GBrowse 2.23 released

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GBrowse 2.23 released

Lincoln Stein
Hi All,


IMPORTANT: This release corrects a security issue in which the default users.sqlite user account database could be created in the root directory under some circumstances. If you installed versions 2.20-2.22, please check for the presence of /users.sqlite and delete it if it is present. Also check the ownership of /, because the install process may have set it to www-data.

This release also corrects some of the "session lock timeout" issues that people have been experiencing. Note, however, that certain long operations, such as file uploads, will continue to create timeouts for individual users; these are usually safe to ignore. Finally, the bug in which the account "Registration" link is missing has been fixed.

Here are the complete release notes:

Version 2.23 (bugfix release)
   * SECURITY ISSUE: Fixed default SQLite user account database to be created in /var/www/gbrowse2/databases rather
     than in / (root) directory.
   * Added an "example_scripts" directory that contains a perl scripts that show how to manipulate
     sessions, upload custom tracks, and get basic information about services. This directory accompanies
     new REST API documentation located at http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
   * Fixed missing "registration" link in login dialog. This occurred when openid was unavailable.
   * Fixed popup dialogs in the "Help" menu so that they appear again.
   * Fixed file upload status display to prevent upload details section from disappearing when
     uploading very small files.
   * Tinkered with session settings to minimize session lock timeouts.
   * Removed some dangling warnings in the track sharing module.
   * Made SQLite the default user account database.
Lincoln

--
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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Re: GBrowse 2.23 released

Keiran Raine
Hi all,

Just something to note for anyone not using the default system version of perl for their gbrowse setup (normally occurs when you have a site wide perl version), e.g.:

~: perl -v
This is perl, v5.8.8 built for x86_64-linux-thread-multi....

~: /usr/bin/perl -v
This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....

As we don't have 5.10 as our default perl I run the installation manually as follows:

/usr/bin/perl Build.PL --prefix /gbrowse
./Build
./Build test
./Build install

Which results in the following failure when the gbrowse_metadb_config.pl script tries to execute:

Updating user account database...
Base class package "Bio::Graphics::FeatureFile" is empty.
    (Perhaps you need to 'use' the module which defines that package first.)
 at /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 5
BEGIN failed--compilation aborted at /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 5.
Compilation failed in require at (eval 5) line 3.
...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
Compilation failed in require at bin/gbrowse_metadb_config.pl line 6.
BEGIN failed--compilation aborted at bin/gbrowse_metadb_config.pl line 6.

If I just ran this manually with the pathed perl I use at the beginning of the install process it woks fine:

/usr/bin/perl -c bin/gbrowse_metadb_config.pl
bin/gbrowse_metadb_config.pl syntax OK

Hope this is of use to anyone having issues.

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 30 Jan 2011, at 20:22, Lincoln Stein wrote:

Hi All,


IMPORTANT: This release corrects a security issue in which the default users.sqlite user account database could be created in the root directory under some circumstances. If you installed versions 2.20-2.22, please check for the presence of /users.sqlite and delete it if it is present. Also check the ownership of /, because the install process may have set it to www-data.

This release also corrects some of the "session lock timeout" issues that people have been experiencing. Note, however, that certain long operations, such as file uploads, will continue to create timeouts for individual users; these are usually safe to ignore. Finally, the bug in which the account "Registration" link is missing has been fixed.

Here are the complete release notes:

Version 2.23 (bugfix release)
   * SECURITY ISSUE: Fixed default SQLite user account database to be created in /var/www/gbrowse2/databases rather
     than in / (root) directory.
   * Added an "example_scripts" directory that contains a perl scripts that show how to manipulate
     sessions, upload custom tracks, and get basic information about services. This directory accompanies
     new REST API documentation located at http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
   * Fixed missing "registration" link in login dialog. This occurred when openid was unavailable.
   * Fixed popup dialogs in the "Help" menu so that they appear again.
   * Fixed file upload status display to prevent upload details section from disappearing when
     uploading very small files.
   * Tinkered with session settings to minimize session lock timeouts.
   * Removed some dangling warnings in the track sharing module.
   * Made SQLite the default user account database.
Lincoln

--
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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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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Re: GBrowse 2.23 released

Karthik-7

Hello Lincoln
I installed gbrowse2.23 from cpan. I get the following error :

Successfully upgraded schema from 0 to 1.
Sharing table didn't exist, creating...
DBD::mysql::st execute failed: Unknown column 'users' in 'field list' at
bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
upgrade failed due to DBD::mysql::st execute failed: Unknown column 'users'
in 'field list' at bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
. Rolling back at bin/gbrowse_metadb_config.pl line 846, <STDIN> line 2.
Can't upgrade from version 1 to version 2 at bin/gbrowse_metadb_config.pl
line 627, <STDIN> line 2.

