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Electronic Lab Notebook

Home Page: https://www.chemotion.net

License: GNU Affero General Public License v3.0

Ruby 38.84% JavaScript 58.59% CSS 0.39% HTML 0.27% Shell 0.08% PLpgSQL 0.14% SCSS 1.41% Haml 0.27%

eln rdm smart-lab fair-data

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chemotion_eln's Issues

Improve Docker setup

I've spend the whole day getting Chemotion to run with Docker according to INSTALL.md - including high levels of frustration. These are my impressions:

docker-compose build runs through smoothly.
Don't execute docker-compose more than once as this creates new containers over and over again. For step 2 I used the interactive shell after running docker-compose up (ONCE!).
'bundle exec rake db:migrate' fails, because it is unable to to find storage.yml and database.yml. I'm not sure if the cp command for them is done in the right directory in Dockerfile.
rake ketcherails:import:common_templates fails:
unknown file type: /usr/local/rvm/gems/ruby-2.3.3/bundler/gems/ketcher-rails-bbc54084cd63/public/images/ketcherails/seeds/icons/icon/AA3.png
/usr/local/rvm/gems/ruby-2.3.3/bundler/gems/ketcher-rails-bbc54084cd63/lib/tasks/ketcherails.rake:17:in `block in copy_icons_files' ...
Exposing port 80 instead of 3000 would be more intuitive.

Bug/Issue: chemotion_ELN_install.sh fails on Ubuntu Server 18.04.04 LTS

Hello chemotion_ELN developers,

I am trying to run a direct production install with chemotion_ELN_install.sh (dockerless).
The installation went quite bumpy until PART 8 (I had to do several adjustments to come so far),
but in the Installer section 8 I am lost:
The error happens during the capistrano deploy task in these lines of the install script:

sharpi 'starting capistrano deploy task' sudo -H -u $PROD bash -c "cd $TMP_DIR && source ~/.rvm/scripts/rvm && rvm use $RUBY_VERSION && cap local_deploy deploy"

The Error message is:

      07 ln -s /var/www/chemotion_ELN/shared/.env /var/www/chemotion_ELN/releases/20210226072953/.env
    ✔ 07 production@localhost 0.050s
      08 ln -s /var/www/chemotion_ELN/shared/.ruby-version /var/www/chemotion_ELN/releases/20210226072953/.ruby-version
    ✔ 08 production@localhost 0.050s
00:05 deploy:symlink:linked_dirs
      01 mkdir -p /var/www/chemotion_ELN/releases/20210226072953/backup /var/www/chemotion_ELN/releases/20210226072953 /var/www/chemotion_ELN/releases/2021022…
    ✔ 13 production@localhost 0.047s
      14 ln -s /var/www/chemotion_ELN/shared/tmp/sockets /var/www/chemotion_ELN/releases/20210226072953/tmp/sockets
        12: from /home/production/.rvm/gems/ruby-2.6.6/gems/sshkit-1.21.0/lib/sshkit/backends/abstract.rb:31:in `run'
 DEBUG [3cdd28dd] Command: [ -L /var/www/chemotion_ELN/releases/20210226072953/public/assets ]

 DEBUG [3cdd28dd] Finished in 0.049 seconds with exit status 1 (failed).

 DEBUG [70478ff2] Running [ -d /var/www/chemotion_ELN/releases/20210226072953/public/assets ] as production@localhost

 DEBUG [70478ff2] Command: [ -d /var/www/chemotion_ELN/releases/20210226072953/public/assets ]

 DEBUG [70478ff2] Finished in 0.048 seconds with exit status 1 (failed).

  INFO [c7fb8b73] Running /usr/bin/env ln -s /var/www/chemotion_ELN/shared/public/assets /var/www/chemotion_ELN/releases/20210226072953/public/assets as production@localhost

 DEBUG [c7fb8b73] Command: ( export NODE_VERSION="v12.18.3" ; /usr/bin/env ln -s /var/www/chemotion_ELN/shared/public/assets /var/www/chemotion_ELN/releases/20210226072953/public/assets )

  INFO [c7fb8b73] Finished in 0.050 seconds with exit status 0 (successful).

  INFO [77a874dc] Running find  /var/www/chemotion_ELN/shared/node_modules/. -name . -o -prune -exec rm -rf -- {} + as production@localhost

 DEBUG [77a874dc] Command: find  /var/www/chemotion_ELN/shared/node_modules/. -name . -o -prune -exec rm -rf -- {} +

  INFO [77a874dc] Finished in 0.046 seconds with exit status 0 (successful).

 DEBUG [afc6dcc7] Running if test ! -d /var/www/chemotion_ELN/releases/20210226072953; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20210226072953'" 1>&2; false; fi as production@localhost

 DEBUG [afc6dcc7] Command: if test ! -d /var/www/chemotion_ELN/releases/20210226072953; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20210226072953'" 1>&2; false; fi

 DEBUG [afc6dcc7] Finished in 0.046 seconds with exit status 0 (successful).

  INFO [e48c87ee] Running /tmp/chemotion/nvm-exec.sh npm install --production --silent --no-progress as production@localhost

 DEBUG [e48c87ee] Command: cd /var/www/chemotion_ELN/releases/20210226072953 && ( export NODE_VERSION="v12.18.3" ; /tmp/chemotion/nvm-exec.sh npm install --production --silent --no-progress )

 DEBUG [e48c87ee]       Now using node v12.18.3 (npm v6.14.6)

Do you have any idea, how to resolve this issue ? (it might be related to #369 )
Thanks for your help.

Issues with installing on Ubuntu 20.04 focal on Hyper-V

Hello, Chemotion team!

We have read your paper and are eager to see Chemotion in action!

Unfortunatelly, we could not as yet install it. We tried several approaches:

Using docker - development branch
Using the script - development branch.
Using docker - master branch.

Approach 1. Using docker - development branch:

The docker image was pulled. On starting the service to initialize the database container, it notifies us we need to install missing gems and stops.
So using
#docker-compose run app bash
app_container# bundle install
app_container# bundle exec rake db:create
app_container# bundle exec rake db:migrate
In config/datacollectors.yml.example, a “ ‘ “ character seems to be missing at the end of line 37 (the last line on screenshot below), which causes errors with db:seed step or importing common_templates.

Adding the “ ‘ “ character.
app_container# bundle exec rake db:seed
app_container# rake ketcherails:import:common_templates
Until now everything seems to work, except it keeps saying required Ruby is not installed. The version installed in the pulled container differs very slightly, and doing ‘# rvm install “ruby-2.5.6” did not help in the past, so this time I’ll leave ruby as is.

