Merge development to master : AgroPortal release 2.4.5 (#196)

* merge to "development"

* refactoring

* unsubscribe feat

* remove no more used code

* remove submissions.js.erb

* add unsubscribe

* add and use Loader view component

* [ontoportal-bot] Gemfile.lock update

* Update users_controller.rb

* add tests && refacto

* add switch input view component

* extract submission save and update concerns

* update latest_submission_attributes helper name

* update turbo alerts helpers to have custom id

* update submission from to use SwitchComponent and move out hidden_field

* update admin metadata section style& add show all submissions  switch

* update curator result to implement submissions & show edit_metadata_btn

* update the edit action to add error handling and remove useless code

* add submission inline editable attribute views and action

* update metadata bulk edit form to use turbo modal

* update curator result table style and attribute_inline_editable partial

* update curator "update" to use a concern & handle multiple submissions

* add route to ontologies_metadata_curator#show_metadata_by_ontology

* add ontology_submission_id_label and ontology_and_submission_id helpers

* add tests and refacto

* fix empty chosen not sent in the request

* fix response_success? test when response.status is string

* fix submission form show_sections  value

* on submission save/update permit arrays of hash or values

* Update users_controller.rb

* Update Dockerfile

* fix empty scheme ids show

* fix turbo frame error catching by preventing event

* se turbo config method to use Alertify.confirm

* add remove turbo_stream helper

* update admin submission delete to handle turbo_stream

* make submission edit action use submission Id

* add edit and delete actions to ontology submissions table

* fix response_errors to use response body

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* fix a typo in ontologies_metadata_curator

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* Revert "Merge branch 'fix/docker' into fix/add-to-our-mailing-list"

This reverts commit 55d8627, reversing
changes made to a0352e8.

* remove duplicated code

* remove unused submission_attributes helper

* update submission_editable_properties  to use equivalent_properties

* display equivalent attributes on display_submission_attributes

* replace equivalent arguments, with equivalent_properties helper

* use equivalent_properties in the metadata curator result

* use the same submission_editable_properties in the curator

* display attrbiute_inline for equivalent_properties

* usen CGI.escape for escaping URIs

* [ontoportal-bot] Gemfile.lock update

* use Chosen for no multiple  select also

* make the select component select an empty value by default

* permit submission array and hash attributes

* add a turbo_frame_tag for format section in the submission form

* remove docker-entrypoint-web file

* disable  workers and threads defaults

* [ontoportal-bot] Gemfile.lock update

* Update docker-compose.yml

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* fix escaping URIs issue

* add less to the Dockerfile used by binding.pry

* [ontoportal-bot] Gemfile.lock update

* Add check icon

* Add unescape() function

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* Update the design of the feedback page

* catch send exceptions for submission attributes

* make form_group_component asterik configurable

* use the required option from form_group_attribute

* don't collapse sections if new submission

* disable submission form filters if  new submission or error state

* show only required properties if new submissions

* disable filter if create or update submission action

* show backend errors in the submission form

* add ID column for submissions table  if ontology admin

* change submission+ontology ID label to use # instead of / as joiner

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* Extract popup message

Extract the popup we're using to show success messages ... to make it reusable

* Update application.css.scss.erb

* delete replacable classes by bootstrap

* Update feedback.html.haml

* Add tags field

* Create notifier.rb

* Add tags (checks)

* Replace fixed colors by variables

* Change the name to card_message

* Update and rename popup_message.scss to card_message.scss

* Update and rename popup_message_component.rb to card_message_component.rb

* Rename the message card component

* Delete app/components/popup_message_component directory

* Update card_message.scss

* Update card_message_component.rb

* Update card_message_component.html.haml

* set ontology viewer section frame target to  top

* disable turbo cache on browser back

* fix ontology_picker_advanced that didn't work on browser back

* Add OntologySubscribeButton component

* move external stimulus controller to application.js

* add subscribe_button helper

* use the subscribe_button component in the user page

* remove old subscribe_ontology_button helper

* remove old subscribeToNotes js code

* remove the bp_ontology_viewer.js file

* remove duplicate code in _submissions.html.haml to toggle the table

* use turbo modal instead of jquery facebox to show the fair score details

* wrap the fair score details pop view in a turbo_frame

* Extract note table line and use turbo modal to show details

* wrap note detail view in a modal turbo_frame

* extract notes table partial

* re-use the notes table partial in the ontology and concept notes views

* add the new_comment action and view

* add new proposal action and view

* add new reply action and view

* update the notes creation action to render streams

* add notes destroy action if portal admin

* add helpers for add_comment, add_proposal and add_reply buttons

* make render_alerts_container use a custom id

* extract reply list and show partials from the thread view

* remove no more used JS code in bp_notes.js

* add route  get 'ontologies/:ontology/notes'

