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  • healthkit-to-sqlite · 1 ✖
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 reactions draft state_reason
1515883470 I_kwDOC8tyDs5aWovO 24 DOC: xml.etree.ElementTree.ParseError due to healthkit version 12 mmngreco 6231413 open 0     2 2023-01-01T23:00:38Z 2023-03-30T10:17:31Z   NONE  

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:

bash (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:

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

  2. Create a patch.txt with the following content

    ```diff --- 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
 healthkit-to-sqlite 197882382 issue     
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