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[protege-discussion] Protege db schema conversion

Timothy Redmond tredmond at stanford.edu
Wed Dec 12 08:40:02 PST 2012


Sorry - I forgot to do this before.  I put the working sql dump over 
here [1].

-Timothy

[1] http://protege.stanford.edu/fileshare/tredmond/fmafromclips.sql.zip


On 12/10/2012 08:31 AM, Timothy Redmond wrote:
>
> I don't know if this is good news or bad news but when I converted the 
> clips file to the database format I had no problems.  I made a mysql 
> dump, reloaded it and that was fine also.   Later - when I have a 
> faster connection - I will give a link to the sql dump file.
>
> Did you notice the problem right after doing the conversion to 
> database format or did it only occur after making a sql dump and 
> reloading it?  I am trying to figure out what is different about how I 
> did things and how you did things.
>
> -Timothy
>
>
> On 12/07/2012 10:49 AM, Todd Detwiler wrote:
>> Timothy,
>> Thank you very much for the info. Yes this is helpful. I hadn't 
>> noticed that all of the is_template values were set to true. Now the 
>> question is, is this happening when converting the clips project into 
>> a db project. If you have any time to look at my clips files, I have 
>> posted them here: 
>> http://dl.dropbox.com/u/2527438/FMA3.3/fma_3.3_frames_clips.zip. I 
>> must warn you, however, that they require a large heap to open in 
>> this format (I generally use 1.5G) and it takes a bit of time to open.
>>
>> Even if you don't have time to investigate, I appreciate your effort 
>> and feedback so far. Unfortunately it still means that I have a 
>> migration path problem.
>>
>> Thanks,
>> Todd
>>
>> Landon Todd Detwiler
>> Structural Informatics Group (SIG)
>> University of Washington
>>
>> phone: 206-616-2336
>>
>> On 12/6/12 12:03 PM, protege-discussion-request at lists.stanford.edu 
>> wrote:
>>> Message: 1
>>> Date: Thu, 06 Dec 2012 10:59:21 -0800
>>> From: Timothy Redmond<tredmond at stanford.edu>
>>> To:protege-discussion at lists.stanford.edu
>>> Subject: Re: [protege-discussion] Protege db schema conversion
>>> Message-ID:<50C0EB09.2080000 at stanford.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>>
>>>> >
>>>> >Yes, I have loaded the clips project (in multiple Protege versions)
>>>> >and attempted to "Convert project to format" frames database. But it
>>>> >does not look the same in Protege (as the clips version). None of the
>>>> >classes have any info in the right frame (as though they were
>>>> >un-typed). Also, many leaf concepts don't appear at all (in the 
>>>> tree).
>>>> >I can query the database and find the missing classes. And, they have
>>>> >valid types. I am using MySQL for my database backend. In fact, I am
>>>> >using the same instance of MySQL that the initial db was in (before
>>>> >upconverting the schema). I can send you the file, but it is too 
>>>> large
>>>> >for email, even when compressed. So I've uploaded it here:
>>>> >http://dl.dropbox.com/u/2527438/FMA3.3/fma_3_3.sql.zip 
>>> Ok - I am a bit confused but there may be a hint here.  The database
>>> dump that you sent me is bad.  The problem that it has is that all of
>>> the is_template values in the database are set to 'true'.  You can see
>>> this in the sql dump because one of the typical entries looks like 
>>> this:
>>>
>>>        (':THING',6,':DIRECT-SUBCLASSES','','^A',0,do 6,'Anatomical 
>>> entity',NULL)
>>>
>>>
>>> where the ^A represents the binary character control-A (I think that
>>> this is a 1 in ascii).  You can see this in the database by running an
>>> sql query:
>>>
>>> mysql> select * from fma where is_template=false;
>>> Empty set (0.00 sec)
>>> mysql>
>>>
>>> This is why when I load this database and read it into Protege, I don't
>>> see any subclass relationships.  Protege looks for :DIRECT-SUBCLASSES
>>> with a isTemplate value of false and the database only has entries with
>>> an isTemplate value of true.
>>>
>>> Now this is where I become uncertain.  Interestingly the symptoms 
>>> that I
>>> described are similar to some of the symptoms that you described (e.g.,
>>> the subclass relationships are in the database in some sense but don't
>>> appear in Protege).  The problem with the database dump is clear enough
>>> but it is not clear when in the process it got corrupted.
>>>
>>> It seems like I have found a problem but not the problem that you
>>> originally described.  I think that you indicated that you had a valid
>>> clips file that lost data when converted to a database project. If I am
>>> going to replicate this, it would seem that maybe I need to start with
>>> the clips file.
>>>
>>> What is the next step?  Does the new information help?
>>>
>>> -Timothy
>>>
>>>
>>>
>>> On 12/03/2012 03:04 PM, Todd Detwiler wrote:
>>>> >Please see my answers to follow-up questions below.
>>>> >Thanks,
>>>> >Todd
>>>> >
>>>> >Landon Todd Detwiler
>>>> >Structural Informatics Group (SIG)
