From 50f64bc155f46c10c1bdad6a6ea92a7e7d9f23ee Mon Sep 17 00:00:00 2001
From: Harsha Kethineni <harshakethineni@flywheel.io>
Date: Mon, 25 Jun 2018 12:11:26 -0500
Subject: [PATCH 1/2] use python to parse configs

---
 Dockerfile    |  4 ++--
 manifest.json |  7 ++++---
 run           | 56 ---------------------------------------------------
 run.py        | 15 ++++++++++++++
 4 files changed, 21 insertions(+), 61 deletions(-)
 delete mode 100755 run
 create mode 100644 run.py

diff --git a/Dockerfile b/Dockerfile
index c169d74..a34cbab 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 # curate-bids
 
-FROM flywheel/bids-client:0.6.2
+FROM flywheel/bids-client:0.6.3
 MAINTAINER Flywheel <support@flywheel.io>
 
 # 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
diff --git a/manifest.json b/manifest.json
index 0328795..3a8b972 100644
--- a/manifest.json
+++ b/manifest.json
@@ -6,9 +6,9 @@
   "maintainer": "Flywheel <support@flywheel.io>",
   "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"
 }
diff --git a/run b/run
deleted file mode 100755
index fd2cc8a..0000000
--- a/run
+++ /dev/null
@@ -1,56 +0,0 @@
-#! /bin/bash
-#
-# Run script for flywheel/curate-bids Gear
-# Authorship: Jennifer Reiter
-
-# Define directory names and containers
-
-FLYWHEEL_BASE=/flywheel/v0
-CONFIG_FILE=$FLYWHEEL_BASE/config.json
-
-
-##############################################################################
-# Parse configuration options
-
-# If config.json exists, then we parse config file and cast vals to ENV Vars
-# (Flywheel gear run). Otherwise we parse manifest.json and cast the values to
-# ENV Vars from manifest (Docker run) Note value.default is used to grab the
-# configured defaults.
-
-if [[ -f $CONFIG_FILE ]]; then
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\"\(.value)\""' $CONFIG_FILE)
-else
-  CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
-  eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value.default)"' $CONFIG_FILE)
-fi
-
-# Get API KEY
-APIKEY=$(jq -r '.inputs.api_key.key' $CONFIG_FILE)
-
-# Get Session ID
-CONFIG_SESSIONID=$(jq -r '.destination.id' $CONFIG_FILE)
-
-# Boolean parsing of reset config option
-if [[ $config_reset == 'true' ]]; then
-  RESET_FLAG='--reset'
-else
-  RESET_FLAG=''
-fi
-
-##############################################################################
-# Notify User that BIDS curation is being run on project label
-echo "BIDS Curation templates are being run on entire Project for session: $CONFIG_SESSIONID"
-
-# Run curate_bids python script
-curate_bids --api-key $APIKEY --session "$CONFIG_SESSIONID" ${RESET_FLAG}
-curate_exit_status=$?
-
-##############################################################################
-# Handle Exit status
-if [[ $curate_exit_status == 0 ]]; then
-  echo -e "${CONTAINER} Success!"
-  exit 0
-else
-  echo "${CONTAINER}  Something went wrong! Curate BIDS exited non-zero!"
-  exit 1
-fi
diff --git a/run.py b/run.py
new file mode 100644
index 0000000..d8e1adf
--- /dev/null
+++ b/run.py
@@ -0,0 +1,15 @@
+import json
+from flywheel_bids.curate_bids import main_with_args
+
+if __name__ == '__main__':
+
+    # Grab Config
+    config = '/flywheel/v0/config.json'
+    with open(config) as configFile:
+        CONFIG = json.load(configFile)
+
+    api_key = CONFIG['inputs']['api_key']['key']
+    session_id = CONFIG['destination']['id']
+    reset = CONFIG['config']['reset']
+
+    main_with_args(api_key, session_id, reset)

From bf52e2da00d9663108698221a77652c00017d81d Mon Sep 17 00:00:00 2001
From: Harsha Kethineni <harshakethineni@flywheel.io>
Date: Mon, 25 Jun 2018 12:43:44 -0500
Subject: [PATCH 2/2] Style changes

---
 run.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/run.py b/run.py
index d8e1adf..9bd8f92 100644
--- a/run.py
+++ b/run.py
@@ -4,12 +4,12 @@
 if __name__ == '__main__':
 
     # Grab Config
-    config = '/flywheel/v0/config.json'
-    with open(config) as configFile:
-        CONFIG = json.load(configFile)
+    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']
+    api_key = config['inputs']['api_key']['key']
+    session_id = config['destination']['id']
+    reset = config['config']['reset']
 
     main_with_args(api_key, session_id, reset)