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2374 commits

Author SHA1 Message Date
artoscinote 888131a465
Merge branch 'features/bioeddie-integration' into ma_SCI_5879 2021-07-20 09:48:13 +02:00
aignatov-bio 53456988ba
Add bioEddie activities and user licenses [SCI-5845][SCI-5842] (#3411) 
* Add bio eddie licens to users [SCI-5845]

* Add activities for BioEddie [SCI-5842]
 2021-07-19 21:33:28 +02:00
Oleksii Kriuchykhin 1c8b32dffc Add biomolecular toolkit API proxying endpoint [SCI-5843] 2021-07-16 15:58:40 +02:00
Martin Artnik 96a5b97bdb Implement Save & Register molecule [SCI-5879] 2021-07-15 12:37:04 +02:00
Martin Artnik ff0ac9f497 Fix free invite users modal [SCI-5900] 2021-07-13 15:51:05 +02:00
Martin Artnik 3cb395db15 Use where_attributes like in team search [SCI-5099] 2021-07-09 10:49:11 +02:00
Martin Artnik fb040bee07 Fix styling, functionality issues with invite users modal [SCI-5099] 2021-07-08 16:10:20 +02:00
Oleksii Kriuchykhin 549fc8e5a0 Fix repository cell joining and preloading [SCI-5847] 2021-07-07 17:43:51 +02:00
Oleksii Kriuchykhin d1208bad0b Merge branch 'develop' into features/new_permissions 2021-07-07 13:44:36 +02:00
artoscinote 52946d18e0
Merge pull request #3416 from artoscinote/ma_SCI_5099 
Rework the team invite modal functionality on members page [SCI-5099]
 2021-07-05 12:41:04 +02:00
Martin Artnik 5f528fcdb5 Rework the team invite modal functionality on members page [SCI-5099] 2021-07-05 12:39:54 +02:00
aignatov-bio bef57eacac Add missed activtiy for tag removing [SCI-5568] 2021-06-30 13:34:02 +02:00
artoscinote 9804e1bd28
Merge pull request #3400 from artoscinote/ma_SCI_5701 
Reworked task view sidebar [SCI-5701]
 2021-06-29 11:26:56 +02:00
zmagoD 9c812e84bd setup logic to group assign all team members and handle the unassignments logic 2021-06-27 13:22:19 +02:00
aignatov-bio 786e74e4de
Add BioEddie integration [SCI-5654][SCI-5657][SCI-5658][SCI-5670] (#3391) 
* Add backend for bioeddie [SCI-5654]

* Add modal for bioeddie [SCI-5654]

* Add bio eddie editor to steps and results [SCI-5654]

* Fix markup and code styling
 2021-06-23 19:48:44 +02:00
Martin Artnik c6c5f75262 Remove unncessary newline 2021-06-22 14:53:03 +02:00
zmagoD ad10befcc4 add new manage access permission to PET levels 2021-06-19 17:17:57 +02:00
Martin Artnik b6588c2334 Reworked task view sidebar [SCI-5701] 2021-06-18 16:52:19 +02:00
Oleksii Kriuchykhin bb458abec6 Remove old reports code [SCI-5650] 2021-06-18 10:40:00 +02:00
Oleksii Kriuchykhin 1e3197875c Fix repositories selection in report wizard and deleted repositories handling [SCI-5831] 2021-06-17 16:23:27 +02:00
Martin Artnik 47071e23a1 Added specs for webhooks 2021-06-17 14:54:30 +02:00
Alex Kriuchykhin b73972dbbf
Merge pull request #3389 from artoscinote/ma_SCI_5819 
Set scinote template if missing when generating reports [SCI-5819]
 2021-06-16 12:27:02 +02:00
aignatov-bio 7313b5fa16
Add archived and deleted repositories to reports [SCI-5781] (#3387) 
* Add archived and deleted repositories to reports [SCI-5781]

