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665 commits

Author SHA1 Message Date
zmagod
90faeec410 fixes typos and protocol step links 2017-04-10 11:21:28 +02:00
zmagod
9bb1bb3f9b refactor [fixes SCI-825] 2017-04-06 15:08:03 +02:00
zmagod
d331911ffe completed step annotations 2017-04-06 08:42:16 +02:00
Mojca Lorber
a0fe47a05d change helper method for user info popover 2017-04-04 15:22:41 +02:00
zmagod
99c116f257 first run 2017-04-04 09:19:43 +02:00
Oleksii Kriuchykhin
2faa137f67 Add user popover method for users [SCI-1127] 2017-04-03 15:10:00 +02:00
zmagod
239a44c26b change send to public_send 2017-03-24 16:25:50 +01:00
zmagod
4635a3320d Merge branch 'master' of https://github.com/biosistemika/scinote-web into zd_SCI_1003_add_extends 2017-03-24 16:09:28 +01:00
zmagod
5cc6cd094e refactor 2017-03-17 16:47:58 +01:00
zmagod
95a0f596b7 adds file link 2017-03-17 16:40:57 +01:00
zmagod
856a4611c6 Merge branch 'master' of https://github.com/biosistemika/scinote-web into zd_SCI_1003_add_extends 2017-03-14 15:58:08 +01:00
zmagod
b821fff4a5 adds non breaking space between file name and buttons 2017-03-13 14:14:44 +01:00
zmagod
7b16e5643e fix assets preprocesor for wopi files 2017-03-13 13:20:49 +01:00
zmagod
0c2523beca Merge branch 'master' of https://github.com/biosistemika/scinote-web into office_integration 2017-03-10 16:21:43 +01:00
mlorb
39e1ac4b26 Merge pull request #512 from biosistemika/ml_sci_1074 
Fix permissions for experiment actions [SCI-1074]
 2017-03-10 11:44:27 +01:00
Mojca Lorber
1ba5f1748f fix permissions for experiment actions 2017-03-09 17:45:34 +01:00
zmagod
1d42d46c02 fixes bug with step comments 2017-03-09 16:02:52 +01:00
zmagod
9939d8df06 refactor 2017-03-09 10:51:54 +01:00
zmagod
f78ef8c82a fixes hound 2017-03-08 14:41:42 +01:00
zmagod
5c2e9a4b04 adds extends and fixes report methods 2017-03-08 14:14:03 +01:00
Oleksii Kriuchykhin
0f8336e5a5 Refactoring of the comments using STI [SCI-1090] 2017-03-08 13:18:20 +01:00
Mojca Lorber
f84611f558 fix report - checklist items are in separate row than checkboxes 2017-02-22 15:51:26 +01:00
okriuchykhin
8e18ff44a6 Merge pull request #479 from okriuchykhin/ok_SCI_999 
Add task complete/uncomplete functionality [SCI-999]
 2017-02-20 15:19:00 +01:00
Oleksii Kriuchykhin
218e96b1f0 Code style fixes [SCI-999] 2017-02-16 11:45:07 +01:00
Luka Murn
164bd787e9 Merge pull request #481 from Ducz0r/lm-sci-958-fix 
Team administrators are Viewers of all Projects in Team [SCI-958]
 2017-02-15 10:40:52 +01:00
Nbernot
97584aabb3 Updated the lists of office online file extensions 
Extended the list of file extensions that receive office online icons and 'open in' text.
 2017-02-14 16:44:03 +01:00
Luka Murn
c6ed73bc82 Allow team admins to see all projects, even hidden ones 2017-02-13 13:42:53 +01:00
Oleksii Kriuchykhin
cf8566df33 Add task complete/uncomplete functionality [SCI-999] 2017-02-10 14:27:20 +01:00
Luka Murn
f7bd62547e Refactor teams settings into its own controllers 2017-02-09 14:37:59 +01:00
Luka Murn
7bee3a4ea0 Move user profile to settings 2017-02-09 11:34:52 +01:00
Mojca Lorber
d3e0eca44e redesign individual team page 2017-02-01 14:44:47 +01:00
zmagod
e59b2e039a Merge branch 'master' of https://github.com/biosistemika/scinote-web into zd_SCI_939 2017-01-27 11:15:31 +01:00
Luka Murn
3bf447b0f4 Fix bug where reCaptcha form wasn't working 2017-01-26 16:06:29 +01:00
Luka Murn
0baaf12de3 Re-display images & checkboxes in PDF reports 
Closes SCI-953.
