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Extending chemotion_ELN with Repository functions
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In short:
- data submission feature added to user ELN page
- Review page for internal reviewing
- Public page to browse published sample/reaction data

Contributors:
Chia-Lin Lin
Pei-Chi Huang
Pierre Tremouilhac
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Chemotion authored and PiTrem committed Apr 17, 2020
1 parent 9c6d718 commit 14676fd
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Showing 320 changed files with 24,210 additions and 830 deletions.
37 changes: 28 additions & 9 deletions .env.development → .env.dev.example
Original file line number Diff line number Diff line change
@@ -1,16 +1,7 @@
SFTP_HOST=sftp
SFTP_PORT=22
SFTP_UPLOAD_FOLDER=uploads
SFTP_USER=sftp_test
SFTP_PASSWORD=sftp_test

MESSAGE_ENABLE=false
MESSAGE_AUTO_INTERNAL=6000
MESSAGE_IDLE_TIME=12

# JWT key for novnc target encryption
NOVNC_SECRET='secret'

# Allow unconfirmed email: leave blank for always, or set a number of days (integer);
# also set 0 to have email being confirmed before first sign in.
DEVISE_ALLOW_UNCONFIRMED=''
Expand All @@ -22,3 +13,31 @@ DEVISE_DISABLED_SIGN_UP=''
# Any new account to be inactive by default => only admin can (de)activate
DEVISE_NEW_ACCOUNT_INACTIVE=false

# email of the Repository user
SYS_EMAIL='[email protected]'

# id of public collection
PUBLIC_COLL_ID=0
SCHEME_ONLY_REACTIONS_COLL_ID=0

DOI_SYMBOL='DOI_SYMBOL'
DOI_PWD='DOI_PWD'
DOI_PREFIX='10.XXXX'
DOI_DOMAIN='DOI.DOMA.IN'

PUBCHEM_LOGIN='PUBCHEM_LOGIN'
PUBCHEM_PASSWORD='PUBCHEM_PW'


PUBLISH_MODE='staging'

ARTICLE_PATH='public/newsroom/'

# user ids of howto editors
# HOWTO_EDITOR='1,2,3'

# user ids of news editors
# NEWSROOM_EDITOR='1,2,3'

# user ids of reviewers
# REVIEWERS='1,2,3'
3 changes: 2 additions & 1 deletion .eslintrc
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Expand Up @@ -11,6 +11,7 @@
"rules": {
"no-console": ["off"],
"comma-dangle": [1,"only-multiline"],
"react/jsx-filename-extension": [1, { "extensions": [".js", ".jsx"] }]
"react/jsx-filename-extension": [1, { "extensions": [".js", ".jsx"] }],
"react/no-multi-comp": [0, { "ignoreStateless": true }]
}
}
15 changes: 15 additions & 0 deletions .gitignore
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Expand Up @@ -23,6 +23,9 @@
.coveralls.yml

.env
.env.development
.env.test
.env.production

/config/mailcollector.yml
/config/datamailcollector.yml
Expand All @@ -32,12 +35,19 @@
!/config/data_collector_keys/.keep

/config/database.yml
/config/repository_database.yml
/config/storage.yml
/config/spectra.yml
/config/editors.yml

/node_modules

/public/newsroom/*
!/public/newsroom/.keep
/public/howto/*
!/public/howto/.keep

!/public/images/molecules/.keep
/public/images/molecules/*
!/public/images/molecules/.keep

Expand Down Expand Up @@ -68,6 +78,7 @@
/public/images/*
!/public/images/wild_card/
!/public/images/ghs/
!/public/images/creative_common/

/public/ontologies/*
!/public/ontologies/.keep
Expand All @@ -77,6 +88,10 @@
!/public/ontologies/rxno.default.json
!/public/ontologies/rxno.default.edited.json

/public/directives/*
!/public/images/directives/.keep
!/public/images/directives/directives.html

/uploads/*
!/public/attachments/.keep

Expand Down
10 changes: 9 additions & 1 deletion Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@ gem 'bibtex-ruby'
# state machine
gem 'aasm'

gem 'bootsnap', require: false

group :development do
gem 'sdoc', '~> 0.4.0', group: :doc

Expand Down Expand Up @@ -91,6 +93,7 @@ gem 'kaminari-grape'
gem "rdkit_chem", git: "https://github.com/CamAnNguyen/rdkit_chem"

gem 'api-pagination'
gem 'rack-cors'

gem 'pundit'

