[MOBY-dev] Compiling datatypes

[Martin Senger]

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

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger