testing xpaths

output_xpath.txt

> library(xml2)

> mzml_file <- "test_mzml.mzML"

> doc <- read_xml(mzml_file)

> xml_find_all(doc, "//cvParam")
{xml_nodeset (0)}

> ns <- xml_ns(doc)

> xml_find_all(doc, "//cvParam", ns = ns["d1"])
{xml_nodeset (0)}

> xml_find_all(doc, "//cvParam", ns = ns["xsi"])
{xml_nodeset (0)}

solution_xpath.R

# upgrade to xml2 v1.0.0
# then use namespace specification
# thanks @hadley
# https://twitter.com/hadleywickham/status/747515633835769857

library(xml2)

mzml_file <- "test_mzml.mzML"

doc <- read_xml(mzml_file)

xml_find_all(doc, "//d1:cvParam")

test_mzml.mzML

<?xml version="1.0" encoding="utf-8"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="SBC110871exopos" version="1.1.0">
    <cvList count="2">
      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
    </cvList>
    <fileDescription>
      <fileContent>
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
      </fileContent>
      <sourceFileList count="1">
        <sourceFile id="RAW1" name="SBC110871exopos.raw" location="file:///">
          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b2ca9b83d6752f533dd7d964613c29d44f0c5753"/>
        </sourceFile>
      </sourceFileList>
    </fileDescription>
    <referenceableParamGroupList count="1">
      <referenceableParamGroup id="CommonInstrumentParams">
        <cvParam cvRef="MS" accession="MS:1002416" name="Orbitrap Fusion" value=""/>
        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="FSN10352"/>
      </referenceableParamGroup>
    </referenceableParamGroupList>
    <softwareList count="2">
      <software id="Xcalibur" version="1.1.982">
        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
      </software>
      <software id="pwiz" version="3.0.9205">
        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
      </software>
    </softwareList>
    <instrumentConfigurationList count="2">
      <instrumentConfiguration id="IC1">
        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
        <componentList count="4">
          <source order="1">
            <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>
            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
          </source>
          <analyzer order="2">
            <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/>
          </analyzer>
          <analyzer order="3">
            <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>
          </analyzer>
          <detector order="4">
            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
          </detector>
        </componentList>
        <softwareRef ref="Xcalibur"/>
      </instrumentConfiguration>
      <instrumentConfiguration id="IC2">
        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
        <componentList count="4">
          <source order="1">
            <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>
            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
          </source>
          <analyzer order="2">
            <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/>
          </analyzer>
          <analyzer order="3">
            <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>
          </analyzer>
          <detector order="4">
            <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
          </detector>
        </componentList>
        <softwareRef ref="Xcalibur"/>
      </instrumentConfiguration>
    </instrumentConfigurationList>
    <dataProcessingList count="1">
      <dataProcessing id="pwiz_Reader_Thermo_conversion">
        <processingMethod order="0" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
      </dataProcessing>
    </dataProcessingList>
  </mzML>
</indexedmzML>  

test_xpath.R

library(xml2)

mzml_file <- "test_mzml.mzML"

doc <- read_xml(mzml_file)

xml_find_all(doc, "//cvParam")

ns <- xml_ns(doc)

xml_find_all(doc, "//cvParam", ns = ns["d1"])

xml_find_all(doc, "//cvParam", ns = ns["xsi"])