On the precompiling step, there is an error:

Installing browserify:
app_container# npm i browserify

Next attempt at precompiling also returns an error: this time it looks for rfb.js not where it is installed.

Correcting the path in /app/assets/javascripts/libCnC/CnC.js:

From

To

Now react-svg-file-zoom-pan-latest is declared to be missing:

Installing it:
app_container# npm i react-svg-file-zoom-pan-latest

Trying precompile step again

Reading here, it seems like the problem might be the new babel that comes with the new browserify.
Trying
app_container#npm i browserify@~8.0.0

Then precompile again. Another error:

Trying npx browserlist@latest --update-db, as advised in the output, doesn’t help.

If I skip the precompile step, the same errors come later when the system is up and I’m trying to connect to the server via browser:

To make that work, I modified the run.sh to include the steps we’ve just gone through:

As seen from the browser:

2. Approach 2 - using the script (dev. branch)

After linking
#sudo ln -s /bin/mkdir /usr/bin/mkdir
to avoid the error while nokogiri installation, at the end we get:

3. Approach 3 - docker with master branch

When, analogous to approach 1, I do
app_container# bundle install
I get denied access to the fttp server with the specified ketcher-rails gem:

Thanks for your time!
I sincerely hope it might help with debugging!
If the problem lies with me - please tell me the right way.

Best regards,
Denys

Create a full list of features implemented

Install script failed at capistrano deploy

Hello !

I am trying to install chemotion on a server with a fresh install of Ubuntu 18.04 but I get an error during the capistrano deploy ending the script :

00:04 deploy:check:linked_files
      ERROR linked file /var/www/chemotion_ELN/shared/config/datacollectors.yml does not exist on localhost

This error might be related to this recent commit. Would it be possible to add an empty datacollectors.yml file in the config folder without repercussions on the install ?

Thanks !

select box generic segment/element

it would be great if one could see additional information in the select box which is then not used for the data entry. e.g.
molecule name - string
only string is used for the data entry
This could help to identify the right component in the selectbox

Cosmetics: ActionController::RoutingError (No route matches [GET] "/favicon.ico")

While there is a favicon in:
https://github.com/ComPlat/chemotion_ELN/blob/development/public/favicon.ico
included from:

chemotion_ELN/app/assets/javascripts/components/ChemrepoLabels.js

Line 13 in 8e2e507

 <img src="/favicon.ico" className="pubchem-logo" alt="Chemotion Repository" title="Chemotion Repository" /> 

I get the message

[FATAL]:  | ActionController::RoutingError (No route matches [GET] "/favicon.ico")

and no favicon. Mon dieu, I can't live without the favicon !
Unfortunately I am no ruby hacker, so no PR to fix this today :-(
Yours, Steffen

docker-compose build fails

Hi,

I am trying to get Chemotion ELN running using docker on Centos 7, but so far I don't have much luck. I attach an Ansible playbook that should transform a Centos 7 machine into one with Chemotion ELN installed. Essentially I am trying to encode the installation instructions into an Ansible playbook. Hopefully this playbook is understandable even for people that are not familiar with Ansible. The playbook fails in the step that does a 'docker-compose build'.

The playbook file is:
chemotion.yml

The output is:

Step 1/26 : FROM phusion/passenger-ruby25:1.0.6
 ---> 3ca356ec3178
Step 2/26 : ENV PATH /usr/local/rvm/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
 ---> Using cache
 ---> b253d337d096
Step 3/26 : ENV APP_HOME /home/app/chemotion_ELN
 ---> Using cache
 ---> cc9b4f952a09
Step 4/26 : ENV BUNDLE_PATH /bundle
 ---> Using cache
 ---> 1fb83b799063
Step 5/26 : ENV HOME /root
 ---> Using cache
 ---> ba01d0321515
Step 6/26 : CMD ["/sbin/my_init"]
 ---> Using cache
 ---> 018c86946fdc
Step 7/26 : EXPOSE 3000
 ---> Using cache
 ---> 050da1641065
Step 8/26 : RUN add-apt-repository ppa:inkscape.dev/stable &&   apt-get -y update --fix-missing &&   apt-get -y install ca-certificates apt-transport-https git       imagemagick libmagic-dev libmagickcore-dev libmagickwand-dev curl       libappindicator1 swig       fonts-liberation xvfb gconf-service libasound2 libgconf-2-4 cmake       libnspr4 libnss3 libpango1.0-0 libxss1 xdg-utils libpq-dev       gtk2-engines-pixbuf xfonts-cyrillic xfonts-100dpi xfonts-75dpi       xfonts-base xfonts-scalable apt-utils cmake inkscape       libeigen3-dev build-essential wget nodejs sudo postgresql-client       libmagickcore-dev libmagickwand-dev imagemagick tzdata gnupg2       python-dev libsqlite3-dev libboost-all-dev p7zip-full       --fix-missing
 ---> Using cache
 ---> 77ded9588a7b
Step 9/26 : RUN mkdir /usr/local/nvm
 ---> Using cache
 ---> e3f2fe5bc4dc
Step 10/26 : RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.34.0/install.sh | NVM_DIR=/usr/local/nvm bash
 ---> Using cache
 ---> c90121fdd227
Step 11/26 : RUN mkdir -p $APP_HOME
 ---> Using cache
 ---> 91bafab2385a
Step 12/26 : WORKDIR $APP_HOME
 ---> Using cache
 ---> 5eda62398821
Step 13/26 : ADD . $APP_HOME
 ---> Using cache
 ---> 004faa4cf94c
Step 14/26 : RUN /bin/bash -c 'bundle install'
 ---> Using cache
 ---> f08c64286ca1
Step 15/26 : RUN /bin/bash -c 'source /usr/local/nvm/nvm.sh;  nvm install;  nvm use;  npm install'
 ---> Running in 1b10aa7928ac
N/A: version "v10.15.3 -> N/A" is not yet installed.

