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

[MICHAEL L. <lu...@cs...>]

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
> > >
> > >
> > >
> > >
> > >
> > >-------------------------------------------------------
> > >This SF.Net email is sponsored by: IBM Linux Tutorials
> > >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > >GenToo technologies. Learn everything from fundamentals to system
> > >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > >_______________________________________________
> > >Gusdev-gusdev mailing list
> > >Gus...@li...
> > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>