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426 commits

Author SHA1 Message Date
Urban Rotnik 6cbece9f86 Add service for multiple share 2019-08-09 14:15:49 +02:00
Mojca Lorber 3c1f28ec06 fix smart annotation permission check 2019-08-09 14:13:03 +02:00
Mojca Lorber 71b881cbdf fix failing tests 2019-08-09 14:13:03 +02:00
Mojca Lorber 4c7c7ccdf1 Add ability to browse through shared inventories to smart annotations 2019-08-09 14:13:03 +02:00
Mojca Lorber cac7dab440 Show shared inventories in left navigation and fix read repository permission 2019-08-09 14:13:00 +02:00
Urban Rotnik 077369d960 Update permissions for Repositories 2019-08-09 14:12:59 +02:00
aignatov-bio 6e5f078dea
Add activities for marvinJS [SCI-3630] (#1950) 
* Add marvinJs activities to step and results

* Add activities for TinyMCE marvinJS assets

* Fix markup
 2019-08-09 09:47:07 +02:00
Oleksii Kriuchykhin d52df56fc4 Fix production build and update packages [SCI-3678] 2019-08-08 14:03:15 +02:00
Oleksii Kriuchykhin 973efa55e1 Merge branch 'master' into ok_SCI_3678 2019-08-08 11:17:07 +02:00
Oleksii Kriuchykhin 973fc775c0 Enforce file size limits for direct uploads on S3 [SCI-3681] 2019-08-06 17:09:00 +02:00
Anton Ignatov e2e876b2a3 Merge branch 'activestorage_migration' into ai-sci-3728-fix-active-storage-tests 2019-08-05 13:51:04 +02:00
Oleksii Kriuchykhin a2fe4bee94 Add text extraction from MarvinJS for search [SCI-3643] 2019-08-02 15:17:28 +02:00
Anton Ignatov f35f4886a3 Fix markup 2019-07-29 10:18:34 +02:00
Anton Ignatov 618f0cc334 Fix tests for services 2019-07-26 14:16:44 +02:00
Anton Ignatov 84fe10df47 Fix tests for models and tema import/export 2019-07-26 12:40:36 +02:00
Anton Ignatov 0702dacc5b Security fixes 2019-07-19 14:10:38 +02:00
Anton Ignatov ad7130d3b2 Simplify TinyMCE assets for MarvinJS 2019-07-19 09:27:03 +02:00
Anton Ignatov bdc2dbbac1 Simplify image creation 2019-07-18 14:29:24 +02:00
Anton Ignatov 1e8663548e Add MarvinJS assets to TinyMCE 2019-07-16 13:40:54 +02:00
Anton Ignatov 3339c1fbbf Add MarvinJS to Result and TinyMce MarvinJS refactor 2019-07-15 17:17:14 +02:00
Miha Mencin 47d3315d82 SCI-3702 revert the fix and use local variables 2019-07-15 16:20:39 +02:00
Miha Mencin 1c84e46a21 Revert "SCI-3702 replace _to_text with _to_html" 
This reverts commit 93b7c472ac.
 2019-07-15 16:18:26 +02:00
Miha Mencin 93b7c472ac SCI-3702 replace _to_text with _to_html 2019-07-15 16:16:41 +02:00
Jure Grabnar a372d4056d Add last_published protocols.io endpoint 2019-07-14 19:24:53 +02:00
Anton Ignatov ffd415d409 Inital refactor for Assets model 2019-07-12 15:02:06 +02:00
Anton Ignatov 7831b0a089 Merge branch 'activestorage_migration' into features/marvinjs-integration 2019-07-12 15:00:07 +02:00
aignatov-bio 4bae87e3f7
Styling changes in DOCX report [SCI-3633] (#1899) 
* Styling changes in DOCX report

* Update result comments in docx report

* Fix markup
 2019-07-12 13:48:14 +02:00
aignatov-bio 5ca822a7d8
Add archive lables and fix bright colors in RTE fields (#1923) 2019-07-12 11:38:48 +02:00
Anton Ignatov 57a273d5d0 Merge branch 'activestorage_migration' into features/marvinjs-integration 2019-07-12 11:34:41 +02:00
Oleksii Kriuchykhin 64b7a5646a Implement custom document file previewer [SCI-3677] 2019-07-10 14:37:23 +02:00
Urban Rotnik cc3cd43270 Log to console when error occur on ProtocolsImport actions 2019-07-09 15:32:43 +02:00
Oleksii Kriuchykhin a1941a21dc Futher refactoring of old Paperclip methods [SCI-3539] 2019-07-09 10:28:15 +02:00
