extras/ExampleOfHowToCreateStudyPackageWithHydra.R

In OHDSI/CohortDiagnostics: Diagnostics for OHDSI Cohorts

# please ensure you have the latest version of Hydra. As of 08/13/2021 - CohortDiagnostics support for Hydra is still in develop branch.
# please check hydra release notes and update hydra
remotes::install_github("OHDSI/Hydra", ref = "develop")
outputFolder <- "d:/temp/output"  # location where you study package will be created


########## Please populate the information below #####################
version <- "v0.1.0"
name <- "Thrombosis With Thrombocytopenia Syndrome cohorts - an OHDSI network study"
packageName <- "ThrombosisWithThrombocytopeniaSyndrome"
skeletonVersion <- "v0.0.1"
createdBy <- "rao@ohdsi.org"
createdDate <- Sys.Date() # default
modifiedBy <- "rao@ohdsi.org"
modifiedDate <- Sys.Date()
skeletonType <- "CohortDiagnosticsStudy"
organizationName <- "OHDSI"
description <- "Cohort diagnostics on Thrombosis With Thrombocytopenia Syndrome cohorts."


library(magrittr)
# Set up
baseUrl <- Sys.getenv("baseUrl")
# if you have security enabled, please authorize the use - example below
# ROhdsiWebApi::authorizeWebApi(baseUrl, 'windows')
cohortIds <- c(22040,
               22042,
               22041,
               22039,
               22038,
               22037,
               22036,
               22035,
               22034,
               22033,
               22031,
               22032,
               22030,
               22028,
               22029)



################# end of user input ##############
webApiCohorts <- ROhdsiWebApi::getCohortDefinitionsMetaData(baseUrl = baseUrl)
studyCohorts <-  webApiCohorts %>%
        dplyr::filter(id %in% cohortIds)

# compile them into a data table
cohortDefinitionsArray <- list()
for (i in (1:nrow(studyCohorts))) {
        cohortDefinition <-
                ROhdsiWebApi::getCohortDefinition(cohortId = studyCohorts$id[[i]],
                                                  baseUrl = baseUrl)
        cohortDefinitionsArray[[i]] <- list(
                id = studyCohorts$id[[i]],
                createdDate = studyCohorts$createdDate[[i]],
                modifiedDate = studyCohorts$createdDate[[i]],
                logicDescription = studyCohorts$description[[i]],
                name = stringr::str_trim(stringr::str_squish(cohortDefinition$name)),
                expression = cohortDefinition$expression
        )
}

tempFolder <- tempdir()
unlink(x = tempFolder, recursive = TRUE, force = TRUE)
dir.create(path = tempFolder, showWarnings = FALSE, recursive = TRUE)

specifications <- list(id = 1,
                       version = version,
                       name = name,
                       packageName = packageName,
                       skeletonVersion = skeletonVersion,
                       createdBy = createdBy,
                       createdDate = createdDate,
                       modifiedBy = modifiedBy,
                       modifiedDate = modifiedDate,
                       skeletonType = skeletonType,
                       organizationName = organizationName,
                       description = description,
                       cohortDefinitions = cohortDefinitionsArray)

jsonFileName <- paste0(file.path(tempFolder, "CohortDiagnosticsSpecs.json"))
write(x = specifications %>% RJSONIO::toJSON(pretty = TRUE, digits = 23), file = jsonFileName)


##############################################################
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#######       Get skeleton from github            ############
#######       Uncomment if you want to use latest ############
#######       skeleton only - for advanced user   ############
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#### get the skeleton from github
# download.file(url = "https://github.com/OHDSI/SkeletonCohortDiagnosticsStudy/archive/refs/heads/main.zip",
#                          destfile = file.path(tempFolder, 'skeleton.zip'))
# unzip(zipfile =  file.path(tempFolder, 'skeleton.zip'), 
#       overwrite = TRUE,
#       exdir = file.path(tempFolder, "skeleton")
#         )
# fileList <- list.files(path = file.path(tempFolder, "skeleton"), full.names = TRUE, recursive = TRUE, all.files = TRUE)
# DatabaseConnector::createZipFile(zipFile = file.path(tempFolder, 'skeleton.zip'), 
#                                  files = fileList, 
#                                  rootFolder = list.dirs(file.path(tempFolder, 'skeleton'), recursive = FALSE))

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#######               Build package              #############
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#### Code that uses the ExampleCohortDiagnosticsSpecs in Hydra to build package
hydraSpecificationFromFile <- Hydra::loadSpecifications(fileName = jsonFileName)
unlink(x = outputFolder, recursive = TRUE)
dir.create(path = outputFolder, showWarnings = FALSE, recursive = TRUE)
Hydra::hydrate(specifications = hydraSpecificationFromFile,
               outputFolder = outputFolder
)

# for advanced user using skeletons outside of Hydra
# Hydra::hydrate(specifications = hydraSpecificationFromFile,
#                outputFolder = outputFolder, 
#                skeletonFileName = file.path(tempFolder, 'skeleton.zip')
# )


unlink(x = tempFolder, recursive = TRUE, force = TRUE)


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######       Build, install and execute package           #############
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