Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

TASK-7358 - Memory problem when unlinking some files #2552

Merged
merged 2 commits into from
Feb 24, 2025
+114 −3
Merged

TASK-7358 - Memory problem when unlinking some files #2552

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3e2ea59
catalog: store a small part of the file in job, #TASK-7358
pfurio Feb 24, 2025
d210db4
app: add job migration, #TASK-7358
pfurio Feb 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
70 changes: 70 additions & 0 deletions ...ain/java/org/opencb/opencga/app/migrations/v3/v3_5_0/MinimiseFileDataInJob_TASK_7358.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
package org.opencb.opencga.app.migrations.v3.v3_5_0;

import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Projections;
import com.mongodb.client.model.UpdateOneModel;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.opencb.opencga.catalog.db.api.FileDBAdaptor;
import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor;
import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
import org.opencb.opencga.catalog.migration.Migration;
import org.opencb.opencga.catalog.migration.MigrationTool;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

@Migration(id = "minimize_file_data_in_job_7358",
description = "Minimize file data in Job #7358", version = "3.5.0",
language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20250224)
public class MinimiseFileDataInJob_TASK_7358 extends MigrationTool {

@Override
protected void run() throws Exception {
Bson query = Filters.or(
Filters.exists("attributes._opencga.deletedInputFiles.attributes" , true),
Filters.exists("attributes._opencga.deletedOutputFiles.attributes" , true)
);
Bson projection = Projections.include("uid", "attributes");
migrateCollection(Arrays.asList(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_JOB_COLLECTION),
query, projection, (document, bulk) -> {
MongoDBAdaptor.UpdateDocument updateDocument = new MongoDBAdaptor.UpdateDocument();
Document ocgaAttributes = document.get("attributes", Document.class).get("_opencga", Document.class);

// Process deleted input files list
List<Document> deletedInputFiles = ocgaAttributes.getList("deletedInputFiles", Document.class);
if (deletedInputFiles != null) {
List<Document> reducedDeletedInputFiles = new ArrayList<>(deletedInputFiles.size());
for (Document deletedInputFile : deletedInputFiles) {
reducedDeletedInputFiles.add(getReducedFileDocument(deletedInputFile));
}
updateDocument.getSet().put("attributes._opencga.deletedInputFiles", reducedDeletedInputFiles);
}

// Process deleted output files list
List<Document> deletedOutputFiles = ocgaAttributes.getList("deletedOutputFiles", Document.class);
if (deletedOutputFiles != null) {
List<Document> reducedDeletedOutputFiles = new ArrayList<>(deletedOutputFiles.size());
for (Document deletedOutputFile : deletedOutputFiles) {
reducedDeletedOutputFiles.add(getReducedFileDocument(deletedOutputFile));
}
updateDocument.getSet().put("attributes._opencga.deletedOutputFiles", reducedDeletedOutputFiles);
}

bulk.add(new UpdateOneModel<>(Filters.eq("_id", document.get("_id")), updateDocument.toFinalUpdateDocument()));
});
}

private Document getReducedFileDocument(Document file) {
return new Document()
.append(FileDBAdaptor.QueryParams.ID.key(), file.get(FileDBAdaptor.QueryParams.ID.key()))
.append(FileDBAdaptor.QueryParams.UUID.key(), file.get(FileDBAdaptor.QueryParams.UUID.key()))
.append(FileDBAdaptor.QueryParams.PATH.key(), file.get(FileDBAdaptor.QueryParams.PATH.key()))
.append(FileDBAdaptor.QueryParams.URI.key(), file.get(FileDBAdaptor.QueryParams.URI.key()))
.append(FileDBAdaptor.QueryParams.TYPE.key(), file.get(FileDBAdaptor.QueryParams.TYPE.key()))
.append(FileDBAdaptor.QueryParams.FORMAT.key(), file.get(FileDBAdaptor.QueryParams.FORMAT.key()))
.append(FileDBAdaptor.QueryParams.BIOFORMAT.key(), file.get(FileDBAdaptor.QueryParams.BIOFORMAT.key()));
}

}
15 changes: 12 additions & 3 deletions opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/JobMongoDBAdaptor.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -740,6 +740,15 @@ public void forEach(Query query, Consumer<? super Object> action, QueryOptions o
void removeFileReferences(ClientSession clientSession, long studyUid, long fileUid, Document file) {
UpdateDocument document = new UpdateDocument();

Document fileCopy = new Document()
.append(FileDBAdaptor.QueryParams.ID.key(), file.get(FileDBAdaptor.QueryParams.ID.key()))
.append(FileDBAdaptor.QueryParams.UUID.key(), file.get(FileDBAdaptor.QueryParams.UUID.key()))
.append(FileDBAdaptor.QueryParams.PATH.key(), file.get(FileDBAdaptor.QueryParams.PATH.key()))
.append(FileDBAdaptor.QueryParams.URI.key(), file.get(FileDBAdaptor.QueryParams.URI.key()))
.append(FileDBAdaptor.QueryParams.TYPE.key(), file.get(FileDBAdaptor.QueryParams.TYPE.key()))
.append(FileDBAdaptor.QueryParams.FORMAT.key(), file.get(FileDBAdaptor.QueryParams.FORMAT.key()))
.append(FileDBAdaptor.QueryParams.BIOFORMAT.key(), file.get(FileDBAdaptor.QueryParams.BIOFORMAT.key()));

