Merge branch 'release-1.6.9'

.gitignore

@@ -41,23 +41,15 @@ Thumbs.db
 .idea/
 .project
 .pydevproject
-/refinery/*.pid
-/refinery/solr/*/data
-/refinery/solr/lib/
-/refinery/solr/*/conf/custom-synonyms.txt
+*.pid
 /refinery/solr/**/conf/solrconfig.xml
 supervisord.conf
 codekit-config.json
 .vagrant/
 /deployment/puppet/.librarian/
-/deployment/puppet/.tmp/
 /deployment/puppet/Puppetfile.lock
-/deployment/aws-config/config.yaml
-/deployment/aws-config/tags.yaml
 /refinery/celerybeat-schedule*
 /refinery/config/config.json
-/refinery/static/production/
-/refinery/static/development/
 /refinery/ui/production/
 /refinery/ui/development/
 /refinery/ui/bower_components/
@@ -68,6 +60,7 @@ codekit-config.json
 /refinery/ui/cypress/screenshots/
 /refinery/ui/cypress/videos/
 /import/
+/media/
 /static/
 /transfer/
 *.conflict
@@ -77,10 +70,6 @@ codekit-config.json
 /refinery/coverage.xml
 .cache/
 
-# to be moved into refinery/ui
-refinery/static/styles/css/font-awesome*.css
-refinery/static/styles/css/refinery-style*.css
-
 ### Terraform template
 # Compiled files
 *.tfstate

.travis.yml

@@ -61,7 +61,7 @@ before_script:
   - cd ../
 
   # Required for cypress tests; TODO: Move to puppet.
-  # TODO: Start up solr (and neo4j?)
+  # TODO: Start up solr
   - python manage.py loaddata guest.json
   - python manage.py activate_user guest
   - python manage.py add_users_to_public_group
@@ -85,7 +85,7 @@ script:
   - echo 'travis_fold:end:django-tests'
 
   - echo 'travis_fold:start:cypress'
-  - pushd ui && node_modules/.bin/cypress run --record && popd
+  - pushd ui && node_modules/.bin/cypress run && popd
   - echo 'travis_fold:end:cypress'
 
   - set +e # Currently, codecov does not always exit with 0, but that should not cause travis to fail.

Vagrantfile

@@ -18,43 +18,26 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
 
   config.vm.provider "virtualbox" do |v|
     v.memory = 2048
-    v.cpus = 1
+    v.cpus = 2
     # To increase guest network performance (https://superuser.com/a/850389)
     v.customize ["modifyvm", :id, "--nictype1", "virtio"]
   end
 
   config.ssh.forward_agent = true  # to enable cloning from Github over SSH
 
-  # If you'd like to be able to copy data from an instance of Galaxy
-  # that's installed on the host, set $GALAXY_DATABSE_DIR environment
-  # variable to the absolute path of the $GALAXY_ROOT/database folder
-  if ENV['GALAXY_DATABASE_DIR']
-#    puts("INFO: Using host directory #{ENV['GALAXY_DATABASE_DIR']} to exchange data with Galaxy.")
-    config.vm.synced_folder ENV['GALAXY_DATABASE_DIR'], ENV['GALAXY_DATABASE_DIR']
-  else
-    config.vm.provision :shell, :inline =>
-<<GALAXY_WARNING_SCRIPT
-    echo 1>&2 'WARNING: $GALAXY_DATABASE_DIR is not set: copying files from local Galaxy instance will not work.'
-GALAXY_WARNING_SCRIPT
-  end
-
   # If you'd like to be able to copy data from your host into the VM, set
-  # REFINERY_VM_TRANSFER_DIR on the host to a directory of your choice.
+  # REFINERY_VM_TRANSFER_DIR on the host to a directory of your choice
   if ENV['REFINERY_VM_TRANSFER_DIR']
     config.vm.synced_folder ENV['REFINERY_VM_TRANSFER_DIR'], "/vagrant/transfer"
-#    puts("INFO: Using host directory #{ENV['REFINERY_VM_TRANSFER_DIR']} to import datasets.")
-  else
-#   puts("WARNING: $REFINERY_VM_TRANSFER_DIR is not set: importing datasets from the command line will not work.")
   end
 
   # Install Librarian-puppet and modules before puppet provisioning
   config.vm.provision :shell, path: "deployment/bootstrap.sh"
 
   config.vm.provision :puppet do |puppet|
     puppet.manifests_path = "deployment/puppet/manifests"
-    puppet.manifest_file  = "vagrant.pp"
-    puppet.module_path = "deployment/puppet/modules"  # requires modules dir to exist when this file is parsed
-    puppet.options = "--hiera_config /vagrant/deployment/puppet/hiera.yaml"  # to avoid missing file warning
+    puppet.manifest_file  = "site.pp"
+    puppet.hiera_config_path = "deployment/puppet/hiera.yaml"  # to avoid missing file warning
   end
 
   # workaround for services that start on boot before /vagrant is available

backup.sh

@@ -24,7 +24,6 @@ BACKUP_TEMP="/tmp/backups"
 REFINERY_BASE_DIR="/vagrant/refinery"
 CONFIG_DIR="config"
 CONFIG_FILE="config.json"
-NEO4J_DATA="/var/lib/neo4j/data/graph.db/"
 
 DEFAULT="\e[39m"
 DIM="\e[2m"
@@ -76,19 +75,6 @@ TIME_INTERMEDIATE_END=$(date +"%s")
 TIME_INTERMEDIATE_DIFF=$(($TIME_INTERMEDIATE_END-$TIME_INTERMEDIATE_START))
 echo -e "copied! $DIM($(($TIME_INTERMEDIATE_DIFF / 60)) min and $(($TIME_INTERMEDIATE_DIFF % 60)) sec)$RESET"
 
-# Backup Neo4J
-echo -e "Neo4J graph db... \c"
-TIME_INTERMEDIATE_START=$(date +"%s")
-
-mkdir -p "$BACKUP_TEMP/$NOW/neo4j"
-sudo service neo4j-service stop
-sudo rsync -az --partial "$NEO4J_DATA" "$BACKUP_TEMP/$NOW/neo4j"
-sudo service neo4j-service start > /dev/null
-
-TIME_INTERMEDIATE_END=$(date +"%s")
-TIME_INTERMEDIATE_DIFF=$(($TIME_INTERMEDIATE_END-$TIME_INTERMEDIATE_START))
-echo -e "copied! $DIM($(($TIME_INTERMEDIATE_DIFF / 60)) min and $(($TIME_INTERMEDIATE_DIFF % 60)) sec)$RESET"
-
 # Compress backup and copy it to the final destination
 echo -e "Compressing... \c"
 TIME_INTERMEDIATE_START=$(date +"%s")

deployment/bootstrap.sh

@@ -5,10 +5,18 @@
 # https://serverfault.com/a/670688
 export DEBIAN_FRONTEND=noninteractive
 
-/usr/bin/apt-get clean && /usr/bin/apt-get -qq update && /usr/bin/apt-get autoremove
+# print commands and their expanded arguments
+set -x
 
-/usr/bin/apt-get -q -y install git ruby-dev
+/usr/bin/apt-get clean
+/usr/bin/apt-get -qq update
+/usr/bin/apt-get -y autoremove
+
+/usr/bin/apt-get -q -y install git htop nmon ruby-dev tree
 
 /usr/bin/gem install librarian-puppet -v 2.2.3 --no-rdoc --no-ri
 
-cd /vagrant/deployment/puppet && librarian-puppet install
+cd /vagrant/deployment/puppet
+librarian-puppet config path /usr/share/puppet/modules --local
+librarian-puppet config tmp /tmp --local
+librarian-puppet install

deployment/puppet/manifests/site.pp

@@ -0,0 +1,21 @@
+node default {
+  if $::domain == 'ec2.internal' {
+    class { 'refinery::params':
+      deployment_platform => 'aws',
+    }
+  }
+  else {
+    class { 'refinery::params':
+      deployment_platform => 'vagrant',
+    }
+  }
+
+  include refinery
+  include refinery::apache2
+  include refinery::django
+  include refinery::docker
+  include refinery::postgresql
+  include refinery::python
+  include refinery::solr
+  include refinery::ui
+}