R/PostgreSQLSupport.R

Defines functions postgresqlTableRef postgresqlQuoteId postgresqlDataType postgresqlBuildTableDefinition postgresqlWriteTable postgresqlImportFile postgresqlReadTable postgresqlCloseResult postgresqlDescribeResult postgresqlResultInfo postgresqlFetch postgresqlDBApply postgresqlDescribeFields postgresqlQuickSQL postgresqlgetResult postgresqlCopyInDataframe postgresqlCopyIn postgresqlpqExecParams postgresqlpqExec postgresqlUnescapeBytea postgresqlEscapeBytea postgresqlEscapeStrings postgresqlExecStatement postgresqlTransactionStatement postgresqlConnectionInfo postgresqlCloseConnection postgresqlDescribeConnection postgresqlCloneConnection postgresqlNewConnection postgresqlDriverInfo postgresqlDescribeDriver postgresqlCloseDriver postgresqlInitDriver

Documented in postgresqlBuildTableDefinition postgresqlCloneConnection postgresqlCloseConnection postgresqlCloseDriver postgresqlCloseResult postgresqlConnectionInfo postgresqlCopyIn postgresqlCopyInDataframe postgresqlDataType postgresqlDBApply postgresqlDescribeConnection postgresqlDescribeDriver postgresqlDescribeFields postgresqlDescribeResult postgresqlDriverInfo postgresqlEscapeBytea postgresqlEscapeStrings postgresqlExecStatement postgresqlFetch postgresqlgetResult postgresqlImportFile postgresqlInitDriver postgresqlNewConnection postgresqlpqExec postgresqlQuickSQL postgresqlQuoteId postgresqlReadTable postgresqlResultInfo postgresqlTableRef postgresqlTransactionStatement postgresqlUnescapeBytea postgresqlWriteTable

## PostgreSQLSupport.R
## $Id$

## This package was developed as a part of Summer of Code program organized by Google.
## Thanks to David A. James & Saikat DebRoy, the authors of RMySQL package.
## Code from RMySQL package was reused with the permission from the authors.
## Also Thanks to my GSoC mentor Dirk Eddelbuettel for helping me in the development.

## create a PostgreSQL database connection manager.  By default we allow
## up to "max.con" connections and single fetches of up to "fetch.default.rec"
## records.  These settings may be changed by re-loading the driver
## using the "force.reload" = T flag (note that this will close all
## currently open connections).
## Returns an object of class "PostgreSQLManger".
## Note: This class is a singleton.
postgresqlInitDriver <- function(max.con=16, fetch.default.rec = 500, force.reload=FALSE) {
   if(fetch.default.rec<=0)
       stop("default num of records per fetch must be positive")
   config.params <- as.integer(c(max.con, fetch.default.rec))
   force <- as.logical(force.reload)
   drvId <- .Call(RS_PostgreSQL_init, config.params, force)
   new("PostgreSQLDriver", Id = drvId)
}

postgresqlCloseDriver <- function(drv, ...) {
   if(!isPostgresqlIdCurrent(drv))
      return(TRUE)
   drvId <- as(drv, "integer")
   .Call(RS_PostgreSQL_closeManager, drvId)
}


## Print out nicely a brief description of the connection Driver
postgresqlDescribeDriver <- function(obj, verbose = FALSE, ...) {
   info <- dbGetInfo(obj)
   print(obj)
   cat("  Driver name: ", info$drvName, "\n")
   cat("  Max  connections:", info$length, "\n")
   cat("  Conn. processed:", info$counter, "\n")
   cat("  Default records per fetch:", info$"fetch_default_rec", "\n")
   if(verbose){
      cat("  DBI API version: ", dbGetDBIVersion(), "\n")
      ##  cat("  PostgreSQL client version: ", info$clientVersion, "\n")  Feature absent
   }
   cat("  Open connections:", info$"num_con", "\n")
   if(verbose && !is.null(info$connectionIds)){
      for(i in seq_along(info$connectionIds)){
         cat("   ", i, " ")
         print(info$connectionIds[[i]])
      }
   }
   invisible(NULL)
}

