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Allow for sync from LIMS to NERSC to occur even when --direct_input is supplied #955

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merged 2 commits into from
Oct 10, 2024
Merged

Allow for sync from LIMS to NERSC to occur even when --direct_input is supplied #955

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6aaef79
Allow for sync from LIMS to NERSC to occur even when --direct_input i…
bkieft-usa Oct 10, 2024
551e70b
Merge branch 'main' into untargeted_dev
bkieft-usa Oct 10, 2024
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2 changes: 1 addition & 1 deletion metatlas/untargeted/run_untargeted_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def main():
logging.info(f'Arguments used: {args}')

##### Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list
new_projects = mzm.update_new_untargeted_tasks(validate_names=args.validate_names, direct_input=args.direct_input,\
new_projects = mzm.update_new_untargeted_tasks(validate_names=args.validate_names, \
output_dir=args.output_dir, raw_data_dir=args.raw_data_dir, raw_data_subdir=args.raw_data_subdir, \
background_designator=args.background_designator,skip_sync=step_bools[0])

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6 changes: 1 addition & 5 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -385,7 +385,7 @@ def rename_untargeted_files_in_archive(
pid = project_name.split('_')[3]
chromatography = project_name.split('_')[7]
else:
logging.warning(tab_print("Warning! Project name %s has fewer than expected fields. Skipping renaming files before zip..."%(project_name), 1))
logging.info(tab_print("Note! Project name %s has fewer than expected fields. Skipping renaming files before zip..."%(project_name), 1))
return

# Check if project name follows the standard naming convention
Expand Down Expand Up @@ -1883,7 +1883,6 @@ def update_new_untargeted_tasks(
validate_names: bool,
skip_sync: bool,
output_dir: str,
direct_input: Optional[str] = None,
raw_data_dir: Optional[str] = None,
raw_data_subdir: Optional[str] = None
) -> None:
Expand All @@ -1901,9 +1900,6 @@ def update_new_untargeted_tasks(
if skip_sync:
logging.info('Skipping Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...')
return
if direct_input is not None:
logging.info('Skipping Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...')
return
logging.info('Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...')
# Get lcmsrun table and subset
df = get_table_from_lims('lcmsrun_plus')
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