Authentication plugin (GGB 2.54) : some troubles

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Authentication plugin (GGB 2.54) : some troubles

Frédéric Sapet
Hello

I have set up a gbrowse (2.54 , from CPAN) with the built-in user account database. It works but I have some concerns about a bug and two other remarks.

The bug (if it's one, and not due to a misunderstanding from myself) is related with both fcgid and authentication. I have a  finder plugin where I use this line of code in dump method : :
my @featureA = $self->database->get_feature_by_name($featureA)
Everything is ok when authentication if OFF (both  when running under CGI or fastCGI mode) but whith authentication ON and when running under FastCGI mode the code $self->database return an empty value and it brokes my plugin.


The fisrt remark is a warning :
[Tue Feb 26 14:55:17 2013] [warn] [client 192.168.109.100] mod_fcgid: stderr: To use the 'require group' limit you must load an authentication plugin. Otherwise use a subroutine to implement role-based authentication.
I don't understand why this warning occurs, I have set user_accounts to 1 in my GBROWSE.conf file and authentication plugin value is set to LDAPAuthenticate. And authentication works fine, but the warning is still there. I try to restrict both source and tracks. I have public and private sources and public and private tracks.

The second remark is maybe a bit more strange and important :
Sometimes, I can see in my Apache log this error messages :
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.

Attempt to free unreferenced scalar: SV 0x1aaa3bb0, Perl interpreter: 0x15cda010 during global destruction.
Attempt to free unreferenced scalar: SV 0x1a9c4930, Perl interpreter: 0x15cda010 during global destruction.

and in the gbrowse slave logs, I can see also some strange messages :
SV = RV(0x3a674e8) at 0x3a674d8
  REFCNT = 1
  FLAGS = (ROK,READONLY)
  RV = 0x39ac0c8
    SV = PVHV(0x3a57880) at 0x39ac0c8
      REFCNT = 1
      FLAGS = (OBJECT,SHAREKEYS)
      STASH = 0x1a14f60 "DBI::dr"
      ARRAY = 0x39c5d08  (0:8, 1:7, 3:1)
      hash quality = 97.7%
      KEYS = 10
      FILL = 8
      MAX = 15
      RITER = -1
      EITER = 0x0
        Elt "Attribution" HASH = 0x3dd36b11
        SV = PV(0x39c9180) at 0x3a670e8
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5dd8 "DBD::mysql by Patrick Galbraith"\0
          CUR = 31
          LEN = 32
        Elt "FetchHashKeyName" HASH = 0xad2a2131
        SV = PV(0x39c9250) at 0x39aac58
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5da8 "NAME"\0
          CUR = 4
          LEN = 8
        Elt "TraceLevel" HASH = 0x825c4531
        SV = IV(0x39c8498) at 0x39c84a0
          REFCNT = 1
          FLAGS = (IOK,pIOK)
          IV = 0

I would like to know what to do. Is this a problem of some perl module deprecated ? Do I need to update some of them ? Storable.pm is currently in version2.39.

Thank you

Fred

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Re: Authentication plugin (GGB 2.54) : some troubles

Lincoln Stein
Is the second remark also associated with authentication, or is this a separate issue?

Lincoln


On Tue, Feb 26, 2013 at 11:22 AM, Frédéric Sapet <[hidden email]> wrote:
Hello

I have set up a gbrowse (2.54 , from CPAN) with the built-in user account database. It works but I have some concerns about a bug and two other remarks.

The bug (if it's one, and not due to a misunderstanding from myself) is related with both fcgid and authentication. I have a  finder plugin where I use this line of code in dump method : :
my @featureA = $self->database->get_feature_by_name($featureA)
Everything is ok when authentication if OFF (both  when running under CGI or fastCGI mode) but whith authentication ON and when running under FastCGI mode the code $self->database return an empty value and it brokes my plugin.


The fisrt remark is a warning :
[Tue Feb 26 14:55:17 2013] [warn] [client 192.168.109.100] mod_fcgid: stderr: To use the 'require group' limit you must load an authentication plugin. Otherwise use a subroutine to implement role-based authentication.
I don't understand why this warning occurs, I have set user_accounts to 1 in my GBROWSE.conf file and authentication plugin value is set to LDAPAuthenticate. And authentication works fine, but the warning is still there. I try to restrict both source and tracks. I have public and private sources and public and private tracks.

