Commit Graph

53 Commits

Author SHA1 Message Date
Dan Funk 11413838a7 Faster lookup fields. We were parsing the spec each time to get details about how to search. We're just grabbing the workflow id and task id now and building that straight into the full text search index for faster lookups. Should be peppy.
Another speed improvement - data in the FileDataModel is deferred, and not queried until it is specifically used, as the new data structures need to use this model frequently.
2020-05-29 01:39:39 -04:00
Dan Funk 22bdb6c760 This migration will clear out any approvals in the database. 2020-05-28 20:13:33 -04:00
Dan Funk 8f41dfa95f forgot the migration. 2020-05-28 10:31:20 -04:00
Dan Funk eb92ee9fb6 Adding missing migration. 2020-05-25 23:47:40 -04:00
Aaron Louie 20bf01a888 Adds cascade to study relationship so data loader doesn't freak out. 2020-05-22 22:04:11 -04:00
Dan Funk 1eb52ed268 Removing duplicate migration. 2020-05-06 13:28:41 -04:00
Dan Funk 07e58e923d Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
# Conflicts:
#	Pipfile.lock

Assuring that all documents from the xls spreadsheet are loaded when doing validations.
2020-05-06 11:25:50 -04:00
Dan Funk 9629b36e92 Setting JSON_SORT_KEYS to false, assuring that Flask does not resort all data returned to the front end.
Updating Spiff Workflow which has some critical behavioral changes around MultiInstance.
2020-05-06 10:59:49 -04:00
Aaron Louie 4ecb0cb3a3 Updates BPMN files 2020-05-05 16:15:38 -04:00
Dan Funk c140637dde Adding Migration, and checking that everything till works the same as before, only a little better. 2020-04-22 15:45:58 -04:00
Dan Funk c30e66d91d Fixing migration. 2020-04-21 17:31:20 -04:00
Dan Funk fd0adb1d43 Updated the study status to use a different enumeration. Migration correctly handles modifying the enum.
INCOMPLETE = 'Incomplete in Protocol Builder',
  ACTIVE = 'Active / Ready to roll',
  HOLD = 'On Hold',
  OPEN = 'Open - this study is in progress',
  ABANDONED = 'Abandoned, it got deleted in Protocol Builder'
2020-04-21 17:13:30 -04:00
Dan Funk 241980f98f If you name add a file to a workflow that has the exact same name as a Task Spec's ID, and an extension of "md", it wll use that file as the markdown content, and ignore the markdown in the documentation on the task spec.
Moving the primary process id from the workflow model to the file model, and assuring it is updated properly.  This was causing a bug that would "lose" the workflow.
2020-04-17 13:30:32 -04:00
Aaron Louie 9a9922c473 Adds display order to Workflow Spec 2020-04-09 14:25:14 -04:00
Dan Funk 2cd5d70a77 missing another migration. This should fix it. 2020-03-30 09:40:56 -04:00
Dan Funk f8cca274d4 Adding a migration for the last commit. 2020-03-30 08:36:10 -04:00
Dan Funk b5fca2f683 Forgot a migration 2020-03-27 12:19:32 -04:00
Aaron Louie f77ebe3177 Adds display order to categories 2020-03-26 15:29:52 -04:00
Dan Funk 473c81ac8b Allow migration even when data exists. 2020-03-23 13:39:54 -04:00
Dan Funk ef0bb7aaaa Allow migration even when data exists. 2020-03-23 13:22:09 -04:00
Dan Funk f205fffc3c Allow migration even when data exists. 2020-03-23 13:03:31 -04:00
Dan Funk 3ec8196979 Cleaning up migration hell. 2020-03-20 11:19:43 -04:00
Dan Funk b35427523d Merge remote-tracking branch 'origin/master' into feature/reference_files
# Conflicts:
#	crc/models/file.py
#	crc/services/file_service.py
#	tests/data/reference/irb_documents.xlsx
#	tests/test_files_api.py
2020-03-20 11:07:55 -04:00
Dan Funk 61a46a9c41 Fixing the primary flag on the file table - it should never be null, it shoud just default to false. 2020-03-20 08:36:50 -04:00
Dan Funk 6e3b6c2635 Assure that files uploaded through web forms and files generated from templates can be cross-referenced to known document requirements from the protocol builder. Configurators can control this by managing an XLS Spreadsheet called "irb_documents.xslx".
