# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
library(plyr)
library(dplyr)
library(readr)
library(stringr)
library(BioChemPantry)
schema <- "csfmetabolome"
pantry <- get_pantry()
pantry %>% create_schema(schema)
pantry_login <- get_pantry_config()$login
staging_directory <- get_staging_directory(schema)
xml_url <- "http://www.csfmetabolome.ca/system/downloads/current/csf_metabolites.zip"
dump_dir <- paste0(staging_directory, "/dump/")
zip_fname <- paste0(dump_dir, "csf_metabolites.zip")
xml_fname <- paste0(dump_dir, "csf_metabolites.xml")
cat("
Downloading CSF Metabolome XML data
url: ", xml_url, "
dump_url: ", dump_dir, "
and loading it into the postgres database
host: ", pantry_login$host, "
port: ", pantry_login$port, "
username: ", pantry_login$user, "
password: **********
schema: ", schema, "
", sep="")
# download and unzip data
paste0("
mkdir -p ", dump_dir, "
cd ", dump_dir, "
wget ", xml_url, "
unzip ", zip_fname, "
") %T>% cat %>% system
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