[protege-owl] Two easy-to-fix bugs

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[protege-owl] Two easy-to-fix bugs

Daniel Elenius
Or so I hope  :)

These have been bothering us greatly here at SRI:

1) When I create a new project from an existing OWL file, and there are
imports for which I need to create repositories, Protege always asks me
to create one repository for each top-level import, even if the first
repository contains the files needed for the second import. For example,
suppose the OWL file is ontologies/A.owl, and this imports B.owl and
C.owl, both of which are located in ontologies/ as well. Protege will
ask me to add a repository for B.owl. So I choose Local Folder
ontologies/. Next, Protege asks me to add a repository for C.owl, even
though it is in the repository I just added!

2) There really really really needs to be a "include subfolders" option
on the Relative Folder repository type.

Daniel
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Re: [protege-owl] Two easy-to-fix bugs

Timothy Redmond

If I understand this request correctly, I think that the first  
feature is already there (?) in the 3.2 beta.   (Sorrry for my  
confusion.)  Here are my steps:

1. I create ontologies A.owl, B.owl, C.owl.  A.owl and B.owl are in  
the same directory and C.owl is in a sub-directory.

2. With the ontology A.owl open I click on the add import button.

3. I click on the option "Import an ontology contained in one of the  
available repositories" and click Next.

4. I click on add repository

5. I select "Local Folder" and click on "Next".

6. I specify the folder and select "Include sub-folders".

7. Both B.owl and C.owl show up (the include sub-folders worked).  I  
can select both of them to import them.  Or I can import them  
separately.

Now it is true at this point that the repository that I just created  
is specific to the A.pprj project.  If I open B.pprj I will not see  
the ontology repository that I just created.  If that is a problem  
then I can remedy that by using the global repositories mechanism.  
To do this, I do the following before importing the ontologies:

1. OWL->Ontology Repositories

2.  Click  on Global repositories and add the repository as before.

Now the repository that was created will be visible to all OWL projects.

It doesn't sound like the request for relative folder repositories  
should be too difficult.  I will make an enhancement request and  
investigate.

-Timothy

On Oct 22, 2006, at 9:28 PM, Daniel Elenius wrote:

> Or so I hope  :)
>
> These have been bothering us greatly here at SRI:
>
> 1) When I create a new project from an existing OWL file, and there  
> are
> imports for which I need to create repositories, Protege always  
> asks me
> to create one repository for each top-level import, even if the first
> repository contains the files needed for the second import. For  
> example,
> suppose the OWL file is ontologies/A.owl, and this imports B.owl and
> C.owl, both of which are located in ontologies/ as well. Protege will
> ask me to add a repository for B.owl. So I choose Local Folder
> ontologies/. Next, Protege asks me to add a repository for C.owl, even
> though it is in the repository I just added!
>
> 2) There really really really needs to be a "include subfolders"  
> option
> on the Relative Folder repository type.
>
> Daniel
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
> faq.html#01a.03

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Re: [protege-owl] Two easy-to-fix bugs

Daniel Elenius
Timothy Redmond wrote:

> If I understand this request correctly, I think that the first  
> feature is already there (?) in the 3.2 beta.   (Sorrry for my  
> confusion.)  Here are my steps:
>
> 1. I create ontologies A.owl, B.owl, C.owl.  A.owl and B.owl are in  
> the same directory and C.owl is in a sub-directory.
>
> 2. With the ontology A.owl open I click on the add import button.
>
>  
I am not talking about adding imports. I am talking about adding
repositories for missing imports, when you create a new project from an
existing OWL file.
See my email again...

