Merge pull request #44 from sanger/next_release

Release 1.7.0

app/models/stock_resource.rb

@@ -0,0 +1,24 @@
+class StockResource < ActiveRecord::Base
+  include ResourceTools
+  include CompositeResourceTools
+
+  has_associated(:study)
+  has_associated(:sample)
+
+  has_composition_keys(:id_stock_resource_lims,:id_sample_tmp)
+
+  json do
+
+    translate(
+      :stock_resource_id => :id_stock_resource_lims,
+      :uuid              => :stock_resource_uuid
+    )
+
+    has_nested_model(:samples) do
+    end
+
+    ignore(:samples)
+
+  end
+
+end

db/migrate/20160919144230_add_stock_resources_table.rb

@@ -0,0 +1,35 @@
+class AddStockResourcesTable < ActiveRecord::Migration
+
+  def change
+    # Using singluar table names to maintain convention with rest of warehouse
+    create_table :stock_resource, primary_key: :id_stock_resource_tmp do |t|
+
+      t.datetime :last_updated,               null: false, comment: 'Timestamp of last update'
+      t.datetime :recorded_at,                null: false, comment: 'Timestamp of warehouse update'
+      t.datetime :created,                    null: false, comment: 'Timestamp of initial registration of stock in LIMS'
+      t.datetime :deleted_at,                 null: true,  comment: 'Timestamp of initial registration of deletion in parent LIMS. NULL if not deleted.'
+
+      t.column :id_sample_tmp,   'integer unsigned',   null: false, comment: 'Sample id, see "sample.id_sample_tmp"'
+      t.column :id_study_tmp,    'integer unsigned',   null: false, comment: 'Sample id, see "study.id_study_tmp"'
+      t.string :id_lims,                   limit:10,   null:false, comment: 'LIM system identifier'
+
+      t.string :id_stock_resource_lims,  limit: 20, null: false, comment: 'Lims specific identifier for the stock'
+      t.string :stock_resource_uuid,        limit: 36,              comment: 'Uuid identifier for the stock'
+
+      t.string :labware_type,            null: false, comment: 'The type of labware containing the stock. eg. Well, Tube'
+
+      t.string :labware_machine_barcode, null: false, comment: 'The barcode of the containing labware as read by a barcode scanner'
+      t.string :labware_human_barcode,   null: false, comment: 'The barcode of the containing labware in human readable format'
+      t.string :labware_coordinate,      null: true,  comment: 'For wells, the coordinate on the containing plate. Null for tubes.'
+
+      t.float :current_volume,           null: true, comment: 'The current volume of material in microlitres based on measurements and know usage'
+      t.float :initial_volume,           null: true, comment: 'The result of the initial volume measurement in microlitres conducted on the material'
+      t.float :concentration,            null: true, comment: 'The concentration of material recorded in the lab in nanograms per microlitre'
+
+      t.string :gel_pass,                null: true, comment: 'The recorded result for the qel QC assay.'
+      t.string :pico_pass,               null: true, comment: 'The recorded result for the pico green assay. A pass indicates a successful assay, not sufficient material.'
+      t.integer :snp_count,              null: true, comment: 'The number of markers detected in genotyping assays'
+      t.string :measured_gender,         null: true, comment: 'The gender call base on the genotyping assay'
+    end
+  end
+end

db/migrate/20170412135215_add_foreigin_key_contraints_to_stock_table.rb

@@ -0,0 +1,15 @@
+class AddForeiginKeyContraintsToStockTable < ActiveRecord::Migration
+
+  require './lib/foreign_key_constraint'
+  include ForeignKeyConstraint
+
+  def up
+    add_constraint :stock_resource, :sample, as: :id_sample_tmp, foreign_key: :id_sample_tmp
+    add_constraint :stock_resource, :study,  as: :id_study_tmp,  foreign_key: :id_study_tmp
+  end
+
+  def down
+    drop_constraint :stock_resource, :sample, as: :id_sample_tmp, foreign_key: :id_sample_tmp
+    drop_constraint :stock_resource, :study,  as: :id_study_tmp,  foreign_key: :id_study_tmp
+  end
+end

