Bugfix

Donders-Institute · Jun 24, 2024 · ee81082 · ee81082
1 parent 7ed6564
commit ee81082
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Showing 6 changed files with 13 additions and 15 deletions.
diff --git a/bidscoin/bcoin.py b/bidscoin/bcoin.py
@@ -51,20 +51,18 @@ def update_to(self, b=1, bsize=1, tsize=None):
         self.update(b * bsize - self.n)  # will also set self.n = b * bsize
 
 
-def drmaa_nativespec(specs: str) -> str:
+def drmaa_nativespec(specs: str, session) -> str:
     """
     Converts native Torque walltime and memory specifications to the DRMAA implementation (currently only Slurm is supported)
 
-    :param specs: Native Torque walltime and memory specifications, e.g. '-l walltime=00:10:00,mem=2gb'
-    :return:      The converted native specifications
+    :param specs:   Native Torque walltime and memory specifications, e.g. '-l walltime=00:10:00,mem=2gb'
+    :param session: The DRMAA session
+    :return:        The converted native specifications
     """
 
-    import drmaa    # Lazy import to avoid import error on non-HPC systems
+    jobmanager = session.drmaaImplementation
 
-    with drmaa.Session() as session:
-        implementation = session.drmaaImplementation
-
-    if 'Slurm' in implementation and '-l ' in specs:
+    if 'Slurm' in jobmanager and '-l ' in specs:
         specs = (specs.replace('-l ', '')
                       .replace(',', ' ')
                       .replace('walltime', '--time')

diff --git a/bidscoin/bidsapps/deface.py b/bidscoin/bidsapps/deface.py
@@ -70,7 +70,7 @@ def deface(bidsfolder: str, pattern: str, participant: list, force: bool, output
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
             jt.remoteCommand       = shutil.which('pydeface')
-            jt.nativeSpecification = drmaa_nativespec(cluster)
+            jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
 
         # Loop over bids subject/session-directories

diff --git a/bidscoin/bidsapps/medeface.py b/bidscoin/bidsapps/medeface.py
@@ -76,7 +76,7 @@ def medeface(bidsfolder: str, pattern: str, maskpattern: str, participant: list,
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
             jt.remoteCommand       = shutil.which('pydeface')
-            jt.nativeSpecification = drmaa_nativespec(cluster)
+            jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
 
         # Loop over bids subject/session-directories to first get all the echo-combined deface masks

diff --git a/bidscoin/bidsapps/skullstrip.py b/bidscoin/bidsapps/skullstrip.py
@@ -84,7 +84,7 @@ def skullstrip(bidsfolder: str, pattern: str, participant: list, masked: str, ou
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
             jt.remoteCommand       = shutil.which('mri_synthstrip')
-            jt.nativeSpecification = drmaa_nativespec(cluster)
+            jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
 
         # Loop over bids subject/session-directories

diff --git a/bidscoin/bidsapps/slicereport.py b/bidscoin/bidsapps/slicereport.py
@@ -123,13 +123,13 @@ def slicer_append(inputimage: Path, operations: str, outlineimage: Path, mainopt
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
             jt.remoteCommand       = str(script)
-            jt.nativeSpecification = drmaa_nativespec(cluster)
+            jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
             jt.jobName             = 'slicereport'
             jt.outputPath          = f"{os.getenv('HOSTNAME')}:{workdir}/{jt.jobName}.out"
             jobid                  = pbatch.runJob(jt)
-        pbatch.deleteJobTemplate(jt)
-        LOGGER.info(f"Your slicereport job has been submitted with ID: {jobid}")
+            pbatch.deleteJobTemplate(jt)
+            LOGGER.info(f"Your slicereport job has been submitted with ID: {jobid}")
 
     else:
         LOGGER.bcdebug(f"Command: {command}")

diff --git a/bidscoin/bidscoiner.py b/bidscoin/bidscoiner.py
@@ -143,7 +143,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
             jt                     = pbatch.createJobTemplate()
             jt.jobEnvironment      = os.environ
             jt.remoteCommand       = shutil.which('bidscoiner') or __file__
-            jt.nativeSpecification = drmaa_nativespec(cluster)
+            jt.nativeSpecification = drmaa_nativespec(cluster, pbatch)
             jt.joinFiles           = True
             jobids                 = []