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TASK-6703 - Fix junit tests #2493

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Aug 8, 2024
Merged

TASK-6703 - Fix junit tests #2493

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86512aa
analysis: Fix ClinicalInterpretationAnalysisTest tests. #TASK-6703
j-coll Jul 11, 2024
d84e860
storage: Fix VariantLocalConflictResolverTest tests. #TASK-6703
j-coll Aug 7, 2024
fab3cab
analysis: Fix test VariantOperationsTest#testCellbaseConfigure #TASK-…
j-coll Jul 12, 2024
ed3efc8
storage: Fix tests VariantQueryExecutorTest. #TASK-6703
j-coll Aug 7, 2024
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8 changes: 6 additions & 2 deletions ...rc/test/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationAnalysisTest.java
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Expand Up @@ -50,6 +50,7 @@
import org.opencb.opencga.core.response.OpenCGAResult;
import org.opencb.opencga.core.testclassification.duration.MediumTests;
import org.opencb.opencga.core.tools.result.ExecutionResult;
import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;

import java.io.File;
Expand Down Expand Up @@ -140,8 +141,11 @@ public void customAnalysisFromClinicalAnalysisTest() throws Exception {
.setConfig(config);

ExecutionResult result = customAnalysis.start();

checkInterpretation(238, result);
int expected = opencga.getVariantStorageManager().get(new VariantQuery(query),
new QueryOptions(QueryOptions.LIMIT, 500), clinicalTest.token)
.getResults().size();
assertNotEquals(0, expected);
checkInterpretation(expected, result);
}

@Test
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11 changes: 9 additions & 2 deletions ...ysis/src/test/java/org/opencb/opencga/analysis/variant/manager/VariantOperationsTest.java
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Expand Up @@ -515,13 +515,20 @@ public void testCellbaseConfigure() throws Exception {
assertEquals("GRCh38", cellBaseUtils.getAssembly());

String newCellbase = "https://uk.ws.zettagenomics.com/cellbase/";
String newCellbaseVersion = "v5.8";
String newCellbaseVersion = "v5.2";
String newCellbaseDataRelease = "1";

assertNotEquals(newCellbase, cellBaseUtils.getURL());
assertNotEquals(newCellbaseVersion, cellBaseUtils.getVersion());
assertNotEquals(newCellbaseDataRelease, cellBaseUtils.getDataRelease());

variantStorageManager.setCellbaseConfiguration(project, new CellBaseConfiguration(newCellbase, newCellbaseVersion, "1", ""), false, null, token);
variantStorageManager.setCellbaseConfiguration(project, new CellBaseConfiguration(newCellbase, newCellbaseVersion, newCellbaseDataRelease, ""), false, null, token);
CellBaseConfiguration cellbaseConfiguration = catalogManager.getProjectManager().get(project, new QueryOptions(), token).first().getCellbase();

assertEquals(newCellbase, cellbaseConfiguration.getUrl());
assertEquals(newCellbaseVersion, cellbaseConfiguration.getVersion());
assertEquals(newCellbaseDataRelease, cellbaseConfiguration.getDataRelease());

// assertTrue(family.getPedigreeGraph() != null);
}

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6 changes: 5 additions & 1 deletion opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java
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Expand Up @@ -319,9 +319,13 @@ private void validateProjectForCreation(Project project, User user) throws Catal
throw new CatalogParameterException("Missing mandatory organism information");
}
try {
//TODO: Should the datarelease be undefined? When undefined, it'd be read from cellbase meta endpoints.
String defaultDataRelease = project.getOrganism().getAssembly().equalsIgnoreCase("grch38")
? ParamConstants.CELLBASE_DATA_RELEASE_GRCH38
: null;
CellBaseConfiguration cellBaseConfiguration = ParamUtils.defaultObject(project.getCellbase(),
new CellBaseConfiguration(ParamConstants.CELLBASE_URL, ParamConstants.CELLBASE_VERSION,
ParamConstants.CELLBASE_DATA_RELEASE, ParamConstants.CELLBASE_APIKEY));
defaultDataRelease, ParamConstants.CELLBASE_APIKEY));
cellBaseConfiguration = CellBaseValidator.validate(cellBaseConfiguration,
project.getOrganism().getScientificName(),
project.getOrganism().getAssembly(), true);
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2 changes: 1 addition & 1 deletion opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java
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Expand Up @@ -77,7 +77,7 @@ public class ParamConstants {

public static final String CELLBASE_URL = "https://ws.zettagenomics.com/cellbase";
public static final String CELLBASE_VERSION = "v5.8";
public static final String CELLBASE_DATA_RELEASE = "7";
public static final String CELLBASE_DATA_RELEASE_GRCH38 = "7";
public static final String CELLBASE_APIKEY = null;

