README.md

In OHDSI/ROhdsiWebApi: Interacting With an OHDSI WebApi Instance

ROhdsiWebApi

ROhdsiWebApi is part of HADES.

Introduction

ROhdsiWebApi is a R based interface to ‘WebApi’ (OHDSI RESTful services), and performs GET/PULL/POST/DELETE calls via the WebApi. All objects starting from R or output to R - are analysis ready R-objects like list and data.frame. The package handles the intermediary steps by converting R-objects to JSON and vice versa. To ensure r-objects are analysis ready, the objects are type converted where possible, e.g. date/date time are converted from string to POSIXct.

This package makes reproducible research easier, by offering ability to retrieve detailed study specifications, transport study specifications from one instance to another, programmatically invoke the generation of a sequence of steps that are part of a study, manage running studies in batch mode.

An example of a WebApi endpoint is “http://server.org:80/WebAPI”.

Generic design pattern:

• Functions that go from WebApi to R: will return a R-object (e.g. list, data frame). The function will handle the conversion of non R-objects like JSON objects into R-objects in the background. The returned objects may be inspected in R. We have ensured that all returned objects are represented in the proper data types e.g. dates in are type date, instead of string, use of integer where appropriate etc.

• Functions that go from R into WebApi: will start with a R-object (e.g. list, data frame). If the WebApi requires a JSON object, the function will handle the conversion of R-object into JSON in the background.

The package follows a consistent naming conventions - with the identifier for the functional category clearly in the name. There are no direct reference to ‘Atlas’, and instead ‘WebApi’ is used = because the package is designed to interface directly with WebApi.

Supported WebApi functional categories.

| Category | Features | | :--------------- | :-------------------------------------------------------- | | ConceptSet | Functions for interfacing with ConceptSet in WebApi | | Cohort | Functions for interfacing with Cohort in WebApi | | IncidenceRate | Functions for interfacing with IncidenceRate in WebApi | | Estimation | Functions for interfacing with Estimation in WebApi | | Prediction | Functions for interfacing with Prediction in WebApi | | Characterization | Functions for interfacing with Characterization in WebApi | | Pathway | Functions for interfacing with Pathway in WebApi |

Technology

ROhdsiWebApi is an R package. Note: ROhdsiWebApi relies on the availability of a WebApi. The documentation of the WebApi (OHDSI RESTful services).

Note: As of V1.0.0, we do not support WebApi that has security enabled. This is considered a road map item.

System Requirements

Requires R. WebApi.

Installation

• In R, use the following commands to download and install ROhdsiWebApi:

remotes::install_github("OHDSI/ROhdsiWebApi")

User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available:

• Vignette

• Package manual

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here how you can contribute to this package.

License

ROhdsiWebApi is licensed under Apache License 2.0

Development

ROhdsiWebApi is being developed in R Studio.

OHDSI/ROhdsiWebApi documentation built on March 15, 2023, 1:23 p.m.