[MOBY-dev] Compiling datatypes

[Kathrin Klee]

Thanks a lot, that worked.

Cheers Kathrin


Martin Senger wrote:
> Hi,
>
> [Sorry for a delayed reply. Thanks to Eddie for helping meantime.]
>
> The problem you have is because you still have an old (not anymore existing)
> datatype GCP_Contact. This is how to get rid of it:
>
> 1) Make sure that you have the latest contents of the registry you want to
> work with. From the dashboard:
>
> a) Select "Known registries" to "testing".
> b) Local Cache -> Update -> select "All" and press "Reload"
>
> When this is done you can check that GCP_Contact is not anymore in your
> cache: Right click on "Data types" subpanel, select "Search" and type
> "GCP_". Look that no GCP_Contact is selected (in red or whatever).
>
> 2) You need also remove the old datatypes from (previously) generated
> sources:
>
> ant clean-datatypes
>
> After this step, you can check that your directory
> "/home/pcb/klee/workspace/jMoby/generated/datatypes" is, indeed, empty.
>
> 3) Now, you can re-generate and compile all datatypes. Remember that if you
> are using command-line (as I did - see below) you need to specify in you
> build.properties which register you are accessing (otherwise it will use the
> default registry). For the "testing" registry, use the following prooerties:
>
> default.endpoint =
> http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
> default.namespace = http://bioinfo.icapture.ubc.ca/MOBY/Central
>
> The command-line is:
>
> ant moses-datatypes
>
> You can see also the number of compiled datatypes. In my case, it was this:
>
> compile-datatypes:
>     [javac] Compiling 586 source files to
> /home/senger/moby-live/Java/build/others/datatypes
>
> while in your case, it was:
>
> compile-datatypes:
>   
>>   [javac] Compiling 587 source files to
>> /home/pcb/klee/workspace/jMoby/build/others/datatypes
>>
>>     
>
> That indicates the culprit.
>
> I hope that this helps you. If not please do not hesitate and contact me
> again.
>
> Cheers,
> Martin
>
>   

-- 

--------------------------------------------------
Kathrin Klee
Bioinformatician
Max Planck Institute for Plant Breeding Research
Plant Computational Biology
Carl-von-Linne Weg 10
50829 Koeln
Germany
+49 (0)221 / 5062 - 449
--------------------------------------------------