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Jeffrey B. Woodward | 1 Oct 2004 01:51
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


I have had the same problem [in some recent experimentation that I was 
doing]; however, I hadn't gotten around to seeing what was going wrong. 
In my case, most all of the form definitions are in a single "included" 
project. I haven't tested if that makes a difference though (i.e., the 
problem occurs if the form definitions are mostly/only in the outter 
most project), but I thought that I would point it out. In my case, the 
database backends tested were MySQL and HSQLDB.

-Jeff

rob wrote:
> Ray Fergerson <fergerson <at> SMI.Stanford.EDU> writes:
> 
> 
>>I forgot to mention, to work around this problem you need to "merge 
>>included projects" and then save to the database.
>>
>>Ray
>>
> 
> Thanks for all of your help Ray, however I still have a question.
> 
> I merged all of my projects into one project, then saved it to the DB and my
> forms still lose thier customization.  Do I have to perform the merge right
> before I save? 
> 
> Thanks,
> Rob
>
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Samson Tu | 1 Oct 2004 16:12
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


The database backend doesn't support inclusion of project. Form 
customization are not saved in the database. Once you merge all included 
projects, you've lost all customizations saved in the included project.

Samson

Jeffrey B. Woodward wrote:

> I have had the same problem [in some recent experimentation that I was 
> doing]; however, I hadn't gotten around to seeing what was going wrong. 
> In my case, most all of the form definitions are in a single "included" 
> project. I haven't tested if that makes a difference though (i.e., the 
> problem occurs if the form definitions are mostly/only in the outter 
> most project), but I thought that I would point it out. In my case, the 
> database backends tested were MySQL and HSQLDB.
> 
> -Jeff
> 
> 
> rob wrote:
> 
>>Ray Fergerson <fergerson <at> SMI.Stanford.EDU> writes:
>>
>>
>>
>>>I forgot to mention, to work around this problem you need to "merge 
>>>included projects" and then save to the database.
>>>
>>>Ray
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Jeffrey B. Woodward | 1 Oct 2004 17:34
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


Samson, do you have any clever suggestion on how/or-if one could 
programmatically "reapply" the customizations from the original included 
project to the resulting merged project?

-Jeff

Samson Tu wrote:
> 
> The database backend doesn't support inclusion of project. Form 
> customization are not saved in the database. Once you merge all included 
> projects, you've lost all customizations saved in the included project.
> 
> Samson
> 
> Jeffrey B. Woodward wrote:
> 
> 
>>I have had the same problem [in some recent experimentation that I was 
>>doing]; however, I hadn't gotten around to seeing what was going wrong. 
>>In my case, most all of the form definitions are in a single "included" 
>>project. I haven't tested if that makes a difference though (i.e., the 
>>problem occurs if the form definitions are mostly/only in the outter 
>>most project), but I thought that I would point it out. In my case, the 
>>database backends tested were MySQL and HSQLDB.
>>
>>-Jeff
>>
>>
>>rob wrote:
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Samson Tu | 2 Oct 2004 00:44
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


Hi,

I might have mis-spoken (at got a few things mixed up):

If you have a file-based project A that includes other projects, and 
merge included projects into project A through Protege GUI, then 
customizations from included projects are saved into the pprj file of A. 
At that point, you can convert your project A to use the database 
backend. You should still have your customizations.

If you convert your Protege project to database back without first doing 
the "Protege merge," then you lose your customizations from included 
project.

If you are saving your project programmatically using 
KnowledgeBaseFactory's saveKnowledgeBase method (as the original poster 
was doing in his first post), you are not saving any customization. You 
should use Project interface's "save" method.

Samson

Jeffrey B. Woodward wrote:
> Samson, do you have any clever suggestion on how/or-if one could 
> programmatically "reapply" the customizations from the original included 
> project to the resulting merged project?
> 
> -Jeff
> 
>
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Jeffrey B. Woodward | 2 Oct 2004 02:47
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


Samson, thank you for the additional information and clarification. In 
my testing thus far, I have been using the ProtegeUI; however, the 
long-term goal would be a fully programmatic method (see my FYI below). 
It was my belief that I tested merging a file-based project to a 
file-based project followed by a "save in format database". However, as 
I am sure you can appreciate, I tried so many things looking for a 
work-around that I can't be 100% sure of anything other than everything 
that I did try didn't work. I will attempt again and let you know.

FYI: In my case, the issue of wanting the database backend is to cut 
down on project load time. With a file-base backend, the project takes 
approx. 1 minute to load while a database backend of the same project 
takes only 4 or 5 seconds to load! Unfortunately, I don't want to 
wholesale convert to a database backend (and manually redo all of the 
form customizations) because I want to continue individual development 
of the "included" projects. Rather, I want to take snapshots to merge 
and convert to a database backend for the end-user consumption while 
keeping the corresponding individual file-based projects accessible to 
the application/ontology developers and data curators. Sorry for the 
long FYI -- this should probably start a new thread!

-Jeff

Samson Tu wrote:
> Hi,
> 
> I might have mis-spoken (at got a few things mixed up):
> 
> If you have a file-based project A that includes other projects, and
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Samson Tu | 4 Oct 2004 21:46
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[protege-discussion] Re: Forms change after ontology is saved to Oracle


Jeffrey B. Woodward wrote:

> FYI: In my case, the issue of wanting the database backend is to cut 
> down on project load time. With a file-base backend, the project takes 
> approx. 1 minute to load while a database backend of the same project 
> takes only 4 or 5 seconds to load! Unfortunately, I don't want to 
> wholesale convert to a database backend (and manually redo all of the 
> form customizations) because I want to continue individual development 
> of the "included" projects. Rather, I want to take snapshots to merge 
> and convert to a database backend for the end-user consumption while 
> keeping the corresponding individual file-based projects accessible to 
> the application/ontology developers and data curators. Sorry for the 
> long FYI -- this should probably start a new thread!
> 

I think you should be able to do what you want to do in Protege:
1. Maintain a set of file-based Protege projects that use inclusion and 
have customized form
2. Periodically, merge included projects and do a "save-as" to a single 
file-based project that retains customization in the pprj file
3. Save the merged project using the database backend that uses the same 
pprj file

Samson
--

-- 
Samson Tu                    email: tu <at> smi.stanford.edu or
Senior Research Scientist           swt <at> stanford.edu
Stanford Medical Informatics phone: 1-650-725-3391
Stanford University          fax: 1-650-725-7944
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