Can this be ignored ?
--
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Re: GBrowse 2.23 released

Lincoln Stein
I'm sorry to everyone, but the recent release introduced a bug into the gbrowse_metadb_config.pl script that causes it to fail when creating a completely new user account database. The fix will be in 2.24, which I will release after some more testing. The patch is as follows:

===================================================================
--- bin/gbrowse_metadb_config.pl (revision 24441)
+++ bin/gbrowse_metadb_config.pl (working copy)
@@ -615,6 +615,19 @@
 
 sub upgrade_schema {
     my $new_version   = shift;
+
+    # probe whether this is a completely empty database
+    {
+ local $database->{PrintWarn}  = 0;
+ local $database->{PrintError} = 0;
+ my ($count) = $database->selectrow_array('select count(*) from users');
+ if (!defined $count) {
+    check_table('dbinfo',$dbinfo_columns);
+    set_schema_version('dbinfo',$new_version);
+    return;
+ }
+    }
+
     my ($old_version) = $database->selectrow_array('SELECT MAX(schema_version) FROM dbinfo LIMIT 1');
     unless ($old_version) {
  # table is missing, so add it

Lincoln

On Mon, Jan 31, 2011 at 10:28 AM, Karthik <[hidden email]> wrote:

Hello Lincoln
I installed gbrowse2.23 from cpan. I get the following error :

Successfully upgraded schema from 0 to 1.
Sharing table didn't exist, creating...
DBD::mysql::st execute failed: Unknown column 'users' in 'field list' at
bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
upgrade failed due to DBD::mysql::st execute failed: Unknown column 'users'
in 'field list' at bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
. Rolling back at bin/gbrowse_metadb_config.pl line 846, <STDIN> line 2.
Can't upgrade from version 1 to version 2 at bin/gbrowse_metadb_config.pl
line 627, <STDIN> line 2.

Can this be ignored ?
--
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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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February 28th, so secure your free ArcSight Logger TODAY!
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Re: GBrowse 2.23 released

Dan Bolser-3
Can I install GBrowse without the user account system?

i.e. is it modular?

On 31 January 2011 16:01, Lincoln Stein <[hidden email]> wrote:

> I'm sorry to everyone, but the recent release introduced a bug into the
> gbrowse_metadb_config.pl script that causes it to fail when creating a
> completely new user account database. The fix will be in 2.24, which I will
> release after some more testing. The patch is as follows:
>
> Index: bin/gbrowse_metadb_config.pl
> ===================================================================
> --- bin/gbrowse_metadb_config.pl (revision 24441)
> +++ bin/gbrowse_metadb_config.pl (working copy)
> @@ -615,6 +615,19 @@
>
>  sub upgrade_schema {
>      my $new_version   = shift;
> +
> +    # probe whether this is a completely empty database
> +    {
> + local $database->{PrintWarn}  = 0;
> + local $database->{PrintError} = 0;
> + my ($count) = $database->selectrow_array('select count(*) from users');
> + if (!defined $count) {
> +    check_table('dbinfo',$dbinfo_columns);
> +    set_schema_version('dbinfo',$new_version);
> +    return;
> + }
> +    }
> +
>      my ($old_version) = $database->selectrow_array('SELECT
> MAX(schema_version) FROM dbinfo LIMIT 1');
>      unless ($old_version) {
>   # table is missing, so add it
>
> Lincoln
>
> On Mon, Jan 31, 2011 at 10:28 AM, Karthik <[hidden email]> wrote:
>>
>> Hello Lincoln
>> I installed gbrowse2.23 from cpan. I get the following error :
>>
>> Successfully upgraded schema from 0 to 1.
>> Sharing table didn't exist, creating...
>> DBD::mysql::st execute failed: Unknown column 'users' in 'field list' at
>> bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>> upgrade failed due to DBD::mysql::st execute failed: Unknown column
>> 'users'
>> in 'field list' at bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>> . Rolling back at bin/gbrowse_metadb_config.pl line 846, <STDIN> line 2.
>> Can't upgrade from version 1 to version 2 at bin/gbrowse_metadb_config.pl
>> line 627, <STDIN> line 2.
>>
>> Can this be ignored ?
>> --
>> View this message in context:
>> http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-2-23-released-tp3363731p3364638.html
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better
>> price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

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Re: GBrowse 2.23 released

Scott Cain
Hi Dan,

I think so--I updated to it on my laptop (where I don't have a user
account system :-) and the update went without a hitch and it seems to
run fine.  Of course, 2.24 will be out soon :-)

