Merge branch 'release-v0.8.0' into 'development'

Release v0.8.0

See merge request ComPlat/chemotion_ELN!1392

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: "complat/complat-ubuntu-runner:0.10.20"
+image: "complat/complat-ubuntu-runner:0.12.20"
 
 services:
   - postgres:12-alpine
@@ -90,7 +90,7 @@ testrb:
   stage: unit
   script:
     # - ln -s /home/gitlab-runner/shared/bundle vendor/bundle
-    - /bin/bash -l -c "source ~/.rvm/scripts/rvm && RAILS_ENV=test bundle exec rake db:schema:load && bundle exec rspec --exclude-pattern spec/{features}/**/*_spec.rb"
+    - /bin/bash -l -c "source ~/.rvm/scripts/rvm && RAILS_ENV=test bundle exec rake db:test:prepare && bundle exec rspec --exclude-pattern spec/{features}/**/*_spec.rb"
   except:
     variables:
     - $CI_COMMIT_MESSAGE =~ /skip[ _-]unitrb/i

.nvmrc

@@ -1 +1 @@
-v12.21.0
+v12.22.1

CHANGELOG.md

@@ -1,6 +1,22 @@
 
 # Chemotion_ELN Changelog
 
+## [v0.8.0]
+> 2021-04-28
+
+* Features
+  * option to decouple sample from molfile defined molecule - enable user custom MW input (Admin has to enable the feature)
+  * research-plan table: switch to using ag-grid - enable moving  row/columns with d-n-d
+  * nmr_sim ELN plugin installed by default
+
+* Fix
+  * Add configurable default profile for Element-Detail tab sortings 
+  * slow opening of reaction panel: rm debounce
+  * green-chemistry: fix checkbox rerendering in table cell
+  * Analytics atom count scenari
+  * default favicon if none present
+
+
 ## [v0.7.1]
 > 2021-03-26
 

Dockerfile

@@ -39,8 +39,8 @@ ADD . $APP_HOME
 
 RUN /bin/bash -c 'bundle install'
 RUN /bin/bash -c 'source /usr/local/nvm/nvm.sh;\
-  nvm install 12.18.3;\
-  nvm use 12.18.3;\
+  nvm install 12.22.1;\
+  nvm use 12.22.1;\
   npm install'
 
 RUN echo '[ -s /usr/local/nvm/nvm.sh ] && . /usr/local/nvm/nvm.sh' >> /home/app/.bashrc

Dockerfile.focal.gitlab-ci

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:focal
 
 ARG DEBIAN_FRONTEND=noninteractive
 
@@ -44,19 +44,17 @@ RUN cat ~/.bash_profile
 RUN mkdir -p shared/bundle/ruby
 RUN mkdir -p shared/node_modules
 RUN ln -s shared/node_modules node_modules
-RUN echo $(ls -1 .)
 
-RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.35.3/install.sh | bash
+RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.38.0/install.sh | bash
 
 COPY Gemfile /home/gitlab-runner/
 COPY Gemfile.lock /home/gitlab-runner/
 COPY package.json /home/gitlab-runner/
 COPY package-lock.json /home/gitlab-runner/
 RUN sudo chmod 666 Gemfile.lock
 RUN sudo chmod 666 package-lock.json
-RUN echo $(ls -1 .)
 
-RUN /bin/bash -l -c "source ~/.nvm/nvm.sh && nvm install 12.21.0 && npm install -g npm@7.6.2 && npm install"
+RUN /bin/bash -l -c "source ~/.nvm/nvm.sh && nvm install 12.22.1 && nvm use 12.22.1 && npm install -g npm && npm install"
 RUN echo $(ls -1 shared/node_modules)
 RUN /bin/bash -l -c "source ~/.rvm/scripts/rvm && rvm install 2.6.6 && gem install bundler -v 1.17.3 && bundle install --path shared/bundle"
 # RUN /bin/bash -l -c "source ~/.rvm/scripts/rvm && chromedriver-update"

