Merge pull request #1997 from effigies/mnt/no_network

CI: Test that Docker image can run a common set of output spaces without network access

Author: effigies

.circleci/config.yml

@@ -365,6 +365,7 @@ jobs:
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
                 -e FMRIPREP_DEV 1 -u $(id -u) \
+                --network none \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --fs-subjects-dir /tmp/ds005/freesurfer \
@@ -393,6 +394,7 @@ jobs:
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
                 -e FMRIPREP_DEV 1 -u $(id -u) \
+                --network none \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --fs-subjects-dir /tmp/ds005/freesurfer \
@@ -422,6 +424,7 @@ jobs:
             rm /tmp/data/ds005/sub-01/func/*_run-01_*
             fmriprep-docker -i poldracklab/fmriprep:latest \
                 -e FMRIPREP_DEV 1 -u $(id -u) \
+                --network none \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --fs-subjects-dir /tmp/ds005/freesurfer \

Dockerfile

@@ -170,7 +170,10 @@ RUN pip install --no-cache-dir "$( grep templateflow fmriprep-setup.cfg | xargs
                tfapi.get('MNI152NLin6Asym', atlas=None, resolution=[1, 2], \
                          desc='brain', extension=['.nii', '.nii.gz']); \
                tfapi.get('MNI152NLin2009cAsym', atlas=None, extension=['.nii', '.nii.gz']); \
-               tfapi.get('OASIS30ANTs', extension=['.nii', '.nii.gz']);" && \
+               tfapi.get('OASIS30ANTs', extension=['.nii', '.nii.gz']); \
+               tfapi.get('fsLR', space='fsaverage', density='164k'); \
+               tfapi.get('fsLR', space=None, density='32k'); \
+               tfapi.get('MNI152NLin6Asym', resolution=2, atlas='HCP', suffix='dseg')" && \
     rm fmriprep-setup.cfg && \
     find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
     find $HOME/.cache/templateflow -type f -exec chmod go=u {} +

wrapper/fmriprep_docker.py

@@ -296,6 +296,9 @@ def get_parser():
                        help='Set custom environment variable within container')
     g_dev.add_argument('-u', '--user', action='store',
                        help='Run container as a given user/uid')
+    g_dev.add_argument('--network', action='store',
+                       help='Run container with a different network driver '
+                            '("none" to simulate no internet connection)')
 
     return parser
 
@@ -434,6 +437,9 @@ def main():
     if opts.shell:
         command.append('--entrypoint=bash')
 
+    if opts.network:
+        command.append('--network=' + opts.network)
+
     command.append(opts.image)
 
     # Override help and version to describe underlying program