Scott


On Mon, Jan 31, 2011 at 11:21 AM, Dan Bolser <[hidden email]> wrote:

> Can I install GBrowse without the user account system?
>
> i.e. is it modular?
>
> On 31 January 2011 16:01, Lincoln Stein <[hidden email]> wrote:
>> I'm sorry to everyone, but the recent release introduced a bug into the
>> gbrowse_metadb_config.pl script that causes it to fail when creating a
>> completely new user account database. The fix will be in 2.24, which I will
>> release after some more testing. The patch is as follows:
>>
>> Index: bin/gbrowse_metadb_config.pl
>> ===================================================================
>> --- bin/gbrowse_metadb_config.pl (revision 24441)
>> +++ bin/gbrowse_metadb_config.pl (working copy)
>> @@ -615,6 +615,19 @@
>>
>>  sub upgrade_schema {
>>      my $new_version   = shift;
>> +
>> +    # probe whether this is a completely empty database
>> +    {
>> + local $database->{PrintWarn}  = 0;
>> + local $database->{PrintError} = 0;
>> + my ($count) = $database->selectrow_array('select count(*) from users');
>> + if (!defined $count) {
>> +    check_table('dbinfo',$dbinfo_columns);
>> +    set_schema_version('dbinfo',$new_version);
>> +    return;
>> + }
>> +    }
>> +
>>      my ($old_version) = $database->selectrow_array('SELECT
>> MAX(schema_version) FROM dbinfo LIMIT 1');
>>      unless ($old_version) {
>>   # table is missing, so add it
>>
>> Lincoln
>>
>> On Mon, Jan 31, 2011 at 10:28 AM, Karthik <[hidden email]> wrote:
>>>
>>> Hello Lincoln
>>> I installed gbrowse2.23 from cpan. I get the following error :
>>>
>>> Successfully upgraded schema from 0 to 1.
>>> Sharing table didn't exist, creating...
>>> DBD::mysql::st execute failed: Unknown column 'users' in 'field list' at
>>> bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>>> upgrade failed due to DBD::mysql::st execute failed: Unknown column
>>> 'users'
>>> in 'field list' at bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>>> . Rolling back at bin/gbrowse_metadb_config.pl line 846, <STDIN> line 2.
>>> Can't upgrade from version 1 to version 2 at bin/gbrowse_metadb_config.pl
>>> line 627, <STDIN> line 2.
>>>
>>> Can this be ignored ?
>>> --
>>> View this message in context:
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-2-23-released-tp3363731p3364638.html
>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>>> Finally, a world-class log management solution at an even better
>>> price-free!
>>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>>> February 28th, so secure your free ArcSight Logger TODAY!
>>> http://p.sf.net/sfu/arcsight-sfd2d
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>> --
>> 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]>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GBrowse 2.23 released

Lincoln Stein
In reply to this post by Dan Bolser-3
Yes, you just set user_accounts=0 in GBrowse.conf (or leave the line out altorgether).

I'm having trouble uploading 2.24 to CPAN, but soon, I hope.


Lincoln

On Mon, Jan 31, 2011 at 11:21 AM, Dan Bolser <[hidden email]> wrote:
Can I install GBrowse without the user account system?

i.e. is it modular?

On 31 January 2011 16:01, Lincoln Stein <[hidden email]> wrote:
> I'm sorry to everyone, but the recent release introduced a bug into the
> gbrowse_metadb_config.pl script that causes it to fail when creating a
> completely new user account database. The fix will be in 2.24, which I will
> release after some more testing. The patch is as follows:
>
> Index: bin/gbrowse_metadb_config.pl
> ===================================================================
> --- bin/gbrowse_metadb_config.pl (revision 24441)
> +++ bin/gbrowse_metadb_config.pl (working copy)
> @@ -615,6 +615,19 @@
>
>  sub upgrade_schema {
>      my $new_version   = shift;
> +
> +    # probe whether this is a completely empty database
> +    {
> + local $database->{PrintWarn}  = 0;
> + local $database->{PrintError} = 0;
> + my ($count) = $database->selectrow_array('select count(*) from users');
> + if (!defined $count) {
> +    check_table('dbinfo',$dbinfo_columns);
> +    set_schema_version('dbinfo',$new_version);
> +    return;
> + }
> +    }
> +
>      my ($old_version) = $database->selectrow_array('SELECT
> MAX(schema_version) FROM dbinfo LIMIT 1');
>      unless ($old_version) {
>   # table is missing, so add it
>
> Lincoln
>
> On Mon, Jan 31, 2011 at 10:28 AM, Karthik <[hidden email]> wrote:
>>
>> Hello Lincoln
>> I installed gbrowse2.23 from cpan. I get the following error :
>>
>> Successfully upgraded schema from 0 to 1.
>> Sharing table didn't exist, creating...
>> DBD::mysql::st execute failed: Unknown column 'users' in 'field list' at
>> bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>> upgrade failed due to DBD::mysql::st execute failed: Unknown column
>> 'users'
>> in 'field list' at bin/gbrowse_metadb_config.pl line 827, <STDIN> line 2.
>> . Rolling back at bin/gbrowse_metadb_config.pl line 846, <STDIN> line 2.
>> Can't upgrade from version 1 to version 2 at bin/gbrowse_metadb_config.pl
>> line 627, <STDIN> line 2.
>>
>> Can this be ignored ?
>> --
>> View this message in context:
>> http://generic-model-organism-system-database.450254.n5.nabble.com/GBrowse-2-23-released-tp3363731p3364638.html
>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better
>> price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
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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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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Re: GBrowse 2.23 released