 2017-01-26 10:46:58 +01:00
Luka Murn
8c5a52417c Merge pull request #445 from okriuchykhin/ok_SCI_940 
Refactor smart annotation/auto_link/simple_format rendering [SCI-940]
 2017-01-25 17:49:38 +01:00
Oleksii Kriuchykhin
c55f3cb99c Add flag to disable simple_format in custom_auto_link [SCI-940] 2017-01-25 17:18:19 +01:00
Oleksii Kriuchykhin
310d8c1920 Refactor smart annotation/auto_link/simple_format rendering [SCI-940] 2017-01-25 17:18:19 +01:00
Oleksii Kriuchykhin
5fe9261595 Fix error when referencing deleted sample in SA [SCI-949] 2017-01-25 15:54:12 +01:00
zmagod
a507bb4d1f hound 2017-01-25 15:40:35 +01:00
zmagod
f04a2f663a renamed organizations in config/ 2017-01-25 12:30:11 +01:00
zmagod
9ae799d52c rename organization/org/Organization to Team in datatables 2017-01-25 09:48:49 +01:00
Luka Murn
53699193a2 Merge branch 'smart-annotations' 
Conflicts:
	app/assets/javascripts/comments.js.erb
	app/assets/javascripts/protocols/index.js
	app/assets/javascripts/protocols/steps.js.erb
	app/assets/javascripts/samples/sample_datatable.js.erb
	app/controllers/my_module_comments_controller.rb
	app/controllers/project_comments_controller.rb
	app/controllers/result_comments_controller.rb
	app/controllers/step_comments_controller.rb
	app/datatables/sample_datatable.rb
	app/views/my_module_comments/_comment.html.erb
	app/views/project_comments/_comment.html.erb
	app/views/projects/show/_experiment.html.erb
	app/views/reports/elements/_experiment_element.html.erb
	app/views/reports/elements/_result_comments_element.html.erb
	app/views/reports/elements/_result_text_element.html.erb
	app/views/reports/elements/_step_checklist_element.html.erb
	app/views/reports/elements/_step_comments_element.html.erb
	app/views/reports/elements/_step_element.html.erb
	app/views/result_comments/_comment.html.erb
	app/views/results/_result_text.html.erb
	app/views/step_comments/_comment.html.erb
	app/views/steps/_step.html.erb
	db/schema.rb
 2017-01-24 14:33:23 +01:00
Zmago Devetak
40bf293ec7 Merge pull request #441 from ZmagoD/zd_SCI_924 
adds smart annotation in task comments, refactor smart_annotation_par…
 2017-01-24 11:18:41 +01:00
okriuchykhin
7fa1f3d966 Merge pull request #438 from okriuchykhin/ok_SCI_921 
Remove unneeded HTML scrubber in protocol importer [SCI-921]
 2017-01-24 11:02:43 +01:00
zmagod
6e7fa21dd3 adds smart annotation in task comments, refactor smart_annotation_parser method, fix the user popover description [fixes SCI-924] 2017-01-24 10:51:12 +01:00
Oleksii Kriuchykhin
2434c73a0c Remove unneeded HTML scrabber in protocol importer [SCI-921] 2017-01-24 09:52:38 +01:00
zmagod
20cde2654b fixed user without permissions bug [fixes SCI-922] 2017-01-23 10:53:42 +01:00
zmagod
9550c6dd35 fixes highlight.js 2017-01-19 17:09:25 +01:00
zmagod
f2d5066dc7 fix some bugs 2017-01-19 11:37:59 +01:00
zmagod
65fa631b1c adding tinyMce first run 2017-01-18 22:40:08 +01:00
Luka Murn
cf72da5635 Merge branch 'improved-files-handling' into 'master' 
Conflicts:
	app/assets/javascripts/protocols/steps.js.erb
	app/helpers/assets_helper.rb
	db/schema.rb
 2017-01-18 11:29:40 +01:00
Zmago Devetak
1b9f7db385 Merge pull request #405 from ZmagoD/zd_SCI_832 
Visualization of User smart annotation after saving the field
 2017-01-18 09:36:42 +01:00
okriuchykhin
781a68e0d5 Merge pull request #415 from okriuchykhin/ok_SCI_888 
Add missed space in the string [SCI-888]
 2017-01-18 09:34:51 +01:00
zmagod
cb0483a6e6 refactor 2017-01-18 08:34:29 +01:00
Oleksii Kriuchykhin
ea8f6a8c6b Fix issue in report editor [SCI-102] 2017-01-17 14:21:59 +01:00
Oleksii Kriuchykhin
0ce71884a5 Add missed space in the string [SCI-888] 2017-01-16 17:09:41 +01:00
Luka Murn
a2935c6620 Add sample info modal popup to sample smart annotations 
This MR also loads datatables.js globally (as it's required by
the modal), so I removed it everywhere in code, and it shouldn't
be used anymore (e.g. '//= require datatables').

