Extract_BioChem_Data <- function(sql_file, data_source, username, password) {
# Function to extract data from a database (e.g. Biochem). The function reads a sql query, opens a
# connection to a database, extracts the data and returns the extracted data and the associated
# sql code.
#
# Input: sql_file : sql filename - string
# data_source : data source name for database - string
# username : username - string
# password: user password - string
#
# Output: data : list of two elements
# data[[1]] : sql code for the query - string
# data[[2]] : data extracted from the database - dataframe
#
# Last update: 20141015
# Benoit.Casault@dfo-mpo.gc.ca
# source custom functions
# source("Read_SQL.R")
# declare empty list to store outputs
data <- list()
# read sql file
data[[1]] <- Read_SQL(sql_file);
# open connection to BioChem
conn <- ROracle::dbConnect( DBI::dbDriver("Oracle"), dbname=data_source, username=username, password=password, believeNRows=F)
# get data from BioChem
data[[2]] <- ROracle::dbGetQuery(conn, data[[1]], nullstring="")
# close BioChem connection
ROracle::dbDisconnect(conn)
# clear variables
rm(conn)
return(data)
}
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