cff270071a
Merge branch 'rrt/dev' into fix/empty_task
2020-06-29 08:41:21 -06:00
a996c81508
Gets mi_index out of Spiff task internal data
2020-06-28 11:35:35 -04:00
d4bcb9af65
Proper error handling in csv/dumps for approvals
2020-06-27 13:59:04 -06:00
848ad563d3
Only filters by mi_index if task has a mult_instance_index
2020-06-26 12:47:42 -04:00
f9f3003ef0
Filters by multi-instance index, if applicable
2020-06-26 12:31:37 -04:00
150117587e
Merge branch 'dev' into feature/parallel_multiinstance_tasks
2020-06-25 23:20:38 -04:00
665faaa175
Send emails from service
2020-06-25 16:18:42 -06:00
44995e3813
Merge branch 'feature/emails-enhancement' of github.com:sartography/cr-connect-workflow into feature/emails-enhancement
2020-06-25 14:37:04 -06:00
c3ceda4c2f
Replaces xml.etree with lxml.etree
2020-06-25 14:02:16 -04:00
7116b582e8
Splitting commands properly without losing double quoted strings
2020-06-25 12:01:24 -06:00
fe5a7ddce3
Merge remote-tracking branch 'origin/rrt/dev' into feature/emails-enhancement
2020-06-25 13:29:06 -04:00
23941d73ad
Fixes variable names. Updates Spiff to STG-26 branch. Updates package versions.
2020-06-25 11:02:57 -04:00
5d1ae402b6
Slight refactor on data passed to template rendering
2020-06-24 22:43:44 -06:00
a0d877e02f
Feedback from PR addressed
2020-06-24 22:23:31 -06:00
5327b469f6
Merge branch 'rrt/dev' into feature/emails-enhancement
2020-06-24 21:46:53 -06:00
a40adeca3a
Merge branch 'dev' into STG-26
2020-06-22 19:57:43 -04:00
dd10e56d1a
Adding forgotten variables to returned dict
2020-06-22 14:56:24 -06:00
bb825f8097
Dropping old parameter from endpoint
2020-06-22 14:09:58 -06:00
dc5ffd29d0
Refactoring shared code
2020-06-22 14:07:57 -06:00
e5541e4950
Enable CSV download
2020-06-22 09:24:58 -06:00
b8d60ca944
Spreadsheet generation
2020-06-22 07:14:00 -06:00
6aec15cc7c
Shifting to a different model, where the TaskEvents store ONLY the form data submitted for that task.
...
In order to allow proper deletion of tasks, we no longer merge data returned from the front end, we set it directly as the task_data.
When returning data to the front end, we take any previous form submission and merge it into the current task data, allowing users to keep their previous submissions.
There is now an "extract_form_data" method that does it's best job to calculate what form data might have changed from the front end.
2020-06-19 08:22:53 -04:00
e6d74aaa1a
Removing extra index when parsing users info
2020-06-18 12:53:50 -06:00
4db815a999
Handling incoming values from processor
2020-06-17 21:11:47 -06:00
e947f40ec7
Merge branch 'rrt/dev' into feature/emails-enhancement
2020-06-17 20:10:11 -06:00
5ce279b663
Dropping silly pdb statement
2020-06-17 17:36:15 -06:00
896ba6b377
Email relies now on markdown content
2020-06-17 17:00:16 -06:00
2ce2dc73b5
Rendering proper content & organizing file structure for email tests
2020-06-17 16:09:38 -06:00
da048d358e
Merge branch 'dev' into feature/refactor_data_loading
2020-06-17 17:14:30 -04:00
3b57adb84c
Continuing a major refactor. Some important points:
...
* TaskEvents now contain the data for each event as it was when the task was completed.
* When loading a task for the front end, if the task was completed previously, we take that data, and overwrite it with the lastest data, allowing users to see previously entered values.
* Pulling in the Admin branch, as there are changes in that branch that are critical to seeing what is happening when we do this thing.
* Moved code for converting a workflow to an API ready data stricture into the Workflow service where it belongs, and out of the API.
* Hard resets just convert to using the latest spec, they don't try to keep the data from the last task. There is a better way.
* Moving to a previous task does not attept to keep the data from the last completed task.
* Added a function that will fix all the existing RRT data by adding critical data into the TaskEvent model. This can be called with from the flask command line tool.
2020-06-17 17:11:15 -04:00
cf09d986ea
Merge branch 'feature/admin' into feature/refactor_data_loading
2020-06-17 16:48:43 -04:00
1844c93919
STG-26 - basic test case for a looping task
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Criteria :
task.multi_instance_type == 'looping'
to terminate, use the standard endpoint for submitting form data with a query variable of terminate_loop=true
Will likely need two buttons:
"Submit and quit"
"Submit and add another"
or something similar
2020-06-17 11:35:06 -04:00
c730a7b1ec
Sending subject and using default sender
2020-06-17 08:53:02 -06:00
40ff3b5fcb
Uses mock LDAP if LDAP_URL environment variable is 'mock'
2020-06-16 21:43:20 -04:00
2ff836019f
Sonarcloud fix
2020-06-16 18:55:18 -06:00
d4a285883f
Email script
2020-06-16 18:42:36 -06:00
59d66be10f
Handling empty task state
2020-06-16 13:13:30 -06:00
1b9166dcb7
Cleaning up the merge, which resulted in some lost code.
2020-06-16 13:34:21 -04:00
c7d8eaff30
Merge branch 'dev' into feature/refactor_data_loading
2020-06-16 13:15:43 -04:00
bd1321baf0
Merge branch 'dev' into feature/admin
2020-06-16 12:29:43 -04:00
0608ffa08a
Restricting the admin endpoints to be admin only, and adding a bit of configuration.
2020-06-16 12:26:25 -04:00
7723862530
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into dev
2020-06-15 16:30:17 -04:00
672ed367e0
Merge branch 'rrt/dev' into feature/admin
2020-06-15 16:13:57 -04:00
706c4afda5
Create a parameter 'lane' since we are using the output from the nav-list as the input to the NavigationItem initializer.
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NB - this doesn't do anything with the lane designation, it just keeps it from blowing up.
2020-06-15 12:33:51 -04:00
92580ee867
adding an additional error check for invalid json returned from the Protocol builder.
2020-06-15 12:26:53 -04:00
eec4b579a7
Don't error out if we don't have a valid study id when doing validation.
2020-06-15 11:27:28 -04:00
5f13b96079
More enhancements
2020-06-12 12:17:08 -06:00
2a84d5196a
filter, not filter_by
2020-06-12 14:13:27 -04:00
e3126620b3
Eschews obfuscation
2020-06-12 14:09:08 -04:00
561e254315
Prevents non-admin users from editing each others' tasks. Fixes bug where test user uid was not being set from token. Moves complete form and get workflow API test utility methods into BaseTest.