You need to run "nvm install v10.15.3" to install it before using it.
rc' with version <v10.15.3>
Downloading and installing node v10.15.3...
Downloading https://nodejs.org/dist/v10.15.3/node-v10.15.3-linux-x64.tar.xz...
######################################################################## 100.0%

atched!
 v6.4.1)
Creating default alias: default -> v10.15.3 *
Found '/home/app/chemotion_ELN/.nvmrc' with version <v10.15.3>
Now using node v10.15.3 (npm v6.4.1)
bed.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/uglify-js-e5732be1/tools/exit.js'
odules/.staging/uglify-js-e5732be1/tools/exports.js'
odules/.staging/uglify-js-e5732be1/tools/node.js'
ats/font.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/uglify-js-e5732be1/tools/props.html'
odules/.staging/xlsx-c7923000/jszip.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/modules/formula.js'
in.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/formats/header.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/modules/history.js'
odules/.staging/quill-12a79c0e/ui/icon-picker.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/ui/icons.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/commonmark-a351681c/dist/commonmark.min.js'
age.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/core-js-98b10bf4/client/library.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/core-js-c07287f3/client/library.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/react-virtualized-select-e95806a2/dist/umd/react-virtualized-select.js.map'
ats/indent.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/d3-b361414b/d3.min.js'
odules/.staging/quill-12a79c0e/blots/inline.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/acorn-31e73d07/dist/acorn.mjs.map'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/formats/italic.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quill-12a79c0e/modules/keyboard.js'
e-corejs2-8cfd7f95/regenerator/index.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/array/from.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/array/is-array.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/array/of.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/date/now.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/json/stringify.js'
ath/acosh.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/asinh.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/atanh.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/immutable-e55696f5/dist/immutable.d.ts'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/cbrt.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/clz32.js'
ath/cosh.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/expm1.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/fround.js'
odules/.staging/react-vis-f3b8b926/dist/index.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/hypot.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/imul.js'
odules/.staging/react-vis-f3b8b926/dist/legends'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/log10.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/log1p.js'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/legends'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/log2.js'
ath/sign.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/legends'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/sinh.js'
ath/tanh.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/eslint-ca3e3534/LICENSE'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/legends'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/math/trunc.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/eslint-ca3e3534/README.md'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/epsilon.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/legends'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/is-finite.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/is-integer.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/main.scss'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/is-nan.js'
ake-vis-flexible.js'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/is-safe-integer.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/max-safe-integer.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/parallel-coordinates'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/min-safe-integer.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/parse-float.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/plot'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/number/parse-int.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/assign.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/plot'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/create.js'
/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/define-properties.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/plot'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/define-property.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/entries.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/plot'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/@babel/runtime-corejs2-8cfd7f95/core-js/object/freeze.js'
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npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
odules/.staging/react-vis-f3b8b926/dist/radar-chart'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quagga-142272aa/.eslintrc'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/quagga-142272aa/bower.json'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/radial-chart'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/sankey'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/sankey'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/style.css'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/styles'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/styles'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/styles'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/styles'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/styles'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/sunburst'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/theme.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/treemap'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
ap'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/treemap'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/treemap'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
odules/.staging/react-vis-f3b8b926/dist/utils'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/utils'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/utils'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/utils'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/utils'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/react-vis-f3b8b926/dist/utils'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, open '/home/app/chemotion_ELN/node_modules/.staging/sinon-478da3ba/pkg/sinon.js'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/living'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/web-idl'
npm WARN tar ENOENT: no such file or directory, lstat '/home/app/chemotion_ELN/node_modules/.staging/jsdom-78780b12/lib/jsdom/web-idl'
 WARN The package babel-preset-es2015 is included as both a dev and production dependency.
npm WARN The package babel-preset-react is included as both a dev and production dependency.
npm WARN The package bundle-collapser is included as both a dev and production dependency.
npm WARN The package envify is included as both a dev and production dependency.
npm WARN The package react-dom is included as both a dev and production dependency.

npm ERR! Invalid dependency type requested: alias

P.S.:

In the Dockerfile you're twice passing to 'apt-get install' the packages 'cmake' and 'imagemagick'. Harmless, but unnecessary.

Script install issue

Hi !

I am very interested to test chemotion in my lab, but before installing it on our servers, I tested the installation on a VM (Ubuntu Server 18.04) using the corresponding script. Everything runs smoothly until deploy in part 8, where I get an error that seems related to the absence of datacollector.yml config file in the corresponding /var/www/chemotion_ELN/releases directory, ending the script (I have run the script a second time with the same result).
Would you have any hint to how I can fix this problem ?

Thanks !

Issue adding plugins

Hi, I have the ELN running on a Virtualbox VM, Ubuntu 20.04, and was trying to add the extra plugins to my setup.

I've tried in a couple of different ways but can't seem to get it to work, so would appreciate some guidance on where I'm going wrong if possible.

One method I have tried is creating a Gemfile.plugin file based on the Gemfile.plugin.example file in the repository such that I have a file as below:

 gem  'scifinding', '0.1.7', 
  branch: 'upg_oauth2',
  ref: '2c9b4ebb3e3e7044620f90293679a9a8d647b080',
  git: 'https://github.com/ComPlat/scifinding',
  group: [:plugins,:development,:production]
 gem 'nmr_sim', git: 'https://github.com/ComPlat/nmr_sim', ref: '104ac26879ede1f495dd5e90979d6f701a356c9f', group: [:plugins,:development,:production]

(I modified the example file slightly to include the branch, as otherwise the main branch seemed to give another error with issues with faraday dependencies not matching)

but when running the Chemotion_ELN_update.sh script to try and add this I get the following output repeated in multiple places:

You are trying to install in deployment mode after changing
your Gemfile. Run `bundle install` elsewhere and add the
updated Gemfile.lock to version control.

The list of sources changed
The dependencies in your gemfile changed

You have added to the Gemfile:
* source: https://github.com/ComPlat/scifinding (at 2c9b4eb)
* scifinding (= 0.1.7)

I also tried adding the line
gem "scifinding", :git => "git://github.com/complat/scifinding.git" , branch: 'upg_oauth2', :group => [:plugins,:test,:development,:production]

to the end of the main Gemfile, and then running the script but still get the same error.

I understand that potentially I am meant to be running bundle install somewhere to manage to get this working, based on the info on the scifinding repo page, but unfortunately I don't know enough about gems and bundler to know where I'm meant to do this, as any place I try tends to lead to the error: Command 'bundle' not found, but can be installed with: ...

