sartography/cr-connect-workflow
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880 Commits

Author SHA1 Message Date
Dan
e68c95f03c New serialization code, with the ability to load from the old serlializer if needed. 
pipenv insisted on updating some other libraries so slight modifications for markupsafe.
 2022-04-15 10:26:23 -04:00
mike cullerton
be24b598b8 Fix call to set_data_common - no longer have workflow_spec_id, add type of data set 2022-04-13 18:03:23 -04:00
mike cullerton
076eb8747f Finish bug fix for deleting data_stores when value is None or empty string 
Cleanup:
- Make sure workflow_spec_id has a value
- Change extra if conditionals to elif conditionals
 2022-04-13 18:01:52 -04:00
mike cullerton
916daf002c Clean up parameters for set_data_common 
Use key, value instead of args[0], args[1]
 2022-04-13 13:48:35 -04:00
Dan
b455b73c7b Don't freak out if there are not files to delete. 2022-04-12 14:43:34 -04:00
mike cullerton
d04b447c8c Update data stores, rather than creating new ones 
Delete 'extra' data stores
 2022-04-05 18:15:58 -04:00
Dan Funk
6694dc6cb3
Merge pull request #510 from sartography/git-error-filenotfound-690 
Git error filenotfound #690
 2022-04-04 16:53:36 -04:00
Dan Funk
095105e3e6
Merge pull request #508 from sartography/validation-with-data-store-396 
Validation with data store #396
 2022-04-04 16:51:57 -04:00
Dan
e1f9dcded5 Assure we can associate the same person with a workflow under two different roles. 2022-04-04 16:01:48 -04:00
mike cullerton
dd26f8fef7 Update review types 
Remove review types 23, 24
Add review type 21
 2022-03-30 10:29:53 -04:00
mike cullerton
ae66934bf9 Fix bug where we tried to add files to the index that were removed from the repo 2022-03-29 09:49:05 -04:00
Mike Cullerton
6ff0cdbb9d
Merge pull request #507 from sartography/bug/validating_data_security 
Bug/validating data security #684
 2022-03-29 09:41:02 -04:00
mike cullerton
4abdc4920f There was a problem if validate_study_id was 0 (zero). It evaluated to False 2022-03-25 10:04:05 -04:00
mike cullerton
8c88de35cd Modify get_validate_common and set_validate_common methods to use the temporary validate_data_store list 
In get_validate_common, we first look in validate_data_store, then in the real data_store. This allows us the flexibility to use temp values for current workflow or real values set by previous workflows.

Also, lots of cleanup:
- we didn't use the dictionary returned by the set_data_common method, so removed it and only return the value we set.
- this allowed us to delete the `overwritten` method and some other code.
- renamed some variables to better represent what we are doing
 2022-03-25 10:01:31 -04:00
mike cullerton
5bf114b605 Initialize validation_data_store as empty list 2022-03-25 09:50:31 -04:00
mike cullerton
b884ce4c3a Remove debug print statement 2022-03-23 16:49:58 -04:00
mike cullerton
94abd7eebf *** WIP *** 
Add a temporary data store for validation
 2022-03-23 15:15:01 -04:00
Dan
7dfb0bbba9 assure we can use the right data when determining if a field is hidden. 2022-03-23 14:25:29 -04:00
alicia pritchett
487a1a3987 Fixes #667- Validate Lane Variables 2022-03-21 12:18:40 -04:00
Dan
befc299475 Merge branch 'dev' into chore/fix_validation_errors 2022-03-19 09:53:12 -04:00
mike cullerton
05c0e4f96c Put default back to False 2022-03-18 16:55:38 -04:00
Dan
e44ea6e13c merging in from dev. 2022-03-18 16:22:33 -04:00
mike cullerton
f4d6b07467 In get study, only process categories when we ask 2022-03-18 16:03:50 -04:00
Dan
a401c41b23 Setting a minimum date for which to import studies. 
Merging in code to improve performance of calculating percent complete for a study.
