Merge pull request #6 from flywheel-apps/docker-refactor

Base container off bids-client

Dockerfile

@@ -1,44 +1,16 @@
 # curate-bids
 
-FROM python:2.7
+FROM flywheel/bids-client:0.5.2
 MAINTAINER Flywheel <[email protected]>
 
 # Install JQ to parse config file
-RUN apt-get update && apt-get -y install jq
-
-# Install jsonschema and dateutil
-RUN pip install jsonschema==2.6.0 python-dateutil==2.6.1
-
-# Install python SDK
-RUN pip install https://github.com/flywheel-io/sdk/releases/download/0.3.0/flywheel-0.3.0-py2-none-linux_x86_64.whl
+RUN apk add --no-cache jq
 
 # Make directory for flywheel spec (v0)
 ENV FLYWHEEL /flywheel/v0
 RUN mkdir -p ${FLYWHEEL}
 COPY run ${FLYWHEEL}/run
 COPY manifest.json ${FLYWHEEL}/manifest.json
 
-# Copy code into place
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/curate_bids.py ${FLYWHEEL}/curate_bids.py
-
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/__init__.py ${FLYWHEEL}/supporting_files/__init__.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/bidsify_flywheel.py ${FLYWHEEL}/supporting_files/bidsify_flywheel.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/classifications.py ${FLYWHEEL}/supporting_files/classifications.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/project_tree.py ${FLYWHEEL}/supporting_files/project_tree.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/resolver.py ${FLYWHEEL}/supporting_files/resolver.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/templates.py ${FLYWHEEL}/supporting_files/templates.py
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/supporting_files/utils.py ${FLYWHEEL}/supporting_files/utils.py
-
-ADD https://raw.githubusercontent.com/flywheel-io/bids-client/master/templates/bids-v1.json ${FLYWHEEL}/templates/bids-v1.json 
-
-RUN chmod +x ${FLYWHEEL}/curate_bids.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/__init__.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/bidsify_flywheel.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/classifications.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/project_tree.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/resolver.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/templates.py
-RUN chmod +x ${FLYWHEEL}/supporting_files/utils.py
-
 # Set the entrypoint
 ENTRYPOINT ["/flywheel/v0/run"]

manifest.json

@@ -6,9 +6,9 @@
   "maintainer": "Flywheel <[email protected]>",
   "source": "https://github.com/flywheel-apps/curate-bids",
   "url": "http://bids.neuroimaging.io/",
-  "version": "0.3.6",
+  "version": "0.5.0",
   "custom": {
-    "docker-image": "flywheel/curate-bids:v0.3.6"
+    "docker-image": "flywheel/curate-bids:v0.5.0"
   },
   "license": "BSD-3-Clause",
   "inputs": {

run

@@ -42,7 +42,7 @@ fi
 echo "BIDS Curation templates are being run on entire Project for session: $CONFIG_SESSIONID"
 
 # Run curate_bids python script
-python /flywheel/v0/curate_bids.py --api-key $APIKEY --session "$CONFIG_SESSIONID" ${RESET_FLAG}
+curate_bids --api-key $APIKEY --session "$CONFIG_SESSIONID" ${RESET_FLAG}
 curate_exit_status=$?
 
 ##############################################################################