The second remark is maybe a bit more strange and important :
Sometimes, I can see in my Apache log this error messages :
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.

Attempt to free unreferenced scalar: SV 0x1aaa3bb0, Perl interpreter: 0x15cda010 during global destruction.
Attempt to free unreferenced scalar: SV 0x1a9c4930, Perl interpreter: 0x15cda010 during global destruction.

and in the gbrowse slave logs, I can see also some strange messages :
SV = RV(0x3a674e8) at 0x3a674d8
  REFCNT = 1
  FLAGS = (ROK,READONLY)
  RV = 0x39ac0c8
    SV = PVHV(0x3a57880) at 0x39ac0c8
      REFCNT = 1
      FLAGS = (OBJECT,SHAREKEYS)
      STASH = 0x1a14f60 "DBI::dr"
      ARRAY = 0x39c5d08  (0:8, 1:7, 3:1)
      hash quality = 97.7%
      KEYS = 10
      FILL = 8
      MAX = 15
      RITER = -1
      EITER = 0x0
        Elt "Attribution" HASH = 0x3dd36b11
        SV = PV(0x39c9180) at 0x3a670e8
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5dd8 "DBD::mysql by Patrick Galbraith"\0
          CUR = 31
          LEN = 32
        Elt "FetchHashKeyName" HASH = 0xad2a2131
        SV = PV(0x39c9250) at 0x39aac58
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5da8 "NAME"\0
          CUR = 4
          LEN = 8
        Elt "TraceLevel" HASH = 0x825c4531
        SV = IV(0x39c8498) at 0x39c84a0
          REFCNT = 1
          FLAGS = (IOK,pIOK)
          IV = 0

I would like to know what to do. Is this a problem of some perl module deprecated ? Do I need to update some of them ? Storable.pm is currently in version2.39.

Thank you

Fred

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
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--
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 <[hidden email]>

------------------------------------------------------------------------------
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Download AppDynamics Lite for free today:
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Re: Authentication plugin (GGB 2.54) : some troubles

Frédéric Sapet
Hello

For the second remark, I'm pretty sure it's related to authentication. These messages ( Can't store GLOB  and Attempt to free unreferenced scalar issues) are not shown when user_accounts = 0. 

For the first bug, it seems to be difficult to reproduce it. I have tried few minutes ago, and $self->database gives me a value now... I started and stopped the Apache server several times since. 
Nevertheless, I've got clickable images (using an image map) at the top of my browser (ie : image of chrosomoses like here : http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/), and sometimes (not easy to reproduce here again) links are broken, and I can't switch for a chromosome to another by clicking it on the image. When this occurs, I see that the "on mouse-over" event, something happens in LDAPauthenticate.pm plugin, the method user_in_group is called (I have noticed this because I have added a warning in _ldap_connect method for the debuging process, the first time I tried setting up the authentication process).

I'm sorry, my problems are a bit twisted, I don't know exactly what to do to be more precise. It looks like my browser becomes crazy and I have to stop and start again the apache server (each time, I flush all the sessions in mysql database and in /var/tmp directory) . After that, the genome browser works well and is very fast.

Fred



2013/2/26 Lincoln Stein <[hidden email]>
Is the second remark also associated with authentication, or is this a separate issue?

Lincoln


On Tue, Feb 26, 2013 at 11:22 AM, Frédéric Sapet <[hidden email]> wrote:
Hello

I have set up a gbrowse (2.54 , from CPAN) with the built-in user account database. It works but I have some concerns about a bug and two other remarks.

The bug (if it's one, and not due to a misunderstanding from myself) is related with both fcgid and authentication. I have a  finder plugin where I use this line of code in dump method : :
my @featureA = $self->database->get_feature_by_name($featureA)
Everything is ok when authentication if OFF (both  when running under CGI or fastCGI mode) but whith authentication ON and when running under FastCGI mode the code $self->database return an empty value and it brokes my plugin.


The fisrt remark is a warning :
[Tue Feb 26 14:55:17 2013] [warn] [client 192.168.109.100] mod_fcgid: stderr: To use the 'require group' limit you must load an authentication plugin. Otherwise use a subroutine to implement role-based authentication.
I don't understand why this warning occurs, I have set user_accounts to 1 in my GBROWSE.conf file and authentication plugin value is set to LDAPAuthenticate. And authentication works fine, but the warning is still there. I try to restrict both source and tracks. I have public and private sources and public and private tracks.

