[Gmod-gbrowse] 2.06 may break CHADO adaptor

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[Gmod-gbrowse] 2.06 may break CHADO adaptor

lpritc@scri.ac.uk
Hi,

Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to one
that won't render details of the annotation from a CHADO database.  2.06
still works fine on the sample yeast databases, however.

The onscreen error I can see is the pink background for each track, and the
truncated message:

"""
Rendering error: Can't call method "prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
"""

Happily, the httpd error log has the full thing (several times):

"""
[Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
"prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
[Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
"prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
[Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
"prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
[Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
"prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
[Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
"prepare" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
"""

I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08

Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.

Cheers,

L.

--
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

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Re: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Scott Cain
Hi Leighton,

Thanks for the bug report--I should have a fix by the end of the day.

Scott


On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]> wrote:

> Hi,
>
> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to one
> that won't render details of the annotation from a CHADO database.  2.06
> still works fine on the sample yeast databases, however.
>
> The onscreen error I can see is the pink background for each track, and the
> truncated message:
>
> """
> Rendering error: Can't call method "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
> """
>
> Happily, the httpd error log has the full thing (several times):
>
> """
> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
> "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
> "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
> "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
> "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
> "prepare" on an undefined value at
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> """
>
> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
>
> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
>
> Cheers,
>
> L.
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [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: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Scott Cain
Hi Leighton,

I think the attached copy of Chado.pm fixes this problem.  Could you
try replacing your copy of Chado.pm (in a directory something like
..../Bio/DB/Das/) and, assuming it works for you too, I'll release
version 0.26.

Thanks,
Scott


On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:

> Hi Leighton,
>
> Thanks for the bug report--I should have a fix by the end of the day.
>
> Scott
>
>
> On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]> wrote:
>> Hi,
>>
>> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to one
>> that won't render details of the annotation from a CHADO database.  2.06
>> still works fine on the sample yeast databases, however.
>>
>> The onscreen error I can see is the pink background for each track, and the
>> truncated message:
>>
>> """
>> Rendering error: Can't call method "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
>> """
>>
>> Happily, the httpd error log has the full thing (several times):
>>
>> """
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> """
>>
>> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
>>
>> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
>>
>> Cheers,
>>
>> L.
>>
>> --
>> Dr Leighton Pritchard MRSC
>> D131, Plant Pathology Programme, SCRI
>> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
>> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
>> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>>
>>
>> ______________________________________________________
>> SCRI, Invergowrie, Dundee, DD2 5DA.
>> The Scottish Crop Research Institute is a charitable company limited by guarantee.
>> Registered in Scotland No: SC 29367.
>> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>>
>>
>> DISCLAIMER:
>>
>> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
>> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>>
>> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
>> ______________________________________________________
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [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
>


--
------------------------------------------------------------------------
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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Chado.pm (78K) Download Attachment
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Re: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Lincoln Stein
Hi Scott,

How did I manage to break the chado adaptor? I didn't think I touched anything that might have affected it.

Lincoln

On Fri, May 14, 2010 at 11:33 AM, Scott Cain <[hidden email]> wrote:
Hi Leighton,

I think the attached copy of Chado.pm fixes this problem.  Could you
try replacing your copy of Chado.pm (in a directory something like
..../Bio/DB/Das/) and, assuming it works for you too, I'll release
version 0.26.

Thanks,
Scott


On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
> Hi Leighton,
>
> Thanks for the bug report--I should have a fix by the end of the day.
>
> Scott
>
>
> On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]> wrote:
>> Hi,
>>
>> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to one
>> that won't render details of the annotation from a CHADO database.  2.06
>> still works fine on the sample yeast databases, however.
>>
>> The onscreen error I can see is the pink background for each track, and the
>> truncated message:
>>
>> """
>> Rendering error: Can't call method "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
>> """
>>
>> Happily, the httpd error log has the full thing (several times):
>>
>> """
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>> "prepare" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> """
>>
>> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
>>
>> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
>>
>> Cheers,
>>
>> L.
>>
>> --
>> Dr Leighton Pritchard MRSC
>> D131, Plant Pathology Programme, SCRI
>> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
>> [hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
>> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>>
>>
>> ______________________________________________________
>> SCRI, Invergowrie, Dundee, DD2 5DA.
>> The Scottish Crop Research Institute is a charitable company limited by guarantee.
>> Registered in Scotland No: SC 29367.
>> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>>
>>
>> DISCLAIMER:
>>
>> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
>> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>>
>> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
>> ______________________________________________________
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [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
>



--
------------------------------------------------------------------------
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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--
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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[Gmod-gbrowse] FW: 2.06 may break CHADO adaptor

lpritc@scri.ac.uk
In reply to this post by lpritc@scri.ac.uk
Hi Scott,

That's done the trick - GBROWSE 2.06 can see the database again.

