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3
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1 #!/usr/bin/env Rscript
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2
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3 ## begin warning handler
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4 withCallingHandlers({
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5
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6 library(methods) # Because Rscript does not always do this
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7
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8 options('useFancyQuotes' = FALSE)
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9
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10 suppressPackageStartupMessages(library("optparse"))
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11 suppressPackageStartupMessages(library("RGalaxy"))
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12
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13
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14 option_list <- list()
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15
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16 option_list$number1 <- make_option('--number1', type='numeric')
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17 option_list$number2 <- make_option('--number2', type='numeric')
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18 option_list$sum <- make_option('--sum', type='character')
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19
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20
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21 opt <- parse_args(OptionParser(option_list=option_list))
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22
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23 suppressPackageStartupMessages(library(RSclient))
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24
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25 ## function body not needed here, it is in package
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26
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27 params <- list()
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28 for(param in names(opt))
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29 {
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30 if (!param == "help")
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31 params[param] <- opt[param]
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32 }
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33
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34 setClass("GalaxyRemoteError", contains="character")
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35 wrappedFunction <- function(f)
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36 {
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37 tryCatch(do.call(f, params),
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38 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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39 }
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40
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41
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42 c <- RS.connect(host='localhost', port=6311)
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43 RS.eval(c, options('useFancyQuotes' = FALSE))
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44 RS.eval(c, suppressPackageStartupMessages(library(RGalaxy)))
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45 RS.assign(c, 'params', params)
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46 RS.assign(c, 'wrappedFunction', wrappedFunction)
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47 RS.eval(c, setClass('GalaxyRemoteError', contains='character'))
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48 res <- RS.eval(c, wrappedFunction(addTwoNumbers))
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49 RS.close(c)
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50 if(is(res, 'GalaxyRemoteError'))RGalaxy::gstop(res)
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51
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52 ## end warning handler
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53 }, warning = function(w) {
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54 cat(paste("Warning:", conditionMessage(w), "\n"))
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55 invokeRestart("muffleWarning")
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56 })
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