Follow the steps on the synthea wiki to run the program and generate the files. This builder works off of the csv files, not the fhir files. To do this the
exporter.csv.export option in the
./src/main/resources/synthea.properties file needs to be set to TRUE.
devtools::install_github("OHDSI/ETL-Synthea") library(ETLSyntheaBuilder) # We are loading a version 5.4 CDM into a local PostgreSQL database called "synthea10". # The ETLSyntheaBuilder package leverages the OHDSI/CommonDataModel package for CDM creation. # Valid CDM versions are determined by executing CommonDataModel::listSupportedVersions(). # The strings representing supported CDM versions are currently "5.3" and "5.4". # The Synthea version we use in this example is 2.7.0. Since Synthea's MASTER branch is always active, we currently # only support version 2.7.0. # The schema to load the Synthea tables is called "native". # The schema to load the Vocabulary and CDM tables is "cdm_synthea10". # The username and pw are "postgres" and "lollipop". # The Synthea and Vocabulary CSV files are located in /tmp/synthea/output/csv and /tmp/Vocabulary_20181119, respectively. # For those interested in seeing the CDM changes from 5.3 to 5.4, please see: http://ohdsi.github.io/CommonDataModel/cdm54Changes.html cd <- DatabaseConnector::createConnectionDetails( dbms = "postgresql", server = "localhost/synthea10", user = "postgres", password = "lollipop", port = 5432, pathToDriver = "d:/drivers" ) cdmSchema <- "cdm_synthea10" cdmVersion <- "5.4" syntheaVersion <- "2.7.0" syntheaSchema <- "native" syntheaFileLoc <- "/tmp/synthea/output/csv" vocabFileLoc <- "/tmp/Vocabulary_20181119" ETLSyntheaBuilder::CreateCDMTables(connectionDetails = cd, cdmSchema = cdmSchema, cdmVersion = cdmVersion) ETLSyntheaBuilder::CreateSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaVersion = syntheaVersion) ETLSyntheaBuilder::LoadSyntheaTables(connectionDetails = cd, syntheaSchema = syntheaSchema, syntheaFileLoc = syntheaFileLoc) ETLSyntheaBuilder::LoadVocabFromCsv(connectionDetails = cd, cdmSchema = cdmSchema, vocabFileLoc = vocabFileLoc) ETLSyntheaBuilder::LoadEventTables(connectionDetails = cd, cdmSchema = cdmSchema, syntheaSchema = syntheaSchema, cdmVersion = cdmVersion, syntheaVersion = syntheaVersion)