Gemfile

@@ -228,6 +228,8 @@ group :test do
   gem 'rspec-repeat'
 end
 
+gem 'nmr_sim', git: 'https://github.com/ComPlat/nmr_sim', ref: 'e2f91776aafd8eb1fa9d88c8ec2291b02201f222', group: [:plugins,:development, :test, :production]
+
 # Chemotion plugins: list your ELN specific plugin gems in the Gemfile.plugin
 eln_plugin = File.join(File.dirname(__FILE__), "Gemfile.plugin")
 if File.exists?(eln_plugin)

Gemfile.lock

@@ -34,6 +34,14 @@ GIT
       rails (~> 4.2.11)
       sprite-factory (= 1.7.1)
 
+GIT
+  remote: https://github.com/ComPlat/nmr_sim
+  revision: e2f91776aafd8eb1fa9d88c8ec2291b02201f222
+  ref: e2f91776aafd8eb1fa9d88c8ec2291b02201f222
+  specs:
+    nmr_sim (0.0.3)
+      rails (~> 4.2)
+
 GIT
   remote: https://github.com/ComPlat/openbabel-gem.git
   revision: 3e25548fd95c2ac83c7fb5d9544ed2cf6ae1344b
@@ -716,6 +724,7 @@ DEPENDENCIES
   meta_request
   net-sftp
   net-ssh
+  nmr_sim!
   nokogiri
   openbabel (= 2.4.90.3)!
   pandoc-ruby

Gemfile.plugin.example

@@ -4,4 +4,4 @@
 #  git: 'https://github.com/ComPlat/scifinding',
 #  group: [:plugins,:development,:production]
 #  # path: '../scifinding',
-# gem 'nmr_sim', git: 'https://github.com/ComPlat/nmr_sim', ref: '104ac26879ede1f495dd5e90979d6f701a356c9f', group: [:plugins,:development,:production]
+# gem 'nmr_sim', git: 'https://github.com/ComPlat/nmr_sim', ref: 'e2f91776aafd8eb1fa9d88c8ec2291b02201f222', group: [:plugins,:development,:production]

INSTALL.md

@@ -64,27 +64,9 @@ NB:
 
 ## Using Docker
 
+see online ![docs](https://www.chemotion.net/chemotionsaurus/docs/eln/docker_installation)
 
 
-This is a setup for a 'pseudo' production stage using passenger and aimed for user testing.
-(For the development environment, change 'RAILS_ENV' to 'development' in docker-compose.yml)
-**Make sure you have finished the BASIC SETUP FIRST**
-
-1. Build the image from Dockerfile `docker-compose build` or pull the image: `docker-compose pull`
-2. Initialize database FIRST:
-  * `docker-compose run app bundle exec rake db:create`
-  * `docker-compose run app bundle exec rake db:migrate`
-  * `docker-compose run app bundle exec rake db:seed` (optional). A "seed"
-    user will be inserted into the db with the information as below: [email protected] - password: "@eln.edu"
-  * `docker-compose run app rake ketcherails:import:common_templates` (optional)
-3. Precompile assets: `docker-compose run app bundle exec rake assets:precompile`
-4. To start the server: `docker-compose up` or start server and detach: `docker-compose up -d`
-
-* Start interactive shell with docker: `docker-compose run app /bin/bash`
-* NOTE: In this Docker image, we disabled the email verification progress
-
-* To enable email confirmation, uncomment ":confirmable" at line 5 of `app/models/user.rb`, stop the `docker-compose` by `docker-compose stop` and start `docker-compose`.
-
 
 # Basic Development Setup
 

README.md

@@ -28,10 +28,13 @@ Copyright (C) 2015-current  Nicole Jung (nicole.jung(at)kit.edu) of the Karlsruh
 
 
 
-## Install
+## Installation
 
 see [INSTALL.md][INSTALL]
 
+## User Documentation
+
+see online ![docs](https://www.chemotion.net/chemotionsaurus/docs/eln/about)
 
