Brian, The Ubuntu libsaxonb-java package in the universe repository installs the script /usr/bin/saxonb-xslt which fires up saxonb under Java. It expects filenames to be specified as the TPP does to Xalan, i.e.
saxonb-xslt <xml file> <xsl file> ... so it will work if you just replace references to /usr/bin/ xsltproc with /usr/bin/saxonb-xslt in the pl scripts. My quick tests were done on a command-line xslt transform. Actual performance when using protxml2html.pl via a web browser doesn't improve as much since the resulting html is still huge, and takes time to transfer and for the browser to display. It does seem very useful for getting huge results files out into text format quickly by invoking protxml2html on the command line though. Another thing to note is that on very small files xsltproc is probably still faster due to the overhead of starting up a JVM for Saxon. The commercial Saxon-EE is very impressive with its 28x speed-up, but the free speedup of 7.5x with saxonb is still very nice. I also tested Saxon-HE (new open source version that is replacing Saxonb, but not packaged for Ubuntu), and it's about the same as saxonb. DT On Dec 2, 4:53 pm, Brian Pratt <[email protected]> wrote: > Impressive! I'm unclear, though, on the practicalities of how it replaces > xsltproc (which is an executable) - presumably there's a script that invokes > java? In which case we have a TPP java dependency we didn't have before - > not that this is necessarily an insurmountable problem, and one we'll > probably have to address sooner than later anyway. > > Brian Pratt > > On Wed, Dec 2, 2009 at 4:28 AM, dctrud <[email protected]> wrote: > > Have obtained a Saxon-EE evaluation to try it. Same .prot.xml file, > > same server - 35.04s (3.5% of the xsltproc run-time). Down side is > > that it costs 300 GBP per server. > > > DT > > > On Dec 2, 10:45 am, dctrud <[email protected]> wrote: > > > I've just done a quick comparison of the speeds of various XSLT > > > processors for transforming .prot.xml to html. There is a marked > > > difference between the processors, and xsltproc which is the TPP > > > default is not the quickest. > > > > Tests performed on Ubuntu 9.0x 64-bit on a DELL R600 Dual Xeon 5500 > > > 32GB RAM. All processors are installed from their Ubuntu packages. > > > Input document was a large 200Mb .prot.xml file resulting from OMSSA > > > search of the 72-run MaxQuant dataset downloaded from ProteomeCommons: > > > > xsltproc - 1011.96s > > > xalan - 1206.95 > > > saxon-xslt - 491.95s > > > saxonb-xslt - 132.19s > > > > saxonb-xslt works for me as a direct replacement for xsltproc in the > > > $xsltproc definition in protxml2html.pl > > > > I've not tried the commercial Saxon-SA / Saxon-EE from Saxonica.com, > > > but they are supposedly faster still. > > > > DT > > > -- > > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]<spctools-discuss%[email protected]> > > . > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