aignatov-bio c8b0d87054
Fix global links in reports (#1894) 2019-07-09 09:35:43 +02:00
mlorb 7272d838b6
Merge pull request #1875 from mlorb/ml-sci-3618 
Remove unassign_user_from_project notification…[SCI-3618]
 2019-07-08 15:23:06 +02:00
Jure Grabnar ae7da78bff
Merge pull request #1897 from jbargu/jg_sci_3646 
[SCI-3646] Add paging functionality to external protocols
 2019-07-08 13:06:19 +02:00
aignatov-bio 0d1ec0d4ed
Fix I18n and constants in DOCX report (#1901) 2019-07-08 12:51:26 +02:00
Alex Kriuchykhin 82708f0124
Merge pull request #1891 from okriuchykhin/ok_SCI_3654 
Fix project page view saving [SCI-3654]
 2019-07-08 11:46:54 +02:00
Oleksii Kriuchykhin 9d926dc956 Refactor TinyMce assets, user avatars, zip files [SCI-3539] 2019-07-05 16:56:05 +02:00
Jure Grabnar dc7fee51fa Add Show more protocols functionality to external protocols 
Closes SCI-3646
 2019-07-04 15:35:18 +02:00
Oleksii Kriuchykhin c0c8e0e1a3 Refactor Experiment workflow images [SCI-3539] 2019-07-04 09:33:12 +02:00
Jure Grabnar 20134c9f8a
Features/protocolsio integration (#1893) 
Features/protocolsio integration
 2019-07-03 17:32:20 +02:00
Oleksii Kriuchykhin e16cb513e1 Fix project page view saving [SCI-3654] 2019-07-03 15:34:16 +02:00
Oleksii Kriuchykhin 028e647f4d Upgrade to Rails 5.2.3 [SCI-3651] 2019-07-03 11:15:13 +02:00
Jure Grabnar 4715e8ec4b Fix building of zero steps protocls 
Close SCI-3648
 2019-07-03 09:34:15 +02:00
aignatov-bio b1a74a893c
Remove strange symbol (#1874) 2019-07-02 11:21:14 +02:00
Mojca Lorber 41935a9471 Remove unassign_user_from_project notification and change code to use helper method for assignment notification generation 2019-07-01 13:44:27 +02:00
Anton Ignatov 1f40fa69fc Merge branch 'features/marvinjs-integration' of https://github.com/biosistemika/scinote-web into features/marvinjs-integration 2019-07-01 11:51:27 +02:00
aignatov-bio a08d93376c
Add promo modal when MarvinJS disabled (#1872) 2019-07-01 11:51:13 +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
Anton Ignatov 390002f40f Merge branch 'ok_SCI_3539' of https://github.com/okriuchykhin/scinote-web into okriuchykhin-ok_SCI_3539 2019-07-01 10:12:26 +02:00
Oleksii Kriuchykhin 5acb16d43e Update Asset helper methods [SCI-3539] 2019-06-28 08:17:09 +02:00
Jure Grabnar bc4b07cc0f Refactor hardcoded protocol_source in SearchService 2019-06-28 02:26:31 +02:00
Jure Grabnar 0a77cedaf8 Fix sorting of external protocols and start showing results 2019-06-27 22:48:56 +02:00
Urban Rotnik 9cb4454537 New implementation for attachments creation 2019-06-27 17:02:06 +02:00
Urban Rotnik 2761079479 Add modal for import 2019-06-27 16:46:02 +02:00
Jure Grabnar 06b8d1fda7 Update ApiClient tests 
Closes SCI-3434
 2019-06-27 14:54:19 +02:00
Jure Grabnar d31f978e55 DRY up protocols importer services errors 2019-06-27 10:11:36 +02:00
Mojca Lorber 9fd83d54a0 Put network error handeling into api and refactor errors 2019-06-26 14:04:03 +02:00
Mojca Lorber ebcaa4b014 Implement protocols.io error handling for api client and normalizer 2019-06-18 14:01:57 +02:00
Urban Rotnik c691ad80b5 Add fields to query params for ApiClient 2019-06-17 12:24:16 +02:00
Urban Rotnik 88d96c0938 Use service in controller 2019-06-17 12:24:15 +02:00
Urban Rotnik 7fad5fc594 Add search service and normalizer for list 2019-06-17 12:24:15 +02:00
Jure Grabnar eb0d677a36 Refactor pio_protocol -> built_protocol 2019-06-17 12:24:13 +02:00
Urban Rotnik 0d43ecdfab Import protocol service after object is built 2019-06-17 12:24:11 +02:00
