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293 commits

Author SHA1 Message Date
Oleksii Kriuchykhin
ab395f46d0 Add paperclip for backward compatibility [SCI-3949] 2019-10-09 10:28:02 +02:00
Oleksii Kriuchykhin
260fcd6e89 Remove Paperclip from codebase [SCI-3908] 2019-10-02 19:45:14 +02:00
Urban Rotnik
e5933091d9 Add rubocop-rails gem 2019-09-17 13:42:43 +02:00
Oleksii Kriuchykhin
bc38c6b29e Fix failing test [SCI-3745] 2019-09-16 10:26:13 +02:00
Oleksii Kriuchykhin
c068901b00 Upgrade Rails to 6.0 [SCI-3745] 2019-09-12 17:24:08 +02:00
Oleksii Kriuchykhin
3a87296c7b Fix cucumber tests, switch to chromium-driver [SCI-3786] 2019-08-22 13:38:02 +02:00
Oleksii Kriuchykhin
973efa55e1 Merge branch 'master' into ok_SCI_3678 2019-08-08 11:17:07 +02:00
Jure Grabnar
d9f6c249f9 Fix CVE-2015-9284 omniauth security precautions 
Close SCI-3588
 2019-07-31 16:59:38 +02:00
Jure Grabnar
6546bd1532 Add omniauth-rails_csrf_protection gem 
Close SCI-3588
 2019-07-31 16:05:06 +02:00
Anton Ignatov
f35f4886a3 Fix markup 2019-07-29 10:18:34 +02:00
Anton Ignatov
a4b2825258 Fix tests for active storage 2019-07-26 15:58:51 +02:00
Luka Murn
a568d39f4c Remove commit_param_routing Gem 
This Gem was only used for certain sample controller actions.
 2019-07-26 10:18:31 +02:00
aignatov-bio
2fae7d8208
Fix issue in report (#1941) 2019-07-19 10:37:44 +02:00
Oleksii Kriuchykhin
a1941a21dc Futher refactoring of old Paperclip methods [SCI-3539] 2019-07-09 10:28:15 +02:00
Oleksii Kriuchykhin
028e647f4d Upgrade to Rails 5.2.3 [SCI-3651] 2019-07-03 11:15:13 +02:00
Jure Grabnar
4bdefda2af Upgrade webpacker to ~> 4.0.0 2019-07-02 13:30:13 +02:00
aignatov-bio
2793777463
Features/docx report (#1873) 
* Initial setup for docx report

