问题
I am using the xml2 package in R to access xml data, and found that it behaves different on different xml_documents.
On this pet example
library(xml2)
doc <- read_xml( "<MEMBERS>
<CUSTOMER>
<ID>178</ID>
<FIRST.NAME>Alvaro</FIRST.NAME>
<LAST.NAME>Juarez</LAST.NAME>
<ADDRESS>123 Park Ave</ADDRESS>
<ZIP>57701</ZIP>
</CUSTOMER>
<CUSTOMER>
<ID>934</ID>
<FIRST.NAME>Janette</FIRST.NAME>
<LAST.NAME>Johnson</LAST.NAME>
<ADDRESS>456 Candy Ln</ADDRESS>
<ZIP>57701</ZIP>
</CUSTOMER>
</MEMBERS>")
doc
{xml_document}
<MEMBERS>
[1] <CUSTOMER>\n <ID>178</ID>\n <FIRST.NAME>Alvaro</FIRST.NAME>\n <LAST.NAME>Juarez</LAST.NAME>\n <ADDRESS>12 ...
[2] <CUSTOMER>\n <ID>934</ID>\n <FIRST.NAME>Janette</FIRST.NAME>\n <LAST.NAME>Johnson</LAST.NAME>\n <ADDRESS> ...
I can run the following code
xml_find_all(doc, "//FIRST.NAME")
{xml_nodeset (2)}
[1] <FIRST.NAME>Alvaro</FIRST.NAME>
[2] <FIRST.NAME>Janette</FIRST.NAME>
giving me the expected output (finding all nodes with 'FIRST.NAME' tags).
However, if I perform the same action on this xml file:
example <- read_xml(file.path("~/Downloads", "uniprot_subset.xml"))
> example
{xml_document}
<uniprot>
[1] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2019-01-16" version="35">\n <accession>Q6GZX4</accession>\n <name>001R_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Putative tr ...
[2] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2019-01-16" version="36">\n <accession>Q6GZX3</accession>\n <name>002L_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacter ...
[3] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2009-06-16" modified="2018-06-20" version="22">\n <accession>Q197F8</accession>\n <name>002R_IIV3</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacteri ...
[4] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2009-06-16" modified="2017-09-27" version="18">\n <accession>Q197F7</accession>\n <name>003L_IIV3</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacteri ...
[5] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2019-01-16" version="31">\n <accession>Q6GZX2</accession>\n <name>003R_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacter ...
[6] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2017-09-27" version="29">\n <accession>Q6GZX1</accession>\n <name>004R_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacter ...
[7] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2009-06-16" modified="2017-09-27" version="24">\n <accession>Q197F5</accession>\n <name>005L_IIV3</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacteri ...
[8] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2019-01-16" version="38">\n <accession>Q6GZX0</accession>\n <name>005R_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacter ...
[9] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2009-06-16" modified="2019-01-16" version="44">\n <accession>Q91G88</accession>\n <name>006L_IIV6</name>\n <protein>\n <recommendedName>\n <fullName>Putative Kil ...
[10] <entry xmlns="http://uniprot.org/uniprot" dataset="Swiss-Prot" created="2011-06-28" modified="2017-09-27" version="27">\n <accession>Q6GZW9</accession>\n <name>006R_FRG3G</name>\n <protein>\n <recommendedName>\n <fullName>Uncharacter ...
it behaves differently
xml_find_all(example, "//accession")
{xml_nodeset (0)}
Basically, it will not find any nodes with the 'accession' tag, even though they exist and can be accessed by different functions, for instance using
xml_children(xml_children(example)[1])[1]
{xml_nodeset (1)}
[1] <accession>Q6GZX4</accession>
Can anyone tell me why the xml_find_all function does not find any nodes in the latter example?
回答1:
This happens because your pet example does not contain namespaces, but the second XML file does.
example %>% xml_ns()
d1 <-> http://uniprot.org/uniprot
d2 <-> http://uniprot.org/uniprot
d3 <-> http://uniprot.org/uniprot
d4 <-> http://uniprot.org/uniprot
d5 <-> http://uniprot.org/uniprot
d6 <-> http://uniprot.org/uniprot
d7 <-> http://uniprot.org/uniprot
d8 <-> http://uniprot.org/uniprot
d9 <-> http://uniprot.org/uniprot
d10 <-> http://uniprot.org/uniprot
Since each entry has the same namespace, in this case the simplest approach is probably to strip (remove) the namespaces:
example %>% xml_ns_strip()
And xml_find_all
should now work as expected:
example %>% xml_find_all("//accession")
{xml_nodeset (10)}
[1] <accession>Q6GZX4</accession>
[2] <accession>Q6GZX3</accession>
[3] <accession>Q197F8</accession>
[4] <accession>Q197F7</accession>
[5] <accession>Q6GZX2</accession>
[6] <accession>Q6GZX1</accession>
[7] <accession>Q197F5</accession>
[8] <accession>Q6GZX0</accession>
[9] <accession>Q91G88</accession>
[10] <accession>Q6GZW9</accession>
If you wanted to retain the namespaces, you could access accessions like so:
example %>% xml_find_all("//d1:accession")
which works in this case because the default name d1
given to the namespace for the first entry maps to the same namespace for all entries.
来源:https://stackoverflow.com/questions/55727236/xml-find-all-function-from-xml2-package-r-does-not-find-relevant-nodes