Refactor Sample Details, add external_label to samples.

app/api/chemotion/sample_api.rb

@@ -76,6 +76,7 @@ module Chemotion
       params do
         requires :id, type: Integer, desc: "Sample id"
         optional :name, type: String, desc: "Sample name"
+        optional :external_label, type: String, desc: "Sample external label"
         optional :amount_value, type: Float, desc: "Sample amount_value"
         optional :amount_unit, type: String, desc: "Sample amount_unit"
         optional :description, type: String, desc: "Sample description"
@@ -106,6 +107,7 @@ module Chemotion
       desc "Create a sample"
       params do
         requires :name, type: String, desc: "Sample name"
+        optional :external_label, type: String, desc: "Sample external label"
         requires :amount_value, type: Float, desc: "Sample amount_value"
         requires :amount_unit, type: String, desc: "Sample amount_unit"
         requires :description, type: String, desc: "Sample description"

app/assets/javascripts/components/actions/ElementActions.js

@@ -152,6 +152,7 @@ class ElementActions {
       id: '_new_',
       type: 'sample',
       name: 'New Sample',
+      external_label: '',
       amount_value: 0,
       amount_unit: 'g',
       description: '',

app/assets/javascripts/components/fetchers/SamplesFetcher.js

 import 'whatwg-fetch';
 import Sample from '../models/Sample';
+import SampleProxy from '../proxies/SampleProxy';
 
 
 // TODO: SamplesFetcher also updates Samples and so on...naming?
@@ -11,7 +12,7 @@ export default class SamplesFetcher {
       .then((response) => {
         return response.json()
       }).then((json) => {
-        return new Sample(json.sample);
+        return new SampleProxy(json.sample);
       }).catch((errorMessage) => {
         console.log(errorMessage);
       });
@@ -52,6 +53,7 @@ export default class SamplesFetcher {
       },
       body: JSON.stringify({
         name: paramObj.name,
+        external_label: paramObj.external_label,
         amount_value: paramObj.amount_value,
         amount_unit: paramObj.amount_unit,
         description: paramObj.description,
@@ -79,6 +81,7 @@ export default class SamplesFetcher {
       },
       body: JSON.stringify({
         name: paramObj.name,
+        external_label: paramObj.external_label,
         amount_value: paramObj.amount_value,
         amount_unit: paramObj.amount_unit,
         description: paramObj.description,

app/assets/javascripts/components/models/Sample.js

@@ -6,6 +6,11 @@ export default class Sample {
     Object.assign(this, args);
   }
 
+  // methods regarding sharing and sample detail levels
+  isRestricted() {
+    return this.is_restricted;
+  }
+
   get name() {
     return this._name
   }
@@ -14,10 +19,42 @@ export default class Sample {
     this._name = name
   }
 
+  get external_label() {
+    return this._external_label;
+  }
+
+  set external_label(label) {
+    this._external_label = label;
+  }
+
+  get location() {
+    return this._location;
+  }
+
+  set location(location) {
+    this._location = location;
+  }
+
+  get description() {
+    return this._description;
+  }
+
+  set description(description) {
+    this._description = description;
+  }
+
+  get impurities() {
+    return this._impurities;
+  }
+
+  set impurities(impurities) {
+    this._impurities = impurities;
+  }
+
   get amount() {
     return({
-      value: amount_value,
-      unit: amount_unit
+      value: this.amount_value,
+      unit: this.amount_unit
     })
   }
 
@@ -66,11 +103,17 @@ export default class Sample {
         return amount_mg;
         break;
       case 'ml':
-        return amount_mg / this.molecule_density;
-        break;
+        let molecule_density = this.molecule_density;
+        if(molecule_density) {
+          return amount_mg / this.molecule_density;
+          break;
+        }
       case 'mmol':
-        return amount_mg * this.purity / this.molecule_molecular_weight;
-        break;
+        let molecule_molecular_weight = this.molecule_molecular_weight
+        if (molecule_molecular_weight) {
+          return amount_mg * this.purity / molecule_molecular_weight;
+          break;
+        }
       default:
         return amount_mg
     }
@@ -96,10 +139,38 @@ export default class Sample {
     return this.molecule && this.molecule.density || 1.0
   }
 