* Add render for project, experiment, my_module

* Implement converter for RTE fields

* Add all report elements

* fix markup

* Change headers, remove empty blocks, refactored repository draw

* Add smart annotations support

* Fix justify fields

* Prepare for addons integration

* Fix markup

* Add comments to GemFile

* Fix TinyMCE error

* Change UI for new report download selector

* Fix file error in inventory cell for docx

* Fix i18n object for header
 2019-07-01 10:14:16 +02:00
Oleksii Kriuchykhin
ba2daede0b Add migration scripts [SCI-3539] 2019-06-24 15:17:42 +02:00
Oleksii Kriuchykhin
109793c7fb Upgrade to Rails 5.2.3 and add ActiveStorage [SCI-3539] 2019-06-13 12:10:44 +02:00
Jure Grabnar
bbfe2b9c89
Merge pull request #1798 from biosistemika/jg_sci_3145_thumbnail_preview 
File preview on new attachments layout [SCI-3145]
 2019-06-10 17:59:12 +02:00
Urban Rotnik
17f987e7c8 Add rubocop-perfromance after Rubocop has been updated 2019-06-10 12:24:04 +02:00
Oleksii Kriuchykhin
e543a849d4 Add document file preview generation with LibreOffice [SCI-3145] 2019-06-05 14:52:30 +02:00
Anton Ignatov
995408e7fc Fix protocol update error, rollback bootstrap gems and fix step name 2019-05-08 17:18:19 +02:00
Anton Ignatov
d36160386f Merge branch 'master' into master-with-note-section 2019-05-07 13:26:55 +02:00
Oleksii Kriuchykhin
4522e6bf06 Update Ruby to 2.5.5, Rails to 5.1.7 and Devise to 4.6.2 [SCI-3401] 2019-04-30 17:04:48 +02:00
Anton Ignatov
aa2dab2014 Merge branch 'features/note-section' into master-with-note-section 2019-04-23 10:31:37 +02:00
Oleksii Kriuchykhin
572f28f0b8 Remove unused devise_security_extension dependency [SCI-3347] 2019-04-16 13:08:15 +02:00
aignatov-bio
8d7cc57da1
Add zoom to image annotation and check jpeg file quality before save [SCI-3300] (#1654) 
* Add zoom to image annotation and check jpeg file quality before save
* Move compression to front end
* Move quality extractor to paperclip processor
 2019-04-15 09:49:44 +02:00
aignatov-bio
9fff93ab0e
Merge pull request #1576 from biosistemika/image-editor-prototype 
Feature/Image annotation
 2019-03-22 16:31:00 +01:00
Oleksii Kriuchykhin
a822227383 Add rich text editor to task and protocol description [SCI-3062][SCI-3071] 2019-03-14 16:27:33 +01:00
Oleksii Kriuchykhin
0b0141de5f Update Rails to 5.1.6.2 2019-03-13 20:32:29 +01:00
Anton Ignatov
b6480b04a9 Fixed conflicts 2019-03-11 15:36:56 +01:00
Oleksii Kriuchykhin
9bbdc8fc89 Include tui image editor with webpack [SCI-2856] 2019-03-11 15:12:38 +01:00
Urban Rotnik
d3d9868ba4 Set version for HTTParty dependency, add opts in mailer 2019-02-19 11:23:01 +01:00
Urban Rotnik
5b55860dea Add scheduler 2019-02-13 15:48:15 +01:00
Urban Rotnik
9f3187abdf Add service for sync system notifications 2019-02-13 15:48:15 +01:00
aignatov-bio
5c85595ab4
System Notifications - View All Page [SCI-2956 and SCI-3001] (#1482) 
* System notification view and notification partial (SCI 2956 and SCI 3001)
 2019-02-13 13:06:14 +01:00
Urban Rotnik
457e9990c5 Add overcommit gem for git hooks (rubocop) 2019-01-18 16:56:28 +01:00
Urban Rotnik
6cf4717ab3 Add envirnoments to run app without docker, reorder Gemfile 
- Reorder Gemfile into alphabet order (rule by Rubocop)
- Add extra ENV variable for custom DB settings locally
- Add extra ENV for disable spoof check on Paperclip
 2019-01-18 16:01:09 +01:00
Oleksii Kriuchykhin
1d4fc7172d Update Ruby to 2.4.5 and add jemalloc package 2019-01-15 17:10:10 +01:00
Luka Murn
e9c0b34662 Merge branch 'core-api' into 'master' 
Conflicts:
	Gemfile
	app/services/api.rb
	config/initializers/api.rb
	config/initializers/extends.rb
	config/routes.rb
	db/schema.rb
	spec/controllers/api/api_controller_spec.rb
 2018-11-14 16:59:04 +01:00
Luka Murn
84df2c81f9 Merge branch 'features/export-all' 
Conflicts:
	app/controllers/experiments_controller.rb
	app/controllers/my_modules_controller.rb
	db/schema.rb
 2018-11-13 09:14:02 +01:00
Oleksii Kriuchykhin
0e192cc830 Ensure that temporary report is always deleted [SCI-2834] 2018-11-06 09:33:18 +01:00
Alex Kriuchykhin
e9b64b65a3
Merge pull request #1330 from okriuchykhin/ok_SCI_2770 
Add request rate throttling for API [SCI-2770]
 2018-10-19 09:38:31 +02:00
Oleksii Kriuchykhin
b9320b3b1d Update sdoc gem [SCI-2765] 2018-10-16 16:50:42 +02:00
Oleksii Kriuchykhin
f6b039d54e Merge latest core-api branch [SCI-2765] 2018-10-16 12:07:47 +02:00
Oleksii Kriuchykhin
8cf59d8d22 Add request rate throttling for API [SCI-2770] 2018-10-11 09:48:06 +02:00
Oleksii Kriuchykhin
