diff --git a/circle.yml b/circle.yml index 57d6c71aec83358170c8dea3b6f1e72988de332c..214ae0f450380b1ef0f2ec387e7bdbbda18e9119 100644 --- a/circle.yml +++ b/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: diff --git a/run.py b/run.py index a419b268f3998efb85eb6e689575cf6ab371d204..0acad792350d45dc5e6b6927a348823281812057 100755 --- a/run.py +++ b/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))