Merge branch 'development' into '243-report-format-spaces-before-rf'

# Conflicts:
#   app/assets/javascripts/components/report/SectionSiSynthesis.js

Capfile

@@ -3,7 +3,8 @@ require 'capistrano/setup'
 
 # Include default deployment tasks
 require 'capistrano/deploy'
-
+require "capistrano/scm/git"
+install_plugin Capistrano::SCM::Git
 require 'capistrano/rvm' # Ruby version manager
 require 'capistrano/nvm' # Node version manager
 require 'capistrano/npm' # Node package manager
@@ -12,6 +13,7 @@ require 'capistrano/rails/assets'
 require 'capistrano/rails/migrations'
 #require 'capistrano/delayed_job'
 require 'whenever/capistrano'
-
+require 'slackistrano/capistrano'
+require_relative 'lib/slackistrano_custom_messaging'
 # Load custom tasks from `lib/capistrano/tasks` if you have any defined
 Dir.glob('lib/capistrano/tasks/*.rake').each { |r| import r }

Gemfile

@@ -99,6 +99,7 @@ gem 'paranoia', '~> 2.0'
 
 gem 'backup'
 gem 'whenever', require: false
+gem 'rubocop', require: false
 gem 'yaml_db'
 
 gem 'ruby-ole'
@@ -160,13 +161,14 @@ group :development, :test do
   # Remove all assets requests
   gem 'quiet_assets'
 
-  gem 'capistrano', '3.4.1'
+  gem 'capistrano', '3.9.1'
   gem 'capistrano-bundler'
   gem 'capistrano-npm'
   gem 'capistrano-nvm', require: false
   gem 'capistrano-rails'
   gem 'capistrano-rvm'
   # gem 'capistrano3-delayed-job'
+  gem 'slackistrano'
 end
 
 group :test do

Gemfile.lock

@@ -101,11 +101,14 @@ GEM
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
     addressable (2.4.0)
+    airbrussh (1.3.0)
+      sshkit (>= 1.6.1, != 1.7.0)
     ancestry (2.1.0)
       activerecord (>= 3.0.0)
     archive-zip (0.7.0)
       io-like (~> 0.3.0)
     arel (6.0.4)
+    ast (2.3.0)
     autoprefixer-rails (6.3.6)
       execjs
     awesome_print (1.6.1)
@@ -139,10 +142,11 @@ GEM
       uniform_notifier (~> 1.10.0)
     byebug (8.2.5)
     callsite (0.0.11)
-    capistrano (3.4.1)
+    capistrano (3.9.1)
+      airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
-      sshkit (~> 1.3)
+      sshkit (>= 1.9.0)
     capistrano-bundler (1.1.4)
       capistrano (~> 3.1)
       sshkit (~> 1.2)
@@ -291,7 +295,7 @@ GEM
     httparty (0.13.7)
       json (~> 1.8)
       multi_xml (>= 0.5.2)
-    i18n (0.7.0)
+    i18n (0.8.6)
     i18n_data (0.7.0)
     ice_nine (0.11.2)
     io-like (0.3.0)
@@ -353,7 +357,7 @@ GEM
       net-ssh (>= 2.6.5)
     net-sftp (2.1.2)
       net-ssh (>= 2.6.5)
-    net-ssh (3.1.1)
+    net-ssh (4.2.0)
     nokogiri (1.6.7.2)
       mini_portile2 (~> 2.0.0.rc2)
     open4 (1.3.4)
@@ -364,14 +368,18 @@ GEM
       cocaine (~> 0.5.5)
       mime-types
       mimemagic (~> 0.3.0)
+    parallel (1.11.2)
     paranoia (2.1.5)
       activerecord (~> 4.0)
+    parser (2.4.0.0)
+      ast (~> 2.2)
     pdf-core (0.6.1)
     pg (0.18.4)
     pg_search (1.0.5)
       activerecord (>= 3.1)
       activesupport (>= 3.1)
       arel
+    powerpack (0.1.1)
     prawn (2.1.0)
       pdf-core (~> 0.6.1)
       ttfunk (~> 1.4.0)
@@ -416,7 +424,9 @@ GEM
       activesupport (= 4.2.0)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (12.0.0)
+    rainbow (2.2.2)
+      rake
+    rake (12.1.0)
     rb-fsevent (0.9.7)
     rb-inotify (0.9.7)
       ffi (>= 0.5.0)
@@ -449,8 +459,16 @@ GEM
       rspec-support (~> 3.4.0)
     rspec-support (3.4.1)
     rtf (0.3.3)
+    rubocop (0.49.1)
+      parallel (~> 1.10)
+      parser (>= 2.3.3.1, < 3.0)
+      powerpack (~> 0.1)
+      rainbow (>= 1.99.1, < 3.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (~> 1.0, >= 1.0.1)
     ruby-mailchecker (3.0.27)
     ruby-ole (1.2.12)
+    ruby-progressbar (1.8.1)
     ruby_parser (3.8.4)
       sexp_processor (~> 4.1)
     rubyzip (1.1.7)
@@ -483,6 +501,8 @@ GEM
     skinny (0.2.4)
       eventmachine (~> 1.0.0)
       thin (>= 1.5, < 1.7)
+    slackistrano (3.8.1)
+      capistrano (>= 3.8.1)
     spring (1.7.1)
     sprite-factory (1.7.1)
     sprockets (3.7.1)
@@ -493,7 +513,7 @@ GEM
       activesupport (>= 4.0)
       sprockets (>= 3.0.0)
     sqlite3 (1.3.11)
-    sshkit (1.10.0)
+    sshkit (1.14.0)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     stackprof (0.2.10)
@@ -517,6 +537,7 @@ GEM
       thread_safe (~> 0.1)
     uglifier (3.0.0)
       execjs (>= 0.3.0, < 3)
+    unicode-display_width (1.2.1)
     unicode_utils (1.4.0)
     uniform_notifier (1.10.0)
     virtus (1.0.5)
@@ -562,7 +583,7 @@ DEPENDENCIES
   browserify-rails (~> 3.0.1)
   bullet
   byebug
-  capistrano (= 3.4.1)
+  capistrano (= 3.9.1)
   capistrano-bundler
   capistrano-npm
   capistrano-nvm
@@ -621,12 +642,14 @@ DEPENDENCIES
   rqrcode
   rspec-rails
   rtf
+  rubocop
   ruby-mailchecker
   ruby-ole
   sablon!
   sass-rails (~> 5.0, >= 5.0.6)
   sdoc (~> 0.4.0)
   selenium-webdriver (~> 3.0.5)
+  slackistrano
   spring
   stackprof
   swot
@@ -640,4 +663,4 @@ DEPENDENCIES
   yaml_db
 
