Merge pull request #8 from flywheel-apps/python-run

Use python to parse configs

Dockerfile

@@ -1,6 +1,6 @@
 # curate-bids
 
-FROM flywheel/bids-client:0.6.2
+FROM flywheel/bids-client:0.6.3
 MAINTAINER Flywheel <[email protected]>
 
 # Install JQ to parse config file
@@ -9,7 +9,7 @@ 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 run.py ${FLYWHEEL}/run.py
 COPY manifest.json ${FLYWHEEL}/manifest.json
 
 # Set the entrypoint

manifest.json

@@ -6,9 +6,9 @@
   "maintainer": "Flywheel <[email protected]>",
   "source": "https://github.com/flywheel-apps/curate-bids",
   "url": "http://bids.neuroimaging.io/",
-  "version": "0.6.2",
+  "version": "0.6.3",
   "custom": {
-    "docker-image": "flywheel/curate-bids:v0.6.2"
+    "docker-image": "flywheel/curate-bids:v0.6.3"
   },
   "license": "BSD-3-Clause",
   "inputs": {
@@ -22,5 +22,6 @@
       "type": "boolean",
       "default": false
     }
-  }
+  },
+  "command": "python run.py"
 }

run.py

@@ -0,0 +1,15 @@
+import json
+from flywheel_bids.curate_bids import main_with_args
+
+if __name__ == '__main__':
+
+    # Grab Config
+    CONFIG_FILE_PATH = '/flywheel/v0/config.json'
+    with open(CONFIG_FILE_PATH) as config_file:
+        config = json.load(CONFIG_FILE)
+
+    api_key = config['inputs']['api_key']['key']
+    session_id = config['destination']['id']
+    reset = config['config']['reset']
+
+    main_with_args(api_key, session_id, reset)