Re: Bio/Graphics/Browser2/UserDB.pm : possibleupdate ?

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Re: Bio/Graphics/Browser2/UserDB.pm : possibleupdate ?

Keiran Raine
Hi Lincoln,
Do you know when you will be able to look at this problem?  Presenting data that has access agreements is becoming a real issue for us and this appears to be the best solution for us.
Thanks
Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H204


I will be reviewing the whole authentication/authorization system. Sounds
like these are related bugs.

Lincoln


On Tue, Mar 5, 2013 at 3:10 AM, Keiran Raine <kr2@...> wrote:

> Hi Lincoln,
>
> Would this explain why I'm having trouble getting PAM group level
> authentication to work?
>
> Issue:
> Mark datasource as 'restrict group xxx'.
> Login as appropriate user.
> Tracks intermittently don't render and logs show 'UNAUTHORIZED ATTEMPT'.
>
> I'm working with an older version of the browser and was waiting to try in
> a newer release before reporting but as this is likely related thought I
> should mention it now.
>
> Keiran
>
> Sent from my Android phone using TouchDown (www.nitrodesk.com)
>
>
> -----Original Message-----
> From: Lincoln Stein [lincoln.stein@...]
> Received: Monday, 04 Mar 2013, 19:11
> To: Frédéric Sapet [frederic.sapet@...]
> CC: gmod-gbrowse@... [Gmod-gbrowse@...
> ]
> Subject: Re: [Gmod-gbrowse] Bio/Graphics/Browser2/UserDB.pm :
> possibleupdate ?
>
>
> The db handle caching system must not be working correctly. I will fix it.
>
> L
>
> On Monday, March 4, 2013, Frédéric Sapet wrote:
>
> > i have noticed that my sessions database was overwhelmed by connections.
> >
> > It's in a way the same problem I have noticed with LDAPAuthenticate.pm,
> > the first connection is no saved, so each time you need data from the
> > database, GGB will create a new one !
> >
> > This is related to a bug described in
> > Bio/Graphics/Browser2/UserTracks/Database.pm
> > # BUG: Two copies of UserDB; one here and one in the Render object
> >
> > I have done something, which is not maybe the best way to do this, but it
> > does the trick.
> >
> > I've added a class variable in Bio/Graphics/Browser2/UserDB.pm :
> >
> > our $alreadyLoggedIn;
> >
> > and then the new method will become :
> >
> > sub new {
> >   my $class   = shift;
> >   my $globals = shift;
> >
> >   my $VERSION = '0.5';
> >   my $credentials  = $globals->user_account_db
> >       || "DBI:mysql:gbrowse_login;user=gbrowse;password=gbrowse";
> >   my $login;
> >   if (!defined $alreadyLoggedIn) {
> >     $login = DBI->connect($credentials);
> >     $alreadyLoggedIn = $login;
> >   }
> >   else {
> >     $login = $alreadyLoggedIn;
> >   }
> >   unless ($login) {
> >       confess "Could not open login database $credentials";
> >   }
> >
> >   my $self = bless {
> >       dbi      => $login,
> >       globals  => $globals,
> >       openid   => HAVE_OPENID,
> >       register => HAVE_SMTP,
> >   }, ref $class || $class;
> >
> >   return $self;
> > }
> >
> > it avoids some connections to the database.
> >
> > By the way, I have a question about the $globals object. This is a
> > Bio::Graphics::Browser2 object.  I have noticed that this object is not
> > always the same through the different calls of
> > Bio/Graphics/Browser2/UserDB.pm even when I work with the same datasource
> > on the interface. I though that the same object should be reused ? (and
> so
> > the class variable be more powerfull)
> >
> > thank you.
> >
> > Fred
> >
> >
>
> --
> 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@...>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
>


-- 
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@...>


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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