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

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.

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.

Value

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

Details

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

Examples

if (FALSE) {
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)
}