renderTranslateQueryApplyBatched: Render, translate, and perform process to batches of data.

In DatabaseConnector: Connecting to Various Database Platforms

Render, translate, and perform process to batches of data.

Description

This function renders, and translates SQL, sends it to the server, processes the data in batches with a call back function. Note that this function should perform a row-wise operation. This is designed to work with massive data that won't fit in to memory.

The batch sizes are determined by the java virtual machine and will depend on the data.

Usage

renderTranslateQueryApplyBatched(
  connection,
  sql,
  fun,
  args = list(),
  errorReportFile = file.path(getwd(), "errorReportSql.txt"),
  snakeCaseToCamelCase = FALSE,
  oracleTempSchema = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  integerAsNumeric = getOption("databaseConnectorIntegerAsNumeric", default = TRUE),
  integer64AsNumeric = getOption("databaseConnectorInteger64AsNumeric", default = TRUE),
  ...
)

Arguments

connection	The connection to the database server created using either connect() or dbConnect().
sql	The SQL to be send.
fun	Function to apply to batch. Must take data.frame and integer position as parameters.
args	List of arguments to be passed to function call.
errorReportFile	The file where an error report will be written if an error occurs. Defaults to 'errorReportSql.txt' in the current working directory.
snakeCaseToCamelCase	If true, field names are assumed to use snake_case, and are converted to camelCase.
oracleTempSchema	DEPRECATED: use tempEmulationSchema instead.
tempEmulationSchema	Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
integerAsNumeric	Logical: should 32-bit integers be converted to numeric (double) values? If FALSE 32-bit integers will be represented using R's native Integer class.
integer64AsNumeric	Logical: should 64-bit integers be converted to numeric (double) values? If FALSE 64-bit integers will be represented using bit64::integer64.
...	Parameters that will be used to render the SQL.

Details

This function calls the render and translate functions in the SqlRender package before calling querySql().

Value

Invisibly returns a list of outputs from each call to the provided function.

Examples

## Not run: 
connectionDetails <- createConnectionDetails(
  dbms = "postgresql",
  server = "localhost",
  user = "root",
  password = "blah",
  schema = "cdm_v4"
)
connection <- connect(connectionDetails)

# First example: write data to a large CSV file:
filepath <- "myBigFile.csv"
writeBatchesToCsv <- function(data, position, ...) {
  write.csv(data, filepath, append = position != 1)
  return(NULL)
}
renderTranslateQueryApplyBatched(connection,
  "SELECT * FROM @schema.person;",
  schema = "cdm_synpuf",
  fun = writeBatchesToCsv
)

# Second example: write data to Andromeda
# (Alternative to querySqlToAndromeda if some local computation needs to be applied)
bigResults <- Andromeda::andromeda()
writeBatchesToAndromeda <- function(data, position, ...) {
  data$p <- EmpiricalCalibration::computeTraditionalP(data$logRr, data$logSeRr)
  if (position == 1) {
    bigResults$rrs <- data
  } else {
    Andromeda::appendToTable(bigResults$rrs, data)
  }
  return(NULL)
}
sql <- "SELECT target_id, comparator_id, log_rr, log_se_rr FROM @schema.my_results;"
renderTranslateQueryApplyBatched(connection,
  sql,
  fun = writeBatchesToAndromeda,
  schema = "my_results",
  snakeCaseToCamelCase = TRUE
)

disconnect(connection)

## End(Not run)

DatabaseConnector documentation built on May 29, 2024, 6:14 a.m.