xnatqa 0.0.16__tar.gz → 0.0.17__tar.gz

{xnatqa-0.0.16/xnatqa.egg-info → xnatqa-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.16
+Version: 0.0.17
 Summary: A workflow for automatically tagging MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT

{xnatqa-0.0.16 → xnatqa-0.0.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "xnatqa"
-version = "0.0.16"
+version = "0.0.17"
 authors = [
   { name="Kyle Kurkela", email="kkurkela@bu.edu" },
 ]

{xnatqa-0.0.16 → xnatqa-0.0.17}/xnatqa/launch.py

@@ -12,9 +12,11 @@ def main():
     # parse input arguments
     parser = argparse.ArgumentParser(description="XNAT QA Workflow")
     parser.add_argument("--experiment", default = "", required=True)
+    parser.add_argument("--dryrun", default = "", action='store_true', help="Run in dry run mode: No launching of jobs")
 
     args, unknown_args = parser.parse_known_args()
     MRsession = args.experiment
+    dryrun    = args.dryrun
 
     # authenticate with xnat using the ~/.xnat_auth file created earlier in the workflow
     auth = yaxil.auth(alias = 'xnat')
@@ -33,12 +35,16 @@ def main():
 
             # if that note has a "#BOLD" tag...
             if '#BOLD' in note:
-                print('Run BOLDQC')
-                os.system(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
+                print('Run BOLDQC:')
+                print(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
+                if not dryrun:
+                    os.system(f'qsub -P cncxnat boldqc.qsub {MRsession} {b}')
                 b+=1
 
             # if that note has a "#T1w" tag...
             if '#T1w' in note:
-                print('Run ANATQC')
-                os.system(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
+                print('Run ANATQC:')
+                print(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
+                if not dryrun:
+                    os.system(f'qsub -P cncxnat anatqc.qsub {MRsession} {a}')
                 a+=1

{xnatqa-0.0.16 → xnatqa-0.0.17}/xnatqa/tag/__init__.py

@@ -188,11 +188,12 @@ def update_xnat_tags(MRsession):
     # run the command
     os.system(f'xnat_tagger.py --label {MRsession} --target-modality all --xnat-alias xnat --config tagger.yaml')
 
-def tag_scans(dicom_dir, MRsession):
+def tag_scans(dicom_dir, MRsession, dryrun):
     
     # generate the xnattag config file
     generate_tagger_config(dicom_dir)
     
     # update the xnat tags
-    update_xnat_tags(MRsession)
+    if not dryrun:
+        update_xnat_tags(MRsession)
 

{xnatqa-0.0.16 → xnatqa-0.0.17}/xnatqa/xnatqa.py

@@ -8,17 +8,19 @@ def main():
     parser = argparse.ArgumentParser(description="XNAT QA Workflow")
     parser.add_argument("--dicom_dir", default="/input", help = "where the DICOMs are located", required=True)
     parser.add_argument("--experiment", default = "", required=True)
+    parser.add_argument("--dryrun", default = "", action='store_true', help="Run in dry run mode: No upload to XNAT")
 
     args, unknown_args = parser.parse_known_args()
     dicom_dir  = os.path.join(args.dicom_dir, 'SCANS')
     experiment = args.experiment
+    dryrun     = args.dryrun
 
     # run xnat authentication for this container. writes an ~/.xnat_auth file to the home directory
     # this file is used in all subsequent calls to XNAT
     os.system(f'xnat_auth --alias xnat --url $XNAT_HOST --username $XNAT_USER --password $XNAT_PASS')
 
     # tag all scans in this session
-    tag_scans(dicom_dir, experiment)
+    tag_scans(dicom_dir, experiment, dryrun)
 
 if __name__ == "__main__":
     main()

{xnatqa-0.0.16 → xnatqa-0.0.17/xnatqa.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xnatqa
-Version: 0.0.16
+Version: 0.0.17
 Summary: A workflow for automatically tagging MRI scans within XNAT
 Author-email: Kyle Kurkela <kkurkela@bu.edu>
 License-Expression: MIT