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Fix depracation warnings in untargeted tools modules #926

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merged 2 commits into from
Sep 21, 2024
Merged

Fix depracation warnings in untargeted tools modules #926

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80f5f2a
Fix depracation warnings in untargeted tools modules
bkieft-usa Sep 21, 2024
4f7dea6
Merge branch 'main' into untargeted_python_env
bkieft-usa Sep 21, 2024
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23 changes: 13 additions & 10 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -339,7 +339,7 @@ def untargeted_file_rename(target_dir="", abridged_filenames=True):
submitter = old_project_name.split('_')[2]
pid = old_project_name.split('_')[3]
chromatography = old_project_name.split('_')[7]
polarity = old_project_name.split('_')[9]
polarity = old_project_name.split('_')[-1] # Sometimes things get added to the end of a project name

# Check if project name follows the standard naming convention
if not any(substring.lower() in department.lower() for substring in ['JGI', 'EB', 'EGSB']) or \
Expand Down Expand Up @@ -717,16 +717,19 @@ def update_table_in_lims(df,table,method='update',max_size=1000,pause_time=None)
whatever is in 'name' or 'Key' will replace whatever used to be there with the other columns
"""
N = math.ceil(float(df.shape[0]) / max_size)
for sub_df in np.array_split(df, N):
for i in range(N):
start_idx = i * max_size
end_idx = min((i + 1) * max_size, df.shape[0])
sub_df = df.iloc[start_idx:end_idx]
payload = sub_df.to_dict('records')
if method=='update':
api.query.update_rows('lists', table, payload,timeout=10000)
elif method=='insert':
api.query.insert_rows('lists', table, payload,timeout=10000)
elif method=='delete':
api.query.delete_rows('lists', table, payload,timeout=10000)
if method == 'update':
api.query.update_rows('lists', table, payload, timeout=10000)
elif method == 'insert':
api.query.insert_rows('lists', table, payload, timeout=10000)
elif method == 'delete':
api.query.delete_rows('lists', table, payload, timeout=10000)
else:
logging.critical(tab_print('ERROR: Nothing to do. Method %s is not programmed'%(method), 2))
logging.critical(tab_print('ERROR: Nothing to do. Method %s is not programmed' % (method), 2))
if pause_time is not None:
time.sleep(pause_time)

Expand Down Expand Up @@ -809,7 +812,7 @@ def mirror_mzmine_results_to_gnps2(project: str, polarity: str, username="bpbowe
logging.error(tab_print("Password is required to mirror data to GNPS2. Exiting", 3))
sys.exit(1)

logging.info(tab_print("Mirroring MZmine results for %s to GNPS2...", 3))
logging.info(tab_print("Mirroring MZmine results for %s to GNPS2..."%(project), 3))

project_directory = f"{project}_{polarity}"
local_directory = f"/global/cfs/cdirs/metatlas/projects/untargeted_tasks/{project_directory}"
Expand Down
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