 ## Code Status
 

VERSION

@@ -1,3 +1,3 @@
-version: 0.7.1
+version: 0.8.0-pre
 base_revision: e8f0a99c4d6d024499cdef3feda77ec0d2c2e760 
 current_revision: 0

app/assets/javascripts/components/SampleDetails.js

@@ -982,7 +982,7 @@ export default class SampleDetails extends React.Component {
       <Tab
         eventKey={ind}
         title={title}
-        key
+        key={key}
       >
         <ListGroupItem style={{ paddingBottom: 20 }}>
           <ComputedPropsContainer sample={sample} />

config/application.rb

@@ -36,11 +36,6 @@ class Application < Rails::Application
 
     config.active_job.queue_adapter = :delayed_job
 
-    # copy favicon if not present in app
-    favicon_example_file = Rails.public_path.join('favicon.ico.example')
-    favicon_file = Rails.public_path.join('favicon.ico')
-    `cp #{favicon_example_file} #{favicon_file}` unless File.exist?(favicon_file)
-
     # Chemotion Plugin configuration
 
     # list of registered plugins (from the plugins group of the Gemfile):

config/deploy.rb

@@ -15,8 +15,8 @@
 set :bundle_jobs, 4 # parallel bundler
 
 set :nvm_type, :user
-set :nvm_node, File.exist?('.nvmrc') && File.read('.nvmrc').strip || 'v12.21.0'
-set :npm_version, File.exist?('.npm-version') && File.read('.npm-version').strip || '7.6.2'
+set :nvm_node, File.exist?('.nvmrc') && File.read('.nvmrc').strip || 'v12.22.1'
+set :npm_version, File.exist?('.npm-version') && File.read('.npm-version').strip || '7.11.1'
 set :nvm_map_bins, fetch(:nvm_map_bins, []).push('rake')
 set :nvm_map_bins, fetch(:nvm_map_bins, []).push('bundle')
 # Default value for :format is :pretty

config/deploy/server.rb.example

@@ -16,7 +16,7 @@ set :linked_files, fetch(:linked_files, []).push(
   # '.ruby-gemset',
 )
 
-set :npm_version, '7.6.2'
+set :npm_version, '7.11.1'
 set :deploy_to, '/var/www/chemotion_ELN'
 set :user, user
 set :bundle_path, nil

config/initializers/favicon.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+# copy favicon if not present in app
+favicon_example_file = Rails.public_path.join('favicon.ico.example')
+begin
+  favicon_file = Rails.public_path.join('favicon.ico')
+  `cp #{favicon_example_file} #{favicon_file}` unless File.exist?(favicon_file)
+  favicon_file = Rails.public_path.join('images', 'favicon.ico')
+  `cp #{favicon_example_file} #{favicon_file}` unless File.exist?(favicon_file)
+rescue
+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: 20210303140000) do
+ActiveRecord::Schema.define(version: 20210416075103) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -499,6 +499,19 @@
   add_index "molecules", ["deleted_at"], name: "index_molecules_on_deleted_at", using: :btree
   add_index "molecules", ["inchikey", "is_partial"], name: "index_molecules_on_inchikey_and_is_partial", unique: true, using: :btree
 
+  create_table "nmr_sim_nmr_simulations", force: :cascade do |t|
+    t.integer  "molecule_id"
+    t.text     "path_1h"
+    t.text     "path_13c"
+    t.text     "source"
+    t.datetime "deleted_at"
+    t.datetime "created_at",  null: false
+    t.datetime "updated_at",  null: false
+  end
+
+  add_index "nmr_sim_nmr_simulations", ["deleted_at"], name: "index_nmr_sim_nmr_simulations_on_deleted_at", using: :btree
+  add_index "nmr_sim_nmr_simulations", ["molecule_id", "source"], name: "index_nmr_sim_nmr_simulations_on_molecule_id_and_source", unique: true, using: :btree
+
   create_table "notifications", force: :cascade do |t|
     t.integer  "message_id"
     t.integer  "user_id"
@@ -1121,7 +1134,7 @@
   SQL
 
   create_trigger :update_users_matrix_trg, sql_definition: <<-SQL
-      CREATE TRIGGER update_users_matrix_trg AFTER INSERT OR UPDATE ON public.matrices FOR EACH ROW EXECUTE PROCEDURE update_users_matrix()
+      CREATE TRIGGER update_users_matrix_trg AFTER INSERT OR UPDATE ON public.matrices FOR EACH ROW EXECUTE FUNCTION update_users_matrix()
   SQL
 
