Upload results to the database server.

Requires the results data model tables have been created using following the specifications, generateSqlSchema function.

Results files should be in the snake_case format for table headers and not camelCase

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

uploadResults(
  connection = NULL,
  connectionDetails = NULL,
  schema,
  resultsFolder,
  tablePrefix = "",
  forceOverWriteOfSpecifications = FALSE,
  purgeSiteDataBeforeUploading = TRUE,
  databaseIdentifierFile = "cdm_source_info.csv",
  runCheckAndFixCommands = FALSE,
  warnOnMissingTable = TRUE,
  purgeDataModel = FALSE,
  specifications
)

Arguments

connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.

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.

resultsFolder

The path to the folder containing the results to upload. See unzipResults for more information.

tablePrefix

String to prefix table names with - default is empty string

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 results folder contains the full data for that data site.

databaseIdentifierFile

File contained that references databaseId field (used when purgeSiteDataBeforeUploading == TRUE). You may specify a relative path for the cdmSourceFile and the function will assume it resides in the resultsFolder. Alternatively, you can provide a path outside of the resultsFolder for this file.

runCheckAndFixCommands

If TRUE, the upload code will attempt to fix column names, data types and duplicate rows. This parameter is kept for legacy reasons - it is strongly recommended that you correct errors in your results where those results are assembled instead of relying on this option to try and fix it during upload.

warnOnMissingTable

Boolean, print a warning if a table file is missing.

purgeDataModel

This function will purge all data from the tables in the specification prior to upload. Use with care. If interactive this will require further input.

specifications

A tibble data frame object with specifications.