Todd Harris
In reply to this post by Keiran Raine
Hi Keiran -

Yes, I've noticed this same problem building against a local perl and
installing into a non-privileged path. I resolved in the same manner
as you.

To simplify installation and avoid library conflicts, we maintain all
of our gbrowse installations and prerequisites in local paths.  This
works well but I've also been a little unsettled when the GBrowse
installer requests root privileges.

I wonder if it might be cleaner to assume a non-privileged, non-system
install, loading into system paths only if requested.

Todd

On Mon, Jan 31, 2011 at 6:50 AM, Keiran Raine <[hidden email]> wrote:

> Hi all,
> Just something to note for anyone not using the default system version of
> perl for their gbrowse setup (normally occurs when you have a site wide perl
> version), e.g.:
> ~: perl -v
> This is perl, v5.8.8 built for x86_64-linux-thread-multi....
> ~: /usr/bin/perl -v
> This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....
> As we don't have 5.10 as our default perl I run the installation manually as
> follows:
> /usr/bin/perl Build.PL --prefix /gbrowse
> ./Build
> ./Build test
> ./Build install
> Which results in the following failure when the gbrowse_metadb_config.pl
> script tries to execute:
> Updating user account database...
> Base class package "Bio::Graphics::FeatureFile" is empty.
>     (Perhaps you need to 'use' the module which defines that package first.)
>  at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
> line 5
> BEGIN failed--compilation aborted at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
> line 5.
> Compilation failed in require at (eval 5) line 3.
> ...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
> BEGIN failed--compilation aborted at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
> Compilation failed in require at bin/gbrowse_metadb_config.pl line 6.
> BEGIN failed--compilation aborted at bin/gbrowse_metadb_config.pl line 6.
> If I just ran this manually with the pathed perl I use at the beginning of
> the install process it woks fine:
> /usr/bin/perl -c bin/gbrowse_metadb_config.pl
> bin/gbrowse_metadb_config.pl syntax OK
> Hope this is of use to anyone having issues.
> Regards,
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
> On 30 Jan 2011, at 20:22, Lincoln Stein wrote:
>
> Hi All,
> I have just released GBrowse 2.23 to
> CPAN http://search.cpan.org/~lds/GBrowse-2.23/ and Ssourceforge
> (http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.23/GBrowse-2.23.tar.gz/download).
> IMPORTANT: This release corrects a security issue in which the default
> users.sqlite user account database could be created in the root directory
> under some circumstances. If you installed versions 2.20-2.22, please check
> for the presence of /users.sqlite and delete it if it is present. Also check
> the ownership of /, because the install process may have set it to www-data.
> This release also corrects some of the "session lock timeout" issues that
> people have been experiencing. Note, however, that certain long operations,
> such as file uploads, will continue to create timeouts for individual users;
> these are usually safe to ignore. Finally, the bug in which the account
> "Registration" link is missing has been fixed.
> Here are the complete release notes:
>
> Version 2.23 (bugfix release)
>    * SECURITY ISSUE: Fixed default SQLite user account database to be
> created in /var/www/gbrowse2/databases rather
>      than in / (root) directory.
>    * Added an "example_scripts" directory that contains a perl scripts that
> show how to manipulate
>      sessions, upload custom tracks, and get basic information about
> services. This directory accompanies
>      new REST API documentation located at
> http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
>    * Fixed missing "registration" link in login dialog. This occurred when
> openid was unavailable.
>    * Fixed popup dialogs in the "Help" menu so that they appear again.
>    * Fixed file upload status display to prevent upload details section from
> disappearing when
>      uploading very small files.
>    * Tinkered with session settings to minimize session lock timeouts.
>    * Removed some dangling warnings in the track sharing module.
>    * Made SQLite the default user account database.
>
> Lincoln
>
> --
> 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]>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a compa ny
> registered in England with number 2742969, whose registered office is 2 15
> Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

------------------------------------------------------------------------------
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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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Re: GBrowse 2.23 released

Lincoln Stein
Hi Todd, Keiran,

I'm working on the problem with the "empty Bio::Graphics::FeatureFile base" now. The issue is that gbrowse_metadb_config.pl isn't being passed the prefix when it is invoked. This ought to be an easy fix and will be in 2.25.

