Failure to understand namespaces in XML::getNodeSet
Hadley, It?s sometimes amazing the mistakes I can make. No, it did not do what I wanted, which was read_xml(str_c(with_ns_xml, collapse = ?") Reproducible example follows: library(stringr) library(xml2) ## Given the correct argument value for collapse, the next two lines work no_ns <- read_xml(str_c(no_ns_xml, collapse = "")) with_ns <- read_xml(str_c(with_ns_xml, collapse = "")) ## The next line finds the node in the XML without a namespace xml_find_all(no_ns, "//WorkSet//Description") ## With a namespace designated in the XML ## Neither of the next two work, though I thought the second should xml_find_all(with_ns, "//WorkSet//Description") xml_find_all(with_ns, "/WorkSet//Description", ns = xml_ns(with_ns)) ## Using xml_ns_strip() works as predicted xml_find_all(xml_ns_strip(with_ns), "//WorkSet//Description") ## I was surprised to find the incorrect namespace value did not matter xml_find_all(no_ns, "//WorkSet//Description", ns = xml_ns(with_ns)) ## This also seems to ignore the namespace argument value xml_find_all(xml_ns_strip(with_ns), "/WorkSet//Description", ns = xml_ns(with_ns)) Full output follows:
## Given the correct argument value for collapse, the next two lines work no_ns <- read_xml(str_c(no_ns_xml, collapse = "")) with_ns <- read_xml(str_c(with_ns_xml, collapse = "")) ## The next line finds the node in the XML without a namespace xml_find_all(no_ns, "//WorkSet//Description")
{xml_nodeset (1)}
[1] <Description>MFIA 9-Plex (CharlesRiver)</Description>
## With a namespace designated in the XML ## Neither of the next two work, though I thought the second should xml_find_all(with_ns, "//WorkSet//Description")
{xml_nodeset (0)}
xml_find_all(with_ns, "/WorkSet//Description", ns = xml_ns(with_ns))
{xml_nodeset (0)}
## Using xml_ns_strip() works as predicted xml_find_all(xml_ns_strip(with_ns), "//WorkSet//Description")
{xml_nodeset (1)}
[1] <Description>MFIA 9-Plex (CharlesRiver)</Description>
## I was surprised to find the incorrect namespace value did not matter xml_find_all(no_ns, "//WorkSet//Description", ns = xml_ns(with_ns))
{xml_nodeset (1)}
[1] <Description>MFIA 9-Plex (CharlesRiver)</Description>
## This also seems to ignore the namespace argument value xml_find_all(xml_ns_strip(with_ns), "/WorkSet//Description", ns = xml_ns(with_ns))
{xml_nodeset (1)}
[1] <Description>MFIA 9-Plex (CharlesRiver)</Description>
R. Mark Sharp, Ph.D.
msharp at TxBiomed.org
On Jan 31, 2017, at 5:52 PM, Hadley Wickham <h.wickham at gmail.com> wrote:
I think you want
x <- read_xml('<?xml version="1.0" ?>
<WorkSet xmlns="http://labkey.org/etl/xml">
<Description>MFIA 9-Plex (CharlesRiver)</Description>
</WorkSet>')
The collapse argument do what you think it does.
Hadley
On Tue, Jan 31, 2017 at 5:36 PM, Mark Sharp <msharp at txbiomed.org> wrote:
Hadley,
Thank you. I am able to get the xml_ns_strip() function to work with my file directly so I will likely be able to reach my immediate goal.
However, I still have had no success with understanding the namespace problem. I am not able to use read_xml() using the object I generated for the reproducible example, which is simply a character vector of length 4 having the contents of the XML file as produce by readLines(). I then used dput() to define the structure. The resulting structure apparently is not to the liking of read_xml(). I have reproduced the necessary code here for your convenience. There error is below.
##
library(xml2)
library(stringr)
with_ns_xml <- c("<?xml version=\"1.0\" ?>",
"<WorkSet xmlns=\"http://labkey.org/etl/xml\">",
"<Description>MFIA 9-Plex (CharlesRiver)</Description>",
"</WorkSet>")
## without str_c() collapse it complain of a vector of length > 1 also.
read_xml(str_c(with_ns_xml, collapse = TRUE))
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, :
Start tag expected, '<' not found [4]
## produces the following error message.
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, :
Start tag expected, '<' not found [4]
I have similar issues with xml2::xml_find_all
xml_find_all(str_c(with_ns_xml, collapse = TRUE), "/WorkSet//Description")
## Produces the following error message.
Error in UseMethod("xml_find_all") :
no applicable method for 'xml_find_all' applied to an object of class "character"
R. Mark Sharp, Ph.D.
msharp at TxBiomed.org
On Jan 31, 2017, at 4:27 PM, Hadley Wickham <h.wickham at gmail.com> wrote: See the last example in ?xml2::xml_find_all or use xml2::xml2::xml_ns_strip() Hadley On Tue, Jan 31, 2017 at 9:43 AM, Mark Sharp <msharp at txbiomed.org> wrote:
I am trying to read a series of XML files that use a namespace and I have failed, thus far, to discover the proper syntax. I have a reproducible example below. I have two XML character strings defined: one without a namespace and one with. I show that I can successfully extract the node using the XML string without the namespace and fail when using the XML string with the namespace.
Mark
PS I am having the same problem with the xml2 package and am hoping understanding one with help with the other.
##
library(XML)
## The first XML text (no_ns_xml) does not have a namespace defined
no_ns_xml <- c("<?xml version=\"1.0\" ?>", "<WorkSet>",
"<Description>MFIA 9-Plex (CharlesRiver)</Description>",
"</WorkSet>")
l_no_ns_xml <-xmlTreeParse(no_ns_xml, asText = TRUE, getDTD = FALSE,
useInternalNodes = TRUE)
## The node is found
getNodeSet(l_no_ns_xml, "/WorkSet//Description")
## The second XML text (with_ns_xml) has a namespace defined
with_ns_xml <- c("<?xml version=\"1.0\" ?>",
"<WorkSet xmlns=\"http://labkey.org/etl/xml\">",
"<Description>MFIA 9-Plex (CharlesRiver)</Description>",
"</WorkSet>")
l_with_ns_xml <-xmlTreeParse(with_ns_xml, asText = TRUE, getDTD = FALSE,
useInternalNodes = TRUE)
## The node is not found
getNodeSet(l_with_ns_xml, "/WorkSet//Description")
## I attempt to provide the namespace, but fail.
ns <- "http://labkey.org/etl/xml"
names(ns)[1] <- "xmlns"
getNodeSet(l_with_ns_xml, "/WorkSet//Description", namespaces = ns)
R. Mark Sharp, Ph.D.
Director of Data Science Core
Southwest National Primate Research Center
Texas Biomedical Research Institute
P.O. Box 760549
San Antonio, TX 78245-0549
Telephone: (210)258-9476
e-mail: msharp at TxBiomed.org
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