77e2371091 Add tests for inventory cell endpoints [SCI-2765] 2018-10-08 13:25:03 +02:00
Luka Murn
9f4cb02fba Update doorkeeper gem to >= 4.6 2018-10-05 11:50:17 +02:00
Luka Murn
5e797c5dae
Remove double 'kaminari' Gem inclusion in Gemfile 2018-09-28 10:47:33 +02:00
Luka Murn
00c714be07
Merge pull request #1299 from Ducz0r/lm-fix-rubocop 
Update rubocop to 0.59.0, fix the config to be compliant
 2018-09-24 10:27:19 +02:00
Oleksii Kriuchykhin
49e788a9ad Mergre latest core-api [SCI-2515] 2018-09-14 10:24:05 +02:00
Luka Murn
0a2be5072a Update rubocop to 0.59.0, fix the config to be compliant 2018-09-12 17:17:55 +02:00
Luka Murn
99c156de94 Fix (hopefully) the TinyMCE files from being cached 
Closes SCI-2717.
 2018-09-12 15:28:21 +02:00
Alex Kriuchykhin
1832c0e806
Merge pull request #1262 from okriuchykhin/ok_SCI_2614 
Add read inventories and inventory items endpoints [SCI-2614][SCI-2616][SCI-2617]
 2018-08-24 15:22:13 +02:00
Oleksii Kriuchykhin
ecde634a2c Add OAuth2 provider [SCI-2515] 2018-08-17 13:17:59 +02:00
Zanz2
2608561560
Merge branch 'master' into zz_protocols_edit_rtf_form_bug_sci2305_v2 2018-08-09 11:38:15 +02:00
Zanz2
1de9e4b360 changed version 2018-08-09 11:35:50 +02:00
Oleksii Kriuchykhin
938ec5acb8 Change primary key to bigint on repositories [SCI-2614][SCI-2616][SCI-2617] 2018-08-08 17:01:49 +02:00
Alex Kriuchykhin
6004f8411b
Merge pull request #1260 from okriuchykhin/ok_SCI_2611 
Add GET teams and team API endpoints [SCI-2611][SCI-2612]
 2018-08-08 16:59:42 +02:00
okriuchykhin
bb5d029c30
Merge pull request #1251 from okriuchykhin/ok_SCI_2253 
Upgrade to Turbolinks 5 [SCI-2253]
 2018-08-02 14:43:19 +02:00
Oleksii Kriuchykhin
22e12d8fc3 Add GET teams and team API endpoints [SCI-2611][SCI-2612] 2018-07-31 13:40:27 +02:00
Oleksii Kriuchykhin
b2bd1cb849 Upgrade to Turbolinks 5 [SCI-2253] 2018-07-27 17:26:46 +02:00
Oleksii Kriuchykhin
0e372af729 Adds API authentication with Azure AD [SCI-2608] 2018-07-24 14:21:33 +02:00
Zanz2
eab389c0dd Fixes tinymce editor not displaying, updated tinymce-rails gem to 4.7.11 2018-07-17 16:06:00 +02:00
Oleksii Kriuchykhin
6c914d2a73 Upgrade Rails to version 5.1.6, Sprockets to 3.7.2 2018-06-20 10:46:41 +02:00
zmagod
b13e39a0d9 adds discard gem, move deletion of repositories in a rake task to run in background worker [fixes SCI-2448] 2018-05-24 14:39:25 +02:00
Luka Murn
cb6fe50832 Merge branch 'master' into ux-release-1 
Conflicts:
	app/assets/javascripts/repositories/index.js
 2018-04-26 11:38:54 +02:00
Luka Murn
9bf8b5d864 Merge branch 'ok_SCI_1860' of https://github.com/okriuchykhin/scinote-web into okriuchykhin-ok_SCI_1860 
Conflicts:
	Makefile
	app/assets/javascripts/projects/index.js.erb
	app/assets/stylesheets/themes/scinote.scss
	config/locales/en.yml
 2018-04-12 13:16:46 +02:00
Luka Murn
159078170a Update Paperclip library to 5.3 version 2018-04-05 13:23:34 +02:00
Zanz2
7f36ab3e5e deleted require and gemfile entry for remotipart 2018-04-04 11:12:39 +02:00
Zanz2
1606982966 found a hackish fix by doing a manual ajax call and some other things with jquery 2018-04-02 19:56:25 +02:00
Oleksii Kriuchykhin
f656ad1561 Fix fa icons [SCI-2217] 2018-03-30 17:03:44 +02:00
okriuchykhin
145f49de2d
Revert "Update turbolinks and fix repository table init [SCI-2251]" 2018-03-26 17:38:48 +02:00
Oleksii Kriuchykhin
83c7539156 Update turbolinks and fix repository table init [SCI-2251] 2018-03-25 19:44:58 +02:00
Oleksii Kriuchykhin
a105e61d48 Remove tutorial [SCI-1860] 2018-03-18 13:18:05 +01:00
zmagod
1cdba5e0d3 Merge branch 'samples_to_repositories_table_migration' of https://github.com/biosistemika/scinote-web into zd_SCI_2068 2018-03-16 11:05:16 +01:00
zmagod
d69754af04 implement search on list items dropdown, update, create actions [fixes SCI-2070] 2018-03-15 15:43:16 +01:00
zmagod
dd2f7dd417 Merge branch 'master' of https://github.com/biosistemika/scinote-web into samples_to_repositories_table_migration 2018-03-13 13:24:36 +01:00
zmagod
41db1a9ab3 update bootstrap to v 3.3.7 2018-03-12 08:57:02 +01:00
mlorb
08439e7f58 sign up with linkedIn account 2018-02-28 18:12:21 +01:00
Oleksii Kriuchykhin
16e1d072b9 Improve files handling in protocol clonning [SCI-2003] 2018-02-01 15:44:08 +01:00
Oleksii Kriuchykhin
b8b13b2086 Update Ruby version to 2.4.3 2018-01-31 10:02:45 +01:00
zmagod
c6f44e799c fixes JWT dependency issues 2018-01-23 16:25:59 +01:00
zmagod
88d7429041 1. fixes failing unit and integration tests 
2. fixes gem dependencies issues
3. fixes failing migrations
4. updates depricated factory_girl => factory_bot and fixes related issues

