Mercurial > repos > prog > lcmsmatching

annotate UrlRequestScheduler.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents 3afe41d3e9e7
children b8f70d8216b3
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1 #############
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2 # CONSTANTS #
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3 #############
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5 BIODB.GET <- 'GET'
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6 BIODB.POST <- 'POST'
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8 #####################
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9 # CLASS DECLARATION #
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10 #####################
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12 UrlRequestScheduler <- methods::setRefClass("UrlRequestScheduler", fields = list(.n = "numeric", .t = "numeric", .time.of.last.request = "ANY", .useragent = "character", .ssl.verifypeer = "logical", .nb.max.tries = "integer", .verbose = "integer"))
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14 # n: number of connections
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15 # t: time (in seconds)
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17 # The scheduler restrict the number of connections at n per t seconds.
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19 ###############
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20 # CONSTRUCTOR #
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21 ###############
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23 UrlRequestScheduler$methods( initialize = function(n = 1, t = 1, useragent = NA_character_, ssl.verifypeer = TRUE, ...) {
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24 .n <<- n
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25 .t <<- t
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26 .time.of.last.request <<- -1
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27 .useragent <<- useragent
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28 .nb.max.tries <<- 10L
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29 .ssl.verifypeer <<- ssl.verifypeer
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30 .verbose <<- 0L
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31 callSuper(...) # calls super-class initializer with remaining parameters
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32 })
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1
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34 ##################
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35 # SET USER AGENT #
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36 ##################
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38 UrlRequestScheduler$methods( setUserAgent = function(useragent) {
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39 .useragent <<- useragent
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40 })
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42 ###############
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43 # SET VERBOSE #
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44 ###############
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46 UrlRequestScheduler$methods( setVerbose = function(verbose) {
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47 .verbose <<- verbose
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48 })
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1
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50 ##################
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51 # WAIT AS NEEDED #
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52 ##################
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54 # Wait the specified between two requests.
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55 UrlRequestScheduler$methods( .wait.as.needed = function() {
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56
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57 # Compute minimum waiting time between two URL requests
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58 waiting_time <- .self$.t / .self$.n
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59
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60 # Wait, if needed, before previous URL request and this new URL request.
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61 if (.self$.time.of.last.request > 0) {
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62 spent_time <- Sys.time() - .self$.time.of.last.request
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63 if (spent_time < waiting_time)
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64 Sys.sleep(waiting_time - spent_time)
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65 }
0
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66
1
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67 # Store current time
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68 .time.of.last.request <<- Sys.time()
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69 })
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71 #########################
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72 # GET CURL OPTIONS {{{1 #
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73 #########################
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75 UrlRequestScheduler$methods( .get.curl.opts = function(opts = list()) {
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76 opts <- RCurl::curlOptions(useragent = .self$.useragent, timeout.ms = 60000, verbose = FALSE, .opts = opts)
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77 return(opts)
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78 })
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79
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80 ###################
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81 # DO GET URL {{{1 #
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82 ###################
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83
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84 UrlRequestScheduler$methods( .doGetUrl = function(url, params = list(), method = BIODB.GET, opts = .self$.get.curl.opts()) {
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85
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86 content <- NA_character_
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87
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88 # Use form to send URL request
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89 if ( method == BIODB.POST || ( ! is.null(params) && ! is.na(params) && length(params) > 0)) {
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90 switch(method,
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91 GET = { content <- RCurl::getForm(url, .opts = opts, .params = params) },
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92 POST = { content <- RCurl::postForm(url, .opts = opts, .params = params) },
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93 stop(paste('Unknown method "', method, '".'))
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94 )
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95 }
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96
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97 # Get URL normally
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98 else {
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99 content <- RCurl::getURL(url, .opts = opts, ssl.verifypeer = .self$.ssl.verifypeer)
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100 }
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101 return(content)
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102 })
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103
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104 ##########################
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105 # SEND SOAP REQUEST {{{1 #
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106 ##########################
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107
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108 UrlRequestScheduler$methods( sendSoapRequest = function(url, request) {
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109 header <- c(Accept="text/xml", Accept="multipart/*", 'Content-Type'="text/xml; charset=utf-8")
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110 opts <- .self$.get.curl.opts(list(httpheader = header, postfields = request))
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111 results <- .self$getUrl(url, method = BIODB.POST, opts = opts)
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112 return(results)
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113 })
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114
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115 ################
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116 # GET URL {{{1 #
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117 ################
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118
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119 UrlRequestScheduler$methods( getUrl = function(url, params = list(), method = BIODB.GET, opts = .self$.get.curl.opts()) {
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120
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121 content <- NA_character_
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122
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123 # Wait required time between two requests
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124 .self$.wait.as.needed()
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125
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126 # Run query
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127 for (i in seq(.self$.nb.max.tries)) {
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128 tryCatch({ content <- .self$.doGetUrl(url, params = params, method = method, opts = opts) },
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129 error = function(e) { if (.self$.verbose > 0) print("Retry connection to server...") } )
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130 if ( ! is.na(content))
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131 break
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132 }
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133
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134 return(content)
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135 })