   create_view "v_samples_collections", sql_definition: <<-SQL

lib/import/import_collections.rb

@@ -136,12 +136,12 @@ def import_samples
         # look for the molecule for this sample and add the molecule name
         # neither the Molecule or the MoleculeName are created if they already exist
         molfile = fields.fetch('molfile')
-        molecule = fields.fetch('decoupled') && molfile.blank? ? Molecule.find_or_create_dummy : Molecule.find_or_create_by_molfile(molfile)
-        molecule.create_molecule_name_by_user(molecule_name_name, @current_user_id) unless fields.fetch('decoupled') && molfile.blank?
+        molecule = fields.fetch('decoupled', nil) && molfile.blank? ? Molecule.find_or_create_dummy : Molecule.find_or_create_by_molfile(molfile)
+        molecule.create_molecule_name_by_user(molecule_name_name, @current_user_id) unless fields.fetch('decoupled', nil) && molfile.blank?
 
         # get the molecule_name from the list of molecule names in molecule
         # this seems a bit cumbersome, but fits in with the methods of Molecule and MoleculeName
-        molecule_name = molecule.molecule_names.find_by(name: molecule_name_name) unless fields.fetch('decoupled') && molfile.blank?
+        molecule_name = molecule.molecule_names.find_by(name: molecule_name_name) unless fields.fetch('decoupled', nil) && molfile.blank?
 
         # create the sample
         sample = Sample.create!(fields.slice(

lib/import/import_sdf.rb

@@ -5,6 +5,7 @@ class Import::ImportSdf
                :inchi_array, :raw_data, :rows, :custom_data_keys, :mapped_keys
 
   SIZE_LIMIT = 40 # MB
+  MOLFILE_BLOCK_END_LINE = 'M  END'
 
   def initialize(args)
     @raw_data = args[:raw_data] || []
@@ -30,7 +31,7 @@ def read_data
     if file_path
       size = File.size(file_path)
       if size.to_f < SIZE_LIMIT * 10**6
-        @raw_data = File.read(file_path).split(/\${4}\r?\n/)
+        @raw_data = File.binread(file_path).encode('utf-8', universal_newline: true, invalid: :replace, undef: :replace).scrub.split(/\${4}\r?\n/)
       else
         @message[:error] << "File too large (over #{SIZE_LIMIT}MB). "
       end
@@ -51,7 +52,7 @@ def find_or_create_mol_by_batch(batch_size = 50)
     n = batch_size - 1
     inchikeys = []
     @processed_mol = []
-    data = raw_data.dup
+    data = raw_data.dup 
     until data.empty?
       batch = data.slice!(0..n)
       molecules = find_or_create_by_molfiles(batch)
@@ -102,14 +103,15 @@ def create_samples
             next unless row
 
             molfile = row['molfile']
-            babel_info = Chemotion::OpenBabelService.molecule_info_from_molfile(molfile)
+            san_molfile = sanitize_molfile(molfile)
+            babel_info = Chemotion::OpenBabelService.molecule_info_from_molfile(san_molfile)
             inchikey = babel_info[:inchikey]
             is_partial = babel_info[:is_partial]
             next unless inchikey.presence && (molecule = Molecule.find_by(inchikey: inchikey, is_partial: is_partial))
 
             sample = Sample.new(
               created_by: current_user_id,
-              molfile: molfile,
+              molfile: san_molfile,
               molfile_version: babel_info[:molfile_version],
               molecule_id: molecule.id
             )
@@ -150,7 +152,7 @@ def find_or_create_by_molfiles(molfiles)
     babel_info_array = Chemotion::OpenBabelService.molecule_info_from_molfiles(molfiles)
 
     babel_info_array.map.with_index do |babel_info, i|
-      if babel_info[:inchikey]
+      if babel_info[:inchikey].present?
         mf = molfiles[i]
         m = Molecule.find_or_create_by_molfile(mf, babel_info)
         process_molfile_opt_data(mf).merge(
@@ -171,4 +173,10 @@ def process_molfile_opt_data(molfile)
       [k, value.strip]
     end]
   end
+
+  def sanitize_molfile(mf)
+#TODO check for residue polymer thingy
+    mf.encode('utf-8', universal_newline: true, invalid: :replace, undef: :replace).scrub.split(/^(#{MOLFILE_BLOCK_END_LINE}(\r?\n)?)/).first.concat(MOLFILE_BLOCK_END_LINE)
+
+  end
 end