postgresqlDriverInfo <- function(obj, what="", ...) {
    if(!isPostgresqlIdCurrent(obj))
        stop(paste("expired", class(obj)))
    drvId <- as(obj, "integer")
    info <- .Call(RS_PostgreSQL_managerInfo, drvId)
    ## replace drv/connection id w. actual drv/connection objects
    conObjs <- vector("list", length = info$"num_con")
    ids <- info$connectionIds
    for(i in seq_along(ids))
        conObjs[[i]] <- new("PostgreSQLConnection", Id = c(drvId, ids[i]))
    info$connectionIds <- conObjs
    info$managerId <- new("PostgreSQLDriver", Id = drvId)
    if(!missing(what))
        info[what]
    else
        info
}

## All NULL values are changed to empty strings (""). 
## These are treated as default values.
postgresqlNewConnection <- function(drv, user = "", password = "",
                                    host = "", dbname = "",
                                    port = "", tty = "", options = "", forceISOdate=TRUE) {
    if(!isPostgresqlIdCurrent(drv))
        stop("expired manager")
    if(is.null(user))
        user=""
    if(is.null(password))
        password=""
    if(is.null(host))
        host=""
    if(is.null(dbname))
        dbname=""
    if(is.null(port))
        port=""
    if(is.null(tty))
        tty=""
    if(is.null(options))
        options=""

    con.params <- as.character(c(user, password, host,
                                 dbname, port,
                                 tty, options))

    drvId <- as(drv, "integer")
    conId <- .Call(RS_PostgreSQL_newConnection, drvId, con.params)
    con <- new("PostgreSQLConnection", Id = conId)
    if(forceISOdate){
      dbGetQuery(con, "set datestyle to ISO")      
    }
    con
}

postgresqlCloneConnection <- function(con, ...) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    newId <- .Call(RS_PostgreSQL_cloneConnection, conId)
    new("PostgreSQLConnection", Id = newId)
}

postgresqlDescribeConnection <- function(obj, verbose = FALSE, ...) {
    info <- dbGetInfo(obj)
    print(obj)
    cat("  User:", info$user, "\n")
    cat("  Host:", info$host, "\n")
    cat("  Dbname:", info$dbname, "\n")

    ## cat("  Connection type:", info$conType, "\n")     function absent

    if(verbose){
        cat("  PostgreSQL server version: ", info$serverVersion, "\n")
        ##     cat("  PostgreSQL client version: ",
        ##         dbGetInfo(as(obj, "PostgreSQLDriver"), what="clientVersion")[[1]], "\n")           feature absent
        cat("  PostgreSQL protocol version: ", info$protocolVersion, "\n")
        cat("  PostgreSQL server thread id: ", info$threadId, "\n")
    }
    if (length(info$rsId)>0) {
        for (i in seq_along(info$rsId)) {
            cat("   ", i, " ")
            print(info$rsId[[i]])
        }
    } else {
        cat("  No resultSet available\n")
    }
    invisible(NULL)
}

postgresqlCloseConnection <- function(con, ...) {
    if(!isPostgresqlIdCurrent(con))
        return(TRUE)
    rs <- dbListResults(con)
    if(length(rs)>0){
        if(dbHasCompleted(rs[[1]]))
            dbClearResult(rs[[1]])
        else
            stop("connection has pending rows (close open results set first)")
    }
    conId <- as(con, "integer")
    .Call(RS_PostgreSQL_closeConnection, conId)
}

postgresqlConnectionInfo <- function(obj, what="", ...) {
    if(!isPostgresqlIdCurrent(obj))
        stop(paste("expired", class(obj), deparse(substitute(obj))))
    id <- as(obj, "integer")
    info <- .Call(RS_PostgreSQL_connectionInfo, id)
    rsId <- vector("list", length = length(info$rsId))
    for(i in seq_along(info$rsId))
        rsId[[i]] <- new("PostgreSQLResult", Id = c(id, info$rsId[i]))
    info$rsId <- rsId
    if(!missing(what))
        info[what]
    else
        info
}

