imports issue

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imports issue

Simon Jupp
Hi,
Nice simple one for you. When I try and import from a file located in  
the web, I see in my shell that an exception has been thrown but the  
imports wizard just hangs trying to fetch it.
Cheers,
Simon


Simon Jupp
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http://www.cs.man.ac.uk/~sjupp/




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Re: imports issue

Timothy Redmond

Send the exception and we will probably get it.

Unfortunately  for me  the two symptoms have conflicting obvious  
explanations.   The obvious explanation for the exception is that you  
had an i/o error.  The obvious explanation for the hanging is that it  
is timing out on the network and  eventually will return.  (I have  
seen this before on certain bad imports).  A possible explanation for  
both is that you found a bug and something broke.

One other possibility.  Usually if  there is an exception chasing a  
bad import, Protege will come back with a  dialog window asking if you  
want to try  to resolve the import.  I don't know if this is possible  
but perhaps this window got lost behind another window or is hiding on  
some other virtual  desktop?

Perhaps Nick or Matthew will see the truth without the exception.

-Timothy


On Aug 1, 2008, at 2:31 AM, Simon Jupp wrote:

> Hi,
> Nice simple one for you. When I try and import from a file located in
> the web, I see in my shell that an exception has been thrown but the
> imports wizard just hangs trying to fetch it.
> Cheers,
> Simon
>
>
> Simon Jupp
> [hidden email]
> http://www.cs.man.ac.uk/~sjupp/
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: imports issue

Simon Jupp
Hi Timothy,

You should be able to replicate the problem. I can open this ontology  
from the specified URI (http://potato.cs.man.ac.uk/2008/05/), however,  
when I use the import wizard it won't open it. Matthew tells me that  
the request type sent from the Wizard is not correct.

Cheers,
Simon

On 1 Aug 2008, at 17:01, Timothy Redmond wrote:

>
> Send the exception and we will probably get it.
>
> Unfortunately  for me  the two symptoms have conflicting obvious
> explanations.   The obvious explanation for the exception is that you
> had an i/o error.  The obvious explanation for the hanging is that it
> is timing out on the network and  eventually will return.  (I have
> seen this before on certain bad imports).  A possible explanation for
> both is that you found a bug and something broke.
>
> One other possibility.  Usually if  there is an exception chasing a
> bad import, Protege will come back with a  dialog window asking if you
> want to try  to resolve the import.  I don't know if this is possible
> but perhaps this window got lost behind another window or is hiding on
> some other virtual  desktop?
>
> Perhaps Nick or Matthew will see the truth without the exception.
>
> -Timothy
>
>
> On Aug 1, 2008, at 2:31 AM, Simon Jupp wrote:
>
>> Hi,
>> Nice simple one for you. When I try and import from a file located in
>> the web, I see in my shell that an exception has been thrown but the
>> imports wizard just hangs trying to fetch it.
>> Cheers,
>> Simon
>>
>>
>> Simon Jupp
>> [hidden email]
>> http://www.cs.man.ac.uk/~sjupp/
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback



Simon Jupp
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http://www.cs.man.ac.uk/~sjupp/




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Re: imports issue

Matthew Horridge
I can't remember exactly, because it is such a long time ago since I  
implemented the imports wizard, but if I recall correctly, the wizard  
opens a stream from the specified URI to check to see if there is an  
ontology at the URI and to see if it can be parsed -- I'm guessing  
that the request type is not set property in the wizard. The OWL API  
uses the following request types:


"application/rdf+xml, application/xml; q=0.5, text/xml; q=0.3, */*;  
q=0.2"

Cheers,

Matthew



On 4 Aug 2008, at 14:03, Simon Jupp wrote:

> Hi Timothy,
>
> You should be able to replicate the problem. I can open this ontology
> from the specified URI (http://potato.cs.man.ac.uk/2008/05/), however,
> when I use the import wizard it won't open it. Matthew tells me that
> the request type sent from the Wizard is not correct.
>
> Cheers,
> Simon
>
> On 1 Aug 2008, at 17:01, Timothy Redmond wrote:
>
>>
>> Send the exception and we will probably get it.
>>
>> Unfortunately  for me  the two symptoms have conflicting obvious
>> explanations.   The obvious explanation for the exception is that you
>> had an i/o error.  The obvious explanation for the hanging is that it
>> is timing out on the network and  eventually will return.  (I have
>> seen this before on certain bad imports).  A possible explanation for
>> both is that you found a bug and something broke.
>>
>> One other possibility.  Usually if  there is an exception chasing a
>> bad import, Protege will come back with a  dialog window asking if  
>> you
>> want to try  to resolve the import.  I don't know if this is possible
>> but perhaps this window got lost behind another window or is hiding  
>> on
>> some other virtual  desktop?
>>
>> Perhaps Nick or Matthew will see the truth without the exception.
>>
>> -Timothy
>>
>>
>> On Aug 1, 2008, at 2:31 AM, Simon Jupp wrote:
>>
>>> Hi,
>>> Nice simple one for you. When I try and import from a file located  
>>> in
>>> the web, I see in my shell that an exception has been thrown but the
>>> imports wizard just hangs trying to fetch it.
>>> Cheers,
>>> Simon
>>>
>>>
>>> Simon Jupp
>>> [hidden email]
>>> http://www.cs.man.ac.uk/~sjupp/
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>
>
> Simon Jupp
> [hidden email]
> http://www.cs.man.ac.uk/~sjupp/
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: imports issue

Timothy Redmond

I still wasn't able to replicate Simon's  issue but you are  right  
Matthew about the importer.

