cbioportal.legacy.persistence.mybatisclickhouse;
package org.cbioportal.infrastructure.repository.clickhouse;

import org.junit.BeforeClass;

import org.junit.ClassRule;
import org.springframework.boot.test.util.TestPropertyValues;
import org.springframework.context.ApplicationContextInitializer;
Expand Down Expand Up @@ -32,6 +31,7 @@ public static class Initializer implements ApplicationContextInitializer<Configu

@Override
public void initialize(ConfigurableApplicationContext configurableApplicationContext) {
clickhouseContainer.start();
TestPropertyValues values = TestPropertyValues.of(
"spring.datasource.clickhouse.url=" + clickhouseContainer.getJdbcUrl(),
"spring.datasource.clickhouse.password=" + clickhouseContainer.getPassword(),
Expand Down
265 changes: 265 additions & 0 deletions ...ortal/infrastructure/repository/clickhouse/alteration/ClickhouseAlterationMapperTest.java
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147 changes: 74 additions & 73 deletions ...StudyViewMapperClinicalDataCountTest.java → ...ata/ClickhouseClinicalDataMapperTest.java
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
package org.cbioportal.legacy.persistence.mybatisclickhouse;
package org.cbioportal.infrastructure.repository.clickhouse.clinical_data;

import org.cbioportal.domain.studyview.StudyViewFilterFactory;
import org.cbioportal.infrastructure.repository.clickhouse.AbstractTestcontainers;
import org.cbioportal.infrastructure.repository.clickhouse.config.MyBatisConfig;
import org.cbioportal.legacy.model.ClinicalDataCount;
import org.cbioportal.legacy.persistence.helper.StudyViewFilterHelper;
import org.cbioportal.legacy.persistence.mybatisclickhouse.config.MyBatisConfig;
import org.cbioportal.legacy.web.parameter.ClinicalDataFilter;
import org.cbioportal.legacy.web.parameter.DataFilterValue;
import org.cbioportal.legacy.web.parameter.StudyViewFilter;
Expand All @@ -20,39 +21,38 @@
import java.util.Collections;
import java.util.List;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.*;

@RunWith(SpringRunner.class)
@Import(MyBatisConfig.class)
@DataJpaTest
@DirtiesContext
@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
public class StudyViewMapperClinicalDataCountTest extends AbstractTestcontainers {
public class ClickhouseClinicalDataMapperTest {
private static final String STUDY_ACC_TCGA = "acc_tcga";
private static final String STUDY_GENIE_PUB = "study_genie_pub";

@Autowired
private StudyViewMapper studyViewMapper;
private static final String STUDY_GENIE_PUB = "study_genie_pub";

@Autowired
private ClickhouseClinicalDataMapper mapper;

@Test
public void getMutationCounts() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("mutation_count"),
Collections.emptyList()
var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("mutation_count"),
Collections.emptyList()
);

var mutationsCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();

assertTrue(mutationsCountsOptional.isPresent());
var mutationsCounts = mutationsCountsOptional.get().getCounts();

assertEquals(6, mutationsCounts.size());
assertEquals(1, findClinicaDataCount(mutationsCounts, "11"));
assertEquals(1, findClinicaDataCount(mutationsCounts, "6"));
Expand All @@ -62,20 +62,20 @@ public void getMutationCounts() {
// 1 empty string + 1 'NAN' + 15 samples with no data
assertEquals(17, findClinicaDataCount(mutationsCounts, "NA"));
}

@Test
public void getCenterCounts() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

var clinicalDataCounts = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("center"),
Collections.emptyList()
var clinicalDataCounts = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("center"),
Collections.emptyList()
);

var categoricalClinicalDataCountsOptional = clinicalDataCounts.stream()
.filter(c -> c.getAttributeId().equals("center")).findFirst();
.filter(c -> c.getAttributeId().equals("center")).findFirst();

assertTrue(categoricalClinicalDataCountsOptional.isPresent());
var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts();
Expand All @@ -96,14 +96,14 @@ public void getDeadCounts() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

var clinicalDataCounts = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("dead"),
Collections.emptyList()
var clinicalDataCounts = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("dead"),
Collections.emptyList()
);

var categoricalClinicalDataCountsOptional = clinicalDataCounts.stream()
.filter(c -> c.getAttributeId().equals("dead")).findFirst();
.filter(c -> c.getAttributeId().equals("dead")).findFirst();

assertTrue(categoricalClinicalDataCountsOptional.isPresent());
var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts();
Expand All @@ -127,10 +127,10 @@ public void getMutationAndCenterCounts() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

var combinedClinicalDataCounts = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("mutation_count", "center"),
Collections.emptyList()
var combinedClinicalDataCounts = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("mutation_count", "center"),
Collections.emptyList()
);

assertEquals(2, combinedClinicalDataCounts.size());
Expand All @@ -141,20 +141,20 @@ public void getAgeCounts() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("age"),
Collections.emptyList()
var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("age"),
Collections.emptyList()
);

var ageCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("age")).findFirst();
.filter(c -> c.getAttributeId().equals("age")).findFirst();

assertTrue(ageCountsOptional.isPresent());
var ageCounts = ageCountsOptional.get().getCounts();
var ageCounts = ageCountsOptional.get().getCounts();

assertAgeCounts(ageCounts);