Here is the scoop on why gbrowse_metadb_config.pl requests root privileges. Among the various things this script does is to create the user accounts database and to fix directory permissions so that uploads and upload sharing works properly. Both the database (in the case of using SQLite) and the directories need to be writable by the web user in order for things to work properly. So the installer requests root privileges in order to set ownership. For a non-privileged install I can deactivate all this, but I will have to assume that Apache is running under the same user as the person who is installing GBrowse. Do you think this is an acceptable condition?

Lincoln


On Mon, Jan 31, 2011 at 12:24 PM, Todd Harris <[hidden email]> wrote:
Hi Keiran -

Yes, I've noticed this same problem building against a local perl and
installing into a non-privileged path. I resolved in the same manner
as you.

To simplify installation and avoid library conflicts, we maintain all
of our gbrowse installations and prerequisites in local paths.  This
works well but I've also been a little unsettled when the GBrowse
installer requests root privileges.

I wonder if it might be cleaner to assume a non-privileged, non-system
install, loading into system paths only if requested.

Todd

On Mon, Jan 31, 2011 at 6:50 AM, Keiran Raine <[hidden email]> wrote:
> Hi all,
> Just something to note for anyone not using the default system version of
> perl for their gbrowse setup (normally occurs when you have a site wide perl
> version), e.g.:
> ~: perl -v
> This is perl, v5.8.8 built for x86_64-linux-thread-multi....
> ~: /usr/bin/perl -v
> This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....
> As we don't have 5.10 as our default perl I run the installation manually as
> follows:
> /usr/bin/perl Build.PL --prefix /gbrowse
> ./Build
> ./Build test
> ./Build install
> Which results in the following failure when the gbrowse_metadb_config.pl
> script tries to execute:
> Updating user account database...
> Base class package "Bio::Graphics::FeatureFile" is empty.
>     (Perhaps you need to 'use' the module which defines that package first.)
>  at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
> line 5
> BEGIN failed--compilation aborted at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
> line 5.
> Compilation failed in require at (eval 5) line 3.
> ...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
> BEGIN failed--compilation aborted at
> /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
> Compilation failed in require at bin/gbrowse_metadb_config.pl line 6.
> BEGIN failed--compilation aborted at bin/gbrowse_metadb_config.pl line 6.
> If I just ran this manually with the pathed perl I use at the beginning of
> the install process it woks fine:
> /usr/bin/perl -c bin/gbrowse_metadb_config.pl
> bin/gbrowse_metadb_config.pl syntax OK
> Hope this is of use to anyone having issues.
> Regards,
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> [hidden email]
>
>
>
>
> On 30 Jan 2011, at 20:22, Lincoln Stein wrote:
>
> Hi All,
> I have just released GBrowse 2.23 to
> CPAN http://search.cpan.org/~lds/GBrowse-2.23/ and Ssourceforge
> (http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.23/GBrowse-2.23.tar.gz/download).
> IMPORTANT: This release corrects a security issue in which the default
> users.sqlite user account database could be created in the root directory
> under some circumstances. If you installed versions 2.20-2.22, please check
> for the presence of /users.sqlite and delete it if it is present. Also check
> the ownership of /, because the install process may have set it to www-data.
> This release also corrects some of the "session lock timeout" issues that
> people have been experiencing. Note, however, that certain long operations,
> such as file uploads, will continue to create timeouts for individual users;
> these are usually safe to ignore. Finally, the bug in which the account
> "Registration" link is missing has been fixed.
> Here are the complete release notes:
>
> Version 2.23 (bugfix release)
>    * SECURITY ISSUE: Fixed default SQLite user account database to be
> created in /var/www/gbrowse2/databases rather
>      than in / (root) directory.
>    * Added an "example_scripts" directory that contains a perl scripts that
> show how to manipulate
>      sessions, upload custom tracks, and get basic information about
> services. This directory accompanies
>      new REST API documentation located at
> http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
>    * Fixed missing "registration" link in login dialog. This occurred when
> openid was unavailable.
>    * Fixed popup dialogs in the "Help" menu so that they appear again.
>    * Fixed file upload status display to prevent upload details section from
> disappearing when
>      uploading very small files.
>    * Tinkered with session settings to minimize session lock timeouts.
>    * Removed some dangling warnings in the track sharing module.
>    * Made SQLite the default user account database.
>
> Lincoln
>
> --
> 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]>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a compa ny
> registered in England with number 2742969, whose registered office is 2 15
> Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
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]>

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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|

Re: GBrowse 2.23 released

Todd Harris
Hi Lincoln -

Thanks for the explanation.

