extras/CodeToRun.R

In EHDEN/CdmInspection: R Package to support quality control inspection of an OMOP-CDM instance

# *******************************************************
# -----------------INSTRUCTIONS -------------------------
# *******************************************************
#
#-----------------------------------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------
# This CodeToRun.R is provided as an example of how to run this package.
# Below you will find 2 sections: the 1st is for installing the dependencies
# required to run the package and the 2nd for running the package.
#
# The code below makes use of R environment variables (denoted by "Sys.getenv(<setting>)") to
# allow for protection of sensitive information. If you'd like to use R environment variables stored
# in an external file, this can be done by creating an .Renviron file in the root of the folder
# where you have cloned this code. For more information on setting environment variables please refer to:
# https://stat.ethz.ch/R-manual/R-devel/library/base/html/readRenviron.html
#
# Below is an example .Renviron file's contents.
# Remove the "#" below as these too are interpreted as comments in the .Renviron file.
#
#    DBMS = "postgresql"
#    DB_SERVER = "database.server.com"
#    DB_PORT = 5432
#    DB_USER = "database_user_name_goes_here"
#    DB_PASSWORD = "your_secret_password"
#    PATH_TO_DRIVER = "C:/path_to_jdbc_driver"
#
# The following describes the settings
#    DBMS, DB_SERVER, DB_PORT, DB_USER, DB_PASSWORD := These are the details used to connect
#    to your database server. For more information on how these are set, please refer to:
#    http://ohdsi.github.io/DatabaseConnector/
#
# Once you have established an .Renviron file, you must restart your R session for R to pick up these new
# variables.
#
# In section 2 below, you will also need to update the code to use your site specific values. Please scroll
# down for specific instructions.
#-----------------------------------------------------------------------------------------------
#
#
# *******************************************************
# SECTION 1: Make sure to install all dependencies (not needed if already done) -------------------------------
# *******************************************************
#
# Prevents errors due to packages being built for other R versions:
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = TRUE)
#
# First, it probably is best to make sure you are up-to-date on all existing packages.
# Important: This code is best run in R, not RStudio, as RStudio may have some libraries
# (like 'rlang') in use.
#update.packages(ask = "graphics")

# When asked to update packages, select '1' ('update all') (could be multiple times)
# When asked whether to install from source, select 'No' (could be multiple times)
#install.packages("devtools")
#devtools::install_github("EHDEN/CdmInspection.R")

# *******************************************************
# SECTION 2: Set Local Details
# *******************************************************
library(CdmInspection)

# Details for connecting to the server:
dbms <- Sys.getenv("DBMS")
user <- Sys.getenv("DB_USER")
password <- Sys.getenv("DB_PASSWORD")
server <- Sys.getenv("DB_SERVER")
port <- Sys.getenv("DB_PORT")
pathToDriver <- Sys.getenv("PATH_TO_DRIVER")
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = dbms,
  server = server,
  port = port,
  user = user,
  password = password,
  pathToDriver = pathToDriver
)

# Details specific to the database:
cdmDatabaseSchema <- Sys.getenv("CDM_SCHEMA")
resultsDatabaseSchema <- Sys.getenv("RESULTS_SCHEMA")
vocabDatabaseSchema <- cdmDatabaseSchema

# Database metadata
databaseId <- "MyDatabaseId"
authors <- '<author_1>,<author_2>' # used on the title page
databaseName <- "MyDatabaseName"
databaseDescription <- "Lorem Ipsum Loriat"

# For Oracle: define a schema that can be used to emulate temp tables:
oracleTempSchema <- NULL

# Details for connecting to the CDM and storing the results
outputFolder <- file.path(getwd(), "results", databaseId)


# Url to check the version of your local Atlas
baseUrl <- "<your_baseUrl>" # example: "http://atlas.your.organisation.com/WebAPI"

# All results smaller than this value are removed from the results.
smallCellCount <- 5

verboseMode <- TRUE

# *******************************************************
# SECTION 3: Run the package
# *******************************************************
results <- cdmInspection(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = cdmDatabaseSchema,
  resultsDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = vocabDatabaseSchema,
  oracleTempSchema = oracleTempSchema,
  databaseId = databaseId,
  databaseName = databaseName,
  databaseDescription = databaseDescription,
  runVocabularyChecks = TRUE,
  runDataTablesChecks = TRUE,
  runPerformanceChecks = TRUE,
  runWebAPIChecks = TRUE,
  smallCellCount = smallCellCount,
  baseUrl = baseUrl,
  sqlOnly = FALSE,
  outputFolder = outputFolder,
  verboseMode = verboseMode
)

generateResultsDocument(
  results,
  outputFolder,
  authors = authors,
  databaseId = databaseId,
  databaseName = databaseName,
  databaseDescription = databaseDescription,
  smallCellCount = smallCellCount
)