2020-06-12 13:46:10 -04:00
691258a4fb
Fixes bug where approvals counts were off by 1. Tests CSV export and all approvals endpoints with lots of records.
2020-06-11 17:15:44 -04:00
f51e5e4e6b
Adds tests for approval counts and all approvals endpoints
2020-06-11 16:39:00 -04:00
768f14b3ac
Cleans up console logging
2020-06-11 13:42:44 -04:00
312eef4d40
Raises 403 error if no user found
2020-06-11 13:07:27 -04:00
cccff9b856
Fixes broken unit tests. But still broken.
2020-06-11 11:29:58 -04:00
1f5554d0d8
Merge branch 'rrt/dev' into feature/swagger_admin_authentication
2020-06-11 08:55:29 -04:00
e9e805b2c9
Storing emails in database
2020-06-09 22:57:56 -06:00
5c1c0f685e
Tests update
2020-06-08 16:17:41 -06:00
777e429382
Merging production back into dev, because we got out of whack somehow.
2020-06-08 14:19:30 -04:00
8cf420b781
Default mail user name and password to blank.
2020-06-08 14:15:56 -04:00
e370148380
Merge pull request #112 from sartography/rrt/dev
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Rrt/dev
2020-06-08 13:18:41 -04:00
0351b3548a
Adding bcc to all emails sent
2020-06-08 11:17:17 -06:00
f91fbf76b9
Capturing explicit errors from mails
2020-06-08 09:16:26 -06:00
87e2379871
Merge branch 'rrt/dev' into feature/swagger_admin_authentication
2020-06-08 10:30:16 -04:00
4cf52b527c
Adding admin dashboard
2020-06-08 07:14:31 -06:00
1c8c085afe
Merge branch 'rrt/dev' into rrt/testing
2020-06-07 22:39:34 -04:00
049424d01b
Adds back an endpoint that returns all approvals across all statuses or users
2020-06-07 22:38:21 -04:00
af1c848f65
Merge branch 'rrt/dev' into rrt/testing
2020-06-07 19:57:09 -04:00
0774942b99
Merge branch 'feature/better_approval_status' into rrt/dev
2020-06-05 22:19:58 -04:00
1d3f98b381
Adds endpoint to quickly get counts of approvals in each status group for a user
2020-06-05 22:19:37 -04:00
213d3f3501
Merge branch 'feature/better_approval_status' into rrt/dev
2020-06-05 19:11:16 -04:00
6861991d8f
Allow setting the type of approvals you want back, by status.
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Some very minor performance enhancements, that will add up on the Approvers page.
2020-06-05 17:49:55 -04:00
f0904e75a6
Sets main approval status after related approvals have been populated
2020-06-05 15:54:53 -04:00
663da57d8b
Config can read smtp values from environment now
2020-06-05 13:54:37 -06:00
57a7c7fa54
Approve/deny fixes
2020-06-05 13:39:52 -06:00
1f32a99efe
Some approval statuses coming back as null., fixed
2020-06-05 14:55:49 -04:00
16ca4fa2c0
Merge branch 'rrt/dev' into feature/mail-system
2020-06-05 12:35:05 -06:00
f0db5b70fc
Adding some additional logic to the approval endpoint so that we take related approvals into account when setting the status. In addtion to prevous status options, there is a new status of "AWAITING" which means there are pending approvals before this approval that still need to be approved or canceled.
2020-06-05 14:33:00 -04:00
4fc1b51cbc
Approve/denied emails
2020-06-05 12:08:31 -06:00
4727d87adb
Hooking up emails into process - start
2020-06-04 20:37:28 -06:00
b6abb0cbe2
using a restartable strategy to get around login errors
2020-06-04 18:03:59 -04:00
9cfe00dfd0
Don't bind all the time.
2020-06-04 15:38:45 -04:00
fed6e86f92
Trying to fix LDAP issues on production. Changing LDAP to static only methods, caching the connection and calling bind before all connection requests.
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Also assuring we don't load the documents.xls file over and over again.
2020-06-04 14:59:36 -04:00
8c36d9f367
Email calls outline
2020-06-04 11:43:10 -06:00
50d2acac9c
Made a very stupid mistake with LDAP connections, pushing up quickly to production.
2020-06-04 11:57:00 -04:00
68aeaf1273
BE VERY CAREFUL where you create a new LdapService() - construction is expensive.
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Adding a few more details to the "csv" endpoint for RRT.
2020-06-04 10:33:17 -04:00
bbcbfef1ba
Fixing the migrations so I don't break the universe.
2020-06-04 10:09:36 -04:00
1324533865
Some additional cleanup - when a file is "archived" it is no longer returned for any endpoints about files, but it
...
is directly accessible via id, in the event some request is made for it at a later date.
2020-06-04 09:49:42 -04:00
f581bd9f2b
Mails for approval process
2020-06-04 00:35:59 -06:00
217ecfc911
When you can't delete a file, mark it as archived. Don't include archived files in new approval requests.
2020-06-03 17:34:27 -04:00
c179c7781b
Do not process or return cancelled approvals via the API.
2020-06-03 16:50:47 -04:00
e102214809
minor cleanup of error codes.
2020-06-03 15:03:22 -04:00
299ad4fc8b
Adding more details to the csv output, and assuring we don't miss people with outstanding approvals that were cancelled.
2020-06-03 07:58:48 -04:00
4bf13b0718
Doing everything I can imagine to get a CSV dump out tomorrow.
2020-06-02 22:01:49 -04:00
2424b9d78c
Don't overwrite the approval, just allow minor changes.
2020-06-02 19:36:06 -04:00
c7484267e1
For the main approval endpoints - we now group the approvals by study. So you get one record back for each study, but it may have other approvals along with it as "related_approvals".
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We now cache the LDAP records - so we look in our own database for the record before calling out to ldap for the details when given a straight up computing id like dhf8r.
Added "date_approved" to the approval model.
And moved the approver and primary investigator into real associated models to make it easier to dump.
Fixed a problem with the validation that was causing it to throw incorrect errors on valid workflows. Getting it to behave a little more like the front end behaves, and respecting the read-only fields. But it was mainly to do with always returning all the data with each form submission.
2020-06-02 18:17:00 -04:00
59e91ec414
Don't add an empty approval record.
2020-06-02 08:35:19 -04:00
d8329e9eff
I completely missed pushing up my changes last night before handing back over to Carlos. Sorry about that.
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Added checks to assure the approver matches g.uid of the current user - otherwise don't modify the approval record.
2020-06-02 07:43:19 -04:00
4090667a5d
Missed committing a pile of changes last night.
2020-06-02 07:08:29 -04:00
a78db8834c
Merge pull request #99 from sartography/feature/sentry
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Enabling Sentry for boxes with the flag set
2020-06-02 06:28:06 -04:00
d0918e9ed3
Merge pull request #98 from sartography/fix/approvals-info
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Approval info addition
2020-06-02 06:26:56 -04:00
95a3b22bf0
Enabling Sentry for boxes with the flag set
2020-06-01 19:59:55 -06:00
c2a1b0175a
Tweaks to approvals
2020-06-01 21:49:30 -04:00
1db9401166
Don't put all the data into Spiff Tasks on a reload or backtrack, just store the data that gets submitted each time in the task log, and use that.
