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  • healthkit-to-sqlite · 10
id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association pull_request body repo type active_lock_reason
519038979 MDU6SXNzdWU1MTkwMzg5Nzk= 10 Failed to import workout points simonw 9599 closed 0     4 2019-11-07T04:50:22Z 2019-11-08T01:18:37Z 2019-11-08T01:18:37Z MEMBER  

I just ran the script and it failed to import any workout_points, though it did import workouts.

healthkit-to-sqlite 197882382 issue  
472429048 MDU6SXNzdWU0NzI0MjkwNDg= 9 Too many SQL variables tholo 166463 closed 0     4 2019-07-24T18:24:17Z 2019-07-26T10:01:05Z 2019-07-26T10:01:05Z NONE  

Decided to try importing my data, and ran into this:

Traceback (most recent call last):
  File "/Users/tholo/Source/health/bin/healthkit-to-sqlite", line 10, in <module>
    sys.exit(cli())
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/healthkit_to_sqlite/cli.py", line 50, in cli
    convert_xml_to_sqlite(fp, db, progress_callback=bar.update)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/healthkit_to_sqlite/utils.py", line 41, in convert_xml_to_sqlite
    write_records(records, db)
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/healthkit_to_sqlite/utils.py", line 80, in write_records
    column_order=["startDate", "endDate", "value", "unit"],
  File "/Users/tholo/Source/health/lib/python3.7/site-packages/sqlite_utils/db.py", line 911, in insert_all
    result = self.db.conn.execute(sql, values)
sqlite3.OperationalError: too many SQL variables

Added some debug output in sqlite_utils/db.py, which resulted in:

                INSERT INTO [rBodyMassIndex] ([creationDate], [endDate], [metadata_HKWasUserEntered], [metadata_Health Mate App Version], [metadata_Modified Date], [metadata_Withings Link], [metadata_Withings User Identifier], [sourceName], [sourceVersion], [startDate], [unit], [value]) VALUES
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                ;

with the attached data:

['2019-06-27 22:55:10 -0700', '2011-06-22 21:05:53 -0700', '0', '4.4.2', '2011-06-23 04:05:53 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1308801953&type=1', '301293', 'Health Mate', '4040200', '2011-06-22 21:05:53 -0700', 'count', '30.0926', '2019-06-27 22:55:10 -0700', '2011-06-23 09:36:27 -0700', '0', '4.4.2', '2011-06-23 16:36:59 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1308846987&type=1', '301293', 'Health Mate', '4040200', '2011-06-23 09:36:27 -0700', 'count', '30.0926', '2019-06-27 22:55:10 -0700', '2011-06-23 23:54:07 -0700', '0', '4.4.2', '2011-06-24 06:55:19 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1308898447&type=1', '301293', 'Health Mate', '4040200', '2011-06-23 23:54:07 -0700', 'count', '30.679', '2019-06-27 22:55:10 -0700', '2011-06-24 09:13:40 -0700', '0', '4.4.2', '2011-06-24 16:14:35 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1308932020&type=1', '301293', 'Health Mate', '4040200', '2011-06-24 09:13:40 -0700', 'count', '30.3549', '2019-06-27 22:55:10 -0700', '2011-06-25 08:30:08 -0700', '0', '4.4.2', '2011-06-25 15:30:49 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309015808&type=1', '301293', 'Health Mate', '4040200', '2011-06-25 08:30:08 -0700', 'count', '30.3395', '2019-06-27 22:55:10 -0700', '2011-06-26 07:47:51 -0700', '0', '4.4.2', '2011-06-26 14:48:27 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309099671&type=1', '301293', 'Health Mate', '4040200', '2011-06-26 07:47:51 -0700', 'count', '30.2315', '2019-06-27 22:55:10 -0700', '2011-06-28 08:48:26 -0700', '0', '4.4.2', '2011-06-28 15:49:13 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309276106&type=1', '301293', 'Health Mate', '4040200', '2011-06-28 08:48:26 -0700', 'count', '30.0617', '2019-06-27 22:55:10 -0700', '2011-06-29 09:21:16 -0700', '0', '4.4.2', '2011-06-29 16:21:59 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309364476&type=1', '301293', 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healthkit-to-sqlite 197882382 issue  
472097220 MDU6SXNzdWU0NzIwOTcyMjA= 7 Script uses a lot of RAM simonw 9599 closed 0     3 2019-07-24T06:11:11Z 2019-07-24T06:35:52Z 2019-07-24T06:35:52Z MEMBER  

I'm using an XML pull parser which should avoid the need to slurp the whole XML file into memory, but it's not working - the script still uses over 1GB of RAM when it runs according to Activity Monitor.

