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TASK-3836 - Fix CellBase data release usage #2242

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merged 2 commits into from
Jan 27, 2023
Merged

TASK-3836 - Fix CellBase data release usage #2242

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9330745
analysis: fix CellBase data release usage, #TASK-3836
jtarraga Jan 17, 2023
bff2e12
analysis: fix CellBase data release usage #TASK-3836
j-coll Jan 19, 2023
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7 changes: 5 additions & 2 deletions ...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java
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Expand Up @@ -222,7 +222,8 @@ public OpenCGAResult<GeneCoverageStats> coverageStats(String studyIdStr, String
// Get species and assembly from catalog
OpenCGAResult<Project> projectQueryResult = catalogManager.getProjectManager().search(
new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyIdStr),
new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), token);
new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(ProjectDBAdaptor.QueryParams.ORGANISM.key(),
ProjectDBAdaptor.QueryParams.CELLBASE.key())), token);
if (projectQueryResult.getNumResults() != 1) {
throw new CatalogException("Error getting species and assembly from catalog");
}
Expand Down Expand Up @@ -438,7 +439,9 @@ public List<Region> mergeRegions(List<Region> regions, List<String> genes, boole
// Get species and assembly from catalog
OpenCGAResult<Project> projectQueryResult = catalogManager.getProjectManager().search(
new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), study),
new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), token);
new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
ProjectDBAdaptor.QueryParams.ORGANISM.key(),
ProjectDBAdaptor.QueryParams.CELLBASE.key())), token);
if (projectQueryResult.getNumResults() != 1) {
throw new CatalogException("Error getting species and assembly from catalog");
}
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2 changes: 1 addition & 1 deletion ...opencb/opencga/analysis/variant/manager/operations/VariantAnnotationOperationManager.java
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Expand Up @@ -121,7 +121,7 @@ private void annotate(String projectStr, List<String> studies, String loadFileSt
}

private void synchronizeProjectMetadata(String projectStr, String token) throws CatalogException, StorageEngineException {
Project project = catalogManager.getProjectManager().get(projectStr, null, token).first();
Project project = catalogManager.getProjectManager().get(projectStr, QueryOptions.empty(), token).first();
ProjectOrganism organism = project.getOrganism();
int currentRelease = project.getCurrentRelease();
CatalogStorageMetadataSynchronizer.updateProjectMetadata(variantStorageEngine.getMetadataManager(), organism, currentRelease,
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6 changes: 3 additions & 3 deletions ...pencb/opencga/analysis/variant/manager/operations/VariantFileIndexerOperationManager.java
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Expand Up @@ -61,8 +61,7 @@

import static org.opencb.opencga.catalog.db.api.FileDBAdaptor.QueryParams.ID;
import static org.opencb.opencga.catalog.db.api.FileDBAdaptor.QueryParams.UID;
import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.CURRENT_RELEASE;
import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.ORGANISM;
import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.*;

/**
* Created by imedina on 17/08/16.
Expand Down Expand Up @@ -163,7 +162,8 @@ private void updateProject(String studyFqn, String token) throws CatalogExceptio
Project project = catalogManager
.getProjectManager()
.get(projectFqn,
new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(CURRENT_RELEASE.key(), ORGANISM.key())), token).first();
new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(CURRENT_RELEASE.key(), ORGANISM.key(), CELLBASE.key())),
token).first();
release = project.getCurrentRelease();

// Add species, assembly and release
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3 changes: 2 additions & 1 deletion ...java/org/opencb/opencga/analysis/variant/metadata/CatalogStorageMetadataSynchronizer.java
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Expand Up @@ -110,7 +110,8 @@ public static void updateProjectMetadata(CatalogManager catalog, VariantStorageM
throws CatalogException, StorageEngineException {
final Project p = catalog.getProjectManager().get(project,
new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
ProjectDBAdaptor.QueryParams.ORGANISM.key(), ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key())),
ProjectDBAdaptor.QueryParams.ORGANISM.key(), ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key(),
ProjectDBAdaptor.QueryParams.CELLBASE.key())),
sessionId)
.first();

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2 changes: 1 addition & 1 deletion ...a/org/opencb/opencga/app/migrations/v2_1_0/storage/AddCellbaseConfigurationToProject.java
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Expand Up @@ -23,7 +23,7 @@ protected void run() throws Exception {
// StorageEngineFactory engineFactory = StorageEngineFactory.get(storageConfiguration);
// VariantStorageManager variantStorageManager = new VariantStorageManager(catalogManager, engineFactory);

for (Project project : catalogManager.getProjectManager().search(new Query(), new QueryOptions(), token).getResults()) {
for (Project project : catalogManager.getProjectManager().search(new Query(), QueryOptions.empty(), token).getResults()) {
if (project.getInternal() == null || project.getCellbase() == null) {
String userToken = catalogManager.getUserManager()
.getNonExpiringToken(project.getFqn().split(USER_PROJECT_SEPARATOR)[0], token);
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2 changes: 1 addition & 1 deletion ...rc/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java
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Expand Up @@ -22,7 +22,7 @@ public class AddCellbaseDataRelease extends StorageMigrationTool {
protected void run() throws Exception {
VariantStorageManager variantStorageManager = getVariantStorageManager();
for (String projectFqn : getVariantStorageProjects()) {
Project project = catalogManager.getProjectManager().get(projectFqn, new QueryOptions(), token).first();
Project project = catalogManager.getProjectManager().get(projectFqn, QueryOptions.empty(), token).first();
CellBaseConfiguration cellbase = project.getCellbase();
CellBaseUtils cellBaseUtils = getVariantStorageEngineByProject(projectFqn).getCellBaseUtils();
boolean updateCellbase = false;
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1 change: 1 addition & 0 deletions ...ore/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
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Expand Up @@ -57,6 +57,7 @@ public void before() throws Exception {
protected void loadFiles() throws Exception {
variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
variantStorageEngine.getConfiguration().getCellbase().setVersion("v5.1");
variantStorageEngine.getConfiguration().getCellbase().setDataRelease("2");
variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
variantStorageEngine.reloadCellbaseConfiguration();

Expand Down