SOLVED: (mostly)
So I'll post this here in case it helps someone in the future.
fileName <- '001.xml'
doc <- xmlTreeParse(fileName,
handlers=list("comment"=function(x,...){NULL}), asTree = TRUE)
root <- xmlRoot(doc)
Connected_To <- xmlToDataFrame(getNodeSet(root,
'//ccd:el-e3657392-8e26-42a4-a996-258f9e645c46',"ccd"))
Must use xmlTreeParse.
Connected_To is a dataframe with the element names as colnames and the rows
are for each instance in the file.
I still get an warning:
Namespace prefix ccd on el-e3657392-8e26-42a4-a996-258f9e645c46 is not defined
I haven't quite found the solution for this namespace problem. I have tried
a few functions/examples from the XML package but they usually return a
list instead of a character vector. But the result dataframe from the XML
is correct and that is my initial goal.
Cheers,
Tim
On Thu, Apr 17, 2014 at 3:54 PM, Timothy W. Cook <t...@mlhim.org> wrote:
> Apologies, I forgot to add details:
> platform x86_64-pc-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major 3
> minor 0.1
> year 2013
> month 05
> day 16
> svn rev 62743
> language R
> version.string R version 3.0.1 (2013-05-16)
> nickname Good Sport
>
> Executed inside R Studio Version 0.98.501
>
>
>
> On Thu, Apr 17, 2014 at 12:35 PM, Timothy W. Cook <t...@mlhim.org> wrote:
>
>> R newbie, experienced software developer.
>>
>> I have a bit of confusion regarding using this function. See the XML
>> fragment at the end of the post.
>>
>> This works as far as retrieving the nodeset:
>>
>> > fileName <- '/home/tim/MLHIM/git/EpiS3/test_ccd/inst/examples/001.xml'
>>
>> > doc <- xmlInternalTreeParse(fileName)> nodes <-
>> > getNodeSet(doc,'//ccd:el-e3657392-8e26-42a4-a996-258f9e645c46')>
>> > Connected_To=xmlToDataFrame(nodes)
>>
>>
>> The result is:
>>
>> > str(Connected_To)'data.frame': 1 obs. of 7 variables:
>> $ comment : Factor w/ 1 level " DvURI ": 1
>> $ data-name : Factor w/ 1 level "Connected To": 1
>> $ valid-time-begin: Factor w/ 1 level " Use any subtype of ExceptionalValue
>> here when a value is missing": 1
>> $ valid-time-end : Factor w/ 1 level "2020-06-07T01:31:49Z": 1
>> $ DvURI-dv : Factor w/ 1 level "2009-01-20T08:40:53Z": 1
>> $ relation : Factor w/ 1 level "http://www.ccdgen.com": 1
>> $ NA : Factor w/ 1 level "connected to": 1
>>
>>
>> The line:
>>
>> $ valid-time-begin: Factor w/ 1 level " Use any subtype of ExceptionalValue
>> here when a value is missing": 1
>>
>> has a value that is a comment that occurs before the element. Then each
>> value is shifted by one place with an extra one at the end.
>>
>> My desired solution would be to remove commenteds from the parsed tree.
>> So I did this:
>>
>> > doc <- xmlInternalTreeParse(fileName,
>> > handlers=list("comment"=function(x,...){NULL}), useInternalNodes = TRUE)
>>
>> But now when I attempt to get the nodes I get an error.
>>
>> > nodes <-
>> > getNodeSet(doc,'//ccd:el-e3657392-8e26-42a4-a996-258f9e645c46')Error in
>> > UseMethod("xpathApply") :
>> no applicable method for 'xpathApply' applied to an object of class "list"
>>
>>
>> I am not sure what the error is telling me nor how to fix it.
>>
>>
>> All suggestions are welcome and appreciated. Maybe I should be using a
>> different approach to solving the issue with extracting the data.frame?
>>
>> Regads,
>> Tim
>>
>>
>>
>>
>> XML fragment:
>> <ccd:el-e3657392-8e26-42a4-a996-258f9e645c46>
>> <!-- DvURI -->
>> <data-name>Connected To</data-name>
>> <!-- Use any subtype of ExceptionalValue here when a value is
>> missing-->
>> <valid-time-begin>2020-06-07T01:31:49Z</valid-time-begin>
>> <valid-time-end>2009-01-20T08:40:53Z</valid-time-end>
>> <DvURI-dv>http://www.ccdgen.com</DvURI-dv>
>> <relation>connected to</relation>
>> </ccd:el-e3657392-8e26-42a4-a996-258f9e645c46>
>>
>> --
>> MLHIM VIP Signup: http://goo.gl/22B0U
>> ============================================
>> Timothy Cook, MSc +55 21 994711995
>> MLHIM http://www.mlhim.org
>> Like Us on FB: https://www.facebook.com/mlhim2
>> Circle us on G+: http://goo.gl/44EV5
>> Google Scholar: http://goo.gl/MMZ1o
>> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>>
>
>
>
> --
> MLHIM VIP Signup: http://goo.gl/22B0U
> ============================================
> Timothy Cook, MSc +55 21 994711995
> MLHIM http://www.mlhim.org
> Like Us on FB: https://www.facebook.com/mlhim2
> Circle us on G+: http://goo.gl/44EV5
> Google Scholar: http://goo.gl/MMZ1o
> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>
--
============================================
Timothy Cook
LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
MLHIM http://www.mlhim.org
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