...
This should correct issues with parallel tasks and other complex areas - so we don't have tasks seeing data that isn't along their path.
2020-06-01 17:42:39 -04:00
3c2849f40d
Approval info addition
2020-06-01 15:29:59 -06:00
51accc350c
Updates doc template
2020-06-01 13:37:44 -04:00
885ce5668e
Updates RRT workflow spec files
2020-06-01 13:29:57 -04:00
c790737bf0
The complete_template script might not grab the correct document when validating, fixed.
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Updated to latest RRT files, and passing.
2020-06-01 12:33:58 -04:00
b6bf843f6e
used 'name' rather than 'value' in the lookup options during validation, causing a disconnect with how this is processed on the front end.
2020-06-01 11:00:56 -04:00
7c8b7829ea
Merge branch 'rrt/dev' into feature/approvals_enhancements
2020-06-01 00:41:51 -04:00
1702ab2576
Fixes decision tables that were causing failing tests
2020-06-01 00:36:25 -04:00
ea441dbff5
More updates
2020-06-01 00:28:37 -04:00
8092bbe682
Wrong file in wrong place.
2020-06-01 00:17:20 -04:00
7351dc4a43
Updates RRT workflow spec files for reals this time
2020-06-01 00:14:09 -04:00
2d5eb740ef
Updates RRTworkflow spec files
2020-06-01 00:07:50 -04:00
bec11980eb
Fixing broken test by using proper FileSchema
2020-05-31 22:00:52 -06:00
b2e56f797b
Converting ApprovalModel to Approval in order to serialize properly the result
2020-05-31 21:02:47 -06:00
cd16b984e0
Adds workflow spec title to workflow api schema
2020-05-31 22:46:56 -04:00
f0bd8d4f9e
Adds approvals to study schema. Adds approvals endpoint
2020-05-31 22:46:32 -04:00
9c7de39b09
This adds additional file data details to the study model as well.
2020-05-31 21:15:40 -04:00
dd6c1d2b42
Renaming approval files
2020-05-31 18:16:42 -06:00
2e54f07095
Adding more info to files and renaming approval waiting status
2020-05-31 17:24:23 -06:00
c4a84ac509
Work in progress: Trying to get Swagger to use verify_token_admin to protect admin endpoints. Not working for some reason, though.
2020-05-31 18:01:08 -04:00
be9b613bbb
Refactors user authentication endpoints so we can use the Swagger UI in production mode
2020-05-31 16:49:39 -04:00
26809d1470
Waiting status renaming
2020-05-31 13:35:42 -06:00
2bc735a3f0
Kelly wrote a beautiful method for resetting the workflow that doesn't loose data when reset inside a parallel task, all I needed to do was use it.
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Catching TypeErrors and reporting them back to the UI so we don't 500 in a bad way (but we still 500)
2020-05-31 13:48:00 -04:00
98fb305868
Run the validation process twice, each time it is requested, first populating everything, and then a second time
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using on the required form fields.
2020-05-30 18:43:20 -04:00
1f0e8741ba
Run the validation twice, once completing all of the data, and a second time, completing only the required fields.
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Also, add a helper method to reduce boiler plate code around Workflow Exceptions.
2020-05-30 17:26:27 -04:00
860c475b29
Fill out repeating sections during validation process.
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Also, when returning error messages, attempt to include the task data for the task that caused the error.
Also, when attempting to delete any file, respond with an API error explaining the issue, and log the details.
2020-05-30 15:37:04 -04:00
d51fbe51e0
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2020-05-29 15:18:41 -04:00
4e4cc7884c
Better ldap searching.
2020-05-29 15:17:51 -04:00
34b812b74e
Updates RRT workflow spec files
2020-05-29 10:49:47 -04:00
895d2f8852
Slight change to the way the approval model is connected.
2020-05-29 05:04:18 -04:00
0ba2819867
Merge branch 'dev' into feature/approval_request_script
2020-05-29 04:51:50 -04:00
afb6be7c60
re-working the way the redirects function, so we pass arguments as a get parameter. Just trying to get rid of the weird lag on production.
...
I noticed the validation sometimes looks ahead for files, so looking at all the tasks now, not just the ready tasks for the lookup field.
Ran into an issue with validation where a workflow model was required, so I create one and delete it. Another refactor for another day.
2020-05-29 04:42:48 -04:00
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.
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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
aea78de066
Merge remote-tracking branch 'origin/dev' into feature/file_refactor_part2
2020-05-28 20:06:32 -04:00
dba41f4759
Ludicrously stupid launch in a refactor of the way all files work in the system at a time where I crave sleep and peace above all other things.
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Added a File class, that we wrap around the FileModel so the api endpoints don't change, but File no longer holds refences to versions or dates of the file_data model, we
figure this out based on a clean database structure.
The ApprovalFile is directly related to the file_data_model - so no chance that a reviewer would review the incorrect version of a file.py
Noticed that our FileType enum called "bpmn" "bpmm", hope this doesn't screw someone up.
Workflows are directly related to the data_models that create the workflow spec it needs. So the files should always be there. There are no more hashes, and thus no more hash errors where it can't find the files to rebuild the workflow.py
Not much to report here, other than I broke every single test in the system at one point. So I'm super concerned about this, and will be testing it a lot before creating the pull request.
2020-05-28 20:03:50 -04:00
dedec02d48
Updates RRT workflow spec files
2020-05-28 10:43:03 -04:00
41b26e28bd
Merge branch 'dev' into feature/approval_request_script
2020-05-28 08:11:31 -06:00
cd7f67ab48
A major refactor of how we search and store files, as there was a lot of confusing bits in here.
...
From an API point of view you can do the following (and only the following)
/files?workflow_spec_id=x
* You can find all files associated with a workflow_spec_id, and add a file with a workflow_spec_id
/files?workflow_id=x
* You can find all files associated with a workflow_id, and add a file that is directly associated with the workflow
/files?workflow_id=x&form_field_key=y
* You can find all files associated with a form element on a running workflow, and add a new file.
Note: you can add multiple files to the same form_field_key, IF they have different file names. If the same name, the original file is archived,
and the new file takes its place.
The study endpoints always return a list of the file metadata associated with the study. Removed /studies-files, but there is an
endpoint called
/studies/all - that returns all the studies in the system, and does include their files.
On a deeper level:
The File model no longer contains:
- study_id,
- task_id,
- form_field_key
Instead, if the file is associated with workflow - then that is the one way it is connected to the study, and we use this relationship to find files for a study.
A file is never associated with a task_id, as these change when the workflow is reloaded.
