Merge branch 'develop' of https://github.com/parklab/refinery-platform …

…into scottx611x/django_1.6_upgrade

deployment/Makefile

@@ -7,7 +7,7 @@ web-stack: web.json .PHONY
 	aws cloudformation create-stack --stack-name refinery-web-$$(date +%Y%m%dT%H%M) --template-body file://web.json
 
 volume.json: .PHONY
-	cfn_py_generate volume_cfn.py volume.json
+	python volume_cfn.py > volume.json
 
 volume-stack: volume.json .PHONY
 	aws cloudformation create-stack --stack-name refinery-volume-$$(date +%Y%m%dT%H%M) --template-body file://volume.json

deployment/aws-config/10default.yaml

@@ -35,10 +35,14 @@
 
 # The name of the pre-existing RDS instance to connect to.
 # (must use the PostgreSQL engine)
-# RDS_SUPERUSER_NAME: "rds-refinery"
+# RDS_NAME: "rds-refinery"
 
 # The name of the RDS superuser account.
+# RDS_SUPERUSER_NAME:
 # FIXED to "root"
 
 # The password for the RDS superuser account.
 # RDS_SUPERUSER_PASSWORD: "mypassword"
+
+# The name of the PostgreSQL role to create.
+RDS_ROLE: "refinery"

deployment/aws-tags/hms.yaml

@@ -0,0 +1,9 @@
+# AWS tags,
+# as per https://github.com/parklab/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
+environment: dev
+project: scc
+product: refinery
+subproduct: platform

deployment/aws.sh

@@ -27,9 +27,14 @@ cd /srv/refinery-platform/deployment
 
 # Discover IP endpoint for our PostgreSQL RDS, and place it in
 # environment variables for puppet/facter to use
-bin/aws-rds-endpoint db20160111 > /home/ubuntu/rds
+: ${RDS_NAME?RDS_NAME must be set}
+bin/aws-rds-endpoint "$RDS_NAME" > /home/ubuntu/rds
+
+# FACTER environment variables become facts for puppet;
+# see https://puppetlabs.com/blog/facter-part-1-facter-101
 export FACTER_RDS_HOST=$(jq -r .Address /home/ubuntu/rds)
 export FACTER_RDS_PORT=$(jq -r .Port /home/ubuntu/rds)
+export FACTER_RDS_ROLE="$RDS_ROLE"
 
 # Create RDS user and database here, instead of using puppet
 # (because drj couldn't work out how to do it in puppet)

deployment/bin/ensure-postgresql-role

@@ -1,6 +1,7 @@
 #!/bin/sh
 
-USER=ubuntu
+# Name and password of PostgreSQL role to create.
+USER=${RDS_ROLE:-refinery}
 PASSWORD=${PASSWORD-password}
 
 HOST=$(jq -r .Address /home/ubuntu/rds)

deployment/stack.py

@@ -41,6 +41,8 @@
 # https://pypi.python.org/pypi/PyYAML/3.11
 import yaml
 
+import tags
+
 # Simulate the environment that "cfn_generate" runs scripts in.
 # http://cfn-pyplates.readthedocs.org/en/latest/advanced.html#generating-templates-in-python
 from cfn_pyplates.core import *
@@ -70,6 +72,7 @@ def main():
         "#!/bin/sh\n",
         "RDS_NAME=", config['RDS_NAME'], "\n",
         "RDS_SUPERUSER_PASSWORD=", config['RDS_SUPERUSER_PASSWORD'], "\n",
+        "RDS_ROLE=", config['RDS_ROLE'], "\n",
         "GIT_BRANCH=", commit, "\n",
         "\n",
         open('bootstrap.sh').read(),
@@ -83,7 +86,7 @@ def main():
             'UserData': base64(user_data_script),
             'KeyName': 'id_rsa',
             'IamInstanceProfile': 'refinery-web',
-            'Tags': [{'Key': 'refinery', 'Value': 'refinery'}],
+            'Tags': tags.load(),
         })
     )
 

deployment/tags.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+
+"""
+Tags local module.
+"""
+
+import glob
+import os       # for os.popen
+
+import yaml
+
+# Get the local user's email address
+email = os.popen("git config --get user.email").read().rstrip()
+
+
+def load():
+    """
+    Tags come from the YAML files in the aws-tags directory,
+    additionally, the tag `owner` if it is not set by those YAML
+    files, will be set to the email address of the local git
+    user.
+    """
+
+    tags = {}
+    for filename in sorted(glob.glob("aws-tags/*")):
+        with open(filename) as f:
+            tags.update(yaml.load(f))
+    if 'owner' not in tags:
+        tags['owner'] = email
+
+    return [{'Key': k, 'Value': v} for k, v in tags.items()]

deployment/volume_cfn.py

@@ -15,8 +15,18 @@
 # AWS Cloudformation
 #   https://aws.amazon.com/cloudformation/
 
+import glob
 import os       # for os.popen
 
+import yaml
+
+import tags
+
+# Simulate the environment that "cfn_generate" runs scripts in.
+# http://cfn-pyplates.readthedocs.org/en/latest/advanced.html#generating-templates-in-python
+from cfn_pyplates.core import *
+from cfn_pyplates.functions import *
+
 cft = CloudFormationTemplate(description="refinery EBS volume.")
 
 # http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-ec2-ebs-volume.html
@@ -26,10 +36,12 @@
         'AvailabilityZone': 'us-east-1b',
         'Encrypted': True,
         'Size': 10,
-        # 'Tags': foo,
+        'Tags': tags.load(),
         'VolumeType': 'gp2'
     })
 )
 
 cft.outputs.ebs = Output(
      "Volume", ref('RefineryData'), "Volume ID")
+
+print(str(cft))

refinery/config/config.json.erb

@@ -24,7 +24,7 @@
         "NAME": "refinery",
         "PASSWORD": "<%= @rds_role_password %>",
         "PORT": "<%= @rds_port %>",
-        "USER": "<%= @app_user || "vagrant" %>"
+        "USER": "<%= @rds_role || "vagrant" %>"
     }
   },
   "DEFAULT_FROM_EMAIL": "webmaster@localhost",