Also track exceptions

Donders-Institute · Sep 29, 2023 · 36492df · 36492df
1 parent 008011d
commit 36492df
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Showing 12 changed files with 177 additions and 116 deletions.
diff --git a/bidscoin/bcoin.py b/bidscoin/bcoin.py
@@ -524,6 +524,7 @@ def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins
 
     if not success:
         LOGGER.warning('Not all tests finishd successfully (this may be ok, but check the output above)')
+        trackusage('bidscoin_error')
     else:
         LOGGER.success('All tests finished successfully :-)')
 
@@ -557,6 +558,7 @@ def pulltutorialdata(tutorialfolder: str) -> None:
         LOGGER.success(f"Done")
     except Exception as unpackerror:
         LOGGER.error(f"Could not unpack: {tutorialtargz}\n{unpackerror}")
+        trackusage('bidscoin_error')
 
 
 def settracking(value: str):
@@ -596,14 +598,19 @@ def main():
     # Parse the input arguments and run bidscoiner(args)
     args = get_parser().parse_args(None if sys.argv[1:] else ['--help'])
 
-    list_executables(show=args.list)
-    list_plugins(show=args.plugins)
-    uninstall_plugins(filenames=args.uninstall)
-    install_plugins(filenames=args.install)
-    pulltutorialdata(tutorialfolder=args.download)
-    test_bidscoin(bidsmapfile=args.test)
-    test_bidsmap(bidsmapfile=args.bidsmaptest)
-    settracking(value=args.tracking)
+    try:
+        list_executables(show=args.list)
+        list_plugins(show=args.plugins)
+        uninstall_plugins(filenames=args.uninstall)
+        install_plugins(filenames=args.install)
+        pulltutorialdata(tutorialfolder=args.download)
+        test_bidscoin(bidsmapfile=args.test)
+        test_bidsmap(bidsmapfile=args.bidsmaptest)
+        settracking(value=args.tracking)
+
+    except Exception:
+        trackusage('bidscoin_exception')
+        raise
 
 
 if __name__ == "__main__":

diff --git a/bidscoin/bidsapps/deface.py b/bidscoin/bidsapps/deface.py
@@ -152,17 +152,22 @@ def main():
 
     from bidscoin.cli._deface import get_parser
 
-    trackusage('deface')
-
     args = get_parser().parse_args()
-    deface(bidsdir    = args.bidsfolder,
-           pattern    = args.pattern,
-           subjects   = args.participant_label,
-           force      = args.force,
-           output     = args.output,
-           cluster    = args.cluster,
-           nativespec = args.nativespec,
-           kwargs     = args.args)
+
+    trackusage('deface')
+    try:
+        deface(bidsdir    = args.bidsfolder,
+               pattern    = args.pattern,
+               subjects   = args.participant_label,
+               force      = args.force,
+               output     = args.output,
+               cluster    = args.cluster,
+               nativespec = args.nativespec,
+               kwargs     = args.args)
+
+    except Exception:
+        trackusage('deface_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidsapps/echocombine.py b/bidscoin/bidsapps/echocombine.py
@@ -200,17 +200,22 @@ def main():
 
     from bidscoin.cli._echocombine import get_parser
 
-    trackusage('echocombine')
-
     # Parse the input arguments and run bidscoiner(args)
     args = get_parser().parse_args()
-    echocombine(bidsdir   = args.bidsfolder,
-                pattern   = args.pattern,
-                subjects  = args.participant_label,
-                output    = args.output,
-                algorithm = args.algorithm,
-                weights   = args.weights,
-                force     = args.force)
+
+    trackusage('echocombine')
+    try:
+        echocombine(bidsdir   = args.bidsfolder,
+                    pattern   = args.pattern,
+                    subjects  = args.participant_label,
+                    output    = args.output,
+                    algorithm = args.algorithm,
+                    weights   = args.weights,
+                    force     = args.force)
+
+    except Exception:
+        trackusage('echocombine_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidsapps/medeface.py b/bidscoin/bidsapps/medeface.py
@@ -200,18 +200,23 @@ def main():
 
     from bidscoin.cli._medeface import get_parser
 
-    trackusage('medeface')
-
     args = get_parser().parse_args()
-    medeface(bidsdir     = args.bidsfolder,
-             pattern     = args.pattern,
-             maskpattern = args.maskpattern,
-             subjects    = args.participant_label,
-             force       = args.force,
-             output      = args.output,
-             cluster     = args.cluster,
-             nativespec  = args.nativespec,
-             kwargs      = args.args)
+
+    trackusage('medeface')
+    try:
+        medeface(bidsdir     = args.bidsfolder,
+                 pattern     = args.pattern,
+                 maskpattern = args.maskpattern,
+                 subjects    = args.participant_label,
+                 force       = args.force,
+                 output      = args.output,
+                 cluster     = args.cluster,
+                 nativespec  = args.nativespec,
+                 kwargs      = args.args)
+
+    except Exception:
+        trackusage('medeface_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidsapps/skullstrip.py b/bidscoin/bidsapps/skullstrip.py
@@ -208,17 +208,22 @@ def main():
 
