fix/wip: updated kube stuff and added a WIP to data

Author: akeshavan

dmriprep/data.py

@@ -435,6 +435,11 @@ def postprocess(self, subject):
                                 stdout=fnull1,
                                 stderr=subprocess.STDOUT)
 
+            # now check that the AP/PA files are named correctly
+            # eg it should look like "sub-{id}_dir-{dir}_acq-dwi_epi.nii.gz
+            # but sometimes it looks like sub-{id}_acq-dwi_run-01_epi.nii.gz
+            # which is silly. the direction should be in the filename.
+
 
 class Subject:
     """A single dMRI study subject"""

kubernetes/docker/build_tag_push.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
-docker build -t dmriprep:kube1 -f dockerfile-dmriprep-kube .
-docker tag dmriprep:kube1 gcr.io/dmriprep/dmriprep:kube1
-docker push gcr.io/dmriprep/dmriprep:kube1
+docker build -t dmriprep:kube3 -f dockerfile-dmriprep-kube .
+docker tag dmriprep:kube3 gcr.io/dmriprep/dmriprep:kube3
+docker push gcr.io/dmriprep/dmriprep:kube3

kubernetes/run_dmriprep.yml.tmpl

@@ -7,7 +7,7 @@ spec:
     spec:
       containers:
       - name: dmriprep-subject
-        image: gcr.io/dmriprep/dmriprep:kube1
+        image: gcr.io/dmriprep/dmriprep:kube3
         command: ["/neurodocker/startup.sh", "./dmriprep_all.sh",  "{{subject}}", "{{access_key}}", "{{secret_key}}"]
       restartPolicy: Never
   backoffLimit: 1