Mercurial > repos > prog > lcmsmatching

comparison HmdbConn.R @ 1:253d531a0193 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
author prog
date Sat, 03 Sep 2016 17:02:01 -0400
parents e66bb061af06
children 20d69a062da3
comparison
equal deleted inserted replaced
0:e66bb061af06 1:253d531a0193
1 if ( ! exists('HmdbConn')) { # Do not load again if already loaded 1 if ( ! exists('HmdbConn')) { # Do not load again if already loaded
2 2
3 source('BiodbConn.R') 3 source('RemotedbConn.R')
4 source('HmdbCompound.R') 4 source('HmdbCompound.R')
5 5
6 ##################### 6 #####################
7 # CLASS DECLARATION # 7 # CLASS DECLARATION #
8 ##################### 8 #####################
9 9
10 HmdbConn <- setRefClass("HmdbConn", contains = "BiodbConn") 10 HmdbConn <- setRefClass("HmdbConn", contains = "RemotedbConn")
11 11
12 ########################## 12 ##########################
13 # GET ENTRY CONTENT TYPE # 13 # GET ENTRY CONTENT TYPE #
14 ########################## 14 ##########################
15 15
16 HmdbConn$methods( getEntryContentType = function(type) { 16 HmdbConn$methods( getEntryContentType = function(type) {
17 return(RBIODB.XML) 17 return(BIODB.XML)
18 }) 18 })
19 19
20 ##################### 20 #####################
21 # GET ENTRY CONTENT # 21 # GET ENTRY CONTENT #
22 ##################### 22 #####################
23 23
24 HmdbConn$methods( getEntryContent = function(type, id) { 24 HmdbConn$methods( getEntryContent = function(type, id) {
25 25
26 if (type == RBIODB.COMPOUND) { 26 if (type == BIODB.COMPOUND) {
27 27
28 # Initialize return values 28 # Initialize return values
29 content <- rep(NA_character_, length(id)) 29 content <- rep(NA_character_, length(id))
30 30
31 # Request 31 # Request
32 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.HMDB, x, content.type = RBIODB.XML)), FUN.VALUE = '') 32 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(BIODB.HMDB, x, content.type = BIODB.XML)), FUN.VALUE = '')
33 33
34 return(content) 34 return(content)
35 } 35 }
36 36
37 return(NULL) 37 return(NULL)
40 ################ 40 ################
41 # CREATE ENTRY # 41 # CREATE ENTRY #
42 ################ 42 ################
43 43
44 HmdbConn$methods( createEntry = function(type, content, drop = TRUE) { 44 HmdbConn$methods( createEntry = function(type, content, drop = TRUE) {
45 return(if (type == RBIODB.COMPOUND) createHmdbCompoundFromXml(content, drop = drop) else NULL) 45 return(if (type == BIODB.COMPOUND) createHmdbCompoundFromXml(content, drop = drop) else NULL)
46 }) 46 })
47 47
48 } # end of load safe guard 48 } # end of load safe guard