Signed-off-by: zmagod <zmago_devetak@yahoo.com>
 2018-01-23 14:54:15 +01:00
zmagod
f8a3fca2db Merge branch 'master' of https://github.com/biosistemika/scinote-web into decoupling 2018-01-23 11:06:33 +01:00
Matej Zrimšek
9ef04a6a2b Set strict version for rubocop gem, because the new one is not compatible with the previously used one. Also updated it to the newest version. 2018-01-16 17:01:44 +01:00
Oleksii Kriuchykhin
b98241ef61 Fix bootstrap select dropdown [SCI-1895][SCI-1896] 2017-12-22 09:52:00 +01:00
Luka Murn
704bd31fef Set wicked_pdf version to ~> 1.0.6 2017-12-20 10:53:53 +01:00
Oleksii Kriuchykhin
1a81a99ff0 Remove Creek XLSX parser gem as it causes conflicts [SCI-1891] 2017-12-19 16:17:11 +01:00
Luka Murn
cf291bf887 Merge branch 'gilson-iot-rails4' 
Conflicts:
	Gemfile.lock
 2017-12-19 10:56:39 +01:00
Oleksii Kriuchykhin
9408b29768 Update Rails version to 4.2.10 [SCI-1845] 2017-11-29 16:49:50 +01:00
zmagod
930e3a86dc Merge branch 'decoupling-settings-page' of https://github.com/biosistemika/scinote-web into zd_SCI_1762 2017-11-23 13:56:17 +01:00
Luka Murn
c51a85a161
Merge pull request #888 from biosistemika/lm-sci-1795 
Setup main architecture for permissions refactoring [SCI-1795]
 2017-11-23 12:32:49 +01:00
Zmago Devetak
2f66c1df25
adds travis config file (#873) 
* adds travis config file

