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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata

‎DESCRIPTION

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Package: micerest
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Type: Package
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Title: Server Helper for Webmice RESTFUL API
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Version: 0.1.0
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Description: Webmice is an online service for running mice through a
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RESTFUL API. The micerest package bundles the R functions needed to
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define the end points.
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License: GPL (>= 3)
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Encoding: UTF-8
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LazyData: true
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Authors@R:
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person("Christine", "Staiger", , "[email protected]",
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role = c("aut", "cre"), comment = c(ORCID = "YOUR-ORCID-ID"))
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Depends:
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RestRserve,
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mice

‎LICENSE.md

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‎NAMESPACE

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exportPattern("^[[:alpha:]]+")

‎R/webmice.R

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library(RestRserve)
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library(mice, warn.conflicts = FALSE)
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library(jsonlite)
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library(readr)
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library(digest)
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#' Parameters
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#' Code location in Docker, set through bash variable
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base_folder <- Sys.getenv("WEBMICE_LOC")
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if(base_folder == "") {
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base_folder <- getwd()
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print('No base folder for webmice set (export WEBMICE_LOC="directory").')
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print(paste("Set to: ", base_folder))
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}
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#' Imports
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source(file.path(base_folder, "webmice_handlers.R"))
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source(file.path(base_folder, "webmice_functions.R"))
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#' Data upload location
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data_uploads = file.path(base_folder, "data_uploads")
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if(!file.exists(data_uploads)){
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dir.create(data_uploads)
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}
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#' Application
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webmice = Application$new()
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#' Endpoints
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webmice$add_post(
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path = "/data",
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FUN = function(request, response) {
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cnt <- request$get_file("csvfile") # 'csv' from the upload form field
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# parse CSV
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dt <- read_csv(cnt)
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hash <- md5_string(request$parameters_body$csvfile)
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tmp <- file.path(data_uploads, hash)
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write_csv(dt, tmp)
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# set output body
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response$append_header("data_token", hash)
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}
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)
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webmice$add_get(path = "/version", FUN = mice_version_handler)
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webmice$add_get(path = "/exampledata", FUN = example_data_handler)
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webmice$add_get(path = "/long", FUN = impute_longfmt_handler)
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webmice$add_get(path = "/fit", FUN = fit_handler)
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webmice$add_get(path = "/pool", FUN = pool_handler)
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#' Swagger
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yaml_file = file.path(base_folder, "openapi.yaml")
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webmice$add_openapi(path = "/openapi.yaml", file_path = yaml_file)
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webmice$add_swagger_ui(path = "/doc", path_openapi = "/openapi.yaml", use_cdn = TRUE)
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backend = BackendRserve$new()
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backend$start(webmice, http_port = 8080)

‎R/webmice_functions.R

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#' Data
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#' Fetches example data from mice, returns data as json
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example_data_to_json = function(name) {
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result = tryCatch({
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return(toJSON(get(name)))
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}, error = function(e) {
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err <- c()
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err$error <- "Error: data name not found"
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return(toJSON(err))
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})
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return(result)
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}
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#' Reads a csv file
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read_file = function(path){
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tryCatch({
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data <- read.csv(path)
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return(data)
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}, error = function(e){
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return(NULL)
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})
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}
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#' Creates a hash for a data file name
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md5_string = function(string) {
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return(digest(paste(Sys.time(), string), algo="md5", serialize=F))
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}
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#' Convert JSON to R
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#' Takes a json string and returns it as R list
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#' Test:
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#' input <- list(data="nhanes", maxit=2, m=2, seed=1)
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json_to_parameters = function(json_payload){
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result = tryCatch({
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params = fromJSON(json_payload)
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return(params)
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}, error = function(e) {
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return(NULL)
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})
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}
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#' Mice return functions
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#' Takes the result of the imputation and returns the long format of the data
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imp_result_long_fmt = function(imp){
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return(toJSON(complete(imp, "long")))
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}
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imp_result_pred_matrix = function(imp){
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res <- c()
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res$error <- "not implemented"
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return(toJSON(res))
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}
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#' Mice functions
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impute = function(data, maxit, m, seed) {
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imp <- list()
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imp$error <- ""
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result = tryCatch({
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imp <- mice(data, maxit=maxit, m=m, seed=seed)
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return(imp)
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}, error = function(e) {
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return("Failure: mice")
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})
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if(result == "Failure: mice"){
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imp$error <- result
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return(imp)
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}
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}
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#' Calls mice's imputation function with parameters provided in a list 'params'
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#' Expected: params$data, params$maxit, params$m, params$seed
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#' data: example data name, a hash from an uploaded file, or a csv filee
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call_mice = function(params){
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imp <- list()
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result = tryCatch({
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data <- get(params$data)
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}, error = function(e){
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return(-1)
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})
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if(typeof(result) == "list") {
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print("DEBUG: Imputation on example data set")
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imp <- impute(data, maxit=params$maxit, m=params$m, seed=params$seed)
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return(imp)
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}
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if(typeof(params$data) == "character" && endsWith(params$data, ".csv")){
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print("DEBUG: Imputation on local csv file")
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df <- read_file(params$data)
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if(is.null(df)){
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imp$error <- "Failure: reading local csv file"
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return(imp)
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}
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imp <- impute(nhanes, maxit=params$maxit, m=params$m, seed=params$seed)
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return(imp)
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}
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if(typeof(params$data) == "character"){
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print("DEBUG: Imputation on uploaded file")
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df <- read_file(file.path(data_uploads, params$data))
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if(is.null(df)){
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imp$error <- "Failure: reading file, not an example dataset or file on server"
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return(imp)
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}
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imp <- impute(df, maxit=params$maxit, m=params$m, seed=params$seed)
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return(imp)
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}
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}
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call_with = function(data, model, formula){
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fit <- c()
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if(model == "lm"){
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fit <- with(data, lm(as.formula(formula)))
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}
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if(model == "glm"){
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fit <- with(data, glm(as.formula(formula)))
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}
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fit$error <- "Model not known"
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return(toJSON(summary(fit), force=TRUE))
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}
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call_pool = function(data){
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pool <- c()
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if(packageVersion("mice") < "3.16.4" ){
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pool$error <- "ERROR pool.table: need mice version 3.16.4 or higher"
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return(toJSON(pool, force=TRUE))
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}
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if(typeof(data) == "list"){
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pool <- pool.table(data)
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} else {
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pool$error <- "Input data not of correct type (summary(fit))"
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}
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return(toJSON(pool, force=TRUE))
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}

