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https://issues.apache.org/jira/browse/BEAM-7866?focusedWorklogId=288220&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-288220
]
ASF GitHub Bot logged work on BEAM-7866:
----------------------------------------
Author: ASF GitHub Bot
Created on: 02/Aug/19 20:12
Start Date: 02/Aug/19 20:12
Worklog Time Spent: 10m
Work Description: jkff commented on pull request #9233: [BEAM-7866] Fix
python ReadFromMongoDB potential data loss issue
URL: https://github.com/apache/beam/pull/9233#discussion_r310264499
##########
File path: sdks/python/apache_beam/io/mongodbio.py
##########
@@ -139,50 +143,77 @@ def __init__(self,
self.filter = filter
self.projection = projection
self.spec = extra_client_params
- self.doc_count = self._get_document_count()
- self.avg_doc_size = self._get_avg_document_size()
- self.client = None
def estimate_size(self):
- return self.avg_doc_size * self.doc_count
+ with MongoClient(self.uri, **self.spec) as client:
+ size = client[self.db].command('collstats', self.coll).get('size')
+ if size is None or size <= 0:
+ raise ValueError('Collection %s not found or total doc size is '
+ 'incorrect' % self.coll)
+ return size
def split(self, desired_bundle_size, start_position=None,
stop_position=None):
# use document cursor index as the start and stop positions
if start_position is None:
- start_position = 0
+ epoch = datetime.datetime(1970, 1, 1)
Review comment:
* Please add a comment that this is an object id smaller than any possible
actual object id
* Does Mongo actually guarantee this property? Maybe it makes sense to
explicitly query for the smallest and largest object id in the database, if it
can be done quickly?
* Using start and end position that are far removed from the actual ids of
present objects risks having most of the splits be empty, or at least having a
couple of splits at the edges that are difficult to liquid-shard. This is a
known issue with e.g. bigtable and shuffle sources in Dataflow. In this sense
too, querying for smallest and largest id would be better.
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Issue Time Tracking
-------------------
Worklog Id: (was: 288220)
> 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: 1.5h
> 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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