In light of it, I think I would keep the installer as-is.  At least in
my case, apache is usually running as a user like www-data or nobody.

Todd

On Mon, Jan 31, 2011 at 11:28 AM, Lincoln Stein <[hidden email]> wrote:

> Hi Todd, Keiran,
> I'm working on the problem with the "empty Bio::Graphics::FeatureFile base"
> now. The issue is that gbrowse_metadb_config.pl isn't being passed the
> prefix when it is invoked. This ought to be an easy fix and will be in 2.25.
> Here is the scoop on why gbrowse_metadb_config.pl requests root privileges.
> Among the various things this script does is to create the user accounts
> database and to fix directory permissions so that uploads and upload sharing
> works properly. Both the database (in the case of using SQLite) and the
> directories need to be writable by the web user in order for things to work
> properly. So the installer requests root privileges in order to set
> ownership. For a non-privileged install I can deactivate all this, but I
> will have to assume that Apache is running under the same user as the person
> who is installing GBrowse. Do you think this is an acceptable condition?
> Lincoln
>
> On Mon, Jan 31, 2011 at 12:24 PM, Todd Harris <[hidden email]> wrote:
>>
>> Hi Keiran -
>>
>> Yes, I've noticed this same problem building against a local perl and
>> installing into a non-privileged path. I resolved in the same manner
>> as you.
>>
>> To simplify installation and avoid library conflicts, we maintain all
>> of our gbrowse installations and prerequisites in local paths.  This
>> works well but I've also been a little unsettled when the GBrowse
>> installer requests root privileges.
>>
>> I wonder if it might be cleaner to assume a non-privileged, non-system
>> install, loading into system paths only if requested.
>>
>> Todd
>>
>> On Mon, Jan 31, 2011 at 6:50 AM, Keiran Raine <[hidden email]> wrote:
>> > Hi all,
>> > Just something to note for anyone not using the default system version
>> > of
>> > perl for their gbrowse setup (normally occurs when you have a site wide
>> > perl
>> > version), e.g.:
>> > ~: perl -v
>> > This is perl, v5.8.8 built for x86_64-linux-thread-multi....
>> > ~: /usr/bin/perl -v
>> > This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....
>> > As we don't have 5.10 as our default perl I run the installation
>> > manually as
>> > follows:
>> > /usr/bin/perl Build.PL --prefix /gbrowse
>> > ./Build
>> > ./Build test
>> > ./Build install
>> > Which results in the following failure when the gbrowse_metadb_config.pl
>> > script tries to execute:
>> > Updating user account database...
>> > Base class package "Bio::Graphics::FeatureFile" is empty.
>> >     (Perhaps you need to 'use' the module which defines that package
>> > first.)
>> >  at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5
>> > BEGIN failed--compilation aborted at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5.
>> > Compilation failed in require at (eval 5) line 3.
>> > ...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
>> > BEGIN failed--compilation aborted at
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
>> > Compilation failed in require at bin/gbrowse_metadb_config.pl line 6.
>> > BEGIN failed--compilation aborted at bin/gbrowse_metadb_config.pl line
>> > 6.
>> > If I just ran this manually with the pathed perl I use at the beginning
>> > of
>> > the install process it woks fine:
>> > /usr/bin/perl -c bin/gbrowse_metadb_config.pl
>> > bin/gbrowse_metadb_config.pl syntax OK
>> > Hope this is of use to anyone having issues.
>> > Regards,
>> > Keiran Raine
>> > Senior Computer Biologist
>> > The Cancer Genome Project
>> > Ext: 7703
>> > [hidden email]
>> >
>> >
>> >
>> >
>> > On 30 Jan 2011, at 20:22, Lincoln Stein wrote:
>> >
>> > Hi All,
>> > I have just released GBrowse 2.23 to
>> > CPAN http://search.cpan.org/~lds/GBrowse-2.23/ and Ssourceforge
>> >
>> > (http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.23/GBrowse-2.23.tar.gz/download).
>> > IMPORTANT: This release corrects a security issue in which the default
>> > users.sqlite user account database could be created in the root
>> > directory
>> > under some circumstances. If you installed versions 2.20-2.22, please
>> > check
>> > for the presence of /users.sqlite and delete it if it is present. Also
>> > check
>> > the ownership of /, because the install process may have set it to
>> > www-data.
>> > This release also corrects some of the "session lock timeout" issues
>> > that
>> > people have been experiencing. Note, however, that certain long
>> > operations,
>> > such as file uploads, will continue to create timeouts for individual
>> > users;
>> > these are usually safe to ignore. Finally, the bug in which the account
>> > "Registration" link is missing has been fixed.
>> > Here are the complete release notes:
>> >
>> > Version 2.23 (bugfix release)
>> >    * SECURITY ISSUE: Fixed default SQLite user account database to be
>> > created in /var/www/gbrowse2/databases rather
>> >      than in / (root) directory.
>> >    * Added an "example_scripts" directory that contains a perl scripts
>> > that
>> > show how to manipulate
>> >      sessions, upload custom tracks, and get basic information about
>> > services. This directory accompanies
>> >      new REST API documentation located at
>> > http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
>> >    * Fixed missing "registration" link in login dialog. This occurred
>> > when
>> > openid was unavailable.
>> >    * Fixed popup dialogs in the "Help" menu so that they appear again.
>> >    * Fixed file upload status display to prevent upload details section
>> > from
>> > disappearing when
>> >      uploading very small files.
>> >    * Tinkered with session settings to minimize session lock timeouts.
>> >    * Removed some dangling warnings in the track sharing module.
>> >    * Made SQLite the default user account database.
>> >
>> > Lincoln
>> >
>> > --
>> > 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]>
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> > Finally, a world-class log management solution at an even better
>> > price-free!
>> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> > February 28th, so secure your free ArcSight Logger TODAY!
>> >
>> > http://p.sf.net/sfu/arcsight-sfd2d_______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>> > -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> > Limited, a charity registered in England with number 1021457 and a compa
>> > ny
>> > registered in England with number 2742969, whose registered office is 2
>> > 15
>> > Euston Road, London, NW1 2BE.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> > Finally, a world-class log management solution at an even better
>> > price-free!
>> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> > February 28th, so secure your free ArcSight Logger TODAY!
>> > http://p.sf.net/sfu/arcsight-sfd2d
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>
>
>
> --
> 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]>
>

