afaecfa21c
Catching an error when variables conflict with repeating section variables.
2021-08-18 13:38:34 -04:00
feb72af32e
Update workflow.py
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Just completing a comment so I understood
2021-08-18 13:27:28 -04:00
b4ecb0f97a
Add backref cascade and make changes to the spot where we delete so it loads objects into memory and then uses the SQLAlchemy plumbing to make sure that the db object gets cleaned up.
2021-08-18 08:25:17 -04:00
032aad9bc4
Fixes #383 - Timestamp on files is UTC?
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also this includes the shield test thing for the boolean_type property whoopsie
2021-08-17 13:04:24 -04:00
7a8eeab820
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-17 11:16:03 -04:00
6ce560cc2d
Made a stupid mistake in a hot fix, causing the builds to fail.
2021-08-17 10:14:49 -04:00
c831ee7e4a
Merge pull request #357 from sartography/426-remove-hsr-number
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remove hsr number #426
2021-08-17 09:58:56 -04:00
78f79a67b7
removing exectue flag.
2021-08-17 09:52:02 -04:00
4e0e162fd6
Removing the execution flag Nile keeps adding to files.
2021-08-17 09:50:57 -04:00
77de2a8f47
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-17 09:47:09 -04:00
0a2597ae36
Just a quick hot fix so that when can still report errors back to the UI even when the task_data can't be serialized, which can happen when functions are defined.
2021-08-17 09:43:08 -04:00
07ffcd7c76
Dependencies In Testing are behind this avoids that issue. https://sonarcloud.io/project/issues?id=sartography_cr-connect-workflow&pullRequest=356&resolved=false&types=BUG
2021-08-16 23:46:39 -04:00
2a2fd710c4
Merge branch 'dev' into dmn-from-spreadsheet-395
2021-08-16 14:22:02 -04:00
3f44c202ca
Merge branch '417-hsr-open-to-enrollment-bug' into 426-remove-hsr-number
2021-08-16 12:55:24 -04:00
b3fd72de8b
Remove hsr_number from Study Schema
2021-08-16 12:51:48 -04:00
1f82143aea
Remove HSR Number from models
2021-08-16 12:50:09 -04:00
46d7b13326
Start to remove HSR Number
2021-08-16 12:09:02 -04:00
0a232dace6
assertEquals -> assertEqual
2021-08-16 10:25:41 -04:00
f8dd4c3eb9
Check Study Associates Endpoint
2021-08-16 09:32:02 -04:00
bd4a9cced3
We no longer use HSRNUMBER to automatically set Study Status to `Open for Enrollment`
2021-08-13 12:06:27 -04:00
4a2581e938
get studies raises and error when invalid studies are the only studies associated with the user
2021-08-12 14:03:44 -04:00
7027392a1b
Merge remote-tracking branch 'origin/bug/missing_pi_name_246' into bug/missing_pi_name_246
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# Conflicts:
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 13:01:41 -04:00
e32c1db4c8
Merge remote-tracking branch 'origin/dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/models/study.py
# crc/services/study_service.py
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 12:59:15 -04:00
000de03733
Just a quick hot fix so that when can still report errors back to the UI even when the task_data can't be serialized, which can happen when functions are defined.
2021-08-12 12:49:19 -04:00
41e27cb454
Merge remote-tracking branch 'origin/dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/models/study.py
# crc/services/study_service.py
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 12:39:04 -04:00
d20b68e483
Fixed Deprecation Warnings in Test Files
2021-08-12 12:33:27 -04:00
2732071585
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-12 12:07:25 -04:00
40727c7ce6
avoid erroring out when unable to calculate a value expression as a part of finding a default value.
2021-08-12 11:35:05 -04:00
adb1b74822
Merge pull request #352 from sartography/post-process-empty-field-408
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Post process empty field #408
2021-08-12 10:53:26 -04:00
d07bac27ca
Fix for hidden file data field.
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We were processing a field that didn't have a value.
Ticket 408
2021-08-11 16:43:50 -04:00
318cd34f81
bouncing to fix a bug in SpiffWorkflow that was holding outo outdated data deed within the python_script_engine.
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This caused validation to fail for valid repeat sections, so including a fix to allow that validation to continue.
2021-08-11 14:21:23 -04:00
05e7f5e253
Worksheet for Alex
2021-08-11 10:06:12 -04:00
19e0caa700
API endpoint for creating a DMN table from a spreadsheet
2021-08-11 08:55:10 -04:00
848c2e622f
Always use a schema to define what is being returned, it enforces consistency of the API and internally we can depend on well defined objects.