Jure Grabnar eb275c4d12 Add tests for BuildProtocolService and fix bugs 2019-06-17 12:24:11 +02:00
Jure Grabnar 362b0cd45d Hound fixes 2019-06-17 12:24:11 +02:00
Jure Grabnar 640f6c1211 Fix tests after BuildProtocolFromClientService refactor 
Closes SCI-3544
 2019-06-17 12:24:11 +02:00
Jure Grabnar 1e8627c450 Refactor ImportProtocol service to BuildProtocolService 
Closes SCI-3544
 2019-06-17 12:24:10 +02:00
Urban Rotnik a15596a126 Add ImportProtocolService 2019-06-17 12:24:10 +02:00
Oleksii Kriuchykhin 8920d38a02 Make repositories more extendable [SCI-3528] 2019-06-06 17:28:59 +02:00
Alex Kriuchykhin 36255f82ed
Merge pull request #1817 from okriuchykhin/ok_SCI_3522 
Add system notifications service to health check endpoint [SCI-3522]
 2019-06-04 14:41:43 +02:00
Oleksii Kriuchykhin 552f69b9b1 Add system notifications service to health check endpoint [SCI-3522] 2019-05-31 15:52:47 +02:00
Luka Murn b21bdddf15 Rename permision_eval - permission_eval 
Hopefully this will help with getting rid of all the errors
that we've been receiving for PermissionEval.

Closes SCI-2991.
 2019-05-31 09:56:54 +02:00
Oleksii Kriuchykhin 5a9640c5d1 Add aditional checks for inventory state objects [SCI-3412] 2019-05-27 17:32:21 +02:00
Mojca Lorber 5c847d5b5d Change author of copied inventory item 2019-05-13 15:37:36 +02:00
Anton Ignatov 652fba0e23 Merge branch 'master-with-note-section' 2019-05-13 11:08:11 +02:00
Urban Rotnik 2364c2653f Add bulk insert for UserSystemNotifications, New service for sending emails 2019-05-08 08:38:10 +02:00
Anton Ignatov 7f296b35fa Update team exporter for new tinymce images 2019-05-07 13:22:55 +02:00
Oleksii Kriuchykhin 3c1774d330 Fix sorting by user name with search parameter in inventories [SCI-3391] 2019-04-25 16:29:41 +02:00
aignatov-bio 6968060078
Fix user order bug (#1687) 2019-04-19 15:24:13 +02:00
Alex Kriuchykhin 8fa6bbc0ab
Merge pull request #1679 from okriuchykhin/ok_SCI_3177 
Improve experiment preview image generation [SCI-3177]
 2019-04-17 20:35:29 +02:00
Alex Kriuchykhin b4cf665c21
Merge pull request #1673 from okriuchykhin/ok_SCI_3294 
Fix team export/import for new activities [SCI-3294]
 2019-04-17 12:49:45 +02:00
Oleksii Kriuchykhin f9832013b0 Improve experiment preview image generation [SCI-3177] 2019-04-17 12:06:46 +02:00
Oleksii Kriuchykhin 2320941b5d Fix team export/import for new activities [SCI-3294] 2019-04-15 15:13:10 +02:00
Alex Kriuchykhin 3250ab70f4
Merge pull request #1668 from okriuchykhin/ok_SCI_3292_v2 
Switch to kaminari pagination in global activities [SCI-3292]
 2019-04-12 16:04:48 +02:00
Oleksii Kriuchykhin 231106e131 Switch to kaminari pagination in global activities [SCI-3292] 2019-04-12 15:37:45 +02:00
aignatov-bio 8ba0555922
Add check for tasks complete in project notifications (#1657) 2019-04-12 09:17:34 +02:00
Oleksii Kriuchykhin d378e33038 Improve global activities pagination and fetching [SCI-3292] 2019-04-10 15:45:17 +02:00
Oleksii Kriuchykhin 01ffb43c23 Include old activites assigned to the task [SCI-3285] 2019-04-02 18:37:55 +02:00
Urban Rotnik 86ddbc68b6 fixup! Show date actual value without link 2019-04-02 14:21:06 +02:00
Urban Rotnik 8eaeeee9f8 Show date actual value without link 2019-04-02 13:15:34 +02:00
Urban Rotnik 6ec22c0b3b
Merge pull request #1618 from urbanrotnik/ur-sci-3240-missing-activities-of-intentory 
Missing activities, fix for showing report name, add step positions, fixed links [SCI-3240] [SCI-3246]
 2019-04-02 11:02:57 +02:00
