-
Notifications
You must be signed in to change notification settings - Fork 97
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
app: fix cohort-sample references, #TASK-6998
- Loading branch information
Showing
3 changed files
with
81 additions
and
83 deletions.
There are no files selected for viewing
30 changes: 2 additions & 28 deletions
30
.../java/org/opencb/opencga/app/migrations/v2/v2_12_4/catalog/FixStatusIndexesMigration.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,46 +1,20 @@ | ||
| package org.opencb.opencga.app.migrations.v2.v2_12_4.catalog; | ||
|
|
||
| import org.bson.Document; | ||
| 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.Arrays; | ||
|
|
||
| @Migration(id = "fix_status_indexes" , | ||
| description = "Replace 'status.name' indexes for 'status.id'", | ||
| version = "2.12.4", | ||
| domain = Migration.MigrationDomain.CATALOG, | ||
| language = Migration.MigrationLanguage.JAVA, | ||
| date = 20240328 | ||
| date = 20240328, | ||
| deprecatedSince = "3.3.0" | ||
| ) | ||
| public class FixStatusIndexesMigration extends MigrationTool { | ||
|
|
||
| @Override | ||
| protected void run() throws Exception { | ||
| Document statusIndex = new Document() | ||
| .append("status.name", 1) | ||
| .append("studyUid", 1); | ||
| dropIndex(Arrays.asList(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION, OrganizationMongoDBAdaptorFactory.FILE_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION, OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION, OrganizationMongoDBAdaptorFactory.INDIVIDUAL_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.INDIVIDUAL_ARCHIVE_COLLECTION, OrganizationMongoDBAdaptorFactory.FAMILY_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.FAMILY_ARCHIVE_COLLECTION, OrganizationMongoDBAdaptorFactory.PANEL_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.PANEL_ARCHIVE_COLLECTION), statusIndex); | ||
|
|
||
| Document internalStatusIndex = new Document() | ||
| .append("internal.status.name", 1) | ||
| .append("studyUid", 1); | ||
| dropIndex(Arrays.asList(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION, OrganizationMongoDBAdaptorFactory.FILE_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION, OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION, OrganizationMongoDBAdaptorFactory.INDIVIDUAL_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.INDIVIDUAL_ARCHIVE_COLLECTION, OrganizationMongoDBAdaptorFactory.FAMILY_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.FAMILY_ARCHIVE_COLLECTION, OrganizationMongoDBAdaptorFactory.PANEL_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.PANEL_ARCHIVE_COLLECTION, OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION, OrganizationMongoDBAdaptorFactory.INTERPRETATION_ARCHIVE_COLLECTION), | ||
| internalStatusIndex); | ||
|
|
||
| catalogManager.installIndexes(token); | ||
| } | ||
|
|
||
| } |
57 changes: 2 additions & 55 deletions
57
...ain/java/org/opencb/opencga/app/migrations/v2/v2_12_6/SyncCohortsAndSamplesMigration.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,73 +1,20 @@ | ||
| package org.opencb.opencga.app.migrations.v2.v2_12_6; | ||
|
|
||
| import com.mongodb.client.MongoCollection; | ||
| import com.mongodb.client.model.Filters; | ||
| import com.mongodb.client.model.Projections; | ||
| import com.mongodb.client.model.Updates; | ||
| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.bson.Document; | ||
| import org.bson.conversions.Bson; | ||
| import org.opencb.opencga.catalog.db.api.CohortDBAdaptor; | ||
| import org.opencb.opencga.catalog.db.api.SampleDBAdaptor; | ||
| 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.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Migration(id = "syncCohortsAndSamplesMigration" , | ||
| description = "Sync array of samples from cohort with array of cohortIds from Sample", | ||
| version = "2.12.6", | ||
| domain = Migration.MigrationDomain.CATALOG, | ||
| language = Migration.MigrationLanguage.JAVA, | ||
| date = 20240621 | ||
| date = 20240621, | ||
| deprecatedSince = "3.3.0" | ||
| ) | ||
| public class SyncCohortsAndSamplesMigration extends MigrationTool { | ||
|
|
||
| @Override | ||
| protected void run() throws Exception { | ||
| MongoCollection<Document> sampleCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION); | ||
| MongoCollection<Document> sampleArchiveCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION); | ||
|
|
||
| queryMongo(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION, new Document(), | ||
| Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key()), | ||
| cohortDoc -> { | ||
| String cohortId = cohortDoc.getString(CohortDBAdaptor.QueryParams.ID.key()); | ||
| List<Document> samples = cohortDoc.getList(CohortDBAdaptor.QueryParams.SAMPLES.key(), Document.class); | ||
| if (CollectionUtils.isNotEmpty(samples)) { | ||
| List<Long> sampleUids = samples | ||
| .stream() | ||
| .map(s -> s.get(SampleDBAdaptor.QueryParams.UID.key(), Number.class).longValue()) | ||
| .collect(Collectors.toList()); | ||
| // Ensure all those samples have a reference to the cohortId | ||