Closes SCI-892.
 2017-01-16 15:52:02 +01:00
okriuchykhin
02bfd19d1c Merge pull request #385 from okriuchykhin/ok_SCI_102 
Fix XSS on activites and throghout the rest of app [SCI-102]
 2017-01-16 11:41:38 +01:00
zmagod
1b2fa78e42 adds user preview to user smart annotation [fixes SCI-832] 2017-01-13 11:34:10 +01:00
Luka Murn
8b01f912a0 Fix new year problems with activities 
Closes SCI-876.
 2017-01-12 14:47:15 +01:00
Oleksii Kriuchykhin
d05c16b0ba Added auto_link wrapper with custom sanitization [SCI-102] 2017-01-11 17:02:17 +01:00
Oleksii Kriuchykhin
0546716a0b Improve user input sanitization, fix bugs [SCI-102] 2017-01-11 15:50:11 +01:00
zmagod
3a1ec0eb5e refactor [fixes SCI-834] [fixes SCI-837] [fixes SCI-823] [fixes SCI-835] [fixes SCI-836] [fixes SCI-824] 2017-01-11 14:56:47 +01:00
zmagod
a4aa933151 refactor smart annotation parser helper 2017-01-11 10:34:14 +01:00
zmagod
a903772de8 style dropdown 2017-01-10 17:05:32 +01:00
zmagod
e0e998a0d8 add smart annotation parser helper 2017-01-10 14:14:21 +01:00
mz3944
ef431da2db Merge pull request #389 from mz3944/mz-sci-848 
Unable to delete samples [SCI-848]
 2017-01-09 11:57:48 +01:00
Matej Zrimšek
5d104981fd Fixed sample deletion on experiments level. Minor refactoring. [SCI-848] 2017-01-06 14:23:20 +01:00
Mojca Lorber
aad2eadeae syntax fix 2017-01-06 10:46:36 +01:00
Mojca Lorber
4e7e261225 fix protocol preview 2017-01-06 10:10:33 +01:00
Oleksii Kriuchykhin
9987993ce0 Avoid sanitizing of data attributes [SCI-102] 2017-01-05 16:05:48 +01:00
Oleksii Kriuchykhin
1009347026 Add list of whitelisted attributes [SCI-102] 2017-01-05 15:33:41 +01:00
Oleksii Kriuchykhin
0ecb6904d4 Add user input sanitizing in the models [SCI-102] 2017-01-05 13:31:35 +01:00
Oleksii Kriuchykhin
cd3924afd3 Sanitize .html_safe marked strings which contain tags [SCI-102] 2017-01-05 13:04:19 +01:00
Oleksii Kriuchykhin
9c4191a1e0 Initial code commit [SCI-102] 2017-01-05 13:04:19 +01:00
Luka Murn
3bee9d2e12 Save an (yet unworking) version of user smart annotations 
Used so other devs can start working on smart annotations.
