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Handle exceptions when FBMN fails and reattempt submission #989

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merged 2 commits into from
Nov 15, 2024
Merged

Handle exceptions when FBMN fails and reattempt submission #989

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a9349b5
Handle exceptions when FBMN fails and reattempt submission
bkieft-usa Nov 15, 2024
60d39fe
Merge branch 'main' into untargeted_dev
bkieft-usa Nov 15, 2024
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4 changes: 3 additions & 1 deletion metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1290,15 +1290,16 @@ def submit_fbmn_jobs(
subdir = raw_data_subdir

# Get mzmine results files and raw data to GNPS2 before starting FBMN job
logging.info(tab_print("Ensuring MZmine results are at GNPS2 before submitting FBMN job...", 2))
if skip_mirror_mzmine_results is False:
logging.info(tab_print("Ensuring MZmine results are at GNPS2 before submitting FBMN job...", 2))
mirror = mirror_mzmine_results_to_gnps2(project=project_name,polarity=polarity,output_dir=output_dir,username="bpbowen")
if mirror == "Failed":
logging.warning(tab_print("Skipping FBMN submission for %s mode because of MZmine results upload failure"%(polarity), 3))
continue
else:
logging.info(tab_print("Skipping MZmine results mirroring to GNPS2...", 2))
if skip_mirror_raw_data is False:
logging.info(tab_print("Ensuring raw mzML data are at GNPS2 before submitting FBMN job...", 2))
mirror = mirror_raw_data_to_gnps2(project=project_name,polarity=polarity,username="bpbowen",raw_data_dir=raw_data_dir,raw_data_subdir=subdir)
if mirror == "Failed":
logging.info(tab_print("Notice! Proceeding with FBMN submission for %s mode even though raw data mirror failed"%(polarity), 3))
Expand All @@ -1315,6 +1316,7 @@ def submit_fbmn_jobs(
if mgf_lines == 0:
logging.info(tab_print("Note! MGF file in %s mode has no MSMS data. Updating FBMN status to '12 not relevant'"%(polarity), 2))
df.loc[i,'%s_%s_status'%(tasktype,polarity_short)] = '12 not relevant'
index_list.append(i)
continue
params = set_fbmn_parameters(description, quant_file, spectra_file, metadata_file, raw_data)
job_id = submit_quickstart_fbmn(params, "bpbowen")
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