Mercurial > repos > prog > lcmsmatching

annotate ChebiConn.R @ 3:abfba8eb1c8d draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 494194bb501d1d7033613131865f7bd68976041c
author prog
date Tue, 14 Mar 2017 12:35:23 -0400
parents 45e985cd8e9e
children
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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1 #####################
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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2 # CLASS DECLARATION #
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3 #####################
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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5 ChebiConn <- methods::setRefClass("ChebiConn", contains = "RemotedbConn")
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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7 ##########################
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8 # GET ENTRY CONTENT TYPE #
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9 ##########################
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11 ChebiConn$methods( getEntryContentType = function() {
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12 return(BIODB.HTML)
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13 })
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15 #####################
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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16 # GET ENTRY CONTENT #
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17 #####################
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19 ChebiConn$methods( getEntryContent = function(id) {
0
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21 # Initialize return values
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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22 content <- rep(NA_character_, length(id))
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1
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24 # Request
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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25 content <- vapply(id, function(x) .self$.get.url(get.entry.url(BIODB.CHEBI, x)), FUN.VALUE = '')
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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27 return(content)
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28 })
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1
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30 ################
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31 # CREATE ENTRY #
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32 ################
0
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34 ChebiConn$methods( createEntry = function(content, drop = TRUE) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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35 return(createChebiEntryFromHtml(content, drop = drop))
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36 })
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1
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38 ##################
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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39 # GET NB ENTRIES #
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40 ##################
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1
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42 ChebiConn$methods( getNbEntries = function() {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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43 return(NA_integer_)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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44 })
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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46 #################
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47 # GET ENTRY IDS #
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48 #################
0
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1
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50 ChebiConn$methods( getEntryIds = function(max.results = NA_integer_) {
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51 request <- "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><SOAP-ENV:Envelope xmlns:SOAP-ENV=\"http://schemas.xmlsoap.org/soap/envelope/\" xmlns:tns=\"http://www.ebi.ac.uk/webservices/chebi\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:soap=\"http://schemas.xmlsoap.org/wsdl/soap/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" ><SOAP-ENV:Body><tns:getLiteEntity xmlns:tns=\"http://www.ebi.ac.uk/webservices/chebi\"><tns:search>1*</tns:search><tns:searchCategory>CHEBI ID</tns:searchCategory><tns:maximumResults>100</tns:maximumResults><tns:stars></tns:stars></tns:getLiteEntity></SOAP-ENV:Body></SOAP-ENV:Envelope>"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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52 print('********************************************************************************')
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53 print('********************************************************************************')
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54 results <- .self$.scheduler$sendSoapRequest('http://www.ebi.ac.uk:80/webservices/chebi/2.0/webservice', request)
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55 print(results)
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56 print('********************************************************************************')
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57 print('********************************************************************************')
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58 return(NULL)
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59 })