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931 Commits

Author SHA1 Message Date
mike cullerton
070c3cfd5d *** WIP *** 
New API endpoints, and associated methods.
Services for the new endpoints
Minimal test
 2022-02-01 10:49:35 -05:00
mike cullerton
c07c429ae1 Fix for new version of Pandas. They check data type now. 2022-02-01 10:42:18 -05:00
mike cullerton
c9b7d95a83 *** WIP *** 
Beginning of Git integration
- added gitpython to Pipfile
- started additions for api, model, service, and a test
 2022-01-28 16:11:36 -05:00
Dan
4c00a5762f partial commit - new spec_file_service, and new spec_file_api endpoints that use spec and file name, not file id. 
removed worklow_sync
cleaned up file and workflow models
most of the test are broken.
 2022-01-28 06:42:37 -05:00
Dan Funk
97c29bf77c
Merge pull request #449 from sartography/files-to-filesystem-572 
Files to filesystem 572
 2022-01-26 10:11:26 -05:00
mike cullerton
d82367ab2a Move temp_migration_service code into migration 7225d990740e 
Delete test_files_to_filesystem and test_files_from_filesystem--they were only used to give me access to the migration methods
 2022-01-26 09:58:46 -05:00
Dan
f3637ee6a0 resolving todos, as they are done, and removing commented out code that is no longer in use. 2022-01-25 16:37:17 -05:00
Dan
8529465322 Removed the method get_spec_data_files completly - using get_spec_files and get_spec_data to get this information instead. 
Only load the spec data files if you are creating a new workflow, otherwise just deserialize the json.
Removed the stuff about calculaing the version of the spec, as we don't use it.
 2022-01-25 16:10:54 -05:00
mike cullerton
ae86ab4790 Make erroring workflows visible 
The `process_erroring_workflows` method is called by our scheduler in __init__.py
 2022-01-25 12:18:29 -05:00
mike cullerton
91fa44b2ab ** WIP ** 
Committing so I can work on another ticket.
 2022-01-21 14:37:11 -05:00
mike cullerton
ca54b850cd UNDO my previous commit regarding get_files needs to have workflow_spec_id 
We need to call `get_spec_files` instead now
 2022-01-20 14:57:32 -05:00
Dan
f815add699 1. Add a default directory for the location of SYNC files. 
2. Added a last_updated column to the lookup table
3. The Lookup service now uses the above, and compares it to the actual file date, we can then rebuild the lookup if needed.
4. That 755 migration loads up the models, so when you change the models, the migration starts to fail.  Not really sure what to do here, but modify the migration while we are in process.
 2022-01-20 13:05:58 -05:00
mike cullerton
9ea1399578 get_files needs to have workflow_spec_id 2022-01-20 09:54:22 -05:00
mike cullerton
68820c67cb Removed (almost) all references to WorkflowSpecDependencyFile 
(There is still a call in the lookup service, but we need to decide how to fix that)
 2022-01-19 16:12:54 -05:00
mike cullerton
16a9a18c5b Fixed get reference file info, and added test 2022-01-19 15:17:35 -05:00
mike cullerton
091d71eb0f Cleaned up code around differences between file info and file data 
Cleaned up some api code around differences between file, spec_file, and reference_file
Cleaned up some api code around differences between file info and file data
Fixed some tests for file api
 2022-01-19 13:47:14 -05:00
mike cullerton
d83f28e1a7 Pushed so Dan can play 2022-01-18 15:55:49 -05:00
mike cullerton
68ac056457 Merge branch 'dev' into files-to-filesystem-572 2022-01-18 08:18:14 -05:00
mike cullerton
6da6e05171 *** WIP *** 
code for updating spec files
some cleanup

tests pass, but we don't have all the tests we need.
 2022-01-13 15:24:29 -05:00
mike cullerton
b99ed73951 Remove unused imports 2022-01-12 15:00:26 -05:00
mike cullerton
cfa9f00bf3 *** WIP *** 
Moved reference files to their own service
 2022-01-12 14:37:33 -05:00
mike cullerton
b6b9482a64 *** WIP *** 
Incremental commit. Mainly cleaning up failing tests.
 2022-01-12 13:16:09 -05:00
Dan
d346589e07 1. added the ability to filter on level and user. 
2. added a total to the response, so you can see what the total count of users is.
3. adding user_uid to the task_log table.
 2022-01-12 08:58:50 -05:00
mike cullerton
9cc91f92c3 *** WIP *** 
cleanup - removing commented code
 2022-01-11 15:55:08 -05:00
mike cullerton
4df2ed6ce4 *** WIP *** 
Failing tests, and missing functionality.
Committing to get stuff on Github.
 2022-01-11 15:30:22 -05:00
Dan
962d05c875 1. Created a TaskLoggingService to encapsulate what we are doing with Task Logging through BPMN Script calls and API calls from the front end. 
2. Added two api endpoints that will allow us to get all the logs for a specific workflow or study.
3. Assured that requests for logs are paginated, sortable, and can be limited to a specific code if needed.
4. Assure that we only use logging levels that match the log levels of Python.
 2022-01-10 13:16:54 -05:00
mike cullerton
f537fd7fbf *** WIP *** 2022-01-07 15:58:23 -05:00
mike cullerton
dc27f795c8 *** WIP *** 
Committing because it is Friday afternoon, and my computer is acting flaky
 2022-01-07 15:34:51 -05:00
mike cullerton
86a6039dc8 *** WIP *** 
**Many** tests are failing!

