run_setup: Run Athena Setup

In patelm9/setupAthena: Setup or Update a Postgres Instance of the Athena Vocabularies

Run Athena Setup

Description

Stepwise process of instantiating the Athena Vocabularies. Steps can be skipped using the steps argument though the order cannot be changed.

Usage

run_setup(
  conn,
  conn_fun = "pg13::local_connect()",
  target_schema = "omop_athena",
  steps = c("drop_tables", "copy", "log", "indices", "constraints"),
  postprocessing = c("omop_atc_classification"),
  path_to_csvs,
  release_version,
  umls_api_key = Sys.getenv("UMLS_API_KEY"),
  verbose = TRUE,
  render_sql = TRUE,
  render_only = FALSE,
  checks = ""
)

Arguments

conn	A Postgres connection object from the DatabaseConnector package. The user must either be a superuser or a member of the pg_read_server_files role.
conn_fun	Character string of the expression used to connect to the target database for the setup. The user must either be a superuser or a member of the pg_read_server_files role.This option automatically closes the connection on exit.
target_schema	Schema where the OMOP Vocabulary Tables will be written to.
steps	Options include c("prepare_cpt4", "drop_tables","copy", "indices", "constraints", "log"). Each step corresponds to the function used and may be independently executed.
path_to_csvs	Path to folder containing the unpacked vocabularies as csv files, downloaded as a zip from athena.ohdsi.org.
release_version	Release version as an exact string provided vocabulary download link delivery via email.
umls_api_key	UMLS API Key for CPT4 reconstitution.
verbose	If TRUE, prints back activity in the R console as it is occurring.
render_sql	If TRUE, the SQL statement is printed back in the R console for reference.

Value

Updated OMOP Vocabulary (Athena) CONCEPT_ANCESTOR, C ONCEPT_CLASS, CONCEPT_RELATIONSHIP, CONCEPT_SYNONYM, CONCEPT, DOMAIN, DRUG_STRENGTH, RELATIONSHIP, and VOCABULARY Tables in the given target schema.

patelm9/setupAthena documentation built on June 11, 2024, 4:23 a.m.