Any help would be much appreciated! Thanks

Installation failed

Hello I tried to use docker installation method but that is failed with these errors

rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/tr46': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/transmitter': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/traverse': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/trim-right': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/tryit': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/tty-browserify': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/tunnel-agent': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/tweetnacl': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/type-check': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/typedarray': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/ua-parser-js': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uglify-js': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uglify-to-browserify': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uglifyify': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/umd': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uncontrollable': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uniq': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/url': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/urllite': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/util': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/util-deprecate': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/uuid': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/validate-npm-package-license': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/verror': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/vm-browserify': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/warning': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/webidl-conversions': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/webrtc-adapter': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/whatwg-encoding': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/whatwg-fetch': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/whatwg-url': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/which': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/window-size': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/wordwrap': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/wrappy': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/write': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/xml-name-validator': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/xmlhttprequest': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/xtend': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/yallist': Directory not empty
rm: cannot remove '/tmp/npm-637-7d2033e1/registry.npmjs.org/yargs': Directory not empty
ERROR: Service 'app' failed to build: The command '/bin/sh -c apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*' returned a non-zero code: 1

use no structure sample in reactions: copy

It would be good if one could copy "no structure samples" into a reaction table (generating a new number). At the moment, only "split" is supported for "no structure samples".

chemotion_ELN yield calculation

Hello,
I’m using chemotion_ELN, Version: 0.6.0.
Recently I realized that for some reaction the yield is not calculated properly. For example in a condensation reaction, there the ratio between the components is 2:3 (1:1.5). Theoretical yield of the product is calculated based on the assumption, that ration between ref. starting material and product is 1:1, but in the described case it is 2:1. May be there is a work around for this problem, but I did not find out how to do this.

Browserslist: caniuse-lite is outdated and Cannot find module '@novnc/noVNC/lib/rfb'

Hi,
I am playing with the dockerised chemotion. I get the messages below, and I think I have
two separate issues: 1) Browserslist: caniuse-lite is outdated and Cannot find module '@novnc/noVNC/lib/rfb'
I'd need a quick heads-up if that might be an issue in the container, or me starting the whole thing.
Thanks in advance,
yours,
Steffen

...
rake aborted!
BrowserifyRails::BrowserifyError: Error while running `/home/app/chemotion_ELN/node_modules/.bin/browserify -t [ babelify --presets [ @babel/preset-env  @babel/preset-react ] --plugins [ @babel/plugin-proposal-object-rest-spread ] ] -g uglifyify  --list -o "/home/app/chemotion_ELN/tmp/cache/browserify-rails/output20210310-569-n7ls79" -`:

Browserslist: caniuse-lite is outdated. Please run:
npx browserslist@latest --update-db
events.js:183
      throw er; // Unhandled 'error' event
      ^

Error: Can't walk dependency graph: Cannot find module '@novnc/noVNC/lib/rfb' from '/home/app/chemotion_ELN/app/assets/javascripts/libCnC/CnC.js'
    required by /home/app/chemotion_ELN/app/assets/javascripts/libCnC/CnC.js
    at /home/app/chemotion_ELN/node_modules/browser-resolve/node_modules/resolve/lib/async.js:115:35
    at processDirs (/home/app/chemotion_ELN/node_modules/browser-resolve/node_modules/resolve/lib/async.js:268:39)
    at isdir (/home/app/chemotion_ELN/node_modules/browser-resolve/node_modules/resolve/lib/async.js:275:32)
    at /home/app/chemotion_ELN/node_modules/browser-resolve/node_modules/resolve/lib/async.js:25:69
    at FSReqWrap.oncomplete (fs.js:152:21)
/home/app/chemotion_ELN/app/assets/config/manifest.js:3

Typo in error message in the error mentioned in issue #390

The error message is:
"Error: can not find one of items in sequnce. Some items are not known".
An alternative:
"Error: cannot find one or more items in the sequence. Some items are not known"

"can not" should be replaced with "cannot".
"sequnce" should be replaced with "sequence".

provide easy to reuse Docker image via DockerHub

I found https://hub.docker.com/r/complat/chemotion-runner/ but I am not sure if that is the Docker for the ELN. Some documentation on DockerHub would be welcome, if it is.

Installation script fails at Capistrano deploy stage

I attempted to install on a Ubuntu 18.04 server running on VirtualBox using the installation script as described here: https://github.com/ComPlat/chemotion_ELN/blob/development/INSTALL.md but get the message "An error has occured" during the Capistrano deploy stage.

The code running appears as below:

01:22 deploy:migrating
      01 /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate
      01 Now using node v12.16.1 (npm v6.13.7)
      01 rake aborted!
      01 LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/rdkit/Code/lib/RDKitChem
      01 /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `require_relative'
      01 /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `<top (required)>'
      01 /var/www/chemotion_ELN/releases/20200503174904/config/application.rb:18:in `<top (required)>'
      01 /var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `require'
      01 /var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `<top (required)>'
      01 /home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
      01 /home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
      01 /home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
      01 (See full trace by running task with --trace)

and later on

Deploy failed code

** DEPLOY FAILED
** Refer to log/capistrano.log for details. Here are the last 20 lines:


 DEBUG [f39b2619] Finished in 2.334 seconds with exit status 0 (successful).

  INFO The Gemfile's dependencies are satisfied, skipping installation

  INFO [deploy:migrate] Run `rake db:migrate`

 DEBUG [70435082] Running if test ! -d /var/www/chemotion_ELN/releases/20200503174904; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200503174904'" 1>&2; false; fi as production@localhost

 DEBUG [70435082] Command: if test ! -d /var/www/chemotion_ELN/releases/20200503174904; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200503174904'" 1>&2; false; fi

 DEBUG [087bae83] Finished in 0.042 seconds with exit status 0 (successful).

  INFO [5c8b6d67] Running /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate as production@localhost

 DEBUG [5c8b6d67] Command: cd /var/www/chemotion_ELN/releases/20200503174904 && ( export NODE_VERSION="v12.16.1" RAILS_ENV="production" ; /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate )

 DEBUG [54da2d1a] 	Now using node v12.16.1 (npm v6.13.7)

 DEBUG [54da2d1a] 	rake aborted!

 DEBUG [54da2d1a] 	LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/rdkit/Code/lib/RDKitChem

 DEBUG [54da2d1a] 	/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `require_relative'

/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200503174904/config/application.rb:18:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `require'

/var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'

 DEBUG [54da2d1a] 	(See full trace by running task with --trace)

removing tmp files..
removing tmp repo..
An error has occured
** DEPLOY FAILED
** Refer to log/capistrano.log for details. Here are the last 20 lines:


 DEBUG [f39b2619] Finished in 2.334 seconds with exit status 0 (successful).

  INFO The Gemfile's dependencies are satisfied, skipping installation

  INFO [deploy:migrate] Run `rake db:migrate`

 DEBUG [70435082] Running if test ! -d /var/www/chemotion_ELN/releases/20200503174904; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200503174904'" 1>&2; false; fi as production@localhost

 DEBUG [70435082] Command: if test ! -d /var/www/chemotion_ELN/releases/20200503174904; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200503174904'" 1>&2; false; fi

 DEBUG [087bae83] Finished in 0.042 seconds with exit status 0 (successful).

