Update references to current repo for new refinery-platform organiz…

…ation (#1574)

README.md

@@ -1,7 +1,7 @@
-# <img src="https://pbs.twimg.com/profile_images/519505652083748864/bG9itLTl_400x400.png" height=30px width=30px>&nbsp;Refinery Platform [![Build Status](https://travis-ci.org/parklab/refinery-platform.svg?branch=develop)](https://travis-ci.org/parklab/refinery-platform) [![Coverage Status](https://img.shields.io/codecov/c/github/parklab/refinery-platform/develop.svg)](https://codecov.io/github/parklab/refinery-platform?branch=develop)
+# <img src="https://pbs.twimg.com/profile_images/519505652083748864/bG9itLTl_400x400.png" height=30px width=30px>&nbsp;Refinery Platform [![Build Status](https://travis-ci.org/refinery-platform/refinery-platform.svg?branch=develop)](https://travis-ci.org/refinery-platform/refinery-platform) [![Coverage Status](https://img.shields.io/codecov/c/github/refinery-platform/refinery-platform/develop.svg)](https://codecov.io/github/refinery-platform/refinery-platform?branch=develop)
 
-* Additional information about how to administer and develop Refinery can be found in the [wiki](http://github.com/parklab/refinery-platform/wiki)
-* [Production deployments](https://github.com/parklab/refinery-platform/wiki/AWS-installation) require access to Amazon Web Services
+* Additional information about how to administer and develop Refinery can be found in the [wiki](http://github.com/refinery-platform/refinery-platform/wiki)
+* [Production deployments](https://github.com/refinery-platform/refinery-platform/wiki/AWS-installation) require access to Amazon Web Services
 * Supported web browsers: Chrome 54 (Linux and OS X), Firefox 49 (Linux and OS X), Safari 9.0.0 (OS X)
 
 ## Installing and Launching for Development
@@ -13,7 +13,7 @@
 
 ### Configure and Load Virtual Machine
 ```bash
-$ git clone git@github.com:parklab/refinery-platform.git
+$ git clone git@github.com:refinery-platform/refinery-platform.git
 $ cd refinery-platform
 $ vagrant up
 ```
@@ -60,7 +60,7 @@ Log in to Refinery (<http://192.168.50.50:8000/>) with the default guest user ac
 
 Log in to Django admin UI (<http://192.168.50.50:8000/admin/>) with the default superuser account (username: admin, password: refinery).
 
-Please see [installation notes](https://github.com/parklab/refinery-platform/wiki/setting-up-galaxy) for more details, including information on how to configure Galaxy for this setup.
+Please see [installation notes](https://github.com/refinery-platform/refinery-platform/wiki/setting-up-galaxy) for more details, including information on how to configure Galaxy for this setup.
 
 ## Troubleshooting
 

deployment/aws-tags/hms.yaml

@@ -1,5 +1,5 @@
 # AWS tags,
-# as per https://github.com/parklab/refinery-platform/issues/839
+# as per https://github.com/refinery-platform/refinery-platform/issues/839
 # Other groups may want to remove this file and use it as a
 # suggestion for their own tagging scheme.
 department: dbmi

deployment/aws.sh

@@ -24,7 +24,7 @@ printf '%s' "${CONFIG_JSON}" | base64 -d > /home/ubuntu/config.json
 mkdir /srv/refinery-platform
 chown ubuntu:ubuntu /srv/refinery-platform
 sudo su -c '
-  git clone https://github.com/parklab/refinery-platform.git /srv/refinery-platform
+  git clone https://github.com/refinery-platform/refinery-platform.git /srv/refinery-platform
   cd /srv/refinery-platform
   git checkout '"$GIT_BRANCH"'
 ' ubuntu

deployment/manifests/aws.pp

@@ -10,7 +10,7 @@
 $import_dir = "/data/import"
 $solr_custom_synonyms_file =
   "${django_root}/solr/core/conf/custom-synonyms.txt"
-# As per https://github.com/parklab/refinery-platform/issues/1153
+# As per https://github.com/refinery-platform/refinery-platform/issues/1153
 $solr_lib_dir = "/opt/solr/server/solr-webapp/webapp/WEB-INF/lib"
 $email_host = "email-smtp.us-east-1.amazonaws.com"
 # $email_host_user set by Facter

deployment/stack.py

@@ -19,7 +19,8 @@
 # It generates one or more
 # CloudFormation JSON files.
 #
-# See https://github.com/parklab/refinery-platform/wiki/AWS-installation
+# See
+# https://github.com/refinery-platform/refinery-platform/wiki/AWS-installation
 # for notes on how to use this to deploy to Amazon AWS.
 #
 # Instances are configured using CloudInit.

refinery/config/settings/aws.py

@@ -1,6 +1,6 @@
 # Django settings specialised for the AWS environment.
 #
-# See https://github.com/parklab/refinery-platform/wiki/AWS for
+# See https://github.com/refinery-platform/refinery-platform/wiki/AWS for
 # more details.
 
 import requests
@@ -10,7 +10,7 @@
 
 # Ensure that the AWS private IP is an Allowed Host.
 # (required for ELB pings to work,
-# see https://github.com/parklab/refinery-platform/issues/1239)
+# see https://github.com/refinery-platform/refinery-platform/issues/1239)
 
 # Not checking for exceptions: if we can't get EC2 instance metadata,
 # something horrible is wrong.

refinery/core/tests.py

@@ -423,7 +423,7 @@ def test_get_nodeset_list_without_login(self):
         response = self.api_client.get(nodeset_uri, format='json')
         self.assertHttpUnauthorized(response)
 
-    # See https://github.com/parklab/refinery-platform/issues/586
+    # See https://github.com/refinery-platform/refinery-platform/issues/586
     # def test_get_nodeset_without_owner(self):
     #     """Test retrieving an existing NodeSet that belongs to no one.
     #     """
@@ -441,7 +441,7 @@ def test_get_nodeset_list_without_login(self):
     #     )
     #     self.assertHttpNotFound(response)
 
-    # See https://github.com/parklab/refinery-platform/issues/586
+    # See https://github.com/refinery-platform/refinery-platform/issues/586
     # def test_get_nodeset_without_permission(self):
     #     """Test retrieving an existing NodeSet that belongs to a different
     #     user

refinery/ui/package.json

@@ -10,12 +10,12 @@
   },
   "repository": {
     "type": "git",
-    "url": "git@github.com:parklab/refinery-platform.git"
+    "url": "git@github.com:refinery-platform/refinery-platform.git"
   },
   "author": "",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/parklab/refinery-platform/issues"
+    "url": "https://github.com/refinery-platform/refinery-platform/issues"
   },
   "devDependencies": {
     "codecov.io": "0.1.6",