Thread: [PyWrapper-devel] MOBY service
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From: Javier de la T. <ja...@gm...> - 2006-11-17 12:54:10
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Hi Milko, I have to watch out the refresh issue in moby. Adding the possibility to choose a moby central should not be complicate with an important consideration. Should we allow users to have services registered in different MOBY registries? If so, the configuration files must be changed to use as a service identifier the serviceName, authURI and THE REGISTRY were it was registered. This is important to know from where to register and deregister the services. If a pywrapper installation can work only with one single MOBY registry then it is easier, I can just add an input field in the configtool to allow users to write the endpoint of the registry they wanna use. I believe that the correct solution is to be "multiple registries aware" in pywrapper, but this will take a little bit more of time, meanwhile this weekend I can add you the simple solution... Cheers. On 17/11/2006, at 13:44, Skofic A. Milko (IPGRI) wrote: > Javier, I finally made my first MOBy service, getTaxaOfBoundingBox, > if you are interested in adding it to the examples I send you the > files, remember to change the links in the files, they point to the > eurisco site. > > There is a problem when you register a new MOBY service: TAPIR > takes a while before recognising that the service is up and > running; when testing one must manually delete the cache files to > test it with Dashboard. > > Do you think we can get a way to set the MOBY central? > > Ciao! > > Milko > > <getTaxaOfBoundingBox.bmtts.xml> > This is the BMTTS section. > > <getTaxaOfBoundingBox.bmtts.xml> > This is the output model. > > <BoundingBox.xslt> > This is the input transformation stylesheet. > > <TaxonScientificName.xsd> > This is the schema for the MOBY taxon name. > > |
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From: Skofic A. M. (IPGRI) <m.s...@cg...> - 2006-11-19 12:24:55
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I realise it could become a mess, since you wouldn't know where you have registered your services. For the moment let's go for the simple solution: a field where you set the registry and that's all. Once we have released TAPIR can we have a skype or talk to see what we can do in the future? What are the plans for the future, Could we make a wish list and plan how we can implement it? Bye! Milko On Nov 17, 2006, at 13:53 , Javier de la Torre wrote: > Hi Milko, > > I have to watch out the refresh issue in moby. Adding the > possibility to choose a moby central should not be complicate with > an important consideration. Should we allow users to have services > registered in different MOBY registries? If so, the configuration > files must be changed to use as a service identifier the > serviceName, authURI and THE REGISTRY were it was registered. This > is important to know from where to register and deregister the > services. > > If a pywrapper installation can work only with one single MOBY > registry then it is easier, I can just add an input field in the > configtool to allow users to write the endpoint of the registry > they wanna use. > > I believe that the correct solution is to be "multiple registries > aware" in pywrapper, but this will take a little bit more of time, > meanwhile this weekend I can add you the simple solution... > > Cheers. > > > On 17/11/2006, at 13:44, Skofic A. Milko (IPGRI) wrote: > >> Javier, I finally made my first MOBy service, >> getTaxaOfBoundingBox, if you are interested in adding it to the >> examples I send you the files, remember to change the links in the >> files, they point to the eurisco site. >> >> There is a problem when you register a new MOBY service: TAPIR >> takes a while before recognising that the service is up and >> running; when testing one must manually delete the cache files to >> test it with Dashboard. >> >> Do you think we can get a way to set the MOBY central? >> >> Ciao! >> >> Milko >> >> <getTaxaOfBoundingBox.bmtts.xml> >> This is the BMTTS section. >> >> <getTaxaOfBoundingBox.bmtts.xml> >> This is the output model. >> >> <BoundingBox.xslt> >> This is the input transformation stylesheet. >> >> <TaxonScientificName.xsd> >> This is the schema for the MOBY taxon name. >> >> > Milko A. Skofic (IPGRI) International Plant Genetic Resources Institute Via dei Tre Denari, 472/a 00057 Maccarese (RM) ITALY E-mail: m.s...@cg... Tel: +30 06 6118286 |
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From: Javier de la T. <ja...@gm...> - 2006-11-19 19:12:15
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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. |
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From: Skofic A. M. (IPGRI) <m.s...@cg...> - 2006-11-19 21:54:34
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I will try it tomorrow, I also didn't know the address of the IRRI registry, but Martin told me to update Dashboard and in the new version you have a popup list with all the registries. Will let you know. Chao! 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. Milko A. Skofic (IPGRI) International Plant Genetic Resources Institute Via dei Tre Denari, 472/a 00057 Maccarese (RM) ITALY E-mail: m.s...@cg... Tel: +30 06 6118286 |