Many thanks for the incredibly quick fix.

Cheers,

L.


On 14/05/2010 Friday, May 14, 16:33, "Scott Cain" <[hidden email]>
wrote:

> Hi Leighton,
>
> I think the attached copy of Chado.pm fixes this problem.  Could you
> try replacing your copy of Chado.pm (in a directory something like
> ..../Bio/DB/Das/) and, assuming it works for you too, I'll release
> version 0.26.
>
> Thanks,
> Scott
>
>
> On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
>> Hi Leighton,
>>
>> Thanks for the bug report--I should have a fix by the end of the day.
>>
>> Scott
>>
>>
>> On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]>
>> wrote:
>>> Hi,
>>>
>>> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to one
>>> that won't render details of the annotation from a CHADO database.  2.06
>>> still works fine on the sample yeast databases, however.
>>>
>>> The onscreen error I can see is the pink background for each track, and the
>>> truncated message:
>>>
>>> """
>>> Rendering error: Can't call method "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
>>> """
>>>
>>> Happily, the httpd error log has the full thing (several times):
>>>
>>> """
>>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>>> "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>>> "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>>> "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>>> "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>>> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call method
>>> "prepare" on an undefined value at
>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>>> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>>> """
>>>
>>> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
>>>
>>> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
>>>
>>> Cheers,
>>>
>>> L.
>>>
>>> --
>>> Dr Leighton Pritchard MRSC
>>> D131, Plant Pathology Programme, SCRI
>>> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
>>> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
>>> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>>>
>>>
>>> ______________________________________________________
>>> SCRI, Invergowrie, Dundee, DD2 5DA.
>>> The Scottish Crop Research Institute is a charitable company limited by
>>> guarantee.
>>> Registered in Scotland No: SC 29367.
>>> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>>>
>>>
>>> DISCLAIMER:
>>>
>>> This email is from the Scottish Crop Research Institute, but the views
>>> expressed by the sender are not necessarily the views of SCRI and its
>>> subsidiaries.  This email and any files transmitted with it are confidential
>>> to the intended recipient at the e-mail address to which it has been
>>> addressed.  It may not be disclosed or used by any other than that
>>> addressee.
>>> If you are not the intended recipient you are requested to preserve this
>>> confidentiality and you must not use, disclose, copy, print or rely on this
>>> e-mail in any way. Please notify [hidden email] quoting the name of
>>> the sender and delete the email from your system.
>>>
>>> Although SCRI has taken reasonable precautions to ensure no viruses are
>>> present in this email, neither the Institute nor the sender accepts any
>>> responsibility for any viruses, and it is your responsibility to scan the
>>> email and the attachments (if any).
>>> ______________________________________________________
>>>
>>> ----------------------------------------------------------------------------
>>> --
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [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
>>


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
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Re: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Scott Cain
In reply to this post by Lincoln Stein
Yeah, it's not clear to me either.  The chado adaptor creates a
database handle when the constructor is called for the database
adaptor (Chado.pm), and it appears that somehow, GBrowse was bypassing
the constructor, because the database handle wasn't getting created.
Fortunately, access to the database handle in the chado adaptor is
through a method that caches the handle, so I just added a check to
make sure dbh exists, and if it doesn't, it creates it inside the
caching method.  What is really baffling to me is that the database
connection parameters are also cached in the constructor, and that is
what the dbh method uses to to "recreate" the handle.  I really don't
understand how those values were cached, but the db handle wasn't
created.