  INFO [5c8b6d67] Running /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate as production@localhost

 DEBUG [5c8b6d67] Command: cd /var/www/chemotion_ELN/releases/20200503174904 && ( export NODE_VERSION="v12.16.1" RAILS_ENV="production" ; /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate )

 DEBUG [54da2d1a] 	Now using node v12.16.1 (npm v6.13.7)

 DEBUG [54da2d1a] 	rake aborted!

 DEBUG [54da2d1a] 	LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/rdkit/Code/lib/RDKitChem

 DEBUG [54da2d1a] 	/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `require_relative'

/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib/rdkit_chem.rb:1:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200503174904/config/application.rb:18:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `require'

/var/www/chemotion_ELN/releases/20200503174904/Rakefile:4:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'

 DEBUG [54da2d1a] 	(See full trace by running task with --trace)

removing tmp files..
removing tmp repo..
An error has occured

It appears that
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/rdkit/Code/lib/RDKitChem

is not a valid path, as the lib directory does not exist in this directory, but is instead found at the path:

/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-6777f2b2c749/lib

I don't understand enough whether this is an issue with the script or my set up, so any advice would be appreciated. I checked the other closed issue that talked about issues with the installation script but this doesn't appear to be the same thing?

Thanks

install issues

when i installed the chemotion _ELN, An error has occured: curl: (7) Failed to connect to raw.githubusercontent.com port 443: Connection refused
How can i solve this problem？
thanks！

Install issue on Ubuntu 20 with VirtualBox [macOS 10.13.6]

Tried to install Chemotion on Ubuntu 20 with VirtualBox using chemotion_ELN_install.sh script. Got error at PART 8 (see snapshot)

Improved yield calculation for reactions including e.g. dimerization

Reactions that include the consumption of 2 equiv of starting material (of reagent) for the generation of 1 formal equivalent of product are at the moment entered via a work-around: 1 equiv of the material is set as starting material, 1 equiv added as reagent. If would be nice to adapt this process: e.g.

offer a check box for "set stoichiometry"
if checked, allow the user to enter a number indicating that the material is consumed in an so far not considered manner
adapt yield calculation according to the number given in the stoichiometry entry field (if stoichiometry is 2, then yieldx2 etc).

Install issue

Hello, I am attempting to install Chemotion on a Ubuntu server and when I run the install script I get the following error "E: The repository 'http://cran.rstudio.com/bin/linux/ubuntu bionic/ Release' does not have a Release file.". Do you know what may be causing this issue?

Markdown Language support

For a more general usage of chemotion the support for mathematical formulars through markdown language (LaTeX math) in (some) text fields might increase the range of possible users.

It could increase the render quality of certain analytics:

${}^1\text{H-NMR} (400 \text{ MHz, ppm}) \delta = 2.3, 7.5, 7.6$

And add the possiblity for many formulas:
$\hat{F} | \phi_m> = \epsilon_m|\phi_m>$

$F_i = - \dfrac{\partial V(r)}{\partial r_i}$

I think that this could be especially useful with the Research Plan feature.

Some resources I stumbled across:
https://github.com/gettalong/kramdown // https://kramdown.gettalong.org/syntax.html#math-blocks
https://github.com/vmg/redcarpet

Generic segment/element

It would be great to have the generic element/segment formula field adapted (or another field generated) to be able to work with text instead of integer also. E.g. for the definition of identifers for MOFs, that would be great. E.g. if there is an building block for metals and one for organic compounds and we know the necessary descriptions for that, one could combine this with the formula field working with text.
Please see the attached picture for the requirements for the identifiers and the other picture for the current plan in ELN generic segment. If one allows to give e.g. "inorganic building block"+"."+"organic building block"+"Format signature"+"catenation"+"topology"+"comment" and creating the string für MOFs with this, this could solve a lot of problems.

What we would need in addition: being able to combine fields of other layers within one formula (or text-formula) field

Add structure by molfile without using ketcher editor

A users request: can we enable to add chemical structures by adding molfile without using ketcher editor? e.g. in a comparable way to SMILES entries in the identifier list?

consider using Zenodo to archive releases

It's fairly easy. See https://guides.github.com/activities/citable-code/

Upload option in generic element/segment

It would be great to have the option to upload a file in the generic segment/element to be stored with the element. The upload function should be given with another input field that can be used for a label (e.g. CIF for MOF or similar). We could use that later on to retrieve information from this data.

Inconsistent uploads

Container attachments are stored in uploads
ResearchPlan attachments are stored in tmp/uploads

Tabs in reaction interface are hidden by default

Expected appearance

To have all the tabs shown by default

Current appearance

Only Scheme tab is shown, other tabs need to be dragged and dropped to appear.

Steps to Reproduce

Create a new reaction or open an already existing one.
Click the tabs layout button.
Drag the tabs shown in grey and drop them in the white section (e.g. on scheme tab).
Click out of the tabs layout window.
The reaction interface should refresh and the chosen tabs will appear.

Context

production ready - tested in FSU.

Failure Logs / Screenshots

"Recyclable" checkbox can't be ticked in the "Green Chemistry" tab in the reaction interface

Expected Behavior

Having the checkbox checked

Current Behavior

Nothing happens

Steps to Reproduce

"Green Chemistry" tab is hidden, follow instructions from issue #392 to show it.
Tick the "Recyclable" checkbox.

Context

production ready tested in FSU.

A bug during editing a reaction

When I'm trying to edit an existing reaction it just goes into infinite updating. If I manually refresh the page none of changes are saved. I've recorded this:
youtube

Drag sample/molecule in generic segment

It would be great if we could have the function "drag molecule" also in the generic segment (perhaps also drag sample but molecule is more important).
For MOFs, it will then be important to see/copy the InChiKey or Smiles code from the assigned molecule. Sample is probably not that important.

Error during installation on Ubuntu 18.04

extconf failed, exit code 1

Gem files will remain installed in /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rinchi-gem-214f7db7947c for inspection.
Results logged to /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/extensions/x86_64-linux/2.5.0/rinchi-gem-214f7db7947c/gem_make.out

An error occurred while installing rinchi-gem (1.0.1), and Bundler cannot continue.

Collections Interface Improvement

Using Version 0.7.1

The Collections Tab has a black selection bar

and the update button is not intuitive to use to save.

Also, if you add a subcollection it immediatly appears on the navigation, but dissapears again, when update is not beeing pressed.

Maybe add a warning of unsaved changes if leaving the collection settings.

