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TASK-6754: Create cohort with more than 1000 samples lead to MongoDB restarts #97

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Merged
pfurio merged 5 commits into from
Oct 22, 2024
Merged

TASK-6754: Create cohort with more than 1000 samples lead to MongoDB restarts #97

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d798a26
datastore: support transactions in mongodb aggregations, #TASK-6754
pfurio Aug 22, 2024
534f4ff
datastore: remove copyDocuments method, #TASK-6754
pfurio Aug 22, 2024
e93dc0a
Merge branch 'release-5.x.x' into TASK-6754
pfurio Oct 11, 2024
85f8fa4
datastore: remove unused imports, #TASK-6754
pfurio Oct 11, 2024
a24758f
Merge branch 'release-5.x.x' into TASK-6754
pfurio Oct 15, 2024
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11 changes: 10 additions & 1 deletion ...tastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -323,17 +323,26 @@ public <T> List<DataResult<T>> privateFind(List<? extends Bson> queries, Bson pr
return queryResultList;
}

public DataResult<Document> aggregate(ClientSession clientSession, List<? extends Bson> operations,
QueryOptions options) {
return aggregate(clientSession, operations, null, options);
}

public DataResult<Document> aggregate(List<? extends Bson> operations, QueryOptions options) {
return aggregate(operations, null, options);
}

public <T> DataResult<T> aggregate(List<? extends Bson> operations, ComplexTypeConverter<T, Document> converter,
QueryOptions options) {
return aggregate(null, operations, converter, options);
}

public <T> DataResult<T> aggregate(ClientSession clientSession, List<? extends Bson> operations,
ComplexTypeConverter<T, Document> converter, QueryOptions options) {
long start = startQuery();

DataResult<T> queryResult;
MongoDBIterator<T> iterator = mongoDBNativeQuery.aggregate(operations, converter, options);
MongoDBIterator<T> iterator = mongoDBNativeQuery.aggregate(clientSession, operations, converter, options);
// MongoCursor<Document> iterator = output.iterator();
List<T> list = new LinkedList<>();
if (queryResultWriter != null) {
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