Mercurial > repos > prog > lcmsmatching

comparison LipidmapsConn.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('LipdmapsConn')) { # Do not load again if already loaded 1 if ( ! exists('LipdmapsConn')) { # Do not load again if already loaded
2 2
3 source('BiodbConn.R') 3 source('RemotedbConn.R')
4 source('LipidmapsCompound.R') 4 source('LipidmapsCompound.R')
5 5
6 ##################### 6 #####################
7 # CLASS DECLARATION # 7 # CLASS DECLARATION #
8 ##################### 8 #####################
9 9
10 LipidmapsConn <- setRefClass("LipidmapsConn", contains = "BiodbConn") 10 LipidmapsConn <- setRefClass("LipidmapsConn", contains = "RemotedbConn")
11 11
12 ############### 12 ###############
13 # CONSTRUCTOR # 13 # CONSTRUCTOR #
14 ############### 14 ###############
15 15
22 ########################## 22 ##########################
23 # GET ENTRY CONTENT TYPE # 23 # GET ENTRY CONTENT TYPE #
24 ########################## 24 ##########################
25 25
26 LipidmapsConn$methods( getEntryContentType = function(type) { 26 LipidmapsConn$methods( getEntryContentType = function(type) {
27 return(RBIODB.CSV) 27 return(BIODB.CSV)
28 }) 28 })
29 29
30 ##################### 30 #####################
31 # GET ENTRY CONTENT # 31 # GET ENTRY CONTENT #
32 ##################### 32 #####################
33 33
34 LipidmapsConn$methods( getEntryContent = function(type, id) { 34 LipidmapsConn$methods( getEntryContent = function(type, id) {
35 35
36 if (type == RBIODB.COMPOUND) { 36 if (type == BIODB.COMPOUND) {
37 37
38 # Initialize return values 38 # Initialize return values
39 content <- rep(NA_character_, length(id)) 39 content <- rep(NA_character_, length(id))
40 40
41 # Request 41 # Request
42 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(RBIODB.LIPIDMAPS, x, content.type = RBIODB.CSV)), FUN.VALUE = '') 42 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(BIODB.LIPIDMAPS, x, content.type = BIODB.CSV)), FUN.VALUE = '')
43 43
44 return(content) 44 return(content)
45 } 45 }
46 46
47 return(NULL) 47 return(NULL)
50 ################ 50 ################
51 # CREATE ENTRY # 51 # CREATE ENTRY #
52 ################ 52 ################
53 53
54 LipidmapsConn$methods( createEntry = function(type, content, drop = TRUE) { 54 LipidmapsConn$methods( createEntry = function(type, content, drop = TRUE) {
55 return(if (type == RBIODB.COMPOUND) createLipidmapsCompoundFromCsv(content, drop = drop) else NULL) 55 return(if (type == BIODB.COMPOUND) createLipidmapsCompoundFromCsv(content, drop = drop) else NULL)
56 }) 56 })
57 } 57 }