The form_field_key must match the irb_doc_code, so when requesting files for a form field, we just look up the irb_doc_code.
2020-05-28 08:27:26 -04:00
97cdbfce94
Deletes extra line break
2020-05-27 23:48:48 -04:00
77f72e408f
Lookup Service now raises exact matches to the top. Very hackish, but it works.
2020-05-27 14:36:10 -04:00
54640988a7
Update endpoint fixes
2020-05-27 12:06:32 -06:00
d5e075db82
Order search results by relevancy in the lookup service.
2020-05-27 09:47:44 -04:00
397cb23b52
Is true "true", yes it is true. So true, is "false", so true, it is true.
2020-05-26 23:38:57 -04:00
0025931a2e
Trying hard to figure out why the DCOS servers think the protocol builder is enabled.
2020-05-26 23:18:14 -04:00
7869fa596e
Protocol Builder isn't disabled on the dcos servers, trying to figure out why, and assure it isn't some sort of weird race condition.
2020-05-26 22:42:49 -04:00
eb15d172c1
I absolutely must fix our cascade deletes, but I sort of like the horror such chunks of code cause, we really need to protect these endpoints, and assure they never get called under normal circumstances, and raise some thoughtful errors.
2020-05-26 21:18:09 -04:00
ccbf374b40
Loads of bug fixes.
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Modifed the request_approval to take a list of arguments, which works better for us... today.
UpdateStudy correctly handles validation.
WorkflowService correctly populates random values from lookup tables.
And several fixes down in Spiffworkflow, including a big bug where only the last item in a decision table made it through.
2020-05-26 20:06:50 -04:00
987790164e
use redirect, not redirect_url.
2020-05-26 15:09:57 -04:00
7ed9411c74
Handling unavailability of ldap connection
2020-05-26 11:29:24 -06:00
72b59deeaf
Completing tests
2020-05-26 10:21:36 -06:00
a14168362a
Merge branch 'feature/support_ui_dashboard' into dev
2020-05-25 21:31:16 -04:00
1231b963d0
Enabling ldap lookup
2020-05-25 17:30:16 -06:00
727274ae33
Using full approval payload to update record
2020-05-25 15:40:24 -06:00
13186176ba
Improved LDAP searches, allow filtering on last name as well as uva id.
2020-05-25 16:00:36 -04:00
be057e8758
Adding an "UpdateStudy" task that is able to update the data on the study model, useful for setting core data points on the model, such as setting the Primary Investigator, or altering the Study Title.
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Fixing a bug where the validation of forms did not correctly process auto-complete fields.
Fixing a bug where the approvals script and the update study script could not process dot notation correctly.
Moved populate_random_data into the WorkflowService where it makes more sense.
2020-05-25 15:30:06 -04:00
6cd4ef64d1
Fixing add_study api endpoint, so you can actually add a new "Study" with just some basic information.
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Using the LDAP service for checking user details in development mode - even if you are using the back door.
Added a new Flask fucntion load-example-rrt-data that loads the rrt workflow, and not the CRC wrokflows.
Modified the "load-example-data" in the tests to use some test data, rather than loading up all the workflows[
in CRC each time, with a parameter to load crc data if that is required - which is enabled for just a handful of tests.
(Tests run in 1/4 the time now)
2020-05-25 12:29:05 -04:00
971d9a58e9
As we now have an approval_service.py, I moved all the business logic into this service and out of the request_approval.py script. And moved all tests for these features into a test file for the service. Will make it easier to cross reference what is happening, as everything all happens in one file.
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As many of the scripts need to know the workflow, and it's down in a weird parameter, moved this so it is passed in each time.
2020-05-24 16:13:15 -04:00
e9bd19b112
Fixing broken test
2020-05-24 01:22:14 -06:00
49eb4b3f98
Making working endpoints for approvals
2020-05-23 23:53:48 -06:00
4eaee57076
Apparently, APPLICATION_ROOT does something.
2020-05-24 00:05:13 -04:00
68084a84cf
Adds base href environment variable. Sets base path for API and all routes from BASE_HREF environment variable.
2020-05-23 22:07:22 -04:00
e5e7eb3dd3
Fixing broken tests by making version parameter optional in get file data endpoint
2020-05-23 15:37:03 -06:00
d5c91e575f
stuff that might be broken.
2020-05-23 15:21:30 -04:00
d39ef658a2
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval
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Added the following columns:
* date_created - so we know when the file was created
* renamed workflow_version to just "version", because everything has a version, this is the version of the request.
* workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out.
* study - a quick relationship link to the study, so that this model is easier to use.
* workflow - ditto
* approval_files - these is a list from a new link table that links an approval to specific files and versions.
The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram.
Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as
users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this.
The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently.
Lots more tests around the file service to make sure it is versioning user uploaded files correctly.
The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
2020-05-23 15:08:17 -04:00
6c14248ef9
Adds 'v1.0/' to login route
2020-05-23 14:49:02 -04:00
20bf01a888
Adds cascade to study relationship so data loader doesn't freak out.
2020-05-22 22:04:11 -04:00
49c322177b
Merge pull request #76 from sartography/feature/rrp-endpoints
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Feature/rrp endpoints
2020-05-22 19:38:26 -04:00
148e86bb42
Building out the boilerplate code to make pushing forward on this a little friendlier.
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There is an approval api file, and approval model file and an approval test file.
2020-05-22 18:25:00 -04:00
571c1d7d24
Merge branch 'feature/rrp-endpoints' into feature/disable_protocol_builder
2020-05-22 16:18:33 -04:00
1017bb1897
On the tools/render_docx api, allow sending the json data in the body, rather than as a ludicrous long get parameter. Silly Dan.
2020-05-22 15:30:22 -04:00
503c1c8f18
Allow disabling the Protocol Builder
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PB_ENABLED can be set to false in the configuration (either in a file called instance/config.py, or as an environment variable)
Added a check in the base_test, to assure that we are always running tests with the test configuration, and bail out otherwise. Setting TESTING=true as an environment variable will get this, but so well the correct ordering of imports. Just be dead certain the first file every test file imports is base_test.py.
Aaron was right, and we call the Protocol Builder in all kinds of awful places. But we don't do this now. So Carlos, you should have the ability to reuse a lot of the logic in the study_service now.
I dropped the poorly named "study-update" endpoint completely. We weren't using it. POST and PUT to Study still work just fine for doing exactly that.
All the tests now run and pass with the Protocol builder disabled. Tests that specifically check PB behavior turn it back on for the test, or mock it out.
2020-05-22 14:37:49 -04:00
992a85e9a5
Rough idea of what the Approvals model will look like.
2020-05-22 11:56:43 -04:00
a0c884499e
Merge branch 'feature/rrp-endpoints' of github.com:sartography/cr-connect-workflow into feature/rrp-endpoints
2020-05-22 09:46:25 -06:00
1ed7930aab
Endpoint for studies with files
2020-05-22 09:46:03 -06:00
8b3dc8e0ca
Merge branch 'dev' into feature/rrp-endpoints
2020-05-22 11:41:11 -04:00
b490005af7
dropping the remaining config stuff for flask_sso.
