Internal error: null when using "Create Ontology From Query"

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Start "OBO Release manager" in Windows 8
2. As Input, select cl.owl (attached)
3. As output, any directory (bug: expects file, but works)
4. In the query ontology tab, select cl.owl again
5. In “Identified by IRI” enter "http://purl.obolibrary.org/obo/CL_0000202"
6. Hit "Make Release"

(Tried with Label: "auditory hair cell" but same null error)

What is the expected output? What do you see instead?
Expected to see an owl file with just that class and subclasses.
What I get is "internal error: null"

What version of the product are you using? On what operating system?
OBOReleaseManager_windows-x64_0.4.0-20130521.exe
Windows 8 64 bit

Please provide any additional information below.
Log output:
2014-11-13 14:33:21 INFO Starting release manager process
2014-11-13 14:33:21 INFO Using staging folder for release manager: 
C:\Users\paty\OORT\staging
2014-11-13 14:33:21 INFO Using the following ontologies: 
[C:\Dev\Ontologies\cl.owl, C:\Dev\Ontologies\cl.owl]
2014-11-13 14:33:27 ERROR Internal error: 
null

Thanks for your help!

Paty

Original issue reported on code.google.com by 4pa...@gmail.com on 13 Nov 2014 at 7:34

Attachments:

• cl.owl

[GoogleCodeExporter]

Hello and thank you for reporting the issue.

I can reproduce the error, but after investigating the issue, I can't offer a 
quick solution.
The problem is that you want to use the same ontology for query and load. 
During the load this leads to an internal error (OWLAPI ontology already 
exists, which has a null error message, grr)

But as you might have already tested, you can't just skip one of the files. I'm 
not sure when we are able to work on this issue.

Maybe you can provide more input on what the use-case is you are trying to 
solve. 
Depending on what you want to create, OORT might not be the correct tool to 
use. The command-line OWTools (although a beast of its own) might be a better 
alternative.

Original comment by HDie...@lbl.gov on 13 Nov 2014 at 9:32

[GoogleCodeExporter]

Thanks for the reply!

Are there any "Windows" command-line OWTools?

this is what I'd like to do: 
https://code.google.com/p/owltools/wiki/OortExtractingModules

Extract a class and all its subclasses and create an owl ontology from it.

Is that possible?

Maybe I should try owltools on a Linux VM?

Paty

Original comment by 4pa...@gmail.com on 13 Nov 2014 at 9:48

[GoogleCodeExporter]

> Are there any "Windows" command-line OWTools?
No, not specifically. But it is not that hard to get OWLTools running on Windows

The wrapper script is written for a Linux/Unix like environment, but it just 
assembles the relevant details for memory setting and other setup details. 
Using a VM might be a bit of an overkill for that.

You can download the required jar for owltools here:
http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar

In theory you just can to run that jar using Java:
java -Xmx2048M -jar  owltools-runner-all.jar 

> Extract a class and all its subclasses and create an owl ontology from it.
Definitely possible (OORT is not the recommended tool for that)

The relevant owltools option is '--extract-module' to extract an ontology 
modules for a given set of classes. Using the sub option '-d' (for deepening) 
will retrieve all subclasses of the initial set before extracting the module. 
Using '--elk' flag will use the efficient elk reasoner to retrieve the 
subclasses

So in total the command could be:
java -Xmx4G -jar  owltools-runner-all.jar --elk cl.owl --extract-module -d 
http://purl.obolibrary.org/obo/CL_0000202 -o cl-module.owl

Original comment by HDie...@lbl.gov on 13 Nov 2014 at 10:14

[GoogleCodeExporter]

Hello,
is there any more input required for the issue? Did the work around using 
owltools help?

Original comment by HDie...@lbl.gov on 21 Nov 2014 at 7:03

[GoogleCodeExporter]

As no further input from the original requester is available, assume the 
problem has been resolved with the provided work-around.

Original comment by HDie...@lbl.gov on 4 Dec 2014 at 9:56

• Changed state: Done