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From: Javier de la T. <ja...@gm...> - 2006-11-19 19:24:05
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Hi Milko, > Once we have released TAPIR can we have a skype or talk to see what > we can do in the future? What are the plans for the future, Could > we make a wish list and plan how we can implement it? > I prefer if you express your wishes here on the public list so that people knows what is going on. Maybe your wishes are the same as others and there is someone already planning it. After expressing the wishes here on the list then we can add the to the trac where there is already 10 or more wishes of things we would like to see in pywrapper. Cheers. JAvi. > Bye! > > Milko > > On Nov 17, 2006, at 13:53 , Javier de la Torre wrote: > >> Hi Milko, >> >> I have to watch out the refresh issue in moby. Adding the >> possibility to choose a moby central should not be complicate with >> an important consideration. Should we allow users to have services >> registered in different MOBY registries? If so, the configuration >> files must be changed to use as a service identifier the >> serviceName, authURI and THE REGISTRY were it was registered. This >> is important to know from where to register and deregister the >> services. >> >> If a pywrapper installation can work only with one single MOBY >> registry then it is easier, I can just add an input field in the >> configtool to allow users to write the endpoint of the registry >> they wanna use. >> >> I believe that the correct solution is to be "multiple registries >> aware" in pywrapper, but this will take a little bit more of time, >> meanwhile this weekend I can add you the simple solution... >> >> Cheers. >> >> >> On 17/11/2006, at 13:44, Skofic A. Milko (IPGRI) wrote: >> >>> Javier, I finally made my first MOBy service, >>> getTaxaOfBoundingBox, if you are interested in adding it to the >>> examples I send you the files, remember to change the links in >>> the files, they point to the eurisco site. >>> >>> There is a problem when you register a new MOBY service: TAPIR >>> takes a while before recognising that the service is up and >>> running; when testing one must manually delete the cache files to >>> test it with Dashboard. >>> >>> Do you think we can get a way to set the MOBY central? >>> >>> Ciao! >>> >>> Milko >>> >>> <getTaxaOfBoundingBox.bmtts.xml> >>> This is the BMTTS section. >>> >>> <getTaxaOfBoundingBox.bmtts.xml> >>> This is the output model. >>> >>> <BoundingBox.xslt> >>> This is the input transformation stylesheet. >>> >>> <TaxonScientificName.xsd> >>> This is the schema for the MOBY taxon name. >>> >>> >> > > > Milko A. Skofic (IPGRI) > International Plant Genetic Resources Institute > Via dei Tre Denari, 472/a > 00057 Maccarese (RM) > ITALY > E-mail: m.s...@cg... > Tel: +30 06 6118286 > > |
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From: Skofic A. M. (IPGRI) <m.s...@cg...> - 2006-11-19 21:55:51
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No problem, I have no problem in sharing views, do you prefer an e- mail discussion or a series of tickets? On Nov 19, 2006, at 20:23 , Javier de la Torre wrote: > Hi Milko, > >> Once we have released TAPIR can we have a skype or talk to see >> what we can do in the future? What are the plans for the future, >> Could we make a wish list and plan how we can implement it? >> > > I prefer if you express your wishes here on the public list so that > people knows what is going on. Maybe your wishes are the same as > others and there is someone already planning it. > > After expressing the wishes here on the list then we can add the to > the trac where there is already 10 or more wishes of things we > would like to see in pywrapper. > > Cheers. > > JAvi. > >> Bye! >> >> Milko >> >> On Nov 17, 2006, at 13:53 , Javier de la Torre wrote: >> >>> Hi Milko, >>> >>> I have to watch out the refresh issue in moby. Adding the >>> possibility to choose a moby central should not be complicate >>> with an important consideration. Should we allow users to have >>> services registered in different MOBY registries? If so, the >>> configuration files must be changed to use as a service >>> identifier the serviceName, authURI and THE REGISTRY were it was >>> registered. This is important to know from where to register and >>> deregister the services. >>> >>> If a pywrapper installation can work only with one single MOBY >>> registry then it is easier, I can just add an input field in the >>> configtool to allow users to write the endpoint of the registry >>> they wanna use. >>> >>> I believe that the correct solution is to be "multiple registries >>> aware" in pywrapper, but this will take a little bit more of >>> time, meanwhile this weekend I can add you the simple solution... >>> >>> Cheers. >>> >>> >>> On 17/11/2006, at 13:44, Skofic A. Milko (IPGRI) wrote: >>> >>>> Javier, I finally made my first MOBy service, >>>> getTaxaOfBoundingBox, if you are interested in adding it to the >>>> examples I send you the files, remember to change the links in >>>> the files, they point to the eurisco site. >>>> >>>> There is a problem when you register a new MOBY service: TAPIR >>>> takes a while before recognising that the service is up and >>>> running; when testing one must manually delete the cache files >>>> to test it with Dashboard. >>>> >>>> Do you think we can get a way to set the MOBY central? >>>> >>>> Ciao! >>>> >>>> Milko >>>> >>>> <getTaxaOfBoundingBox.bmtts.xml> >>>> This is the BMTTS section. >>>> >>>> <getTaxaOfBoundingBox.bmtts.xml> >>>> This is the output model. >>>> >>>> <BoundingBox.xslt> >>>> This is the input transformation stylesheet. >>>> >>>> <TaxonScientificName.xsd> >>>> This is the schema for the MOBY taxon name. >>>> >>>> >>> >> >> >> Milko A. Skofic (IPGRI) >> International Plant Genetic Resources Institute >> Via dei Tre Denari, 472/a >> 00057 Maccarese (RM) >> ITALY >> E-mail: m.s...