2021-08-10 16:16:08 -04:00
913c12c02d
Merge branch 'dev' into bug/pi_name_missing_246
2021-08-10 15:06:52 -04:00
dce95189cb
Merge branch 'dev' into dmn-from-spreadsheet-395
2021-08-10 09:39:42 -04:00
960d302c03
Finish #367 - Make sure that we only use a primary_id if it is in the workflow that we are currently working on - otherwise it is a library and might have its own primary id.
2021-08-10 09:15:38 -04:00
c153c5e344
Another test spreadsheet
2021-08-09 13:27:58 -04:00
deebc49a82
Removed test files - don't need under version control
2021-08-03 12:20:25 -04:00
0e20480f52
Removed test files - don't need under version control
2021-08-03 12:17:54 -04:00
64576ee8fd
It now adds the dmn file to the DB.
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Added annotations.
Still need to move it out of a script.
Maybe a new API endpoint and a new method in file_service
2021-08-03 11:55:50 -04:00
6e1fedb704
Add tests for libraries, remove an API endpoint that didn't make sense after recent changes and remove some commented out sections that were not needed after some decisions about the api endpoints were made
2021-08-03 10:02:22 -04:00
deb16740f6
First attempt at creating dmn from spreadsheet.
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xml template and example spreadsheet
2021-08-02 10:04:25 -04:00
e1aee0f635
First attempt at creating dmn table from spreadsheet.
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Starting as a script
2021-08-02 10:03:10 -04:00
41ad7935f8
Merge branch 'dev' into 367-Call-Activity
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# Conflicts:
# Pipfile.lock
2021-07-29 09:28:21 -04:00
217e61eed3
next_task returns the next available task, except when the task is completed when it returns the EndEvent -
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The problem was that it was returning the first EndEvent it found, not the last one. This caused a problem when we had a CallActivity which has its own EndEvent.
Fixes #399
2021-07-27 09:19:08 -04:00
b857fddbad
commit in intermediate changes to work on a bug
2021-07-26 13:00:11 -04:00
25e00823a7
Merge pull request #342 from sartography/enum-file-data-375
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Enum file data #375
2021-07-23 13:47:57 -04:00
4c8a86f9bf
Fixed bug where processing file data only worked for enums.
2021-07-23 11:24:17 -04:00
7f5c7417d8
Print out some additional debugging information in the email script so we can tell what is happening and where.
2021-07-22 16:02:08 -04:00
38b8c7fcdf
Fixed email_cc test
2021-07-22 15:08:28 -04:00
b94d49076d
Fixed Associate API Endpoint description
2021-07-22 14:36:00 -04:00
90425ebbb3
Merge branch 'bug/missing_pi_name_246' of https://github.com/sartography/cr-connect-workflow into bug/missing_pi_name_246
2021-07-22 14:09:34 -04:00
a73d1794eb
Fixed Associate API Endpoint description
2021-07-22 14:09:24 -04:00
61504664d4
Merge pull request #346 from sartography/bug/346_timer_fails_to_send_email
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fixes #346 , allow emails to fire in scheduled events
2021-07-22 13:40:12 -04:00
2009a794ea
We were depending on an active http request existing in order to fire emails, using that request to determine the front end url. We have the frontend url in our config file, and we don't have a request object when running scheduled tasks, so I just use our configuration setting instead.
2021-07-22 13:25:06 -04:00
1cfb7f96fa
Missing uid declaration in study service corrected
2021-07-22 11:28:11 -04:00
8df1145471
Modify the LDAP service to only use lowercase UIDs.
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UVA always returns the UID as lowercase.
This caused a postgres unique value problem for us.
2021-07-22 10:46:09 -04:00
428802b9d0
Modify LDAP script so that it doesn't raise an error when we don't get a record back from LDAP.
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We now return an empty dictionary
2021-07-22 10:44:41 -04:00
48516e4009
Parent side working
2021-07-22 10:23:05 -04:00
2455495457
got library side working - still need to have parent working
2021-07-22 10:20:34 -04:00
3906580604
Merges getStudyAssociates() endpoint
2021-07-20 14:25:01 -04:00
a263447806
Merges getStudyAssociates() endpoint
2021-07-20 13:57:32 -04:00
4632c6374f
Merge branch 'dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/api.yml
# crc/services/study_service.py
2021-07-20 11:44:11 -04:00
354e20c34b
Use the data_store_service to set the data_store, rather than access DB directly.