------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
Gmod-gbrowse mailing list
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Re: GBrowse 2.23 released

Lincoln Stein
I put in code to avoid sudo'ing when not necessary, but this will be a rare occurrence!

Lincoln

On Mon, Jan 31, 2011 at 2:56 PM, Todd Harris <[hidden email]> wrote:
Hi Lincoln -

Thanks for the explanation.

In light of it, I think I would keep the installer as-is.  At least in
my case, apache is usually running as a user like www-data or nobody.

Todd

On Mon, Jan 31, 2011 at 11:28 AM, Lincoln Stein <[hidden email]> wrote:
> Hi Todd, Keiran,
> I'm working on the problem with the "empty Bio::Graphics::FeatureFile base"
> now. The issue is that gbrowse_metadb_config.pl isn't being passed the
> prefix when it is invoked. This ought to be an easy fix and will be in 2.25.
> Here is the scoop on why gbrowse_metadb_config.pl requests root privileges.
> Among the various things this script does is to create the user accounts
> database and to fix directory permissions so that uploads and upload sharing
> works properly. Both the database (in the case of using SQLite) and the
> directories need to be writable by the web user in order for things to work
> properly. So the installer requests root privileges in order to set
> ownership. For a non-privileged install I can deactivate all this, but I
> will have to assume that Apache is running under the same user as the person
> who is installing GBrowse. Do you think this is an acceptable condition?
> Lincoln
>
> On Mon, Jan 31, 2011 at 12:24 PM, Todd Harris <[hidden email]> wrote:
>>
>> Hi Keiran -
>>
>> Yes, I've noticed this same problem building against a local perl and
>> installing into a non-privileged path. I resolved in the same manner
>> as you.
>>
>> To simplify installation and avoid library conflicts, we maintain all
>> of our gbrowse installations and prerequisites in local paths.  This
>> works well but I've also been a little unsettled when the GBrowse
>> installer requests root privileges.
>>
>> I wonder if it might be cleaner to assume a non-privileged, non-system
>> install, loading into system paths only if requested.
>>
>> Todd
>>
>> On Mon, Jan 31, 2011 at 6:50 AM, Keiran Raine <[hidden email]> wrote:
>> > Hi all,
>> > Just something to note for anyone not using the default system version
>> > of
>> > perl for their gbrowse setup (normally occurs when you have a site wide
>> > perl
>> > version), e.g.:
>> > ~: perl -v
>> > This is perl, v5.8.8 built for x86_64-linux-thread-multi....
>> > ~: /usr/bin/perl -v
>> > This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi....
>> > As we don't have 5.10 as our default perl I run the installation
>> > manually as
>> > follows:
>> > /usr/bin/perl Build.PL --prefix /gbrowse
>> > ./Build
>> > ./Build test
>> > ./Build install
>> > Which results in the following failure when the gbrowse_metadb_config.pl
>> > script tries to execute:
>> > Updating user account database...
>> > Base class package "Bio::Graphics::FeatureFile" is empty.
>> >     (Perhaps you need to 'use' the module which defines that package
>> > first.)
>> >  at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5
>> > BEGIN failed--compilation aborted at
>> >
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
>> > line 5.
>> > Compilation failed in require at (eval 5) line 3.
>> > ...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
>> > BEGIN failed--compilation aborted at
>> > /var/tmp/kr2/GBrowse-2.23/bin/../lib/Bio/Graphics/Browser2.pm line 9.
>> > Compilation failed in require at bin/gbrowse_metadb_config.pl line 6.
>> > BEGIN failed--compilation aborted at bin/gbrowse_metadb_config.pl line
>> > 6.
>> > If I just ran this manually with the pathed perl I use at the beginning
>> > of
>> > the install process it woks fine:
