Oops, I should add - the reason I can't use an itertools counter to
pre-assign IDs is because the table is potentially being dumped to by
multiple scripts, which is why I have to commit the parts prior to the
segments (since engine.execute can't return multiple insert_ids).
On Monday, 24 March 2014 14:40:52 UTC+8, James Meneghello wrote:
>
> Thanks for the quick reply!
>
> This seems to work pretty well. I took out the batching (as it's already
> batched at a higher level) and modified it to suit the insertion of
> children as well (and reducded the unique to a single field) , and it
> appears to work.
>
> with db_session() as db:
> existing_entries = dict(
> ((entry.subject, entry) for entry in
>
> db.query(Entry).filter(Entry.subject.in_(entries.keys())).options(subqueryload('segments')).all()
> )
> )
>
> segment_inserts = []
> for subject, entry in entries.items():
> existing_entry = existing_entries.get(subject, None)
> if existing_entry:
> segments = dict(((s.segment, s) for s in
> existing_entry.segments))
> for segment_number, segment in entry['segments'].items():
> if int(segment_number) not in segments:
> segment['entry_id'] = existing_entry.id
> segment_inserts.append(segment)
> else:
> entry_id = engine.execute(Entry.__table__.insert(),
> entry).inserted_primary_key
> for segment in entry['segments'].values():
> segment['entry_id'] = entry_id[0]
> segment_inserts.append(segment)
>
> engine.execute(Segment.__table__.insert(), segment_inserts)
>
>
> For 20,000 segments, this ends up being about 45 seconds and 1650 queries
> - 2 to select all the entries and segments, 1 to insert the segments and
> the rest to insert parts. From here, however, I rewrote it a bit:
>
> with db_session() as db:
> existing_entries = dict(
> ((entry.subject, entry) for entry in
>
> db.query(Entry).filter(Entry.subject.in_(entries.keys())).all()
> )
> )
>
> entry_inserts = []
> for subject, entry in entries.items():
> existing_entry = existing_entries.get(subject, None)
> if not existing_entry:
> entry_inserts.append(entry)
>
> engine.execute(Entry.__table__.insert(), entry_inserts)
>
> existing_entries = dict(
> ((entry.subject, entry) for entry in
>
> db.query(Entry).filter(Entry.subject.in_(entries.keys())).options(subqueryload('segments')).all()
> )
> )
>
> segment_inserts = []
> for subject, entry in entries.items():
> existing_entry = existing_entries.get(subject, None)
> if existing_entry:
> segments = dict(((s.segment, s) for s in
> existing_entry.segments))
> for segment_number, segment in entry['segments'].items():
> if int(segment_number) not in segments:
> segment['entry_id'] = existing_entry.id
> segment_inserts.append(segment)
> else:
> log.error('i\'ve made a huge mistake')
>
> engine.execute(Segment.__table__.insert(), segment_inserts)
>
> This ends up being about 19 seconds, 6 queries for a clean dump, and a bit
> less if the table is already populated. Removing the unique indexes on both
> the entries and segments tables and replacing them with standard indexes
> saves about a second in a full dump, and about 6 seconds for an update. I'm
> pretty happy with where it is now, and I suspect most of the time (aside
> from the two insert calls) is being spent in Python. That said, if you have
> any tips for improvements I'd be all ears.
>
> Thanks for the help!
>
> On Monday, 24 March 2014 09:19:25 UTC+8, Michael Bayer wrote:
>>
>>
>> On Mar 23, 2014, at 11:33 AM, James Meneghello <muro...@gmail.com> wrote:
>>
>> I'm having a few issues with unique constraints and bulk inserts. The
>> software I'm writing takes data from an external source (a lot of it,
>> anywhere from 1,000 rows per minute to 100-200k+), crunches it down into
>> its hierarchy and saves it to the DB, to be aggregated in the background.
>> The function handling the initial DB save is designed to work with about
>> 20-50k rows at a time - very little modification takes place, it's pretty
>> much just grabbed and thrown into the table. Obviously the amount of data
>> being saved somewhat excludes the use of the ORM in this particular table,
>> but there are a number of other tables that benefit from using the ORM.
>> Hence, the small stuff uses the ORM and the big stuff uses the Core.
>>
>> The main problem I'm having is with the initial save. The data comes in
>> unordered and sometimes contains duplicates, so there's a UniqueConstraint
>> on Entry on sub, division, created. Unfortunately, this hampers the bulk
>> insert - if there's a duplicate, it rolls back the entire insert and hence
>> the entries aren't available to be referenced by the segments later.