Sign In messages at unexpected times

Version: 0.7.1

If you log in and then click on affiliations Signed in successfully. appears.

If you log out You need to sign in or sign up before continuing. appears all the time

Typo in config

There seems to be a typo in the storage config:
secundary should probably be secondary

Chemotion on Windows Server

Thanks for the great software. IF I want to install chemotion on windows, is it only possible by using Docker?

Tags for certain input fields giving dates

User-request: it would be great if one could have a tag for certain fields in the ELN that can be filled with the date on that that the content was generated and last updated. Most important for research plan (text fields) and reaction description (reactions)

Update from Version: 0.7.1 -> 0.8.0 fails

We are trying to update to the new Version 0.8.0 via the update script. I haven't altered the script and run it as is.

It seems to have an issue with the database migrations:

== 20201109012155 CreateTextTemplates: migrating ==============================

-- create_table(:text_templates)

001:29 removing tmp files..
001:29 removing tmp repo..
001:29 An error has occured

Looking more closley

00:25 deploy:migrating
01 /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.6.6 do bundle exec rake db:migrate
01 Now using node v12.22.1 (npm v7.11.1)
01 /home/production/.rvm/gems/ruby-2.6.6/gems/activesupport-4.2.11.3/lib/active_support/core_ext/object/duplicable.rb:111: warning: BigDecimal.new is deprecated; use BigDecimal() method instead.
01 rake aborted!
01 StandardError: An error has occurred, this and all later migrations canceled:
01 
01 PG::DuplicateTable: ERROR:  relation "text_templates" already exists
01 : CREATE TABLE "text_templates" ("id" serial primary key, "type" character varying, "user_id" integer NOT NULL, "name" character varying, "data" jsonb DEFAULT '{}', "deleted_at" timestamp, "created_at" timestamp NOT NULL, "updated_at" timestamp NOT NULL)

[...]

== 20201109012155 CreateTextTemplates: migrating ==============================
-- create_table(:text_templates)
rake stderr: /home/production/.rvm/gems/ruby-2.6.6/gems/activesupport-4.2.11.3/lib/active_support/core_ext/object/duplicable.rb:111: warning: BigDecimal.new is deprecated; use BigDecimal() method instead.
rake aborted!
StandardError: An error has occurred, this and all later migrations canceled:

PG::DuplicateTable: ERROR:  relation "text_templates" already exists
: CREATE TABLE "text_templates" ("id" serial primary key, "type" character varying, "user_id" integer NOT NULL, "name" character varying, "data" jsonb DEFAULT '{}', "deleted_at" timestamp, "created_at" timestamp NOT NULL, "updated_at" timestamp NOT NULL)

it looks like, it doesn't try to migrate but recreate the entire database.
I attached the full log.
Do I have to make some changes to the update script?

Best
Fabian

update_production.log

Error during deployment

I'm trying to install ELN on clean Ubuntu 18.04 instance via the script.
Everything goes fine until deployment stage, looks like it cannot find some ruby gem.
Here is the error message:

01:39 bundler:install
      The Gemfile's dependencies are satisfied, skipping installation
01:39 deploy:migrate
      [deploy:migrate] Run `rake db:migrate`
01:39 deploy:migrating
      01 /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db…
      01 Now using node v12.16.1 (npm v6.13.7)
      01 rake aborted!
      01 LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.…
      01 /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890…
      01 /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890…
      01 /var/www/chemotion_ELN/releases/20200819151752/config/application.rb:1…
      01 /var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
      01 /var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (re…
      01 /home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in …
      01 /home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in …
      01 /home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in …
      01 (See full trace by running task with --trace)
#<Thread:0x000055df7bdacea0@/home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:10 run> terminated with exception (report_on_exception is true):
Traceback (most recent call last):
	1: from /home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:11:in `block (2 levels) in execute'
/home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:15:in `rescue in block (2 levels) in execute': Exception while executing as production@localhost: rake exit status: 1 (SSHKit::Runner::ExecuteError)
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)
#<Thread:0x000055df7bdaed40@/home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:10 run> terminated with exception (report_on_exception is true):
Traceback (most recent call last):
	1: from /home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:11:in `block (2 levels) in execute'
/home/production/.rvm/gems/ruby-2.5.6/gems/sshkit-1.18.2/lib/sshkit/runners/parallel.rb:15:in `rescue in block (2 levels) in execute': Exception while executing as production@localhost: Exception while executing as production@localhost: rake exit status: 1 (SSHKit::Runner::ExecuteError)
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)
(Backtrace restricted to imported tasks)
cap aborted!
SSHKit::Runner::ExecuteError: Exception while executing as production@localhost: Exception while executing as production@localhost: rake exit status: 1
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)


Caused by:
SSHKit::Runner::ExecuteError: Exception while executing as production@localhost: rake exit status: 1
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)


Caused by:
SSHKit::Command::Failed: rake exit status: 1
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)

Tasks: TOP => deploy:migrate
(See full trace by running task with --trace)
The deploy has failed with an error: Exception while executing as production@localhost: Exception while executing as production@localhost: rake exit status: 1
rake stdout: Now using node v12.16.1 (npm v6.13.7)
rake stderr: rake aborted!
LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'
/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'
/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'
/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'
(See full trace by running task with --trace)


** DEPLOY FAILED
** Refer to log/capistrano.log for details. Here are the last 20 lines:


 DEBUG [c15e4829] Finished in 2.686 seconds with exit status 0 (successful).

  INFO The Gemfile's dependencies are satisfied, skipping installation

  INFO [deploy:migrate] Run `rake db:migrate`

 DEBUG [d5e87a8a] Running if test ! -d /var/www/chemotion_ELN/releases/20200819151752; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200819151752'" 1>&2; false; fi as production@localhost

 DEBUG [d5e87a8a] Command: if test ! -d /var/www/chemotion_ELN/releases/20200819151752; then echo "Directory does not exist '/var/www/chemotion_ELN/releases/20200819151752'" 1>&2; false; fi

 DEBUG [3996b1c0] Finished in 0.044 seconds with exit status 0 (successful).

  INFO [b758ceb0] Running /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate as production@localhost

 DEBUG [b758ceb0] Command: cd /var/www/chemotion_ELN/releases/20200819151752 && ( export NODE_VERSION="v12.16.1" RAILS_ENV="production" ; /tmp/chemotion/nvm-exec.sh ~/.rvm/bin/rvm 2.5.6 do bundle exec rake db:migrate )

 DEBUG [a93c4ab2] 	Now using node v12.16.1 (npm v6.13.7)

 DEBUG [a93c4ab2] 	rake aborted!

