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Convert an Apple Healthkit export zip to a SQLite database

Home Page: https://datasette.io/tools/healthkit-to-sqlite

License: Apache License 2.0

Python 100.00%

healthkit sqlite datasette dogsheep datasette-io datasette-tool

healthkit-to-sqlite's Introduction

healthkit-to-sqlite

Convert an Apple Healthkit export zip to a SQLite database

How to install

$ pip install healthkit-to-sqlite

How to use

First you need to export your Apple HealthKit data.

On your iPhone, open the "Health" app
Click the profile icon in the top right
Click "Export Health Data" at the bottom of that page
Save the resulting file somewhere you can access it, or AirDrop it directly to your laptop.

Now you can convert the resulting export.zip file to SQLite like so:

$ healthkit-to-sqlite export.zip healthkit.db

A progress bar will be displayed. You can disable this using --silent.

Importing from HealthKit  [#-------------]    5%  00:01:33

You can explore the resulting data using Datasette like this:

$ datasette healthkit.db

healthkit-to-sqlite's People

Contributors

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Forkers

cwkendall tomaskrehlik ryancheley n8henrie fabianhertwig badboy ibombonato linuxul koljamalz

healthkit-to-sqlite's Issues

Datetime columns are not properly formatted to be recognizes as datetime

Currently, the datetimes are formatted in a way that is not recognized by datasette-vega for plotting with a Date/time type for the axis.

For example, if you have datasette running locally with datasette-vega installed and have a database that includes resting heart rate:

http://localhost:8001/healthkit/rRestingHeartRate#g.mark=line&g.x_column=startDate&g.x_type=temporal&g.y_column=value&g.y_type=quantitative

The plot is blank unless you choose Label as the type for the date data.

The startDate (and creationDate and endDate) columns appear like: 2019-11-14 18:22:18 -0700

If instead the format for this column is changed slightly: 2019-11-14T18:22:18-07:00 they are recognized as proper dates and the charting works as expected.

I have a PR that addresses this issue, will submit shortly.

