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Automating protocol writing (generated cohort description into appendix document)

(Vojtech Huser) #1

Atlas provides Graphical View and Text View of the cohort. Is this functionality driven by an webAPI call ?

I would like to develop R code that calls the API with call something like
getTextViewForCohortID(1770614) and will get me text I can render using pander into .docx file (as appendix to a study protocol) (for skeleton study)

E.g., for 10 definitions, it would save me clicking 10 times copy to clipboard and grabing the text. (same for graphical view)

Is this possible? (mainly for the web experts out there) @Chris_Knoll ?
(picture is from this url http://atlas-demo.ohdsi.org/#/cohortdefinition/100792

(Chris Knoll) #2

The UI is a distinct component from the WebAPI call. Meaning: the WebAPI provides the services of saving/loading/querying and security fuctions, but the rendering and display is handled by code in atlas. It is feasible to provide a word/markdown export capability directly in WebAPI, but the reason it exists as a capability found in Atlas was just a matter of simpler implementation. An issue is already open to provide a markdown export here: https://github.com/OHDSI/Atlas/issues/1181. This is probably something that should be baked directly in to WebAPI so it can be used independently of Atlas (like you describe as accessed directly from R).

It just would take someone from the community to step up and deliver the feature.

(Vojtech Huser) #3

Thank you for reply. Our current solution is a work around https://github.com/vojtechhuser/SkeletonDescriptiveStudy/blob/master/extras/PackageMaintenance.R#L63

(appendix with links to Atlas) (see the htm file in the same folder as protocol) (the actual links are butchered by github html preview)