Re: [PyWrapper-devel] MOBY registries in PyWrapper

[Skofic A. M. (B. - HQ) <m.s...@cg...>]

I checked the data types, and they are there; I think it has to do  
with something else.

On Nov 21, 2006, at 8:27 , Javier de la Torre wrote:

> 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.
>>>>
>>>
>>
>