Create MutantSampleFileFormatter

[ChrOertlin]

Description

Create class MutantSampleNameGenerator

1. Create sample file names for mutant sample files

Reason: since we require to rename files in the upload as well as delivery this module should be atomic as possible for re-use.

Create class MutantSampleFileFormatter

responsibilities

1. create sample folders
2. create sample file names
3. rename sample files with appropriate names
4. Needs to concatenate fastq files
5. Make use of MutantSampleNameGenerator

Implementation

Create class MutantFileFormatter that inherit SampleFileConcatenationFormatter

init super (requires concatenation service)
inject lims api

def format_files()
    formatted_files = super().format_files
    meta_data_files= _add_lims_meta_data(formatted_files)
    return self._format_sample_files(meta_data_files)

Add function s

def _add_lims_metadata():
# for sample file in formatted_files.sample_file
# call get lims meta data(sample_id)

    def get_lims_naming_metadata(self, sample_id -> str | None:
        region_code = self.lims_api.get_sample_attribute(
            lims_id=sample.internal_id, key="region_code"
        ).split(" ")[0]
        lab_code = self.lims_api.get_sample_attribute(
            lims_id=sample.internal_id, key="lab_code"
        ).split(" ")[0]

        return f"{region_code}_{lab_code}"

[Vince-janv]

Current naming is done by this function: cg.meta.workflow.fastq.FastqHandler.get_concatenated_name

[Vince-janv]

We should compare the new directory structure with the current one and notify the customer (via KN or MAR) if this will change. Just to not crash any automation they might have

[Vince-janv]

Can you add that the FASTQ files should be concatenated?