> 3. I click on the option "Import an ontology contained in one of the  
> available repositories" and click Next.
>
> 4. I click on add repository
>
> 5. I select "Local Folder" and click on "Next".
>
> 6. I specify the folder and select "Include sub-folders".
>
> 7. Both B.owl and C.owl show up (the include sub-folders worked).  I  
> can select both of them to import them.  Or I can import them  
> separately.
>
> Now it is true at this point that the repository that I just created  
> is specific to the A.pprj project.  If I open B.pprj I will not see  
> the ontology repository that I just created.  If that is a problem  
> then I can remedy that by using the global repositories mechanism.  
> To do this, I do the following before importing the ontologies:
>
> 1. OWL->Ontology Repositories
>
> 2.  Click  on Global repositories and add the repository as before.
>
> Now the repository that was created will be visible to all OWL projects.
>
> It doesn't sound like the request for relative folder repositories  
> should be too difficult.  I will make an enhancement request and  
> investigate.
>
> -Timothy
>
> On Oct 22, 2006, at 9:28 PM, Daniel Elenius wrote:
>
>  
>> Or so I hope  :)
>>
>> These have been bothering us greatly here at SRI:
>>
>> 1) When I create a new project from an existing OWL file, and there  
>> are
>> imports for which I need to create repositories, Protege always  
>> asks me
>> to create one repository for each top-level import, even if the first
>> repository contains the files needed for the second import. For  
>> example,
>> suppose the OWL file is ontologies/A.owl, and this imports B.owl and
>> C.owl, both of which are located in ontologies/ as well. Protege will
>> ask me to add a repository for B.owl. So I choose Local Folder
>> ontologies/. Next, Protege asks me to add a repository for C.owl, even
>> though it is in the repository I just added!
>>
>> 2) There really really really needs to be a "include subfolders"  
>> option
>> on the Relative Folder repository type.
>>
>> Daniel
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
>> faq.html#01a.03
>>    
>
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Re: [protege-owl] Two easy-to-fix bugs

Tania Tudorache
Daniel,

Thank you for the clarification. What version of Protege are you using?
The latest Protege 3.2 beta (342) supports this feature for the "Local
folder" repositories. When you are prompted to add a repository for a
missing import and you select the "Local folder" option, if you enable
the "include sub-folders" checkbox, then the C.owl will be found
automatically and you will not have to add a new repository.

You are right, the "Include sub-folder" option is not available for the
"Relative folder" repository, but only for the "Local folder". I have
added an enhancement request for this.

Tania


Daniel Elenius wrote:

> Timothy Redmond wrote:
>  
>> If I understand this request correctly, I think that the first  
>> feature is already there (?) in the 3.2 beta.   (Sorrry for my  
>> confusion.)  Here are my steps:
>>
>> 1. I create ontologies A.owl, B.owl, C.owl.  A.owl and B.owl are in  
>> the same directory and C.owl is in a sub-directory.
>>
>> 2. With the ontology A.owl open I click on the add import button.
>>
>>  
>>    
> I am not talking about adding imports. I am talking about adding
> repositories for missing imports, when you create a new project from an
> existing OWL file.
> See my email again...
>  
>> 3. I click on the option "Import an ontology contained in one of the  
>> available repositories" and click Next.
>>
>> 4. I click on add repository
>>
>> 5. I select "Local Folder" and click on "Next".
>>
>> 6. I specify the folder and select "Include sub-folders".
>>
>> 7. Both B.owl and C.owl show up (the include sub-folders worked).  I  
>> can select both of them to import them.  Or I can import them  
>> separately.
>>
>> Now it is true at this point that the repository that I just created  
>> is specific to the A.pprj project.  If I open B.pprj I will not see  
>> the ontology repository that I just created.  If that is a problem  
>> then I can remedy that by using the global repositories mechanism.  
>> To do this, I do the following before importing the ontologies:
>>
>> 1. OWL->Ontology Repositories
>>
>> 2.  Click  on Global repositories and add the repository as before.
>>
>> Now the repository that was created will be visible to all OWL projects.
>>
>> It doesn't sound like the request for relative folder repositories  
>> should be too difficult.  I will make an enhancement request and  
>> investigate.
>>
>> -Timothy
>>
>> On Oct 22, 2006, at 9:28 PM, Daniel Elenius wrote:
>>
>>  
>>    
>>> Or so I hope  :)
>>>
>>> These have been bothering us greatly here at SRI:
>>>
>>> 1) When I create a new project from an existing OWL file, and there  
>>> are
>>> imports for which I need to create repositories, Protege always  
>>> asks me
>>> to create one repository for each top-level import, even if the first
>>> repository contains the files needed for the second import. For  
>>> example,
>>> suppose the OWL file is ontologies/A.owl, and this imports B.owl and
>>> C.owl, both of which are located in ontologies/ as well. Protege will
>>> ask me to add a repository for B.owl. So I choose Local Folder
>>> ontologies/. Next, Protege asks me to add a repository for C.owl, even
>>> though it is in the repository I just added!
>>>
>>> 2) There really really really needs to be a "include subfolders"  
>>> option
>>> on the Relative Folder repository type.
>>>
>>> Daniel
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
>>> faq.html#01a.03
>>>    
>>>      
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>  
>>    
>
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>  