Too many SQL variables

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', 'Health Mate', '4040200', '2011-06-29 09:21:16 -0700', 'count', '29.9537', '2019-06-27 22:55:10 -0700', '2011-06-30 08:41:46 -0700', '0', '4.4.2', '2011-06-30 15:42:30 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309448506&type=1', '301293', 'Health Mate', '4040200', '2011-06-30 08:41:46 -0700', 'count', '29.8302', '2019-06-27 22:55:10 -0700', '2011-07-01 09:05:28 -0700', '0', '4.4.2', '2011-07-01 16:06:24 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309536328&type=1', '301293', 'Health Mate', '4040200', '2011-07-01 09:05:28 -0700', 'count', '29.8611', '2019-06-27 22:55:10 -0700', '2011-07-02 08:58:50 -0700', '0', '4.4.2', '2011-07-02 15:59:40 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309622330&type=1', '301293', 'Health Mate', '4040200', '2011-07-02 08:58:50 -0700', 'count', '29.8765', '2019-06-27 22:55:10 -0700', '2011-07-04 09:33:43 -0700', '0', '4.4.2', '2011-07-04 16:34:19 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309797223&type=1', '301293', 'Health Mate', '4040200', '2011-07-04 09:33:43 -0700', 'count', '30.0309', '2019-06-27 22:55:10 -0700', '2011-07-06 09:40:23 -0700', '0', '4.4.2', '2011-07-06 16:41:02 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1309970423&type=1', '301293', 'Health Mate', '4040200', '2011-07-06 09:40:23 -0700', 'count', '30.1852', '2019-06-27 22:55:10 -0700', '2011-07-08 08:08:48 -0700', '0', '4.4.2', '2011-07-08 15:09:51 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310137728&type=1', '301293', 'Health Mate', '4040200', '2011-07-08 08:08:48 -0700', 'count', '30.0309', '2019-06-27 22:55:10 -0700', '2011-07-09 08:31:05 -0700', '0', '4.4.2', '2011-07-09 15:31:48 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310225465&type=1', '301293', 'Health Mate', '4040200', '2011-07-09 08:31:05 -0700', 'count', '29.9537', '2019-06-27 22:55:10 -0700', '2011-07-10 08:14:36 -0700', '0', '4.4.2', '2011-07-10 15:15:12 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310310876&type=1', '301293', 'Health Mate', '4040200', '2011-07-10 08:14:36 -0700', 'count', '30.0926', '2019-06-27 22:55:10 -0700', '2011-07-12 07:55:21 -0700', '0', '4.4.2', '2011-07-12 14:55:59 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310482521&type=1', '301293', 'Health Mate', '4040200', '2011-07-12 07:55:21 -0700', 'count', '30.108', '2019-06-27 22:55:10 -0700', '2011-07-13 08:48:05 -0700', '0', '4.4.2', '2011-07-13 15:48:42 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310572085&type=1', '301293', 'Health Mate', '4040200', '2011-07-13 08:48:05 -0700', 'count', '30', '2019-06-27 22:55:10 -0700', '2011-07-14 09:05:16 -0700', '0', '4.4.2', '2011-07-14 16:05:57 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310659516&type=1', '301293', 'Health Mate', '4040200', '2011-07-14 09:05:16 -0700', 'count', '29.9074', '2019-06-27 22:55:10 -0700', '2011-07-15 07:09:56 -0700', '0', '4.4.2', '2011-07-15 14:10:35 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310738996&type=1', '301293', 'Health Mate', '4040200', '2011-07-15 07:09:56 -0700', 'count', '29.9537', '2019-06-27 22:55:10 -0700', '2011-07-16 09:26:04 -0700', '0', '4.4.2', '2011-07-16 16:26:44 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310833564&type=1', '301293', 'Health Mate', '4040200', '2011-07-16 09:26:04 -0700', 'count', '29.7531', '2019-06-27 22:55:10 -0700', '2011-07-17 09:52:59 -0700', '0', '4.4.2', '2011-07-17 16:53:38 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1310921579&type=1', '301293', 'Health Mate', '4040200', '2011-07-17 09:52:59 -0700', 'count', '29.8765', '2019-06-27 22:55:10 -0700', '2011-07-19 08:56:16 -0700', '0', '4.4.2', '2011-07-19 15:57:03 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1311090976&type=1', '301293', 'Health Mate', '4040200', '2011-07-19 08:56:16 -0700', 'count', 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'withings-bd2://timeline/measure?userid=301293&date=1355760820&type=1', '301293', 