chore: 🔨 outline pytask flow for staging data#152
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martonvago
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Jul 2, 2026
| env_key="REDC_CPH_API_KEY", url="https://redcap.regionh.dk/api/" | ||
| ) | ||
| Odense = APIConfig(env_key="REDC_ODN_API_KEY", url="https://redcap.sdu.dk/api/") | ||
| Test = APIConfig(env_key="TEST_API_KEY", url="https://redcap.au.dk/api/") |
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Can this live here for testing?
martonvago
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Jul 2, 2026
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This is all stuff we had before
lwjohnst86
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Jul 2, 2026
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Hmm, there are too many things going on here in this PR. Can you start very small, with just a task for downloading the dictionary? Then build PRs from there that add one task at a time?
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I was thinking that seeing the whole flow with the function stubs is useful, but if not then sure!
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martonvago
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Jul 2, 2026
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If we don't want to keep passing the paths around that declare task dependencies, we can move them into a data catalog
martonvago
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Jul 2, 2026
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| def task_download_data( | ||
| raw_data_dir: Annotated[ | ||
| Path, | ||
| DirectoryNode(root_dir=RAW_REDCAP, pattern="*.csv.gz"), | ||
| Product, | ||
| ], | ||
| ) -> None: | ||
| """Download the latest data from all centers to `RAW_REDCAP/<timestamp>.csv.gz`.""" | ||
| for center in [Center.Copenhagen]: | ||
| download_redcap_data(raw_data_dir, center) |
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Some notes here:
- Dealing with the different centers is a work in progress, but this is a nod in that direction
- pytask doesn't have an "always run this task" option, so data download will only run on
uv run pytaskif theRAW_REDCAPfolder is empty. We can force execution with e.g.
uv run pytask -k download_data --force
uv run pytask
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Closing in favour of #153 |
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Description
This PR outlines how the pytask pipeline could be structured for staging data (see
build.py). I pulled out some common code (dealing with the API, reading/writing JSON) to make the structure clearer.I deliberately removed the implementation of the tasks to focus on where things should be saved and how the tasks should be organised. There is a working draft of the implementation on https://github.com/onlimit-study/feasibility-data/tree/feat/pytask-wip if it's helpful.
Closes #97
Needs a thorough review.
Checklist
just run-all-- well, bits of it