## checks for any open resultsets, and closes them if completed.
## the statement is then executed on the connection, and returns
## whether it executed without an error or not.
postgresqlTransactionStatement <- function(con, statement) {
    ## are there resultSets pending on con?
    if(length(dbListResults(con)) > 0){
        res <- dbListResults(con)[[1]]
        if(!dbHasCompleted(res)){
            stop("connection with pending rows, close resultSet before continuing")
        }
        dbClearResult(res)
    }

    rc <- try(dbGetQuery(con, statement))
    !inherits(rc, ErrorClass)
}


## submits the sql statement to PostgreSQL and creates a
## dbResult object if the SQL operation does not produce
## output, otherwise it produces a resultSet that can
## be used for fetching rows.
postgresqlExecStatement <- function(con, statement, params, ...) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    statement <- as(statement, "character")
    if(missing(params)){
        rsId <- .Call(RS_PostgreSQL_exec, conId, statement)
    }else{
        rsId <- .External(RS_PostgreSQL_pqexecparams, conId, statement, as(params, "character"), ...)
    }
    new("PostgreSQLResult", Id = rsId)
}

postgresqlEscapeStrings <- function(con, preescapedstring) {
    conId <- as(con, "integer")
    preescapedstring <- as(preescapedstring, "character")
    escapedstring <- .Call(RS_PostgreSQL_escape, conId, preescapedstring)
    return(escapedstring)
}
postgresqlEscapeBytea <- function(con, raw_data) {
    conId <- as(con, "integer")
    raw_data <- as(raw_data, "raw")
    escapedstring <- .Call(RS_PostgreSQL_escape_bytea, conId, raw_data)
    return(escapedstring)
}
postgresqlUnescapeBytea <- function(escapedbytea) {
    escapedbytea <- as(escapedbytea, "character")
    raw_data <- .Call(RS_PostgreSQL_unescape_bytea, escapedbytea)
    return(raw_data)
}
postgresqlpqExec <- function(con, statement) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    statement <- as(statement, "character")
    .Call(RS_PostgreSQL_pqexec, conId, statement)
}
postgresqlpqExecParams <- function(con, statement, ...) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    statement <- as(statement, "character")
    .External(RS_PostgreSQL_pqexecparams, conId, statement, ...)
}

postgresqlCopyIn <- function(con, filename) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    filename <- as(filename, "character")
    .Call(RS_PostgreSQL_CopyIn, conId, filename)
}
postgresqlCopyInDataframe <- function(con, dataframe) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    nrow <- nrow(dataframe)
    p <- ncol(dataframe)
    .Call(RS_PostgreSQL_CopyInDataframe, conId, dataframe, nrow, p)
}
postgresqlgetResult <- function(con) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    conId <- as(con, "integer")
    rsId <- .Call(RS_PostgreSQL_getResult, conId)
    new("PostgreSQLResult", Id = rsId)
}


## helper function: it exec's *and* retrieves a statement. It should
## be named somehting else.
postgresqlQuickSQL <- function(con, statement, ...) {
    if(!isPostgresqlIdCurrent(con))
        stop(paste("expired", class(con)))
    rsList <- dbListResults(con)
    if (length(rsList)>0){  # clear results
        dbClearResult(rsList[[1]])
    }
    rs <- try(dbSendQuery(con, statement, ...))
    if (inherits(rs, ErrorClass)){
        warning("Could not create execute: ", statement)
        return(NULL)
    }
    if(dbHasCompleted(rs)){
        dbClearResult(rs)            ## no records to fetch, we're done
        invisible()
        return(data.frame()) # data.frame of 0 row 0 columns
    }
    res <- fetch(rs, n = -1)
    if(dbHasCompleted(rs))
        dbClearResult(rs)
    else
        warning("pending rows")  # shouldn't occur...
    res
}

postgresqlDescribeFields <- function(res, ...) {
    flds <- dbGetInfo(res, "fieldDescription")[[1]][[1]]
    if(!is.null(flds)){
        flds$Sclass <- .Call(RS_DBI_SclassNames, flds$Sclass)