I think this is because I'm still causing the full root element to be incrementally loaded into memory just in case I try and access it later.

http://effbot.org/elementtree/iterparse.htm says I should use elem.clear() as I go. It also says:

The above pattern has one drawback; it does not clear the root element, so you will end up with a single element with lots of empty child elements. If your files are huge, rather than just large, this might be a problem. To work around this, you need to get your hands on the root element.

So I will try that recipe and see if it helps.

healthkit-to-sqlite 197882382 issue  
472104705 MDExOlB1bGxSZXF1ZXN0MzAwNTgwMjIx 8 Use less RAM simonw 9599 closed 0     0 2019-07-24T06:35:01Z 2019-07-24T06:35:52Z 2019-07-24T06:35:52Z MEMBER dogsheep/healthkit-to-sqlite/pulls/8

Closes #7

healthkit-to-sqlite 197882382 pull  
470691622 MDU6SXNzdWU0NzA2OTE2MjI= 5 Add progress bar simonw 9599 closed 0     2 2019-07-20T16:29:07Z 2019-07-22T03:30:13Z 2019-07-22T02:49:22Z MEMBER  

Showing a progress bar would be nice, using Click.

The easiest way to do this would probably be be to hook it up to the length of the compressed content, and update it as this code pushes more XML bytes through the parser:

https://github.com/dogsheep/healthkit-to-sqlite/blob/d64299765064501f4efdd9a0b21dbdba9ec4287f/healthkit_to_sqlite/utils.py#L6-L10

healthkit-to-sqlite 197882382 issue  
470856782 MDU6SXNzdWU0NzA4NTY3ODI= 6 Break up records into different tables for each type simonw 9599 closed 0     1 2019-07-22T01:54:59Z 2019-07-22T03:28:55Z 2019-07-22T03:28:50Z MEMBER  

I don't think there's much benefit to having all of the different record types stored in the same enormous table. Here's what I get when I use _facet=type:

I'm going to try splitting these up into separate tables - so HKQuantityTypeIdentifierBodyMassIndex becomes a table called rBodyMassIndex - and see if that's nicer to work with.

healthkit-to-sqlite 197882382 issue  
470637152 MDU6SXNzdWU0NzA2MzcxNTI= 2 Import workouts simonw 9599 closed 0     1 2019-07-20T05:20:21Z 2019-07-20T06:21:41Z 2019-07-20T06:21:41Z MEMBER  

From #1

healthkit-to-sqlite 197882382 issue  
470640505 MDU6SXNzdWU0NzA2NDA1MDU= 4 Import Records simonw 9599 closed 0     1 2019-07-20T06:11:20Z 2019-07-20T06:21:41Z 2019-07-20T06:21:41Z MEMBER  

From #1:

 'Record': {'attr_counts': {'creationDate': 2672233,
                            'device': 2665111,
                            'endDate': 2672233,
                            'sourceName': 2672233,
                            'sourceVersion': 2671779,
                            'startDate': 2672233,
                            'type': 2672233,
                            'unit': 2650012,
                            'value': 2672232},
            'child_counts': {'HeartRateVariabilityMetadataList': 2318,
                             'MetadataEntry': 287974},
            'count': 2672233,
            'parent_counts': {'Correlation': 2, 'HealthData': 2672231}},
healthkit-to-sqlite 197882382 issue  
470637206 MDU6SXNzdWU0NzA2MzcyMDY= 3 Import ActivitySummary simonw 9599 closed 0     0 2019-07-20T05:21:00Z 2019-07-20T05:58:07Z 2019-07-20T05:58:07Z MEMBER  

From #1

  'ActivitySummary': {'attr_counts': {'activeEnergyBurned': 980,
                                     'activeEnergyBurnedGoal': 980,
                                     'activeEnergyBurnedUnit': 980,
                                     'appleExerciseTime': 980,
                                     'appleExerciseTimeGoal': 980,
                                     'appleStandHours': 980,
                                     'appleStandHoursGoal': 980,
                                     'dateComponents': 980},
                     'child_counts': {},
                     'count': 980,
                     'parent_counts': {'HealthData': 980}},
healthkit-to-sqlite 197882382 issue  
470637068 MDU6SXNzdWU0NzA2MzcwNjg= 1 Use XML Analyser to figure out the structure of the export XML simonw 9599 closed 0     1 2019-07-20T05:19:02Z 2019-07-20T05:20:09Z 2019-07-20T05:20:09Z MEMBER  

https://github.com/simonw/xml_analyser

healthkit-to-sqlite 197882382 issue  

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