'Health Mate', '4040200', '2012-12-17 09:13:40 -0700', 'count', '29.784', '2019-06-27 22:55:10 -0700', '2012-12-19 11:09:55 -0700', '0', '4.4.2', '2012-12-19 18:10:37 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1355940595&type=1', '301293', 'Health Mate', '4040200', '2012-12-19 11:09:55 -0700', 'count', '29.6914', '2019-06-27 22:55:10 -0700', '2012-12-25 10:37:41 -0700', '0', '4.4.2', '2012-12-25 17:38:25 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1356457061&type=1', '301293', 'Health Mate', '4040200', '2012-12-25 10:37:41 -0700', 'count', '29.8765', '2019-06-27 22:55:10 -0700', '2013-01-01 10:44:02 -0700', '0', '4.4.2', '2013-01-01 17:44:46 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1357062242&type=1', '301293', 'Health Mate', '4040200', '2013-01-01 10:44:02 -0700', 'count', '30.0772', '2019-06-27 22:55:10 -0700', '2013-01-15 09:10:46 -0700', '0', 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'2013-02-07 09:07:06 -0700', '0', '4.4.2', '2013-02-07 16:07:49 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1360253226&type=1', '301293', 'Health Mate', '4040200', '2013-02-07 09:07:06 -0700', 'count', '30.1389', '2019-06-27 22:55:10 -0700', '2013-02-19 08:49:57 -0700', '0', '4.4.2', '2013-02-19 15:50:39 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1361288997&type=1', '301293', 'Health Mate', '4040200', '2013-02-19 08:49:57 -0700', 'count', '30.1235', '2019-06-27 22:55:10 -0700', '2013-03-02 11:20:54 -0700', '0', '4.4.2', '2013-03-02 18:21:38 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1362248454&type=1', '301293', 'Health Mate', '4040200', '2013-03-02 11:20:54 -0700', 'count', '30', '2019-06-27 22:55:10 -0700', '2013-04-23 08:05:30 -0700', '0', '4.4.2', '2013-04-23 15:06:59 +0000', 'withings-bd2://timeline/measure?user                    """
id=301293&date=1366729530&type=1', '301293', 'Health Mate', '4040200', '2013-04-23 08:05:30 -0700', 'count', '30.5247', '2019-06-27 22:55:10 -0700', '2013-05-09 09:49:18 -0700', '0', '4.4.2', '2013-05-09 16:50:02 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1368118158&type=1', '301293', 'Health Mate', '4040200', '2013-05-09 09:49:18 -0700', 'count', '30.4167', '2019-06-27 22:55:10 -0700', '2013-06-09 09:28:47 -0700', '0', '4.4.2', '2013-06-09 16:29:30 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1370795327&type=1', '301293', 'Health Mate', '4040200', '2013-06-09 09:28:47 -0700', 'count', '30.8333', '2019-06-27 22:55:10 -0700', '2013-07-09 08:00:17 -0700', '0', '4.4.2', '2013-07-09 15:01:00 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1373382017&type=1', '301293', 'Health Mate', '4040200', '2013-07-09 08:00:17 -0700', 'count', '30.8179', '2019-06-27 22:55:10 -0700', '2013-07-28 09:16:55 -0700', '0', '4.4.2', '2013-07-28 16:17:39 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1375028215&type=1', '301293', 'Health Mate', '4040200', '2013-07-28 09:16:55 -0700', 'count', '30.5556', '2019-06-27 22:55:10 -0700', '2013-09-13 09:22:19 -0700', '0', '4.4.2', '2013-09-13 16:23:08 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1379089339&type=1', '301293', 'Health Mate', '4040200', '2013-09-13 09:22:19 -0700', 'count', '30.9568', '2019-06-27 22:55:10 -0700', '2013-09-24 08:08:23 -0700', '0', '4.4.2', '2013-09-24 15:09:03 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1380035303&type=1', '301293', 'Health Mate', '4040200', '2013-09-24 08:08:23 -0700', 'count', '31.4352', '2019-06-27 22:55:10 -0700', '2013-10-01 08:15:13 -0700', '0', '4.4.2', '2013-10-01 15:15:57 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1380640513&type=1', '301293', 'Health Mate', '4040200', '2013-10-01 08:15:13 -0700', 'count', '31.2037', '2019-06-27 22:55:10 -0700', '2013-10-23 09:31:25 -0700', '0', '4.4.2', '2013-10-23 16:32:13 +0000', 'withings-bd2://timeline/measure?userid=301293&date=1382545885&type=1', '301293', 'Health Mate', '4040200', '2013-10-23 09:31:25 -0700', 'count', '31.8056']

