TASK-8038 - Recover opencga-storage-mongodb

[j-coll]

Summary

Support work in java-common-libs for recovering opencga-storage-mongodb (TASK-8038).
Adds MongoDB aggregation support in persistent cursors, a parallel DataWriter.tee
primitive, and an embedded MongoDB test harness, plus an NPE fix in ProgressLogger.

Changes

• commons-datastore-mongodb
  • MongoPersistentCursor: support aggregation pipelines
  • New EmbeddedMongoDBManager / EmbeddedMongoDBRule for tests
  • Added MongoPersistentCursorTest
• commons-lib
  • DataWriter: new tee (sequential + parallel) with bounded queues; fix hang when a background thread dies with a full queue
  • Task: new tee, deprecated Task.join
  • ProgressLogger.asTask(): fix NPE

Testing

• New unit tests: DataWriterTest, TaskTest, MongoPersistentCursorTest
• Embedded MongoDB via EmbeddedMongoDBRule

Related

• ClickUp: TASK-8038

[imedina]

Task linked: TASK-8038 Recover opencga-storage-mongodb

[j-coll]

Hi @pfurio, ready for review. This is the supporting work for TASK-8038 — MongoDB cursor aggregation, embedded MongoDB test harness, DataWriter.tee, and a couple of small fixes (see PR description).

Goes together with zetta-genomics/opencga#2635 (main PR, also yours). Thanks!