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Re: [protege-owl] Two easy-to-fix bugs

Daniel Elenius
Tania Tudorache wrote:

> Daniel,
>
> Thank you for the clarification. What version of Protege are you using?
> The latest Protege 3.2 beta (342) supports this feature for the "Local
> folder" repositories. When you are prompted to add a repository for a
> missing import and you select the "Local folder" option, if you enable
> the "include sub-folders" checkbox, then the C.owl will be found
> automatically and you will not have to add a new repository.
>  
>  
I am using 342, and it doesn't work for me. I did discover that there is
an additional qualification to make the bug appear: A.owl must be in a
different folder from its imports (B.owl and C.owl), because Protege
always looks in the folder of the importing ontology, I guess.

Try these steps.

1) In a folder, e.g. Temp, create B.owl and C.owl. Any namespace, and
nothing needs to be put in the ontologies.
2) Create a subfolder Temp/A, and in the subfolder, cretae A.owl. Add
B.owl and C.owl as imports to A.owl.
3) Now, create new project from existing owl file, and select A.owl.
4) Protege will ask for where to find B.owl (or whatever the namespace
is of B.owl). Chose "Local folder", select the "Temp" folder where B is
located.
5) Now -- the bug! -- Protege asks for where to find C.owl, even though
it's in a folder (Temp) for which we've already created a Local Folder
repository!

Note that this problem has nothing to do with the "include sub-folders"
option (AFAIK).


> You are right, the "Include sub-folder" option is not available for the
> "Relative folder" repository, but only for the "Local folder". I have
> added an enhancement request for this.
>
>  
Thank you.
I wonder why it wasn't already there. It looks like just an omission,
but perhaps there is some very intricate technical reason?