UNIQUE constraint failed: workouts.id

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

Use XML Analyser to figure out the structure of the export XML

https://github.com/simonw/xml_analyser

Some workout columns should be float, not text

Columns duration, totalDistance and totalEnergyBurned should be converted to float.

healthkit-to-sqlite/healthkit_to_sqlite/utils.py

Lines 50 to 57 in 71e36e1

 def workout_to_db(workout, db, zipfile=None): 

 record = dict(workout.attrib) 

 # add metadata entry items as extra keys 

 for el in workout.findall("MetadataEntry"): 

 record["metadata_" + el.attrib["key"]] = el.attrib["value"] 

 # Dump any WorkoutEvent in a nested list for the moment 

 record["workout_events"] = [el.attrib for el in workout.findall("WorkoutEvent")] 

 pk = db["workouts"].insert(record, alter=True, hash_id="id").last_pk

Add index on workout_points.date

Sorting that by date makes sense for seeing most recent points, and my DB has 2.5m points in so it's an expensive sort!

Duplicate Column

Hey, thank you for this repo!

When I try to convert my export, I get a multiple column error. Here is the stack trace:

(.venv) (base) computer:bodyweight_app user$ healthkit-to-sqlite ./data/Health_export.zip ./data/healthkit.db
Importing from HealthKit  [###############################-----]   87%  00:00:22
Traceback (most recent call last):
  File "/MyProject/.venv/bin/healthkit-to-sqlite", line 10, in <module>
    sys.exit(cli())
  File "/MyProject/.venv/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/MyProject/.venv/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/MyProject/.venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/MyProject/.venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/MyProject/.venv/lib/python3.7/site-packages/healthkit_to_sqlite/cli.py", line 57, in cli
    convert_xml_to_sqlite(fp, db, progress_callback=bar.update, zipfile=zf)
  File "/MyProject/.venv/lib/python3.7/site-packages/healthkit_to_sqlite/utils.py", line 41, in convert_xml_to_sqlite
    write_records(records, db)
  File "/MyProject/.venv/lib/python3.7/site-packages/healthkit_to_sqlite/utils.py", line 146, in write_records
    batch_size=50,
  File "/MyProject/.venv/lib/python3.7/site-packages/sqlite_utils/db.py", line 2579, in insert_all
    extracts=extracts,
  File "/MyProject/.venv/lib/python3.7/site-packages/sqlite_utils/db.py", line 1246, in create
    extracts=extracts,
  File "/MyProject/.venv/lib/python3.7/site-packages/sqlite_utils/db.py", line 767, in create_table
    self.execute(sql)
  File "/MyProject/.venv/lib/python3.7/site-packages/sqlite_utils/db.py", line 421, in execute
    return self.conn.execute(sql)
sqlite3.OperationalError: duplicate column name: metadata_Meal

export.xml file name varies with different language settings

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.

Import ActivitySummary

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}},

table activity_summary has no column named appleMoveTime

Got this error today against a fresh export:

table activity_summary has no column named appleMoveTime

Failed to import workout points

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

Add progress bar

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:

healthkit-to-sqlite/healthkit_to_sqlite/utils.py

Lines 6 to 10 in d642997

 while True: 

 chunk = fp.read(1024 * 1024 * 8) 

 if not chunk: 

 break 

 parser.feed(chunk)

Import Records

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}},

Break up records into different tables for each type

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.

DOC: xml.etree.ElementTree.ParseError due to healthkit version 12

Hi @simonw

I hope you find this issue ok, the idea is provide some documentation to other users like me about how to solve this problem and save some time.

Following the instructions from the README.md I've faced this error:

(venv) mgreco@pop-os apple-health master* (23:44|0s)
$ healthkit-to-sqlite apple_health_export/export.xml healthkit.db --xml
Importing from HealthKit  [------------------------------------]    0%
Traceback (most recent call last):
  File "/home/mgreco/github/mmngreco/apple-health/venv/bin/healthkit-to-sqlite", line 33, in <module>
    sys.exit(load_entry_point('healthkit-to-sqlite', 'console_scripts', 'healthkit-to-sqlite')())
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/mgreco/github/mmngreco/apple-health/.deps/healthkit-to-sqlite/healthkit_to_sqlite/cli.py", line 57, in cli
    convert_xml_to_sqlite(fp, db, progress_callback=bar.update, zipfile=zf)
  File "/home/mgreco/github/mmngreco/apple-health/.deps/healthkit-to-sqlite/healthkit_to_sqlite/utils.py", line 25, in convert_xml_to_sqlite
    for tag, el in find_all_tags(
  File "/home/mgreco/github/mmngreco/apple-health/.deps/healthkit-to-sqlite/healthkit_to_sqlite/utils.py", line 12, in find_all_tags
    for event, el in parser.read_events():
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/xml/etree/ElementTree.py", line 1324, in read_events
    raise event
  File "/home/mgreco/github/mmngreco/apple-health/venv/lib/python3.10/xml/etree/ElementTree.py", line 1296, in feed
    self._parser.feed(data)
xml.etree.ElementTree.ParseError: syntax error: line 156, column 0

So, after debugging and searching on internet I found this useful link: https://discussions.apple.com/thread/254202523 (etresoft, the real hero). Which basically says that the xml given by the health app (healthkit version 12) has some bugs but fortunately, they can be solved with a couple of commads:

Uncompress the zip and move the new folder where export.xml is.