aignatov-bio daaa6a367b
Adding custom scrollbar to global activities [SCI-3206] (#1623) 
* Adding custom scrollbar to global activities
 2019-04-02 09:56:50 +02:00
Urban Rotnik b91f08fe99 Add activity for copying Inventory and Invetory item 2019-04-01 15:40:00 +02:00
Alex Kriuchykhin b3aa6be23d
Merge pull request #1621 from okriuchykhin/ok_SCI_3255 
Add global activities to reports [SCI-3255]
 2019-04-01 15:07:06 +02:00
Jure Grabnar e165459ef5
Merge pull request #1574 from jbargu/jg_sci_3149_3163 
Valid smart annotation links of smart annotation imported within protocol [SCI-3149, 3163]
 2019-04-01 14:32:54 +02:00
Jure Grabnar 83130426e2
Merge pull request #1617 from jbargu/jg_3244 
Duplicated activity, report activity ... [SCI-3244]
 2019-04-01 14:31:53 +02:00
Jure Grabnar 111b0e2b7f
Merge pull request #1615 from jbargu/jg_sci_3252 
Change breadcrumbs for copy as template experiment, missing activity for move workflow [SCI-3252]
 2019-04-01 12:30:48 +02:00
Oleksii Kriuchykhin 98e58ff7eb Add global activities to reports [SCI-3255] 2019-04-01 11:26:51 +02:00
Jure Grabnar 3a79f7ca01 Add activity to save_pdf_to_inventory_item 2019-03-29 16:01:36 +01:00
Jure Grabnar 8bc10e1ca7 Change breadcrumbs for cloning experiment to destination project 2019-03-29 09:52:07 +01:00
aignatov-bio b51dcc9d75
Adding children selector to global activities subjects [SCI-3247] (#1605) 
* Adding children selector to global activities subjects

* Fix naming, add seperate check for project id
 2019-03-29 09:26:27 +01:00
Oleksii Kriuchykhin d7d45bec70 Fix links for archived objects in global activities [SCI-3229] 2019-03-28 13:43:50 +01:00
Matej Zrimšek 318c322a1c Fix sorting of custom columns on repository datatables 2019-03-27 12:58:55 +01:00
Matej Zrimšek 632835cf30 Fix fetching assigned repository rows when using filter & refactor it 2019-03-27 12:58:55 +01:00
Oleksii Kriuchykhin 2ff43a3320 Change filtering logic when no filters are selected [SCI-3223] 2019-03-26 16:04:03 +01:00
Alex Kriuchykhin 935e3a65cf
Merge pull request #1586 from okriuchykhin/ok_SCI_3199 
Fix multiple bugs in global activities [SCI-3197][SCI-3199][SCI-3213][SCI-3225]
 2019-03-26 16:02:44 +01:00
Miha Mencin 9a30d7be9d SCI-3232 renaming the attribute name so it doesnt get 'constantized' 2019-03-26 11:39:54 +01:00
Oleksii Kriuchykhin e3a3ec4491 Fix multiple bugs in global activities [SCI-3197][SCI-3199][SCI-3213][3225] 2019-03-25 17:38:13 +01:00
Miha Mencin 4a87216a3d
Merge branch 'master' into features/global-activities 2019-03-25 14:35:24 +01:00
Jure Grabnar 5de51f9c58 Prevent smart annotations accessing other teams when importing protocol 
Closes SCI-3163
 2019-03-20 12:58:22 +01:00
Mojca Lorber 4f9814b884 Merge branch 'features/global-activities' of github.com:biosistemika/scinote-web into ml-sci-3021 2019-03-20 11:03:00 +01:00
Anton Ignatov 29b67be127 Fix team selection in global activities and add link from navbar 2019-03-20 10:33:22 +01:00
Mojca Lorber 70eebca5ee experiment activities refactoring 2019-03-19 15:33:57 +01:00
Urban Rotnik 1017836c0e Activities service fix 2019-03-19 14:12:39 +01:00
Urban Rotnik fe35c805b7 Add model breadcrumbs, update activities_helper 2019-03-19 14:01:06 +01:00
Anton Ignatov 87280f083a [SCI-3166] Finalize global activities front end 2019-03-19 13:50:55 +01:00
Oleksii Kriuchykhin 0c71493fdb Add viewing permissions for global activities [SCI-2997] 2019-03-18 15:38:19 +01:00
Urban Rotnik b8e84b5685 Add logic for saving message items values and types 2019-03-11 08:37:22 +01:00