 BUNDLED WITH
-   1.15.3
+   1.15.4

app/api/chemotion/molecule_api.rb

@@ -42,6 +42,26 @@ module Chemotion
         molecule.load_cas if molecule
         molecule
       end
+
+      desc 'return names of the molecule'
+      params do
+        requires :inchikey, type: String, desc: 'Molecule inchikey'
+        optional :new_name, type: String, desc: 'New molecule_name'
+      end
+      get :names do
+        inchikey = params[:inchikey]
+        new_name = params[:new_name]
+
+        mol = Molecule.find_by(inchikey: inchikey)
+        return [] if mol.blank?
+
+        user_id = current_user.id
+        mol.create_molecule_name_by_user(new_name, user_id) if new_name.present?
+
+        mol.molecule_names.map do |mn|
+          { id: mn.id, name: mn.name }
+        end
+      end
     end
   end
 end

app/api/chemotion/report_api.rb

@@ -13,15 +13,15 @@ module Chemotion
 
       def excluded_field
         %w(
-          id molecule_id created_by deleted_at
-          user_id fingerprint_id sample_svg_file xref
+          id molecule_id created_by deleted_at identifier molecule_name_id
+          user_id fingerprint_id sample_svg_file xref impurities ancestry
         )
       end
 
       def included_field
         %w(
-          molecule.cano_smiles molecule.sum_formular
-          molecule.inchistring molecule.molecular_weight
+          molecule.cano_smiles molecule.sum_formular molecule_name
+          molecule.inchistring molecule.molecular_weight molecule.inchikey
         )
       end
 
@@ -31,11 +31,11 @@ module Chemotion
         elements = "#{type}s".to_sym
         if checkedAll
           Collection.find(currentCollection)
-                    .send(elements).where.not(id: uncheckedIds)
+                    .send(elements).where.not(id: uncheckedIds).order(updated_at: :desc)
         else
           Collection.find(currentCollection)
                     .send(elements).where(id: checkedIds)
-                    .order("position(samples.id::text in '#{checkedIds}')")
+                    .order("position(#{type}s.id::text in '#{checkedIds}')")
         end
       end
 