Create a patch.txt with the following content

--- export.xml	2022-09-18 15:17:09.000000000 -0400
+++ export-fixed.xml	2022-09-18 16:37:08.000000000 -0400
@@ -15,6 +15,7 @@
   HKCharacteristicTypeIdentifierBiologicalSex       CDATA #REQUIRED
   HKCharacteristicTypeIdentifierBloodType           CDATA #REQUIRED
   HKCharacteristicTypeIdentifierFitzpatrickSkinType CDATA #REQUIRED
+  HKCharacteristicTypeIdentifierCardioFitnessMedicationsUse CDATA #IMPLIED
 >
 <!ELEMENT Record ((MetadataEntry|HeartRateVariabilityMetadataList)*)>
 <!ATTLIST Record
@@ -39,7 +40,7 @@
   startDate     CDATA #REQUIRED
   endDate       CDATA #REQUIRED
 >
-<!ELEMENT Workout ((MetadataEntry|WorkoutEvent|WorkoutRoute)*)>
+<!ELEMENT Workout ((MetadataEntry|WorkoutEvent|WorkoutRoute|WorkoutStatistics)*)>
 <!ATTLIST Workout
   workoutActivityType   CDATA #REQUIRED
   duration              CDATA #IMPLIED
@@ -63,7 +64,7 @@
   duration             CDATA #IMPLIED
   durationUnit         CDATA #IMPLIED
 >
-<!ELEMENT WorkoutEvent EMPTY>
+<!ELEMENT WorkoutEvent (MetadataEntry?)>
 <!ATTLIST WorkoutEvent
   type                 CDATA #REQUIRED
   date                 CDATA #REQUIRED
@@ -79,6 +80,7 @@
   minimum              CDATA #IMPLIED
   maximum              CDATA #IMPLIED
   sum                  CDATA #IMPLIED
+  unit                 CDATA #IMPLIED
 >
 <!ELEMENT WorkoutRoute ((MetadataEntry|FileReference)*)>
 <!ATTLIST WorkoutRoute
@@ -153,6 +155,7 @@
   dateIssued       CDATA #REQUIRED
   expirationDate   CDATA #REQUIRED
   brand            CDATA #IMPLIED
+>
 <!ELEMENT RightEye EMPTY>
 <!ATTLIST RightEye
   sphere           CDATA #IMPLIED
@@ -203,13 +206,6 @@
   diameter         CDATA #IMPLIED
   diameterUnit     CDATA #IMPLIED
 >
-  device           CDATA #IMPLIED
-<!ELEMENT MetadataEntry EMPTY>
-<!ATTLIST MetadataEntry
-  key              CDATA #IMPLIED
-  value            CDATA #IMPLIED
->
->
 ]>
 <HealthData>
  <ExportDate/>

Apply the path with the command: patch < patch.txt
Fix endDates with the command sed 's/startDate/endDate/2' export.xml > export-fixed.xml
Try again healthkit-to-sqlite export-fixed.xml healthkit.db --xml

Script uses a lot of RAM

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.

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	def workout_to_db(workout, db, zipfile=None):
	record = dict(workout.attrib)
	# add metadata entry items as extra keys
	for el in workout.findall("MetadataEntry"):
	record["metadata_" + el.attrib["key"]] = el.attrib["value"]
	# Dump any WorkoutEvent in a nested list for the moment
	record["workout_events"] = [el.attrib for el in workout.findall("WorkoutEvent")]
	pk = db["workouts"].insert(record, alter=True, hash_id="id").last_pk

	while True:
	chunk = fp.read(1024 * 1024 * 8)
	if not chunk:
	break
	parser.feed(chunk)