Re: [PyWrapper-devel] MOBY registries in PyWrapper

[Javier de la T. <ja...@gm...>]

Uhmmm... I am going to have to trace this down with a tracer tool.  
The python library I am using does not give you much information when  
it crashes connecting to the server.
But usually this means that there is no connection with this url or  
it is limited. If there will be an error on biomoby then the library  
catches the errors fine.

You have to be careful that you have all the necessary data types in  
the IRRI registry for the template that you are going to use, but I  
doubt this is the problem because then you would get a warning about it.

I will let you know.

Javier.

On 20/11/2006, at 14:25, Skofic A. Milko (IPGRI) wrote:

> 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.
>>>
>>
>