* Small markup fix [SCI-5781]
 2021-06-16 10:56:08 +02:00
Martin Artnik 2427086372 Set scinote template if missing when generating reports [SCI-5819] 2021-06-15 12:54:48 +02:00
Miha Mencin 60c309e1cd
Merge pull request #3375 from artoscinote/ma_SCI_5787 
Fix changing report project, fix typo [SCI-5787]
 2021-06-09 13:43:23 +02:00
aignatov-bio afe2a19c88
Add webhooks management [SCI-5767] (#3376) 
* Add webhooks managment [SCI-5767]

* Markup fixes [SCI-5676]
 2021-06-09 12:53:11 +02:00
Martin Artnik 6d98b7eb2b Fix changing report project, fix typo [SCI-5787] 2021-06-08 15:07:00 +02:00
Oleksii Kriuchykhin 86fcda3c09 Fix date formatting for the API [SCI-5785] 2021-06-07 10:34:58 +02:00
zmagoD 784e43e328 create user_assignments for all child objects when the user is attached to the project 2021-06-06 09:54:47 +02:00
aignatov-bio 9559ed88aa
Add webhooks index page [SCI-5766] (#3366) 2021-06-03 14:00:43 +02:00
zmagoD 3d79dd32ad update endpoint type 2021-05-31 21:48:18 +02:00
aignatov-bio 3c7592657c Add activity filters [SCI-5765] 2021-05-31 13:39:10 +02:00
zmagoD debff7bc85 fix code style 2021-05-29 19:25:46 +02:00
zmagoD 28cb7ee81d add user roles enpoint and update scenarios 2021-05-29 15:28:10 +02:00
Alex Kriuchykhin 967ec1fdbf
Merge pull request #3349 from aignatov-bio/ai-sci-5758-small-report-wizard-fixes 
Small report wizard fixes [SCI-5758]
 2021-05-27 14:28:21 +02:00
Oleksii Kriuchykhin 7a5c7e0526 Fix reports docx job arguments [SCI-5763] 2021-05-26 14:34:58 +02:00
aignatov-bio f586865696 Small report wizard fixes [SCI-5758] 2021-05-25 13:14:57 +02:00
zmagoD 7e6789200a fix new API endpoints and add test cases 2021-05-23 17:31:02 +02:00
zmagoD 300c1521fd add new API endpoints and fix/update ExperimentMember and MyModuleMember modules 2021-05-22 18:36:30 +02:00
zmagoD be94cb09c2 fix code style 2021-05-22 14:41:56 +02:00
Oleksii Kriuchykhin 64ce35c8da Refactor DOCX report generator [SCI-5735] 2021-05-21 16:40:38 +02:00
Oleksii Kriuchykhin 29c83ffbb1 Merge branch 'develop' into features/new-reports 2021-05-21 11:04:17 +02:00
Miha Mencin 6142c2d89d
Merge pull request #3336 from aignatov-bio/ai-sci-5740-default-template-selection 
Add default template selection [SCI-5740]
 2021-05-20 15:11:33 +02:00
Oleksii Kriuchykhin 7bfde7dc1e Render report element children container only if children are present [SCI-5739] 2021-05-20 14:16:39 +02:00
aignatov-bio 1b56190116 Add default template selection [SCI-5740] 2021-05-20 13:18:57 +02:00
aignatov-bio c961b493fc
Small fixes in reports templates [SCI-5723] (#3327) 
* Small fixes in reports templates [SCI-5723]