 2017-01-04 10:54:02 +01:00
zmagod
a434649f42 Merge branch 'master' of https://github.com/biosistemika/scinote-web into office_integration 2017-01-03 16:35:25 +01:00
Zmago Devetak
c8631077df Merge pull request #361 from biosistemika/improved-sample-table 
Improved sample table
 2016-12-16 15:37:54 +01:00
zmagod
6d2fb3b02c Merge branch 'improved-sample-table' of https://github.com/biosistemika/scinote-web into zd_SCI_790 2016-12-14 17:05:00 +01:00
zmagod
1ff98bb6df adds tooltip to samples dropdown and column names 2016-12-14 13:36:10 +01:00
zmagod
9037ab3f48 fixed navigation link 2016-12-14 10:35:48 +01:00
zmagod
8dd8a7e7cd Merge branch 'improved-sample-table' of https://github.com/biosistemika/scinote-web into zd_improved_samples_table_SCI_774_775_778_777 2016-12-12 15:52:25 +01:00
zmagod
8bb452e4f7 trim long names [fixes SCI-774] adds secondary navigation and sidebar [fixes SCI-775] 2016-12-12 10:30:03 +01:00
zmagod
de3099e4d1 removes asset_helper, fixes loading of processed thumbnails in results and steps and when loading protocols from repository 2016-12-09 13:59:49 +01:00
Luka Murn
da630ac2cb Make edit, delete buttons clickable & hide them if neccesary 2016-12-09 13:18:59 +01:00
zmagod
83aae59eed adds sample groups index page 2016-12-02 09:33:09 +01:00
Luka Murn
76ec77fce4 Merge pull request #329 from biosistemika/simplify-signup 
Merge simplify-signup into master
 2016-11-30 09:41:20 +01:00
Luka Murn
6491cf1806 Refactor & fix sign up constraints 2016-11-29 16:53:40 +01:00
Luka Murn
b1b095910c Merge pull request #309 from Ducz0r/lm-remove-unused-files 
Brace for impact...
 2016-11-25 10:00:29 +01:00
Zmago Devetak
341fb13a26 Merge pull request #310 from ZmagoD/zd_add_email_login_constraints 
adds rake task that creates a sign up email domain constraint
 2016-11-23 09:16:24 +01:00
zmagod
d75d58b159 moved email constraint to database_helper 2016-11-23 09:13:09 +01:00
Mojca Lorber
48ac289b6e put recaptcha in helper method 2016-11-22 17:57:42 +01:00
Luka Murn
595b213b1a Changes up to samples in views folder 2016-11-19 16:51:40 +01:00
Luka Murn
f5795f5516 Remove unused assets & helpers 2016-11-18 11:30:03 +01:00
Luka Murn
08c6210f7c Also employ "no format" Nokogiri strategy when sanitizing 
Closes SCI-691.
 2016-11-17 16:43:14 +01:00
Luka Murn
26d04b1f3c Merge branch 'rich-text-formatting' into 'master' 
Conflicts:
	Gemfile.lock
	app/assets/stylesheets/themes/scinote.scss
 2016-11-17 16:39:33 +01:00
Luka Murn
a3bbf94643 Add a smart_text_area tag & implement it throughout application 
This fixes the mentioned issues @mlorb mentioned.
Closes SCI-637.
 2016-11-16 17:57:01 +01:00
Mojca Lorber
6f1c9ffb81 refactoring 2016-11-08 11:20:14 +01:00
Mojca Lorber
63eb4eeaf8 fix hound 2016-11-07 15:33:21 +01:00
Mojca Lorber
27c83992b4 refactoring notification method 2016-11-07 15:31:06 +01:00
zmagod
a116feac9c fixed typos and added truncation to org name 2016-10-17 15:21:19 +02:00
zmagod
bb9c03df24 fixes controllers 2016-10-17 15:10:26 +02:00
zmagod
d7f514db09 fixes search 2016-10-17 15:10:26 +02:00
Matej Zrimšek
a6a2a237aa Removed unneeded ERB tags, which caused error. Minor refactoring. 2016-10-17 11:57:47 +02:00
Matej Zrimšek
0780bd2416 Ruby constants are now automatically available in JS. Refactoring was needed. 2016-10-17 11:57:37 +02:00
Matej Zrimšek
a3dfb59558 Added remaining constants. 2016-10-17 11:30:05 +02:00
Luka Murn
02d3e03f75 Bugfix for notification emails 
The URLs in notification emails didn't get server URL prepended,
so users could not click on them.
