Re: [PyWrapper-devel] MOBY registries in PyWrapper

[Skofic A. M. (IPGRI) <m.s...@cg...>]

I have tried to register a service in the IRRI registry, these are  
the parameters:
End-point: http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl
Namespace: http://cropwiki.irri.org/MOBY/Central

TAPIR returns the following error:
Sorry, the service was not registred. The BioMOBY end point and  
namespace you have configured is not accessible. Are you sure this is  
a MOBY registry?

What should I ask the IRRI people to solve the problem?

I took the end-point and namespace from Dashboard, so it should be  
the correct information.

By the way, I registered in their registry the TapirProvider service  
type.

On Nov 20, 2006, at 10:45 , Javier de la Torre wrote:

> Aghh,
>
> Thats because your old biomoby-settings file is not now up to date,  
> the services now in the config file have information about which  
> registry was used to register them but in your case because your  
> files are not updated, see the empty parethesys close to the  
> service name? the configtool does not know from where to doregister.
>
> If you want send me your biomoby-settings file and I will update it  
> accordely to the new version, then it will work.
>
> Javi.
>
> On 20/11/2006, at 10:35, Skofic A. Milko (IPGRI) wrote:
>
>> I am trying now with the changes. I had to update the moby  
>> configuration files to get into the user interface.
>>
>> First of all, I think that having one registry per data source is  
>> fine, if you need to register a service in different registries  
>> why not create a new data source and point to the other registry  
>> from there? The need to be able to select a registry is crucial  
>> for us, but once it is selected I don't think it should change.
>>
>> Now for the tests, I wanted to deregister the current services  
>> before changing registry, but it doesn't allow me to do so, it  
>> says that:
>>
>> BioMOBY Settings
>>
>> The service <b>getTaxaOfBoundingBox</b> could not be deregistered.  
>> Is the central MOBY registry accesible?
>>
>> 1) Services you are already publishing and registry where you  
>> registered them:
>>
>> TestServiceABCD ()Deregister
>> getTaxaOfBoundingBox ()Deregister
>> Deregister all
>> 2) Considering the mappings that you already have done, you could  
>> be publishing:
>>
>> There are no other services available to register
>> General settings
>> BioMOBY registry end point
>>
>> BioMOBY registry Namespace
>>
>> bmttsUrl
>>
>> ServiceNs
>>
>> AuthURI
>>
>> ContactEmail
>>
>> databaseName
>>
>>
>> Save
>>
>>
>> It looks as if it cannot communicate with the registry end point  
>> (I left the Canada one).
>>
>> During the startup process of TAPIR I got a strange message:
>>
>> ERROR! from pywrapper: REQ_READ_MODEL_FAILED:::The requested model  
>> TCS 1.01 could not be read. Reason: Could not access external  
>> model component(s)
>> Traceback (most recent call last):
>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/ 
>> pywrapper/model.py", line 252, in __readFile__
>>     self.parser.parse( file(filename) )
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 109, in  
>> parse
>>     xmlreader.IncrementalParser.parse(self, source)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/xmlreader.py", line 123, in  
>> parse
>>     self.feed(buffer)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 216, in  
>> feed
>>     self._parser.Parse(data, isFinal)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 353, in  
>> start_element_ns
>>     AttributesNSImpl(newattrs, qnames))
>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/tools/ 
>> saxhandler_extended.py", line 100, in startElementNS
>>     self.startSimpleElement(ns, localname.lower(), attributes)
>>   File "/Library/WebServer/Services/pywrapper/lib/biocase/ 
>> pywrapper/model_handler.py", line 69, in startSimpleElement
>>     parser.parse(attrs.get('location'))
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/expatreader.py", line 103, in  
>> parse
>>     source = saxutils.prepare_input_source(source)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/site-packages/_xmlplus/sax/saxutils.py", line 523, in  
>> prepare_input_source
>>     f = urllib2.urlopen(source.getSystemId())
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 130, in urlopen
>>     return _opener.open(url, data)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 358, in open
>>     response = self._open(req, data)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 376, in _open
>>     '_open', req)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 337, in _call_chain
>>     result = func(*args)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 1021, in http_open
>>     return self.do_open(httplib.HTTPConnection, req)
>>   File "/Library/WebServer/Services/pywrapper/tools/python/lib/ 
>> python2.4/urllib2.py", line 996, in do_open
>>     raise URLError(err)
>> URLError: <urlopen error (60, 'Operation timed out')>
>> WARNING! from pywrapper: The model http://rs.tdwg.org/tapir/cs/ 
>> tcs1.01/model/tcs101.xml could not be loaded. It might be corrupt.
>>
>> It looks like the TCS model is corrupt.
>>
>> Let me know if you need other information.
>>
>> Ciao!
>>
>> Milko
>>
>> On Nov 19, 2006, at 20:11 , Javier de la Torre wrote:
>>
>>> Hi Milko,
>>>
>>> Ok. I have implemented some sort of multiple biomoby registry  
>>> awareness in pywrapper.
>>>
>>> Now in the MOBY tab there are two new fields in the General  
>>> Settings:
>>>
>>> "BioMOBY registry end point" and "BioMOBY registry Namespace".
>>>
>>> This let you choose the registry you want to use. This  
>>> information is saved as a general setting for this datasource.  
>>> But preparing the work for the future now when you register a  
>>> service the information of the end point and the namespace is  
>>> stored in the service on the config files, thats allowing the  
>>> same service to be register in multiple biomoby registries.
>>>
>>> When you click on register a service the configtool uses the  
>>> registry specify at this moment on the general settings, but when  
>>> you click on Deregister it uses the registry that was used for  
>>> registration.
>>>
>>> By default I have left configured the CENTRAL MOBY REGISTRY in  
>>> Canada. Milko, if you think more people are going to use the IRRI  
>>> one I can change it, give me the end point and ns and I change it  
>>> on the default config file so that new installations will appear  
>>> with this.
>>>
>>> There are some limitations still that I hope will not prevent us  
>>> from delopying right now:
>>>
>>> -Althought the config tool stores the info on the registry that  
>>> was used for registering a service, the interface will still not  
>>> offer you the possibility to register the same service in  
>>> multiple registries. If the config tool detects that a certain  
>>> service has been already registered in a registry is not offered  
>>> as a potential service. In the config files is still possible to  
>>> configure the same service in multiple registries, altought you  
>>> would have to manually register them using Dashboard or something  
>>> like this...
>>>
>>> -The BMTTS file gives pywrapper a list of service templates, but  
>>> it does not tell you for what registry this templates are  
>>> designed. Different registries have different data types. So a  
>>> service template for the IRRI server does not necessarily have to  
>>> work with the Central one in Canada... Therefore is needed that  
>>> the BMTTS stores information about to which registry a certain  
>>> template was designed. Then the config tool should read this info  
>>> and react according to this...
>>>
>>> I have only tried it with the central moby registry in Canada,  
>>> but I suppose it should work with others. I havent tried because  
>>> I dont have the url of the IRRI registry and the  
>>> getCoordinatesOfTaxon service template will probably not work  
>>> with the data types there... Could you try Milko with yours?
>>>
>>>
>>> It is commited now.
>>>
>>> Javi.
>>
>