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Update Tutorial authored by alabarga's avatar alabarga
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Tutorial.md
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......@@ -53,6 +53,8 @@ library(ETLSyntheaBuilder)
# Download drivers
DatabaseConnector::downloadJdbcDrivers('postgresql', '.')
# Connect to your database
cd <- DatabaseConnector::createConnectionDetails(
dbms = "postgresql",
server = "localhost/demo_omop",
......@@ -62,6 +64,8 @@ cd <- DatabaseConnector::createConnectionDetails(
pathToDriver = "./"
)
# OMOP-CDM Database configuration
cdmSchema <- "cdm"
cdmVersion <- "5.4"
syntheaVersion <- "2.7.0"
......@@ -69,13 +73,21 @@ syntheaSchema <- "native"
syntheaFileLoc <- "./csv"
vocabFileLoc <- "./vocabulary_download_v5_minimal"
# Create OMOP-CDM tables
ETLSyntheaBuilder::CreateCDMTables(connectionDetails = cd, cdmSchema = cdmSchema, cdmVersion = cdmVersion)
# Load OMOP vocabularies
ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc)
# Load Synthea data
ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion)
ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaFileLoc = syntheaFileLoc)
ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc)
# Execute ETL
ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)
......