Statistical Analysis: an Introduction using R/Contributors/uploadToCommons.r

### Call this function as in the following example:
###
###  uploadToCommons("username", "password", c("R-example_plot_1.r", R-example_plot_2.r), "svg", 2, 4, 8)
###
### This will generate and upload an svg graphics file called "R-example_plot_1.svg" from the R code specified in "R-example_plot_1.r".
###
### Notes:
### 1) extra arguments (e.g. the "2, 4, 8" above) are passed to the graphics device (here "svg")
### 2) the R code should NOT include a call to a graphics device (e.g. svg(), pdf(), etc.).
###This is generated automatically by the script (within an R session, this allows you to produce an on-screen test plot by using source())
### 3) you can also test the script by specifying "dummy.run=TRUE" in the call, which will attempt to generate a file and display in in a web browser window

uploadToCommons <- function(wikiuser, wikipass, file.names, graphics.func, ..., 
                              description="{{en|1=Unspecified plot generated from R}}",
                              description.language="en",
                              plotfile.names=sub(
                                ##make up the plot name by removing ".r" if necessary
                                ##then appending .`graphics.func`
                                pattern='(\\.r)?$',
                                replacement=switch(graphics.func,
                                  cairo_pdf=".pdf",
                                  CairoSVG=".svg",
                                  paste(".", graphics.func, sep="")),
                                x=basename(file.names),
                                ignore.case=TRUE),
                                plotfile.contentType=switch(graphics.func,
                                  ##Of the R devices, wikicommons allows SVG, PNG, JPEG, PDF
                                  CairoSVG="image/svg+xml",
                                  svg="image/svg+xml",
                                  png="image/png",
                                  jpg="image/jpeg",
                                  pdf="application/pdf"),
                              dummy.run=FALSE,
                              view.files.in.browser=dummy.run
                              ) {
  require(RCurl) #for the uploading via http

  ##Here are the defaults for the information template submitted to wikicommons
  list(Description=description,
       Source="Own work by uploader",
       Author=paste("[[User:", wikiuser, "|", wikiuser, "]]", sep=""),
       Date=as.character(Sys.Date()),
       Permission="",
       other_versions="") -> info
  
    save.dir <- getwd() #note that all plots will be saved in your R working directory


  getCurlHandle(cookiefile="", cookiejar=file.path(save.dir, "temp.cookie"), ssl.verifyhost=0, ssl.verifypeer=0, followlocation=0) -> cHandle

  if (identical(dummy.run, FALSE)) {
    #postForm("https://secure.wikimedia.org/wikipedia/commons/w/index.php?title=Special:UserLogin&action=submitlogin&type=login",
    postForm("http://commons.wikimedia.org/w/index.php?title=Special:UserLogin&action=submitlogin&type=login",
             wpName=wikiuser,
             wpPassword=wikipass,
             wpRemember="1",
             wpLoginAttempt="Log in",
             curl=cHandle) -> page1
  }
  mapply(function(codefile, plotfile) {
    ##run the R code: 
    graphics.call <- do.call(call, append(list(graphics.func, file=plotfile), list(...)))
    eval(graphics.call)
    source(codefile)
    dev.off()
    
    code <- readLines(codefile)
    
    ##assume that first line, if starting with a "#", is the description
    ##this code should probably check for disallowed wikitext (e.g. "=" and "}}")
    if(substring(code[1], 1, 1)=="#")  info$Description <-if(is.null(description.language)) substring(code[1], 2) else paste("{{en|1=", substring(code[1], 2), "}}", sep="")

    ## construct the wikitext version of the information
    paste("{{Information",
          paste("|",names(info),"=", info, sep="", collapse="\n"), 
          "}}",
          "{{Created with R}} using the following commands",
          "<pre>",
          paste(deparse(graphics.call, width.cutoff = 500), collapse=""),
          paste(code, collapse="\n"),
          "dev.off()",
          "

",

         sep="\n") -> wikiInfoText

   if (identical(dummy.run, FALSE)) {
     getURL(paste("http://commons.wikimedia.org/wiki", plotfile, sep="/"), curl=cHandle) -> page2
     postForm("http://commons.wikimedia.org/wiki/Special:Upload",
              wpUploadFile=fileUpload(file.path(save.dir,plotfile), contentType=plotfile.contentType),
              wpSourceType='file',
              wpDestFile=plotfile,
              wpUploadDescription=wikiInfoText,
              wpLicense="PD-self",
              wpIgnoreWarning='true',
              wpUpload="Upload file",
              wpDestFileWarningAck="1",
              curl=cHandle) -> page3
     if (length(grep("No file by this name exists", page2)) > 0) #a file existed before
       {

      1. TO DO: should overwite original summary here
         warning("This file already exists: overwriting (you may need to change the summary information by hand)")
       }
   } else {
     cat(wikiInfoText)
     if(view.files.in.browser)
       browseURL(paste("file:/",getwd(), plotfile, sep="/"))
   }
   
   }, file.names, plotfile.names) -> dummy
 rm(cHandle)
 gc() #force writing the cookie file

}

Last modified on 23 July 2009, at 20:01