‎R/webmice_handlers.R

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pool_handler = function(.req, .res) {
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poolJson <- ''
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json_payload <- as.character(.req$parameters_query[["payload"]])
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if (length(json_payload) == 0L) {raise(HTTPError$bad_request())}
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params <- json_to_parameters(json_payload)
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if(is.null(params$data)) {poolJson <- "Error: no data"}
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if(poolJson == ''){
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print("DEBUG: Calling pool.table (requires 3.16.4)")
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poolJson <- call_pool(params$data)
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}
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.res$set_body(poolJson)
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.res$set_content_type("text/plain")
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}
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fit_handler = function(.req, .res) {
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fitJson <- ''
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json_payload <- as.character(.req$parameters_query[["payload"]])
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# if answers are copied straight from the Swagger interface, there are too many backslashes
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# json_payload <- gsub('\\\\', '', input)
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if (length(json_payload) == 0L) {raise(HTTPError$bad_request())}
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params <- json_to_parameters(json_payload)
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if(is.null(params$data)) {fitJson <- "Error: no data"}
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if(is.null(params$model)) {fitJson <- "Error: no model"}
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if(is.null(params$formula)) {fitJson <- "Error: no formula"}
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if(fitJson == ''){
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print("DEBUG: Calling with (fitting function)")
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fitJson <- call_with(params$data, params$model, params$formula)
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}
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.res$set_body(fitJson)
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.res$set_content_type("text/plain")
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}
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impute_longfmt_handler = function(.req, .res) {
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json_payload <- as.character(.req$parameters_query[["payload"]])
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if (length(json_payload) == 0L) {raise(HTTPError$bad_request())}
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# check if convertible to json
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params <- json_to_parameters(json_payload)
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# impute function needs data, maxit, m, seed
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if(is.null(params$data)) {raise(HTTPError$not_acceptable())}
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if(is.null(params$maxit)) {raise(HTTPError$not_acceptable())}
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if(is.null(params$m)) {raise(HTTPError$not_acceptable())}
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if(is.null(params$seed)) {raise(HTTPError$not_acceptable())}
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print("DEBUG: Calling mice")
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imp <- call_mice(params)
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if(is.null(imp$error)){
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.res$set_body(imp_result_long_fmt(imp))
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} else{
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.res$set_body(toJSON(imp))
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}
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.res$set_content_type("text/plain")
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}
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example_data_handler = function(.req, .res) {
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example_name <- as.character(.req$parameters_query[["name"]])
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.res$set_body(example_data_to_json(example_name))
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.res$set_content_type("text/plain")
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}
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mice_version_handler = function(.req, .res) {
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version <- list()
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version$mice <- sessionInfo("mice")$otherPkgs$mice$Version
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.res$set_body(toJSON(version))
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.res$set_content_type("text/plain")
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}

‎micerest.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source

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