* Update template name validation [SCI-5723]
 2021-05-18 15:19:51 +02:00
aignatov-bio e8b115ca7a Change results sorting [SCI-5727] 2021-05-17 15:17:32 +02:00
Miha Mencin d952edd389
Merge pull request #3316 from okriuchykhin/ok_SCI_5702 
Add generation error states to reports [SCI-5702]
 2021-05-17 10:16:06 +02:00
zmagoD c23c01c01c remove user projects enpoints, fix the role name display 2021-05-16 12:03:16 +02:00
Oleksii Kriuchykhin a175e83a16 Add generation error states to reports [SCI-5702] 2021-05-11 14:52:02 +02:00
aignatov-bio 44a17dc014 Fix ordering tasks in report and wizard [SCI-5706] 2021-05-11 09:40:51 +02:00
zmagoD 5ee38966a0 Merge branch 'features/new_permissions' of https://github.com/biosistemika/scinote-web into new_perimssions-managing-project-ui 2021-05-11 08:36:39 +02:00
Miha Mencin 56a6c0825d
Merge pull request #3296 from okriuchykhin/ok_SCI_5699 
Improve handling of selected inventories in reports [SCI-5699]
 2021-05-10 10:48:09 +02:00
Miha Mencin b4b7783cd3
Merge pull request #3301 from okriuchykhin/ok_SCI_5691 
Hide empty projects in reports editor [SCI-5691]
 2021-05-10 10:47:23 +02:00
Miha Mencin 4886a78be9
Merge pull request #3297 from okriuchykhin/ok_SCI_5694 
Add flash messages for report generation [SCI-5694]
 2021-05-10 10:46:49 +02:00
zmagoD d145dd6d36 add my module assigments modals 2021-05-09 16:59:10 +02:00
zmagoD ac91d9c2c4 add assign user permission to experiment level 2021-05-08 18:06:07 +02:00
Oleksii Kriuchykhin b056eb797f Hide empty projects in reports editor [SCI-5691] 2021-05-07 18:28:13 +02:00
Oleksii Kriuchykhin e4d852b9f5 Fix report PDF generation job params [SCI-5708] 2021-05-07 17:00:34 +02:00
Oleksii Kriuchykhin 06109889c5 Add flash messages for report generation [SCI-5694] 2021-05-07 16:23:35 +02:00
Oleksii Kriuchykhin 62b919cd8f Improve handling of selected inventories in reports [SCI-5699] 2021-05-07 14:55:01 +02:00
Alex Kriuchykhin 7bc6abd9bb
Merge pull request #3290 from okriuchykhin/ok_SCI_5614 
Improve report saving performance and error handling [SCI-5614]
 2021-05-07 11:51:57 +02:00
Alex Kriuchykhin eb773d94c5
Merge pull request #3294 from okriuchykhin/ok_SCI_5619 
Add default settings to existing reports [SCI-5619][SCI-5672]
 2021-05-07 11:38:41 +02:00
Alex Kriuchykhin 7a256838c1
Merge pull request #3292 from aignatov-bio/ai-sci-5638-add-missing-activities-for-new-reports 
Add new activities to reports [SCI-5638]
 2021-05-07 11:26:21 +02:00
Oleksii Kriuchykhin b67f2a21f5 Add default settings to existing reports [SCI-5619][SCI-5672] 2021-05-06 17:33:58 +02:00
aignatov-bio 2fc5bd2521
Fix report processing state after create and update [SCI-5678] (#3276) 2021-05-06 14:22:02 +02:00
aignatov-bio bb5f985630 Add new activities to reports [SCI-5638] 2021-05-06 14:03:45 +02:00
Oleksii Kriuchykhin c0ef2eef3c Improve report saving performance and error handling [SCI-5614] 2021-05-06 10:53:40 +02:00
miha 36788db816 SCI-5698 Make the decision to redirect to 2fa more readable 2021-05-06 08:14:39 +02:00
miha f23ff73610 SCI-5693 skip 2fa if bypass is set 2021-05-05 17:29:21 +02:00
miha 136f0cd17f SCI-5693 refactor of 2fa procedure 2021-05-04 20:51:34 +02:00
Oleksii Kriuchykhin a307a16033 Fix handsontable assets inclusion in report templates [SCI-5692] 2021-05-04 16:05:19 +02:00
zmagoD 47cb1b31dc fix code style 2021-05-02 11:36:10 +02:00
zmagoD c1d98f421d update scenarios and UI logic to handle project page reload after modal close 2021-05-02 11:22:59 +02:00
zmagoD 11e5662c47 add fe logic for disable/enable fields 2021-04-30 13:26:06 +02:00
aignatov-bio 86854b015d Add third template to reports [SCI-5618] 2021-04-29 15:21:58 +02:00
zmagoD 8a74546cdf fix the logic for addin/editing new project members 2021-04-28 18:02:18 +02:00
aignatov-bio 7c75f170d0
Add repositories settings to report wizard [SCI-5648] (#3269) 
* Add repositories settings to report wizard [SCI-5648]