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Pass the label explicitly (as the value)
2021-07-15 13:09:40 -04:00
dd67a5e650
Never set the date to datetime.utcnow() on DateTime fields. We want this to fall back on the func.now() method and allow the database to set the time on insert.
2021-07-12 15:58:32 -04:00
522ca9d164
Merge pull request #340 from sartography/bug/better_errors_on_scheduled_tasks
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Assure we log reasonably clear errors when executing scheduled tasks …
2021-07-12 10:13:02 -04:00
d1bf370a39
Merge pull request #339 from sartography/restrict-loaded-studies-374
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Restrict loaded studies #374
2021-07-12 10:11:34 -04:00
7070761089
Merge pull request #338 from sartography/document-spreadsheet-name-380
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Document spreadsheet name #380
2021-07-12 10:11:16 -04:00
f982745d32
fixing a failing test, don't assume the study and workflow ids will always be 1.
2021-07-12 10:00:39 -04:00
1916c4ff54
Assure we log reasonably clear errors when executing scheduled tasks in the background, so that sentry can pick them up and they can be addressed effectively.
2021-07-12 09:43:12 -04:00
690c059335
get_studies_for_user is no longer a static method
2021-07-09 10:37:57 -04:00
dad2de9f0c
get_user_studies now checks study_details['REVIEW_TYPE'] before displaying a study.
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This corresponds to REVIEWTYPENAME being `Full Committee`, `Expedited`, `Non-UVA IRB Full Board`, or `Non-UVA IRB Expedited`
2021-07-09 10:37:25 -04:00
79c69037dd
Filter out Library categories from the list returned
2021-07-08 08:57:40 -04:00
d6f9b013f7
Change `irb_documents` to `documents`
2021-07-07 12:54:03 -04:00
23180908c8
Undo change. Wrong branch
2021-07-07 12:43:51 -04:00
c39e08972d
Change irb_documents to documents
2021-07-07 12:42:01 -04:00
3c52453c26
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:35:24 -04:00
2ed436327f
Merge pull request #333 from sartography/check-study-script-273
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Check study script #273
2021-07-07 11:28:32 -04:00
db9b228735
Merge pull request #334 from sartography/WaitingEventsHotPatch
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Make a change so that anything that has a waiting event is labeled in…
2021-07-07 11:27:10 -04:00
2a45f2fcda
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:24:00 -04:00
b0cf74fa3d
Merge branch 'dev' into add-by-user-61
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# Conflicts:
# tests/files/test_files_api.py
2021-07-07 10:46:50 -04:00
c11b5cfb29
Add user_uid to api output
2021-07-07 08:18:02 -04:00
fb54edac1c
Adding additional details to error messages, and cleaning up the cruft around these messages to keep them clear and succinct.
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Most noteable is the addition of the line on which the error occurs for script tasks. It will report the line number and pass back the content of
the line that failed.
The validator only returns the first error it encounters, as it's clear that all we ever get right now is two of the same error.
Did a lot of work between this and spiffworkflow to remove all the places where we obfuscate or drop details as we converted between workflowExceptions and APIExceptions.
Dropped the python levenshtein dependency, in favor of just rolling a simple one ourselves in Spiffworkflow.
2021-07-07 00:53:49 -04:00
894377a607
Add user_uid to FileDataModel calls
2021-07-06 17:09:00 -04:00
23be257db0
Add user_uid column to file_data table
2021-07-06 17:07:47 -04:00
a9805ad40c
Adding some documentation for clarity.
2021-07-06 14:40:20 -04:00
cafdc4d100
Removing an unneeded modification to the database structure for lookup tables.
2021-07-06 14:02:07 -04:00
04842aa66b
Undo change to 1 minute.
2021-07-06 13:13:07 -04:00
7aa4b0833c
Merge remote-tracking branch 'origin/dev' into feature/documents_xls_refactor
2021-07-06 13:11:08 -04:00
1b1a994360
Refactoring Reference files to use the lookup table, rather than parsing the results directly out of the spreadsheet, or attempting to cache them.
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Adding a DocumentService to clean up the FileService, and get Documents well seperated, as it seems likely be pulled out or seperated in the future, there is now a Documents api file as well, for the same reason.
Some other minor changes are just fixing white space to assure our code is linting correctly.
I removed _create_study_workflow_approvals from the base test, as we don't use approvals like this anymore.