db/structure.sql

@@ -206,6 +206,43 @@ CREATE TABLE `schema_migrations` (
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
+--
+-- Table structure for table `stock_resource`
+--
+
+DROP TABLE IF EXISTS `stock_resource`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `stock_resource` (
+  `id_stock_resource_tmp` int(11) NOT NULL AUTO_INCREMENT,
+  `last_updated` datetime NOT NULL COMMENT 'Timestamp of last update',
+  `recorded_at` datetime NOT NULL COMMENT 'Timestamp of warehouse update',
+  `created` datetime NOT NULL COMMENT 'Timestamp of initial registration of stock in LIMS',
+  `deleted_at` datetime DEFAULT NULL COMMENT 'Timestamp of initial registration of deletion in parent LIMS. NULL if not deleted.',
+  `id_sample_tmp` int(10) unsigned NOT NULL COMMENT 'Sample id, see "sample.id_sample_tmp"',
+  `id_study_tmp` int(10) unsigned NOT NULL COMMENT 'Sample id, see "study.id_study_tmp"',
+  `id_lims` varchar(10) COLLATE utf8_unicode_ci NOT NULL COMMENT 'LIM system identifier',
+  `id_stock_resource_lims` varchar(20) COLLATE utf8_unicode_ci NOT NULL COMMENT 'Lims specific identifier for the stock',
+  `stock_resource_uuid` varchar(36) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Uuid identifier for the stock',
+  `labware_type` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The type of labware containing the stock. eg. Well, Tube',
+  `labware_machine_barcode` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The barcode of the containing labware as read by a barcode scanner',
+  `labware_human_barcode` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The barcode of the containing labware in human readable format',
+  `labware_coordinate` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'For wells, the coordinate on the containing plate. Null for tubes.',
+  `current_volume` float DEFAULT NULL COMMENT 'The current volume of material in microlitres based on measurements and know usage',
+  `initial_volume` float DEFAULT NULL COMMENT 'The result of the initial volume measurement in microlitres conducted on the material',
+  `concentration` float DEFAULT NULL COMMENT 'The concentration of material recorded in the lab in nanograms per microlitre',
+  `gel_pass` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'The recorded result for the qel QC assay.',
+  `pico_pass` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'The recorded result for the pico green assay. A pass indicates a successful assay, not sufficient material.',
+  `snp_count` int(11) DEFAULT NULL COMMENT 'The number of markers detected in genotyping assays',
+  `measured_gender` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'The gender call base on the genotyping assay',
+  PRIMARY KEY (`id_stock_resource_tmp`),
+  KEY `fk_stock_resource_to_sample` (`id_sample_tmp`),
+  KEY `fk_stock_resource_to_study` (`id_study_tmp`),
+  CONSTRAINT `fk_stock_resource_to_sample` FOREIGN KEY (`id_sample_tmp`) REFERENCES `sample` (`id_sample_tmp`),
+  CONSTRAINT `fk_stock_resource_to_study` FOREIGN KEY (`id_study_tmp`) REFERENCES `study` (`id_study_tmp`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
 --
 -- Table structure for table `study`
 --
@@ -290,7 +327,7 @@ CREATE TABLE `study_users` (
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2016-08-10 11:13:37
+-- Dump completed on 2017-04-12 14:56:42
 INSERT INTO schema_migrations (version) VALUES ('20141113110635');
 
 INSERT INTO schema_migrations (version) VALUES ('20141113130813');
@@ -341,3 +378,7 @@ INSERT INTO schema_migrations (version) VALUES ('20160621125538');
 
 INSERT INTO schema_migrations (version) VALUES ('20160810093024');
 
+INSERT INTO schema_migrations (version) VALUES ('20160919144230');
+
+INSERT INTO schema_migrations (version) VALUES ('20170412135215');
+