 DEBUG [a93c4ab2] 	LoadError: cannot load such file -- /home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/rdkit_chem/lib/RDKitChem

 DEBUG [a93c4ab2] 	/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `require_relative'

/home/production/.rvm/gems/ruby-2.5.6/bundler/gems/rdkit_chem-cf8a3890c5aa/lib/rdkit_chem.rb:3:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200819151752/config/application.rb:18:in `<top (required)>'

/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `require'

/var/www/chemotion_ELN/releases/20200819151752/Rakefile:4:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `eval'

/home/production/.rvm/gems/ruby-2.5.6/bin/ruby_executable_hooks:24:in `<main>'

 DEBUG [a93c4ab2] 	(See full trace by running task with --trace)

removing tmp files..
removing tmp repo..
An error has occured

The funding info in the README is not correctly formatted

Installation script doesn't work

I've tried the installation script on new Vultr VDS using clean Ubuntu 18.04. It runs well until PART 4, when it asks for production user password, which, as far as I understand, is automatically generated. I run the script as root if it is important.

Searching for binary rubies, this might take some time.
Found remote file https://rvm_io.global.ssl.fastly.net/binaries/ubuntu/18.04/x86_64/ruby-2.5.6.tar.bz2
Checking requirements for ubuntu.
Installing requirements for ubuntu.
Updating systemproduction password required for 'apt-get --quiet --yes update': ..-
production password required for 'apt-get --quiet --yes update':
production password required for 'apt-get --quiet --yes update':
..
Error running 'requirements_debian_update_system ruby-2.5.6',
please read /home/production/.rvm/log/1573551803_ruby-2.5.6/update_system.log
Requirements installation failed with status: 1.
removing tmp files..
An error has occured

Install script issue in part 1

I am setting up a

production
development environment

Failure Information

Hi ! I just wanted to report an issue observed when trying to install chemotion on a fresh Ubuntu server install on a VM, in the part 1 of the script.

I didn't quite understand what was the issue, I then manually installed all the dependencies listed in the script in part 1 without any problem, except for the three fonts package listed below which seems to be for Ubuntu 20.04 only.

After running the script another time with part 1 commented, the rest of the install went fine and I ended up with a working version of chemotion.

Context

Fresh install of Ubuntu server 18.04.5 on a virtual machine (> 3 Gb ram and two core allocated).

I am

using Docker
not using Docker
OS: Ubuntu Server 18.04.5
ELN version, or branch, or commit : development branch

Steps to Reproduce

Just running the script.

Failure Logs / Screenshots

000:00 ##########################################
000:00 Running installation for Ubuntu 18.04.5 LTS
000:00 ##########################################
000:00 ##########################################
000:00 PART 0
000:00 ##########################################
000:00 ##########################################
000:00 updating OS
000:00 ##########################################
Hit:1 http://fr.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://fr.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://fr.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://fr.archive.ubuntu.com/ubuntu bionic-security InRelease
Ign:5 https://oss-binaries.phusionpassenger.com/apt/passenger bionic InRelease
Hit:6 https://oss-binaries.phusionpassenger.com/apt/passenger bionic Release
Reading package lists... Done
Building dependency tree
Reading state information... Done
All packages are up to date.
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
000:06 done updating OS

000:06 ##########################################
000:06 PART 1
000:06 ##########################################
000:06 ##########################################
000:06 installing debian dependencies
000:06 ##########################################
Hit:1 http://fr.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://fr.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://fr.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://fr.archive.ubuntu.com/ubuntu bionic-security InRelease
Ign:5 https://oss-binaries.phusionpassenger.com/apt/passenger bionic InRelease
Hit:6 https://oss-binaries.phusionpassenger.com/apt/passenger bionic Release
Reading package lists... Done
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libxslt1-dev' instead of 'libxslt-dev'
E: Unable to locate package fonts-noto-core
E: Unable to locate package fonts-noto-extra
E: Unable to locate package fonts-noto-ui-core
000:10 removing tmp files..
000:10 removing tmp repo..
000:10 An error has occured

Install script issue

Hello!

I am trying to install chemotion on Ubuntu Server 20.4 (fresh install with no additional packages) following the instructions in INSTALL.md. The script stops at the following step and does nothing anymore:

00:04 npm:install

      01 /tmp/chemotion/nvm-exec.sh npm install --production --silent --no-progress

      01 Now using node v12.18.3 (npm v6.14.6)

I am a bit lost how to look for the problem. Any help would be appreciated.

docker-compose method of settting up development environment fails

I am trying to set up a development environment using Docker. Following the instructions found here I manage to initialize the database container, however, at the next step to install dependencies missing from the container, an error is raised.

The problem is with executing this command

docker-compose run app /bin/bash -c 'source /usr/local/nvm/nvm.sh;\
 cd node_modules/@novnc/noVNC;\
 npx babel-upgrade --write; npm i; npm i pako; npm i @babel/preset-env;\
 mkdir -p utils;\
 curl https://raw.githubusercontent.com/novnc/noVNC/master/utils/use_require.js > utils/use_require.js;\
 node utils/use_require.js --clean; true'

The output is as follows:

WARNING: Found orphan containers (build_db_data_1) for this project. If you removed or renamed this service in your compose file, you can run this command with the --remove-orphans flag to clean it up.
Starting build_postgres_1 ... done
Starting build_sftp_1     ... done
/bin/bash: line 1: cd: node_modules/@novnc/noVNC: No such file or directory
🙌  Thanks for trying out https://github.com/babel/babel-upgrade !

Updating .babelrc config at .babelrc
Index: .babelrc
===================================================================
--- .babelrc	Before Upgrade
+++ .babelrc	After Upgrade


Updating closest package.json dependencies
Index: /home/app/chemotion_ELN/package.json
===================================================================
--- /home/app/chemotion_ELN/package.json	Before Upgrade
+++ /home/app/chemotion_ELN/package.json	After Upgrade
@@ -112,9 +112,9 @@
     ]
   },
   "devDependencies": {
     "@babel/register": "^7.11.5",
-    "babel-eslint": "7.2.2",
+    "babel-eslint": "^9.0.0",
     "enzyme": "^3.7.0",
     "enzyme-adapter-react-16": "^1.6.0",
     "eslint": "^4.19.1",
     "eslint-config-airbnb": "^16.1.0",


npm WARN deprecated [email protected]: babel-eslint is now @babel/eslint-parser. This package will no longer receive updates.
npm WARN @citation-js/[email protected] requires a peer of @citation-js/core@^0.4.2 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of [email protected] - 0.14 || ^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.5.4 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14 || ^15.0.0-rc || ^15.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14.0 || ^15.0.0-rc.1 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of sinon@^1.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of webpack@^4.0.0 || ^5.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: [email protected] (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

added 1 package, removed 6 packages, updated 1 package and audited 1904 packages in 5.62s

