Merge pull request #42 from ninjaconcept/37-molecule-model

Creation of the Molecule model

app/models/molecule.rb

+class Molecule < ActiveRecord::Base
+  has_many :samples
+
+  validates_uniqueness_of :inchikey
+end

app/models/sample.rb

@@ -9,6 +9,8 @@ class Sample < ActiveRecord::Base
   has_many :reactions_as_starting_material, through: :reactions_starting_material_samples, source: :reaction
   has_many :reactions_as_reactant, through: :reactions_reactant_samples, source: :reaction
   has_many :reactions_as_product, through: :reactions_product_samples, source: :reaction
+
+  belongs_to :molecule
   
   composed_of :amount, mapping: %w(amount_value, amount_unit)
 end

db/migrate/20150817200859_create_molecules.rb

+class CreateMolecules < ActiveRecord::Migration
+  def change
+    create_table :molecules do |t|
+      t.string :inchikey
+      t.string :inchistring
+      t.float :density
+      t.float :molecular_weight
+      t.binary :molfile
+      t.float :melting_point
+      t.float :boiling_point
+      t.string :sum_formular
+      t.string :names, array: true, default: []
+      t.string :iupac_name
+      t.string :molecule_svg_file
+
+      t.timestamps null: false
+    end
+
+    add_index :molecules, :inchikey, unique: true
+  end
+end

db/migrate/20150818100730_add_molecule_id_to_samples.rb

+class AddMoleculeIdToSamples < ActiveRecord::Migration
+  def change
+    add_column :samples, :molecule_id, :integer
+  end
+end

db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20150817085601) do
+ActiveRecord::Schema.define(version: 20150818100730) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -49,6 +49,25 @@ ActiveRecord::Schema.define(version: 20150817085601) do
   add_index "collections_samples", ["collection_id"], name: "index_collections_samples_on_collection_id", using: :btree
   add_index "collections_samples", ["sample_id"], name: "index_collections_samples_on_sample_id", using: :btree
 
+  create_table "molecules", force: :cascade do |t|
+    t.integer  "sample_id"
+    t.string   "inchikey"
+    t.string   "inchistring"
+    t.float    "density"
+    t.float    "molecular_weight"
+    t.binary   "molfile"
+    t.float    "melting_point"
+    t.float    "boiling_point"
+    t.string   "sum_formular"
+    t.string   "names",             default: [],              array: true
+    t.string   "iupac_name"
+    t.string   "molecule_svg_file"
+    t.datetime "created_at",                     null: false
+    t.datetime "updated_at",                     null: false
+  end
+
+  add_index "molecules", ["inchikey"], name: "index_molecules_on_inchikey", unique: true, using: :btree
+
   create_table "reactions", force: :cascade do |t|
     t.string   "name"
     t.datetime "created_at", null: false
@@ -86,6 +105,7 @@ ActiveRecord::Schema.define(version: 20150817085601) do
     t.datetime "created_at",                null: false
     t.datetime "updated_at",                null: false
     t.text     "description",  default: ""
+    t.integer  "molecule_id"
   end
 
   create_table "users", force: :cascade do |t|

spec/factories/molecules.rb

+FactoryGirl.define do
+  factory :molecule do
+  	sample_id         "1"
+    inchikey          "inchikey"
+    inchistring       "inchistring"
+    density           0.12345
+    molecular_weight  0.54321
+    molfile           ""
+    melting_point     150.00
+    boiling_point     100.00
+    sum_formular      "sum_formular"
+    names             %w(name1 name2 name3)
+    iupac_name        "iupac_name"
+    molecule_svg_file "molecule_svg_file"
+  end
+end

spec/models/molecule_spec.rb

+require 'rails_helper'
+require 'digest'
+
+RSpec.describe Molecule, type: :model do
+  
+  describe 'creation' do
+    let(:molecule) { create(:molecule) }
+    it 'is possible to create a valid molecule' do
+      expect(molecule.valid?).to be(true)
+    end
+
+    it 'should have a unique inchikey' do
+      molecule.save
+      invalid_molecule = Molecule.new
+      invalid_molecule.inchikey = molecule.inchikey
+      expect {invalid_molecule.save!}.to raise_error
+    end
+  end
+
+  describe 'persistance' do
+    let (:molecule) { build(:molecule) }
+    it 'should persist array of names' do
+      molecule.names = %w(foo bar quz)
+      molecule.save
+      persisted_molecule = Molecule.last
+      expect(persisted_molecule.names).to match_array(molecule.names)
+    end
+
+    it 'should persist the binary molfile' do
+      molfile_example = File.open("spec/models/molecule_spec.rb", "rb")
+      molecule.molfile = molfile_example.read
+      molfile_example.close
+      molecule.save
+      persisted_molecule = Molecule.last
+      persisted_molfile_SHA =
+        (Digest::SHA256.new << persisted_molecule.molfile).hexdigest
+      molfile_SHA =
+        (Digest::SHA256.new << molecule.molfile).hexdigest
+      expect(persisted_molfile_SHA).to be === (molfile_SHA)
+    end
+  end
+end

spec/models/sample_spec.rb

@@ -11,4 +11,18 @@ RSpec.describe Sample, type: :model do
 
 
 
+  context 'with molecule' do
+
+    let(:sample) { build(:sample) }
+    let(:molecule) {create(:molecule)}
+
+    it 'it should belong to a sample' do
+      sample.molecule = molecule
+      sample.save
+
+      persisted_sample = Sample.last
+      expect(persisted_sample.molecule).to be === (molecule)
+    end
+  end
+
 end