@@ -69,7 +69,7 @@ module Chemotion
         requires :uncheckedIds, type: Array
         requires :checkedAll, type: Boolean
         requires :currentCollection, type: Integer
-        requires :removedColumns, type: Array
+        requires :removedColumns, type: Array[String]
         requires :exportType, type: Integer
       end
       post :export_samples_from_selections do
@@ -101,7 +101,7 @@ module Chemotion
           type, checkedAll, checkedIds, uncheckedIds, currentCollection
         )
         samples = if type == 'sample'
-                    elements.includes(:molecule)
+                    elements.includes([:molecule,:molecule_name])
                   elsif type == 'reaction'
                     elements.map { |r|
                       r.starting_materials + r.reactants + r.products

app/api/chemotion/sample_api.rb

@@ -247,6 +247,7 @@ module Chemotion
         optional :residues, type: Array
         optional :elemental_compositions, type: Array
         optional :xref, type: Hash
+        optional :molecule_name_id, type: Integer
         requires :container, type: Hash
         #use :root_container_params
       end
@@ -316,6 +317,7 @@ module Chemotion
         optional :residues, type: Array
         optional :elemental_compositions, type: Array
         optional :xref, type: Hash
+        optional :molecule_name_id, type: Integer
         requires :container, type: Hash
       end
       post do
@@ -343,7 +345,8 @@ module Chemotion
           residues: params[:residues],
           elemental_compositions: params[:elemental_compositions],
           created_by: current_user.id,
-          xref: params[:xref]
+          xref: params[:xref],
+          molecule_name_id: params[:molecule_name_id]
         }
 
         # otherwise ActiveRecord::UnknownAttributeError appears

app/assets/javascripts/components/QuillEditor.js

 import React from 'react';
 import ReactDOM from 'react-dom';
+import PropTypes from 'prop-types';
 
 import Quill from 'quill';
 import Delta from 'quill-delta';
@@ -256,18 +257,18 @@ export default class QuillEditor extends React.Component {
 }
 
 QuillEditor.propTypes = {
-  value: React.PropTypes.object,
-  customToolbar: React.PropTypes.object,
-  toolbarSymbol: React.PropTypes.array,
-  theme: React.PropTypes.string,
-  height: React.PropTypes.string,
-  disabled: React.PropTypes.bool,
-  onChange: React.PropTypes.func,
+  value: PropTypes.object,
+  customToolbar: PropTypes.oneOfType([PropTypes.object, PropTypes.string]),
+  toolbarSymbol: PropTypes.array,
+  theme: PropTypes.string,
+  height: PropTypes.string,
+  disabled: PropTypes.bool,
+  onChange: PropTypes.func,
 };
 
 QuillEditor.defaultProps = {
   value: {},
-  customToolbar: "",
+  customToolbar: '',
   toolbarSymbol: [],
   theme: 'snow',
   height: '230px',

app/assets/javascripts/components/SampleDetailsContainersAux.js

@@ -150,7 +150,7 @@ const HeaderNormal = ({ sample, container, mode, readOnly, isDisabled, serial,
   const kind = container.extended_metadata.kind || '';
   const status = container.extended_metadata.status || '';
   const previewImg = previewImage(container);
-  const content = container.extended_metadata.content;
+  const content = container.extended_metadata.content || { ops: [{ insert: '' }] };
   const contentOneLine = {
     ops: content.ops.map((x) => {
       const c = Object.assign({}, x);

app/assets/javascripts/components/SampleForm.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { Button, Checkbox, FormGroup, FormControl, InputGroup, ControlLabel,
   Table, Glyphicon } from 'react-bootstrap';
 import Select from 'react-select';
-
+import DetailActions from './actions/DetailActions';
 import NumeralInputWithUnitsCompo from './NumeralInputWithUnitsCompo';
 import { solventOptions } from './staticDropdownOptions/options';
 
@@ -13,9 +13,16 @@ export default class SampleForm extends React.Component {
     this.state = {
       sample: props.sample,
       molarityBlocked: (props.sample.molarity_value || 0) <= 0,
+      isMolNameLoading: false,
     };
 
     this.handleFieldChanged = this.handleFieldChanged.bind(this);
+    this.updateMolName = this.updateMolName.bind(this);
+    this.addMolName = this.addMolName.bind(this);
+  }
+
+  componentWillReceiveProps(nextProps) {
+    this.setState({ isMolNameLoading: false });
   }
 
   handleAmountChanged(amount) {
@@ -74,18 +81,53 @@ export default class SampleForm extends React.Component {
     return (<span />);
   }
 