2021-07-06 13:10:20 -04:00
9803a04d6d
Make a change so that anything that has a waiting event is labeled in the database as waiting, even if it is sitting around waiting on a user input task that is ready
2021-07-06 11:46:47 -04:00
dce1d86e93
commit changes before looking at something else
2021-07-06 10:34:57 -04:00
f647390e1c
Added description and validate_only
2021-07-02 15:51:24 -04:00
9690c69b6c
added check_study method to protocol_builder service for new endpoint
2021-07-02 15:25:33 -04:00
cd26654b3a
Script to call new pb mock api endpoint `check_study`
2021-07-02 15:21:35 -04:00
db44882733
When we encounter a name error running a script, look in the task data and see if there is a variable with a similar name.
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If a variable with a similar name exists, add it to the ApiError as a hint
2021-07-01 15:38:45 -04:00
98d641f54d
Merge branch 'dev' into partial_testing
2021-06-30 16:13:31 -04:00
508ef1ff2b
Readded exit_at to workflow param
2021-06-30 11:15:48 -04:00
9a32fadc2f
Merge branch 'dev' into 346-waiting-task-schedule
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# Conflicts:
# Pipfile.lock
# crc/services/workflow_service.py
2021-06-30 10:14:37 -04:00
a79ba22410
fixes to get the tests passing. We were missing a dependency in the Pipfile and the data_store had some invalid imports.
2021-06-30 10:06:57 -04:00
2ba52a7095
Merge remote-tracking branch 'origin/HEAD' into partial_testing
2021-06-29 11:21:49 -04:00
187221537b
fixing a corner case around file_data attributes.
2021-06-25 16:18:28 -04:00
628a587d97
We weren't committing to the database in the correct spot, so the delete wasn't sticking, and we were ending up with test workflows showing up in the main interface.
2021-06-23 16:39:58 -04:00
48bf721b23
Merge pull request #331 from sartography/bug/356_duplicate_workflow
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Bug/356 duplicate workflow
2021-06-22 17:42:24 -04:00
92ca506c8e
Calls to eval no longer return the data, rather it will accept and return a key, allowing the front end to cache similar queries and not re-execute them.
2021-06-22 17:23:18 -04:00
61ad371680
Clean up the file api so we don't have a bunch of extra stuff in there. Just include the raw data from the document spraedsheet if it is available.
2021-06-22 15:08:08 -04:00
1f3febe2df
Fix the panda warnings, which means we only support xlsx files now.
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Include the document details when reutnring a file from the file model.
Improve the validation of file form elements.
2021-06-22 14:58:52 -04:00
369b518384
Removed WorkflowService.delete_test_data()
2021-06-22 11:29:00 -04:00
07eb3f9ca8
Moving metrics into SpiffWorkflow so we can run the performance metrics deeply across both systems simultaniously.
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Upgrading libraries.
Fixing deprication issue with Pandas and numpy.
We can only process xlsx files now, plain oldschool xls is fully removed.
2021-06-18 16:41:55 -04:00
4ca94b39ce
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-17 15:12:28 -04:00
19d63e2aa2
Merge pull request #328 from sartography/restart-workflow-programmatically-347
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Restart workflow programmatically #347
2021-06-17 10:36:46 -04:00
a4caae8d64
when validating, we need to take every step to remove the workflows we create during the validation.
2021-06-16 14:40:20 -04:00
acae6030f5
The API for evaluating python expressions should not raise an error, it can simply return a result of false, and provide an error to explain the problem. In this way the front end doesn't error out when it's running the script tasks but doesn't have enough information to get a valid response back.
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The validation should take into account that repeating sections must be evaluated in the context of the data within the repeating section, not outside of it.
2021-06-15 16:17:15 -04:00
02949dc6e2
WorkflowProcessor handles this error
2021-06-15 11:12:50 -04:00
5c5b966bc4
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-15 09:11:18 -04:00
c8f8888c17
Script to reset workflow. Requires workflow spec name.
2021-06-14 14:51:16 -04:00
738a984dcd
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-06-11 17:21:47 -04:00
879d6e1df3
missed a critical change on the backend with the recent file updates, this assures that we properly handle repeating sections during the post process,
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and we update the file doc code in those repeating sections.
2021-06-11 17:20:25 -04:00
7282419174
modified the tools api to return the expression and data with the result, making it easier to cash results on the front end, This should help drastically reduce the calls to the python_eval from the front end.
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The post processors for form submissions needs to take repeating sections into account, or it won't find the files it is looking for.
