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cr-connect-workflow
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19 Commits

Author SHA1 Message Date
mike cullerton 22b3230243 Added service `get_irb_info` to `crc.services.protocol_builder.ProtocolBuilderService` 
Added environment variable `PB_IRB_INFO_URL` for new `get_irb_info` service
 2021-05-01 15:20:47 -04:00
Kelly McDonald 2931f45187 Add 'sponsors' to study_info call 2020-11-04 14:34:10 -05:00
Dan Funk 5be35e8bab Adding a study sponsors script to return details about study sponsors 2020-08-25 10:30:46 -04:00
Aaron Louie c25536dcca Makes Sonar happy. 2020-08-04 16:42:35 -04:00
Dan Funk 92580ee867 adding an additional error check for invalid json returned from the Protocol builder. 2020-06-15 12:26:53 -04:00
Dan Funk e102214809 minor cleanup of error codes. 2020-06-03 15:03:22 -04:00
Dan Funk d5e075db82 Order search results by relevancy in the lookup service. 2020-05-27 09:47:44 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk 6cd4ef64d1 Fixing add_study api endpoint, so you can actually add a new "Study" with just some basic information. 
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
Dan Funk 503c1c8f18 Allow disabling the Protocol Builder 
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
Dan Funk 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. 
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
Dan Funk 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
Dan Funk c9900d787e Every good deed goes punished. 2020-03-27 15:48:21 -04:00
Dan Funk 7194d7d374 Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory. 
Adding a new script that script tasks can use to add in data about the study.

Moving all the test workflow specifications out of the main load.

fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
 2020-03-03 13:52:45 -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 27d7afb656 Adds Protocol Builder models and schemas. Reorganizes and cleans up some files. 2020-02-27 09:54:46 -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
Dan Funk 2cc6010c8d Protocol builder connections 2020-02-20 13:30:04 -05:00