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# INSERT MISSING SPECIES into TAXONOMY TABLE
# package: megaptera
# called by: stepC
# author: Christoph Heibl
# last update: 2014-09-23
dbAutoFillTaxonomy <- function(x){
## DEFINITIONS
## -----------
gene <- sql.conform(x$gene)
acc.tab <- paste("acc", gsub("^_", "", gene), sep = "_")
## open database connection
## ------------------------
conn <- dbConnect(PostgreSQL(), host = x$db[["host"]],
port = x$db[["port"]], dbname = x$db[["dbname"]],
user = x$db[["user"]], password = x$db[["password"]])
SQL <- paste("SELECT taxon from", acc.tab,
"WHERE status != 'excluded' OR status IS NULL",
"EXCEPT SELECT spec from taxonomy")
spec <- dbGetQuery(conn, SQL)$taxon
autoFill <- function(z, conn){
zz <- paste("SELECT * FROM taxonomy WHERE",
sql.wrap(strip.spec(z), term = "gen"))
zz <- dbGetQuery(conn, zz)
if ( nrow(zz) == 0 ) {
warning("genus '", strip.spec(z), "' not in taxonomy")
SQL <- paste("UPDATE", acc.tab,
"SET", sql.wrap("excluded", term = "status"),
"WHERE", sql.wrap(z, term = "taxon", operator = "~", BOOL = NULL))
dbSendQuery(conn, SQL)
} else {
zz <- zz[, -which(colnames(zz) == "spec")]
zz <- unique(zz)[1, ]
zz <- data.frame(zz, spec = z, stringsAsFactors = FALSE)
SQL <- paste("INSERT INTO taxonomy",
paste("(", paste(names(zz), collapse = ", "), ")", sep = ""),
"VALUES",
paste("(", paste(paste("'", zz, "'", sep = ""), collapse = ", "), ")", sep = ""))
dbSendQuery(conn, SQL)
}
}
lapply(spec, autoFill, conn = conn)
dbDisconnect(conn)
}
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