 2016-10-13 12:12:28 +02:00
Oleksii Kriuchykhin
8dc956010c Initial code commit [SCI-443] 2016-10-11 16:43:17 +02:00
Jure Grabnar
0c7cd52dba Add WOPI icons/buttons to files 2016-10-04 12:34:43 +02:00
Jure Grabnar
03567d6208 Prevent archive of locked result asset 2016-10-03 17:07:57 +02:00
Oleksii Kriuchykhin
a39c948c5f System notifications code rework 2016-10-03 15:21:26 +02:00
Oleksii Kriuchykhin
f5cc2fe225 Code style fixes 2016-09-30 09:34:58 +02:00
Oleksii Kriuchykhin
036bda3afa Initial code for system notifications [SCI-444] 2016-09-29 16:51:27 +02:00
Matej Zrimšek
76ff34a8a9 URL presigning is now used only when using S3 file uploading (caused error for local uploading) [fixes SCI-447], along with some refactoring. 2016-09-13 18:56:47 +02:00
Zmago Devetak
b26bf7b183 Merge pull request #136 from ZmagoD/zd_SCI_370 
Enabled to delete results in task archive [fixes SCI-370]
 2016-09-13 15:22:08 +02:00
zmagod
691ae94d2c enabled to delete results in task archive [fixes SCI-370] 2016-09-13 13:26:04 +02:00
zmagod
faed0500c7 set move and clone permissions to also validate the user on the organizational level [fixes SCI-372] 2016-09-08 09:23:29 +02:00
Luka Murn
a0311970f8 Add missing commits for showing image and not able to preview 2016-08-26 16:49:32 +02:00
Matej Zrimšek
e3a7f45fdf Merge branch 'master' into mz_file_upload_and_client_side_upgrade 
Conflicts:
	app/assets/javascripts/application.js
	app/views/results/_result_asset.html.erb
	app/views/steps/_step.html.erb
 2016-08-26 11:13:40 +02:00
Matej Zrimšek
782d384e26 Spinner now doesn't hide prematurally on file uploading. Some recently introduced bugs quickfixes (report images not showing, locale missplealing, client-side blank tables deletion deleted all tables, error if no asset present in a step). 2016-08-25 22:26:53 +02:00
Luka Murn
8018cff02e Merge pull request #103 from Ducz0r/bb_edit_delete_comments 
Edit&delete comments
 2016-08-25 17:18:48 +02:00
Luka Murn
24dd25d9f5 Add edit/delete result comment functionality 
Lessons learned during this fix:
Don't use dependant: :destroy on both ends of association
between 2 ActiveRecords, or you will run into stack overflow.
 2016-08-25 13:51:31 +02:00
Luka Murn
bac0455435 Add edit&delete functionality to step comments 
This commit also:
* fixes a bug in permission_helper.rb,
* fixes comments.js a bit,
* adds 2 more re-renders of dropdown position calculations to canvas.js and projects/index.js.
 2016-08-25 13:51:31 +02:00
Luka Murn
8a73a3ab5c Update permission_helper.rb and routes.rb 2016-08-25 13:51:30 +02:00
Luka Murn
319bcc7850 Add permissions for comments to permission_helper.rb 2016-08-25 13:51:30 +02:00
zmagod
1120ef1407 adds experiment and team to tag search resuls [fixes SCI-381] 2016-08-25 10:40:03 +02:00
Jure Grabnar
00da7efb44 Merge remote-tracking branch 'origin/jg_SCI_328_moving_workflows' 
Conflicts:
	app/models/experiment.rb

SCI-328 #close
 2016-08-24 13:11:10 +02:00
Zmago Devetak
afaeab492d Merge pull request #87 from ZmagoD/zd_SCI_371 
hide the dropdown if user has no permissions(technician) [fixes SCI-371]
 2016-08-24 11:56:29 +02:00
zmagod
27d77bc73f added new permission for dropdown actions 2016-08-24 10:56:30 +02:00
Jure Grabnar
a091571d9c Add consistent links for archive for all entities 2016-08-24 09:14:29 +02:00
Jure Grabnar
0cdb18ffcd Update experiment links on sidebar between actions 2016-08-24 09:05:57 +02:00