// 1 empty string + 1 'NAN' + 1 'N/A' + 1 patient without data
assertEquals(4, findClinicaDataCount(ageCounts, "NA"));
}
Expand All @@ -164,29 +164,29 @@ public void getAgeCountsForMultipleStudies() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB, STUDY_ACC_TCGA));

var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("age"),
Collections.emptyList()
var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("age"),
Collections.emptyList()
);

var ageCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("age")).findFirst();
.filter(c -> c.getAttributeId().equals("age")).findFirst();

assertTrue(ageCountsOptional.isPresent());
var ageCounts = ageCountsOptional.get().getCounts();

// everything should be exactly the same as single study (STUDY_GENIE_PUB) filter
// except NA counts
assertAgeCounts(ageCounts);

// 1 empty string + 1 'NAN' + 1 'N/A' + 1 GENIE_PUB patient without data + 4 ACC_TCGA data without data
assertEquals(8, findClinicaDataCount(ageCounts, "NA"));
}

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

assertEquals(3, findClinicaDataCount(ageCounts, "<18"));
assertEquals(1, findClinicaDataCount(ageCounts, "18"));
assertEquals(1, findClinicaDataCount(ageCounts, "22"));
Expand All @@ -203,25 +203,25 @@ private void assertAgeCounts(List<ClinicalDataCount> ageCounts) {
assertEquals(2, findClinicaDataCount(ageCounts, ">89"));
assertEquals(1, findClinicaDataCount(ageCounts, "UNKNOWN"));
}

@Test
public void getMutationCountsFilteredByAge() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));

// filter patients with age between 20 and 70
// (there are 5 patients within this range, which are 307..311)
ClinicalDataFilter filter = buildClinicalDataFilter("age", 20, 70);
studyViewFilter.setClinicalDataFilters(List.of(filter));
var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("mutation_count"),
Collections.emptyList()

var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("mutation_count"),
Collections.emptyList()
);

var mutationsCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();

assertTrue(mutationsCountsOptional.isPresent());
var mutationCountsFiltered = mutationsCountsOptional.get().getCounts();
Expand All @@ -242,26 +242,26 @@ public void getMutationCountsFilteredByAgeWithOpenStartValues() {
ClinicalDataFilter filter = buildClinicalDataFilter("age", null, 20);
studyViewFilter.setClinicalDataFilters(List.of(filter));

var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("mutation_count"),
Collections.emptyList()
var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("mutation_count"),
Collections.emptyList()
);

var mutationsCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();

assertTrue(mutationsCountsOptional.isPresent());
var mutationCountsFiltered = mutationsCountsOptional.get().getCounts();

assertEquals(4, mutationCountsFiltered.size());
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306

// no patients/samples with NA
assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA"));
assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA"));
}

@Test
Expand All @@ -274,14 +274,14 @@ public void getMutationCountsFilteredByAgeWithOpenEndValues() {
ClinicalDataFilter filter = buildClinicalDataFilter("age", 80, null);
studyViewFilter.setClinicalDataFilters(List.of(filter));

var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts(
StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()),
List.of("mutation_count"),
Collections.emptyList()
var clinicalDataCountItems = mapper.getClinicalDataCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
List.of("mutation_count"),
Collections.emptyList()
);

var mutationsCountsOptional = clinicalDataCountItems.stream()
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();
.filter(c -> c.getAttributeId().equals("mutation_count")).findFirst();

assertTrue(mutationsCountsOptional.isPresent());
var mutationCountsFiltered = mutationsCountsOptional.get().getCounts();
Expand All @@ -293,7 +293,7 @@ public void getMutationCountsFilteredByAgeWithOpenEndValues() {
// patients/samples with NA data: 317, 318, and 319
assertEquals(3, findClinicaDataCount(mutationCountsFiltered, "NA"));
}

private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) {
DataFilterValue value = new DataFilterValue();
if (start != null) {
Expand All @@ -306,13 +306,14 @@ private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer s
ClinicalDataFilter filter = new ClinicalDataFilter();
filter.setAttributeId(attributeId);
filter.setValues(List.of(value));

return filter;
}

private int findClinicaDataCount(List<ClinicalDataCount> counts, String attrValue) {
var count = counts.stream().filter(c -> c.getValue().equals(attrValue)).findAny().orElse(null);

return count == null ? 0 : count.getCount();
}
}

}
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