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Refactor metaproteomics aggregation script #27

Merged
merged 16 commits into from
Dec 3, 2024
Merged

Refactor metaproteomics aggregation script #27

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c2eeb64
Start to refactor metaproteomics aggregation class
kheal Nov 7, 2024
1981145
Subclass aggregation scripts
kheal Nov 8, 2024
a828bb1
Restructure to fetch bearer token from username and pw
kheal Nov 8, 2024
226b816
Fix sweep_success function
kheal Nov 11, 2024
b02e320
Change to was_generated_by
kheal Nov 20, 2024
62b3e12
Update scripts to use single base url set as optional environmental v…
kheal Nov 20, 2024
7e726ad
Remove _dev from call
kheal Nov 25, 2024
a944777
Adjust API call for functional_annotation_agg query
kheal Nov 26, 2024
143c60c
Fix json construction
kheal Nov 27, 2024
a3d814c
Add logging for exceptions
kheal Nov 27, 2024
5767452
Lint metap agg script
kheal Nov 27, 2024
4304e6e
Modify shell to accept logging
kheal Nov 27, 2024
088fa48
feat: make regex a "prefix expression"
dwinston Nov 27, 2024
4c8fcfa
Modify FIXME note to point to new bug
kheal Dec 2, 2024
5e3e245
Remove pagination for both collection endpoint calls
kheal Dec 2, 2024
a0c81df
Fix page_token parameter in collection endpoint
kheal Dec 2, 2024
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -65,6 +65,9 @@ Now that the container image is hosted there, you can configure a Spin workload
- `POLL_TIME`: Number of seconds to sleep between each run (Default: `14400`, which is 4 hours)
- `NMDC_BASE_URL`: Base URL to access the data (Default: `https://data.microbiomedata.org/data`)
- `NMDC_BASE_PATH`: Base path to the data on disk (Default: `/global/cfs/cdirs/m3408/results`)
- `NMDC_CLIENT_ID`: Client ID for interacting with NMDC's runtime API
- `NMDC_CLIENT_PW`: Password for interacting with NMDC's runtime API
- `NMDC_API_URL`: Base url for NMCD runtime API (Default: `https://api-dev.microbiomedata.org`, which is the dev url)

## Release Notes

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