| Bson query = Filters.and( | ||
| Filters.in(SampleDBAdaptor.QueryParams.UID.key(), sampleUids), | ||
| Filters.eq(MongoDBAdaptor.LAST_OF_VERSION, true) | ||
| ); | ||
| Bson update = Updates.addToSet(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId); | ||
| long addedMissingCohort = sampleCollection.updateMany(query, update).getModifiedCount(); | ||
| sampleArchiveCollection.updateMany(query, update); | ||
|
|
||
| // Ensure there aren't any samples pointing to this cohort that are not in the samples array | ||
| query = Filters.and( | ||
| Filters.nin(SampleDBAdaptor.QueryParams.UID.key(), sampleUids), | ||
| Filters.eq(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId), | ||
| Filters.eq(MongoDBAdaptor.LAST_OF_VERSION, true) | ||
| ); | ||
| update = Updates.pull(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId); | ||
| long removedNonAssociatedCohort = sampleCollection.updateMany(query, update).getModifiedCount(); | ||
| sampleArchiveCollection.updateMany(query, update); | ||
|
|
||
| if (addedMissingCohort > 0 || removedNonAssociatedCohort > 0) { | ||
| logger.info("Fixed cohort '{}' references. " | ||
| + "Added missing reference to {} samples. " | ||
| + "Removed non-associated reference from {} samples.", | ||
| cohortId, addedMissingCohort, removedNonAssociatedCohort); | ||
| } | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| } |
77 changes: 77 additions & 0 deletions
77
.../java/org/opencb/opencga/app/migrations/v3/v3_3_0/CatalogFixCohortAndSampleMigration.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| package org.opencb.opencga.app.migrations.v3.v3_3_0; | ||
|
|
||
| import com.mongodb.client.MongoCollection; | ||
| import com.mongodb.client.model.Filters; | ||
| import com.mongodb.client.model.Projections; | ||
| import com.mongodb.client.model.Updates; | ||
| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.bson.Document; | ||
| import org.bson.conversions.Bson; | ||
| import org.opencb.opencga.catalog.db.api.CohortDBAdaptor; | ||
| import org.opencb.opencga.catalog.db.api.SampleDBAdaptor; | ||
| import org.opencb.opencga.catalog.db.api.StudyDBAdaptor; | ||
| 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.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Migration(id = "syncCohortsAndSamplesMigration" , | ||
| description = "Sync array of samples from cohort with array of cohortIds from Sample", | ||
| version = "3.3.0", | ||
| domain = Migration.MigrationDomain.CATALOG, | ||
| language = Migration.MigrationLanguage.JAVA, | ||
| date = 20240926 | ||
| ) | ||
| public class CatalogFixCohortAndSampleMigration extends MigrationTool { | ||
|
|
||
| @Override | ||
| protected void run() throws Exception { | ||
| MongoCollection<Document> sampleCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION); | ||
| MongoCollection<Document> sampleArchiveCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION); | ||
|
|
||
| // Fill map study uid - fqn | ||
| Map<Long, String> uidFqnMap = new HashMap<>(); | ||
| Bson studyProjection = Projections.include(StudyDBAdaptor.QueryParams.UID.key(), StudyDBAdaptor.QueryParams.FQN.key()); | ||
| queryMongo(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION, new Document(), studyProjection, study -> { | ||
| long studyUid = study.get(StudyDBAdaptor.QueryParams.UID.key(), Number.class).longValue(); | ||
| String studyFqn = study.getString(StudyDBAdaptor.QueryParams.FQN.key()); | ||
| uidFqnMap.put(studyUid, studyFqn); | ||
| }); | ||
|
|
||
| queryMongo(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION, new Document(), | ||
| Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key(), | ||
| CohortDBAdaptor.QueryParams.STUDY_UID.key()), | ||
| cohortDoc -> { | ||
| String cohortId = cohortDoc.getString(CohortDBAdaptor.QueryParams.ID.key()); | ||
| List<Document> samples = cohortDoc.getList(CohortDBAdaptor.QueryParams.SAMPLES.key(), Document.class); | ||
| if (CollectionUtils.isNotEmpty(samples)) { | ||
| List<Long> sampleUids = samples | ||
| .stream() | ||
| .map(s -> s.get(SampleDBAdaptor.QueryParams.UID.key(), Number.class).longValue()) | ||
| .collect(Collectors.toList()); | ||
| // Ensure all those samples have a reference to the cohortId | ||
| Bson query = Filters.and( | ||
| Filters.in(SampleDBAdaptor.QueryParams.UID.key(), sampleUids), | ||
| Filters.eq(MongoDBAdaptor.LAST_OF_VERSION, true) | ||
| ); | ||
| Bson update = Updates.addToSet(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId); | ||
| long addedMissingCohort = sampleCollection.updateMany(query, update).getModifiedCount(); | ||
| sampleArchiveCollection.updateMany(query, update); | ||
|
|
||
| if (addedMissingCohort > 0) { | ||
| long studyUid = cohortDoc.get(CohortDBAdaptor.QueryParams.STUDY_UID.key(), Number.class).longValue(); | ||
|
|
||
| logger.info("Fixed cohort '{}' references from study '{}'. " | ||
| + "Added missing reference to {} samples.", | ||
| cohortId, uidFqnMap.get(studyUid), addedMissingCohort); | ||
| } | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| } |