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varfish-org / varfish-cli

VarFish REST API client (CLI + Python package)
MIT License
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feat: add index option to case import #136

Closed tedil closed 2 weeks ago

tedil commented 2 weeks ago

Resolves #133

Summary by CodeRabbit

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πŸ“₯ Commits Reviewing files that changed from the base of the PR and between bce42d84411ad15765647ff2066dad32996444a8 and b6e869b73c390f570a17885effc05368c20a960b.

Walkthrough

The changes introduce a new command-line option to the cli_caseimportinfo_create function, allowing users to specify an index case in the pedigree. This is achieved by adding an optional index parameter, which is incorporated into the CaseImportOptions and CaseImporter classes. The logic for selecting the index case has been updated to use this parameter if provided, enhancing the flexibility of the case import process without altering existing functionalities.

Changes

File Path Change Summary
varfish_cli/cli/importer/init.py Added index parameter to cli_caseimportinfo_create function, allowing specification of index case.
varfish_cli/cli/importer/create.py Updated CaseImportOptions and CaseImporter classes to include index attribute; modified logic in _create_case_import_info method to use self.index if provided.

Assessment against linked issues

Objective Addressed Explanation
Add option to specify index patient during import (#133) βœ…

πŸ‡ In the meadow, where bunnies play,
A new option has come to stay.
Specify your index with ease and cheer,
No more defaults, the choice is clear!
With each import, hop with delight,
The right case chosen, everything feels right! 🌼

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Nicolai-vKuegelgen commented 2 weeks ago

If no manual index is specified, ideally the index should be assigned to the first affected sample in the pedigree, not just the first sample overall.

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 80.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 83.33%. Comparing base (878af61) to head (0e78d9b). Report is 19 commits behind head on main.

Files with missing lines Patch % Lines
varfish_cli/cli/importer/create.py 80.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #136 +/- ## ========================================== - Coverage 83.99% 83.33% -0.67% ========================================== Files 21 21 Lines 1506 1452 -54 ========================================== - Hits 1265 1210 -55 - Misses 241 242 +1 ``` | [Files with missing lines](https://app.codecov.io/gh/varfish-org/varfish-cli/pull/136?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org) | Coverage Ξ” | | |---|---|---| | [varfish\_cli/cli/importer/\_\_init\_\_.py](https://app.codecov.io/gh/varfish-org/varfish-cli/pull/136?src=pr&el=tree&filepath=varfish_cli%2Fcli%2Fimporter%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-dmFyZmlzaF9jbGkvY2xpL2ltcG9ydGVyL19faW5pdF9fLnB5) | `92.00% <ΓΈ> (-0.16%)` | :arrow_down: | | [varfish\_cli/cli/importer/create.py](https://app.codecov.io/gh/varfish-org/varfish-cli/pull/136?src=pr&el=tree&filepath=varfish_cli%2Fcli%2Fimporter%2Fcreate.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-dmFyZmlzaF9jbGkvY2xpL2ltcG9ydGVyL2NyZWF0ZS5weQ==) | `76.87% <80.00%> (-0.37%)` | :arrow_down: | ... and [17 files with indirect coverage changes](https://app.codecov.io/gh/varfish-org/varfish-cli/pull/136/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org)