+  set molecule_density(density) {
+    this.molecule.density = density;
+  }
+
   get molecule_molecular_weight() {
     return this.molecule && this.molecule.molecular_weight
   }
 
+  get molecule_formula() {
+    return this.molecule && this.molecule.sum_formular;
+  }
+
+  get molecule_inchistring() {
+    return this.molecule && this.molecule.inchistring;
+  }
+
+  get molecule_boiling_point() {
+    return this.molecule && this.molecule.boiling_point;
+  }
+
+  set molecule_boiling_point(bp) {
+    this.molecule.boiling_point = bp;
+  }
+
+  get molecule_melting_point() {
+    return this.molecule && this.molecule.melting_point;
+  }
+
+  set molecule_melting_point(mp) {
+    this.molecule.melting_point = mp;
+  }
+
   get purity() {
     return this._purity || 1.0
   }
@@ -115,5 +186,4 @@ export default class Sample {
   set molecule(molecule) {
     this._molecule = new Molecule(molecule)
   }
-
 };

app/assets/javascripts/components/proxies/SampleProxy.js

+import Sample from '../models/Sample';
+import Molecule from '../models/Molecule';
+
+export default class SampleProxy extends Sample {
+  constructor(args) {
+    super(args)
+
+    let sampleMethodsWithGetAndSet = [
+      'name', 'external_label', 'location', 'description', 'impurities', 'amount_unit', 'amount_value', 'purity'
+    ]
+
+    sampleMethodsWithGetAndSet.forEach((m) => {
+      Object.defineProperty(this, m, {
+        get: function() { return this.methodOrRestrictionPattern(m) },
+        set: function(arg) { super[m] = arg }
+      })
+    })
+
+    let sampleMethodsWithGet = [
+      'amount_mg', 'amount_ml', 'amount_mmol'
+    ]
+
+    sampleMethodsWithGet.forEach((m) => {
+      Object.defineProperty(this, m, {
+        get: function() { return this.methodOrRestrictionPattern(m) },
+      })
+    })
+
+    let moleculeMethodsWithGetAndSet = [
+      'molecule_density', 'molecule_boiling_point', 'molecule_melting_point'
+    ]
+
+    moleculeMethodsWithGetAndSet.forEach((m) => {
+      Object.defineProperty(this, m, {
+        get: function() { return this.methodOnMoleculeOrRestrictionPattern(m) },
+        set: function(arg) { super[m] = arg }
+      })
+    })
+
+    let moleculeMethodsWithGet = [
+      'molecule_molecular_weight', 'molecule_formula', 'molecule_inchistring'
+    ]
+
+    moleculeMethodsWithGet.forEach((m) => {
+      Object.defineProperty(this, m, {
+        get: function() { return this.methodOnMoleculeOrRestrictionPattern(m) },
+      })
+    })
+  }
+
+  get restrictionPattern() {
+    return '***';
+  }
+
+  methodOrRestrictionPattern(method) {
+    if(super.isRestricted && super[method] == undefined) {
+      return this.restrictionPattern;
+    } else {
+      return super[method];
+    }
+  }
+
+  methodOnMoleculeOrRestrictionPattern(method) {
+    if(super.isRestricted && super.molecule == undefined) {
+      return this.restrictionPattern;
+    } else {
+      return super[method];
+    }
+  }
+
+  get amount() {
+    return({
+      value: this.amount_value,
+      unit: this.amount_unit
+    })
+  }
+
+  get molecule() {
+    return this.methodOrRestrictionPattern('molecule');
+  }
+
+  set molecule(molecule) {
+    super.molecule = new Molecule(molecule)
+  }
+}

app/models/user.rb

@@ -18,4 +18,8 @@ class User < ActiveRecord::Base
   def owns_unshared_collections?(collections)
     owns_collections?(collections) && collections.pluck(:is_shared).none?
   end
+
+  def name
+    "#{first_name} #{last_name}"
+  end
 end

app/proxies/sample_proxy.rb

@@ -18,7 +18,7 @@ class SampleProxy
       sample_attr.each do |attr|
         new_sample_hash[attr] = s[attr]
       end
-      new_sample_hash[:is_scoped] = true
+      new_sample_hash[:is_restricted] = true
 