* Move repositories from report settings to content [SCI-5648]
 2021-04-28 09:54:00 +02:00
zmagoD c136d953d0 create form object for role assigment, create helper object for project member, added new user_projects modal 2021-04-24 18:43:28 +02:00
Oleksii Kriuchykhin a67cc619ec Add additional custom fields for reports [SCI-5609] 2021-04-20 13:57:09 +02:00
aignatov-bio d18a54c874
Update create and update action for reports controller [SCI-5641] (#3260) 
Update create and update action [SCI-5641]
 2021-04-20 13:35:40 +02:00
zmagoD 04ef7a4478 add show and edit permissions modal 2021-04-18 17:19:16 +02:00
zmagoD 3333241c9a add CTA for project members modal SCI-5645 2021-04-18 12:23:29 +02:00
Miha Mencin f95e9402bd
Merge pull request #3258 from okriuchykhin/ok_SCI_5613 
Fix save report PDF to Inventory [SCI-5613]
 2021-04-15 09:30:04 +02:00
Alex Kriuchykhin 80827ce761
Merge pull request #3257 from biosistemika/SCI-5623-add-external-id-to-user 
SCI-5623 add external id to user
 2021-04-14 16:15:43 +02:00
Oleksii Kriuchykhin f13f3691b1 Fix blob permissions check to support multiple attachments [SCI-5613] 2021-04-14 16:07:01 +02:00
Oleksii Kriuchykhin fe8f006f6e Fix save report PDF to Inventory [SCI-5613] 2021-04-14 16:06:59 +02:00
Oleksii Kriuchykhin 0a9a656313 Add flash message and notification for generated reports [SCI-5552] 2021-04-14 15:45:51 +02:00
Oleksii Kriuchykhin a2a0aabb62 Implement pooling for Report document creation status [SCI-5557] 2021-04-14 15:16:08 +02:00
Oleksii Kriuchykhin df8354bde3 Move the docx creation to the Delayed job [SCI-5560] 2021-04-14 12:39:36 +02:00
aignatov-bio bccd474cc6 Add edit mode for report [SCI-5620] 2021-04-14 11:51:03 +02:00
miha e610683d5c [SCI-5623] added external_id setting to user 2021-04-14 09:44:09 +02:00
Alex Kriuchykhin 1df86c36d9
Merge pull request #3254 from okriuchykhin/ok_SCI_5637 
Implement PDF report generation in delayed job [SCI-5637]
 2021-04-13 16:37:16 +02:00
Oleksii Kriuchykhin f864f551d5 Implement PDF report generation in delayed job [SCI-5637] 2021-04-12 13:04:02 +02:00
miha 56ebc3dc07 [SCI-5635] add a migration to fix broken steps, fix the api so it sets last_modified_by_id, minor step model refactor 
migration fix

remove the conditoin for set_last_modified_by callback

set the last_modified_by_id in before_save callback (in case it is not set yet)