Scott


On Fri, May 14, 2010 at 11:56 AM, Lincoln Stein <[hidden email]> wrote:

> Hi Scott,
> How did I manage to break the chado adaptor? I didn't think I touched
> anything that might have affected it.
> Lincoln
>
> On Fri, May 14, 2010 at 11:33 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Leighton,
>>
>> I think the attached copy of Chado.pm fixes this problem.  Could you
>> try replacing your copy of Chado.pm (in a directory something like
>> ..../Bio/DB/Das/) and, assuming it works for you too, I'll release
>> version 0.26.
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
>> > Hi Leighton,
>> >
>> > Thanks for the bug report--I should have a fix by the end of the day.
>> >
>> > Scott
>> >
>> >
>> > On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]>
>> > wrote:
>> >> Hi,
>> >>
>> >> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to
>> >> one
>> >> that won't render details of the annotation from a CHADO database.
>> >>  2.06
>> >> still works fine on the sample yeast databases, however.
>> >>
>> >> The onscreen error I can see is the pink background for each track, and
>> >> the
>> >> truncated message:
>> >>
>> >> """
>> >> Rendering error: Can't call method "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
>> >> """
>> >>
>> >> Happily, the httpd error log has the full thing (several times):
>> >>
>> >> """
>> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
>> >> method
>> >> "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> >>
>> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
>> >> method
>> >> "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> >>
>> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
>> >> method
>> >> "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> >>
>> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
>> >> method
>> >> "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> >>
>> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
>> >> method
>> >> "prepare" on an undefined value at
>> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
>> >>
>> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
>> >> """
>> >>
>> >> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
>> >>
>> >> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
>> >>
>> >> Cheers,
>> >>
>> >> L.
>> >>
>> >> --
>> >> Dr Leighton Pritchard MRSC
>> >> D131, Plant Pathology Programme, SCRI
>> >> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
>> >> e:[hidden email]
>> >> w:http://www.scri.ac.uk/staff/leightonpritchard
>> >> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>> >>
>> >>
>> >> ______________________________________________________
>> >> SCRI, Invergowrie, Dundee, DD2 5DA.
>> >> The Scottish Crop Research Institute is a charitable company limited by
>> >> guarantee.
>> >> Registered in Scotland No: SC 29367.
>> >> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>> >>
>> >>
>> >> DISCLAIMER:
>> >>
>> >> This email is from the Scottish Crop Research Institute, but the views
>> >> expressed by the sender are not necessarily the views of SCRI and its
>> >> subsidiaries.  This email and any files transmitted with it are confidential
>> >> to the intended recipient at the e-mail address to which it has been
>> >> addressed.  It may not be disclosed or used by any other than that
>> >> addressee.
>> >> If you are not the intended recipient you are requested to preserve
>> >> this confidentiality and you must not use, disclose, copy, print or rely on
>> >> this e-mail in any way. Please notify [hidden email] quoting the name
>> >> of the sender and delete the email from your system.
>> >>
>> >> Although SCRI has taken reasonable precautions to ensure no viruses are
>> >> present in this email, neither the Institute nor the sender accepts any
>> >> responsibility for any viruses, and it is your responsibility to scan the
>> >> email and the attachments (if any).
>> >> ______________________________________________________
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >>
>> >> _______________________________________________
>> >> Gmod-gbrowse mailing list
>> >> [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
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> 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]>
>



--
------------------------------------------------------------------------
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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[Gmod-gbrowse] Re: 2.06 may break CHADO adaptor

Siddhartha Basu
Well,  the chado adaptor caches the dbh in every instantiated object,
however as far as my understanding it does not gurantee an active
database handler when run under persistent environment(mod_perl/fcgi)
where forking/threading is prevalent. And i believe it would be a frequent scenario for chado adaptor
when being called from gbrowse.
In case of a forking where the child wishes to use the parent's
dbh,the 'InactiveDestroy' attribute of DBI would be the likely solution.
So,  the DBI keeps the parent's connection alive when the dbh variable is destroyed.
perlmonks discussion: http://www.perlmonks.org/?node_id=594175
DBI documentation:
http://search.cpan.org/~timb/DBI/DBI.pm#InactiveDestroy_(boolean)
However,  this solution does not work for oracle driver.

The other solution is to create a new handle inside a new fork/thread.
And DBIx::Connector module
http://search.cpan.org/~dwheeler/DBIx-Connector-0.34 seems to be an apt
solution which takes these situations into consideration. I am using it
at dictyBase in our custom chado Oracle adaptor along with gbrowse2.
Most of our previous connection related issues seems to be taken care
of.

