4

I am trying to parse an XML file with xml2. But I cannot for the life of me figure out how to do it by specifying the name.

This works:

library(xml2)
library(dplyr)

xml <- read_xml(file)

-->

> xml
{xml_document}
<indexedmzML schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
[1] <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  ...
[2] <indexList count="2">\n  <index name="spectrum">\n    <offset idRef="scanId=3027">15181</offset>\n    <offset idRef="scanId=3524">30052</offset> ...
[3] <indexListOffset>73363063</indexListOffset>
[4] <fileChecksum>b8f69d6276d9c4929e74416bc9e3446a173d1894</fileChecksum>

And I can extract by position both step-by-step and with xpath:

xml_child(xml, 1) %>% xml_child(7) %>% xml_attr("startTimeStamp")

_

xml_child(xml, "/*[1]/*[7]") %>% xml_attr("startTimeStamp")



However my attemps to select by name are failing.

> xml_child(xml, "indexedmzML")
{xml_missing}
<NA>
> xml_child(xml, "mzML")
{xml_missing}
<NA>

and 

> xml_child(xml, "/indexedmzML")
{xml_missing}
<NA>
> xml_child(xml, "/mzML")
{xml_missing}
<NA>

and 

> xml_child(xml, "/mzML/run")
{xml_missing}
<NA>



Can somehow point me to the solution that is somehow escaping me?



EDIT:

OK here is a data example. With that data what I want is

xml_child(xml, 1) %>% xml_child(2) %>% xml_attr("startTimeStamp")

But selected by name.

<?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="0001_LIP1p_20150803_008_CHCl3-MeOH_1_1" version="1.1.0">

      <dataProcessing id="pwiz_Reader_Agilent_conversion">
        <processingMethod order="0" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
        </processingMethod>
        <processingMethod order="1" softwareRef="pwiz">
          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
          <userParam name="Agilent/MassHunter peak picking"/>
        </processingMethod>
      </dataProcessing>

    <run id="_x0030_001_LIP1p_20150803_008_CHCl3-MeOH_1_1" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2015-08-03T14:34:14Z" defaultSourceFileRef="MSScan.bin">

    </run>
  </mzML>
</indexedmzML>
4

1 回答 1

6

如果startTimeStamp要从 XML 文件中提取所有值，可以执行以下操作：

xml %>% xml_find_all("//@startTimeStamp") %>% xml_text()

编辑：

如果要按名称选择它，则需要担心名称空间。

的确，

xml %>% xml_child("mzML")

将返回

{xml_missing}
<NA>

您首先需要检查与您的 XML 文件关联的名称空间：

xml_ns(xml)
# d1   <-> http://psi.hupo.org/ms/mzml
# d2   <-> http://psi.hupo.org/ms/mzml
# xsi  <-> http://www.w3.org/2001/XMLSchema-instance
# xsi1 <-> http://www.w3.org/2001/XMLSchema-instance

所以你需要使用：

xml %>% xml_child("d1:mzML")

对于您感兴趣的属性的完整路径：

xml %>% xml_child("d1:mzML") %>% xml_child("d1:run") %>% xml_attr("startTimeStamp")

的文档xml_ns()提供了更多信息，并鼓励您使用更多信息名称重命名命名空间。

于 2016-12-05T15:54:16.343 回答