remove trailing spaces

Set last modified in protocl import service
 2021-04-12 09:59:00 +02:00
Oleksii Kriuchykhin 67302da968 Add settings to reports [SCI-5612] 2021-04-08 17:40:16 +02:00
aignatov-bio e6edbf55f3 Add report wizard step 2 [SCI-5572] 2021-04-08 12:00:08 +02:00
Alex Kriuchykhin aa21d7e415
Merge pull request #3247 from okriuchykhin/ok_SCI_5591 
Add dynamic form elements in report wizard step 1 [SCI-5591]
 2021-04-07 12:05:10 +02:00
aignatov-bio a46b9cb8ea Add document preview to reports [SCI-5559] 2021-04-07 11:15:22 +02:00
Oleksii Kriuchykhin a9ac8452f2 Add dynamic form elements in report wizard step 1 [SCI-5591] 2021-04-06 13:56:24 +02:00
miha 961fa9ab4e [SCI-5631] Add ordering to index endpoint so pagination works, limit maximum page size for kaminari 2021-04-06 09:59:24 +02:00
aignatov-bio 82be23db81 Add project and template selector [SCI-5570] 2021-03-31 15:32:03 +02:00
Alex Kriuchykhin c9688a58f7
Merge pull request #3241 from aignatov-bio/ai-sci-5571-add-template-partial-to-report 
Add template partials to reports [SCI-5571]
 2021-03-31 11:36:56 +02:00
aignatov-bio d04858d26e Fix markup [SCI-5571] 2021-03-30 23:47:34 +02:00
aignatov-bio ecca155fab Added layout for footer and header [SCI-5571] 2021-03-30 23:43:34 +02:00
aignatov-bio ad8e404bca Add template partials to reports [SCI-5571] 2021-03-30 13:40:36 +02:00
aignatov-bio 1c93131ff1 Fix folders breadcrumbs [SCI-5597] 2021-03-26 11:58:18 +01:00
aignatov-bio b5cb46908c
Merge pull request #3225 from aignatov-bio/ai-sci-5563-add-reload-action-to-inline-asset 
Add reload action for assets [SCI-5563]
 2021-03-25 15:40:36 +01:00
Oleksii Kriuchykhin 943c01cada Remove simple_token_authentication [SCI-5595] 2021-03-25 14:55:22 +01:00
aignatov-bio 0920d0a5cd Add reports wizzard layout [SCI-5569] 2021-03-25 13:21:54 +01:00
aignatov-bio 7c573a1ee9 Add reload action for assets [SCI-5563] 2021-03-22 13:02:13 +01:00
Oleksii Kriuchykhin d315b1327b Implement missing missing user smart annotation notifications [SCI-5575] 2021-03-19 17:11:19 +01:00
Oleksii Kriuchykhin 413187e6da Fix filtering on current tasks widget [SCI-5555] 2021-03-12 13:33:37 +01:00
Urban Rotnik 8bacc74c17
Merge pull request #3187 from urbanrotnik/ur-sci-5439 
Fix report completed_on time and username [SCI-5439]
 2021-03-09 13:27:24 +01:00
Urban Rotnik e1db291729
Merge pull request #3200 from urbanrotnik/ur-sci-5525 
Add breadcrumbs on Experiments and Tasks pages [SCI-5525]
 2021-03-08 14:13:44 +01:00
Urban Rotnik a4112984ea fixup! Add breadcrumbs on Experiments and Tasks pages 2021-03-08 11:51:11 +01:00
Urban Rotnik 96ef0c10da
Merge pull request #3148 from urbanrotnik/ur-sci-5450-remamber-user-view-mode 
Store Table/Cards view setting per user [SCI-5450]
 2021-03-08 11:48:33 +01:00
aignatov-bio df4297f6f7 Merge branch 'develop' into features/local_file_previews 2021-03-08 11:30:47 +01:00
Urban Rotnik 235f19cf25 Store Table/Cards view setting per user 
SCI-5450
 2021-03-04 14:56:59 +01:00
Oleksii Kriuchykhin d557739f2e Remove notification service check from health check endpoint [SCI-5526] 2021-03-04 09:38:25 +01:00
Urban Rotnik 401224ae11 Add breadcrumbs on Experiments and Tasks pages 2021-03-04 09:00:58 +01:00
Urban Rotnik 8ca8c84efd Fix report completed_on time and username (partially) 
SCI-5439