>> You should be able to replicate the problem. I can open this ontology
>> from the specified URI (http://potato.cs.man.ac.uk/2008/05/


This didn't open for me in Protege 4 or  in the owl api:

         OWLOntologyManager manager =  
OWLManager.createOWLOntologyManager();
         OWLOntology ontology =  
manager.loadOntologyFromPhysicalURI(new URI("http://potato.cs.man.ac.uk/2008/05/ 
"));

Both of these used Matthew's request type below.

> The OWL API
> uses the following request types:
>
>
> "application/rdf+xml, application/xml; q=0.5, text/xml; q=0.3, */*;
> q=0.2"

You are right the importer  doesn't seem to use  this.

I know nothing about this.  But I do see a lot of magic in the owl api  
method AbstractOWLParser.getInputStream(URI). What I am wondering is  
whether  this routine should be  more exposed if it is the right way  
of opening a URI.  Perhaps this routine should be the implementation  
of PhysicalURIInputSource.getInputStream()?  Or maybe  this would  
break a lot of stuff? Or I will steal the code and  put it in some  
URIUtilities  class.

-Timothy





On Aug 4, 2008, at 6:22 AM, Matthew Horridge wrote:

> I can't remember exactly, because it is such a long time ago since I
> implemented the imports wizard, but if I recall correctly, the wizard
> opens a stream from the specified URI to check to see if there is an
> ontology at the URI and to see if it can be parsed -- I'm guessing
> that the request type is not set property in the wizard. The OWL API
> uses the following request types:
>
>
> "application/rdf+xml, application/xml; q=0.5, text/xml; q=0.3, */*;
> q=0.2"
>
> Cheers,
>
> Matthew
>
>
>
> On 4 Aug 2008, at 14:03, Simon Jupp wrote:
>
>> Hi Timothy,
>>
>> You should be able to replicate the problem. I can open this ontology
>> from the specified URI (http://potato.cs.man.ac.uk/2008/05/),  
>> however,
>> when I use the import wizard it won't open it. Matthew tells me that
>> the request type sent from the Wizard is not correct.
>>
>> Cheers,
>> Simon
>>
>> On 1 Aug 2008, at 17:01, Timothy Redmond wrote:
>>
>>>
>>> Send the exception and we will probably get it.
>>>
>>> Unfortunately  for me  the two symptoms have conflicting obvious
>>> explanations.   The obvious explanation for the exception is that  
>>> you
>>> had an i/o error.  The obvious explanation for the hanging is that  
>>> it
>>> is timing out on the network and  eventually will return.  (I have
>>> seen this before on certain bad imports).  A possible explanation  
>>> for
>>> both is that you found a bug and something broke.
>>>
>>> One other possibility.  Usually if  there is an exception chasing a
>>> bad import, Protege will come back with a  dialog window asking if
>>> you
>>> want to try  to resolve the import.  I don't know if this is  
>>> possible
>>> but perhaps this window got lost behind another window or is hiding
>>> on
>>> some other virtual  desktop?
>>>
>>> Perhaps Nick or Matthew will see the truth without the exception.
>>>
>>> -Timothy
>>>
>>>
>>> On Aug 1, 2008, at 2:31 AM, Simon Jupp wrote:
>>>
>>>> Hi,
>>>> Nice simple one for you. When I try and import from a file located
>>>> in
>>>> the web, I see in my shell that an exception has been thrown but  
>>>> the
>>>> imports wizard just hangs trying to fetch it.
>>>> Cheers,
>>>> Simon
>>>>
>>>>
>>>> Simon Jupp
>>>> [hidden email]
>>>> http://www.cs.man.ac.uk/~sjupp/
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>>
>>
>> Simon Jupp
>> [hidden email]
>> http://www.cs.man.ac.uk/~sjupp/
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
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Re: imports issue

Timothy Redmond
In reply to this post by Simon Jupp

I will put a fix in for this shortly (based on Matthew's  
interpretation).  There is a build going on today for the problem with  
the new data properties and object properties.  The fix won't get in  
there but probably in a svn build immediately thereafter.

-Timothy


On Aug 4, 2008, at 6:03 AM, Simon Jupp wrote:

> Hi Timothy,
>
> You should be able to replicate the problem. I can open this ontology
> from the specified URI (http://potato.cs.man.ac.uk/2008/05/), however,
> when I use the import wizard it won't open it. Matthew tells me that
> the request type sent from the Wizard is not correct.
>
> Cheers,
> Simon
>
> On 1 Aug 2008, at 17:01, Timothy Redmond wrote:
>
>>
>> Send the exception and we will probably get it.
>>
>> Unfortunately  for me  the two symptoms have conflicting obvious
>> explanations.   The obvious explanation for the exception is that you
>> had an i/o error.  The obvious explanation for the hanging is that it
>> is timing out on the network and  eventually will return.  (I have
>> seen this before on certain bad imports).  A possible explanation for
>> both is that you found a bug and something broke.
>>
>> One other possibility.  Usually if  there is an exception chasing a
>> bad import, Protege will come back with a  dialog window asking if  
>> you
>> want to try  to resolve the import.  I don't know if this is possible
>> but perhaps this window got lost behind another window or is hiding  
>> on
>> some other virtual  desktop?
>>
>> Perhaps Nick or Matthew will see the truth without the exception.
>>
>> -Timothy
>>
>>
>> On Aug 1, 2008, at 2:31 AM, Simon Jupp wrote:
>>
>>> Hi,
>>> Nice simple one for you. When I try and import from a file located  
>>> in
>>> the web, I see in my shell that an exception has been thrown but the
>>> imports wizard just hangs trying to fetch it.
>>> Cheers,
>>> Simon
>>>
>>>
>>> Simon Jupp
>>> [hidden email]
>>> http://www.cs.man.ac.uk/~sjupp/
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>
>
> Simon Jupp
> [hidden email]
> http://www.cs.man.ac.uk/~sjupp/
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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