-siddhartha
 



On Fri, 14 May 2010, Scott Cain wrote:

> Yeah, it's not clear to me either.  The chado adaptor creates a
> database handle when the constructor is called for the database
> adaptor (Chado.pm), and it appears that somehow, GBrowse was bypassing
> the constructor, because the database handle wasn't getting created.
> Fortunately, access to the database handle in the chado adaptor is
> through a method that caches the handle, so I just added a check to
> make sure dbh exists, and if it doesn't, it creates it inside the
> caching method.  What is really baffling to me is that the database
> connection parameters are also cached in the constructor, and that is
> what the dbh method uses to to "recreate" the handle.  I really don't
> understand how those values were cached, but the db handle wasn't
> created.
>
> Scott
>
>
> On Fri, May 14, 2010 at 11:56 AM, Lincoln Stein <[hidden email]> wrote:
> > Hi Scott,
> > How did I manage to break the chado adaptor? I didn't think I touched
> > anything that might have affected it.
> > Lincoln
> >
> > On Fri, May 14, 2010 at 11:33 AM, Scott Cain <[hidden email]> wrote:
> >>
> >> Hi Leighton,
> >>
> >> I think the attached copy of Chado.pm fixes this problem.  Could you
> >> try replacing your copy of Chado.pm (in a directory something like
> >> ..../Bio/DB/Das/) and, assuming it works for you too, I'll release
> >> version 0.26.
> >>
> >> Thanks,
> >> Scott
> >>
> >>
> >> On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
> >> > Hi Leighton,
> >> >
> >> > Thanks for the bug report--I should have a fix by the end of the day.
> >> >
> >> > Scott
> >> >
> >> >
> >> > On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]>
> >> > wrote:
> >> >> Hi,
> >> >>
> >> >> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to
> >> >> one
> >> >> that won't render details of the annotation from a CHADO database.
> >> >>  2.06
> >> >> still works fine on the sample yeast databases, however.
> >> >>
> >> >> The onscreen error I can see is the pink background for each track, and
> >> >> the
> >> >> truncated message:
> >> >>
> >> >> """
> >> >> Rendering error: Can't call method "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
> >> >> """
> >> >>
> >> >> Happily, the httpd error log has the full thing (several times):
> >> >>
> >> >> """
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> """
> >> >>
> >> >> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
> >> >>
> >> >> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
> >> >>
> >> >> Cheers,
> >> >>
> >> >> L.
> >> >>
> >> >> --
> >> >> Dr Leighton Pritchard MRSC
> >> >> D131, Plant Pathology Programme, SCRI
> >> >> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> >> >> e:[hidden email]
> >> >> w:http://www.scri.ac.uk/staff/leightonpritchard
> >> >> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
> >> >>
> >> >>
> >> >> ______________________________________________________
> >> >> SCRI, Invergowrie, Dundee, DD2 5DA.
> >> >> The Scottish Crop Research Institute is a charitable company limited by
> >> >> guarantee.
> >> >> Registered in Scotland No: SC 29367.
> >> >> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
> >> >>
> >> >>
> >> >> DISCLAIMER:
> >> >>
> >> >> This email is from the Scottish Crop Research Institute, but the views
> >> >> expressed by the sender are not necessarily the views of SCRI and its
> >> >> subsidiaries.  This email and any files transmitted with it are confidential
> >> >> to the intended recipient at the e-mail address to which it has been
> >> >> addressed.  It may not be disclosed or used by any other than that
> >> >> addressee.
> >> >> If you are not the intended recipient you are requested to preserve
> >> >> this confidentiality and you must not use, disclose, copy, print or rely on
> >> >> this e-mail in any way. Please notify [hidden email] quoting the name
> >> >> of the sender and delete the email from your system.
> >> >>
> >> >> Although SCRI has taken reasonable precautions to ensure no viruses are
> >> >> present in this email, neither the Institute nor the sender accepts any
> >> >> responsibility for any viruses, and it is your responsibility to scan the
> >> >> email and the attachments (if any).
> >> >> ______________________________________________________
> >> >>
> >> >>
> >> >> ------------------------------------------------------------------------------
> >> >>
> >> >> _______________________________________________
> >> >> Gmod-gbrowse mailing list
> >> >> [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
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >>
> >> ------------------------------------------------------------------------------
> >>
> >>
> >> _______________________________________________
> >> 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]>
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------

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Re: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Lincoln Stein
Scott,

GBrowse calls the adaptor's clone() method after forking while in the child process. This would be the place that you can put code that refreshes the connection. If you need it, we can create something that you can call inside the parent process prior to the fork.

