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comparison MirbaseConn.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
parents 253d531a0193
children
comparison
equal deleted inserted replaced
1:253d531a0193 2:20d69a062da3
1 if ( ! exists('MirbaseConn')) { # Do not load again if already loaded 1 #####################
2 # CLASS DECLARATION #
3 #####################
2 4
3 source('RemotedbConn.R') 5 MirbaseConn <- methods::setRefClass("MirbaseConn", contains = "RemotedbConn")
4 source('MirbaseCompound.R')
5 6
6 ##################### 7 ##########################
7 # CLASS DECLARATION # 8 # GET ENTRY CONTENT TYPE #
8 ##################### 9 ##########################
9 10
10 MirbaseConn <- setRefClass("MirbaseConn", contains = "RemotedbConn") 11 MirbaseConn$methods( getEntryContentType = function() {
12 return(BIODB.HTML)
13 })
11 14
12 ########################## 15 #####################
13 # GET ENTRY CONTENT TYPE # 16 # GET ENTRY CONTENT #
14 ########################## 17 #####################
15 18
16 MirbaseConn$methods( getEntryContentType = function(type) { 19 MirbaseConn$methods( getEntryContent = function(ids) {
17 return(BIODB.HTML)
18 })
19 20
20 ##################### 21 # Initialize return values
21 # GET ENTRY CONTENT # 22 content <- rep(NA_character_, length(ids))
22 #####################
23
24 MirbaseConn$methods( getEntryContent = function(type, id) {
25 23
26 if (type == BIODB.COMPOUND) { 24 # Request
25 content <- vapply(ids, function(x) .self$.get.url(get.entry.url(BIODB.MIRBASE, x, content.type = BIODB.HTML)), FUN.VALUE = '')
27 26
28 # Initialize return values 27 return(content)
29 content <- rep(NA_character_, length(id)) 28 })
30 29
31 # Request 30 ################
32 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(BIODB.MIRBASE, x, content.type = BIODB.HTML)), FUN.VALUE = '') 31 # CREATE ENTRY #
32 ################
33 33
34 return(content) 34 MirbaseConn$methods( createEntry = function(content, drop = TRUE) {
35 } 35 return(createMirbaseEntryFromHtml(content, drop = drop))
36 })
36 37
37 return(NULL) 38 ###################
38 }) 39 # FIND ACCESSIONS #
40 ###################
39 41
40 ################ 42 MirbaseConn$methods( findAccessions = function(name) {
41 # CREATE ENTRY #
42 ################
43
44 MirbaseConn$methods( createEntry = function(type, content, drop = TRUE) {
45 return(if (type == BIODB.COMPOUND) createMirbaseCompoundFromHtml(content, drop = drop) else NULL)
46 })
47 43
48 ################### 44 # Get HTML
49 # FIND ACCESSIONS # 45 htmlstr <- .self$.get.url('http://www.mirbase.org/cgi-bin/query.pl', params = c(terms = name, submit = 'Search'))
50 ###################
51 46
52 MirbaseConn$methods( 47 # Parse HTML
53 findAccessions = function(name) { 48 xml <- htmlTreeParse(htmlstr, asText = TRUE, useInternalNodes = TRUE)
54 49
55 # Get HTML 50 # Get accession number
56 htmlstr <- .self$.scheduler$getUrl('http://www.mirbase.org/cgi-bin/query.pl', params = c(terms = name, submit = 'Search')) 51 acc <- unlist(xpathSApply(xml, "//a[starts-with(.,'MIMAT')]", xmlValue))
57 52
58 # Parse HTML 53 return(acc)
59 xml <- htmlTreeParse(htmlstr, asText = TRUE, useInternalNodes = TRUE) 54 })
60
61 # Get accession number
62 acc <- unlist(xpathSApply(xml, "//a[starts-with(.,'MIMAT')]", xmlValue))
63
64 return(acc)
65 })
66 }