67 packages are looking for funding
  run `npm fund` for details

found 29 vulnerabilities (25 low, 1 moderate, 3 high)
  run `npm audit fix` to fix them, or `npm audit` for details
npm WARN @citation-js/[email protected] requires a peer of @citation-js/core@^0.4.2 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of [email protected] - 0.14 || ^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.5.4 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14 || ^15.0.0-rc || ^15.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14.0 || ^15.0.0-rc.1 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of sinon@^1.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of webpack@^4.0.0 || ^5.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: [email protected] (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

+ [email protected]
added 1 package from 6 contributors, updated 1 package and audited 1905 packages in 6.378s

67 packages are looking for funding
  run `npm fund` for details

found 29 vulnerabilities (25 low, 1 moderate, 3 high)
  run `npm audit fix` to fix them, or `npm audit` for details
npm WARN @citation-js/[email protected] requires a peer of @citation-js/core@^0.4.2 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.6.3 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of [email protected] - 0.14 || ^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.5.4 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14 || ^15.0.0-rc || ^15.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^16.8.0 || ^17.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@>=16.6.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^0.14.0 || ^15.0.0-rc.1 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of react-dom@^15.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of sinon@^1.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN [email protected] requires a peer of webpack@^4.0.0 || ^5.0.0 but none is installed. You must install peer dependencies yourself.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: [email protected] (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

+ @babel/[email protected]
added 286 packages from 14 contributors, removed 10 packages, updated 63 packages, moved 2 packages and audited 2181 packages in 14.593s

67 packages are looking for funding
  run `npm fund` for details

found 29 vulnerabilities (25 low, 1 moderate, 3 high)
  run `npm audit fix` to fix them, or `npm audit` for details
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  5103  100  5103    0     0  15187      0 --:--:-- --:--:-- --:--:-- 15187
Removing /home/app/chemotion_ELN/lib
Writing /home/app/chemotion_ELN/lib/vendor/assets/javascripts/autocomplete.min.js
Failure converting modules: Error: ENOENT: no such file or directory, scandir '/home/app/chemotion_ELN/core'

I think the failure message at the bottom is problematic, because the next command that is suggested to verify the installation

docker-compose run app rake ketcherails:import:common_templates

fails as well:

WARNING: Found orphan containers (build_db_data_1) for this project. If you removed or renamed this service in your compose file, you can run this command with the --remove-orphans flag to clean it up.
Starting build_sftp_1     ... done
Starting build_postgres_1 ... done
rake aborted!
NameError: uninitialized constant OnelineLogFormatter
/home/app/chemotion_ELN/config/environments/production.rb:85:in `block in <top (required)>'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/railtie.rb:210:in `instance_eval'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/railtie.rb:210:in `configure'
/home/app/chemotion_ELN/config/environments/production.rb:1:in `<top (required)>'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/engine.rb:598:in `block (2 levels) in <class:Engine>'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/engine.rb:597:in `each'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/engine.rb:597:in `block in <class:Engine>'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:30:in `instance_exec'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:30:in `run'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:55:in `block in run_initializers'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:44:in `each'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:44:in `tsort_each_child'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/initializable.rb:54:in `run_initializers'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/application.rb:352:in `initialize!'
/home/app/chemotion_ELN/config/environment.rb:5:in `<top (required)>'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/application.rb:328:in `require_environment!'
/usr/local/rvm/gems/ruby-2.5.5/gems/railties-4.2.11.3/lib/rails/application.rb:457:in `block in run_tasks_blocks'
/usr/local/rvm/gems/ruby-2.5.5/gems/rake-12.3.3/exe/rake:27:in `<top (required)>'
/usr/local/rvm/gems/ruby-2.5.5/bin/ruby_executable_hooks:24:in `eval'
/usr/local/rvm/gems/ruby-2.5.5/bin/ruby_executable_hooks:24:in `<main>'
Tasks: TOP => ketcherails:import:common_templates => environment
(See full trace by running task with --trace)

Any suggestions on how to debug this would be much appreciated

alignment in analysis section

I would be great if you could change the layout of the analysis section in the part attachments: dependent on the availability of a preview, the content of the layout is a bit shifted: could you place the preview on the right side of the panel (that the text part is not affected by the availability of the image)? (-> or a better solution if there is any)?

References in ELN and Repo

could you please adapt the new field for literature entries in ELN and Repo? At the moment, the new field describing the meaning of the reference (direct reference or reference from someone else) should be more visible/mandatory.
Please also add a new type to have three altogether:

reference citing exactly this experiment/same authors
reference citing the experiment done by others
reference similar experiments or related literature

Error in structur editor when saving file as InChI string

Expected Behavior

Having a text that includes InChI string

Current Behavior

Error message

Steps to Reproduce

Open the structure editor for a certain molecule/sample.
Choose "save as".
In the format field, choose InChI string.

Context

production ready - tested in FSU

Failure Logs / Screenshots

Cannot add literature to research plan

How to reproduce:

Create a new research plan
Click Literatures
Paste a DOI
Click resolve button
Click Plus button

Error in structure editor in building chains of amino acids

Expected Behavior

Building a chain of amino acids.

Current Behavior

Error message: "Error: can not find one of items in sequnce. Some items are not known."

Steps to Reproduce

Create a new sample.
Open its structure editor.
Choose "Build chains".
In the sequence field, type: "A-A-G", press OK.

Context

production ready - tested in FSU

Failure Logs / Screenshots

Upload analytical directories without the need to zip them

Having an Analytical Data Server besides Chemotion, which is used not exclusively by chemotion users it would help to support the upload of directories.

Storing the analytical data in compressed from may cause already existing pipelines with e.g. TopSpin to break.

I've looked up some approaches using JavaScript that either allow to upload directories directly or convert them to a zip file.

Sources:
https://gildas-lormeau.github.io/zip.js/ / https://github.com/gildas-lormeau/zip.js
https://wicg.github.io/directory-upload/index.html

https://stackoverflow.com/questions/42239663/upload-folder-and-all-its-content-in-javascript
https://stackoverflow.com/questions/56731695/javascript-upload-folder-by-zipping-with-same-folder-structure-as-uploaded-folde

This would avoid the extra step of zipping the files (if not possible automatically, because of existing pipelines) and increase the useability of the ChemSpectra editor.

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