String prefix = QueryParams.ATTRIBUTES.key() + "." + Constants.PRIVATE_OPENCGA_ATTRIBUTES + ".";

// INPUT
Expand All @@ -748,7 +757,7 @@ void removeFileReferences(ClientSession clientSession, long studyUid, long fileU
.append(QueryParams.INPUT_UID.key(), fileUid);
document.getPullAll().put(QueryParams.INPUT.key(),
Collections.singletonList(new Document(FileDBAdaptor.QueryParams.UID.key(), fileUid)));
document.getPush().put(prefix + Constants.JOB_DELETED_INPUT_FILES, file);
document.getPush().put(prefix + Constants.JOB_DELETED_INPUT_FILES, fileCopy);
Document updateDocument = document.toFinalUpdateDocument();

logger.debug("Removing file from job '{}' field. Query: {}, Update: {}", QueryParams.INPUT.key(), query.toBsonDocument(),
Expand All @@ -763,7 +772,7 @@ void removeFileReferences(ClientSession clientSession, long studyUid, long fileU
document = new UpdateDocument();
document.getPullAll().put(QueryParams.OUTPUT.key(),
Collections.singletonList(new Document(FileDBAdaptor.QueryParams.UID.key(), fileUid)));
document.getPush().put(prefix + Constants.JOB_DELETED_OUTPUT_FILES, file);
document.getPush().put(prefix + Constants.JOB_DELETED_OUTPUT_FILES, fileCopy);
updateDocument = document.toFinalUpdateDocument();

logger.debug("Removing file from job '{}' field. Query: {}, Update: {}", QueryParams.OUTPUT.key(), query.toBsonDocument(),
Expand All @@ -777,7 +786,7 @@ void removeFileReferences(ClientSession clientSession, long studyUid, long fileU
.append(QueryParams.OUT_DIR_UID.key(), fileUid);
document = new UpdateDocument();
document.getSet().put(QueryParams.OUT_DIR.key(), new Document(FileDBAdaptor.QueryParams.UID.key(), -1));
document.getSet().put(prefix + Constants.JOB_DELETED_OUTPUT_DIRECTORY, file);
document.getSet().put(prefix + Constants.JOB_DELETED_OUTPUT_DIRECTORY, fileCopy);
updateDocument = document.toFinalUpdateDocument();

logger.debug("Removing file from job '{}' field. Query: {}, Update: {}", QueryParams.OUT_DIR.key(), query.toBsonDocument(),
Expand Down
32 changes: 32 additions & 0 deletions opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
import org.opencb.opencga.core.models.family.Family;
import org.opencb.opencga.core.models.file.*;
import org.opencb.opencga.core.models.individual.Individual;
import org.opencb.opencga.core.models.job.Job;
import org.opencb.opencga.core.models.panel.Panel;
import org.opencb.opencga.core.models.sample.Sample;
import org.opencb.opencga.core.models.study.*;
Expand Down Expand Up @@ -1911,6 +1912,37 @@ public void removeFileReferencesFromSamplesOnFileDeleteTest() throws CatalogExce
fileManager.get(studyFqn, fileId, QueryOptions.empty(), ownerToken).first();
}

@Test
public void removeFileReferencesFromJobOnFileDeleteTest() throws CatalogException {
String fileId = "data:test:folder:test_0.1K.png";
File file = fileManager.get(studyFqn, fileId, QueryOptions.empty(), ownerToken).first();
assertFalse(file.getSampleIds().isEmpty());
assertEquals(5, file.getSampleIds().size());

Job job = new Job()
.setId("jobId")
.setInput(Collections.singletonList(file));
job = catalogManager.getJobManager().create(studyFqn, job, INCLUDE_RESULT, ownerToken).first();
assertEquals(1, job.getInput().size());
assertEquals(fileId, job.getInput().get(0).getId());
assertNotNull(job.getInput().get(0).getFormat());
assertTrue(job.getAttributes().isEmpty());

setToPendingDelete(studyFqn, new Query(FileDBAdaptor.QueryParams.ID.key(), fileId));
fileManager.delete(studyFqn, Collections.singletonList(fileId), new QueryOptions(Constants.SKIP_TRASH, true), ownerToken);

Job job1 = catalogManager.getJobManager().get(studyFqn, job.getId(), QueryOptions.empty(), ownerToken).first();
assertEquals(0, job1.getInput().size());
assertFalse(job1.getAttributes().isEmpty());

Map<String, Object> opencgaAttributes = (Map<String, Object>) job1.getAttributes().get(Constants.PRIVATE_OPENCGA_ATTRIBUTES);
List<Map<String, Object>> deletedInputFiles = (List<Map<String, Object>>) opencgaAttributes.get(Constants.JOB_DELETED_INPUT_FILES);
assertEquals(1, deletedInputFiles.size());
assertEquals(fileId, deletedInputFiles.get(0).get("id"));
assertEquals(file.getFormat().name(), deletedInputFiles.get(0).get("format"));
assertFalse(deletedInputFiles.get(0).containsKey("attributes"));
}


@Test
public void testDeleteLeafFolder() throws CatalogException, IOException {
Expand Down
Loading