2021-06-11 08:27:50 -04:00
394906d840
Add refresh_waiting_tasks to the processor do_engine_steps so that if we have a waiting task that has met its condition prior to the scheduler running, it will go ahead and proceed
2021-06-10 08:33:24 -04:00
e1a4a79b03
Added Partial Workflow spec
2021-06-09 15:21:21 -04:00
2364c240b2
Error Text Changed
2021-06-09 14:54:43 -04:00
338fe30984
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-09 14:32:01 -04:00
17077be701
exit at task
2021-06-09 12:40:38 -04:00
5f722d675f
Add a function that gets runs via a background scheduler to look for any workflows that are in a 'waiting' state - it runs the update waiting tasks and does do_engine_steps
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We have a test for the function that runs, but an assumption was made that the scheduler module has its own unit tests and we do not need to test that.
fixes #346
2021-06-09 10:42:34 -04:00
fce9166c4a
Do not require users to be admins for viewing the document directory tab.
2021-06-09 09:51:30 -04:00
0d8d251e8e
Temp save to test dev
2021-06-09 09:24:37 -04:00
286803d10b
fixing a big stupid bug I created when merging all the code and making changes to the files.
2021-06-08 14:24:59 -04:00
586a0f2f1a
Merge pull request #325 from sartography/feature/file_refactor
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Prefer tasks that share a parent over just the the next available tas…
2021-06-08 11:28:23 -04:00
8d79fe9d94
Fixing failing tests, and now asserting that we only perform the post_process_form if we actually have a form.
2021-06-08 11:16:10 -04:00
9c4994581d
Merge pull request #324 from sartography/modify-infinite-loop-312
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Modify infinite loop #312
2021-06-08 10:30:13 -04:00
e10b210302
Merge pull request #323 from sartography/shield-test-issue-344
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Shield test issue #344
2021-06-08 08:59:58 -04:00
a7b208f50a
Merge pull request #322 from sartography/data-store-refactor-330
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Data store refactor #330
2021-06-08 08:58:53 -04:00
6937c33719
Merge pull request #319 from sartography/datastore-file-endpoints-325
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Datastore file endpoints #325
2021-06-08 08:54:43 -04:00
37d4e7cc79
Merge pull request #318 from sartography/340-update_study_associate_change
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Add test and fix to make sure that an empty study associates list (or…
2021-06-08 08:52:44 -04:00
c4a6fbb516
Merge pull request #317 from sartography/337-Data-Store-IRB-Code
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337 partial fix
2021-06-08 08:51:09 -04:00
5881c903ca
Merge pull request #316 from sartography/326-Multi_File_Data_Store
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Make sure we are using the correct script engine
2021-06-08 08:49:43 -04:00
710921cfe1
Merge pull request #314 from sartography/deprecate-study-info-protocol-261
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Remove protocol from study_info script #261
2021-06-08 08:47:43 -04:00
59f605c3df
Prefer tasks that share a parent over just the the next available task when returning the next_task in the workflow processor.
2021-06-08 08:03:14 -04:00
a3a485dd34
Changed do_task_validate_only so it returns a mocked value, instead of True/False.
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True/False caused problems for workflow validations
2021-06-04 11:44:55 -04:00
9a63ab9c4f
Change `do_task_validate_only` in study_info script to call the real do_task.
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We do this so we can seed settings into the workflow for testing different scenarios using the study from validate_study_id
2021-06-03 14:28:24 -04:00
c41657301a
Modify `test_spec` and `make_test_workflow` to accept new optional `validate_study_id` parameter.
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Modify `make_test_workflow` to use study_id when creating test workflow for validation.
2021-06-03 14:22:26 -04:00
0dfc96d7f6
Modified `validate_workflow_specification` to accept new optional `validate_study_id` parameter.
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We then pass validate_study_id on to WorkflowService.test_spec
2021-06-03 14:19:41 -04:00
d657744816
Added optional `validate_study_id` parameter to the validation api endpoint.
2021-06-03 14:17:12 -04:00
7f0d8a131d
Import DataStoreBase from service now
2021-06-02 10:00:55 -04:00
506b84a49a
Import DataStoreBase from service now
2021-06-02 10:00:18 -04:00
e2e35b673d
Moved data store code from script to service
2021-06-02 09:59:41 -04:00
162dee45d3
Unused import
2021-06-01 16:34:21 -04:00
2e3d8c7343
Fix for DataStoreSchema missing the file_id column.
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The file_id column is a foreign key.
2021-06-01 13:51:10 -04:00
Dan
Mike Cullerton
Kelly McDonald
Leashys
nilez
mike cullerton