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https://issues.apache.org/jira/browse/BEAM-7866?focusedWorklogId=290120&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-290120
]
ASF GitHub Bot logged work on BEAM-7866:
----------------------------------------
Author: ASF GitHub Bot
Created on: 07/Aug/19 00:53
Start Date: 07/Aug/19 00:53
Worklog Time Spent: 10m
Work Description: chamikaramj commented on pull request #9233:
[BEAM-7866] Fix python ReadFromMongoDB potential data loss issue
URL: https://github.com/apache/beam/pull/9233#discussion_r311330436
##########
File path: sdks/python/apache_beam/io/mongodbio_test.py
##########
@@ -30,38 +34,136 @@
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
+ start = filter['_id'].get('$gte')
+ end = filter['_id'].get('$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):
+ # simulate mongo db splitVector command, return split keys base on chunk
+ # size, assuming every doc is of size 1mb
+ start_id = min['_id']
Review comment:
Prob. use different variable names since these override system functions.
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Issue Time Tracking
-------------------
Worklog Id: (was: 290120)
Time Spent: 5h 20m (was: 5h 10m)
> 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: 5h 20m
> 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.
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