The second remark is maybe a bit more strange and important :
Sometimes, I can see in my Apache log this error messages :
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.

Attempt to free unreferenced scalar: SV 0x1aaa3bb0, Perl interpreter: 0x15cda010 during global destruction.
Attempt to free unreferenced scalar: SV 0x1a9c4930, Perl interpreter: 0x15cda010 during global destruction.

and in the gbrowse slave logs, I can see also some strange messages :
SV = RV(0x3a674e8) at 0x3a674d8
  REFCNT = 1
  FLAGS = (ROK,READONLY)
  RV = 0x39ac0c8
    SV = PVHV(0x3a57880) at 0x39ac0c8
      REFCNT = 1
      FLAGS = (OBJECT,SHAREKEYS)
      STASH = 0x1a14f60 "DBI::dr"
      ARRAY = 0x39c5d08  (0:8, 1:7, 3:1)
      hash quality = 97.7%
      KEYS = 10
      FILL = 8
      MAX = 15
      RITER = -1
      EITER = 0x0
        Elt "Attribution" HASH = 0x3dd36b11
        SV = PV(0x39c9180) at 0x3a670e8
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5dd8 "DBD::mysql by Patrick Galbraith"\0
          CUR = 31
          LEN = 32
        Elt "FetchHashKeyName" HASH = 0xad2a2131
        SV = PV(0x39c9250) at 0x39aac58
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5da8 "NAME"\0
          CUR = 4
          LEN = 8
        Elt "TraceLevel" HASH = 0x825c4531
        SV = IV(0x39c8498) at 0x39c84a0
          REFCNT = 1
          FLAGS = (IOK,pIOK)
          IV = 0

I would like to know what to do. Is this a problem of some perl module deprecated ? Do I need to update some of them ? Storable.pm is currently in version2.39.

Thank you

Fred

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
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[hidden email]
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
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Re: Authentication plugin (GGB 2.54) : some troubles

Frédéric Sapet
Hello

I've found a way to reproduce the bug ($self->database return an empty value in Finder plugin)

This bug occurs only under FastCGI environnment.

You can try to add a warning in BatchDumper.pm :

 plugins/BatchDumper.pm

 63 my $db = $self->database;
 64 print STDERR "FRED ICI db=$db=\n";
 65
 66   my @segments = map {
 67     ( $self->renderer->name2segments($_,$self->database) )
 68                      } split /\s+/m, $config->{sequence_IDs}||'';


Then I have made a copy of yeast configuration file
cp yeast_simple.conf yeast_simple_private.conf

In GBROWSE.conf I have now two databases fro yeast, one with public acces and another one which requires to be in biogemma group (i'm working with LDAPAuthenticate plugin) :

[yeast]
description   = Yeast chromosomes 1+2 (basic)
path          = yeast_simple.conf

[yeastPRIVATE]
description   = PRIVATE Yeast chromosomes 1+2 (basic)
path          = yeast_simple_private.conf
restrict      = require group biogemma

Then, go to the interface.
Reach yeast database
You're not logged, so yeastPRIVATE is not reachable.
Launch "Download Sequence File" plugin on Yeast database : OK (plugin works and you see in apache log :  mod_fcgid: stderr: FRED ICI db=Bio::DB::SeqFeature::Store::memory=HASH(0xf35fdc0)=)
then Log in.
select yeastPRIVATE
Launch "Download Sequence File" plugin on Yeast database : KO (plugin still works but in apache log :  mod_fcgid: stderr: FRED ICI db==)

BatchDumper.pm seems to be not worried about the fact that $self->database returns nothing.
But some of my plugins need it and I think that CreateBlastDB.pm will be broken too because it uses the database method :  my $db    = $self->database or die "I do not have a database";

As I said, in common CGI environnment, it works, but in this case, all my images map are un-functionnal and each on-mouse-over event (on image map, tracks) make a call to the method user_in_group in LDAPAuthenticate plugin (like I said yesterday). The method user_in_group  is also called several times when you try to select another region to display.

I hope it helps.

Fred




2013/2/26 Frédéric Sapet <[hidden email]>
Hello

For the second remark, I'm pretty sure it's related to authentication. These messages ( Can't store GLOB  and Attempt to free unreferenced scalar issues) are not shown when user_accounts = 0. 