     from bidscoin.cli._skullstrip import get_parser
 
-    trackusage('skullstrip')
-
     args = get_parser().parse_args()
-    skullstrip(bidsdir  = args.bidsfolder,
-               pattern  = args.pattern,
-               subjects = args.participant_label,
-               masked   = args.masked,
-               output   = args.output,
-               force    = args.force,
-               args     = args.args,
-               cluster  = args.cluster)
+
+    trackusage('skullstrip')
+    try:
+        skullstrip(bidsdir  = args.bidsfolder,
+                   pattern  = args.pattern,
+                   subjects = args.participant_label,
+                   masked   = args.masked,
+                   output   = args.output,
+                   force    = args.force,
+                   args     = args.args,
+                   cluster  = args.cluster)
+
+    except Exception:
+        trackusage('skullstrip_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidsapps/slicereport.py b/bidscoin/bidsapps/slicereport.py
@@ -278,22 +278,27 @@ def main():
 
     from bidscoin.cli._slicereport import get_parser
 
-    trackusage('slicereport')
-
     args = get_parser().parse_args()
-    slicereport(bidsdir        = args.bidsfolder,
-                pattern        = args.pattern,
-                outlinepattern = args.outlinepattern,
-                outlineimage   = args.outlineimage,
-                subjects       = args.participant_label,
-                reportdir      = args.reportfolder,
-                crossdirs      = args.xlinkfolder,
-                qccols         = args.qcscores,
-                cluster        = args.cluster,
-                options        = args.options,
-                outputs        = args.outputs,
-                suboptions     = args.suboptions,
-                suboutputs     = args.suboutputs)
+
+    trackusage('slicereport')
+    try:
+        slicereport(bidsdir        = args.bidsfolder,
+                    pattern        = args.pattern,
+                    outlinepattern = args.outlinepattern,
+                    outlineimage   = args.outlineimage,
+                    subjects       = args.participant_label,
+                    reportdir      = args.reportfolder,
+                    crossdirs      = args.xlinkfolder,
+                    qccols         = args.qcscores,
+                    cluster        = args.cluster,
+                    options        = args.options,
+                    outputs        = args.outputs,
+                    suboptions     = args.suboptions,
+                    suboutputs     = args.suboutputs)
+
+    except Exception:
+        trackusage('slicereport_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidscoiner.py b/bidscoin/bidscoiner.py
@@ -346,12 +346,16 @@ def main():
     args = get_parser().parse_args()
 
     trackusage('bidscoiner')
-
-    bidscoiner(rawfolder   = args.sourcefolder,
-               bidsfolder  = args.bidsfolder,
-               subjects    = args.participant_label,
-               force       = args.force,
-               bidsmapfile = args.bidsmap)
+    try:
+        bidscoiner(rawfolder   = args.sourcefolder,
+                   bidsfolder  = args.bidsfolder,
+                   subjects    = args.participant_label,
+                   force       = args.force,
+                   bidsmapfile = args.bidsmap)
+
+    except Exception:
+        trackusage('bidscoiner_exception')
+        raise
 
 
 if __name__ == "__main__":

diff --git a/bidscoin/bidseditor.py b/bidscoin/bidseditor.py
@@ -1693,10 +1693,14 @@ def main():
     args = get_parser().parse_args()
 
     trackusage('bidseditor')
-
-    bidseditor(bidsfolder   = args.bidsfolder,
-               bidsmapfile  = args.bidsmap,
-               templatefile = args.template)
+    try:
+        bidseditor(bidsfolder   = args.bidsfolder,
+                   bidsmapfile  = args.bidsmap,
+                   templatefile = args.template)
+
+    except Exception:
+        trackusage('bidseditor_exception')
+        raise
 
 
 if __name__ == '__main__':

diff --git a/bidscoin/bidsmapper.py b/bidscoin/bidsmapper.py
@@ -240,19 +240,23 @@ def main():
     args = get_parser().parse_args()
 
