Merge pull request #40 from sanger/next_release

release-1.6.0

Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 
 # TODO: We pretty much just use active record and active mailer, do we need rails?
 gem "rails", "~> 4.1"
-gem "mysql2"
+gem "mysql2", "~> 0.3.17"
 
 # TODO: COnsider switching to Bunny if possible
 gem "amqp", "~> 1.5"

Gemfile.lock

@@ -88,7 +88,7 @@ GEM
       sinatra (~> 1.3)
       webmock (~> 1.8)
     multi_json (1.10.1)
-    mysql2 (0.3.16)
+    mysql2 (0.3.21)
     netrc (0.7.7)
     pry (0.10.1)
       coderay (~> 1.1.0)
@@ -179,7 +179,7 @@ DEPENDENCIES
   hashie (~> 3.3)
   migration_comments
   mocktra (~> 1.0.2)
-  mysql2
+  mysql2 (~> 0.3.17)
   psd_logger!
   rails (~> 4.1)
   rest-client

db/migrate/20160420084130_add_library_created_at_to_pac_bio_run.rb

@@ -0,0 +1,7 @@
+class AddLibraryCreatedAtToPacBioRun < ActiveRecord::Migration
+  def change
+    change_table :pac_bio_run do |t|
+      t.datetime :library_created_at,               null: true, comment: 'Timestamp of library creation'
+    end
+  end
+end

db/migrate/20160621125538_add_phenotype_column_to_sample_table.rb

@@ -0,0 +1,7 @@
+class AddPhenotypeColumnToSampleTable < ActiveRecord::Migration
+  def change
+    change_table :sample do |t|
+      t.string   'phenotype', comment: 'The phenotype of the sample as described in Sequencescape'
+    end
+  end
+end

db/migrate/20160810093024_unify_character_encoding_of_all_tables.rb

@@ -0,0 +1,73 @@
+class UnifyCharacterEncodingOfAllTables < ActiveRecord::Migration
+
+  # SQL provided by David Harper
+
+  def up
+    psd_only = ENV['PSD_ONLY']
+    say "Updating PSD tables only" if psd_only
+
+    say "Updating database defaults"
+    ActiveRecord::Base.connection.execute("ALTER DATABASE CHARACTER SET = 'utf8'  COLLATE = 'utf8_unicode_ci';")
+    say "Updating flgen_plate"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `flgen_plate` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating iseq_flowcell"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_flowcell` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating pac_bio_run"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `pac_bio_run` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating sample"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `sample` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating schema_migrations"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `schema_migrations` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating study"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `study` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    say "Updating study_users"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `study_users` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+
+    unless psd_only
+      say "Updating non psd tables"
+      say "Updating iseq_product_metrics",true
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_product_metrics` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+      say "Updating iseq_run_lane_metrics",true
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_lane_metrics` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+      say "Updating iseq_run_status",true
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_status` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+      say "Updating iseq_run_status_dict",true
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_status_dict` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_unicode_ci';")
+    end
+  end
+
+  def down
+    psd_only = ENV['PSD_ONLY']
+    say "Restoring PSD tables only" if psd_only
+
+    say "Restoring database defaults"
+    ActiveRecord::Base.connection.execute("ALTER DATABASE CHARACTER SET = 'latin1'  COLLATE = 'latin1_swedish_ci';")
+
+    say "Restoring flgen_plate"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `flgen_plate` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    say "Restoring iseq_flowcell"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_flowcell` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    say "Restoring pac_bio_run"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `pac_bio_run` CONVERT TO CHARACTER SET 'latin1' COLLATE 'latin1_swedish_ci';")
+    say "Restoring sample"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `sample` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    say "Restoring schema_migrations"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `schema_migrations` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    say "Restoring study"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `study` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    say "Restoring study_users"
+    ActiveRecord::Base.connection.execute("ALTER TABLE `study_users` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+
+    unless psd_only
+      say "Restoring non psd tables"
+      say "Restoring iseq_product_metrics"
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_product_metrics` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+      say "Restoring iseq_run_lane_metrics"
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_lane_metrics` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+      say "Restoring iseq_run_status"
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_status` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+      say "Restoring iseq_run_status_dict"
+      ActiveRecord::Base.connection.execute("ALTER TABLE `iseq_run_status_dict` CONVERT TO CHARACTER SET 'utf8' COLLATE 'utf8_general_ci';")
+    end
+  end
+end