library(DatabaseConnector)
library(SqlRender)
library(tidyverse)
library(FeatureExtraction)
library(hivTestStudy)
# set your db, server, port, user and password,
readRenviron('./.env')
# since connectionDetail doesn't accept more than one schema param
# or other params we need later, store those in 'connp'
# 'connectionDetails' will only be used for creating connections, not
# for referencing connection-related parameters as has been the convention
# in other DatabaseConnector-based studies
connp <- list(dbms = "postgresql",
server = paste0(Sys.getenv("PGHOST"),'/',
Sys.getenv('PGDATABASE')),
port = coalesce(na_if(Sys.getenv("PGPORT"), ""), "5432"),
user = Sys.getenv('PGUSER'),
password = Sys.getenv('PGPASSWORD'),
schema = Sys.getenv('CDM_SCHEMA'),
results_schema = Sys.getenv('RESULTS_SCHEMA')
)
# for params related to this study and package but not to the db connection,
# use another config variable: studyp:
studyp <- list(
tablePrefix <- "hivTestStudy_",
outputFolder <- getwd(), # Sys.getenv('OUTPUT_FOLDER') # /tmp/study_results
packageName <- "hivTestStudy"
)
connectionDetails <- do.call(
createConnectionDetails,
connp[c("dbms","server","port","user","password","schema")])
conn <- connect(connectionDetails)
hivTestStudy::init(connectionDetails = connectionDetails,
targetDatabaseSchema = connp$results_schema,
tablePrefix = studyp$tablePrefix)
# use as example now: https://github.com/OHDSI/StudyProtocols/tree/master/KeppraAngioedema
hivTestStudy::execute(connectionDetails = connectionDetails, outputFolder = outputFolder,
connp$results_schema, tablePrefix)
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