+  openMolName(moleculeNames) {
+    const { sample } = this.state;
+    if (moleculeNames.length <= 1) {
+      this.setState({ isMolNameLoading: true });
+      DetailActions.updateMoleculeNames(sample);
+    }
+  }
+
+  addMolName(moleculeName) {
+    const { sample } = this.state;
+    this.setState({ isMolNameLoading: true });
+    DetailActions.updateMoleculeNames(sample, moleculeName.label);
+  }
+
+  updateMolName(e) {
+    const { sample } = this.state;
+    sample.molecule_name = e;
+    this.props.parent.setState({ sample });
+  }
+
   moleculeInput(sample) {
+    const mnos = sample.molecule_names;
+    const mno = sample.molecule_name;
+    let moleculeNames = mno ? [mno] : [];
+    if (sample && mnos) {
+      moleculeNames = mnos.map(n => (
+        Object.assign({ label: n.name, value: n.id })
+      ));
+    }
+
+    const onOpenMolName = () => this.openMolName(moleculeNames);
+
     return (
       <FormGroup style={{ width: '100%' }}>
         <ControlLabel>Molecule</ControlLabel>
         <InputGroup>
-          <FormControl
-            type="text"
-            ref="moleculeInput"
-            value={sample.molecule_name}
+          <Select.Creatable
+            name="moleculeName"
+            multi={false}
             disabled={!sample.can_update}
-            readOnly={!sample.can_update}
-            onChange={(e) => this.handleFieldChanged(sample, 'molecule_iupac_name', e.target.value)}
+            options={moleculeNames}
+            onOpen={onOpenMolName}
+            onChange={this.updateMolName}
+            isLoading={this.state.isMolNameLoading}
+            value={mno && mno.value}
+            onNewOptionClick={this.addMolName}
+            clearable={false}
           />
           <InputGroup.Button>
             {this.structureEditorButton(!sample.can_update)}

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

@@ -29,6 +29,23 @@ class DetailActions {
       })
     }
   }
+
+  updateMoleculeNames(sample, newMolName = '') {
+    const inchikey = sample.molecule.inchikey;
+    if (!inchikey) { return null; }
+
+    return (dispatch) => {
+      MoleculesFetcher
+        .updateNames(inchikey, newMolName)
+        .then((result) => {
+          const mn = result.find(r => r.name === newMolName);
+          if (mn) sample.molecule_name = { label: mn.name, value: mn.id };
+          sample.molecule_names = result;
+          dispatch(sample);
+        })
+        .catch(errorMessage => console.log(errorMessage));
+    };
+  }
 }
 
 export default alt.createActions(DetailActions)

app/assets/javascripts/components/common/CheckBoxs.js

 import React from 'react'
 import {Table} from 'react-bootstrap'
+import PropTypes from 'prop-types'
 
-const CheckBoxs = ({items, toggleCheckbox, toggleCheckAll, checkedAll}) => {
+const CheckBoxs = ({items, toggleCheckbox, toggleCheckAll, checkedAll, customClass = 'check-box-list' , customStyle = {}}) => {
   let checkBoxs = items.map( (setting, i) => {
     const {text, checked} = setting
     return(
@@ -11,7 +12,10 @@ const CheckBoxs = ({items, toggleCheckbox, toggleCheckAll, checkedAll}) => {
                   toggleCheckbox={toggleCheckbox.bind(null, text, checked)} />
     )
   })
-
+  const lgth = items && items.length
+  if (customClass == 'check-box-list') {
+    customClass =  lgth && lgth < 4 ? `check-box-list-${lgth}` : 'check-box-list'
+  }
   return (
     <Table striped>
       <thead>
@@ -31,7 +35,7 @@ const CheckBoxs = ({items, toggleCheckbox, toggleCheckAll, checkedAll}) => {
       <tbody>
         <tr >
           <td>
-            <ul id="export-import">
+            <ul className={customClass} style={customStyle}>
               {checkBoxs}
             </ul>
           </td>
@@ -41,11 +45,12 @@ const CheckBoxs = ({items, toggleCheckbox, toggleCheckAll, checkedAll}) => {
   )
 }
 CheckBoxs.propTypes = {
-  items: React.PropTypes.array,
-  checkedAll: React.PropTypes.bool,
-  toggleCheckAll: React.PropTypes.func,
-  toggleCheckbox: React.PropTypes.func,
-
+  items: PropTypes.array,
+  checkedAll: PropTypes.bool,
+  toggleCheckAll: PropTypes.func,
+  toggleCheckbox: PropTypes.func,
+  customClass: PropTypes.string,
+  customStyle: PropTypes.object,
 }
 
 const CheckBox = ({text, checked, toggleCheckbox}) => {
@@ -60,10 +65,11 @@ const CheckBox = ({text, checked, toggleCheckbox}) => {
 