zmagod
eab05eb9db adds font-awesome to pdf [fixes SCI-345] 2016-08-22 14:40:09 +02:00
Jure Grabnar
6879521a75 Add missing .experiment to can_unlink_protocol 2016-08-18 10:48:44 +02:00
Matej Zrimšek
4ad384df5a Fixed hound alerts. 2016-08-17 21:02:05 +02:00
Matej Zrimšek
951cf67b3d A lot of file uploading edge cases considered. File uploading is now actually redirected to S3 server, as before was not. Error functions changed and error output format specified, which should be used consistently throughout the application. Some other refactoring. 2016-08-17 18:08:21 +02:00
Jure Grabnar
0cdea0b51a Add modal for moving task on canvas 2016-08-17 15:46:30 +02:00
Jure Grabnar
7f21ae138a Set clone actions/routes/view 
DRY code for showing AJAX on project#show page
 2016-08-11 09:46:15 +02:00
Jure Grabnar
a0fe31479f Fix permissions for archived experiments 2016-08-09 10:00:44 +02:00
Jure Grabnar
0ca5725f9b Archive/restore of experiments now work 2016-08-08 16:35:45 +02:00
Jure Grabnar
2bd74866e0 Fix my_modules archive page 2016-08-08 15:04:02 +02:00
Jure Grabnar
5a023483d7 Prepare views for experiment archive 2016-08-08 14:19:35 +02:00
Jure Grabnar
775a39344c Fix experiment archive permissions 2016-08-08 13:40:08 +02:00
jbargu
3f91e7a476 Merge pull request #47 from biosistemika/jg_explvl_reports 
Update reports with experiment level

[Fixes SCI-35].
 2016-08-08 08:51:23 +02:00
zmagod
9c5c4f0a3a Merge branch 'zd_SCI_44' of https://github.com/ZmagoD/scinote-web into ZmagoD-zd_SCI_44 2016-08-05 15:23:01 +02:00
Jure Grabnar
0c51f7bc8b Saving/editing of reports now works 2016-08-03 13:15:40 +02:00
zmagod
caa80642c0 [fixes SCI-304], [fixes SCI-37] 2016-08-03 09:34:10 +02:00
zmagod
9581e2751f fixes samples page for experiment level [fixes SCI-44] 2016-08-02 08:44:07 +02:00
Luka Murn
40fe4e54a9 Feed the Hound #2 2016-07-29 16:48:56 +02:00
Luka Murn
ecf5b5a2c1 Feed the Hound 2016-07-29 16:46:25 +02:00
Luka Murn
8a2b54819a More fixes on secondary navigation 2016-07-29 16:20:35 +02:00
Luka Murn
b085aa1db3 Remove uneccesary project_activities HTML pages 2016-07-29 16:06:35 +02:00
Luka Murn
34af50a9d0 Fix breadcrumbs & sidebar so it works 2016-07-29 15:47:41 +02:00
Luka Murn
0f0689eddc Fix permission helper 2016-07-29 11:43:15 +02:00
Luka Murn
edafcaeed6 Move route module_archive_project -> module_archive_experiment 
Also add some new routes, move some templates.
 2016-07-29 10:25:02 +02:00
Luka Murn
b64e200b91 Refactor canvas a lot. 
Also refactor localization files concerning canvas.
 2016-07-28 16:41:10 +02:00
zmagod
d16c0fe706 fixed edit canvas 2016-07-28 10:09:05 +02:00
zmagod
54c4051906 added canvas under experiments 2016-07-28 09:01:44 +02:00
Zmago Devetak
c869db2506 Merge pull request #35 from ZmagoD/zd_SCI_40 
Edit canvas controller to work with experiments
 2016-07-27 12:11:19 +02:00
zmagod
485d93f8b9 refactor canvas permissions 2016-07-27 11:35:07 +02:00
Jure Grabnar
690ad0fffa Add a few experiment permissions 2016-07-26 12:26:48 +02:00
zmagod
6053c782f9 fixed permission_helper [fixes SCI-34] 2016-07-25 12:07:10 +02:00
zmagod
426bce48b2 fixed permission_helper 2016-07-25 09:31:40 +02:00
zmagod
389ee7ea43 start fixing modules 2016-07-22 14:31:09 +02:00
Luka Murn
076b67620f Migration GitLab -> GitHub 2016-07-21 13:11:15 +02:00
Luka Murn
055298fee8 Initial commit. 2016-02-12 16:52:43 +01:00