@cg... >> Tel: +30 06 6118286 >> >> > Milko A. Skofic (IPGRI) International Plant Genetic Resources Institute Via dei Tre Denari, 472/a 00057 Maccarese (RM) ITALY E-mail: m.s...@cg... Tel: +30 06 6118286 |
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From: Javier de la T. <ja...@gm...> - 2006-11-20 00:15:53
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Hi Milko, I think we can start discussing on the mailing list and then add tickets when we consider. Javi. On 19/11/2006, at 22:55, Skofic A. Milko (IPGRI) wrote: > No problem, I have no problem in sharing views, do you prefer an e- > mail discussion or a series of tickets? > > On Nov 19, 2006, at 20:23 , Javier de la Torre wrote: > >> Hi Milko, >> >>> Once we have released TAPIR can we have a skype or talk to see >>> what we can do in the future? What are the plans for the future, >>> Could we make a wish list and plan how we can implement it? >>> >> >> I prefer if you express your wishes here on the public list so >> that people knows what is going on. Maybe your wishes are the same >> as others and there is someone already planning it. >> >> After expressing the wishes here on the list then we can add the >> to the trac where there is already 10 or more wishes of things we >> would like to see in pywrapper. >> >> Cheers. >> >> JAvi. >> >>> Bye! >>> >>> Milko >>> >>> On Nov 17, 2006, at 13:53 , Javier de la Torre wrote: >>> >>>> Hi Milko, >>>> >>>> I have to watch out the refresh issue in moby. Adding the >>>> possibility to choose a moby central should not be complicate >>>> with an important consideration. Should we allow users to have >>>> services registered in different MOBY registries? If so, the >>>> configuration files must be changed to use as a service >>>> identifier the serviceName, authURI and THE REGISTRY were it was >>>> registered. This is important to know from where to register and >>>> deregister the services. >>>> >>>> If a pywrapper installation can work only with one single MOBY >>>> registry then it is easier, I can just add an input field in the >>>> configtool to allow users to write the endpoint of the registry >>>> they wanna use. >>>> >>>> I believe that the correct solution is to be "multiple >>>> registries aware" in pywrapper, but this will take a little bit >>>> more of time, meanwhile this weekend I can add you the simple >>>> solution... >>>> >>>> Cheers. >>>> >>>> >>>> On 17/11/2006, at 13:44, Skofic A. Milko (IPGRI) wrote: >>>> >>>>> Javier, I finally made my first MOBy service, >>>>> getTaxaOfBoundingBox, if you are interested in adding it to the >>>>> examples I send you the files, remember to change the links in >>>>> the files, they point to the eurisco site. >>>>> >>>>> There is a problem when you register a new MOBY service: TAPIR >>>>> takes a while before recognising that the service is up and >>>>> running; when testing one must manually delete the cache files >>>>> to test it with Dashboard. >>>>> >>>>> Do you think we can get a way to set the MOBY central? >>>>> >>>>> Ciao! >>>>> >>>>> Milko >>>>> >>>>> <getTaxaOfBoundingBox.bmtts.xml> >>>>> This is the BMTTS section. >>>>> >>>>> <getTaxaOfBoundingBox.bmtts.xml> >>>>> This is the output model. >>>>> >>>>> <BoundingBox.xslt> >>>>> This is the input transformation stylesheet. >>>>> >>>>> <TaxonScientificName.xsd> >>>>> This is the schema for the MOBY taxon name. >>>>> >>>>> >>>> >>> >>> >>> Milko A. Skofic (IPGRI) >>> International Plant Genetic Resources Institute >>> Via dei Tre Denari, 472/a >>> 00057 Maccarese (RM) >>> ITALY >>> E-mail: m.s...@cg... >>> Tel: +30 06 6118286 >>> >>> >> > > > Milko A. Skofic (IPGRI) > International Plant Genetic Resources Institute > Via dei Tre Denari, 472/a > 00057 Maccarese (RM) > ITALY > E-mail: m.s...@cg... > Tel: +30 06 6118286 > > |
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From: Skofic A. M. (IPGRI) <m.s...@cg...> - 2006-11-20 09:35:25
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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.
|
|
From: Javier de la T. <ja...@gm...> - 2006-11-20 09:46:17
|
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.
>
|
|
From: Skofic A. M. (IPGRI) <m.s...@cg...> - 2006-11-20 13:25:38
|
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. >> > |
|
From: Javier de la T. <ja...@gm...> - 2006-11-21 08:20:34
|
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. >>> >> > |
|
From: Skofic A. M. (B. - HQ) <m.s...@cg...> - 2006-11-21 08:51:27
|
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. >>>> >>> >> > |
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