Hi,
On Apr 16, 2013, at 2:49 PM, santiago gil wrote:
>
> 2013/4/14 santiago gil <sg.c...@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.
>>
I have not used xmlToList(), but I find what you try below works if you specify
useInternalNodes = TRUE in your invocation of xmlTreeParse. Often that is the
solution for many issues with xml. Also, I have found it best to write a
relatively generic getter style function. So, in the example below I have
written a function called getPortAttr - it will get attributes for the child
node you name. I used your example as the defaults: "service" is the child to
query and "name" is the attribute to retrieve from that child. It's a heck of
a lot easier to write a function than building the longish parse strings with
lots of [[this]][[and]][[that]] stuff, and it is reusable to boot.
Cheers,
Ben
library(XML)
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>'
mytree<-xmlTreeParse(mydoc, useInternalNodes = TRUE)
myroot<-xmlRoot(mytree)
myports <- myroot[["ports"]]["port"]
getPortAttr <- function(x, child = "service", attr = "name") {
kid <- x[[child]]
att <- xmlAttrs(kid)[[attr]]
att
}
portNames <- sapply(myports, getPortAttr)
#> portNames
# port port
# "msrpc" "netbios-ssn"
portReason <- sapply(myports, getPortAttr, child = "state", attr = "reason")
#> portReason
# port port
#"syn-ack" "syn-ack"
>> 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/
>
> ______________________________________________
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Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org
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