* remove the layout from the notes virtual_show response

* remove the relative link to edit submission

* Feature: Update login page design (#142)

* add new login style

* import the new login style

* update login template

* put colors variables in one globale file

* convert login file from .erb to .haml

* Remove the replaceable classes by bootstrap classes & use css variables instead of fixed values

* import variables file

* Update application.css.scss.erb

* Update application.css.scss.erb

* Update application.css.scss.erb

* Update and rename variables_stage.scss to variables.scss.erb

* Update bioportal.scss

* Update login.scss

* Rename variables.scss.erb to theme-variables.scss.erb

* Update application.css.scss.erb

---------

Co-authored-by: Syphax Bouazzouni <[email protected]>

* Feature: Update lost password page design (#143)

* update login page design

* update the design of lost password page

* update sucess message for password reset

* Update index.html.erb

* Delete login.scss

* Update index.html.erb

* upload arrow-back.svg

* Update lostpassword.scss

* Extract the svg to a file, and convert the file from .erb to .haml

* Use the message card component

* replace fixed colors by variables

* Update lostpassword.scss

* Update lost_password_success.html.haml

* Update lost_password_success.html.haml

* Update lost_password_success.html.haml

---------

Co-authored-by: Syphax Bouazzouni <[email protected]>

* [ontoportal-bot] Gemfile.lock update

* Fix: add user to mailing list on signup (#148)

* update (un)subscribe ui

* Refactor confirmation message and update UI

* Create Sympa mailer with registration and unregistration methods

* Fix subscription logic and add environment example for mailing list

* protect routes

* [ontoportal-bot] Gemfile.lock update

* remove the old reference to subscribe_notes_controller

* Create green-check.svg

* Create red-warning.svg

* Update card_message_component.rb

* Update card_message_component.html.haml

* Update home_controller.rb

* Update feedback.html.haml

* Update and rename feedback_complete.html.erb to feedback_complete.html.haml

* Revert "Add tags field"

This reverts commit 989902d.

* update feedback in the right notifier.rb in mailers not models

* fix feedback popup if location is empty

* remove the old feedback.html.erb file

* remove the auto close of the popup after a timeout

* move the feedback views to home/feedback folder

* reset the portal font

* [ontoportal-bot] Gemfile.lock update

* remove the auto close of the popup after a timeout

* move the feedback views to home/feedback folder

* update switch component to have a boolean version for submissions form

* fix input attribute of type uri getting only the first letter (e.g h)

* don't use response_error? in the admin controller

* update $DATA_CATALOG_VALUES variables values

* update how data_catalog is found

* add display=all parameter to access concept json link

* show ontology pull url in summary page if ontology admin

* remove the option None for all the submission from select attribute

* extract ontology_restricted? helper

* remove unused code in the  ontology 'show' action

* remove no more needed code in the ontology 'summary' action

* add submission index action

* move partial 'submission' to a turbo_frame

* use @submission_latest instead of @Submissions.first to get the latest

* add submission index action route

* don't show Download latest version if no submission latest

* [ontoportal-bot] Gemfile.lock update

* add newrelic configs for ui app

* remove unused stages

* fix typo issue of writing '=' in the statement end where it's not needed

* Remove no title value of the message card component  (#197)

* Feature: Add Newrelic configuration file  (#198)

* [ontoportal-bot] Gemfile.lock update

* add newrelic configs for ui app

* remove unused stages

* fix typo issue of writing '=' in the statement end where it's not needed

---------

Co-authored-by: OntoPortal Bot <[email protected]>
Co-authored-by: HADDAD Zineddine <[email protected]>

* [ontoportal-bot] Gemfile.lock update

* install newrelic_rpm also in :appliance stage

* Revert "Merge pull request #119 from ontoportal-lirmm/fix/browse-search-length-problem"

This reverts commit 0ad14c3.

