Mercurial > repos > prog > lcmsmatching

annotate MassbankConn.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
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 MassbankConn <- methods::setRefClass("MassbankConn", contains = c("RemotedbConn", "MassdbConn"), fields = list( .url = "character" ))
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1
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7 ###############
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8 # CONSTRUCTOR #
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9 ###############
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11 MassbankConn$methods( initialize = function(url = NA_character_, ...) {
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13 # Set URL
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14 .url <<- if (is.null(url) || is.na(url)) BIODB.MASSBANK.EU.WS.URL else url
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1
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16 callSuper(...)
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17 })
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19 ##########################
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20 # GET ENTRY CONTENT TYPE #
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21 ##########################
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23 MassbankConn$methods( getEntryContentType = function() {
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24 return(BIODB.TXT)
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25 })
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27 #####################
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28 # GET ENTRY CONTENT #
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29 #####################
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31 MassbankConn$methods( getEntryContent = function(ids) {
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1
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33 # Debug
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34 .self$.print.debug.msg(paste0("Get entry content(s) for ", length(ids)," id(s)..."))
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36 URL.MAX.LENGTH <- 2083
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1
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38 # Initialize return values
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39 content <- rep(NA_character_, length(ids))
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41 # Loop on all
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42 n <- 0
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43 while (n < length(ids)) {
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44
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45 # Get list of accession ids to retrieve
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46 accessions <- ids[(n + 1):length(ids)]
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1
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48 # Create URL request
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49 x <- get.entry.url(class = BIODB.MASSBANK, accession = accessions, content.type = BIODB.TXT, max.length = URL.MAX.LENGTH, base.url = .self$.url)
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51 # Debug
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52 .self$.print.debug.msg(paste0("Send URL request for ", x$n," id(s)..."))
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54 # Send request
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55 xmlstr <- .self$.get.url(x$url)
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56
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57 # Increase number of entries retrieved
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58 n <- n + x$n
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60 # Parse XML and get text
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61 if ( ! is.na(xmlstr)) {
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62 xml <- xmlInternalTreeParse(xmlstr, asText = TRUE)
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63 ns <- c(ax21 = "http://api.massbank/xsd")
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64 returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
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65 if (length(returned.ids) > 0)
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66 content[match(returned.ids, ids)] <- xpathSApply(xml, "//ax21:info", xmlValue, namespaces = ns)
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67 }
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68
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69 # Debug
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70 .self$.print.debug.msg(paste0("Now ", length(ids) - n," id(s) left to be retrieved..."))
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71 }
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73 return(content)
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74 })
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76 ################
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77 # CREATE ENTRY #
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78 ################
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79
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80 # Creates a Spectrum instance from file content.
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81 # content A file content, downloaded from the public database.
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82 # RETURN A spectrum instance.
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83 MassbankConn$methods( createEntry = function(content, drop = TRUE) {
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84 return(createMassbankEntryFromTxt(content, drop = drop))
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85 })
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86
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87 #################
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88 # GET MZ VALUES #
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89 #################
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90
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91 MassbankConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
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92 })
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93
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94 #################
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95 # GET ENTRY IDS #
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96 #################
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97
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98 MassbankConn$methods( getEntryIds = function(max.results = NA_integer_) {
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99
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100 # Set URL
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101 url <- paste0(.self$.url, 'searchPeak?mzs=1000&relativeIntensity=100&tolerance=1000&instrumentTypes=all&ionMode=Both')
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102 url <- paste0(url, '&maxNumResults=', (if (is.na(max.results)) 0 else max.results))
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103
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104 # Send request
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105 xmlstr <- .self$.get.url(url)
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106
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107 # Parse XML and get text
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108 if ( ! is.na(xmlstr)) {
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109 xml <- xmlInternalTreeParse(xmlstr, asText = TRUE)
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110 ns <- c(ax21 = "http://api.massbank/xsd")
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111 returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
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112 return(returned.ids)
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113 }
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114 })
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115
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116 ##################
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117 # GET NB ENTRIES #
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118 ##################
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119
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120 MassbankConn$methods( getNbEntries = function() {
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121 return(length(.self$getEntryIds()))
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122 })