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XML and str

4 messages · Ashley Ford, Duncan Temple Lang, Martin Maechler

Original
Ashley Ford
# 
If I read in an .xml file eg with
package="XML"))

It appears to be OK however examining it with str() gives an apparent
error
List of 2
 $ doc:List of 3
  ..$ file    : list()
  .. ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
  ..$ version :List of 4
  .. ..- attr(*, "class")= chr "XMLNode"
  ..$ children:Error in obj$children[[...]] : subscript out of bounds

I am unsure if this is a feature or a bug and if the latter whether it
is in XML or str, it is not causing a problem but I would like to
understand what is happening, any ideas ?

examining components eg
List of 2
 $ comment: list()
  ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
etc 

is OK.

XML Version 1.4-1, 
same behaviour on Windows and Linux, R version 2.4.1 (2006-12-18)




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Martin Maechler
# 
Ashley> If I read in an .xml file eg with 

    >> xeg <- xmlTreeParse(system.file("exampleData", "test.xml",
                                       package="XML"))

    Ashley> It appears to be OK however examining it with str() gives an apparent
    Ashley> error

    >> str(xeg, 2)
    Ashley> List of 2
    Ashley> $ doc:List of 3
    Ashley> ..$ file    : list()
    Ashley> .. ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
    Ashley> ..$ version :List of 4
    Ashley> .. ..- attr(*, "class")= chr "XMLNode"
    Ashley> ..$ children:Error in obj$children[[...]] : subscript out of bounds

    Ashley> I am unsure if this is a feature or a bug and if the latter whether it
    Ashley> is in XML or str, it is not causing a problem but I would like to
    Ashley> understand what is happening, any ideas ?

Yes -  thank you for providing a well-reproducible example.
After setting  
      options(error = recover)

I do

   > obj <- xeg$doc
   > mode(obj)     # "list"
   [1] "list"
   > is.list(obj)  # TRUE
   [1] TRUE
   > length(obj)   # 3
   [1] 3
   > obj[[3]]      # ---> the error you see above.
   Error in obj$children[[...]] : subscript out of bounds

   Enter a frame number, or 0 to exit   

   1: obj[[3]]
   2: `[[.XMLDocumentContent`(obj, 3)

   Selection: 0

   > obj$children  # works, should be identical to obj[[3]]
   $comment
   <!--A comment-->

   $foo
   <foo x="1">
    <element attrib1="my value"/>
   ......

This shows that the XML package implements the "[[" method
wrongly IMHO and also inconsistently with the "$" method.
this is not a bug in XML but rather str() which assumes that
x[[length(x)]] works for objects of mode "list" even when they
are not of *class* "list", but I hope he would still rather
consider changing [[.XMLDocumentContent ...

Martin

    Ashley> examining components eg 
    >> str(xeg$doc$children,2)

    Ashley> List of 2
    Ashley> $ comment: list()
    Ashley> ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
    Ashley> etc 

    Ashley> is OK.

    Ashley> XML Version 1.4-1, 
    Ashley> same behaviour on Windows and Linux, R version 2.4.1 (2006-12-18)




    Ashley> The information contained in this E-Mail and any subsequent
    Ashley> correspondence is private and is intended solely for the intended
    Ashley> recipient(s).  The information in this communication may be confidential
    Ashley> and/or legally privileged.  Nothing in this e-mail is intended to
    Ashley> conclude a contract on behalf of QinetiQ or make QinetiQ subject to any
    Ashley> other legally binding commitments, unless the e-mail contains an express
    Ashley> statement to the contrary or incorporates a formal Purchase Order.

    Ashley> For those other than the recipient any disclosure, copying,
    Ashley> distribution, or any action taken or omitted to be taken in reliance on
    Ashley> such information is prohibited and may be unlawful.

    Ashley> Emails and other electronic communication with QinetiQ may be monitored
    Ashley> and recorded for business purposes including security, audit and
    Ashley> archival purposes.  Any response to this email indicates consent to
    Ashley> this.

    Ashley> Telephone calls to QinetiQ may be monitored or recorded for quality
    Ashley> control, security and other business purposes.

    Ashley> QinetiQ Group plc,

    Ashley> Company Registration No: 4586941,  

    Ashley> Registered office: 85 Buckingham Gate, London SW1E 6PD

    Ashley> ______________________________________________
    Ashley> R-help at stat.math.ethz.ch mailing list
    Ashley> https://stat.ethz.ch/mailman/listinfo/r-help
    Ashley> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    Ashley> and provide commented, minimal, self-contained, reproducible code.
2 days later
Duncan Temple Lang
#
Martin Maechler wrote:
More likely, the appropriate fix is to have
length() return the relevant value.
I even recall considering this at the time of writing
the package initially.  But that was back in 1999/2000
and S4 and R/S-Plus compatibility were not what they
are now.  It could be changed.  Not certain when I will
get a chance.

