semi-colons converted to X in config file?
I suspect I've run into a rare XML entity/Cheetah conversion bug. I have a parameter definition like <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> I also am creating a configfile using <configfile name="iniFile"> ... paramSchedule=${schedule} ... </configfile> The file that gets created has ... paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75 ... i.e. the ';' character gets converted to X. I suspect that this is an XML parsing issue (trying to interpret ';' as marking an entity resolution?) but the default value get displayed correctly in the Galaxy UI so it might not be so simple as this. I can't see how Cheetah is converting ';' to 'X' but maybe that's it. I'm planning on hacking around this, but wanted to post to the list to see if anyone else has seen this or has quick recommendations. Jon
Jon, you might want to have a look at the ALLOWED CHARACTERS section of the tool xml configuration pages on the wiki. Need to add these to your config. Seems like the ; gets masked to X. Alex ________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Jon Sorenson [JSorenson@pacificbiosciences.com] Verzonden: zaterdag 28 mei 2011 7:01 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] semi-colons converted to X in config file? I suspect I’ve run into a rare XML entity/Cheetah conversion bug. I have a parameter definition like <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> I also am creating a configfile using <configfile name="iniFile"> … paramSchedule=${schedule} … </configfile> The file that gets created has … paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75 … i.e. the ‘;’ character gets converted to X. I suspect that this is an XML parsing issue (trying to interpret ‘;’ as marking an entity resolution?) but the default value get displayed correctly in the Galaxy UI so it might not be so simple as this. I can’t see how Cheetah is converting ‘;’ to ‘X’ but maybe that’s it. I’m planning on hacking around this, but wanted to post to the list to see if anyone else has seen this or has quick recommendations. Jon
Ah, that's it. Thanks. I had skimmed over the section on the optional sanitizer part of param definitions and didn't realize there was some default sanitization occurring. Without understanding this problem, I had hacked around it with #set $schedule2=$schedule.replace('X',';') in the configfile (and it works for this limited purpose) but adding a custom sanitizer seems like the appropriate and robust thing to do. Thanks, Jon -----Original Message----- From: Bossers, Alex [mailto:Alex.Bossers@wur.nl] Sent: Saturday, May 28, 2011 10:34 AM To: Jon Sorenson; galaxy-dev@lists.bx.psu.edu Subject: RE: semi-colons converted to X in config file? Jon, you might want to have a look at the ALLOWED CHARACTERS section of the tool xml configuration pages on the wiki. Need to add these to your config. Seems like the ; gets masked to X. Alex ________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Jon Sorenson [JSorenson@pacificbiosciences.com] Verzonden: zaterdag 28 mei 2011 7:01 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] semi-colons converted to X in config file? I suspect I've run into a rare XML entity/Cheetah conversion bug. I have a parameter definition like <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> I also am creating a configfile using <configfile name="iniFile"> ... paramSchedule=${schedule} ... </configfile> The file that gets created has ... paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75 ... i.e. the ';' character gets converted to X. I suspect that this is an XML parsing issue (trying to interpret ';' as marking an entity resolution?) but the default value get displayed correctly in the Galaxy UI so it might not be so simple as this. I can't see how Cheetah is converting ';' to 'X' but maybe that's it. I'm planning on hacking around this, but wanted to post to the list to see if anyone else has seen this or has quick recommendations. Jon
participants (2)
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Bossers, Alex -
Jon Sorenson