Fix study/sample metadata updates not updating permissions #318
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The documentation in npg_irods.cli.update_secondary_metadata states that the code can be used for Illumina and ONT data, while we are extending the use to any arbitrary platform. Could the documentation be extended please. |
The enhance-secondary-metadata was omitting permission updates when updating metadata. It was also almost duplicating functions already present in update-secondary-metadata. Remove the enhance-secondary-metadata script. Add a clause to the update-secondary-metadata case statement to capture the cases covered by enhance_secondary_metadata. Refactor to remove duplicate code. Update fixtures and tests with more descriptive names.
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mgcam
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Jun 6, 2024
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It's good to drop code repetitions. Please see a suggestion for a minor change.
@nerdstrike has run the code for Elembio data - thank you, @nerdstrike
| @@ -46,6 +52,7 @@ class Platform(Enum): | |||
| """An analysis platform (instrument or analysis technology), named by manufacturing | |||
| company.""" | |||
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| OTHER = 0 | |||
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For completeness, Elembio platform should be added.
Update the iRODS path for Ultima Genomics from "ug" to "ultimagen"
mgcam
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Jun 6, 2024
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The enhance-secondary-metadata was omitting permission updates when updating metadata. It was also almost duplicating functions already present in update-secondary-metadata.
Remove the enhance-secondary-metadata script.
Add a clause to the update-secondary-metadata case statement to capture the cases covered by enhance_secondary_metadata.
Refactor to remove duplicate code.
Update fixtures and tests with more descriptive names.