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Clinical-Genomics / cg / 8815980126
86%

Build:
DEFAULT BRANCH: master
Ran 24 Apr 2024 11:48AM UTC
Jobs 1
Files 539
Run time 1min
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24 Apr 2024 11:45AM UTC coverage: 84.424% (-0.005%) from 84.429%
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Unify models FlowCellSample and FlowCellBclConvertSample (#3171)

## Description
Remove the model `FlowCellBcl2FastqSample` from cg. Also remove the inheritance model in FlowCellSample, renaming `FlowCellBclConvertSample` to `FlowCellSample`.

### Changed

- Removed `FlowCellSampleBcl2Fastq` and its usages.
- Rename `FlowCellBclConvertSample` to `FlowCellSample`
- Update of usages of abstract class `FlowCellSample`
- The translation of the sample sheet no longer checks if the sample sheet is Bcl2Fastq. If it is not in the correct format, it will just fail sample validation. The checking passed from using `_is_sample_sheet_from_flow_cell_translatable` to directly calling `_are_necessary_files_in_flow_cell`.
- This makes the methods `_is_sample_sheet_bcl2fastq` and `_is_sample_sheet_from_flow_cell_translatable` unused, so they were removed
- Removed Bcl2Fastq-specific index functions and constants in `cg/apps/demultiplex/sample_sheet/index.py`.
- Removed function `get_sample_type_from_content` as we only. use one flow cell sample type (BCLConvert)
- Changed function `get_flow_cell_samples_from_content` so that it no longer receives a sample type as parameter, it uses BCLConvert always
- Removed unused models `SampleSheetBcl2Fastq` and `SampleSheetBCLConvert`
- Modified all functions that took a sample type as parameter to use only BCLConvert
- Removed test functions and fixtures related to removed classes and functions

24 of 25 new or added lines in 7 files covered. (96.0%)

19475 of 23068 relevant lines covered (84.42%)

0.84 hits per line

Jobs
ID Job ID Ran Files Coverage
1 8815980126.1 24 Apr 2024 11:48AM UTC 0
84.42
Source Files on build 8815980126
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