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comparison PeakforestConn.R @ 2:20d69a062da3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
author prog
date Thu, 02 Mar 2017 08:55:00 -0500
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1:253d531a0193 2:20d69a062da3
1 #####################
2 # CLASS DECLARATION #
3 #####################
4 #'A class to connect to peakforest
5 #'@export
6 #'@field .url An urel to the database
7 PeakforestConn <- methods::setRefClass("PeakforestConn", contains = c("RemotedbConn","MassdbConn"), fields = list( .url = "character" )) # TODO Inherits also from MassdbConn
8
9 ##########################
10 # GET ENTRY CONTENT TYPE #
11 ##########################
12
13 PeakforestConn$methods( getEntryContentType = function(type) {
14 return(BIODB.JSON)
15 })
16
17 #####################
18 # GET ENTRY CONTENT #
19 #####################
20
21 PeakforestConn$methods( getEntryContent = function(id) {
22
23
24 # Initialize return values
25 content <- rep(NA_character_, length(id))
26 # Request
27
28 url <- get.entry.url(BIODB.PEAKFOREST, id[i], BIODB.JSON,token = .self$.token)
29 jsonstr <- .self$.get.url(url)
30 if(startsWith("<html>", jsonstr) ){
31 next
32 }
33
34 return(content)
35 })
36
37
38 ##########################################
39 # SEARCH FOR SPECTRA IN GIVEN MASS RANGE #
40 ##########################################
41
42 PeakforestConn$methods( searchMzRange = function(mzmin, mzmax, rtype = c("object","spec","peak")){
43
44 rtype <- match.arg(rtype)
45 if(mzmin>mzmax){
46 stop("mzmin shloud be inferior to mzmax in searchMzRange.")
47 }
48
49 url <- paste0("https://rest.peakforest.org/spectra/lcms/peaks/get-range/",mzmin,"/",mzmax)
50
51 contents <- .self$.get.url(url)
52
53 jsontree <- fromJSON(contents)
54
55 ###No match form the output.
56 if( length(jsontree)==0 ) return(NULL)
57
58 # Getting a list of all the id.
59 lid <- sapply(jsontree,function(x){
60 x$source$id
61 })
62
63 # Returning the content for all the spectra
64 contents <- .self$getEntryContent(lid)
65
66 entries <- .self$createEntry(contents)
67
68 # Checking the return type
69 if( rtype=="object" ){
70 return( entries )
71 }
72
73 ### XXXX See if we don't want to reduce the output and factorize this shit.
74 toreturn <- NULL
75 if( rtype=="spec" ){
76 toreturn <- sapply(entries,function(x){
77 x$getFieldsAsDataFrame()
78 })
79 }
80 if( rtype=="peak" ){
81 toreturn <- lapply(entries,function(x){
82 temp <- as.data.frame( x$getFieldValue( BIODB.PEAKS ))
83 temp$accession = x$getFieldValue( BIODB.ACCESSION)
84 return(temp)
85
86 })
87 }
88 ###Trying to convert in data.frame
89 if(!is.data.frame(toreturn)){
90 temp <- colnames(toreturn[[1]])
91 toreturn <- do.call("rbind.fill",toreturn)
92 colnames(toreturn) <- temp
93 }
94
95 return(toreturn)
96 })
97
98
99 #################################################
100 # SEARCH FOR SPECTRA IN A TOLERANCE AROUND A MZ #
101 #################################################
102
103 PeakforestConn$methods( searchMzTol = function(mz, tol, tolunit=BIODB.MZTOLUNIT.VALS,
104 rtype = c("object","spec","peak")){
105
106 rtype <- match.arg(rtype)
107 tolunit <- match.arg(tolunit)
108
109 if( tolunit == BIODB.MZTOLUNIT.PPM){
110 tol <- tol * mz * 10^-6
111 }
112
113 mzmin <- mz - tol
114 mzmax <- mz + tol
115
116 return(.self$searchMzRange(mzmin, mzmax, rtype = rtype))
117
118 })
119
120 ##################################################
121 # SEARCH FOR MSMS SPECTRA PRECUSOR AROUND A MASS #
122 ##################################################
123
124
125 PeakforestConn$methods(
126 searchSpecPrecTol = function(mz,
127 tol,
128 tolunit = "plain",
129 mode = NULL) {
130 #TODO handle the units
131 #tolunit <- match.arg(tolunit)
132
133 strmode <- ''
134
135 if (!is.null(mode)) {
136 if (mode %in% c(BIODB.MSMODE.NEG, BIODB.MSMODE.POS)) {
137 strmode <- paste0('?polarity=', mode)
138 }
139
140 }
141
142 if (tolunit == BIODB.MZTOLUNIT.PPM) {
143 tol <- tol * mz * 10 ^ -6
144 }
145
146 ##Request which return peak and not spectra.
147 url <-
148 paste0(
149 "https://rest.peakforest.org/spectra/lcms/search-naive/",
150 mz,
151 "/",
152 tol,
153 strmode
154 )
155 contents <- .self$.get.url(url)
156 entries <- .self$createReducedEntry(contents, drop = TRUE)
157 return(entries)
158 }
159 )
160
161
162 ################
163 # CREATE ENTRY #
164 ################
165
166 # Creates a Spectrum instance from file content.
167 # content A file content, downloaded from the public database.
168 # RETURN A spectrum instance.
169 PeakforestConn$methods( createEntry = function(content, drop = TRUE) {
170 return(createPeakforestSpectraFromJSON(content, drop = drop))
171 })
172
173 PeakforestConn$methods( createReducedEntry = function(content , drop = TRUE){
174 entries <- createReducedSpectraFromJSON(content, drop = drop)
175 return(entries)
176 })