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Ran black on new_service.py
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bu_isciii/new_service.py

+9-6
Original file line numberDiff line numberDiff line change
@@ -92,7 +92,9 @@ def __init__(
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def check_md5(self):
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# Path to the .md5 file
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project_name = self.service_samples[0]["project_name"]
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md5_file_path = f'{self.conf["fastq_repo"]}/{project_name}/md5sum_{project_name}.md5'
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md5_file_path = (
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f'{self.conf["fastq_repo"]}/{project_name}/md5sum_{project_name}.md5'
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)
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if not os.path.exists(md5_file_path):
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stderr.print(f"[red]ERROR: .md5 file not found at {md5_file_path}")
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sys.exit(1)
@@ -103,16 +105,17 @@ def check_md5(self):
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# Regex pattern to match sample names in .fastq.gz files
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sample_names_pattern = "|".join(
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[f"{sample['sample_name']}.*\\.fastq\\.gz" for sample in self.service_samples]
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)
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[
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f"{sample['sample_name']}.*\\.fastq\\.gz"
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for sample in self.service_samples
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]
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)
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# md5sum command
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stderr.print(f"[blue]Checking MD5 integrity for {md5_file_path}")
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try:
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cmd = f"grep -E '{sample_names_pattern}' {md5_file_path} | md5sum -c"
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subprocess.run(
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cmd, shell=True, check=True, executable='/bin/bash'
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)
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subprocess.run(cmd, shell=True, check=True, executable="/bin/bash")
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stderr.print("[green]MD5 check passed!")
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except subprocess.CalledProcessError as e:
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stderr.print(f"[red]ERROR: MD5 check failed: {e.stderr}")

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