[R] Parsing large XML documents in R - how to optimize the speed?

[Duncan Temple Lang]

Hi Frederic

  You definitely want to be using xmlParse() (or equivalently
  xmlTreeParse( , useInternalNodes = TRUE)).

  This then allows use of getNodeSet()

  I would suggest you use Rprof() to find out where the bottlenecks arise,
   e.g. in the XML functions or in S4 code, or in your code that assembles the
    R objects from the XML.

  I'm happy to take a look at speeding it up if you can make the test file available
and show me your code.

    D.
On 8/10/12 3:46 PM, Frederic Fournier wrote:
> Hello everyone,
> 
> I would like to parse very large xml files from MS/MS experiments and
> create R objects from their content. (By very large, I mean going up to
> 5-10Gb, although I am using a 'small' 40M file to test my code.)
> 
> My first attempt at parsing the 40M file, using the XML package, took more
> than 2200 seconds and left me quite disappointed.
> I managed to cut that down to around 40 seconds by:
>     -using the 'useInternalNodes' option of the XML package when parsing
> the xml tree;
>     -vectorizing the parsing (i.e., replacing loops like "for(node in
> group.of.nodes) {...}" by "sapply(group.of.node, function(node){...}")
> I gained another 5 seconds by making small changes to the functions used
> (like replacing 'getNodeset' by 'xmlElementsByTagName' when I don't need to
> navigate to the children nodes).
> Now I am blocked at around 35 seconds and I would still like to cut this
> time by a 5x, but I have no clue what to do to achieve this gain. I'll try
> to expose as briefly as possible the relevant structure of the xml file I
> am parsing, the structure of the R object I want to create, and the type of
> functions I am using to do it. I hope that one of you will be able to point
> me towards a better and quicker way of doing the parsing!
> 
> 
> Here is the (simplified) structure of the relevant nodes of the xml file:
> 
> <model> (many many nodes)
>   <protein> (a couple of proteins per model node)
>     <peptide> (1 per protein node)
>       <domain> (1 or more per peptide node)
>         <aa> (0 or more per domain node)
>         </aa>
>       </domain>
>     </peptide>
>   </protein>
> </model>
> 
> Here is the basic structure of the R object that I want to create:
> 
> 'result' object that contains:
>   -various attributes
>   -a list of 'protein' objects, each of which containing:
>       -various attributes
>       -a list of 'peptide' objects, each of which containing:
>         -various attributes
>         -a list of 'aa' objects, each of which consisting of a couple of
> attributes.
> 
> Here is the basic structure of the code:
> 
> xml.doc <- xmlTreeParse("file", getDTD=FALSE, useInternalNodes=TRUE)
> result <- new('S4_result_class')
> result at proteins <- xpathApply(xml.doc, "//model/protein",
> function(protein.node) {
>   protein <- new('S4_protein_class')
>   ## fill in a couple of attributes of the protein object using xmlValue
> and xmlAttrs(protein.node)
>   protein at peptides <- xpathApply(protein.node, "./peptide",
> function(peptide.node) {
>     peptide <- new('S4_peptide_class')
>     ## fill in a couple of attributes of the peptide object using xmlValue
> and xmlAttrs(peptide.node)
>     peptide at aas <- sapply(xmlElementsByTagName(peptide.node, name="aa"),
> function(aa.node) {
>       aa <- new('S4_aa_class')
>       ## fill in a couple of attributes of the 'aa' object using xmlValue
> and xmlAttrs(aa.node)
>     })
>   })
> })
> free(xml.doc)
> 
> 
> Does anyone know a better and quicker way of doing this?
> 
> Sorry for the very long message and thank you very much for your time and
> help!
> 
> Frederic
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> 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.
> 
>