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annotate PubchemCompound.R @ 0:3afe41d3e9e7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
author prog
date Mon, 11 Jul 2016 09:12:03 -0400
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('PubchemCompound')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 source('BiodbEntry.R')
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5 #####################
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6 # CLASS DECLARATION #
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7 #####################
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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9 PubchemCompound <- setRefClass("PubchemCompound", contains = "BiodbEntry")
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11 ###########
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12 # FACTORY #
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13 ###########
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15 createPubchemCompoundFromXml <- function(contents, drop = TRUE) {
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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17 library(XML)
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19 compounds <- list()
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21 # Set XML namespace
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22 ns <- c(pubchem = "http://pubchem.ncbi.nlm.nih.gov/pug_view")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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24 # Define xpath expressions
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25 xpath.expr <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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26 xpath.expr[[RBIODB.ACCESSION]] <- "//pubchem:RecordType[text()='CID']/../pubchem:RecordNumber"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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27 xpath.expr[[RBIODB.INCHI]] <- "//pubchem:Name[text()='InChI']/../pubchem:StringValue"
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28 xpath.expr[[RBIODB.INCHIKEY]] <- "//pubchem:Name[text()='InChI Key']/../pubchem:StringValue"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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30 for (content in contents) {
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32 # Create instance
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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33 compound <- PubchemCompound$new()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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35 # Parse XML
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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36 xml <- xmlInternalTreeParse(content, asText = TRUE)
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38 # Unknown compound
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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39 fault <- xpathSApply(xml, "/pubchem:Fault", xmlValue, namespaces = ns)
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40 if (length(fault) == 0) {
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42 # Test generic xpath expressions
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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43 for (field in names(xpath.expr)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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44 v <- xpathSApply(xml, xpath.expr[[field]], xmlValue, namespaces = ns)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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45 if (length(v) > 0)
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46 compound$setField(field, v)
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47 }
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49 # Get name
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50 name <- NA_character_
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51 tryCatch( { name <- xpathSApply(xml, "//pubchem:Name[text()='IUPAC Name']/../pubchem:StringValue", xmlValue, namespaces = ns) }, warning = function(w) {})
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52 if (is.na(name))
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53 tryCatch( { name <- xpathSApply(xml, "//pubchem:Name[text()='Record Title']/../pubchem:StringValue", xmlValue, namespaces = ns) }, warning = function(w) {})
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54 if ( ! is.na(name))
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55 compound$setField(RBIODB.NAME, name)
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57 }
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59 compounds <- c(compounds, compound)
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60 }
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62 # Replace elements with no accession id by NULL
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63 compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
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65 # If the input was a single element, then output a single object
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66 if (drop && length(contents) == 1)
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67 compounds <- compounds[[1]]
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69 return(compounds)
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70 }
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71 }