* extract metadata table row partial

* make the bulk update refresh the table in the background

* remove the single update option in the bulk popup

* add a help text for the bulk edit button

* fix ontology advancer filter not working in admin because to triggered

* update submission_properties list to include them all

* [ontoportal-bot] Gemfile.lock update

* Feature: Update the style of the mailing list section in the account page  (#202)

* Feature: Extract chips component (#181)

* create chips component file

* Add a function to turn spaces into underscores

* Create chips component design file

* CSS for the chips component

* Change the meaningless argument "text" by "name" & "value"

* Add a component folder for component styles in the styelsheets folder

* Feature: Feedback page uses chips component (#201)

* create chips component file

* Add a function to turn spaces into underscores

* Create chips component design file

* CSS for the chips component

* Add recaptcha tags

* Change the meaningless argument "text" by "name" & "value"

* Use the chips component on the feedback page

* Add a component folder for component styles in the styelsheets folder

* Remove chips component style from feedback page css file

* Feature: Update register template  (#144)

* update login page design

* update the design of lost password page

* update sucess message for password reset

* update register page design

* Delete login.scss

* Delete lostpassword.scss

* Update index.html.erb

* Delete lost_password_success.html.erb

* Update index.html.erb

* Update lost_password.html.erb

* Update routes.rb

* Update index.html.erb

* Update register.scss

* Delete _form.html.erb

* Update _form.html.haml

* Update login_controller.rb

* Add code to remove auto added arrows from number_text_field

* Add the two fields (OrcidID & github)

* Add subscription to mailing list

* Update index.html.erb

* Update _form.html.haml

* Add captacha tag

* Update _form.html.haml

* Add github icon

* Add orcide icon

* Fix recaptacha tags (add "=")

* replace "ORCIDE" by "ORCID"

* Change ORCID ID  input type from 'number' to ‘text’

* Extract orcidId & githubId from URLs

* Extract arrow-back.svg file

* Fix extract id from link

* Resolve conflicts with developement branch

* remove import browse

---------

Co-authored-by: Syphax bouazzouni <[email protected]>

* convert the feedback file from erb to haml

---------

Co-authored-by: HADDAD Zineddine <[email protected]>
Co-authored-by: OntoPortal Bot <[email protected]>
Co-authored-by: Bilelkihal <[email protected]>

.env.sample

@@ -47,8 +47,8 @@ export NODE_ENV=development
 # it's a good idea to use 1 to avoid race conditions when debugging.
 #export WEB_CONCURRENCY=
 #export RAILS_MAX_THREADS=5
-export WEB_CONCURRENCY=1
-export RAILS_MAX_THREADS=1
+#export WEB_CONCURRENCY=1
+#export RAILS_MAX_THREADS=1
 
 # You'll always want to set POSTGRES_USER and POSTGRES_PASSWORD since the
 # postgres Docker image uses them for its default database user and password.

Dockerfile

@@ -14,6 +14,7 @@ RUN apk add --no-cache \
     nodejs \
     tzdata \
     yarn \
+    less \
   && addgroup --gid ${GID} ruby \
   && adduser  -u ${UID} -G ruby -D  ruby \
   && chown ruby:ruby -R /app \
@@ -35,13 +36,14 @@ ENV RAILS_ENV="${RAILS_ENV}" \
 
 COPY --chown=ruby:ruby Gemfile* ./
 RUN bundle install --jobs "$(nproc)"
+RUN gem install rails 
+
 
 
 RUN echo "--modules-folder /node_modules" > .yarnrc
 COPY --chown=ruby:ruby package.json *yarn* ./
 RUN yarn install
 
-ENTRYPOINT ["/app/bin/docker-entrypoint-web"]
 
 EXPOSE 3000
 

Gemfile

@@ -72,7 +72,7 @@ gem 'view_component', '~> 2.72'
 gem 'turnout'
 gem 'will_paginate', '~> 3.0'
 
-gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'master'
+gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'development'
 
 
 group :staging, :production, :appliance do
@@ -119,3 +119,4 @@ end
 
 
 gem "net-ftp", "~> 0.2.0", require: false
+gem "net-http"

