uploadResultsToDatabase: Upload results to the database server.

In ohdsi-studies/LegendT2dm: Large-Scale Evidence Generation and Evaluation in a Network of Databases

Upload results to the database server.

Description

Requires the results data model tables have been created using the createResultsDataModel function.

Set the POSTGRES_PATH environmental variable to the path to the folder containing the psql executable to enable bulk upload (recommended).

Usage

uploadResultsToDatabase(
  connectionDetails,
  schema,
  zipFileName,
  specifications,
  forceOverWriteOfSpecifications = FALSE,
  purgeSiteDataBeforeUploading = FALSE,
  convertFromCamelCase = FALSE,
  replaceInfinities = NULL,
  tempFolder = tempdir()
)

Arguments

connectionDetails	Object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
schema	Schema on the postgres server where the tables have been created.
zipFileName	Name of single or vector of multiple zip files.
specifications	Specification of results tables
forceOverWriteOfSpecifications	If TRUE, specifications of the phenotypes, cohort definitions, and analysis will be overwritten if they already exist on the database. Only use this if these specifications have changed since the last upload.
purgeSiteDataBeforeUploading	If TRUE, before inserting data for a specific databaseId all the data for that site will be dropped. This assumes the input zip file contains the full data for that data site.
convertFromCamelCase	Convert column names from camelCase to snake_case when uploading?
replaceInfinities	Value to which to change infinities, NULL does not change .
tempFolder	Folder on the local file system where the zip files are extracted to. Will be cleaned up when the function is finished. Can be used to specify a temp folder on a drive that has sufficient space if the default system temp space is too limited.

ohdsi-studies/LegendT2dm documentation built on July 4, 2025, 8:25 p.m.