DROID / IHCC-cohorts-data-harmonization / theisuru-patch-14
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Workflow
The following workflow defines all tasks necessary to upload, preprocess, share, and map a new data dictionary.
- Upload cohort data
- Open Google Sheet
- Run automated mapping for new data dictionary
- Share Google Sheet with submitter
- Prepare data dictionary for build
- Run automated validation
- Build data dictionary
- View results
- Add data dictionary to Version Control
- Prepare git commit (click on Commit in Version menu)
- Push changes to GitHub (click on Push in Version menu), and make pull request.
- Delete Google sheet (Caution, cannot be undone)
IHCC Data Admin Tasks
Console
Action all started at 2022-12-01T11:49:25.638Z (2022-12-01T11:49:25.638Z)
ERROR: Exit code 2
$ make -f Makefile all
python3 src/create_xref_template.py build/chop.tsv build/intermediate/gecko_index.tsv build/intermediate/chop-xrefs.tsv
Traceback (most recent call last):
File "src/create_xref_template.py", line 82, in <module>
main()
File "src/create_xref_template.py", line 60, in main
curie = row["ID"].strip()
KeyError: 'ID'
make: *** [Makefile:169: build/intermediate/chop-xrefs.tsv] Error 1
make: *** Deleting file 'build/intermediate/chop-xrefs.tsv'