>>>> >University of Washington
>>>> >
>>>> >phone: 206-616-2336
>>>> >
>>>> >On 12/3/12 2:22 PM,protege-discussion-request at lists.stanford.edu  
>>>> wrote:
>>>>> >>---------------------------------------------------------------------- 
>>>>>
>>>>> >>
>>>>> >>Message: 1
>>>>> >>Date: Mon, 03 Dec 2012 12:37:36 -0800
>>>>> >>From: Timothy Redmond<tredmond at stanford.edu>
>>>>> >>To:protege-discussion at lists.stanford.edu
>>>>> >>Subject: Re: [protege-discussion] Protege db schema conversion
>>>>> >>Message-ID:<50BD0D90.5030501 at stanford.edu>
>>>>> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>> >>
>>>>> >>
>>>>> >>My first reaction was that I am not sure what is wrong but perhaps
>>>>> >>getting some clarification on parts of the message will help me 
>>>>> figure
>>>>> >>out what is wrong.
>>>>> >>
>>>>> >>On 11/28/12 3:17 PM, Todd Detwiler wrote:
>>>>>> >>>Through the life of Protege as a tool, the database schema has
>>>>>> >>>undergone a few changes. As far as I know, the best approach for
>>>>>> >>>upconverting the schema of a database ontology has always been to
>>>>>> >>>first export it to clips (in an older Protege version) and 
>>>>>> then open
>>>>>> >>>that clips file in a newer Protege version and then save it 
>>>>>> out to a
>>>>>> >>>db. This has worked for us reasonably well in the past (we 
>>>>>> have an
>>>>>> >>>ontology for which the developers still use an old Protege 
>>>>>> version).
>>>>>> >>>But lately this isn't working well any more. I can still 
>>>>>> successfully
>>>>>> >>>write out our ontology to clips files. Newer versions of 
>>>>>> Protege (i.e.
>>>>>> >>>3.4.7, 3.4.8, and 3.5beta) can open the clips file and things 
>>>>>> look OK.
>>>>> >>This makes it sound like you have successfully converted the 
>>>>> database
>>>>> >>project to a clips project.  I am also assuming from this 
>>>>> description
>>>>> >>that you are using Protege frames and not Protege OWL.
>>>> >
>>>> >It appears so. I have converted the project to clips and,
>>>> >superficially, it looks fine in Protege. This is a fairly large
>>>> >ontology (the FMA) at 80,000+classes and over 2 million 
>>>> relationships.
>>>> >So, it does take a while to convert to clips and a rather large heap.
>>>> >Oh, and yes it is in frames.
>>>> >
>>>>> >>
>>>>>> >>>But when I try and save it out to a db, things go wrong. The 
>>>>>> resultant
>>>>>> >>>db, in the Protege UI, looks like all of our classes are untyped
>>>>>> >>>(nothing in the right hand pane).
>>>>> >>It sounds like you have taken a valid clips backed Protege frames
>>>>> >>project, converted it to a Protege Database project (not a OWL/RDF
>>>>> >>Database) project.  After doing the conversion, it sounds like the
>>>>> >>database project does not look the same as the clips backed 
>>>>> project.  If
>>>>> >>so, it sounds like this is where the problem occurred. Did you 
>>>>> use one
>>>>> >>of the supported datablases (mysql or postgres)? Is it possible 
>>>>> to send
>>>>> >>us the ontology so that we can try it out?
>>>> >
>>>> >Yes, I have loaded the clips project (in multiple Protege versions)
>>>> >and attempted to "Convert project to format" frames database. But it
>>>> >does not look the same in Protege (as the clips version). None of the
>>>> >classes have any info in the right frame (as though they were
>>>> >un-typed). Also, many leaf concepts don't appear at all (in the 
>>>> tree).
>>>> >I can query the database and find the missing classes. And, they have
>>>> >valid types. I am using MySQL for my database backend. In fact, I am
>>>> >using the same instance of MySQL that the initial db was in (before
>>>> >upconverting the schema). I can send you the file, but it is too 
>>>> large
>>>> >for email, even when compressed. So I've uploaded it here:
>>>> >http://dl.dropbox.com/u/2527438/FMA3.3/fma_3_3.sql.zip
>>>>> >>
>>>>>> >>>Also, lots of leaf classes appear to be missing in the tree. 
>>>>>> Now, if I
>>>>>> >>>query the database, these classes exist and have types.
>>>>> >>Are you talking about sql queries here?
>>>> >
>>>> >Yes, SQL queries.
>>>> >
>>>>> >>
>>>>>> >>>Further, if I open the new database ontology in Protege 
>>>>>> 3.4beta, it
>>>>>> >>>looks fine.
>>>>> >>So the new database project looks fine in one version of Protege
>>>>> >>(3.4.*?) but not in another one (3.5?)?  I believe that the 
>>>>> database
>>>>> >>backend format should be identical between the later 3.4 
>>>>> versions and
>>>>> >>the 3.5 version.
>>>> >
>>>> >That is correct. It does not look fine in 3.4.7, 3.4.8, or 3.5beta.
>>>> >But it does display fine in 3.4beta.
>>>> >
>>>> >Thank you for any help you can offer,
>>>> >Todd
>>>> >
>>>>> >>
>>>>> >>-Timothy
>>>>> >>
>>>>>> >>>What changes have occurred in the database backend, since 
>>>>>> 3.4beta,
>>>>>> >>>that could be causing this?
>>>>>> >>>Thanks,
>>>>>> >>>Todd
>>>>>> >>>
>>>>> >>
>>>>> >>
>>>>> >>
>>>> >
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