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templates.molgenis.R.ftl Maven / Gradle / Ivy
###################################################################
#
# Molgenis R api client.
#
####################################################################
library('RCurl')
library('rjson')
#Prevent scientific notation
options(scipen=999)
#Create a new environment
molgenis.env <- new.env()
local({
molgenis.api.url <- "${api_url}"
<#if token??>
molgenis.token <- "${token}"
<#else>
molgenis.token <- NULL
}, env = molgenis.env)
###################################################################
#
# Login to the rest api and create a session
#
# Parameters:
# username: your username
# password: your password
#
###################################################################
molgenis.login <- local(function(username, password) {
jsonRequest <- toJSON(list(username = username, password = password))
url <- paste0(molgenis.api.url, "login")
jsonResponse <- postForm(url, .opts = list(postfields = jsonRequest, httpheader = c('Content-Type' = 'application/json')))
cat("Login success")
response <- fromJSON(jsonResponse)
molgenis.token <<- response$token
}, molgenis.env)
####################################################################
#
# Logout from the rest api
#
####################################################################
molgenis.logout <- local(function() {
url <- paste0(molgenis.api.url, 'logout')
getURL(url, httpheader = list('x-molgenis-token' = molgenis.token))
cat("Logout success")
}, molgenis.env)
#####################################################################
#
# Query the data api
# Parameters:
# entity: the entityname (required)
# q: the query
# start: the index of the first result to return
# num: the number of results to return (default is 1000, max is 10000)
# attributes: the attributes to return if NULL (default) all attributes are returned
#
# Return:
# Dataframe with the query result
#
# The query must be in fiql/rsql format (see https://github.com/jirutka/rsql-parser)
#
# Example: molgenis.get(entity = "Person", q = "firstName==Piet", start = 6, num = 10)
#######################################################################
molgenis.get <- local(function(entity, q = NULL, start = 0, num = 1000, sortColumn= NULL, sortOrder = NULL, attributes = NULL) {
url <- paste0(molgenis.api.url, "csv/", entity, "?molgenis-token=", molgenis.token, "&start=", start, "&num=", num, "&sortColumn=", sortColumn, "&sortOrder=", sortOrder)
if (!is.null(q)) {
url <- paste0(url, "&q=", curlEscape(q))
}
if (!is.null(attributes)) {
url <- paste0(url, "&attributes=", curlEscape(paste0(attributes, collapse = ",")))
}
# FIXME Check metadata for every column and set a colClass vector corresponding to the correct type
# EXAMPLE: column1 contains strings,
# characterClass <- c("character")
# names(characterClass) <- c("column1")
# read.csv(url, colClass = c(characterClass))
csv <- getURL(url)
dataFrame <- read.csv(textConnection(csv))
return (dataFrame)
}, molgenis.env)
######################################################################
#
# Creates a new entity
#
# Parameters:
# entity: the entityname
# ...: var arg list of attribute name/value pairs
#
# Return:
# the id of the created entity
#
# example: molgenis.add(entity = "Person", firstName = "Piet", lastName = "Paulusma")
#
####################################################################
molgenis.add <- local(function(entity, ...) {
molgenis.addList(entity, list(...))
}, env = molgenis.env)
######################################################################
#
# Creates new entities
#
# Parameters:
# entity: the entityname
# rows: dataFrame where each row is an entity
#
# example:
# firstName <- c("Piet", "Klaas")
# lastName <- c("Paulusma", "de Vries")
# df <- data.frame(firstName, lastName)
# molgenis.addAll("Person", df)
#
####################################################################
molgenis.addAll <- function(entity, rows) {
apply(rows, 1, function(row){
molgenis.addList(entity, row)
})
}
######################################################################
#
# Creates a new entity
#
# Parameters:
# entity: the entityname
# attributeList: list of attribute name/value pairs
#
# Return:
# the id of the created entity
#
#####################################################################
molgenis.addList <- local(function(entity, attributeList) {
url <- paste0(molgenis.api.url, entity)
h <- basicHeaderGatherer()
postForm(url,
.params = attributeList,
style = "POST",
.opts = list(headerfunction = h$update,
httpheader = list("x-molgenis-token" = molgenis.token,
"Content-Type" = "application/x-www-form-urlencoded")))
returnedHeaders <- h$value()
#On success the api returns httpcode 201 CREATED
if (returnedHeaders["status"] != "201") {
stop("Error creating entity")
}
#The entity is created successfully, return the new id
location <- returnedHeaders["Location"]
l <- strsplit(location, "/")[[1]]
return (l[length(l)])
}, env = molgenis.env)
#####################################################################
#
# Updates an existing entity
#
# Parameters:
# entity: the entityname
# id: the id of the entity to update
# ...: var arg list of attribute name/value pairs
#
# example: molgenis.update(entity = "Person", id = 5, firstName = "Piet", lastName = "Paulusma")
#
#####################################################################
molgenis.update <- local(function(entity, id, ...) {
url <- paste0(molgenis.api.url, entity, "/", id)
parameters <- list(...)
parameters <- c(parameters, "_method" = "PUT")
h <- basicHeaderGatherer()
postForm(url,
.params = parameters,
style = "POST",
.opts = list(headerfunction = h$update,
httpheader = list("x-molgenis-token" = molgenis.token,
"Content-Type" = "application/x-www-form-urlencoded")))
returnedHeaders <- h$value()
#On success the api returns httpcode 204 NO_CONTENT
if (returnedHeaders["status"] != "204") {
stop("Error updating entity")
}
}, env = molgenis.env)
#####################################################################
#
# Deletes an existing entity
#
# Parameters:
# entity: entityname
# id: the id of the entity to delete
#
# Example: molgenis.delete(entity = "Person", id = 5)
#
#####################################################################
molgenis.delete <- local(function(entity, id) {
url <- paste0(molgenis.api.url, entity, "/", id)
h <- basicHeaderGatherer()
postForm(url,
.params = c("_method" = "DELETE"),
style = "POST",
.opts = list(headerfunction = h$update,
httpheader = list("x-molgenis-token" = molgenis.token)))
returnedHeaders <- h$value()
#On success the api returns httpcode 204 NO_CONTENT
if (returnedHeaders["status"] != "204") {
stop("Error deleting entity")
}
}, env = molgenis.env)
#####################################################################
#
# Gets entity metadata
#
# Parameters:
# entity: the entityname
# Returns:
# list
#
#####################################################################
molgenis.getEntityMetaData <- local(function(entity) {
url <- paste0(molgenis.api.url, entity, "/meta?expand=attributes")
responseJson <- getURL(url, httpheader = list("x-molgenis-token" = molgenis.token))
response <- fromJSON(responseJson)
return (response)
}, molgenis.env)
#####################################################################
#
# Gets attribute metadata
#
# Parameters:
# entity: the entityname
# attribute: the attributename
# Returns:
# list
#
#####################################################################
molgenis.getAttributeMetaData <- local(function(entity, attribute){
url <- paste0(molgenis.api.url, entity, "/meta/", attribute)
responseJson <- getURL(url, httpheader = list("x-molgenis-token" = molgenis.token))
response <- fromJSON(responseJson)
return (response)
}, molgenis.env)