We cannot realy on last_modified_by, because it can be changed after step completion
 2021-02-25 13:24:21 +01:00
Oleksii Kriuchykhin bdd717b21b Refactor view project users modal [SCI-5387] 2021-02-22 22:37:32 +01:00
Miha Mencin 63dd680385
Merge pull request #3177 from urbanrotnik/ur-sci-5514 
Fix repository empty index show condition [SCI-5514]
 2021-02-22 10:56:02 +01:00
Urban Rotnik 42f8062fe0 Fix repository empty index show condition 2021-02-22 10:18:52 +01:00
aignatov-bio 58a5126a13 Fix normalize_module_position method [SCI-5508] 2021-02-19 14:41:57 +01:00
Urban Rotnik 2daf5aad2a
Merge pull request #3168 from urbanrotnik/ur-sci-5493-external-protocols-preview 2021-02-18 14:50:30 +01:00
Oleksii Kriuchykhin 7d89088b14 Multiple small bugfixes [SCI-5494] 2021-02-18 13:55:03 +01:00
Urban Rotnik 6851746bf6 Fix HTTParty request after gem upgrade 2021-02-17 13:34:26 +01:00
mlorb 20dc9967f5
Merge pull request #3113 from mlorb/ml-sci-5311 
Implement the option of deleting empty folders [SCI-5311]
 2021-02-15 10:27:05 +01:00
Mojca Lorber b600f22248 Add no results page on experiment page 2021-02-12 12:12:26 +01:00
Mojca Lorber 7071f4a6c5 Send selected folders param to modal 2021-02-11 18:27:16 +01:00
aignatov-bio bcc9d6c85c Fix sort for experiments page [SCI-5479] 2021-02-11 15:38:10 +01:00
aignatov-bio 1eff3494fb Fix archived experiments page routes and clean old archive page [SCI-5479] 2021-02-11 14:21:15 +01:00
Mojca Lorber 19733ba7d9 Refactor deleting of empty folders 2021-02-10 22:11:42 +01:00
aignatov-bio 8adbd11197 Fix archived project routes and experiment archived date [SCI-5477] 2021-02-10 15:05:53 +01:00
mlorb 45da42b924
Merge branch 'develop' into ml-sci-5311 2021-02-07 19:20:09 +01:00
aignatov-bio 2972fac96e
Merge pull request #3140 from aignatov-bio/ai-sci-5407-add-folders-link-to-search 
Add folder links to global search [SCI-5407]
 2021-02-05 15:24:23 +01:00
aignatov-bio 7c99eaed8f Add folder links to global search [SCI-5407] 2021-02-05 12:39:26 +01:00
Mojca Lorber ad61e59593 Change the title Projects to folder/subfolder title [SCI-5456] 2021-02-05 11:04:58 +01:00
Oleksii Kriuchykhin c62c464902 Implement editing options and modals for experiment card [SCI-5367] 2021-02-04 12:06:51 +01:00
Alex Kriuchykhin 1466ae114f
Merge pull request #3027 from okriuchykhin/ok_SCI_5246 
Remove Demo project and Samples inventory [SCI-5246][SCI-5248]
 2021-02-04 11:28:09 +01:00
Oleksii Kriuchykhin 8a0a0cbacc Add view only project users modal for project card [SCI-5337] 2021-02-04 11:25:35 +01:00
aignatov-bio a7a948abaf Add archive/restore toolbar buttons and backend [SCI-5457] 2021-02-03 14:29:50 +01:00
aignatov-bio 7726eae4da Add experiments page load logic and connect filters [SCI-5457] 2021-02-03 14:29:50 +01:00
Oleksii Kriuchykhin 6b2a94f045 Add empty repositories index page [SCI-5248] 2021-02-01 15:02:08 +01:00
Oleksii Kriuchykhin 324c268594 Remove Demo project and Samples repository [SCI-5246][SCI-5248] 2021-02-01 15:02:06 +01:00
aignatov-bio 8be9d3b14c
Merge pull request #3126 from biosistemika/features/new-experiments-page 
Features/new experiments page
 2021-01-29 13:28:11 +01:00
Oleksii Kriuchykhin 75da67b937 Update Rails to 6.1.1, ruby to 2.7.2 [SCI-5459] 2021-01-28 14:43:45 +01:00
Oleksii Kriuchykhin b872c6fd14 Add breadrumbs to project experiments page [SCI-5369] 2021-01-25 16:06:48 +01:00