        ## -------
        ## This is actually a bug introduced deliberately. In dbGetInfo, it displays the Sclass for Date/Time datatypes in Pg
        ## as character. But in dbColumnInfo, it displays it as 'POSIXct'. This is because there is no
        ## datatype corresponding to Date/Time defined in R-defines.h & R-internals.h
        for(i in 1:length(flds$type)) {
            if(flds$type[[i]] == 1114) {
                flds$Sclass[[i]] = "POSIXct";
            } else if(flds$type[[i]] == 1082) {
                flds$Sclass[[i]] = "Date";
            } else if(flds$type[[i]] == 1184) {
   		flds$Sclass[[i]] = "POSIXct";
            }
        }
        ## -------

        flds$type <- .Call(RS_PostgreSQL_typeNames, as.integer(flds$type))
        ## no factors
        structure(flds, row.names = paste(seq_along(flds$type)),
                  class = "data.frame")
    }
    else data.frame(flds)
}

## (Experimental)
## This function is meant to handle somewhat gracefully(?) large amounts
## of data from the DBMS by bringing into R manageable chunks (about
## batchSize records at a time, but not more than maxBatch); the idea
## is that the data from individual groups can be handled by R, but
## not all the groups at the same time.
##
## dbApply apply functions to groups of rows coming from a remote
## database resultSet upon the following fetching events:
##   begin         (prior to fetching the first record)
##   group.begin   (the record just fetched begins a new group)
##   new_record    (a new record just fetched)
##   group.end     (the record just fetched ends the current group)
##   end           (the record just fetched is the very last record)
##
## The "begin", "begin.group", etc., specify R functions to be
## invoked upon the corresponding events.  (For compatibility
## with other apply functions the arg FUN is used to specify the
## most common case where we only specify the "group.end" event.)
##
## The following describes the exact order and form of invocation for the
## various callbacks in the underlying  C code.  All callback function
## (except FUN) are optional.
##  begin()
##    group.begin(group.name)
##    new.record(df.record)
##    FUN(df.group, group.name)   (aka group.end)
##  end()
##
## TODO: (1) add argument output=F/T to suppress the creation of
##           an expensive(?) output list.
##       (2) allow INDEX to be a list as in tapply()
##       (3) should we implement a simplify argument, as in sapply()?
##       (4) should report (instead of just warning) when we're forced
##           to handle partial groups (groups larger than maxBatch).
##       (5) extend to the case where even individual groups are too
##           big for R (as in incrementatl quantiles).
##       (6) Highly R-dependent, not sure yet how to port it to S-plus.
##
postgresqlDBApply <- function(res, INDEX, FUN = stop("must specify FUN"),
                              begin = NULL,
                              group.begin =  NULL,
                              new.record = NULL,
                              end = NULL,
                              batchSize = 100, maxBatch = 1e6,
                              ..., simplify = TRUE) {
    if(dbHasCompleted(res))
        stop("result set has completed")
    if(is.character(INDEX)){
        flds <- tolower(as.character(dbColumnInfo(res)$name))
        INDEX <- match(tolower(INDEX[1]), flds, 0)
    }
    if(INDEX<1)
        stop(paste("INDEX field", INDEX, "not in result set"))

    null.or.fun <- function(fun) { # get fun obj, but a NULL is ok
        if(is.null(fun))
            fun
        else
            match.fun(fun)
    }
    begin <- null.or.fun(begin)
    group.begin <- null.or.fun(group.begin)
    group.end <- null.or.fun(FUN)     ## probably this is the most important
    end <- null.or.fun(end)
    new.record <- null.or.fun(new.record)
    rsId <- as(res, "integer")
    con <- as(res, "PostgreSQLConnection")
    on.exit({
        rc <- dbGetException(con)
        if(!is.null(rc$errorNum) && rc$errorNum!=0)
            cat("dbApply aborted with PostgreSQL error ", rc$errorNum,
                " (", rc$errorMsg, ")\n", sep = "")

