run_setup: Instantiate Postgres

In meerapatelmd/setupMetathesaurus: Setup UMLS Metathesaurus

Instantiate Postgres

Description

Instantiate Postgres

Usage

run_setup(
  conn,
  conn_fun = "pg13::local_connect()",
  schema = "umls",
  path_to_rrfs,
  steps = c("reset_schema", "ddl_tables", "copy_rrfs", "add_indexes", "log",
    "setup_crosswalk"),
  postprocess = TRUE,
  mrconso_only = "DEPRECATED",
  omop_only = "DEPRECATED",
  english_only = TRUE,
  log_schema = "public",
  log_table_name = "setup_umls_log",
  log_version,
  log_release_date,
  verbose = TRUE,
  render_sql = TRUE,
  render_only = FALSE
)

Arguments

conn	Database connection via DatabaseConnector.
conn_fun	Instead of supplying of a direct database connection, an expression can be supplied that automatically connects and disconnects the connection once the function is run.
schema	For Postgres executions only, the schema to write all the tables to, Default: 'umls'
mrconso_only	Setup only the MRCONSO Table? Default: FALSE
omop_only	Setup the MRCONSO, MRHIER, MRMAP, MRSMAP, MRSAT, AND MRREL Tables only? Default: FALSE
english_only	Setup only the ENG Tables? Default: TRUE

meerapatelmd/setupMetathesaurus documentation built on May 25, 2022, 6:19 a.m.