Urban Rotnik 117944117b Add service for activity creation 2019-03-11 08:36:15 +01:00
Miha Mencin 6deaff6382 fixing hound errors 2019-03-04 18:36:32 +01:00
Miha Mencin 844303ae7c SCI-3119 schedule the creaton of template 2019-03-01 17:47:04 +01:00
aignatov-bio 9a007b5d75
Merge pull request #1542 from aignatov-bio/ai-sci-3108-missing-user-name-in-activity 
Fix missing user name in activty, when moving experiment [SCI-3108]
 2019-03-01 14:16:59 +01:00
Alex Kriuchykhin 985820a97c
Merge pull request #1527 from okriuchykhin/ok_SCI_3101 
Move templates project creation for new team to delayed job [SCI-3101]
 2019-03-01 13:55:49 +01:00
Oleksii Kriuchykhin 1fedb4c91e Improve speed of index query in projects overview service [SCI-3107] 2019-02-28 17:46:34 +01:00
Anton Ignatov 9e472c0ccf Fix missing user name in activty, when moving experiment 2019-02-28 16:06:23 +01:00
Oleksii Kriuchykhin 0266f6bd3c Change search on subject query constaruction logic [SCI-3014] 2019-02-27 13:21:05 +01:00
Anton Ignatov 978c4bcb69 Fixed, trying to save object instead name 2019-02-27 10:43:46 +01:00
Oleksii Kriuchykhin 74a60d443d Merge branch 'features/global-activities' into ok_SCI_3014_v2 2019-02-26 13:46:25 +01:00
Oleksii Kriuchykhin a0d2f7c676 Move templates project creation for new team to delayed job [SCI-3101] 2019-02-26 13:32:00 +01:00
Oleksii Kriuchykhin 61147b480c Add main global activities bussiness logic [SCI-3014] 2019-02-26 11:01:15 +01:00
Urban Rotnik 5a123d26ac Activity model update 2019-02-26 07:15:05 +01:00
Urban Rotnik 3ad6cee766 Fix tests, remove nullable field 2019-02-25 16:50:38 +01:00
Urban Rotnik 7b6c6c414d Merge branch 'master' into features/templates 2019-02-19 14:46:15 +01:00
aignatov-bio fcdb4e7a92
Merge pull request #1500 from biosistemika/features/system-notifications 
Features/system notifications
 2019-02-19 13:51:18 +01:00
Urban Rotnik f63eaaefe7 Add user_system_notification records when syncing notifications, update email sending 2019-02-19 11:22:58 +01:00
Oleksii Kriuchykhin c186498a5e Merge branch 'features/templates' into ok_SCI_3037 2019-02-15 10:47:38 +01:00
Alex Kriuchykhin 185e3b4832
Merge pull request #1495 from okriuchykhin/ok_SCI_3039 
Create templates project when syncing templates if team doesn't have it [SCI-3039]
 2019-02-14 17:40:01 +01:00
Mojca Lorber 343a46584f Rename scope 2019-02-14 14:54:04 +01:00
Mojca Lorber 0e14c126e5 Add scope instead of method for active my_module_group 2019-02-14 10:53:48 +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
Oleksii Kriuchykhin da30d187a6 Create templates project when syncing templates if team doesn't have it [SCI-3039] 2019-02-13 15:17:33 +01:00
Oleksii Kriuchykhin f3ad4f7fc9 Fix failing test [SCI-3037] 2019-02-12 13:39:38 +01:00
Mojca Lorber d706a18e2d Add flag for archived tasks to experiment exporter 2019-02-12 13:29:48 +01:00
Oleksii Kriuchykhin 7854b9d281 Merge branch 'features/templates' into ok_SCI_3037 2019-02-12 11:18:31 +01:00
Oleksii Kriuchykhin 445098fe45 Fix protocols in team export service [SCI-3037] 2019-02-12 10:56:15 +01:00
Alex Kriuchykhin b71c9d96a2
Merge pull request #1476 from okriuchykhin/ok_SCI_2944 
Add test for templates service [SCI-2944]
 2019-02-12 09:39:03 +01:00
Jure Grabnar 0fa403d6b0 Refactor tests fro experiment import 
Closes [SCI-2946]
 2019-02-06 14:27:43 +01:00
Matej Zrimšek f68adf1e5e Fix workflow image loading for moved experiments [SCI-3003] 2019-02-06 07:51:43 +01:00