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updaing the user 'sso' endpoint to provide additional information for debugging.
Pulling information from ldap to stay super consistent on where we get our information.
2020-05-22 09:50:18 -04:00
1cc9a60bfe
clearing out the remaining references to the flask_sso library.
2020-05-22 08:01:33 -04:00
4627318818
Dropping flask_sso library in favor of reading from the headers directly. Updating login to read from ldap once it has the user_id. Adding more information to the sso endpoint.
2020-05-22 07:55:58 -04:00
0265db7146
adding an /sso endpoint for testing.
2020-05-21 16:02:45 -04:00
4628834106
just a few more logging details.
2020-05-21 12:11:35 -04:00
abc90cdcb1
Adding serialiazer for study files
2020-05-20 15:10:22 -06:00
48f9873548
Adding yet another flush, because Travis builds keep failing due to database race condition issues in this method.
2020-05-20 10:02:30 -04:00
58189285ad
Cleans up
2020-05-20 00:12:48 -04:00
2b5687c3a3
Fixes pernicious bug where template document versions were not being updated properly, and template completion script was not honoring version numbers
2020-05-20 00:10:32 -04:00
481a9ed04c
Gets image ids from task data and Injects images into jinja docx
2020-05-19 21:51:54 -04:00
c4f2bd8dc6
Quick cleanup, adding a space
2020-05-19 16:23:20 -04:00
951710d762
ldap lookup.
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Refactored calls into a new lookup_service to keep things tidy.
New keys for all enum/auto-complete fields:
PROP_OPTIONS_FILE = "spreadsheet.name"
PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
PROP_LDAP_LOOKUP = "ldap.lookup"
FIELD_TYPE_AUTO_COMPLETE = "autocomplete"
2020-05-19 16:11:43 -04:00
5c5c2a7312
Assure that new lines entered in text-fields are correctly added to the final word document.
2020-05-18 11:55:10 -04:00
fc080ce7a8
Don't reset the token to something that already has a token. Terrible things happen and we hit a recursion.
2020-05-17 13:29:36 -04:00
fafdf56ad2
Merge remote-tracking branch 'origin/testing' into feature/navigation
2020-05-16 15:46:14 -04:00
43bf8f5337
Fixing a bug with navigation where elements went missing past exclusive gateways on subsequent forks.
2020-05-16 15:33:06 -04:00
091a1729f8
Removes CORS logging. Allows only specific origins
2020-05-16 11:36:48 -04:00
7d3f139633
Merge branch 'feature/navigation' of github.com:sartography/cr-connect-workflow into feature/navigation
2020-05-15 16:39:25 -04:00
de435bd961
the heck with camel case, what the heck TypeScript? Get a grip. This is a python API.
2020-05-15 16:38:37 -04:00
0f1fbd0249
Merge branch 'dev' into feature/navigation
2020-05-15 16:10:40 -04:00
53255ef35e
massive overhaul of the Workflow API endpoint.
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No Previous Task, No Last Task, No Task List. Just the current task, and the Navigation.
Use the token endpoint to set the current task, even if it is a "READY" task in the api.
Previous Task can be set by identifying the prior task in the Navigation (I'm hoping)
Prefering camel case to snake case on all new apis. Maybe clean the rest up later.
2020-05-15 15:54:53 -04:00
b63ee8159e
We now only return the ready user tasks, not all tasks, and even then the ready user tasks don't come back with the forms and details, just the bare minimum. Speeds things up considerably, and most of this information wasn't used anyway.
2020-05-14 17:13:47 -04:00
f2c9fd5fc4
adding a default url. And some debugging information to see if we hit he endpoint in the logs.
2020-05-14 15:07:05 -04:00
6d4348d644
Fixing some failing tests. Moved the task properties into a dictionary, but moving the form field properties to a dictionary will be a larger effort that we don't want to get into on either the back or front end right this moment.
2020-05-14 14:39:14 -04:00
55a1850e7c
adding a navigation component to the Workflow Model.
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running all extension/properties through the Jinja template processor so you can have custom display names using data, very helpful for building multi-instance displays.
Properties was returned as an array of key/value pairs, which is just mean. Switched this to a dictionary.
2020-05-14 13:43:23 -04:00
3ef07bd8c9
Allows all origins (for troubleshooting)
2020-05-13 12:32:57 -04:00
caf791118f
Allows all resources
2020-05-13 11:00:43 -04:00
fbdff7a5e6
Merge branch 'master' into dev
2020-05-12 22:46:20 -04:00
cdfe45dc00
Turns on flask_cors debugging to troubleshoot CORS issue
2020-05-12 22:42:02 -04:00
77b1908373
Escapes dot characters in CORS domains
2020-05-12 14:27:17 -04:00
ac3f0b401b
Converts list of allowed origins to regexes
2020-05-12 12:23:47 -04:00
e723992fde
Found a number of bugs with the parallel multi-instance - pulling in some recent changes from Spiffworkflow to open things up a bit more to allow functional jumping between tasks.
2020-05-12 12:23:43 -04:00
73ce70b574
Allows CORS connections from frontend
2020-05-12 10:43:52 -04:00
99503fb832
missed a file in the last commit.
2020-05-11 17:42:24 -04:00
b7c11fd893
Merge branch 'master' into feature/investigators_reference_file
2020-05-11 17:36:37 -04:00
02f8764056
Updated to use the latest script engine / evaluation engine that creates a single location where all values used in BPMN/DMN are processed. Right now this is a python based interpreter, but we will eventually base this on FEEL expressions.
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The validation process needs to take the api model into account so we catch errors with bad file names.
2020-05-11 17:04:05 -04:00
c34000d369
Merge branch 'master' into feature/investigators_reference_file
2020-05-07 16:47:24 -04:00
da7cae51b8
Adding a new reference file that provides greater details about the investigators related to a study.
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Improving the study_info script documentation to provide detailed examples of values returned based on arguments.
Making the tests a little more targetted and less subject to breaking through better mocks.
Allow all tests to pass even when ther protocol builder mock isn't running locally.
Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 13:57:24 -04:00
9afcd753c4
No longer requires task_id
2020-05-06 14:27:28 -04:00
1571986c0e
I had to give up and live with the idea that we can only render documentation on the current task, not on the previous or next tasks. I think this is ok. If you want to view a task, you need to make it the active task to assure all the parts and pieces are in place.
2020-05-06 13:01:38 -04:00
8ded625c7d
Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
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# Conflicts:
# Pipfile.lock
Assuring that all documents from the xls spreadsheet are loaded when doing validations.
Fixing some failed tests.
2020-05-06 11:46:19 -04:00
07e58e923d
Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
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# Conflicts:
# Pipfile.lock
Assuring that all documents from the xls spreadsheet are loaded when doing validations.