Lincoln 

On Sat, May 15, 2010 at 8:33 AM, Siddhartha Basu <[hidden email]> wrote:
Well,  the chado adaptor caches the dbh in every instantiated object,
however as far as my understanding it does not gurantee an active
database handler when run under persistent environment(mod_perl/fcgi)
where forking/threading is prevalent. And i believe it would be a frequent scenario for chado adaptor
when being called from gbrowse.
In case of a forking where the child wishes to use the parent's
dbh,the 'InactiveDestroy' attribute of DBI would be the likely solution.
So,  the DBI keeps the parent's connection alive when the dbh variable is destroyed.
perlmonks discussion: http://www.perlmonks.org/?node_id=594175
DBI documentation:
http://search.cpan.org/~timb/DBI/DBI.pm#InactiveDestroy_(boolean)
However,  this solution does not work for oracle driver.

The other solution is to create a new handle inside a new fork/thread.
And DBIx::Connector module
http://search.cpan.org/~dwheeler/DBIx-Connector-0.34 seems to be an apt
solution which takes these situations into consideration. I am using it
at dictyBase in our custom chado Oracle adaptor along with gbrowse2.
Most of our previous connection related issues seems to be taken care
of.

-siddhartha




On Fri, 14 May 2010, Scott Cain wrote:

> Yeah, it's not clear to me either.  The chado adaptor creates a
> database handle when the constructor is called for the database
> adaptor (Chado.pm), and it appears that somehow, GBrowse was bypassing
> the constructor, because the database handle wasn't getting created.
> Fortunately, access to the database handle in the chado adaptor is
> through a method that caches the handle, so I just added a check to
> make sure dbh exists, and if it doesn't, it creates it inside the
> caching method.  What is really baffling to me is that the database
> connection parameters are also cached in the constructor, and that is
> what the dbh method uses to to "recreate" the handle.  I really don't
> understand how those values were cached, but the db handle wasn't
> created.
>
> Scott
>
>
> On Fri, May 14, 2010 at 11:56 AM, Lincoln Stein <[hidden email]> wrote:
> > Hi Scott,
> > How did I manage to break the chado adaptor? I didn't think I touched
> > anything that might have affected it.
> > Lincoln
> >
> > On Fri, May 14, 2010 at 11:33 AM, Scott Cain <[hidden email]> wrote:
> >>
> >> Hi Leighton,
> >>
> >> I think the attached copy of Chado.pm fixes this problem.  Could you
> >> try replacing your copy of Chado.pm (in a directory something like
> >> ..../Bio/DB/Das/) and, assuming it works for you too, I'll release
> >> version 0.26.
> >>
> >> Thanks,
> >> Scott
> >>
> >>
> >> On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
> >> > Hi Leighton,
> >> >
> >> > Thanks for the bug report--I should have a fix by the end of the day.
> >> >
> >> > Scott
> >> >
> >> >
> >> > On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]>
> >> > wrote:
> >> >> Hi,
> >> >>
> >> >> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to
> >> >> one
> >> >> that won't render details of the annotation from a CHADO database.
> >> >>  2.06
> >> >> still works fine on the sample yeast databases, however.
> >> >>
> >> >> The onscreen error I can see is the pink background for each track, and
> >> >> the
> >> >> truncated message:
> >> >>
> >> >> """
> >> >> Rendering error: Can't call method "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line
> >> >> """
> >> >>
> >> >> Happily, the httpd error log has the full thing (several times):
> >> >>
> >> >> """
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> [Fri May 14 15:05:02 2010] [error] [client (redacted)] Can't call
> >> >> method
> >> >> "prepare" on an undefined value at
> >> >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 1472., referer:
> >> >>
> >> >> http://ppserver/cgi-bin/gb2/gbrowse/chado_test/?name=id:146;dbid=general
> >> >> """
> >> >>
> >> >> I'm using Bio::DB::Das::Chado 0.25 and Bio::Graphics 2.08
> >> >>
> >> >> Reverting to GBROWSE 2.04 via CPAN fixes the issue for me.
> >> >>
> >> >> Cheers,
> >> >>
> >> >> L.
> >> >>
> >> >> --
> >> >> Dr Leighton Pritchard MRSC
> >> >> D131, Plant Pathology Programme, SCRI
> >> >> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
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> >> > 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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> >> Scott Cain, Ph. D.                                   scott at scottcain
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> >> Ontario Institute for Cancer Research
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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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> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
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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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Re: [Gmod-gbrowse] 2.06 may break CHADO adaptor

