Re: [Gusdev-gusdev] everything works except commit!

[Steve F. <sfi...@pc...>]

i am not sure about the errors.

but, commit is a basic db term describing "go ahead and *really* update 
the database"

the opposite of commit is rollback.   a transaction (insert or update) 
is either committed or rolled back.

when you run a plugin w/o commit, it runs all the logic, and issues 
commands to insert data, but, at the least minute, oracle rolls back all 
the updates, so the db is not affected.

steve

MICHAEL LUCHTAN wrote:

>And just a clarification, if it is too complicated, don't worry about
>it...
>What exactly does commit do?  Why would it give these errors with commit
>turned on, but not when it is off?
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Mon, 19 Apr 2004, MICHAEL LUCHTAN wrote:
>
>  
>
>>Steve-
>>I will try this.  But some points to consider:
>>1.The previous data was entered using a plugin called
>>LoadBlastSimilaritiesPK.pm, included in the GUS release.
>>2.The "sequences" increments each time regardless of whether commit is
>>turned on.   Maybe not elegant, but I guess this doesn't matter,huh?
>>
>>Thanks,
>>
>>Michael Luchtan
>>http://www.cs.uga.edu/~luchtan
>>
>>
>>On Mon, 19 Apr 2004, Steve Fischer wrote:
>>
>>    
>>
>>>Michael-
>>>
>>>let me try to cobble together an answer.   first, i am the culprit
>>>responsible for that plugin.   but, i think it should be ok.
>>>
>>>about "sequences."    that term refers a database sequence, not a
>>>biological one.   it is a facility supported by oracle (and postgres)
>>>that provides an incremented number.    the plugins and object layer use
>>>such sequences to get the next primary key when inserting a row.
>>>
>>>so, i suspect that your initial data in those tables was added "outside"
>>>the plugin structure.
>>>
>>>i think the thing to do here is:
>>>  1. avoid adding data without using either the plugins/object layer or
>>>using the sequence directly
>>>  2. to correct the out-of-sync sequence, just run it in a loop
>>>advancing it past 3000 or whatever it needs to be.
>>>  3. re-instate the code that uses the sequence
>>>
>>>I would try that first, and then lets see if you still get the
>>>constraint errors.
>>>
>>>steve
>>>
>>>MICHAEL LUCHTAN wrote:
>>>
>>>      
>>>
>>>>Hello everyone-
>>>>I have been attempting to load blast similarities into GUS with the plugin
>>>>LoadBlastSimFast.pm after already loading some data in with the plugin
>>>>LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
>>>>Well, the first thing that LoadBlastSimFast.pm does is start complaining
>>>>about PrimaryKey uniqueness constraints being violated.  It used some
>>>>fancy Oracle SQL that I didn't understand:
>>>>select dots.similarity_SQ.NEXTVAL from DUAL
>>>>Which by debugging I found out started at one, and increased each time we
>>>>tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
>>>>we already had about 3,000 entries in the dots.similarity table and
>>>>we already had a sequence_id with value 1.  There
>>>>was likewise a problem with the dots.similarityspan table.
>>>>
>>>>Since I only having a workingman's knowledge of OracleSQL, I switched it
>>>>so that it starts with
>>>>select count(*) from dots.similarity
>>>>And increases this by one for each entry.  Likewise for
>>>>dots.similarityspan.  This seemed to fix the problem, and the plugin works
>>>>great on each file tested, claims to have entered all the correct data,
>>>>and exits gracefully.  Yet when I run the same command line with --commit
>>>>appended to the end, we start getting these Primary Key constraints
>>>>violated errors again.
>>>>
>>>>Perhaps I do not understand what happens with commit.  I thought that
>>>>these kind of errors would be caught with a regular run without commit
>>>>turned on.
>>>>Any help?
>>>>
>>>>
>>>>
>>>>
>>>>Michael Luchtan
>>>>http://www.cs.uga.edu/~luchtan
>>>>
>>>>
>>>>
>>>>
>>>>
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