>> > /usr/bin/perl -c bin/gbrowse_metadb_config.pl
>> > bin/gbrowse_metadb_config.pl syntax OK
>> > Hope this is of use to anyone having issues.
>> > Regards,
>> > Keiran Raine
>> > Senior Computer Biologist
>> > The Cancer Genome Project
>> > Ext: 7703
>> > [hidden email]
>> >
>> >
>> >
>> >
>> > On 30 Jan 2011, at 20:22, Lincoln Stein wrote:
>> >
>> > Hi All,
>> > I have just released GBrowse 2.23 to
>> > CPAN http://search.cpan.org/~lds/GBrowse-2.23/ and Ssourceforge
>> >
>> > (http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-2.23/GBrowse-2.23.tar.gz/download).
>> > IMPORTANT: This release corrects a security issue in which the default
>> > users.sqlite user account database could be created in the root
>> > directory
>> > under some circumstances. If you installed versions 2.20-2.22, please
>> > check
>> > for the presence of /users.sqlite and delete it if it is present. Also
>> > check
>> > the ownership of /, because the install process may have set it to
>> > www-data.
>> > This release also corrects some of the "session lock timeout" issues
>> > that
>> > people have been experiencing. Note, however, that certain long
>> > operations,
>> > such as file uploads, will continue to create timeouts for individual
>> > users;
>> > these are usually safe to ignore. Finally, the bug in which the account
>> > "Registration" link is missing has been fixed.
>> > Here are the complete release notes:
>> >
>> > Version 2.23 (bugfix release)
>> >    * SECURITY ISSUE: Fixed default SQLite user account database to be
>> > created in /var/www/gbrowse2/databases rather
>> >      than in / (root) directory.
>> >    * Added an "example_scripts" directory that contains a perl scripts
>> > that
>> > show how to manipulate
>> >      sessions, upload custom tracks, and get basic information about
>> > services. This directory accompanies
>> >      new REST API documentation located at
>> > http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
>> >    * Fixed missing "registration" link in login dialog. This occurred
>> > when
>> > openid was unavailable.
>> >    * Fixed popup dialogs in the "Help" menu so that they appear again.
>> >    * Fixed file upload status display to prevent upload details section
>> > from
>> > disappearing when
>> >      uploading very small files.
>> >    * Tinkered with session settings to minimize session lock timeouts.
>> >    * Removed some dangling warnings in the track sharing module.
>> >    * Made SQLite the default user account database.
>> >
>> > Lincoln
>> >
>> > --
>> > 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]>
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> > Finally, a world-class log management solution at an even better
>> > price-free!
>> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> > February 28th, so secure your free ArcSight Logger TODAY!
>> >
>> > http://p.sf.net/sfu/arcsight-sfd2d_______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>> > -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> > Limited, a charity registered in England with number 1021457 and a compa
>> > ny
>> > registered in England with number 2742969, whose registered office is 2
>> > 15
>> > Euston Road, London, NW1 2BE.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> > Finally, a world-class log management solution at an even better
>> > price-free!
>> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> > February 28th, so secure your free ArcSight Logger TODAY!
>> > http://p.sf.net/sfu/arcsight-sfd2d
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>
>
>
> --
> 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]>
>



--
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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Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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