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: fe929a4dd156920d60ecde9e8f9ef30a2cf5088e
-  branch: master
+  revision: 0c8cd2b377d88b66a979664d5b16e5068b6d4548
+  branch: development
   specs:
     ontologies_api_client (2.2.0)
       activesupport
@@ -158,7 +158,7 @@ GEM
     flamegraph (0.9.5)
     globalid (1.1.0)
       activesupport (>= 5.0)
-    graphql (2.0.16)
+    graphql (2.0.17)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
       graphql
@@ -218,6 +218,8 @@ GEM
     net-ftp (0.2.0)
       net-protocol
       time
+    net-http (0.3.2)
+      uri
     net-imap (0.3.4)
       date
       net-protocol
@@ -233,12 +235,12 @@ GEM
     netrc (0.11.0)
     newrelic_rpm (8.16.0)
     nio4r (2.5.8)
-    nokogiri (1.14.1-x86_64-linux)
+    nokogiri (1.14.2-x86_64-linux)
       racc (~> 1.4)
-    oj (3.14.1)
+    oj (3.14.2)
     open_uri_redirections (0.2.1)
     parallel (1.22.1)
-    parser (3.2.0.0)
+    parser (3.2.1.0)
       ast (~> 2.4.1)
     popper_js (1.16.1)
     pry (0.14.2)
@@ -275,8 +277,10 @@ GEM
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.5.0)
       loofah (~> 2.19, >= 2.19.1)
-    rails_autolink (1.1.7)
-      rails (> 3.1)
+    rails_autolink (1.1.8)
+      actionview (> 3.1)
+      activesupport (> 3.1)
+      railties (> 3.1)
     railties (7.0.3)
       actionpack (= 7.0.3)
       activesupport (= 7.0.3)
@@ -292,7 +296,7 @@ GEM
     rdoc (6.3.3)
     recaptcha (5.9.0)
       json
-    regexp_parser (2.6.2)
+    regexp_parser (2.7.0)
     reline (0.3.2)
       io-console (~> 0.5)
     rest-client (2.1.0)
@@ -318,7 +322,7 @@ GEM
       rspec-mocks (~> 3.11)
       rspec-support (~> 3.11)
     rspec-support (3.12.0)
-    rubocop (1.44.1)
+    rubocop (1.45.1)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.2.0.0)
@@ -328,8 +332,8 @@ GEM
       rubocop-ast (>= 1.24.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.24.1)
-      parser (>= 3.1.1.0)
+    rubocop-ast (1.26.0)
+      parser (>= 3.2.1.0)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
     ruby_parser (3.19.2)
@@ -374,7 +378,7 @@ GEM
     tilt (2.0.11)
     time (0.2.1)
       date
-    timeout (0.3.1)
+    timeout (0.3.2)
     turbo-rails (1.3.3)
       actionpack (>= 6.0.0)
       activejob (>= 6.0.0)
@@ -390,6 +394,7 @@ GEM
       unf_ext
     unf_ext (0.0.8.2)
     unicode-display_width (2.4.2)
+    uri (0.12.0)
     view_component (2.82.0)
       activesupport (>= 5.2.0, < 8.0)
       concurrent-ruby (~> 1.0)
@@ -410,7 +415,7 @@ GEM
     will_paginate (3.3.1)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    zeitwerk (2.6.6)
+    zeitwerk (2.6.7)
 
 PLATFORMS
   x86_64-linux
@@ -446,6 +451,7 @@ DEPENDENCIES
   multi_json
   mysql2 (= 0.5.3)
   net-ftp (~> 0.2.0)
+  net-http
   newrelic_rpm
   oj
   ontologies_api_client!
@@ -478,4 +484,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.3.23
+   2.3.15

app/assets/javascripts/application.js

@@ -13,7 +13,6 @@
 //= require bioportal
 //= require admin/licenses
 //= require bp_ajax_controller
-//= require bp_ontology_viewer
 //= require bp_reviews
 //= require bp_notes
 //= require bp_ontolobridge
@@ -32,7 +31,6 @@
 //= require_tree ./components
 //= require ontologies
 //= require projects
-//= require submissions
 //= require tooltipster.bundle.min
 //= require application_esbuild
 customElements.define('data-table-loader', DataTableLoader );