Expand Down Expand Up @@ -150,8 +153,10 @@ gem 'coveralls', require: false
# to compile from github/openbabel/openbabel master
# gem 'openbabel', '2.4.1.2', git: 'https://github.com/ComPlat/openbabel-gem'
# to compile from github/openbabel/openbabel branch openbabel-2-4-x
# gem 'openbabel', '2.4.90.1', git: 'https://github.com/ComPlat/openbabel-gem'
gem 'openbabel', '2.4.90.3', git: 'https://github.com/ComPlat/openbabel-gem.git', branch: 'hot-fix-svg'


gem 'barby'
gem 'prawn'
gem 'prawn-svg'
Expand All @@ -163,13 +168,14 @@ gem 'swot', git: 'https://github.com/leereilly/swot.git', branch: 'master',
ref: 'bfe392b4cd52f62fbc1d83156020275719783dd1'
# gem 'gman', '~> 7.0.3'
gem 'activejob-status'
gem 'moneta'

group :development, :test do
gem 'binding_of_caller'

gem 'annotate'

gem 'mailcatcher', '0.7.1'
# gem 'mailcatcher', '0.7.1'

# Call 'byebug' anywhere in the code to stop execution
# and get a debugger console
Expand Down Expand Up @@ -230,4 +236,6 @@ if File.exists?(eln_plugin)
eval_gemfile eln_plugin
end

#gem 'reposit', git: '[email protected]:complat/reposit.git'

####
48 changes: 18 additions & 30 deletions Gemfile.lock
Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ GEM
api-pagination (4.8.2)
arel (6.0.4)
ast (2.4.0)
autoprefixer-rails (9.6.4)
autoprefixer-rails (9.7.6)
execjs
awesome_print (1.8.0)
axiom-types (0.1.1)
Expand All @@ -164,10 +164,12 @@ GEM
coderay (>= 1.0.0)
erubi (>= 1.0.0)
rack (>= 0.9.0)
bibtex-ruby (5.1.2)
bibtex-ruby (5.1.3)
latex-decode (~> 0.0)
binding_of_caller (0.8.0)
debug_inspector (>= 0.0.1)
bootsnap (1.3.2)
msgpack (~> 1.0)
bootstrap-kaminari-views (0.0.5)
kaminari (>= 0.13)
rails (>= 3.1)
Expand Down Expand Up @@ -239,7 +241,7 @@ GEM
css_parser (1.7.0)
addressable
daemons (1.3.1)
database_cleaner (1.7.0)
database_cleaner (1.8.4)
debug_inspector (0.0.3)
delayed_cron_job (0.7.2)
delayed_job (>= 4.1)
Expand Down Expand Up @@ -369,23 +371,14 @@ GEM
latex-decode (0.3.1)
launchy (2.4.3)
addressable (~> 2.3)
listen (3.1.5)
rb-fsevent (~> 0.9, >= 0.9.4)
rb-inotify (~> 0.9, >= 0.9.7)
ruby_dep (~> 1.2)
loofah (2.4.0)
listen (3.2.1)
rb-fsevent (~> 0.10, >= 0.10.3)
rb-inotify (~> 0.9, >= 0.9.10)
loofah (2.5.0)
crass (~> 1.0.2)
nokogiri (>= 1.5.9)
mail (2.7.1)
mini_mime (>= 0.1.1)
mailcatcher (0.7.1)
eventmachine (= 1.0.9.1)
mail (~> 2.3)
rack (~> 1.5)
sinatra (~> 1.2)
skinny (~> 0.2.3)
sqlite3 (~> 1.3)
thin (~> 1.5.0)
memoist (0.16.0)
memory_profiler (0.9.13)
meta_request (0.7.0)
Expand All @@ -399,6 +392,8 @@ GEM
mini_mime (1.0.2)
mini_portile2 (2.4.0)
minitest (5.12.2)
moneta (1.0.0)
msgpack (1.2.6)
multi_json (1.13.1)
multi_xml (0.6.0)
multipart-post (2.1.0)
Expand Down Expand Up @@ -427,7 +422,7 @@ GEM
parallel (1.17.0)
paranoia (2.4.2)
activerecord (>= 4.0, < 6.1)
parser (2.6.4.1)
parser (2.7.1.0)
ast (~> 2.4.0)
pdf-core (0.7.0)
pg (0.20.0)
Expand All @@ -448,8 +443,7 @@ GEM
rack (>= 0.4)
rack-contrib (1.8.0)
rack (~> 1.4)
rack-protection (1.5.5)
rack
rack-cors (1.0.2)
rack-test (0.6.3)
rack (>= 1.0)
rails (4.2.11.1)
Expand Down Expand Up @@ -546,7 +540,7 @@ GEM
safe_yaml (1.0.5)
sassc (2.2.1)
ffi (~> 1.9)
sassc-rails (2.1.1)
sassc-rails (2.1.2)
railties (>= 4.0.0)
sassc (>= 2.0)
sprockets (> 3.0)
Expand All @@ -568,14 +562,7 @@ GEM
json (>= 1.8, < 3)
simplecov-html (~> 0.10.0)
simplecov-html (0.10.2)
sinatra (1.4.8)
rack (~> 1.5)
rack-protection (~> 1.4)
tilt (>= 1.3, < 3)
sixarm_ruby_unaccent (1.2.0)
skinny (0.2.4)
eventmachine (~> 1.0.0)
thin (>= 1.5, < 1.7)
slackistrano (3.8.4)
capistrano (>= 3.8.1)
spring (2.0.2)
Expand All @@ -588,7 +575,6 @@ GEM
actionpack (>= 4.0)
activesupport (>= 4.0)
sprockets (>= 3.0.0)
sqlite3 (1.4.1)
sshkit (1.18.2)
net-scp (>= 1.1.2)
net-ssh (>= 2.8.0)
Expand All @@ -610,7 +596,7 @@ GEM
parallel (~> 1.0)
railties (>= 4)
sprockets (~> 3.0)
tzinfo (1.2.5)
tzinfo (1.2.7)
thread_safe (~> 0.1)
uglifier (4.1.20)
execjs (>= 0.3.0, < 3)
Expand Down Expand Up @@ -663,6 +649,7 @@ DEPENDENCIES
better_errors
bibtex-ruby
binding_of_caller
bootsnap
bootstrap-sass (~> 3.4.1)
browserify-rails (~> 4.2.0)
bullet
Expand Down Expand Up @@ -710,9 +697,9 @@ DEPENDENCIES
kaminari-grape
ketcherails (~> 0.1.6)!
launchy (~> 2.4.3)
mailcatcher (= 0.7.1)
memory_profiler
meta_request
moneta
net-sftp
net-ssh
nokogiri
Expand All @@ -724,6 +711,7 @@ DEPENDENCIES
prawn
prawn-svg
pundit
rack-cors
rack-mini-profiler!
rails (= 4.2.11.1)
rdkit_chem!
Expand Down
17 changes: 3 additions & 14 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Chemotion Electronic Lab Notebook
# Chemotion REPOSITORY