* add dist to travis

* adds script section

* test env

* remove globals

* adds hashed variables

* add matrix

* removed matrix

* test env

* testing

* test

* update Gemfile

* test travis

* test

* test

* test travis

* test

* build with docker

* test

* test

* ads

* add devise secre

* test travis

* test

* test

* test

* adds travis db configurations

* make travis happy

* test

* test

* test

* test

* test

* test

* testing devise

* test

* test

* teset

* test

* test

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* test

* edit env

* test

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* final commit

* test

* cleanup

* cleanup
 2017-11-23 09:55:57 +01:00
zmagod
70db34090d fixes rspec tests 2017-11-20 09:41:14 +01:00
Luka Murn
ccef5571f1 Add dependency to Canaid, the permission helper library 2017-11-16 15:49:13 +01:00
Oleksii Kriuchykhin
84f4aba213 Pull latest master into gilson-iot-rails4 2017-11-15 15:15:26 +01:00
zmagod
327e27e123 Merge branch 'decoupling-settings-page' of https://github.com/biosistemika/scinote-web into zd_SCI_1576 2017-11-09 15:55:10 +01:00
zmagod
9eac014f1a Merge branch 'decoupling-settings-page' of https://github.com/biosistemika/scinote-web into zd_SCI_1731 2017-11-09 09:05:22 +01:00
zmagod
b036452d8c adds background worker to cucumber tests 2017-11-08 11:59:01 +01:00
mlorb
1c3c822796 change drivers for browser 2017-11-06 14:26:01 +01:00
zmagod
e0323a0a46 fixes failing tests 2017-10-27 09:35:39 +02:00
zmagod
3d22a5404d add scenic gem, teams datatables sql view 2017-10-26 16:59:00 +02:00
zmagod
4de335d189 add whacamole configuration [fixes SCI-1683] 2017-10-25 09:47:26 +02:00
Luka Murn
82f982e983 Merge branch 'rails-5.1' into decoupling-settings-page 
Conflicts:
	Gemfile
	Gemfile.lock
 2017-10-23 10:59:10 +02:00
Luka Murn
e740e586e8 Additional fixes required by latest merge from master (nr. 2) 2017-10-23 10:43:32 +02:00
Luka Murn
8254153bb9 Merge branch 'master' into rails-5.1 
Conflicts:
	Gemfile
	Gemfile.lock
	app/models/connection.rb
	app/models/experiment.rb
	app/models/my_module.rb
 2017-10-23 08:57:57 +02:00
okriuchykhin
8e90e041b9 Merge pull request #825 from okriuchykhin/ok_SCI_1665 
Optimize memory usage in samples/repositories import [SCI-1665]
 2017-10-17 17:26:00 +02:00
Oleksii Kriuchykhin
c8d2ae70fa Move duplicated code to service [SCI-1665] 2017-10-17 14:46:16 +02:00
Oleksii Kriuchykhin
56f52ebfa7 Optimize memory usage in samples/repositories import [SCI-1665] 2017-10-12 14:43:25 +02:00
zmagod
dccf4e34ff fix cucumber settings 2017-10-12 13:50:48 +02:00
mlorb
c358f8fa0c write unit tests for invite users 2017-09-28 14:49:33 +02:00
Oleksii Kriuchykhin
faaa016267 Update AWS SDK v2 [SCI-1623] 2017-09-26 13:41:53 +02:00
mlorb
48c8922604 adds invite users modal 2017-09-21 10:45:35 +02:00
Luka Murn
e078ae4f77 Merge branch 'rails-5.1' into decoupling-settings-page 2017-09-21 08:36:09 +02:00
Luka Murn
beae1b05d8 Merge branch 'master' into rails-5.1 
Conflicts:
	Gemfile
	Gemfile.lock
 2017-09-21 08:27:38 +02:00
Luka Murn
8463c89386 Update Gemfile 2017-09-01 09:36:40 +02:00
Oleksii Kriuchykhin
c3fceb90df Backport API to Rails-4 [SCI-1579] 2017-08-30 13:30:41 +02:00
zmagod
ee054f91b8 adds bullet gem [fixes SCI-1578] 2017-08-30 09:29:45 +02:00
Luka Murn
b6eb46471a Merge pull request #753 from Ducz0r/lm-remove-some-code 
