Use ResearchStudy id from context in AdverseEvent search #101
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
jafeltra
requested review from
Dtphelan1,
dmendelowitz,
julianxcarter and
mgramigna
as code owners
jafeltra
force-pushed
the
adverse-event-uses-study-context
branch
from
fafd5c5 to
80eec9c
Compare
dmendelowitz
approved these changes
Apr 5, 2021
Contributor
dmendelowitz
left a comment
dmendelowitz
left a comment
There was a problem hiding this comment.
This looks good to me and worked when tested from the E-MEF
jafeltra
force-pushed
the
adverse-event-uses-study-context
branch
from
80eec9c to
db5d986
Compare
julianxcarter
approved these changes
Apr 5, 2021
Contributor
julianxcarter
left a comment
julianxcarter
left a comment
There was a problem hiding this comment.
This looks good to me!
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
This PR uses context to find any ResearchStudy ids to be included in the FHIR Adverse Event search.
New behavior
The
FHIRAdverseEventExtractornow looks in context for anyResearchStudyresources. If it finds research study resources, it includes the study ids from all research studies in thethis.studylist of studies to be used when searching for AdverseEvents. If no research study resources are found, the AdverseEvent extractor still proceeds trying to search for AdverseEvents, but does not add any studies beyond the ones that were set in the constructor.It also adds a new context util function for ResearchStudy resources.
Code changes
This includes the new context util function and associated test. It also updates the (string) list of studies that is added in
parametrizeArgsForFHIRModulein theFHIRAdverseEventExtractor. Searching for AdverseEvents using thestudyquery parameter supports searching for multiple study ids in a comma separated list, likestudy=study1,study2.Testing guidance
Ensure that the tests cover the expected behavior. The actual extractor can't really be tested in this repo.