INSERT command denied on Reset, GBrowse 2
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INSERT command denied on Reset, GBrowse 2
by Neil Saunders
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Just noticed something new on a GBrowse 2 installation (CVS, SVN
Bioperl, Ubuntu 9.04, Apache 2.2.11, MySQL 5.0.75). Clicking the 'reset' link gives an incompletely rendered initial display and this error in the Apache log: INSERT command denied to user 'genome'@'localhost' for table 'locationlist' at /usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1466. My impression was that the MySQL user needs only SELECT privilege. Why is this INSERT appearing? thanks Neil Saunders -- Statistical Bioinformatics - Health CSIRO Mathematical and Information Sciences Locked Bag 17, North Ryde, NSW 1670, Australia http://friendfeed.com/neilfws ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Dave Clements, GMOD Help Desk
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Hi Neil,
I can't find any explanation of what is going on here either. As I read the documentation, I don't think that GBrowse should require insert access at run time either. Does anyone on the list know if there is design documentation anywhere for the database schema used by SeqFeature::Store? That might help solve the mystery. Dave C. On Thu, Sep 10, 2009 at 10:45 PM, Neil Saunders <neilfws@...> wrote: > Just noticed something new on a GBrowse 2 installation (CVS, SVN > Bioperl, Ubuntu 9.04, Apache 2.2.11, MySQL 5.0.75). > > Clicking the 'reset' link gives an incompletely rendered initial display > and this error in the Apache log: > > INSERT command denied to user 'genome'@'localhost' for table > 'locationlist' at > /usr/local/share/perl/5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1466. > > My impression was that the MySQL user needs only SELECT privilege. Why > is this INSERT appearing? > > thanks > Neil Saunders > -- > Statistical Bioinformatics - Health > CSIRO Mathematical and Information Sciences > Locked Bag 17, North Ryde, NSW 1670, Australia > > http://friendfeed.com/neilfws > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Lincoln Stein-3
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Hi Neil,
This shouldn't happen. What type of backend are you using? Lincoln On Fri, Sep 11, 2009 at 1:45 AM, Neil Saunders <neilfws@...> wrote: Just noticed something new on a GBrowse 2 installation (CVS, SVN -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Neil Saunders-3
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> This shouldn't happen. What type of backend are you using?
MySQL 5.0.75. I should add that I've only seen this on one of 3 machines with a GBrowse 2 installation. The installation is not the cleanest (have used at various times CVS, downloaded CVS tarballs and CPAN), so could just be a quirk of the machine. Neil -- Statistical Bioinformatics - Health CSIRO Mathematical and Information Sciences Locked Bag 17, North Ryde, NSW 1670, Australia http://friendfeed.com/neilfws ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Lincoln Stein-3
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Are there any plugins installed? GBrowse on its own never tries to update the databases.
Lincoln On Fri, Sep 18, 2009 at 4:16 AM, Neil Saunders <neil.saunders@...> wrote:
-- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Neil Saunders
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> Are there any plugins installed? GBrowse on its own never tries to
> update the databases. Just those that install by default: FastaDumper, RestrictionAnnotator, SequenceDumper, TrackDumper, Submitter Not to worry. I'm quite used to GBrowse2 flakiness :-) Neil -- Statistical Bioinformatics - Health CSIRO Mathematical and Information Sciences Locked Bag 17, North Ryde, NSW 1670, Australia http://friendfeed.com/neilfws ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Lincoln Stein-3
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Hi Neil,
It turns out that there was a bug in DBI/mysql.pm that causes the backend to try to insert a sequence ID whenever it searches for a sequence that is unknown. My guess is that you have your initial feature set to an invalid sequence id, so that when you reset, it searches for that sequence id and fails. The enclosed diff fixes the bug in the mysql adaptor, which is part of BioPerl. It is also in bioperl-live SVN, but unfortunately did not make it into the recent bioperl release. Lincoln
On Fri, Sep 11, 2009 at 1:45 AM, Neil Saunders <neilfws@...> wrote: Just noticed something new on a GBrowse 2 installation (CVS, SVN -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> [insert_bug.diff] Index: Bio/DB/SeqFeature/Store/DBI/mysql.pm =================================================================== --- Bio/DB/SeqFeature/Store/DBI/mysql.pm (revision 16217) +++ Bio/DB/SeqFeature/Store/DBI/mysql.pm (working copy) @@ -1028,7 +1028,7 @@ # the additional join on the location_list table badly impacts performance # so we build a copy of the table in memory - my $seqid = $self->_locationid($seq_id) || 0; # zero is an invalid primary ID, so will return empty + my $seqid = $self->_locationid_nocreate($seq_id) || 0; # zero is an invalid primary ID, so will return empty $start = MIN_INT unless defined $start; $end = MAX_INT unless defined $end; @@ -1487,6 +1487,9 @@ sub _locationid { shift->_genericid('locationlist','seqname',shift,1); } +sub _locationid_nocreate { + shift->_genericid('locationlist','seqname',shift,0); +} sub _attributeid { shift->_genericid('attributelist','tag',shift,1); } ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: INSERT command denied on Reset, GBrowse 2
by Neil Saunders-3
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> The enclosed diff fixes the bug in the mysql adaptor, which is part of BioPerl.
> It is also in bioperl-live SVN, but unfortunately did not make it into the recent bioperl release. That's great, thanks. Will try that out in a couple of weeks (after vacation). Neil -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...>> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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