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annotate w4mcorcov_util.R @ 11:ddcc33ff3205 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
author eschen42
date Wed, 05 Sep 2018 22:31:21 -0400
parents 50f60f94c034
children
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1 # tryCatchFunc wraps an expression that produces a value if it does not stop:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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2 # tryCatchFunc produces a list
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3 # On success of expr(), tryCatchFunc produces
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4 # list(success TRUE, value = expr(), msg = "")
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5 # On failure of expr(), tryCatchFunc produces
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6 # list(success = FALSE, value = NA, msg = "the error message")
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7 tryCatchFunc <- function(expr) {
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8 # format error for logging
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9 format_error <- function(e) {
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10 paste(c("Error { message:", e$message, ", call:", e$call, "}"), collapse = " ")
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11 }
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12 retval <- NULL
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13 tryCatch(
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14 expr = {
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15 retval <- ( list( success = TRUE, value = eval(expr = expr), msg = "" ) )
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16 }
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17 , error = function(e) {
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18 retval <<- list( success = FALSE, value = NA, msg = format_error(e) )
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19 }
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20 )
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21 return (retval)
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22 }
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23
11
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24 errorSink <- function(which_function, ...) {
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25 var_args <- "..."
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26 tryCatch(
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27 var_args <<- (deparse(..., width.cutoff = 60))
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28 , error = function(e) {print(e$message)}
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29 )
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30 if (var_args == "...")
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31 return
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32 # format error for logging
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33 format_error <- function(e) {
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34 sprintf(
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35 "Error\n{ message: %s\n, arguments: %s\n}\n"
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36 , e$message
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37 , Reduce(f = paste, x = var_args)
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38 )
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39 }
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40 format_warning <- function(e) {
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41 sprintf(
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42 "Warning\n{ message: %s\n, arguments: %s\n}\n"
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43 , e$message
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44 , Reduce(f = paste, x = var_args)
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45 )
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46 }
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47 sink_number <- sink.number()
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48 sink(stderr())
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49 tryCatch(
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50 var_args <- (deparse(..., width.cutoff = 60))
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51 , expr = {
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52 retval <- which_function(...)
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53 }
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54 , error = function(e) cat(format_error(e), file = stderr())
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55 , warning = function(w) cat(format_warning(w), file = stderr())
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56 )
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57 while (sink.number() > sink_number) {
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58 sink()
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59 }
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60 }
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61 errorPrint <- function(...) {
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62 errorSink(which_function = print, ...)
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63 }
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64 errorCat <- function(...) {
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65 errorSink(which_function = cat, ..., "\n")
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66 }
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67
0
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68
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69 # # pseudo-inverse - computational inverse of non-square matrix a
0
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70 # p.i <- function(a) {
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71 # solve(t(a) %*% a) %*% t(a)
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72 # }
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73
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74 # vim: sw=2 ts=2 et ai :