CircleCI: Further fixes for new test data

- Delete previous test dataset if present.
- tar file contents get extracted to the directory data/, not a sub-directory thereof.

circle.yml

@@ -11,7 +11,8 @@ dependencies:
     - "~/data"
 
   override:
-    - if [[ ! -d ~/data/mrtrix3_connectome_data_ver2 ]]; then wget -c -P ${HOME}/downloads/ "https://www.dropbox.com/s/u3uvf857jf4iqq1/MRtrix3_connectome_data_ver2.tar" && mkdir -p ${HOME}/data && tar xf ${HOME}/downloads/MRtrix3_connectome_data_ver2.tar -C ${HOME}/data; fi
+    - if [[ -d ~/data/mrtrix3_connectome_data ]]; then rm -rf ${HOME}/data/mrtrix3_connectome_data; fi
+    - if [[ ! -d ~/data ]]; then wget -c -P ${HOME}/downloads/ "https://www.dropbox.com/s/u3uvf857jf4iqq1/MRtrix3_connectome_data_ver2.tar" && mkdir -p ${HOME}/data && tar xf ${HOME}/downloads/MRtrix3_connectome_data_ver2.tar -C ${HOME}/data; fi
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - git describe --tags > version
     - docker build -t bids/${CIRCLE_PROJECT_REPONAME,,} . :
@@ -24,12 +25,12 @@ test:
     # print version
     - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
     # participant level tests for single session dataset
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/mrtrix3_connectome_data_ver2:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 -parc aal -streamlines 100000 -preprocessed :
+    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 -parc aal -streamlines 100000 -preprocessed :
         timeout: 21600
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/mrtrix3_connectome_data_ver2:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 -parc aal -streamlines 100000 -preprocessed :
+    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 -parc aal -streamlines 100000 -preprocessed :
         timeout: 21600
     # group level test for single session dataset
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/mrtrix3_connectome_data_ver2:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group :
+    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data:/bids_dataset -v ${HOME}/outputs:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group :
         timeout: 21600
 
 deployment:

run.py

@@ -475,6 +475,8 @@ def runGroup(output_dir):
       self.label = label
 
   subject_list = ['sub-' + dir.split("-")[-1] for dir in glob.glob(os.path.join(output_dir, 'sub-*'))]
+  if not subject_list:
+    app.error('No processed subject data found in output directory for group analysis')
   subjects = []
   for label in subject_list:
     subjects.append(subjectPaths(label))