Scott Cain
Hi Lincoln,

I'm reasonably happy with my current solution.  Calls to the dbh
method check to make sure it's valid and create it if not.  It
actually seems like the right place to do it anyway; doing it in the
constructor was easy but wrong :-)

Thanks,
Scott


On Saturday, May 15, 2010, Lincoln Stein <[hidden email]> wrote:

> Scott,
> GBrowse calls the adaptor's clone() method after forking while in the child process. This would be the place that you can put code that refreshes the connection. If you need it, we can create something that you can call inside the parent process prior to the fork.
>
> Lincoln
>
> On Sat, May 15, 2010 at 8:33 AM, Siddhartha Basu <[hidden email]> wrote:
>
> Well,  the chado adaptor caches the dbh in every instantiated object,
> however as far as my understanding it does not gurantee an active
> database handler when run under persistent environment(mod_perl/fcgi)
> where forking/threading is prevalent. And i believe it would be a frequent scenario for chado adaptor
> when being called from gbrowse.
> In case of a forking where the child wishes to use the parent's
> dbh,the 'InactiveDestroy' attribute of DBI would be the likely solution.
> So,  the DBI keeps the parent's connection alive when the dbh variable is destroyed.
> perlmonks discussion: http://www.perlmonks.org/?node_id=594175
> DBI documentation:
> http://search.cpan.org/~timb/DBI/DBI.pm#InactiveDestroy_(boolean)
> However,  this solution does not work for oracle driver.
>
> The other solution is to create a new handle inside a new fork/thread.
> And DBIx::Connector module
> http://search.cpan.org/~dwheeler/DBIx-Connector-0.34 seems to be an apt
> solution which takes these situations into consideration. I am using it
> at dictyBase in our custom chado Oracle adaptor along with gbrowse2.
> Most of our previous connection related issues seems to be taken care
> of.
>
> -siddhartha
>
>
>
>
> On Fri, 14 May 2010, Scott Cain wrote:
>
>> Yeah, it's not clear to me either.  The chado adaptor creates a
>> database handle when the constructor is called for the database
>> adaptor (Chado.pm), and it appears that somehow, GBrowse was bypassing
>> the constructor, because the database handle wasn't getting created.
>> Fortunately, access to the database handle in the chado adaptor is
>> through a method that caches the handle, so I just added a check to
>> make sure dbh exists, and if it doesn't, it creates it inside the
>> caching method.  What is really baffling to me is that the database
>> connection parameters are also cached in the constructor, and that is
>> what the dbh method uses to to "recreate" the handle.  I really don't
>> understand how those values were cached, but the db handle wasn't
>> created.
>>
>> Scott
>>
>>
>> On Fri, May 14, 2010 at 11:56 AM, Lincoln Stein <[hidden email]> wrote:
>> > Hi Scott,
>> > How did I manage to break the chado adaptor? I didn't think I touched
>> > anything that might have affected it.
>> > Lincoln
>> >
>> > On Fri, May 14, 2010 at 11:33 AM, Scott Cain <[hidden email]> wrote:
>> >>
>> >> Hi Leighton,
>> >>
>> >> I think the attached copy of Chado.pm fixes this problem.  Could you
>> >> try replacing your copy of Chado.pm (in a directory something like
>> >> ..../Bio/DB/Das/) and, assuming it works for you too, I'll release
>> >> version 0.26.
>> >>
>> >> Thanks,
>> >> Scott
>> >>
>> >>
>> >> On Fri, May 14, 2010 at 10:22 AM, Scott Cain <[hidden email]> wrote:
>> >> > Hi Leighton,
>> >> >
>> >> > Thanks for the bug report--I should have a fix by the end of the day.
>> >> >
>> >> > Scott
>> >> >
>> >> >
>> >> > On Fri, May 14, 2010 at 10:17 AM, Leighton Pritchard <[hidden email]>
>> >> > wrote:
>> >> >> Hi,
>> >> >>
>> >> >> Upgrading from GBROWSE 2.04 to 2.06 goes from a working installation to
>> >> >> one
>> >> >> that won't render details of the annotation from a CHADO database.
>> >> >>  2.06
>> >> >> still works fine on the sample yeast databases, however.
>> >> >>
>> >> >> The onscreen error --
> 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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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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