Metagenomics Exchange upload command and related bookkeeping code #350
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- Refactored the cli wrapper - Refactored the settings to be in line with the rest - Modified the unit tests
The test tests/me/test_populate_metagenomics_exchange.py::TestMeAPI::test_removals_dry_mode it's working now.
…nomics/emgapi into feature/metagenomics_exchange
…ndexed This is needed because RenameField doesn't allow you to change the db_column name. With this change it seems to work, and the data should be kept: ```sql -- -- Alter field last_indexed on analysisjob -- ALTER TABLE "ANALYSIS_JOB" RENAME COLUMN "LAST_INDEXED" TO "LAST_EBI_SEARCH_INDEXED"; -- -- Alter field last_indexed on study -- ALTER TABLE "STUDY" RENAME COLUMN "LAST_INDEXED" TO "LAST_EBI_SEARCH_INDEXED"; -- -- Rename field last_indexed on analysisjob to last_ebi_search_indexed -- -- -- Rename field last_indexed on study to last_ebi_search_indexed -- ```
…change Feature/metagenomics exchange
MGS-sails
reviewed
Feb 12, 2024
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Hi @mberacochea
Thanks for doing this.
Functionally speaking it all looks fine to me.
I just left a few minor comments that could perhaps improve the code in the long term.
But I don't think they are blockers for releasing this.
emgapi/metagenomics_exchange.py
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| logging.warning(f"Get API request failed") | ||
| return analysis_registry_id , metadata_match | ||
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| if response.ok: |
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I think reducing the amount of nesting, can make this code more easier to maintain in the future.
Specifically referring to Lines: 111-141
MGS-sails
reviewed
Feb 12, 2024
SandyRogers
approved these changes
Feb 12, 2024
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Thanks folks. Nothing much to add from me, other than:
- we will need a change to the config repo to add the ME config for dev and prod.
- We now usually include an API version bump on
developso that the pip installing themasterbranch always installs the latest commit.
PR 👍 |
MGS-sails
approved these changes
Feb 13, 2024
Add support for Assembly and Run based jobs (both). Remove the public check, we only submit public data to the exchange. Normalize argument names in the MGX wrapper. Added some docstrings
The MGX API returns a json with the error message, which is useful for debugging.
…hange-bug-fixes Fixes for a few bugs I encountered while testing the command
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