Assureing we have a primary investigator for the front page (another merge)
 2022-03-18 15:27:45 -04:00
Dan
b36ff02517 Merge remote-tracking branch 'origin/chore/study-progress' into staging-500-error 2022-03-18 15:07:14 -04:00
alicia pritchett
3c5a75c976 Change study progress resulting from a query 2022-03-18 14:42:03 -04:00
Dan
405c63aaef Merge remote-tracking branch 'origin/chore/study-progress' into staging-500-error 2022-03-18 12:59:31 -04:00
Dan
b7489aea43 merging in PI Name changes from Alicia's #499 PR. 2022-03-18 12:30:20 -04:00
alicia pritchett
12a0e26ee1 Include the PI name on the study model 2022-03-18 11:03:06 -04:00
Dan
ef5aca4fe4 ReviewType now comes back with the user studies, so we don't need to make an additional query to get it. 2022-03-18 09:59:10 -04:00
mike cullerton
276924960b Merge branch 'dev' into chore/fix_validation_errors 2022-03-18 08:36:03 -04:00
alicia pritchett
2ab96b16a0 Update the study model to include a progress (integer) 2022-03-17 17:20:42 -04:00
mike cullerton
15750beb10 Added a comment on why we moved the session.add(study) line 2022-03-17 15:18:49 -04:00
mike cullerton
be2b7c07ef add the new study to the session after we run update_from_protocol_builder 2022-03-17 14:29:38 -04:00
mike cullerton
69b5d80b23 Included templates wrapped by if clause don't always exist 
Don't raise an error here
 2022-03-16 16:57:26 -04:00
alicia pritchett
c18bc6f876 fix study service 2022-03-16 16:21:02 -04:00
alicia pritchett
5b7e71d42d meta field for categories 2022-03-16 12:49:35 -04:00
alicia pritchett
829c810807 wip 2022-03-15 13:21:58 -04:00
alicia pritchett
37d92c6a5f WIP ~ adding a category metadata object 2022-03-15 10:49:41 -04:00
Dan Funk
791ab20f8c
Merge pull request #494 from sartography/chore/fix_validation_errors 
Chore/fix validation errors
 2022-03-14 16:51:27 -04:00
Dan Funk
8ea8993421
Merge pull request #493 from sartography/jinja-included-includes-670 
Jinja included includes #670
 2022-03-14 16:49:56 -04:00
Dan
483d7e858b Improved Errors - Pick up on the new task_trace information in WorkflowException and pass it on through the api. 
Also:  All script tasks should raise WorkflowTaskExecExceptions - NOT APIExceptions - this is because our scripts are executed by Spiff (not the other way around)  so the errors need to pass fluidly through spiff, and come back to use THEN we can convert them to APIErrors.  Otherwise we lose all kinds of good information about the error.
 2022-03-14 16:00:53 -04:00
mike cullerton
416adcbe69 Recursively parse the included templates 2022-03-14 13:51:41 -04:00
mike cullerton
a6a98bed10 Include workflow_spec_id when adding a log 2022-03-14 11:56:36 -04:00
Dan
90bfbed6fd Merge branch 'dev' into chore/fix_validation_errors 2022-03-14 10:58:01 -04:00
Dan
dec63839f3 Merge remote-tracking branch 'origin/dev' into chore/log-changes-661 2022-03-12 16:19:23 -05:00
Dan
2fc4b44ef3 Create a path to directly download the spreadsheet file (and avoid the weird dance on the front end of making an API call to get file data.) 
Fixing pagination.  Seems the front end uses a page_index that is 0 based, and sqlAlchemy prefers to start at 1.
 2022-03-12 16:19:07 -05:00
Dan
4e9fe3a6bb Merge branch 'dev' into chore/fix_validation_errors 2022-03-12 14:09:40 -05:00
Dan
4ab314c7b8 Be sure to delete the data store items when you delete a study. 2022-03-12 13:38:09 -05:00
Dan
52b5e1d34a Fixing tests. 2022-03-11 18:02:37 -05:00