2020-05-06 11:25:50 -04:00
9629b36e92
Setting JSON_SORT_KEYS to false, assuring that Flask does not resort all data returned to the front end.
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Updating Spiff Workflow which has some critical behavioral changes around MultiInstance.
2020-05-06 10:59:49 -04:00
6c36a32411
Adds DSP
2020-05-06 10:37:43 -04:00
a8827d78c4
Fixes typo
2020-05-05 20:49:07 -04:00
4ecb0cb3a3
Updates BPMN files
2020-05-05 16:15:38 -04:00
ce76b0d3e8
Merge branch 'feature/protocol_status' into feature/previous_task
2020-05-04 11:12:12 -04:00
714b5f3be0
Merge branch 'feature/protocol_status' into feature/previous_task
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# Conflicts:
# crc/services/study_service.py
2020-05-04 11:08:36 -04:00
2699f5c65c
Refactor the stats models, and assure they are very correct across all tests with the workflow api.
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I noticed we were saving the workflow every time we loaded it up, rather than only when we were making changes to it. Refactored this to be a little more careful.
Centralized the saving of the workflow into one location in the processor, so we can make sure we update all the details about that workflow every time we save.
The workflow service has a method that will log any task action taken in a consistent way.
The stats models were removed from the API completely. Will wait for a use case for dealing with this later.
2020-05-04 10:57:09 -04:00
28d5727851
Merge branch 'master' into feature/protocol_status
2020-05-01 22:55:59 -04:00
098cf10926
Fixes Jinja code to match new structure of StudyInfo documents
2020-05-01 22:49:52 -04:00
6a96ccffa2
Updates pipenv hashes. Fixes typo in SpiffWorkflow file name
2020-05-01 21:54:01 -04:00
1f5002680a
Initial work on a "Previous" task.
2020-05-01 12:11:39 -04:00
bec59a71d7
Deleteing stuff is a damn mess, but this is a little cleaner.
2020-04-29 16:07:39 -04:00
f1f8b91c9c
Refactor the document details scripts. Now there is one script, it returns data in a consistent format, and has all the details required. The script is located in StudyInfo, with the argument documents. Make note that it returns a dictionary of ALL the documents, with a field to mark which ones are required according to the protocol builder. Others may become required if a workflow determines such, in which case the workflow will enforce this, and the document will have a count > 0, and additional details in a list of files within the document. I modified the XLS file to use lower case variable names, because it disturbed me, and we have to reference them frequently. Removed devious "as_object" variable on get_required_docs, so it behaves like the other methods all the time, and returns a dictionary. All the core business logic for finding the documents list now resides in the StudyService.
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Because this changes the endpoint for all existing document details, I've modified all the test and static bpmn files to use the new format.
Shorting up the SponsorsList.xls file makes for slightly faster tests. seems senseless to load 5000 everytime we reset the data.
Tried to test all of this carefully in the test_study_details_documents.py test.
2020-04-29 15:08:11 -04:00
beb86f0453
Adds protocol script to study service
2020-04-29 10:21:24 -04:00
13333fb306
Adding an API endpoint that allows setting the token on the workflow to a specific task.
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Added error checking such that attempting to submit data for a task that is not in the "READY" state throws an error message.
For some reason I'm getting lots of errors in the tests as they try to hit API endpoints they were not hitting before, so adding a number of mocks to some of the study service tests.
2020-04-28 17:25:53 -04:00
0088364b1d
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-04-28 13:48:52 -04:00
3e3a249e3c
Verifying Sub-Process works, and adding a field to expose a hint as to the sub-process in which the task occurs.
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Because the name field is now used to expose workflow/sub-process information on tasks, we can't use it to store the workflow_version, so that is now just stored on the database model. Which is much cleaner and removes a duplication.
2020-04-28 13:48:44 -04:00
663a1a00a8
Fixes file name so it matches workflow spec ID
2020-04-28 11:50:10 -04:00
9311a2502a
Fixes broken Formly expression
2020-04-28 09:25:44 -04:00
52fc3c2c2f
Removes xlsx lock file. Adds LibreOffice lock files to gitignore
2020-04-27 22:58:12 -04:00
496e5b7719
Updates all workflow specs to match staging
2020-04-27 22:54:05 -04:00
447f4013f8
Assure that a hard-reset sticks, and the system is properly updated.
2020-04-27 16:08:23 -04:00
1b9743a4d1
Assure that if a form has an enumeration it errors out if that enumeration is empty.
2020-04-27 15:10:09 -04:00
8ed520c6f1
Removes hidden workflows
2020-04-24 09:45:55 -04:00
c85173de88
Sorts approvals by display order
2020-04-24 08:54:14 -04:00
1ccedbc9fd
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-04-24 07:01:40 -04:00
12eb039bc9
Server isn't erroring out, but can't find the lookup table id in the database, so trying to use the in-memory model instead, to give things time to get to the database. Really unsure what is happening here. Hard to see in the database.
2020-04-24 07:01:32 -04:00
af1bb9f80d
Adds more useful metadata to approvals and documents status scripts. Fleshes out and pretties up Documents & Approvals screen
2020-04-23 23:32:20 -04:00
47de010a88
Puts data from sequential calls to StudyInfo into the right place. Sets the required document flag correctly.
2020-04-23 21:02:08 -04:00
d91f690388
Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.
2020-04-23 19:25:01 -04:00
2e601719ad
Fixes broken spec
2020-04-23 17:10:10 -04:00
08140eca17
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-04-23 15:01:02 -04:00
3aeb7ad116
Server isn't erroring out, but can't find the lookup table id in the database, so trying to use the in-memory model instead, to give things time to get to the database. Really unsure what is happening here. Hard to see in the database.
2020-04-23 14:58:17 -04:00
796c109611
Adds approvals to study service
2020-04-23 14:40:05 -04:00
b5b46b7c2c
better overall search results for type ahead. Still dealing with stop words failing.
2020-04-23 12:05:08 -04:00
65b29e1a9d
Don't just bomb out as soon as someone types an empty string.
2020-04-23 09:44:11 -04:00
7b085c9c9d
Adding an API Endpoint that will return a list of LookupValues that match a given query - can be used to populate an auto-complete table.
2020-04-22 19:40:40 -04:00
6de8c8b977
Create lookup tables for XSL files referenced in workflows so we can do full text searches and populate lists on the fly quickly.
2020-04-22 15:37:02 -04:00
79d9a66ce3
Merge pull request #32 from sartography/feature/new_study_states
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Updated the study status to use a different enumeration. Migration c…
2020-04-21 17:21:10 -04:00
fd0adb1d43
Updated the study status to use a different enumeration. Migration correctly handles modifying the enum.
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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
b10f72c085
Updates workflow spec. Removes old DMN files
2020-04-21 14:19:57 -04:00
0a74bf8c44
We can now collect, and provide "extension properties" on a task as set in the camunda modeler.
