According to Rzepa, Henry: > Thanks Gilles. I had actually attempted to mail the developers list with the below, > but although I subscribed, it still refused my posting
That's odd. Geoff and I review postings from non subscribers before tossing out irrelevant ones. I seem to recall Geoff approving one from you a while back, but I never saw any from you recently. In any case, there's no problem discussing configuration issues and troubleshooting on htdig-general. > >The main difference between external_parsers handling between 3.1.5 and > >3.1.6 is that the parser is called directly via fork() and execv() rather > >than by a popen() call which calls the shell to parse a command line > >to call the parser. I don't see how this would prevent it from running > >executables directly, though, as execv can certainly handle executables > >as long as the patch is correct. > > > >I don't see a problem with either of those lines, as long as the paths > >are correct and the programs work. > > We looked very hard, and believe both the above to be true (ie pasting > the entry in the .conf file into a command line runs the program from > the command line with no problem OK, that's good to know. Testing from the command line can rule out all sorts of problems. If we know that works, we can focus on htdig itself. > > I would be interested in knowing > >more about which problems you have with 3.1.6 that you're sure didn't > >happen with 3.1.4 or 3.1.5. If you can pin it down to something solid > >and reproduceable, please let us know the error messages and/or verbose > >output from htdig, as well as details about your platform. > > We bypassed 3.1.5, and had tried only 3.1.4 and 3.1.6, using essentially > the same .conf file for both. The external parser was invoked with no problem > at 3.1.4, but failed to be called at 3.1.6. This on an SGI compilation using > gcc and lib32 libraries. > > I did put up a test page http://www.ch.ic.ac.uk/chemime/test6.html > but in fact it no longer demonstrates the phenomenon (since we fixed > 3.1.6 by calling a script that calls the program, ie > #!/bin/sh > rm -f /var/www/htdig/tmp > /usr/java/bin/java chemical.Htdigfront $1 $2 $3 $4 > /var/www/htdig/tmp > cat < /var/www/htdig/tmp ) > > the line /usr/java/bin/java chemical.Htdigfront (which works on its own > with four parameters) if placed in the conf file fails to index any of the > external files shown in the test page above. We presumed that chemical.Htdigfront > was a local directory chemical containing the main Java class Htdigfront.class > and which sat in the bin directory. Perhaps its the lack of an absolute path > to these java classes that is the problem? Not sure how to put one in though! OK, I'd be interested in knowing what your external_parsers attribute looked like when you tried to call java directly rather than through a script. The 3.1.6 code does have a simple parser to allow passing arguments to the parser, before the standard ones htdig adds, but you have to use a quoted string for the whole command, just as you did in 3.1.4. E.g.: external_parsers: chemical/x-pdb "/usr/java/bin/java chemical.Htdigfront" should do the trick in either 3.1.4 or 3.1.6. On the other hand, if java, or the chemical.Htdigfront program, has problems writing to a pipe, that may be the cause of failure - which would likely have affected 3.1.4 too! I'm curious as to why your script sends java's stdout to a file, and then uses cat to send the file back to stdout. It strikes me as an unnecessary extra step, which would only be needed if the output file wasn't written sequentially (i.e. required seeking) which wouldn't work with a pipe. Did you get any error messages or relevant debugging output from htdig when you tried to run the java program directly, or was the only symptom the fact that searches didn't work or htmerge deleted the chemical/* documents from your database? -- Gilles R. Detillieux E-mail: <[EMAIL PROTECTED]> Spinal Cord Research Centre WWW: http://www.scrc.umanitoba.ca/~grdetil Dept. Physiology, U. of Manitoba Phone: (204)789-3766 Winnipeg, MB R3E 3J7 (Canada) Fax: (204)789-3930 _______________________________________________ htdig-general mailing list <[EMAIL PROTECTED]> To unsubscribe, send a message to <[EMAIL PROTECTED]> with a subject of unsubscribe FAQ: http://htdig.sourceforge.net/FAQ.html
