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.
msh...@txbiomed.org
> On Jan 31, 2017, at 5:52 PM, Hadley Wickham <h.wick...@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 <msh...@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.
>> msh...@txbiomed.org
>>
>>
>>
>>
>>
>>> On Jan 31, 2017, at 4:27 PM, Hadley Wickham <h.wick...@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 <msh...@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: msh...@txbiomed.org
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> CONFIDENTIALITY NOTICE: This e-mail and any files and/or...{{dropped:10}}
>>>>
>>>> ______________________________________________
>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>>
>>> --
>>> http://hadley.nz
>>
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>
>
>
> --
> http://hadley.nz
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