Mercurial > repos > prog > lcmsmatching

annotate PubchemConn.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
parents 3afe41d3e9e7
children
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 PubchemConn <- methods::setRefClass("PubchemConn", contains = "RemotedbConn", fields = list( .db = "character" ))
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7 ###############
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8 # CONSTRUCTOR #
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9 ###############
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11 PubchemConn$methods( initialize = function(db = BIODB.PUBCHEMCOMP, ...) {
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12 .db <<- db
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13 callSuper(...)
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14 })
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16 ##########################
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17 # GET ENTRY CONTENT TYPE #
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18 ##########################
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20 PubchemConn$methods( getEntryContentType = function() {
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21 return(BIODB.XML)
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22 })
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24 #####################
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25 # GET ENTRY CONTENT #
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26 #####################
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28 PubchemConn$methods( getEntryContent = function(ids) {
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30 # Debug
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31 .self$.print.debug.msg(paste0("Get entry content(s) for ", length(ids)," id(s)..."))
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33 URL.MAX.LENGTH <- 2083
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35 # Initialize return values
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36 content <- rep(NA_character_, length(ids))
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38 # Loop on all
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39 n <- 0
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40 while (n < length(ids)) {
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42 # Get list of accession ids to retrieve
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43 accessions <- ids[(n + 1):length(ids)]
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45 # Create URL request
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46 x <- get.entry.url(class = .self$.db, accession = accessions, content.type = BIODB.XML, max.length = URL.MAX.LENGTH)
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48 # Debug
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49 .self$.print.debug.msg(paste0("Send URL request for ", x$n," id(s)..."))
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51 # Send request
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52 xmlstr <- .self$.get.url(x$url)
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54 # Increase number of entries retrieved
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55 n <- n + x$n
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56
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57 # TODO When one of the id is wrong, no content is returned. Only a single error is returned, with the first faulty ID:
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58 # <Fault xmlns="http://pubchem.ncbi.nlm.nih.gov/pug_rest" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:schemaLocation="http://pubchem.ncbi.nlm.nih.gov/pug_rest https://pubchem.ncbi.nlm.nih.gov/pug_rest/pug_rest.xsd">
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59 # <Code>PUGREST.NotFound</Code>
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60 # <Message>Record not found</Message>
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61 # <Details>No record data for CID 1246452553</Details>
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62 # </Fault>
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64 # Parse XML and get included XML
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65 if ( ! is.na(xmlstr)) {
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66 xml <- xmlInternalTreeParse(xmlstr, asText = TRUE)
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67 ns <- c(pcns = "http://www.ncbi.nlm.nih.gov")
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68 returned.ids <- xpathSApply(xml, paste0("//pcns:", if (.self$.db == BIODB.PUBCHEMCOMP) 'PC-CompoundType_id_cid' else 'PC-ID_id'), xmlValue, namespaces = ns)
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69 content[match(returned.ids, ids)] <- vapply(getNodeSet(xml, paste0("//pcns:", if (.self$.db == BIODB.PUBCHEMCOMP) "PC-Compound" else 'PC-Substance'), namespaces = ns), saveXML, FUN.VALUE = '')
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70 }
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72 # Debug
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73 .self$.print.debug.msg(paste0("Now ", length(ids) - n," id(s) left to be retrieved..."))
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74 }
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75
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76 return(content)
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77 })
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78
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79 ################
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80 # CREATE ENTRY #
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81 ################
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82
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83 PubchemConn$methods( createEntry = function(content, drop = TRUE) {
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84 return(if (.self$.db == BIODB.PUBCHEMCOMP) createPubchemEntryFromXml(content, drop = drop) else createPubchemSubstanceFromXml(content, drop = drop))
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85 })
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87 #########################
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88 # GET PUBCHEM IMAGE URL #
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89 #########################
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90
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91 get.pubchem.image.url <- function(id, db = BIODB.PUBCHEMCOMP) {
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92
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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93 url <- paste0('http://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?', (if (db == BIODB.PUBCHEMCOMP) 'cid' else 'sid'), '=', id, '&t=l')
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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94
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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95 return(url)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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96 }