> Tania
>  
>
> Daniel Elenius wrote:
>  
>> Timothy Redmond wrote:
>>  
>>    
>>> If I understand this request correctly, I think that the first  
>>> feature is already there (?) in the 3.2 beta.   (Sorrry for my  
>>> confusion.)  Here are my steps:
>>>
>>> 1. I create ontologies A.owl, B.owl, C.owl.  A.owl and B.owl are in  
>>> the same directory and C.owl is in a sub-directory.
>>>
>>> 2. With the ontology A.owl open I click on the add import button.
>>>
>>>  
>>>    
>>>      
>> I am not talking about adding imports. I am talking about adding
>> repositories for missing imports, when you create a new project from an
>> existing OWL file.
>> See my email again...
>>  
>>    
>>> 3. I click on the option "Import an ontology contained in one of the  
>>> available repositories" and click Next.
>>>
>>> 4. I click on add repository
>>>
>>> 5. I select "Local Folder" and click on "Next".
>>>
>>> 6. I specify the folder and select "Include sub-folders".
>>>
>>> 7. Both B.owl and C.owl show up (the include sub-folders worked).  I  
>>> can select both of them to import them.  Or I can import them  
>>> separately.
>>>
>>> Now it is true at this point that the repository that I just created  
>>> is specific to the A.pprj project.  If I open B.pprj I will not see  
>>> the ontology repository that I just created.  If that is a problem  
>>> then I can remedy that by using the global repositories mechanism.  
>>> To do this, I do the following before importing the ontologies:
>>>
>>> 1. OWL->Ontology Repositories
>>>
>>> 2.  Click  on Global repositories and add the repository as before.
>>>
>>> Now the repository that was created will be visible to all OWL projects.
>>>
>>> It doesn't sound like the request for relative folder repositories  
>>> should be too difficult.  I will make an enhancement request and  
>>> investigate.
>>>
>>> -Timothy
>>>
>>> On Oct 22, 2006, at 9:28 PM, Daniel Elenius wrote:
>>>
>>>  
>>>    
>>>      
>>>> Or so I hope  :)
>>>>
>>>> These have been bothering us greatly here at SRI:
>>>>
>>>> 1) When I create a new project from an existing OWL file, and there  
>>>> are
>>>> imports for which I need to create repositories, Protege always  
>>>> asks me
>>>> to create one repository for each top-level import, even if the first
>>>> repository contains the files needed for the second import. For  
>>>> example,
>>>> suppose the OWL file is ontologies/A.owl, and this imports B.owl and
>>>> C.owl, both of which are located in ontologies/ as well. Protege will
>>>> ask me to add a repository for B.owl. So I choose Local Folder
>>>> ontologies/. Next, Protege asks me to add a repository for C.owl, even
>>>> though it is in the repository I just added!
>>>>
>>>> 2) There really really really needs to be a "include subfolders"  
>>>> option
>>>> on the Relative Folder repository type.
>>>>
>>>> Daniel
>>>> _______________________________________________
>>>> protege-owl mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>>
>>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
>>>> faq.html#01a.03
>>>>    
>>>>      
>>>>        
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>>  
>>>    
>>>      
>> _______________________________________________
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>>
>>  
>>    
>
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Re: [protege-owl] Two easy-to-fix bugs

Tania Tudorache
Daniel,

I have tried to reproduce the bug by following the steps you described
in Protege 3.2 b342, but I couldn't. Did you do a clean install of
Protege b342?

I will close this bug, but leave the enhancement request for adding
"include subfolders" for the relative foldersrepository.

Tania


Daniel Elenius wrote:

