Updating import yaml files to fix fastq.gz.md5 import issues #426
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aclum
reviewed
Mar 11, 2025
aclum
approved these changes
Mar 11, 2025
mbthornton-lbl
requested changes
Mar 12, 2025
tests/test_import_mapper.py
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| @@ -31,6 +31,8 @@ def mock_minted_ids(): | |||
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| def test_update_do_mappings_from_import_files(import_mapper_instance): | |||
| import_mapper_instance.update_do_mappings_from_import_files() | |||
| for fm_all in import_mapper_instance.mappings: | |||
| print(fm_all, "\n\n") | |||
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What is the purpose of this print statement? Can we have an assert statement that confirms that the correct files are being imported?
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I have updated the PR to include an assert statement to test no .md5 files were picked. The print statement helps while testing to quickly skim over the files that are being imported.
mbthornton-lbl
approved these changes
Mar 13, 2025
aclum
approved these changes
Mar 13, 2025
AmitBinf
deleted the
421-import-automation-in-some-cases-picks-up-the-md5-sum-file-instead-of-the-fastq-file
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Changed
import_suffixfordata_object_type: Metagenome Raw Readsinimport.yamlandimport-mt.yamlfrom -->
import_suffix: .[A,C,G,T]+-[A,C,G,T]+.fastq.gzto -->
import_suffix: \.[ACGT]+-[ACGT]+\.fastq\.gz$should resolve this issue.
\.matches a literal dot (.).[ACGT]+matches one or more occurrences of the letters A, C, G, or T.-matches a literal hyphen (-).[ACGT]+matches one or more occurrences of the letters A, C, G, or T again.\.fastq\.gzmatches the literal string .fastq.gz.$ensures that the pattern matches only at the end of the string, so it won’t match.fastq.gz.md5