[R] Problem with handling of attributes in xmlToList in XML package

[David Winsemius]

Yes. This is the third such copy. You can view them all in the Archive, starting with the first one:

https://stat.ethz.ch/pipermail/r-help/2013-April/351504.html

On Apr 16, 2013, at 11:49 AM, santiago gil wrote:

> Are my emails getting through?
> 
> 2013/4/14 santiago gil <sg.ccnr at gmail.com>:
>> Hello all,
>> 
>> I have a problem with the way attributes are dealt with in the
>> function xmlToList(), and I haven't been able to figure it out for
>> days now.
>> 
>> Say I have a document (produced by nmap) like this:
>> 
>>> mydoc <- '<host starttime="1365204834" endtime="1365205860"><status state="up" reason="echo-reply" reason_ttl="127"/>
>>    <address addr="XXX.XXX.XXX.XXX" addrtype="ipv4"/>
>>    <ports><port protocol="tcp" portid="135"><state state="open"
>> reason="syn-ack" reason_ttl="127"/><service name="msrpc"
>> product="Microsoft Windows RPC" ostype="Windows" method="probed"
>> conf="10"><cpe>cpe:/o:microsoft:windows</cpe></service></port>
>>    <port protocol="tcp" portid="139"><state state="open"
>> reason="syn-ack" reason_ttl="127"/><service name="netbios-ssn"
>> method="probed" conf="10"/></port>
>>    </ports>
>>    <times srtt="647" rttvar="71" to="100000"/>
>>    </host>'
>> 
>> I want to store this as a list of lists, so I do:
>> 
>> mytree<-xmlTreeParse(mydoc)
>> myroot<-xmlRoot(mytree)
>> mylist<-xmlToList(myroot)
>> 
>> Now my problem is that when I want to fetch the attributes of the
>> services running of each port, the behavior is not consistent:
>> 
>>> mylist[["ports"]][[1]][["service"]]$.attrs["name"]
>>   name
>> "msrpc"
>>> mylist[["ports"]][[2]][["service"]]$.attrs["name"]
>> Error in trash_list[["ports"]][[2]][["service"]]$.attrs :
>>  $ operator is invalid for atomic vectors
>> 
>> I understand that the way they are dfined in the documnt is not the
>> same, but I think there still should be a consistent behavior. I've
>> tried many combination of parameters for xmlTreeParse() but nothing
>> has helped me. I can't find a way to call up the name of the service
>> consistently regardless of whether the node has children or not. Any
>> tips?
>> 
>> All the best,
>> 
>> 
>> S.G.
>> 
>> --
>> -------------------------------------------------------------------------------
>> http://barabasilab.neu.edu/people/gil/
> 
> 
> 
> -- 
> -------------------------------------------------------------------------------
> http://barabasilab.neu.edu/people/gil/
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.

David Winsemius
Alameda, CA, USA