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These are provided as "properties" on a task, and are identical in structure to properties on a form field.
2020-04-21 12:07:59 -04:00
ec112f52be
Make use of cleaner data provided by Spiffworkflow about multi-instance settings.
2020-04-21 11:43:43 -04:00
ee999a0f15
fixing a bunch of stupid mistakes because I am tried.
2020-04-20 20:28:12 -04:00
d2b31bb3d1
Merge pull request #31 from sartography/feature_personnel_multi_instance
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Feature personnel multi instance
2020-04-20 16:17:43 -04:00
edbd75bb75
Connect LDAP Requests to the StudyInfo service so we get back additional details.
2020-04-20 16:02:13 -04:00
2d3402a719
Ldap Service with Test and mocks.
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LDAP_URL can be set in an environment variable.
2020-04-20 15:16:33 -04:00
194ed55801
Merge remote-tracking branch 'origin/master'
2020-04-20 12:04:18 -04:00
00312d244a
Cleans up debugging config print
2020-04-20 12:04:10 -04:00
d3dd9dcc25
Functional multi-instance - works with no changes to the front end - though I've added some attributes to task so we could give people a sense of how many iterations they will go through.
2020-04-19 15:14:10 -04:00
b099cac174
Merge branch 'master' into feature_personnel_multi_instance
2020-04-17 14:26:23 -04:00
c8b817e98a
Be careful not to clean out all the data when a form is submitted, just merge the data in as it comes.
2020-04-17 13:51:48 -04:00
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.
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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
565ad01393
Merge branch 'master' into feature_personnel_multi_instance
2020-04-16 11:22:50 -04:00
35fa241a4c
Printing out some more stuff for debugging
2020-04-15 14:43:09 -04:00
678a45fa76
Merge branch 'master' into feature_personnel_multi_instance
2020-04-15 12:42:36 -04:00
a5f5468e9a
Merge branch 'master' into feature/customer_lookup
2020-04-15 12:41:35 -04:00
288efff364
Merge branch 'master' into feature_personnel_multi_instance
2020-04-15 12:36:50 -04:00
dc2895cb05
Allow configurators to upload xls files into a workflow for defining enumrations of values for dropdown lists in forms. Fixing lots of tests.
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Found a problem where the documentation for elements was being processed BEFORE data was loaded from a script. There still may be some issues here.
Ran into an issue with circular dependencies - handling it with a new workflow_service, and pulling computational logic out of the api_models - it was the right thing to do.
2020-04-15 11:13:32 -04:00
faf4c0df97
Updates BPMN and DMN files
2020-04-15 10:58:13 -04:00
aa17e30762
Updating libraries, modifying study_info script to save data in a consistent way, waiting on more fixes in spiffworkflow before continuing.
2020-04-13 16:23:31 -04:00
9a9922c473
Adds display order to Workflow Spec
2020-04-09 14:25:14 -04:00
316b9e6e8d
Fixing a stupid mistake - must have typed a ' mark during commit.
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Script should inherit from object.
Updating the ids so I could more easily test and assure things were working correctly.
2020-04-08 13:39:42 -04:00
c79415a794
throw a sensible error when study is not found on get_study (don't 500)
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some ugly fixes in the file_service for improving panda output from spreadsheet processing that I need to revist.
now that the spiff-workflow handles multi-instance, we can't have random multi-instance tasks around.
Improved tests around study deletion.
2020-04-08 13:28:43 -04:00
519a034d87
Updates last_updated when file data is saved. Returns last_updated as lastModified in response header for file data endpoint.
2020-04-08 12:58:55 -04:00
9bf5c9e727
Fixing an error that would prevent the correct counts from displaying if the record didn't come back from the protcol builder.
2020-04-07 14:14:43 -04:00
697127660f
Assure that all script tasks place data in a dictionary that is named exactly the same as the class - which is also the same as the Script tag.
2020-04-07 14:09:21 -04:00
c6b6ee5d70
Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required".
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Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 16:56:00 -04:00
d58a90a727
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-04-06 13:24:01 -04:00
e6550b7e39
Fixes Formly expression syntax error
2020-04-06 13:22:49 -04:00
419d619efa
Updates BPMN & DMN files with latest from staging
2020-04-06 13:12:34 -04:00
e283b86466
Fixing a bug with deleting a study.
2020-04-06 13:08:17 -04:00
a322801c91
Allow a study to be deleted, even if some statistics are laying around.
2020-04-03 16:41:16 -04:00
60a10bb688
Marshmallow isn't the right tool when dealing with large models with lots of null values. Rather than fight the process of mamaging the Study Details, I'm letting that fall through, and we can test on an individual value or maybe set up a constants array when that becomes meaningful.
2020-04-03 16:24:38 -04:00
fe40be752f
fixing a bug in the Protocol builder schema, more to fix there, and deserves a test, but this corrects the investigators
2020-04-03 13:52:12 -04:00
b39e4b382f
Catch more template processing errors.
2020-04-02 15:06:00 -04:00
785918cb7f
Be sure the validation process examines the data located in the documentation and correctly handles boolean fields.
2020-04-02 14:47:20 -04:00
534e8493a4
Deleting was broken because statistics were causing an integrity constraint.
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Updating IDS bpmn to the latest for testing.
Adding a TODO
2020-04-02 12:58:52 -04:00
17796193de
fixing a bug that was causing failing tests.
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Adding id and spec_version to the workflow metadata.
Refactoring the processing of the master_spec so that it doesn't polute the workflow database.
Adding tests to assure that the status and counts are updated on the workflow model as users make progress.
2020-03-30 14:01:57 -04:00
34b6ec92bf
updating the API
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Removing the call for study/workflows - as workflow information is returned with the study by default.
Fixing a bug in the workflow spec model schema.
2020-03-30 10:12:10 -04:00
4a916c1ee3
Created a "StudyService" and moved all complex logic around study manipulation out of the study api, and this service, as things were getting complicated. The Workflow Processor no longer creates the WorkflowModel, the study object handles that, and only passes the model into the workflow processor when it is ready to start the workflow.
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Created a Study object (seperate from the StudyModel) that can cronstructed on request, and contains a different data structure than we store in the DB. This allows us to return underlying Categories and Workflows in a clean way.
Added a new status to workflows called "not_started", meaning we have not yet instantiated a processor or created a BPMN, they have no version yet and no stored data, just the possiblity of being started.
The Top Level Workflow or "Master" workflow is now a part of the sample data, and loaded at all times.
Removed the ability to "add a workflow to a study" and "remove a workflow from a study", a study contains all possible workflows by definition.
Example data no longer creates users or studies, it just creates the specs.
2020-03-30 08:00:16 -04:00
c9900d787e
Every good deed goes punished.
2020-03-27 15:48:21 -04:00
6ebd4dce42
WIP: Adds default workflow spec categories
2020-03-27 15:32:07 -04:00
57f1fa670e
fixing a stupid mistake.