For the first bug, it seems to be difficult to reproduce it. I have tried few minutes ago, and $self->database gives me a value now... I started and stopped the Apache server several times since. 
Nevertheless, I've got clickable images (using an image map) at the top of my browser (ie : image of chrosomoses like here : http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/), and sometimes (not easy to reproduce here again) links are broken, and I can't switch for a chromosome to another by clicking it on the image. When this occurs, I see that the "on mouse-over" event, something happens in LDAPauthenticate.pm plugin, the method user_in_group is called (I have noticed this because I have added a warning in _ldap_connect method for the debuging process, the first time I tried setting up the authentication process).

I'm sorry, my problems are a bit twisted, I don't know exactly what to do to be more precise. It looks like my browser becomes crazy and I have to stop and start again the apache server (each time, I flush all the sessions in mysql database and in /var/tmp directory) . After that, the genome browser works well and is very fast.

Fred



2013/2/26 Lincoln Stein <[hidden email]>
Is the second remark also associated with authentication, or is this a separate issue?

Lincoln


On Tue, Feb 26, 2013 at 11:22 AM, Frédéric Sapet <[hidden email]> wrote:
Hello

I have set up a gbrowse (2.54 , from CPAN) with the built-in user account database. It works but I have some concerns about a bug and two other remarks.

The bug (if it's one, and not due to a misunderstanding from myself) is related with both fcgid and authentication. I have a  finder plugin where I use this line of code in dump method : :
my @featureA = $self->database->get_feature_by_name($featureA)
Everything is ok when authentication if OFF (both  when running under CGI or fastCGI mode) but whith authentication ON and when running under FastCGI mode the code $self->database return an empty value and it brokes my plugin.


The fisrt remark is a warning :
[Tue Feb 26 14:55:17 2013] [warn] [client 192.168.109.100] mod_fcgid: stderr: To use the 'require group' limit you must load an authentication plugin. Otherwise use a subroutine to implement role-based authentication.
I don't understand why this warning occurs, I have set user_accounts to 1 in my GBROWSE.conf file and authentication plugin value is set to LDAPAuthenticate. And authentication works fine, but the warning is still there. I try to restrict both source and tracks. I have public and private sources and public and private tracks.

The second remark is maybe a bit more strange and important :
Sometimes, I can see in my Apache log this error messages :
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.
Can't store GLOB items at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Storable.pm line 339, at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RenderPanels.pm line 783.

Attempt to free unreferenced scalar: SV 0x1aaa3bb0, Perl interpreter: 0x15cda010 during global destruction.
Attempt to free unreferenced scalar: SV 0x1a9c4930, Perl interpreter: 0x15cda010 during global destruction.

and in the gbrowse slave logs, I can see also some strange messages :
SV = RV(0x3a674e8) at 0x3a674d8
  REFCNT = 1
  FLAGS = (ROK,READONLY)
  RV = 0x39ac0c8
    SV = PVHV(0x3a57880) at 0x39ac0c8
      REFCNT = 1
      FLAGS = (OBJECT,SHAREKEYS)
      STASH = 0x1a14f60 "DBI::dr"
      ARRAY = 0x39c5d08  (0:8, 1:7, 3:1)
      hash quality = 97.7%
      KEYS = 10
      FILL = 8
      MAX = 15
      RITER = -1
      EITER = 0x0
        Elt "Attribution" HASH = 0x3dd36b11
        SV = PV(0x39c9180) at 0x3a670e8
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5dd8 "DBD::mysql by Patrick Galbraith"\0
          CUR = 31
          LEN = 32
        Elt "FetchHashKeyName" HASH = 0xad2a2131
        SV = PV(0x39c9250) at 0x39aac58
          REFCNT = 1
          FLAGS = (POK,pPOK)
          PV = 0x39c5da8 "NAME"\0
          CUR = 4
          LEN = 8
        Elt "TraceLevel" HASH = 0x825c4531
        SV = IV(0x39c8498) at 0x39c84a0
          REFCNT = 1
          FLAGS = (IOK,pIOK)
          IV = 0

I would like to know what to do. Is this a problem of some perl module deprecated ? Do I need to update some of them ? Storable.pm is currently in version2.39.

Thank you

Fred

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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