Add nallo upload #4205
Add nallo upload #4205
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…cs/cg into add_nallo_upload
|
| LOG.info( | ||
| f"Upload of case {case.internal_id} was successful. Uploaded at {dt.datetime.now()} in StatusDB" | ||
| ) | ||
| self.update_uploaded_at(analysis=analysis) |
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Maybe very minor but I thought this was done after uploads to Caesar? So after line 43?
| self.case_tags: CaseTags = CaseTags(**NALLO_CASE_TAGS) | ||
| self.sample_tags: SampleTags = SampleTags(**NALLO_SAMPLE_TAGS) |
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| self.case_tags: CaseTags = CaseTags(**NALLO_CASE_TAGS) | |
| self.sample_tags: SampleTags = SampleTags(**NALLO_SAMPLE_TAGS) | |
| self.case_tags = CaseTags(**NALLO_CASE_TAGS) | |
| self.sample_tags = SampleTags(**NALLO_SAMPLE_TAGS) |
| hk_version_obj: Version, | ||
| analysis_obj: Analysis, |
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Out of scope but I do not like designs where we tie the whole class to a single Version/Analysis. It makes it less flexible
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Also out of scope but modifying the input and making all methods return None is confusing to me. If we redesign at some point it might be nice to consider changing.
| def build_load_config(self) -> NalloLoadConfig: | ||
| """Create a NALLO specific load config for uploading analysis to Scout.""" | ||
| LOG.info("Build load config for NALLO case") | ||
| load_config: NalloLoadConfig = NalloLoadConfig( |
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| load_config: NalloLoadConfig = NalloLoadConfig( | |
| load_config = NalloLoadConfig( |
| """Include case level files for NALLO case.""" | ||
| LOG.info("Including NALLO specific case level files") | ||
| for scout_key in NALLO_CASE_TAGS.keys(): | ||
| self._include_case_file(load_config, scout_key) |
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Can we have named arguments?
| """Include the file path associated to a scout configuration parameter if the corresponding housekeeper tags | ||
| are found. Otherwise return None.""" | ||
| file_path = self.get_file_from_hk(getattr(self.case_tags, scout_key)) | ||
| setattr(load_config, scout_key, file_path) |
| samples: list[ScoutNalloIndividual] = [] | ||
| somalier_samples: str | None = None | ||
| somalier_pairs: str | None = None | ||
| vcf_snv: Annotated[str, BeforeValidator(field_not_none)] = None |
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I am very confused by us having a BeforeValidator seemingly avoiding "field not None" behaviour, but also us having a default value of None. Seems a bit contradictory to me.
You can consider it out of scope though, the pattern does not seem introduced by you.
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