       {sample: new_sample_hash}
     else
@@ -54,13 +54,18 @@ class SampleProxy
       [
         :id,
         :type,
-        #:weight
+        :external_label,
+        :amount_value,
+        :amount_unit
       ]
     when 1
       [
         :id,
         :type,
-        :molecule
+        :external_label,
+        :molecule,
+        :amount_value,
+        :amount_unit
       ]
     when 2
 

app/serializers/sample_serializer.rb

 class SampleSerializer < ActiveModel::Serializer
   attributes :id, :type, :name, :description, :created_at, :collection_labels, :amount_value, :amount_unit, :molfile,
-             :purity, :solvent, :impurities, :location, :weight, :volume, :is_top_secret, :is_scoped
+             :purity, :solvent, :impurities, :location, :weight, :volume, :is_top_secret, :is_restricted, :external_label
 
   has_one :molecule
 
@@ -29,7 +29,7 @@ class SampleSerializer < ActiveModel::Serializer
     object.volume
   end
 
-  def is_scoped
+  def is_restricted
     false
   end
 end

app/serializers/user_serializer.rb

@@ -2,7 +2,7 @@ class UserSerializer < ActiveModel::Serializer
   attributes :id, :name, :initials
 
   def name
-    "#{object.first_name} #{object.last_name}"
+    object.name
   end
 
   def initials

config/environments/production.rb

@@ -29,7 +29,7 @@ Rails.application.configure do
   # config.assets.css_compressor = :sass
 
   # Do not fallback to assets pipeline if a precompiled asset is missed.
-  config.assets.compile = false
+  config.assets.compile = true
 
   # Asset digests allow you to set far-future HTTP expiration dates on all assets,
   # yet still be able to expire them through the digest params.

db/migrate/20151005151021_add_external_label_to_samples.rb

+class AddExternalLabelToSamples < ActiveRecord::Migration
+  def change
+    add_column :samples, :external_label, :string, default: ""
+  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: 20151004084416) do
+ActiveRecord::Schema.define(version: 20151005151021) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -145,17 +145,18 @@ ActiveRecord::Schema.define(version: 20151004084416) do
     t.string   "name"
     t.float    "amount_value"
     t.string   "amount_unit"
-    t.datetime "created_at",                    null: false
-    t.datetime "updated_at",                    null: false
-    t.text     "description",   default: ""
+    t.datetime "created_at",                     null: false
+    t.datetime "updated_at",                     null: false
+    t.text     "description",    default: ""
     t.integer  "molecule_id"
     t.binary   "molfile"
     t.float    "purity"
-    t.string   "solvent",       default: ""
-    t.string   "impurities",    default: ""
-    t.string   "location",      default: ""
-    t.boolean  "is_top_secret", default: false
+    t.string   "solvent",        default: ""
+    t.string   "impurities",     default: ""
+    t.string   "location",       default: ""
+    t.boolean  "is_top_secret",  default: false
     t.string   "ancestry"
+    t.string   "external_label", default: ""
   end
 
   add_index "samples", ["molecule_id"], name: "index_samples_on_sample_id", using: :btree

spec/api/collection_api_spec.rb

@@ -9,7 +9,7 @@ describe Chemotion::CollectionAPI do
   }
 
   context 'authorized user logged in' do
-    let(:user)  { create(:user, name: 'Musashi') }
+    let(:user)  { create(:user, first_name: 'Musashi', last_name: 'M') }
     let(:u2)    { create(:user) }
     let!(:c1)   { create(:collection, user: user, is_shared: false) }
     let!(:c2)   { create(:collection, user: user, shared_by_id: user.id, is_shared: true) }
@@ -304,7 +304,7 @@ describe Chemotion::CollectionAPI do
             post '/api/v1/collections/shared', params
 
             # naming convention for shared collections
-            c = Collection.find_by(label: 'My project with Musashi')
+            c = Collection.find_by(label: 'My project with Musashi M')
             expect(c).to_not be_nil
             expect(c.user_id).to eq user.id
             expect(c.samples).to match_array [s1, s2]
@@ -347,7 +347,7 @@ describe Chemotion::CollectionAPI do
           it 'creates no shared collection' do
             post '/api/v1/collections/shared', params
 
-            c = Collection.find_by(label: 'My project with Musashi')
+            c = Collection.find_by(label: 'My project with Musashi M')
             expect(c).to be_nil
           end
         end