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  • healthkit-to-sqlite · 15
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 performed_via_github_app
793907673 MDExOlB1bGxSZXF1ZXN0NTYxNTEyNTAz 15 added try / except to write_records ryancheley 9857779 open 0     0 2021-01-26T03:56:21Z 2021-01-26T03:56:21Z   FIRST_TIME_CONTRIBUTOR dogsheep/healthkit-to-sqlite/pulls/15

to keep the data write from failing if it came across an error during processing. In particular when trying to convert my HealthKit zip file (and that of my wife's) it would consistently error out with the following:

db.py 1709 insert_chunk
result = self.db.execute(query, params)

db.py 226 execute
return self.conn.execute(sql, parameters)

sqlite3.OperationalError:
too many SQL variables

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
db.py 1709 insert_chunk
result = self.db.execute(query, params)

db.py 226 execute
return self.conn.execute(sql, parameters)

sqlite3.OperationalError:
too many SQL variables

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
db.py 1709 insert_chunk
result = self.db.execute(query, params)

db.py 226 execute
return self.conn.execute(sql, parameters)

sqlite3.OperationalError:
table rBodyMass has no column named metadata_HKWasUserEntered

---------------------------------------------------------------------------------------------------------------------------------------------------------------------
healthkit-to-sqlite 8 <module>
sys.exit(cli())

core.py 829 __call__
return self.main(*args, **kwargs)

core.py 782 main
rv = self.invoke(ctx)

core.py 1066 invoke
return ctx.invoke(self.callback, **ctx.params)

core.py 610 invoke
return callback(*args, **kwargs)

cli.py 57 cli
convert_xml_to_sqlite(fp, db, progress_callback=bar.update, zipfile=zf)

utils.py 42 convert_xml_to_sqlite
write_records(records, db)

utils.py 143 write_records
db[table].insert_all(

db.py 1899 insert_all
self.insert_chunk(

db.py 1720 insert_chunk
self.insert_chunk(

db.py 1720 insert_chunk
self.insert_chunk(

db.py 1714 insert_chunk
result = self.db.execute(query, params)

db.py 226 execute
return self.conn.execute(sql, parameters)

sqlite3.OperationalError:
table rBodyMass has no column named metadata_HKWasUserEntered

Adding the try / except in the write_records seems to fix that issue.

healthkit-to-sqlite 197882382 pull    
771608692 MDU6SXNzdWU3NzE2MDg2OTI= 14 UNIQUE constraint failed: workouts.id n8henrie 1234956 open 0     0 2020-12-20T15:11:20Z 2020-12-20T15:11:20Z   NONE  

I'm getting an error on my initial attempt to import data:

$ healthkit-to-sqlite 20201119\ healthkit\ export.zip healthkit.db
Importing from HealthKit  [###################################-]   98%  00:00:01
Traceback (most recent call last):
  File "venv/bin/healthkit-to-sqlite", line 8, in <module>
    sys.exit(cli())
  File "venv/lib/python3.9/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "venv/lib/python3.9/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "venv/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "venv/lib/python3.9/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "venv/lib/python3.9/site-packages/healthkit_to_sqlite/cli.py", line 57, in cli
    convert_xml_to_sqlite(fp, db, progress_callback=bar.update, zipfile=zf)
  File "venv/lib/python3.9/site-packages/healthkit_to_sqlite/utils.py", line 34, in convert_xml_to_sqlite
    workout_to_db(el, db, zipfile)
  File "venv/lib/python3.9/site-packages/healthkit_to_sqlite/utils.py", line 57, in workout_to_db
    pk = db["workouts"].insert(record, alter=True, hash_id="id").last_pk
  File "venv/lib/python3.9/site-packages/sqlite_utils/db.py", line 1660, in insert
    return self.insert_all(
  File "venv/lib/python3.9/site-packages/sqlite_utils/db.py", line 1778, in insert_all
    self.insert_chunk(
  File "venv/lib/python3.9/site-packages/sqlite_utils/db.py", line 1588, in insert_chunk
    result = self.db.execute(query, params)
  File "venv/lib/python3.9/site-packages/sqlite_utils/db.py", line 213, in execute
    return self.conn.execute(sql, parameters)
sqlite3.IntegrityError: UNIQUE constraint failed: workouts.id
healthkit-to-sqlite 197882382 issue    
743071410 MDExOlB1bGxSZXF1ZXN0NTIxMDU0NjEy 13 SQLite does not have case sensitive columns tomaskrehlik 1689944 open 0     0 2020-11-14T20:12:32Z 2020-11-14T20:12:32Z   FIRST_TIME_CONTRIBUTOR dogsheep/healthkit-to-sqlite/pulls/13

This solves a weird issue when there is record with metadata key
that is only different in letter cases.

See the test for details.

healthkit-to-sqlite 197882382 pull    
727848625 MDU6SXNzdWU3Mjc4NDg2MjU= 12 Some workout columns should be float, not text simonw 9599 open 0     0 2020-10-23T02:47:02Z 2020-10-23T02:47:02Z   MEMBER   healthkit-to-sqlite 197882382 issue    
723838331 MDU6SXNzdWU3MjM4MzgzMzE= 11 export.xml file name varies with different language settings jarib 572 closed 0     7 2020-10-17T20:07:18Z 2020-10-17T21:39:15Z 2020-10-17T21:14:10Z NONE  

The XML file exported from my phone has a Norwegian file name – eksport.xml 🙄

I can work around this by unpacking the zip and using --xml, but then I lose the workout points.

Perhaps this could be solved by --localized-xml eksport.xml? Alternatively just fall back to the first XML file in the root folder of the zip.

healthkit-to-sqlite 197882382 issue    
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:

https://user-images.githubusercontent.com/9599/61601118-e2f54d00-abe8-11e9-8bf6-3df2ef969112.png">

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   healthkit-to-sqlite 197882382 issue    

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