Remove some code we're no longer maintaining
 2017-08-22 14:04:04 +02:00
Luka Murn
90188c89c9 Update delayed_paperclip library 
Closes SCI-1376.
 2017-08-22 08:34:58 +02:00
zmagod
c5e32c4ea0 Merge branch 'rails-5.1' of https://github.com/biosistemika/scinote-web into merge-rails-5.1-branch 2017-08-21 09:52:14 +02:00
Luka Murn
13eae287bb Revert "Add core API using JWT authentication and tests for it [SCI-1507]" 2017-08-07 11:54:45 +02:00
Luka Murn
ae5bccf709 Merge branch 'master' into rails-5.1 
Conflicts:
	Gemfile.lock
	app/datatables/repository_datatable.rb
	app/models/repository_cell.rb
 2017-08-07 08:45:53 +02:00
Oleksii Kriuchykhin
e958410261 Add core API using JWT authentication and tests for it [SCI-1507] 2017-08-03 17:00:14 +02:00
zmagod
6ef19725f1 adds redux 2017-08-02 17:27:05 +02:00
Luka Murn
03a7440136 Remove SkyLight stuff (we're not using it any more) 2017-07-27 14:26:44 +02:00
zmagod
416ab8eee3 Merge branch 'rails-5.1' of https://github.com/biosistemika/scinote-web into zd_SCI_1400 2017-07-26 16:20:09 +02:00
Oleksii Kriuchykhin
6c33b46f6a Improve import of repository records plus tsv file import fixes [SCI-1487] 2017-07-20 11:44:10 +02:00
Oleksii Kriuchykhin
ece27b2652 Fix importing files with empty header cells and error messages improvements [SCI-1484] 2017-07-18 14:54:35 +02:00
Oleksii Kriuchykhin
b8e93ee883 Add Webpacker and React [SCI-1461] 2017-07-12 16:41:55 +02:00
zmagod
6636190442 removes unneeded gems, adds validation test to models 2017-07-06 17:37:29 +02:00
zmagod
234ca71f0a removes unneded gems, fixes hound 2017-07-06 09:45:59 +02:00
zmagod
750c82a80f setup testing tools [fixes SCI-1400] 2017-07-06 09:07:05 +02:00
zmagod
bc33883c3c first run fixing addons 2017-06-30 10:23:28 +02:00
zmagod
71aa05bb0e refactor 2017-06-27 14:58:49 +02:00
zmagod
819f47b450 setup sciNote for Rails 5.1 2017-06-23 15:19:08 +02:00
zmagod
1b21f073d7 Rails 5.1.1 2017-06-23 10:34:46 +02:00
zmagod
909a114418 Rails 5.0.0.rc2 2017-06-23 10:08:54 +02:00
zmagod
75507107fd migrate to 4.2.9 2017-06-23 08:50:12 +02:00
Paul Menzel
24b97637b4 Gemfile: Use HTTPS protocol for sneaky-save 
Address the Bundler warning below.

```
Step 6/14 : RUN bundle install
 ---> Running in bfbfa83e61de
The git source `git://github.com/einzige/sneaky-save.git` uses the `git` protocol, which transmits data without encryption. Disable this warning with `bundle config git.allow_insecure true`, or switch to the `https` protocol to keep your data secure.
Your Ruby version is 2.3.4, but your Gemfile specified 2.3.3
The command '/bin/sh -c bundle install' returned a non-zero code: 18
```
 2017-06-07 11:47:16 +02:00
zmagod
10db322307 fixes input sanitize method [fixes SCI-1248] 2017-05-10 14:57:11 +02:00
zmagod
5b58824ec0 refactor 2017-05-03 15:30:08 +02:00
zmagod
550f563666 working version for steps first run 2017-04-21 16:09:04 +02:00
zmagod
c25df63a14 add tinymce img importer and refactor input sanitize helper 2017-04-19 09:11:52 +02:00
Zmago Devetak
9c31239318 Merge pull request #552 from biosistemika/release-1.9.0 
Release 1.9.1
 2017-04-12 13:08:37 +02:00
Luka Murn
e656101c47 Revert Wicked PDF Gem version 2017-04-12 09:27:31 +02:00
Luka Murn
a30c7a77e8 Silence Wicked PDF generation 
Closes SCI-1107.
 2017-04-10 14:00:31 +02:00
zmagod
9a17648eee Adds new relic in sciNote [fixes SCI-1183] 2017-04-07 11:23:45 +02:00