    })
    ## BEGIN event handler (re-entrant, only prior to reading first row)
    if(!is.null(begin) && dbGetRowCount(res)==0)
        begin()
    rho <- environment()
    funs <- list(begin = begin, end = end,
                 group.begin = group.begin,
                 group.end = group.end, new.record = new.record)
    out <- .Call(RS_PostgreSQL_dbApply,
                 rs = rsId,
                 INDEX = as.integer(INDEX-1),
                 funs, rho, as.integer(batchSize), as.integer(maxBatch))
    if(!is.null(end) && dbHasCompleted(res))
        end()
    out
}

## Fetch at most n records from the opened resultSet (n = -1 means
## all records, n=0 means extract as many as "default_fetch_rec",
## as defined by PostgreSQLDriver (see describe(drv, T)).
## The returned object is a data.frame.
## Note: The method dbHasCompleted() on the resultSet tells you whether
## or not there are pending records to be fetched.
##
## TODO: Make sure we don't exhaust all the memory, or generate
## an object whose size exceeds option("object.size").  Also,
## are we sure we want to return a data.frame?
postgresqlFetch <- function(res, n=0, ...) {
    n <- as(n, "integer")
    rsId <- as(res, "integer")
    rel <- .Call(RS_PostgreSQL_fetch, rsId, nrec = n)
    ## create running row index as of previous fetch (if any)
    cnt <- dbGetRowCount(res)
    nrec <- length(rel[[1]])
    indx <- seq(from = cnt - nrec + 1, length = nrec)
    attr(rel, "row.names") <- as.integer(indx)
    if(usingR())
        class(rel) <- "data.frame"
    else
        oldClass(rel) <- "data.frame"

    drop_infinity <- function(x){ if(is.na(x)) NA else if(x == 'infinity' || x == '-infinity'){warning(x, ": infinity in date data detected") ; NA} else x}
    flds <- dbGetInfo(res)$fieldDescription[[1]]$type
    if(length(rel[,1])>0){
        for(i in 1:length(flds)) {
            if(flds[[i]] == 1114) {  ## 1114 corresponds to Timestamp without TZ (mapped to POSIXct class)
                rel[,i] <- sapply(rel[,i], drop_infinity) 
                rel[,i] <- as.POSIXct(rel[,i])
            } else if(flds[[i]] == 1082) {  ## 1082 corresponds to Date (mapped to Date class)
                rel[,i] <- sapply(rel[,i], drop_infinity) 
                rel[,i] <- as.Date(rel[,i])
            } else if(flds[[i]] == 1184)  {  ## 1184 corresponds to Timestamp with TimeZone
                rel[,i] <- sapply(rel[,i], drop_infinity) 
                rel[,i] <- as.POSIXct(sub('([+-]..)$', '\\100', sub(':(..)$','\\1' ,rel[,i])), format="%Y-%m-%d %H:%M:%OS%z")
            }
        }
    }
    rel
}

## Note that originally we had only resultSet both for SELECTs
## and INSERTS, ...  Later on we created a base class dbResult
## for non-Select SQL and a derived class resultSet for SELECTS.
postgresqlResultInfo <- function(obj, what = "", ...) {
    if(!isPostgresqlIdCurrent(obj))
        stop(paste("expired", class(obj), deparse(substitute(obj))))
    id <- as(obj, "integer")
    info <- .Call(RS_PostgreSQL_resultSetInfo, id)
    if(!missing(what))
        info[what]
    else
        info
}

