[MOBY-dev] Moby objects in Taverna. Where do they come from?

[Pieter Neerincx]

Hi Eddie,

On 27-Sep-2005, at 4:55 PM, Pieter Neerincx wrote:
>>
>> Hi Pieter,
>>
>> I found out what you were talking about and you were right
>> on all accounts. I have fixed this *bug* and I created a new
>> version that I am in the process of uploading.
>>
>
> Super, will test it at the end of the day.

Check, it works! Taverna now uses my local central when added to  
taverna/conf/mygrid.porperties.

Ran into a few small other problems though. I'm not sure whether  
these are the result of your custom mod of taverna or whether these  
are generic Taverna bugs...

1. The ~taverna-workbench/runme.sh script to start Taverna was in the  
wrong encoding. It contains windows CR LF line endings. After I  
dos2unix-ed the file it works.

2. I can only add 1 processor to a workflow by "drag and drop".  
Taverna refuses to add any other processor I drag and drop. It  
doesn't matter what kind of processor it is: biomoby service, object,  
local java widget, etc.. I can add more processors to a workflow  
using right-click -> add to workflow.

>
>> Actually, I did notice that I am unable to add services
>> using your endpoint!?! I looked at your service instance rdf
>> and I noticed that you have the descriptions of services
>> available, but all find service calls don't seem to be
>> working. Is this true?
>>
>
> I'll look into it. Might be a problem that I switched off https for  
> my local central, but not for the services themselves. I've been  
> switching between ports, 80, 443, 8080 and 8443 for the past days.  
> Maybe some of my config files are not in sync...

Got that nailed down as well. Wasn't a port problem. I turned on  
debugging in path/to/perl/modules/MOBY/Central.pm this used to simply  
write debug info to /tmp/CentralRegistryLogOut.txt , but with the new  
code base this also generates an "Error 500, internal server error".  
This doesn't happen for all calls to MOBY Central, but it did mess up  
the find services call. The following line:

     $debug && &_LOG("found id $_->{service_instance_id}\n");

occurs several times. Not all of them are fatal, but the ones on line  
1992, 2010, 2028 and 2046 result in the internal server error...  
Don't know how to fix it yet. Turning debugging off must have been  
the easiest work around I applied ever :)

Cheers,

Pieter

>
> Pieter
>
>
>
>>
>> Eddie
>>
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>>
>>
>
>
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
> phone: 0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> pieter.neerincx at wur.nl
>
>
>
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>


Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034
Dreijenlaan 3
6703 HA Wageningen
The Netherlands
phone: 0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl