version 1.00.05

README.md

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+# ClinGen Actionability Curation Interface
+
+The official server with ClinGen Actionability Curation Interface is available at [http://actionability.clinicalgenome.org](http://actionability.clinicalgenome.org). 
+If you want to use Actionability Curation Interface just follow the link and ask for an account on that server.
+
+This repository contains source codes of services provided by the ClinGen Actionability Curation Interface server. 
+You can find installation instruction in the file doc/installation.pdf.
+Installation and source packages can be obtained from [the page with releases](https://github.com/BRL-BCM/actionability/releases).
+You need a server with [Genboree](https://github.com/BRL-BCM/genboree) to install your own instance of Actionability Curation Interface.
+
+Use of this software is governed by a license.  See the file LICENSE for details.

createUser.rb

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+#!/usr/bin/env ruby
+
+require 'genboreeTools'
+
+
+group_name = 'actionability'
+work_kb_name = 'actionability'
+release_kb_name = 'actionability_release'
+
+if ARGV.size < 5
+  puts "Parameters: login firstname lastname email roles ('ac scorer', 'ac consensus scorer', 'ac kst')"
+  exit 1
+end
+
+login=ARGV[0]
+firstname=ARGV[1]
+lastname=ARGV[2]
+email=ARGV[3]
+roles = ARGV[4..-1]
+
+
+genboree_add_user(login, 'actionability', email, firstname, lastname) if not genboree_user_exists(login)
+genboree_assign_user_to_group_as_author(login, group_name)
+redmine_assign_user_to_project(login, 'actionability', roles)
+
+puts "Completed!"

install.rb

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+#!/usr/bin/env ruby
+
+require 'genboreeTools'
+
+
+# copy static files
+`cp ./src/data/conf/actionability.yaml /usr/local/brl/data/conf/`
+`cp -r ./src/data/redmine /usr/local/brl/data/`
+
+# install app
+`./install_app.sh`
+
+
+group_name = 'actionability'
+work_kb_name = 'actionability'
+release_kb_name = 'actionability_release'
+header_file = '/usr/local/brl/data/redmine/html/clingen_actionability_header.html'
+footer_file = '/usr/local/brl/data/redmine/html/clingen_actionability_footer.html'
+
+# genboree group
+api_put("/REST/v1/grp/#{group_name}")
+
+# create KBs
+genboree_add_kb(group_name, work_kb_name)
+genboree_add_kb(group_name, release_kb_name)
+genboree_set_kb_public(group_name, release_kb_name)
+
+# get list of collections
+colls = []
+`ls kb_collections`.each { |x|
+    x.strip!
+    colls << x[0..-6] if x =~ /\.json$/
+}
+
+# create collections
+colls.each { |coll|
+    api_put( "/REST/v1/grp/#{group_name}/kb/#{work_kb_name}/coll/#{coll}/model", File.read("kb_collections/#{coll}.json") )
+    api_put( "/REST/v1/grp/#{group_name}/kb/#{release_kb_name}/coll/#{coll}/model", File.read("kb_collections/#{coll}.json") )
+}
+
+# create project for work
+redmine_add_project("actionability", "Actionability", ['genboree_ac'])
+redmine_configure_project_genboree_ac("actionability", group_name, work_kb_name, work_kb_name, release_kb_name, header_file, footer_file)
+
+# create project for release
+redmine_add_project("actionability_release", "Actionability Release", ['genboree_ac'], true)
+redmine_configure_project_genboree_ac("actionability_release", group_name, release_kb_name, work_kb_name, nil, header_file, footer_file)
+
+# load data to collections
+colls.each { |coll|
+    filename = "kb_data/#{coll}.json.gz"
+    next if coll =~ /^combined_model/ or not File.exist?(filename)
+    puts "Load data from file #{filename}"
+    api_put_from_file_in_chunks( "/REST/v1/grp/#{group_name}/kb/#{work_kb_name}/coll/#{coll}/docs?autoAdjust=true", "#{filename}" )
+}

install_app.sh

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+#!/bin/bash
+
+set -e  # stop on first error
+
+rm -rf /usr/local/brl/local/lib/ruby/site_ruby/1.8/brl/genboree/rest/extensions/clingenActionability
+cp -r src/ruby/brl/genboree/rest/extensions/clingenActionability  /usr/local/brl/local/lib/ruby/site_ruby/1.8/brl/genboree/rest/extensions/
+
+rm -rf /usr/local/brl/local/conf/apiExtensions/clingenActionability
+cp -r src/conf/apiExtensions/clingenActionability  /usr/local/brl/local/conf/apiExtensions/
+
+rm -rf /usr/local/brl/local/rails/redmine/sencha-deploy/genboree_ac
+cp -r src/redmine/sencha-deploy/genboree_ac  /usr/local/brl/local/rails/redmine/sencha-deploy/
+
+rm -rf /usr/local/brl/local/rails/redmine/plugins/genboree_ac
+cp -r src/redmine/plugins/genboree_ac  /usr/local/brl/local/rails/redmine/plugins/
+
+cd ${DIR_TARGET}/rails/redmine
+RAILS_ENV=production rake db:migrate
+RAILS_ENV=production rake redmine:plugins
+cd -