SN DSA Release #277
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SN DSA Release #277
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The tests are failing. I think it's related to your latest change |
| @@ -750,14 +752,20 @@ def get_sex_abbreviation(sex: str) -> str: | |||
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| def get_sequencing_and_assay_codes( | |||
| file: List[Dict[str, Any]], | |||
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Is this correct? Is it a list?
| @@ -816,7 +824,9 @@ def get_analysis( | |||
| software_and_versions, reference_genome_code | |||
| ) | |||
| if file_format_utils.is_chain_file(file_extension): | |||
| value = f"{value}{ANALYSIS_INFO_SEPARATOR}{get_chain_file_value(file)}" | |||
| value = ANALYSIS_INFO_SEPARATOR.join([value,get_chain_file_value(file)]) if value else get_chain_file_value(file) | |||
| if file_format_utils.is_fasta_file(file_extension): | |||
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Not quite sure I understand. You are only testing for fasta file here. Do you always want to appenddsa in that case?
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Great point. I'll add a specification for only DSA fasta files
src/encoded/commands/release_file.py
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| file_constants.DATASET: dataset, | ||
| file_constants.ACCESS_STATUS: access_status, | ||
| file_constants.ANNOTATED_FILENAME: annotated_filename_info.filename, | ||
| } | ||
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| if not supp_file_utils.is_reference_conversion(self.file) and not supp_file_utils.is_reference_genome(self.file): |
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You are making this check already in get_file_sets_from_file. Should we just test here if file_set_accessions is empty?
alexander-veit
approved these changes
Dec 19, 2024
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In
commands/release-file.pyandcommands/create-annotated-filenames.py:haplotype,target_assembly, andsource_assemblyproperties to create annotated filenames for chain and fasta files