     trackusage('bidsmapper')
-
-    bidsmapper(rawfolder    = args.sourcefolder,
-               bidsfolder   = args.bidsfolder,
-               bidsmapfile  = args.bidsmap,
-               templatefile = args.template,
-               plugins      = args.plugins,
-               subprefix    = args.subprefix,
-               sesprefix    = args.sesprefix,
-               unzip        = args.unzip,
-               store        = args.store,
-               noeditor     = args.automated,
-               force        = args.force,
-               noupdate     = args.no_update)
+    try:
+        bidsmapper(rawfolder    = args.sourcefolder,
+                   bidsfolder   = args.bidsfolder,
+                   bidsmapfile  = args.bidsmap,
+                   templatefile = args.template,
+                   plugins      = args.plugins,
+                   subprefix    = args.subprefix,
+                   sesprefix    = args.sesprefix,
+                   unzip        = args.unzip,
+                   store        = args.store,
+                   noeditor     = args.automated,
+                   force        = args.force,
+                   noupdate     = args.no_update)
+
+    except Exception:
+        trackusage('bidsmapper_exception')
+        raise
 
 
 if __name__ == "__main__":

diff --git a/bidscoin/utilities/bidsparticipants.py b/bidscoin/utilities/bidsparticipants.py
@@ -182,14 +182,19 @@ def main():
 
     from bidscoin.cli._bidsparticipants import get_parser
 
-    trackusage('bidsparticipants')
-
     args = get_parser().parse_args()
-    bidsparticipants(rawfolder   = args.sourcefolder,
-                     bidsfolder  = args.bidsfolder,
-                     keys        = args.keys,
-                     bidsmapfile = args.bidsmap,
-                     dryrun      = args.dryrun)
+
+    trackusage('bidsparticipants')
+    try:
+        bidsparticipants(rawfolder   = args.sourcefolder,
+                         bidsfolder  = args.bidsfolder,
+                         keys        = args.keys,
+                         bidsmapfile = args.bidsmap,
+                         dryrun      = args.dryrun)
+
+    except Exception:
+        trackusage('bidsparticipants_exception')
+        raise
 
 
 if __name__ == "__main__":

diff --git a/bidscoin/utilities/dicomsort.py b/bidscoin/utilities/dicomsort.py
@@ -40,6 +40,7 @@ def construct_name(scheme: str, dicomfile: Path, force: bool) -> str:
                 value = int(value.replace('.',''))      # Convert the SeriesInstanceUID to an int
         if not value and value != 0 and not force:
             LOGGER.error(f"Missing '{field}' DICOM field specified in the '{scheme}' folder/naming scheme, cannot find a safe name for: {dicomfile}\n")
+            trackusage('dicomsort_error')
             return ''
         else:
             schemevalues[field] = value
@@ -112,6 +113,7 @@ def sortsession(sessionfolder: Path, dicomfiles: List[Path], folderscheme: str,
             subfolder = construct_name(folderscheme, dicomfile, force)
             if not subfolder:
                 LOGGER.error('Cannot create subfolders, aborting dicomsort()...')
+                trackusage('dicomsort_error')
                 return
             if subfolder not in subfolders:
                 subfolders.append(subfolder)
@@ -162,7 +164,7 @@ def sortsessions(sourcefolder: Path, subprefix: str='', sesprefix: str='', folde
             LOGGER.error(f"Unexpected dicomsource argument '{sourcefolder}', aborting dicomsort()...")
             return []
     elif not sourcefolder.is_dir():
-        print(f"Sourcefolder '{sourcefolder}' not found")
+        LOGGER.error(f"Sourcefolder '{sourcefolder}' not found")
         return []
     if (folderscheme and not validscheme(folderscheme)) or (namescheme and not validscheme(namescheme)):
         LOGGER.error('Wrong scheme input argument(s), aborting dicomsort()...')
@@ -214,20 +216,25 @@ def main():
 
     from bidscoin.cli._dicomsort import get_parser
 
-    trackusage('dicomsort')
+    args = get_parser().parse_args()
 
     # Set-up logging
     bcoin.setup_logging()
 
-    args = get_parser().parse_args()
-    sortsessions(sourcefolder = args.dicomsource,
-                 subprefix    = args.subprefix,
-                 sesprefix    = args.sesprefix,
-                 folderscheme = args.folderscheme,
-                 namescheme   = args.namescheme,
-                 pattern      = args.pattern,
-                 force        = args.force,
-                 dryrun       = args.dryrun)
+    trackusage('dicomsort')
+    try:
+        sortsessions(sourcefolder = args.dicomsource,
+                     subprefix    = args.subprefix,
+                     sesprefix    = args.sesprefix,
+                     folderscheme = args.folderscheme,
+                     namescheme   = args.namescheme,
+                     pattern      = args.pattern,
+                     force        = args.force,
+                     dryrun       = args.dryrun)
+
+    except Exception:
+        trackusage('dicomsort_exception')
+        raise
 
 
 if __name__ == "__main__":