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comparison EnzymeConn.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('EnzymeConn')) { # Do not load again if already loaded 1 #####################
2 # CLASS DECLARATION #
3 #####################
2 4
3 source('RemotedbConn.R') 5 EnzymeConn <- methods::setRefClass("EnzymeConn", contains = "RemotedbConn")
4 source('EnzymeCompound.R')
5 6
6 ##################### 7 ##########################
7 # CLASS DECLARATION # 8 # GET ENTRY CONTENT TYPE #
8 ##################### 9 ##########################
9 10
10 EnzymeConn <- setRefClass("EnzymeConn", contains = "RemotedbConn") 11 EnzymeConn$methods( getEntryContentType = function() {
12 return(BIODB.TXT)
13 })
11 14
12 ########################## 15 #####################
13 # GET ENTRY CONTENT TYPE # 16 # GET ENTRY CONTENT #
14 ########################## 17 #####################
15 18
16 EnzymeConn$methods( getEntryContentType = function(type) { 19 EnzymeConn$methods( getEntryContent = function(id) {
17 return(BIODB.TXT)
18 })
19 20
20 ##################### 21 # Initialize return values
21 # GET ENTRY CONTENT # 22 content <- rep(NA_character_, length(id))
22 #####################
23
24 EnzymeConn$methods( getEntryContent = function(type, id) {
25 23
26 if (type == BIODB.COMPOUND) { 24 # Request
25 content <- vapply(id, function(x) .self$.get.url(get.entry.url(BIODB.ENZYME, accession = x, content.type = BIODB.TXT)), FUN.VALUE = '')
27 26
28 # Initialize return values 27 return(content)
29 content <- rep(NA_character_, length(id)) 28 })
30 29
31 # Request 30 ################
32 content <- vapply(id, function(x) .self$.scheduler$getUrl(get.entry.url(BIODB.ENZYME, accession = x, content.type = BIODB.TXT)), FUN.VALUE = '') 31 # CREATE ENTRY #
32 ################
33 33
34 return(content) 34 EnzymeConn$methods( createEntry = function(content, drop = TRUE) {
35 } 35 return(createEnzymeEntryFromTxt(content, drop = drop))
36 36 })
37 return(NULL)
38 })
39
40 ################
41 # CREATE ENTRY #
42 ################
43
44 EnzymeConn$methods( createEntry = function(type, content, drop = TRUE) {
45 return(if (type == BIODB.COMPOUND) createEnzymeCompoundFromTxt(content, drop = drop) else NULL)
46 })
47 }