 D.
Martin Maechler
# 

        
DTL> Martin Maechler wrote:

        
>>>>>>> "Ashley" == Ashley Ford <ford at signal.QinetiQ.com>
    >>>>>>> on Wed, 07 Feb 2007 17:18:56 +0000 writes:
    >> 
    Ashley> If I read in an .xml file eg with 
    >> 
    >> >> xeg <- xmlTreeParse(system.file("exampleData", "test.xml",
    >> package="XML"))
    >> 
    Ashley> It appears to be OK however examining it with str() gives an apparent
    Ashley> error
    >> 
    >> >> str(xeg, 2)
    Ashley> List of 2
    Ashley> $ doc:List of 3
    Ashley> ..$ file    : list()
    Ashley> .. ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
    Ashley> ..$ version :List of 4
    Ashley> .. ..- attr(*, "class")= chr "XMLNode"
    Ashley> ..$ children:Error in obj$children[[...]] : subscript out of bounds
    >> 
    Ashley> I am unsure if this is a feature or a bug and if the latter whether it
    Ashley> is in XML or str, it is not causing a problem but I would like to
    Ashley> understand what is happening, any ideas ?
    >> 
    >> Yes -  thank you for providing a well-reproducible example.
    >> After setting  
    >> options(error = recover)
    >> 
    >> I do
    >> 
    >> > obj <- xeg$doc
    >> > mode(obj)     # "list"
    >> [1] "list"
    >> > is.list(obj)  # TRUE
    >> [1] TRUE
    >> > length(obj)   # 3
    >> [1] 3
    >> > obj[[3]]      # ---> the error you see above.
    >> Error in obj$children[[...]] : subscript out of bounds
    >> 
    >> Enter a frame number, or 0 to exit   
    >> 
    >> 1: obj[[3]]
    >> 2: `[[.XMLDocumentContent`(obj, 3)
    >> 
    >> Selection: 0
    >> 
    >> > obj$children  # works, should be identical to obj[[3]]
    >> $comment
    >> <!--A comment-->
    >> 
    >> $foo
    >> <foo x="1">
    >> <element attrib1="my value"/>
    >> ......
    >> 
    >> This shows that the XML package implements the "[[" method
    >> wrongly IMHO and also inconsistently with the "$" method.
    >> 
    >>> From a strict OOP view, the XML author could argue that
    >> this is not a bug in XML but rather str() which assumes that
    >> x[[length(x)]] works for objects of mode "list" even when they
    >> are not of *class* "list", but I hope he would still rather
    >> consider changing [[.XMLDocumentContent ...
    >> 


    DTL> More likely, the appropriate fix is to have
    DTL> length() return the relevant value.

Hmm. 

  > library(XML)
  > xeg <- xmlTreeParse(system.file("exampleData", "test.xml", package= "XML"))
  > obj <- xeg$doc
  > mode(obj)     # "list"
  [1] "list"
  > is.list(obj)  # TRUE
  [1] TRUE
  > length(obj)   # 3
  [1] 3
  > obj[[3]]      # ---> the error you see above.
  Error in obj$children[[...]] : subscript out of bounds
  > names(obj)
  [1] "file"     "version"  "children"
  > class(obj)
  [1] "XMLDocumentContent"
  > methods(class=class(obj))
  [1] xmlApply.XMLDocumentContent*  [[.XMLDocumentContent*       
  [3] xmlRoot.XMLDocumentContent*   xmlSApply.XMLDocumentContent*

  > XML:::`[[.XMLDocumentContent`
  function (obj, ...) 
  {
      obj$children[[...]]
  }
  <environment: namespace:XML>

so  length(obj) is 3 and obj is a simple S3 object
which is just a list with 3 named components,
Do you really want to define  length(.) to also return the
length of obj$children instead of the length() of the list
itself?   
With that you'd have your XMLDocumentContent objects ``look''
like lists with three named components on one hand
(and help(xmlTreeParse) does mention these components)
but behave in other contexts as if it was just its own component
'obj$children'.   Of course you then should also define 
  print.XMLDocumentContent() and
  str.XMLDocumentContent()   accordingly, 
so users would barely know about the "file" and "version"
component of 'obj'.
But is this really desirable ?
With the above "[[.XMLDoc..."  you break the basic S-language
premise of  "[[" and "$" to behave accordingly.

You could solve "everything" elegantly if you used S4 instead of S3
classes, since there's no defined correspondence between slot
access and "[[" (and yes, then (with S4), I'd agree that 

setMethod("length", "XMLDocumentContent", 
          function(x) length(x at children))

would be needed too -- and fine.

Martin

    DTL> I even recall considering this at the time of writing
    DTL> the package initially.  But that was back in 1999/2000
    DTL> and S4 and R/S-Plus compatibility were not what they
    DTL> are now.  It could be changed.  Not certain when I will
    DTL> get a chance.


    Ashley> examining components eg 
    >> >> str(xeg$doc$children,2)
    >> 
    Ashley> List of 2
    Ashley> $ comment: list()
    Ashley> ..- attr(*, "class")= chr [1:2] "XMLComment" "XMLNode"
    Ashley> etc 
    >> 
    Ashley> is OK.
    >> 
    Ashley> XML Version 1.4-1, 
    Ashley> same behaviour on Windows and Linux, R version 2.4.1 (2006-12-18)
    >>