Stardog Bug

[Jeff Johnson]

Hi, I'm an undergrad working with Michal Galdzicki on the Synthetic Biology Open Language. I think I found a bug in StarDog--or maybe Java. I put together a demo of the problem, and we've reproduced it on my laptop and a server so far. Here's some info about them:

Ubuntu 11.04

"java-6-sun-1.6.0.26"

java version "1.6.0_26"

Java(TM) SE Runtime Environment (build 1.6.0_26-b03)

Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)

Xubuntu 12.04
java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.1) (6b24-1.11.1-4ubuntu3)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

My test setup is slightly too big to email, so I put it up on the website:
http://sbpkb2.sbols.org/crashtest.zip

Does the same thing crash at your end? It seems obscure with the spaces, but also shows up when I try to build up a complicated query and I've commented out parts of it.
Thanks
Jeff

[Kendall Clark]

Thanks, guys.

Can you also give us a short description of the bug so that it's searchable for the archives?

Cheers,

Kendall

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Cheers,
Kendall

[Kendall]

Jeff,

Thanks for the bug report. There is definitely something weird going on here.

The two queries seem bit for bit identical except for one space character. That shouldn't make a difference. But our CLI handling library does not like the $(cat ...) invocation. Notice that if you just pass the two files to stardog query (instead of using -q) then they both execute perfectly fine.

Hence, there is something amiss in the CLI library. We'll make a ticket and try to close it.

For now, the workaround is to pass the queries in directly in a file and that should work fine.

Cheers,

Kendall

[Kendall]

We'll have a fix for this in Stardog 1.0.1 which will be out soon.

It was some weirdness in some regexes we use to validate inputs.

Thanks for the report.

Cheers,

Kendall

[Michal Galdzicki]

thanks,

the workaround worked for me:

stardog query -c http://localhost:5822/test1 crash_query.txt 

now passes

mike

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