Merge pull request #36 from sanger/next_release

New column 'destination' and travis tests configuration

.ruby-gemset

@@ -0,0 +1 @@
+unified-warehouse

.ruby-version

@@ -0,0 +1 @@
+ruby-2.1.3

.travis.yml

@@ -0,0 +1,6 @@
+language: ruby
+# We don't specify a list of ruby versions, as Travis will fall back to .ruby-version
+# This is the behaviour we want, so no sense in overriding it
+bundler_args: --without deployment
+sudo: false
+cache: bundler

Gemfile

@@ -35,5 +35,5 @@ group :development do
 end
 
 group :deployment do
-  gem "psd_logger", :git => "git+ssh://[email protected]/sanger/psd_logger.git"
+  gem "psd_logger", :github => "sanger/psd_logger"
 end

Gemfile.lock

@@ -1,5 +1,5 @@
 GIT
-  remote: git+ssh://git@github.com/sanger/psd_logger.git
+  remote: git://github.com/sanger/psd_logger.git
   revision: dd2d634114df75b1d8535715c169a7fc99521389
   specs:
     psd_logger (0.1.6)

README

@@ -1,3 +1,12 @@
 Unified Warehouse Builder
 -------------------------
 This application is a denormalised warehouse for multiple LIMS.
+
+To Begin (Development)
+----------------------
+1. Clone the git repository
+2. Ensure ruby-2.1.3 is installed
+3. Install the relevant gems through bundler:
+  - bundle install
+4. Ensure the test suite is running:
+  - rake

Rakefile

@@ -5,3 +5,5 @@
 require File.expand_path('../config/application', __FILE__)
 
 UnifiedWarehouse::Application.load_tasks
+
+task :spec => 'db:setup'

db/migrate/20160120155501_add_data_destination_to_studies_table.rb

@@ -0,0 +1,7 @@
+class AddDataDestinationToStudiesTable < ActiveRecord::Migration
+  def change
+    change_table :study do |t|
+      t.string   'data_destination',  comment: 'The data destination type(s) for the study. It could be \'standard\', \'14mg\' or \'gseq\'. This may be extended, if Sanger gains more external customers. It can contain multiply destinations separated by a space.'
+    end
+  end
+end

db/structure.sql

@@ -1,8 +1,8 @@
--- MySQL dump 10.13  Distrib 5.6.20, for osx10.9 (x86_64)
+-- MySQL dump 10.13  Distrib 5.5.21, for osx10.6 (i386)
 --
 -- Host: localhost    Database: unified_warehouse_development
 -- ------------------------------------------------------
--- Server version	5.6.20
+-- Server version	5.5.21
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -247,6 +247,7 @@ CREATE TABLE `study` (
   `data_access_group` varchar(255) DEFAULT NULL,
   `prelim_id` varchar(20) DEFAULT NULL COMMENT 'The preliminary study id prior to entry into the LIMS',
   `hmdmc_number` varchar(255) DEFAULT NULL COMMENT 'The Human Materials and Data Management Committee approval number(s) for the study.',
+  `data_destination` varchar(255) DEFAULT NULL COMMENT 'The data destination type(s) for the study. It could be ''standard'', ''14mg'' or ''gseq''. This may be extended, if Sanger gains more external customers. It can contain multiply destinations separated by a space.',
   PRIMARY KEY (`id_study_tmp`),
   UNIQUE KEY `study_id_lims_id_study_lims_index` (`id_lims`,`id_study_lims`),
   UNIQUE KEY `study_uuid_study_lims_index` (`uuid_study_lims`),
@@ -285,7 +286,7 @@ CREATE TABLE `study_users` (
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2015-11-27  9:51:34
+-- Dump completed on 2016-01-20 17:12:58
 INSERT INTO schema_migrations (version) VALUES ('20141113110635');
 
 INSERT INTO schema_migrations (version) VALUES ('20141113130813');
@@ -326,3 +327,5 @@ INSERT INTO schema_migrations (version) VALUES ('20151110102754');
 
 INSERT INTO schema_migrations (version) VALUES ('20151127094701');
 
+INSERT INTO schema_migrations (version) VALUES ('20160120155501');
+

spec/models/study_spec.rb

@@ -61,7 +61,8 @@
         "alignments_in_bam" => true,
         "prelim_id" => "A1234",
         # The field may contain multiple numbers, and sometimes has comments.
-        "hmdmc_number" => "H12345; H67890; And then a comment"
+        "hmdmc_number" => "H12345; H67890; And then a comment",
+        "data_destination" => "standard"
       }
     end
 

spec/spec_helper.rb

@@ -14,6 +14,7 @@
   config.include FactoryGirl::Syntax::Methods
 
   config.before(:suite) do
+    ActiveRecord::Migration.maintain_test_schema!
     FactoryGirl.lint
   end