2020-03-27 14:55:53 -04:00
907e1cbbb3
minor fixes that were breaking when connecting to the front end.
2020-03-27 14:27:50 -04:00
b61a35f956
Merge remote-tracking branch 'origin/master' into feature/status_refactor
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Fixing adding a study so all workflows are again added, will add status on those workflows based on output from the master bpmn diagram, which is coming shortly.
2020-03-27 11:55:36 -04:00
c7d2c28178
Vastly more informative ApiError model that provides details on the underlying task where the error occured.
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Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data.
Minor fixes to existing bpmns to allow them to pass.
All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 08:29:31 -04:00
6c832829b0
Merge remote-tracking branch 'origin' into feature/status_refactor
2020-03-26 20:47:37 -04:00
f77ebe3177
Adds display order to categories
2020-03-26 15:29:52 -04:00
e2c408b70d
Removed all self-referential calls in the study_api. One api endpoint should never call another api endpoint. Moved the logic for updating a study to the study Model, rather than checking and setting dictionary values which will become very hard to maintain.
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The protocol builder service now returns real models, not dictionaries, forcing proper validation and fail-fast behavior.
Changed the name of the "status" spec, to "top_level_workflow" and removing any connection a workflow or study has with this specification. It is only unused to determine status in real time, and is not reused or tracked.
Modified the required documents script to return a dictionary and not an array, making it easier to speak to specific values in the BPMN and DMN.
Working on new ways to test the top_level_workflow in the context of updates, this is still a work in progress.
Making use of several modifications to the Spiff library that enables more complex expressions in DMN models. This is evident in the new DMN models for the top_level_workflow
2020-03-26 12:51:53 -04:00
dd5971bea9
Updates workflow specs for data loader
2020-03-25 11:13:52 -04:00
bd92c230e4
Fix the API so we are clear what is being returned when updating a file.
2020-03-25 08:06:58 -04:00
f4342fc785
It became impossible to use the Swagger ui when we started adding authentication to all of the calls. I discovered Connexion and Swagger have a default way of handing JTW authentication and this cleans up our code quite a bit, moves the securing of endpoints into the API Definition, which is quite nice, and removes a whole library dependency (I never get to do that!) I added a SWAGGER_AUTH_KEY that can be used in non-production environments to allow users to quickly authenticate from the Swagger ui. I also removed all api calls to simple little happy api services, because that is just mean and pointless.
2020-03-24 14:15:21 -04:00
0cd584880f
Fixing a bug where the workflow specification can not be deleted.
2020-03-23 12:48:31 -04:00
967ac65d0e
Just raise the ApiError, no need to marshal it.
2020-03-23 12:22:26 -04:00
b35427523d
Merge remote-tracking branch 'origin/master' into feature/reference_files
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# 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
16c6ba9661
Removing unneeded files.
2020-03-20 08:33:37 -04:00
3eb1167b8e
Found a few errors in the sqlalchemy file definition that was causing failures, and had some consistency problems with the IRB Categories file name. The API was bailing out because we had restricted file types to bpmn,svg,or dmn in the connexion config file, I don't restrict this anymore we have plenty of checks elsewhere. Adding xlrd as a dependency - this didn't fail till a push to production.
2020-03-20 08:21:21 -04:00
13a688048c
Fixing failed tests, setting unknown=EXCLUDE on the workflow spec model schema so that it can handle getting back the dump-only workflow_spec_category and just ignore it.
2020-03-20 07:54:01 -04:00
e529e149f6
Assure that reference file exists on data-reload.
2020-03-20 07:41:21 -04:00
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".
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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
dbe6701bb2
Removing the doc_types from the protocol builder, as these will eventually contradict what is coming from IRB and should not be used as an reference. Also fixing a failing test and assuring that only one reference file ever exists with a given name.
2020-03-19 10:40:07 -04:00
560b8a8782
Mergers details from the irb_documents.xlsx into the values returned from the Protocol Builder to create a more complete picture of required document details.
2020-03-19 10:23:50 -04:00
ac7c7b42c4
Revert "Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories"
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This reverts commit 9a26fc8e80
2020-03-18 17:05:13 -04:00
83d859fd3a
Just merging stuff real quick.
2020-03-18 17:03:36 -04:00
9a26fc8e80
Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories
2020-03-18 16:58:57 -04:00
f0678b43d4
Minor fixes
2020-03-18 16:58:50 -04:00
02be8ede75
Merge remote-tracking branch 'origin/master' into feature/reference_files
2020-03-18 15:16:34 -04:00
853b2b2502
Populates category
2020-03-18 15:16:15 -04:00
532d6b5dd6
Adds CRUD endpoints for workflow spec categories
2020-03-16 16:30:56 -04:00
4db456dcea
Adds workflow spec category methods
2020-03-16 16:12:39 -04:00
cbd8d2f46c
Silences SQLALCHEMY_TRACK_MODIFICATIONS warning
2020-03-16 13:47:17 -04:00
40e12f5ab5
Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning
2020-03-16 13:37:31 -04:00
7d31bc24eb
Attempting to address "FutureWarning: Implicit (flask) JSON serialization" warning
2020-03-16 13:24:15 -04:00
a98251237b
Adds workflow spec category to API
2020-03-16 12:10:32 -04:00
6af1693bdc
Fixes SonarCloud issue L23. Verifies that study ids match.
2020-03-16 10:37:06 -04:00
0cc98616fd
Merge branch 'master' into feature/workflow_spec_categories
2020-03-16 10:25:03 -04:00
3885bc7624
Merge remote-tracking branch 'origin/master' into feature/delete_study
2020-03-16 08:49:44 -04:00
cd6a70b747
Fixes code smell issues identified by SonarCloud
2020-03-16 08:31:19 -04:00
f9dbbefe89
Adds status spec to study when workflow is added.
2020-03-16 08:05:30 -04:00
bdd07685c6
Adds status spec when adding a study, and adds/removes workflows from study based on output data from status spec.
2020-03-15 15:54:13 -04:00
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
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
902dba7191
Adds is_status flag to workflow specs
2020-03-13 14:56:46 -04:00
05b39df745
Fixes #12 : Catching some specific common errors and re-raising as APIErrors with detailed codes and descriptions to improve debugging. In doing so, improving the error handling in the event a soft-reset causes an immediate error - and resetting to the original version of the specification in these events, to allow users the chance to try a hard reset instead.
2020-03-11 16:33:18 -04:00
f177e33ad6
Tiny tweak
2020-03-11 15:31:23 -04:00
3262833102
Requires login
2020-03-11 15:27:22 -04:00
e977ee9e0d
Updates task counts when getting workflow
2020-03-11 15:16:42 -04:00
bbfe9291e0
Adds endpoint to get workflow stats. Adds a test for the endpoint.
2020-03-11 14:28:53 -04:00
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
Carlos Lopez
Aaron Louie
Dan Funk
Kelly McDonald