Committing so I can merge dev into this branch
 2022-01-06 11:46:54 -05:00
mike cullerton
7f9519736c fixed some issues with how we look up records. Try to depend on the data_obj 2022-01-04 07:26:12 -05:00
mike cullerton
2cd0f84a47 Merge branch 'dev' into files-to-filesystem-572 2022-01-03 08:06:17 -05:00
Dan
1446302a04 A quick fix for an error we are seeing in testing. 2021-12-30 15:27:31 -05:00
Dan
3480e1c8ab use a signal, in addition to firing off a cancel notify when a workflow is restarted. 2021-12-23 15:30:09 -05:00
Dan
bd3176eea6 Fixes #578 - issue with us displaying an incorrect end event in some cases. 2021-12-22 16:27:52 -05:00
mike cullerton
3fa5505970 Cleanup - remove print statements 2021-12-17 12:30:10 -05:00
mike cullerton
6073412d82 Clean up imports 2021-12-17 12:03:45 -05:00
mike cullerton
aa27df7840 Process the spec files and their metadata 2021-12-17 11:46:21 -05:00
alicia pritchett
a81f25f0ee Just kidding. We should make deepcopy and put in fake data 4 valdiation 
see above. previously i deleted this, because i didnt want unitializsed data in task data. well heres a hint. don't put it in task data. make a deep copy and hold on to that for validation pursposes
 2021-12-16 14:47:04 -05:00
mike cullerton
5c90ce01a6 *** WIP *** 
Temp services `ToFilesystemService` and `FromFilesystemService` for migrating files To and From the filesystem - Not sure where these classes will end up
Tests to call the two services.
upgrade method in migration that writes workflow spec files and metadata to filesystem
 2021-12-16 14:22:37 -05:00
mike cullerton
338352017b *** WIP *** 
Moving files to the filesystem
Tools for reading/writing metadata for categories and specs
 2021-12-16 08:41:49 -05:00
Dan Funk
e62a99af96
Merge pull request #438 from sartography/bug/fix-task-data 
Bug/fix task data
 2021-12-13 13:31:37 -05:00
Dan Funk
b5f2fe05dc
Merge pull request #439 from sartography/workflow-spec-delete-217 
Problem deleting workflow spec #217
 2021-12-13 13:19:56 -05:00
Dan
c46800171d Merge remote-tracking branch 'origin/dev' into bug/fix-task-data 2021-12-13 13:18:00 -05:00
mike cullerton
daebf42a30 Move some of the work in crc.api.workflow.delete_workflow_specification to separate workflow_service methods 
Added a session.commit to `delete_workflow_spec_task_events`
 2021-12-13 11:04:28 -05:00
mike cullerton
acbb8898e4 Merge branch 'more-study-statuses-562' into waiting-workflow-errors-566 2021-12-10 16:52:07 -05:00
mike cullerton
f748fa3db8 Removed unused imports 2021-12-10 16:48:28 -05:00
mike cullerton
9cd5022bf0 Set progress_status to in_progress when creating a new study. 
-- I'm not sure if this is what we want.
 2021-12-10 16:00:33 -05:00
alicia pritchett
f9fbb32641 Take this garbage out 
I can say that because I originally wrote that garbage
 2021-12-10 12:10:08 -05:00
alicia pritchett
962cf7c32c Fixes problem with initializing some task data fields 
we had a problem where sometimes, task data gets some values set in its fields to None, which conflicts with default values. this fixes that
 2021-12-10 11:33:26 -05:00
mike cullerton
52baf25459 In WorkflowService.do_waiting, if a workflow causes an exception, change its status from waiting to erroring so we don't continue to call it in do_waiting. 2021-12-09 15:33:39 -05:00