>> Obviously, capturing it in a try/catch would skip the whole block as well.
>> Both Entry and Segment have the same problem - there are often duplicate
>> segments. Since there's a large amount of data being pushed through it, I
>> assume it's impractical to insert the elements individually - while there's
>> only 100-200 entries per block, there's usually 20-50k segments.
>>
>> Is there any way of forcing the engine to skip over duplicates and not
>> rollback the transaction on exception? Code's below. Using Postgres, with
>> psycopg2 as the driver.
>>
>>
>> engine.execute(Entry.__table__.insert(), entries)
>>
>> segment_list = []
>> for sub, entry in entry.items():
>> segments = entry.pop('segments')
>>
>> e = db.query(Entry)\
>> .filter(Entry.sub==entry['sub'])\
>> .filter(Entry.division==entry['division'])\
>> .filter(Entry.created==entry['created']).first()
>>
>> for segment in segments:
>> segment['entry_id'] = e.id
>> segment_list.append(segment)
>>
>> engine.execute(Segment.__table__.insert(), segment_list)
>>
>>
>>
>>
>> In addition, is there some way to pre-fetch data? Rather than query for
>> each Entry, it'd be nice to pre-load all entries and save a couple hundred
>> queries.
>>
>>
>> you have all the entries in segment_list. Seems like you’d just want to
>> dedupe entries as they enter that list, that’s a pretty simple thing to do
>> with a dictionary. but additionally you’re also emitting a SELECT for
>> every item individually so whatever time you’re saving on that INSERT is
>> just being expended with that huge number of SELECT statements anyway.
>>
>> so yes you certainly want to pre-load everything, since the criteria here
>> is three different things you can use a tuple-based IN clause.
>>
>> below is an example that uses this and also batches so that it won’t run
>> out of memory under any circumstances, it starts with 50K rows in the
>> database and then adds another 50K with 20K overlapping. the whole thing
>> runs in about 28 seconds on my mac.
>>
>> from sqlalchemy import *
>> from sqlalchemy.orm import *
>> from sqlalchemy.ext.declarative import declarative_base
>> import random
>> import itertools
>>
>> Base = declarative_base()
>>
>> class Entry(Base):
>> __tablename__ = 'a'
>>
>> id = Column(Integer, primary_key=True)
>> sub = Column(Integer)
>> division = Column(Integer)
>> created = Column(Integer)
>> __table_args__ = (UniqueConstraint('sub', 'division', 'created'), )
>>
>> e = create_engine("postgresql://scott:tiger@localhost/test", echo=True)
>> Base.metadata.drop_all(e)
>> Base.metadata.create_all(e)
>>
>>
>> a_bunch_of_fake_unique_entries = list(set(
>> (random.randint(1, 100000), random.randint(1, 100000),
>> random.randint(1, 100000))
>> for i in range(100000)
>> ))
>>
>> entries_we_will_start_with = a_bunch_of_fake_unique_entries[0:50000]
>> entries_we_will_merge = a_bunch_of_fake_unique_entries[30000:100000]
>>
>> sess = Session(e)
>>
>> counter = itertools.count(1)
>> sess.add_all([Entry(id=next(counter), sub=sub, division=division,
>> created=created)
>> for sub, division, created in
>> entries_we_will_start_with])
>> sess.commit()
>>
>> # here's where your example begins... This will also batch it
>> # to ensure it can scale arbitrarily
>>
>> while entries_we_will_merge:
>> batch = entries_we_will_merge[0:1000]
>> entries_we_will_merge = entries_we_will_merge[1000:]
>>
>> existing_entries = dict(
>> ((entry.sub, entry.division, entry.created),
>> entry)
>> for entry in sess.query(Entry).filter(
>> tuple_(Entry.sub, Entry.division,
>> Entry.created).in_([
>> tuple_(sub, division, created)
>> for sub, division, created in
>> batch
>> ])
>> )
>> )
>>
>> inserts = []
>> for entry_to_merge in batch:
>> existing_entry = existing_entries.get(entry_to_merge, None)
>> if existing_entry:
>> # do whatever to update existing
>> pass
>> else:
>> inserts.append(
>> dict(
>> id=next(counter),
>> sub=entry_to_merge[0],
>> division=entry_to_merge[1],
>> create_engine=entry_to_merge[2]
>> )
>> )
>> if inserts:
>> sess.execute(Entry.__table__.insert(), params=inserts)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Thanks!
>>
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