postgresqlDescribeResult <- function(obj, verbose = FALSE, ...) {
    if(!isPostgresqlIdCurrent(obj)){
        print(obj)
        invisible(return(NULL))
    }
    print(obj)
    cat("  Statement:", dbGetStatement(obj), "\n")
    cat("  Has completed?", if(dbHasCompleted(obj)) "yes" else "no", "\n")
    cat("  Affected rows:", dbGetRowsAffected(obj), "\n")
    cat("  Rows fetched:", dbGetRowCount(obj), "\n")
    flds <- dbColumnInfo(obj)
    if(verbose && !is.null(flds)){
        cat("  Fields:\n")
        out <- print(dbColumnInfo(obj))
    }
    invisible(NULL)
}

postgresqlCloseResult <- function(res, ...) {
    if(!isPostgresqlIdCurrent(res))
        return(TRUE)
    rsId <- as(res, "integer")
    .Call(RS_PostgreSQL_closeResultSet, rsId)
}

## Use NULL, "", or 0 as row.names to prevent using any field as row.names.
postgresqlReadTable <- function(con, name, row.names = "row.names", check.names = TRUE, ...) {
    out <- dbGetQuery(con, paste("SELECT * from", postgresqlTableRef(name)))
    if(check.names)
        names(out) <- make.names(names(out), unique = TRUE)
    ## should we set the row.names of the output data.frame?
    nms <- names(out)
    j <- switch(mode(row.names),
                "character" = if(row.names=="") 0 else
                match(tolower(row.names), tolower(nms),
                      nomatch = if(missing(row.names)) 0 else -1),
                "numeric" = row.names,
                "NULL" = 0,
                0)
    if(j==0)
        return(out)
    if(j<0 || j>ncol(out)){
        warning("row.names not set on output data.frame (non-existing field)")
        return(out)
    }
    rnms <- as.character(out[,j])
    if(all(!duplicated(rnms))){
        out <- out[,-j, drop = FALSE]
        row.names(out) <- rnms
    } else warning("row.names not set on output (duplicate elements in field)")
    out
}

postgresqlImportFile <- function(con, name, value, field.types = NULL, overwrite = FALSE,
                                 append = FALSE, header, row.names, nrows = 50, sep = ",",
                                 eol="\n", skip = 0, quote = '"', ...) {
    if(overwrite && append)
        stop("overwrite and append cannot both be TRUE")

    new.con <- con

    if(dbExistsTable(con,name)){
        if(overwrite){
            if(!dbRemoveTable(con, name)){
                warning(paste("table", name, "couldn't be overwritten"))
                return(FALSE)
            }
        }
        else if(!append){
            warning(paste("table", name, "exists in database: aborting dbWriteTable"))
            return(FALSE)
        }
    }

    ## compute full path name (have R expand ~, etc)
    fn <- file.path(dirname(value), basename(value))
    if(missing(header) || missing(row.names)){
        f <- file(fn, open="r")
        if(skip>0)
            readLines(f, n=skip)
        txtcon <- textConnection(readLines(f, n=2))
        flds <- count.fields(txtcon, sep)
        close(txtcon)
        close(f)
        nf <- length(unique(flds))
    }
    if(missing(header)){
        header <- nf==2
    }
    if(missing(row.names)){
        if(header)
            row.names <- if(nf==2) TRUE else FALSE
        else
            row.names <- FALSE
    }

    new.table <- !dbExistsTable(con, name)
    if(new.table){
        ## need to init table, say, with the first nrows lines
        d <- read.table(fn, sep=sep, header=header, skip=skip, nrows=nrows, ...)
        sql <-
            postgresqlBuildTableDefinition(new.con, name, obj=d, field.types = field.types,
                                   row.names = row.names)
        rs <- try(dbSendQuery(new.con, sql))
        if(inherits(rs, ErrorClass)){
            warning("could not create table: aborting postgresqlImportFile")
            return(FALSE)
        }
        else
            dbClearResult(rs)
    }
    else if(!append){
        warning(sprintf("table %s already exists -- use append=TRUE?", name))
    }

    fmt <- paste("COPY %s FROM '%s' ","WITH DELIMITER AS '%s' ",
                 if(!is.null(quote)) "CSV  QUOTE AS  '%s'", sep="")

    if(is.null(quote))
        sql <- sprintf(fmt, name,fn, sep)
    else
        sql <- sprintf(fmt, name,fn, sep, quote)

    rs <- try(dbSendQuery(new.con, sql))
    if(inherits(rs, ErrorClass)){
        warning("could not load data into table")
        return(FALSE)
    }
    dbClearResult(rs)
    TRUE
}