An ELN for chemists!
A repository for chemists based on chemotion ELN !

## Funding

Expand All @@ -9,7 +9,7 @@ This project has been funded by the ![DFG](http://www.dfg.de/includes/images/df

## License

Chemotion_ELN: an Electronic Lab Notebook for Chemists.
Chemotion_REPOSITORY for Chemists.

Copyright (C) 2015-current Nicole Jung (nicole.jung(at)kit.edu) of the Karlsruhe Institute of Technology.

Expand All @@ -33,15 +33,4 @@ Copyright (C) 2015-current Nicole Jung (nicole.jung(at)kit.edu) of the Karlsruh
see [INSTALL.md][INSTALL]


## Code Status

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1054134.svg)](https://doi.org/10.5281/zenodo.1054134)

[![Build Status](https://travis-ci.org/ComPlat/chemotion_ELN.svg?branch=master)](https://travis-ci.org/ComPlat/chemotion_ELN)

[![Coverage Status](https://coveralls.io/repos/github/ComPlat/chemotion_ELN/badge.svg)](https://coveralls.io/github/ComPlat/chemotion_ELN)




[INSTALL]: INSTALL.md
6 changes: 5 additions & 1 deletion app/api/api.rb
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,9 @@ def is_public_request?
'/api/v1/chemspectra/',
'/api/v1/ketcher/layout',
'/api/v1/gate/receiving',
'/api/v1/gate/ping'
'/api/v1/gate/ping',
'/api/v1/search/',
'/api/v1/suggestion'
)
end

Expand Down Expand Up @@ -125,4 +127,6 @@ def to_json_camel_case(val)
mount Chemotion::EditorAPI
mount Chemotion::UiAPI
mount Chemotion::OlsTermsAPI
mount Chemotion::RepositoryAPI
mount Chemotion::ArticleAPI
end
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