public static final String POP_FREQ_1000G_CB_V4 = "1kG_phase3";
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2 changes: 1 addition & 1 deletion opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java
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Expand Up @@ -171,7 +171,7 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException
logger.warn("DataRelease not supported on version '" + serverVersion + ".x'");
} else {
String dataRelease = getDataRelease();
if (dataRelease == null) {
if (StringUtils.isEmpty(dataRelease)) {
if (autoComplete) {
cellBaseConfiguration.setDataRelease(getDefaultDataRelease());
} else {
Expand Down
2 changes: 1 addition & 1 deletion opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java
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Expand Up @@ -46,7 +46,7 @@ public class CellBaseConfiguration {
private String apiKey;

public CellBaseConfiguration() {
this(ParamConstants.CELLBASE_URL, ParamConstants.CELLBASE_VERSION, ParamConstants.CELLBASE_DATA_RELEASE,
this(ParamConstants.CELLBASE_URL, ParamConstants.CELLBASE_VERSION, ParamConstants.CELLBASE_DATA_RELEASE_GRCH38,
ParamConstants.CELLBASE_APIKEY);
}

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4 changes: 2 additions & 2 deletions ...re/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineBNDTest.java
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Expand Up @@ -47,7 +47,7 @@ public abstract class VariantStorageEngineBNDTest extends VariantStorageBaseTest
public void before() throws Exception {
variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE_GRCH38);
if (!loaded) {
clearDB(DB_NAME);
loadFiles();
Expand All @@ -58,7 +58,7 @@ public void before() throws Exception {
protected void loadFiles() throws Exception {
variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE_GRCH38);
studyMetadata = new StudyMetadata(1, "s1");
// variantStorageEngine.getOptions().append(VariantStorageOptions.ANNOTATOR_CELLBASE_EXCLUDE.key(), "expression,clinical");
input1 = getResourceUri("variant-test-bnd.vcf");
Expand Down
2 changes: 1 addition & 1 deletion ...ore/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
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Expand Up @@ -60,7 +60,7 @@ public void before() throws Exception {
protected void loadFiles() throws Exception {
variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE_GRCH38);
variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
variantStorageEngine.reloadCellbaseConfiguration();

Expand Down
2 changes: 1 addition & 1 deletion .../test/java/org/opencb/opencga/storage/core/variant/VariantStorageSearchIntersectTest.java
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Expand Up @@ -81,7 +81,7 @@ public void before() throws Exception {
VariantStorageEngine variantStorageEngine = getVariantStorageEngine();
variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE_GRCH38);
dbAdaptor = variantStorageEngine.getDBAdaptor();
if (!loaded) {
loadFile();
Expand Down
4 changes: 2 additions & 2 deletions ...ava/org/opencb/opencga/storage/core/variant/query/executors/VariantQueryExecutorTest.java
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Expand Up @@ -139,8 +139,8 @@ public void testXRefRs() throws StorageEngineException {
with("ConsequenceType", VariantAnnotation::getConsequenceTypes, hasItem(
with("GeneName", ConsequenceType::getGeneName,
is("TEX13B"))))));
matchers.put("COSV60260399", hasAnnotation(with("TraitAssociation", VariantAnnotation::getTraitAssociation, hasItem(
with("Cosmic", EvidenceEntry::getId, is("COSV60260399"))))));
matchers.put("RCV000155534", hasAnnotation(with("TraitAssociation", VariantAnnotation::getTraitAssociation, hasItem(
with("Clinvar", EvidenceEntry::getId, is("RCV000155534"))))));
matchers.put("ENST00000341832.11(ENSG00000248333):c.356-1170A>G", hasAnnotation(with("HGVS", VariantAnnotation::getHgvs, hasItem(
is("ENST00000341832.11(ENSG00000248333):c.356-1170A>G")))));
matchers.put("ENST00000341832.11:c.356-1170A>G", hasAnnotation(with("HGVS", VariantAnnotation::getHgvs, hasItem(
Expand Down
2 changes: 1 addition & 1 deletion ...rg/opencb/opencga/storage/hadoop/variant/archive/mr/VariantLocalConflictResolverTest.java
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Expand Up @@ -169,7 +169,7 @@ public void resolveConflictIndelCase1() throws Exception {
se.setSampleDataKeys(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
se.setSamplesPosition(asMap("S1", 0));
se.addSampleData("S1", Arrays.asList("1/2", "LowGQXHetDel"));
se.getSecondaryAlternates().add(new AlternateCoordinate(null, null, 328, "CTT", "CTTTC", INDEL));
se.getSecondaryAlternates().add(new AlternateCoordinate(null, 328, null, "CTT", "CTTTC", INDEL));
addAttribute(v1, FILTER, "LowGQXHetDel");


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