## Create table "name" (must be an SQL identifier) and populate
## it with the values of the data.frame "value"
## TODO: This function should execute its sql as a single transaction,
##       and allow converter functions.
postgresqlWriteTable <- function(con, name, value, field.types, row.names = TRUE,
                                 overwrite = FALSE, append = FALSE, ..., allow.keywords = FALSE) {
    if(overwrite && append)
        stop("overwrite and append cannot both be TRUE")
    if(!is.data.frame(value))
        value <- as.data.frame(value)
    if(row.names){
        value <- cbind(row.names(value), value)  ## can't use row.names= here
        names(value)[1] <- "row.names"
    }
    if(missing(field.types) || is.null(field.types)){
        ## the following mapping should be coming from some kind of table
        ## also, need to use converter functions (for dates, etc.)
        field.types <- sapply(value, dbDataType, dbObj = con)
    }

    i <- match("row.names", names(field.types), nomatch=0)
    if(i>0) ## did we add a row.names value?  If so, it's a text field.
        ## MODIFIED -- Sameer
        field.types[i] <- dbDataType(dbObj=con, field.types[row.names])
    new.con <- con

    if(dbExistsTable(con,name)){
        if(overwrite){
            if(!dbRemoveTable(con, name)){
                warning(paste("table", name, "couldn't be overwritten"))
                return(FALSE)
            }
        }
        else if(!append){
            warning(paste("table",name,"exists in database: aborting assignTable"))
            return(FALSE)
        }
    }
    if(!dbExistsTable(con,name)){      ## need to re-test table for existance
        ## need to create a new (empty) table
        sql1 <- paste("create table ", postgresqlTableRef(name), "\n(\n\t", sep="")
        sql2 <- paste(paste(postgresqlQuoteId(names(field.types)), field.types), collapse=",\n\t",
                      sep="")
        sql3 <- "\n)\n"
        sql <- paste(sql1, sql2, sql3, sep="")
        rs <- try(dbSendQuery(new.con, sql))
        if(inherits(rs, ErrorClass)){
            warning("could not create table: aborting assignTable")
            return(FALSE)
        } else {
            dbClearResult(rs)
        }
    }

    ## convert columns we can't handle in C code
    value[] <- lapply(value, function(z) {
        if(is.object(z) && !is.factor(z)) as.character(z) else z
    })
    oldenc <- dbGetQuery(new.con, "SHOW client_encoding")
    postgresqlpqExec(new.con, "SET CLIENT_ENCODING TO 'UTF8'")
    sql4 <- paste("COPY", postgresqlTableRef(name),"(",paste(postgresqlQuoteId(names(value)),collapse=","),") FROM STDIN")
    postgresqlpqExec(new.con, sql4)
    postgresqlCopyInDataframe(new.con, value)
    rs<-postgresqlgetResult(new.con)

    retv <- TRUE
    if (inherits(rs, ErrorClass)) {
        warning("could not load data into table")
        retv <- FALSE
    }

    dbClearResult(rs)
    sql5 <- paste("SET CLIENT_ENCODING TO '", oldenc, "'", sep="")
    dbGetQuery(new.con, sql5)

    retv
}

postgresqlBuildTableDefinition <- function(dbObj, name, obj, field.types = NULL, row.names = TRUE, ...) {
    if(!is.data.frame(obj))
        obj <- as.data.frame(obj)
    if(!is.null(row.names) && row.names){
        obj  <- cbind(row.names(obj), obj)  ## can't use row.names= here
        names(obj)[1] <- "row.names"
    }
    if(is.null(field.types)){
        ## the following mapping should be coming from some kind of table
        ## also, need to use converter functions (for dates, etc.)
        field.types <- sapply(obj, dbDataType, dbObj = dbObj)
    }
    i <- match("row.names", names(field.types), nomatch=0)
    if(i>0) ## did we add a row.names value?  If so, it's a text field.
        field.types[i] <- dbDataType(dbObj, field.types$row.names)