> Tania Tudorache wrote:
>> Daniel,
>>
>> Thank you for the clarification. What version of Protege are you
>> using? The latest Protege 3.2 beta (342) supports this feature for
>> the "Local folder" repositories. When you are prompted to add a
>> repository for a missing import and you select the "Local folder"
>> option, if you enable the "include sub-folders" checkbox, then the
>> C.owl will be found automatically and you will not have to add a new
>> repository.
>>  
>>  
> I am using 342, and it doesn't work for me. I did discover that there
> is an additional qualification to make the bug appear: A.owl must be
> in a different folder from its imports (B.owl and C.owl), because
> Protege always looks in the folder of the importing ontology, I guess.
>
> Try these steps.
>
> 1) In a folder, e.g. Temp, create B.owl and C.owl. Any namespace, and
> nothing needs to be put in the ontologies.
> 2) Create a subfolder Temp/A, and in the subfolder, cretae A.owl. Add
> B.owl and C.owl as imports to A.owl.
> 3) Now, create new project from existing owl file, and select A.owl.
> 4) Protege will ask for where to find B.owl (or whatever the namespace
> is of B.owl). Chose "Local folder", select the "Temp" folder where B
> is located.
> 5) Now -- the bug! -- Protege asks for where to find C.owl, even
> though it's in a folder (Temp) for which we've already created a Local
> Folder repository!
>
> Note that this problem has nothing to do with the "include
> sub-folders" option (AFAIK).
>
>
>> You are right, the "Include sub-folder" option is not available for
>> the "Relative folder" repository, but only for the "Local folder". I
>> have added an enhancement request for this.
>>
>>  
> Thank you.
> I wonder why it wasn't already there. It looks like just an omission,
> but perhaps there is some very intricate technical reason?
>
>
>> Tania
>>  
>> Daniel Elenius wrote:
>>  
>>> Timothy Redmond wrote:
>>>      
>>>> If I understand this request correctly, I think that the first  
>>>> feature is already there (?) in the 3.2 beta.   (Sorrry for my  
>>>> confusion.)  Here are my steps:
>>>>
>>>> 1. I create ontologies A.owl, B.owl, C.owl.  A.owl and B.owl are
>>>> in  the same directory and C.owl is in a sub-directory.
>>>>
>>>> 2. With the ontology A.owl open I click on the add import button.
>>>>
>>>>            
>>> I am not talking about adding imports. I am talking about adding
>>> repositories for missing imports, when you create a new project from
>>> an existing OWL file.
>>> See my email again...
>>>      
>>>> 3. I click on the option "Import an ontology contained in one of
>>>> the  available repositories" and click Next.
>>>>
>>>> 4. I click on add repository
>>>>
>>>> 5. I select "Local Folder" and click on "Next".
>>>>
>>>> 6. I specify the folder and select "Include sub-folders".
>>>>
>>>> 7. Both B.owl and C.owl show up (the include sub-folders worked).  
>>>> I  can select both of them to import them.  Or I can import them  
>>>> separately.
>>>>
>>>> Now it is true at this point that the repository that I just
>>>> created  is specific to the A.pprj project.  If I open B.pprj I
>>>> will not see  the ontology repository that I just created.  If that
>>>> is a problem  then I can remedy that by using the global
>>>> repositories mechanism.   To do this, I do the following before
>>>> importing the ontologies:
>>>>
>>>> 1. OWL->Ontology Repositories
>>>>
>>>> 2.  Click  on Global repositories and add the repository as before.
>>>>
>>>> Now the repository that was created will be visible to all OWL
>>>> projects.
>>>>
>>>> It doesn't sound like the request for relative folder repositories  
>>>> should be too difficult.  I will make an enhancement request and  
>>>> investigate.
>>>>
>>>> -Timothy
>>>>
>>>> On Oct 22, 2006, at 9:28 PM, Daniel Elenius wrote:
>>>>
>>>>            
>>>>> Or so I hope  :)
>>>>>
>>>>> These have been bothering us greatly here at SRI:
>>>>>
>>>>> 1) When I create a new project from an existing OWL file, and
>>>>> there  are
>>>>> imports for which I need to create repositories, Protege always  
>>>>> asks me
>>>>> to create one repository for each top-level import, even if the first
>>>>> repository contains the files needed for the second import. For  
>>>>> example,
>>>>> suppose the OWL file is ontologies/A.owl, and this imports B.owl and
>>>>> C.owl, both of which are located in ontologies/ as well. Protege will
>>>>> ask me to add a repository for B.owl. So I choose Local Folder
>>>>> ontologies/. Next, Protege asks me to add a repository for C.owl,
>>>>> even
>>>>> though it is in the repository I just added!
>>>>>
>>>>> 2) There really really really needs to be a "include subfolders"  
>>>>> option
>>>>> on the Relative Folder repository type.
>>>>>
>>>>> Daniel
>>>>> _______________________________________________
>>>>> protege-owl mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>>>
>>>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
>>>>> faq.html#01a.03
>>>>>                  
>>>> _______________________________________________
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>>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>>
>>>> Instructions for unsubscribing:
>>>> http://protege.stanford.edu/doc/faq.html#01a.03             
>>> _______________________________________________
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>>>
>>> Instructions for unsubscribing:
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>>>      
>>
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>
>

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