make default artifacts directory, --run must be an int

harvard-nrg · Dec 7, 2021 · 9cc9dab · 9cc9dab
1 parent eb96f56
commit 9cc9dab
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/anatqc/__version__.py b/anatqc/__version__.py
@@ -1,6 +1,6 @@
 __title__ = 'anatqc'
 __description__ = 'Anatomical QC'
 __url__ = 'https://github.com/harvard-nrg/anatqc'
-__version__ = '0.4.4'
+__version__ = '0.4.5'
 __author__ = 'Neuroinformatics Research Group'
 __author_email__ = '[email protected]'
diff --git a/anatqc/cli/process.py b/anatqc/cli/process.py
@@ -125,6 +125,13 @@ def do(args):
         if not os.path.exists(archive):
             logger.info('creating anat-morph archive %s', archive)
             anatqc.archive(morph_outdir, archive)
+
+    # artifacts directory
+    if not args.artifacts_dir:
+        args.artifacts_dir = os.path.join(
+            morph_outdir,
+            'xnat-artifacts'
+        )
 
     # build data to upload to xnat
     R = Report(args.bids_dir, args.sub, args.ses, args.run)

diff --git a/scripts/anatQC.py b/scripts/anatQC.py
@@ -42,7 +42,7 @@ def main():
         help='BIDS session')
     parser_process.add_argument('--mod', default='T1w',
         help='BIDS modality')
-    parser_process.add_argument('--run', default='1',
+    parser_process.add_argument('--run', default=1, type=int,
         help='BIDS run')
     parser_process.add_argument('--bids-dir', required=True,
         help='BIDS root directory')
@@ -60,7 +60,7 @@ def main():
         help='XNAT username')
     parser_process.add_argument('--xnat-pass',
         help='XNAT password')
-    parser_process.add_argument('--artifacts-dir', default='/artifacts',
+    parser_process.add_argument('--artifacts-dir',
         help='Location for generated assessors and resources')
     parser_process.add_argument('--xnat-upload', action='store_true',
         help='Upload results to XNAT over REST API')
@@ -73,7 +73,7 @@ def main():
         help='XNAT Project name')
     parser_tandem.add_argument('--bids-dir', required=True,
         help='Output BIDS directory')
-    parser_tandem.add_argument('--run', default='1',
+    parser_tandem.add_argument('--run', default=1, type=int,
         help='BIDS run')
     parser_tandem.add_argument('--partition', default='default',
         help='Job scheduler partition')
@@ -97,7 +97,7 @@ def main():
         help='XNAT username')
     parser_tandem.add_argument('--xnat-pass',
         help='XNAT password')
-    parser_tandem.add_argument('--artifacts-dir', default='/artifacts',
+    parser_tandem.add_argument('--artifacts-dir',
         help='Location for generated assessors and resources')
     parser_tandem.add_argument('--xnat-upload', action='store_true',
         help='Upload results to XNAT over REST API')