Required Documents is becoming complicated, so making this it's own script task, removing it from study_info.py
The file_service is now very aware of this irb_documents file, so it will always need to exist.  We seed this file
during setup, but it can be overwritten by the configurator.
2020-03-19 17:14:20 -04:00
Dan Funk 83d859fd3a Just merging stuff real quick. 2020-03-18 17:03:36 -04:00
Dan Funk 02be8ede75 Merge remote-tracking branch 'origin/master' into feature/reference_files 2020-03-18 15:16:34 -04:00
Aaron Louie e4af6f77d0 Adds is_status flag to workflow_spec, status_spec_id & version to study, and is_active flag to WorkflowApi 2020-03-15 15:52:59 -04:00
Dan Funk 779674ab60 Add the ability to upload and request general reference files by name. These will be used across workflows and will frequently contain lookup tables that can be referenced by various script tasks. 2020-03-13 15:03:57 -04:00
Aaron Louie 902dba7191 Adds is_status flag to workflow specs 2020-03-13 14:56:46 -04:00
Aaron Louie be17c2159c Adds workflow stats and task events models and schemas. Updates workflow stats and logs task completion when task data is updated. 2020-03-10 21:29:57 -04:00
Aaron Louie 5bf0eb33d9 Fixes migrations. Will require full database reset. 2020-03-06 09:50:32 -05:00
Dan Funk 9fcd6f38f4 Merge remote-tracking branch 'origin/master' into feature/pb_services 2020-03-05 17:13:41 -05:00
Dan Funk 7b21b78987 Workflow Processor will deserialize workflows using the version of the BPMN files used during creation, but allows for both a soft and hard reset - soft resets will use the new workflow without a restart and will retain full history. A hard-reset will restart the workflow from scratch, but will retain the data from the last completed task. Workflows have a complex version number associated with them that is used during the deserialization to find the correct files. 2020-03-05 15:38:30 -05:00
Dan Funk d0f0acc8cf Missing migration. 2020-03-04 13:48:13 -05:00
Aaron Louie 01720a8bbf Replaces migration and fixes broken tests 2020-03-03 16:02:01 -05:00
Aaron Louie 4534b0c2df Updates study model to better match Protocol Builder. Deletes all migrations and starts over, since Alembic has problems migrating changes to existing column constraints. 2020-02-28 11:14:30 -05:00
Aaron Louie 0cc59d0974 Adds study inactive flag. Sets study to inactive if not found in Protocol Builder. 2020-02-27 11:17:58 -05:00
Aaron Louie 3ef4860391 Adds user_uid and investigator_ids fields to Study. Gets studies from protocol builder and adds them if they aren't already in the database 2020-02-26 18:06:51 -05:00
Aaron Louie 581434b453 Adds SSO header attributes 2020-02-20 15:43:29 -05:00
Dan Funk 705cfc0a35 forgot a critical migration in the last commit. 2020-02-19 12:00:14 -05:00
Aaron Louie 71dac70e1f Updates list of allowed files. Removes unnecessary migrations. Note this will require a full wipe & reset of the database to work. 2020-02-05 17:23:37 -05:00
Aaron Louie 654f39e7fd Adds form field key to file model. 2020-02-05 14:55:31 -05:00
Aaron Louie 3ee0426ba9 Adds workflow_id to file endpoints. 2020-02-04 14:26:53 -05:00
Aaron Louie 098ecb3e87 Wipes out old migrations, since changing foreign key constraints in SQLite requires a full database reset anyways. 2020-02-04 09:57:02 -05:00
Aaron Louie 0368657549 Adds ability to get FileModel records by study and task 2020-02-03 21:56:18 -05:00
Aaron Louie 7fc2e87b84 Adds primary process ID to workflow spec 2020-01-23 10:54:41 -05:00
Aaron Louie c11bf3d286 Adds workflow spec name field 2020-01-21 15:22:44 -05:00
Dan Funk 782271885a Fixing database migrations - will require a delete of the database. 2020-01-02 10:14:48 -05:00
Dan Funk 0685b282e8 Don't put foreign key constraints on primary keys. 2019-12-30 16:00:33 -05:00