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Skip download logging for completed projects so it doesn't fill log out #984

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merged 2 commits into from
Nov 14, 2024
Merged

Skip download logging for completed projects so it doesn't fill log out #984

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7735ea5
Skip download logging for completed projects so it doesn't fill log out
bkieft-usa Nov 14, 2024
3b35d73
Merge branch 'main' into untargeted_dev
bkieft-usa Nov 14, 2024
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38 changes: 18 additions & 20 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -656,22 +656,8 @@ def download_fbmn_results(
if polarity_list is None:
logging.warning(tab_print("Warning! Project %s does not have a negative or a positive polarity directory. Skipping..."%(project_name), 1))
continue

logging.info(tab_print("Working on project %s:"%(project_name), 1))
for polarity in polarity_list:
polarity_short = polarity[:3]

# Bail out conditions
if row['%s_%s_status'%(tasktype,polarity_short)] == '12 not relevant':
logging.info(tab_print("Bailed out because FBMN status for %s mode is '12 not relevant'. Skipping download."%(polarity), 1))
continue
if row['%s_%s_status'%(tasktype,polarity_short)] != '07 complete' and row['%s_%s_status'%("mzmine",polarity_short)] != '07 complete':
logging.info(tab_print("Bailed out because FBMN and/or MZmine status for %s mode is not '07 complete'. Skipping download."%(polarity), 1))
continue # skip this polarity even if the other one is finished
if row['%s_%s_status'%(tasktype,polarity_short)] == '09 error':
logging.info(tab_print("Bailed out because FBMN status for %s mode is '09 error'. Not downloading files."%(polarity), 1))
continue

pathname = os.path.join(output_dir,'%s_%s'%(project_name,polarity))
fbmn_filename = os.path.join(pathname,'%s_%s_gnps2-fbmn-task.txt'%(project_name,polarity))
if os.path.isfile(fbmn_filename)==True:
Expand All @@ -681,26 +667,38 @@ def download_fbmn_results(
results_table_filename = os.path.join(pathname,'%s_%s_gnps2-fbmn-library-results.tsv'%(project_name,polarity))
gnps2_link_filename = os.path.join(pathname,'%s_%s_gnps2-page-link.txt'%(project_name,polarity))
if overwrite_fbmn==False and os.path.exists(graphml_filename) and os.path.exists(results_table_filename) and os.path.exists(gnps2_link_filename):
continue # Skip finished projects unless overwrite is forced
# Bail out conditions
logging.info(tab_print("Working on project %s:"%(project_name), 1))
if row['%s_%s_status'%(tasktype,polarity_short)] == '12 not relevant':
logging.info(tab_print("Bailed out because FBMN status for %s mode is '12 not relevant'. Skipping download."%(polarity), 2))
continue
logging.info(tab_print("Downloading %s mode FBMN results for %s with task ID %s"%(polarity,project_name,taskid), 1))
if row['%s_%s_status'%(tasktype,polarity_short)] != '07 complete' and row['%s_%s_status'%("mzmine",polarity_short)] != '07 complete':
logging.info(tab_print("Bailed out because FBMN and/or MZmine status for %s mode is not '07 complete'. Skipping download."%(polarity), 2))
continue # skip this polarity even if the other one is finished
if row['%s_%s_status'%(tasktype,polarity_short)] == '09 error':
logging.info(tab_print("Bailed out because FBMN status for %s mode is '09 error'. Not downloading files."%(polarity), 2))
continue

logging.info(tab_print("Downloading %s mode FBMN results with task ID %s"%(polarity,taskid), 2))
if overwrite_fbmn == True or not os.path.exists(gnps2_link_filename):
with open(gnps2_link_filename,'w') as fid:
fid.write(f"https://gnps2.org/status?task={taskid}\n")
logging.info(tab_print("Wrote GNPS2 link", 2))
logging.info(tab_print("Wrote GNPS2 link", 3))
if overwrite_fbmn == True or not os.path.exists(graphml_filename):
graphml_download = download_from_url("https://gnps2.org/result?task=%s&viewname=graphml&resultdisplay_type=task"%(taskid), graphml_filename)
if graphml_download:
logging.info(tab_print("Downloaded graphml file", 2))
logging.info(tab_print("Downloaded graphml file", 3))
count += 1
else:
logging.critical(tab_print("Error: Failed to download graphml file", 2))
logging.critical(tab_print("Error: Failed to download graphml file", 3))
if overwrite_fbmn == True or not os.path.exists(results_table_filename):
results_table_download = download_from_url("https://gnps2.org/resultfile?task=%s&file=nf_output/library/merged_results_with_gnps.tsv"%(taskid), results_table_filename)
if results_table_download:
logging.info(tab_print("Downloaded result table file", 2))
logging.info(tab_print("Downloaded result table file", 3))
count += 1
else:
logging.critical(tab_print("Error: Failed to download results table", 2))
logging.critical(tab_print("Error: Failed to download results table", 3))
try:
recursive_chown(pathname, 'metatlas')
except:
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