spec/models/stock_resource_spec.rb

@@ -0,0 +1,160 @@
+require 'spec_helper'
+
+describe StockResource do
+
+  let!(:mock_sample) { create(:sample) }
+  let!(:mock_study)  { create(:study)  }
+
+  before(:each) do
+    mock_sample; mock_study
+  end
+
+  shared_examples_for 'a stock resource' do
+
+    it_behaves_like 'maps JSON fields', {
+    }
+
+    it_behaves_like 'ignores JSON fields', [
+    ]
+
+    it_behaves_like 'belongs to',[
+     :sample,
+     :study
+    ], [:samples]
+
+    it_behaves_like 'a nested resource'
+  end
+
+  context 'for a well' do
+    # We have a row for the lane, the sample and the control
+    let(:expected_entries) { 1 }
+
+    it_behaves_like 'a stock resource'
+
+    let(:json) do
+      {
+        "created_at" => "2012-03-11 10:22:42",
+        "updated_at" => "2012-03-11 10:22:42",
+
+        "samples" => [
+          "sample_uuid" => "000000-0000-0000-0000-0000000000",
+          "study_uuid" => "000000-0000-0000-0000-0000000001"
+        ],
+
+        "stock_resource_id" => "12345",
+        "stock_resource_uuid" => "000000-0000-0000-0000-0000000002",
+
+        # We don't validate the barcode format, other
+        # LIMS might use different standards
+        "labware_machine_barcode" => "1220456987123",
+        "labware_human_barcode" => "DN456987D",
+        "labware_coordinate" => "A1",
+        "labware_type" => "well",
+
+        "current_volume" => 1.23,
+        "initial_volume" => 4.56,
+        "concentration"  => 23.56,
+
+        "gel_pass" => "Pass",
+        "pico_pass" => "Pass",
+        "snp_count" => 2,
+        "measured_gender" => "Unknown"
+
+      }
+    end
+
+    context 'when update with identical tag indexes' do
+
+      let(:example_lims) { 'example' }
+
+      let(:updated_json) do
+        updated_json = json.dup
+        updated_json['current_volume'] = 1.00
+        updated_json['updated_at'] = "2012-03-11 10:22:42"
+        updated_json
+      end
+
+      it 'reuses the existing records' do
+        described_class.create_or_update_from_json(json, example_lims)
+        original_ids = described_class.pluck(:id_stock_resource_tmp,:id_sample_tmp)
+        described_class.create_or_update_from_json(updated_json, example_lims)
+        new_ids = described_class.pluck(:id_stock_resource_tmp,:id_sample_tmp)
+        expect(new_ids).to eq(original_ids)
+      end
+    end
+
+  end
+
+  context 'for a well with SS formatted data' do
+    # We have a row for the lane, the sample and the control
+    let(:expected_entries) { 1 }
+
+    it_behaves_like 'a stock resource'
+
+    let(:json) do
+      {
+        "created_at" => "2012-03-11T10:22:42+00:00",
+        "updated_at" => "2012-03-11T10:22:42+00:00",
+
+        "samples" => [
+          "sample_uuid" => "000000-0000-0000-0000-0000000000",
+          "study_uuid" => "000000-0000-0000-0000-0000000001"
+        ],
+
+        "stock_resource_id" => 12345,
+        "stock_resource_uuid" => "000000-0000-0000-0000-0000000002",
+
+        # We don't validate the barcode format, other
+        # LIMS might use different standards
+        "labware_machine_barcode" => "1220456987123",
+        "labware_human_barcode" => "DN456987D",
+        "labware_coordinate" => "A1",
+        "labware_type" => "well",
+
+        "current_volume" => 1.23,
+        "initial_volume" => 4.56,
+        "concentration"  => 23.56,
+
+        "gel_pass" => "Pass",
+        "pico_pass" => "Pass",
+        "snp_count" => 2,
+        "measured_gender" => "Unknown"
+
+      }
+    end
+
+  end
+
+
+  context 'for a tube' do
+
+    let(:expected_entries) { 1 }
+
+    let(:json) do
+      {
+        "created_at" => "2012-03-11 10:22:42",
+        "updated_at" => "2012-03-11 10:22:42",
+
+        "samples" => [
+          "sample_uuid" => "000000-0000-0000-0000-0000000000",
+          "study_uuid" => "000000-0000-0000-0000-0000000001"
+        ],
+
+        "stock_resource_id" => "12345",
+        "stock_resource_uuid" => "000000-0000-0000-0000-0000000002",
+
+        # We don't validate the barcode format, other
+        # LIMS might use different standards
+        "machine_barcode" => "3040456987123",
+        "human_barcode" => "NT456987D",
+        "labware_type" => "tube"
+
+        # QC data will not always be present, especially for tubes
+        # So lets make sure its absence doesn't cause issues
+
+      }
+    end
+
+  end
+
+end

spec/support/it_behaves_like_belongs_to.rb

@@ -3,13 +3,15 @@
   let!(:json_handler) { described_class.send(:json) }
 
   def find_target(json,graph)
+    return json if graph.nil?
     return json[graph.to_s].first if graph.is_a?(Symbol)
     return json[graph.first.to_s].first if (graph.count==1 && graph.first.is_a?(Symbol))
     k,v = graph.first
     find_target(json[k.to_s].first,v)
   end
 
   def find_handler(handler,graph)
+    return handler if graph.nil?
     return handler.nested_models[graph] if graph.is_a?(Symbol)
     return handler.nested_models[graph.first] if (graph.count==1 && graph.first.is_a?(Symbol))
     k,v = graph.first
@@ -40,6 +42,7 @@ def find_handler(handler,graph)
   end
 
   after(:each) do
-    described_class.send(:create_or_update, subject.detect {|json| json.class == owning_handler })
+    content = subject.is_a?(Array) ? subject.detect {|json| json.class == owning_handler } : subject
+    described_class.send(:create_or_update, content)
   end
 end