mike cullerton
dd26f8fef7
Update review types
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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
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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
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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 ***
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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.
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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
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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
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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
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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.
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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.)
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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
mike cullerton
b753f06394
Changes to remove pagination for the get_logs scripts.
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We only use pagination for the get_logs_for_study API endpoint. (Used on the study page)
2022-03-11 14:03:09 -05:00
mike cullerton
d57d741c10
Added TODO
2022-03-10 12:17:32 -05:00
mike cullerton
423426c2c8
Removed some unused imports
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Finished up get_all_logs_for_download
2022-03-10 12:14:14 -05:00
mike cullerton
9efb4c4fb3
New spreadsheet_service.
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Accepts list of dictionaries, and optional headers and title
Creates spreadsheet from list of dictionaries
Returns the spreadsheet as a binary stream
2022-03-10 12:13:10 -05:00
Dan
c55cc4715d
Fixing a bug that would cause us to evaluate the wrong field almost all of the time.
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We looped over all the other fields in the task, to assure they at least had a null value, but in doing so, we overwrote the variable containing the field we were trying to test.
2022-03-09 15:26:29 -05:00
mike cullerton
bf31364b1f
*** WIP ***
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Committing to fix logging so we can use a level of 'metrics'
2022-03-09 13:07:56 -05:00
Dan
1e9c9919c2
hot fix, missed a critical part of the jinja include syntax when identifying included templates
2022-03-09 11:03:42 -05:00
Dan
ce57a3753a
fixing some comments and error messages for clarity
2022-03-09 10:28:22 -05:00
Dan
e3c1a908fe
A better comment around a tricky part of the code.
2022-03-09 09:43:08 -05:00
