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ASF GitHub Bot logged work on BEAM-7866: ---------------------------------------- Author: ASF GitHub Bot Created on: 08/Aug/19 17:46 Start Date: 08/Aug/19 17:46 Worklog Time Spent: 10m Work Description: y1chi commented on pull request #9233: [BEAM-7866] Fix python ReadFromMongoDB potential data loss issue URL: https://github.com/apache/beam/pull/9233#discussion_r312163044 ########## File path: sdks/python/apache_beam/io/mongodbio_test.py ########## @@ -30,38 +34,138 @@ from apache_beam.io.mongodbio import _BoundedMongoSource from apache_beam.io.mongodbio import _GenerateObjectIdFn from apache_beam.io.mongodbio import _MongoSink +from apache_beam.io.mongodbio import _ObjectIdHelper +from apache_beam.io.mongodbio import _ObjectIdRangeTracker from apache_beam.io.mongodbio import _WriteMongoFn from apache_beam.testing.test_pipeline import TestPipeline from apache_beam.testing.util import assert_that from apache_beam.testing.util import equal_to +class _MockMongoColl(object): + """Fake mongodb collection cursor.""" + + def __init__(self, docs): + self.docs = docs + + def _filter(self, filter): + match = [] + if not filter: + return self + if '$and' not in filter or not filter['$and']: + return self + start = filter['$and'][0]['_id'].get('$gte') + end = filter['$and'][0]['_id'].get('$lt') + assert start is not None + assert end is not None + for doc in self.docs: + if start and doc['_id'] < start: + continue + if end and doc['_id'] >= end: + continue + match.append(doc) + return match + + def find(self, filter=None, **kwargs): + return _MockMongoColl(self._filter(filter)) + + def sort(self, sort_items): + key, order = sort_items[0] + self.docs = sorted(self.docs, + key=lambda x: x[key], + reverse=(order != ASCENDING)) + return self + + def limit(self, num): + return _MockMongoColl(self.docs[0:num]) + + def count_documents(self, filter): + return len(self._filter(filter)) + + def __getitem__(self, index): + return self.docs[index] + + +class _MockMongoDb(object): + """Fake Mongo Db.""" + + def __init__(self, docs): + self.docs = docs + + def __getitem__(self, coll_name): + return _MockMongoColl(self.docs) + + def command(self, command, *args, **kwargs): + if command == 'collstats': + return {'size': 5, 'avgSize': 1} + elif command == 'splitVector': + return self.get_split_key(command, *args, **kwargs) + + def get_split_key(self, command, ns, min, max, maxChunkSize, **kwargs): Review comment: Done ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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For queries about this service, please contact Infrastructure at: us...@infra.apache.org Issue Time Tracking ------------------- Worklog Id: (was: 291466) Time Spent: 9h 40m (was: 9.5h) > Python MongoDB IO performance and correctness issues > ---------------------------------------------------- > > Key: BEAM-7866 > URL: https://issues.apache.org/jira/browse/BEAM-7866 > Project: Beam > Issue Type: Bug > Components: sdk-py-core > Reporter: Eugene Kirpichov > Assignee: Yichi Zhang > Priority: Blocker > Fix For: 2.15.0 > > Time Spent: 9h 40m > Remaining Estimate: 0h > > https://github.com/apache/beam/blob/master/sdks/python/apache_beam/io/mongodbio.py > splits the query result by computing number of results in constructor, and > then in each reader re-executing the whole query and getting an index > sub-range of those results. > This is broken in several critical ways: > - The order of query results returned by find() is not necessarily > deterministic, so the idea of index ranges on it is meaningless: each shard > may basically get random, possibly overlapping subsets of the total results > - Even if you add order by `_id`, the database may be changing concurrently > to reading and splitting. E.g. if the database contained documents with ids > 10 20 30 40 50, and this was split into shards 0..2 and 3..5 (under the > assumption that these shards would contain respectively 10 20 30, and 40 50), > and then suppose shard 10 20 30 is read and then document 25 is inserted - > then the 3..5 shard will read 30 40 50, i.e. document 30 is duplicated and > document 25 is lost. > - Every shard re-executes the query and skips the first start_offset items, > which in total is quadratic complexity > - The query is first executed in the constructor in order to count results, > which 1) means the constructor can be super slow and 2) it won't work at all > if the database is unavailable at the time the pipeline is constructed (e.g. > if this is a template). > Unfortunately, none of these issues are caught by SourceTestUtils: this class > has extensive coverage with it, and the tests pass. This is because the tests > return the same results in the same order. I don't know how to catch this > automatically, and I don't know how to catch the performance issue > automatically, but these would all be important follow-up items after the > actual fix. > CC: [~chamikara] as reviewer. -- This message was sent by Atlassian JIRA (v7.6.14#76016)