Upload results to the database server.

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

uploadResults(
  connectionDetails,
  schema,
  zipFileName,
  forceOverWriteOfSpecifications = FALSE,
  purgeSiteDataBeforeUploading = TRUE,
  tempFolder = tempdir(),
  tablePrefix = "",
  ...
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.

schema

The schema on the postgres server where the tables have been created.

zipFileName

The name of the zip file.

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.

tempFolder

A 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.

tablePrefix

(Optional) string to insert before table names (e.g. "cd_") for database table names

...

See ResultModelManager::uploadResults