Add trackusage for DRMAA jobs

Author: marcelzwiers

bidscoin/bcoin.py

@@ -14,6 +14,7 @@
 import urllib.request
 import time
 import argparse
+import re
 from duecredit.cmdline import cmd_summary
 from functools import lru_cache
 from importlib.metadata import entry_points
@@ -72,17 +73,24 @@ def drmaa_nativespec(specs: str, session) -> str:
     return specs.strip()
 
 
-def synchronize(pbatch, jobids: list, wait: int=15):
+def synchronize(pbatch, jobids: list, event: str, wait: int=15):
     """
     Shows tqdm progress bars for queued and running DRMAA jobs. Waits until all jobs have finished +
     some extra wait time to give NAS systems the opportunity to fully synchronize
 
     :param pbatch: The DRMAA session
     :param jobids: The job ids
+    :param event:  The event that is passed to trackusage()
     :param wait:   The extra wait time for the NAS
     :return:
     """
 
+    if jobids:
+        match = re.search(r"(slurm|pbs|torque|sge|lsf|condor|uge)", pbatch.drmaaImplementation.lower())
+        trackusage(f"{event}_{match.group(1) if match else 'drmaa'}")
+    else:
+        return
+
     with logging_redirect_tqdm():
 
         qbar = tqdm(total=len(jobids), desc='Queued ', unit='job', leave=False, bar_format='{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}]')

bidscoin/bidsapps/deface.py

@@ -151,7 +151,7 @@ def deface(bidsfolder: str, pattern: str, participant: list, force: bool, output
         if cluster and jobids:
             LOGGER.info('')
             LOGGER.info('Waiting for the deface jobs to finish...')
-            bcoin.synchronize(pbatch, jobids, wait=0)
+            bcoin.synchronize(pbatch, jobids, 'deface', wait=0)
             pbatch.deleteJobTemplate(jt)
 
     LOGGER.info('-------------- FINISHED! -------------')

bidscoin/bidsapps/medeface.py

@@ -131,7 +131,7 @@ def medeface(bidsfolder: str, pattern: str, maskpattern: str, participant: list,
         if cluster and jobids:
             LOGGER.info('')
             LOGGER.info('Waiting for the deface jobs to finish...')
-            bcoin.synchronize(pbatch, jobids)
+            bcoin.synchronize(pbatch, jobids, 'medeface')
             pbatch.deleteJobTemplate(jt)
 
     # Loop again over bids subject/session-directories to apply the deface-masks and write metadata

bidscoin/bidsapps/skullstrip.py

@@ -229,7 +229,7 @@ def skullstrip(bidsfolder: str, pattern: str, participant: list, masked: str, ou
         if cluster and jobids:
             LOGGER.info('')
             LOGGER.info('Waiting for the skullstrip jobs to finish...')
-            bcoin.synchronize(pbatch, jobids, wait=0)
+            bcoin.synchronize(pbatch, jobids,'skullstrip', wait=0)
             pbatch.deleteJobTemplate(jt)
 
     LOGGER.info('-------------- FINISHED! -------------')

bidscoin/bidsapps/slicereport.py

@@ -318,7 +318,7 @@ def slicereport(bidsfolder: str, pattern: str, outlinepattern: str, outlineimage
     if cluster:
         from drmaa import Session as drmaasession   # Lazy import to avoid import error on non-HPC systems
         with drmaasession() as pbatch:
-            bcoin.synchronize(pbatch, JOBIDS, 0)
+            bcoin.synchronize(pbatch, JOBIDS, 'slicereport', 0)
 
 
 def main():

bidscoin/bidscoiner.py

@@ -174,7 +174,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
                 return
 
             LOGGER.info('Waiting for the bidscoiner jobs to finish...')
-            bcoin.synchronize(pbatch, jobids)
+            bcoin.synchronize(pbatch, jobids, 'bidscoiner')
 
         # Merge the bids subfolders
         errors             = ''