    ## need to create a new (empty) table
    flds <- paste(postgresqlQuoteId(names(field.types)), field.types)
    paste("CREATE TABLE", postgresqlTableRef(name), "\n(", paste(flds, collapse=",\n\t"), "\n)")
}


## find a suitable SQL data type for the R/S object obj
## TODO: Lots and lots!! (this is a very rough first draft)
## need to register converters, abstract out PostgreSQL and generalize
## to Oracle, Informix, etc.  Perhaps this should be table-driven.
## NOTE: PostgreSQL data types differ from the SQL92 (e.g., varchar truncate
## trailing spaces).
postgresqlDataType <- function(obj, ...) {
    rs.class <- data.class(obj)
    if(rs.class=="numeric"){
        sql.type <- if(is(obj,"integer")) "integer" else  "float8"
    }
    else {
        sql.type <- switch(rs.class,
                           character = "text",
                           logical = "bool",
                           factor = "text",
                           ordered = "text",
                           Date = "date",
                           POSIXct = "timestamp with time zone",
                           "text")
    }
    sql.type
}

postgresqlQuoteId <- function(identifiers){
    ret <- paste('"', gsub('"','""',identifiers), '"', sep="")
    ret
}
postgresqlTableRef <- function(identifiers){
    ret <- paste('"', gsub('"','""',identifiers), '"', sep="", collapse=".")
    ret
}

## the following reserved words were taken from ["RESERVED" of postgres colomn in ] Table C.1 in Appendix C
## of the PostgreSQL Manual 8.3.1.
.PostgreSQLKeywords <- c("ALL", "ANALYSE", "ANALYZE", "AND", "ANY",
                         "ARRAY", "AS", "ASC", "ASYMMETRIC", "AUTHORIZATION", "BETWEEN",
                         "BINARY", "BOTH", "CASE", "CAST", "CHECK", "COLLATE", "COLUMN",
                         "CONSTRAINT", "CREATE", "CROSS", "CURRENT_DATE", "CURRENT_ROLE",
                         "CURRENT_TIME", "CURRENT_TIMESTAMP", "CURRENT_USER", "DEFAULT",
                         "DEFERRABLE", "DESC", "DISTINCT", "DO", "ELSE", "END", "EXCEPT",
                         "FALSE", "FOR", "FOREIGN", "FREEZE", "FROM", "FULL", "GRANT", "GROUP",
                         "HAVING", "ILIKE", "IN", "INITIALLY", "INNER","INTERSECT", "INTO",
                         "IS", "ISNULL", "JOIN", "LEADING", "LEFT", "LIKE", "LIMIT",
                         "LOCALTIME", "LOCALTIMESTAMP", "NATURAL", "NEW", "NOT", "NULL", "OFF",
                         "OFFSET", "OLD", "ON", "ONLY", "OR", "ORDER", "OUTER", "OVERLAPS",
                         "PLACING", "PRIMARY", "REFERENCES", "RESERVED", "SELECT",
                         "SESSION_USER", "SIMILAR", "SOME", "SYMMETRIC", "TABLE", "THEN", "TO",
                         "TRAILING", "TRUE", "UNION", "UNIQUE", "USER", "USING", "VERBOSE",
                         "WHEN", "WHERE", "WITH" )

Try the RPostgreSQL package in your browser

Any scripts or data that you put into this service are public.

RPostgreSQL documentation built on Feb. 16, 2023, 8:53 p.m.