   )
 }
+
 CheckBox.propTypes = {
-  text: React.PropTypes.string,
-  checked: React.PropTypes.bool,
-  toggleCheckbox: React.PropTypes.func,
+  text: PropTypes.string,
+  checked: PropTypes.bool,
+  toggleCheckbox: PropTypes.func,
 }
 
 export default CheckBoxs

app/assets/javascripts/components/common/SampleName.js

-import React, {Component} from 'react';
-import {Tooltip, OverlayTrigger} from 'react-bootstrap';
-import Formula from './Formula'
-//var _ = require('lodash');
+import React from 'react';
+import Formula from './Formula';
 
-export default class SampleName extends React.Component {
-  render() {
-    let {sample} = this.props;
+const sumFormula = sf => <Formula formula={sf} />;
 
-    let molecule_name = sample._molecule.iupac_name
-    let sum_formular = (<Formula formula={sample._molecule.sum_formular}/>)
-    if(sample.contains_residues) {
-      let polymer_name = sample.polymer_type.charAt(0).toUpperCase()
-                          + sample.polymer_type.slice(1);
-      return (
-        <div>
-          <p>
-            {polymer_name.replace('_', '-') + ' - '}
-            {sum_formular}
-          </p>
-          <p>{molecule_name}</p>
-        </div>
-      )
-    } else {
-      return (
-        <div>
-          <p>{sum_formular}</p>
-          <p>{molecule_name}</p>
-        </div>
-      )
-    }
+const sampleNameWithResidues = (polymer_type, sumFormulaCom, moleculeName) => {
+  const polymerName = (polymer_type.charAt(0).toUpperCase()
+    + polymer_type.slice(1)).replace('_', '-') + ' - ';
+
+  return (
+    <div>
+      <p>
+        {polymerName}
+        {sumFormulaCom}
+      </p>
+      <p>{moleculeName}</p>
+    </div>
+  );
+};
+
+const SampleName = ({ sample }) => {
+  const { sum_formular, iupac_name } = sample._molecule;
+  const { contains_residues, polymer_type } = sample;
+  const mnl = sample.molecule_name_label;
+  const moleculeName = mnl && mnl !== sum_formular ? mnl : iupac_name;
+  const sumFormulaCom = sumFormula(sum_formular);
+
+  if (contains_residues) {
+    return sampleNameWithResidues(polymer_type, sumFormulaCom, moleculeName);
   }
-}
+
+  return (
+    <div>
+      <p>{sumFormulaCom}</p>
+      <p>{moleculeName}</p>
+    </div>
+  );
+};
+
+export default SampleName;

app/assets/javascripts/components/contextActions/ModalExport.js

@@ -14,28 +14,30 @@ export default class ModalExport extends React.Component {
       columns: [
         {value: "Image", text: "image", checked: true},
         {value: "name", text: "name", checked: true},
-        {value: "description", text: "description", checked: true},
+        {value: "molecule_name", text: "molecule name", checked: true},
         {value: "cano_smiles", text: "canonical smiles", checked: true},
+        {value: "inchistring", text: "InChIstring", checked: true},
+        {value: "inchikey", text: "InChIkey", checked: true},
         {value: "sum_formular", text: "sum formula", checked: true},
-        {value: "inchistring", text: "inchistring", checked: true},
+        {value: "external_label", text: "external label", checked: false},
+        {value: "short_label", text: "short label", checked: false},
+        {value: "description", text: "description", checked: true},
+        {value: "real_amount_value,real_amount_unit", text: "real amount", checked: false},
         {value: "target_amount_value, target_amount_unit", text: "target amount", checked: false},
-        {value: "created_at", text: "created at", checked: false},
-        {value: "updated_at", text: "updated at", checked: false},
+        {value: "molarity_value, molarity_unit", text: "molarity", checked: false},
+        {value: "density", text: "density", checked: false},
         {value: "molfile", text: "molfile", checked: false},
         {value: "purity", text: "purity", checked: false},
         {value: "solvent", text: "solvent", checked: false},