Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

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Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Fields, Christopher J
Dan.

Is this maybe something for the GBrowse list? (cc'ing there JIC)

chris

On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:

> Seems I still can't log bugs here:
> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>
> Error:
>        Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>
>
> Here I my bug report:
>
> I'm following the tutorial here:
>
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>
>
> I successfully set up and browsed the first database (going no further
> than #data_file). I decided to try switching from an in memory
> (file-based) database to a DBI::mysql database. After taking the
> appropriate steps (see below), I get the following error when viewing
> the database in GB:
>
>        The landmark named ctgA is not recognized. See the help pages
> for suggestions.
>
>
> I'm not sure why the landmark is found using a memory (file-based)
> database, but not found when using the same GFF loaded into mysql.
>
> This is the latest bioperl-live (although I'm still struggling with git).
>
> Any hints on what might be going wrong? I've a feeling I should
> perhaps roll back a few versions, as I noticed some SQL errors coming
> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>
>
> Cheers,
> Dan.
>
>
>
> 1) I loaded the GFF:
>
> bp_seqfeature_load.pl -v -v -f -c -z \
>  --dsn dbi:mysql:mydb:myhost \
>  --namespace volvox \
> --summary \
>  -u me -p secret \
> databases/volvox/volvox_remarks.gff3
>
>
> 2) I changed the volvox.conf file:
>
> #db_args       = -adaptor memory
> #               -dir '$HTDOCS/databases/volvox'
>
> db_args       = -adaptor DBI::mysql
>                -dsn mydb:myhost
>                -namespace volvox
>                -user me
>                -pass secret
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Dan Bolser-3
Cheers Chris,

Is there a known good version of
"perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
I believe that this is one of the more common databases, so I'm
surprised to find it broken.

What would be the git command to roll back to a stable BioPerl / GBrowse?


Sorry for the basic questions,
Dan.

On 12 July 2010 17:56, Chris Fields <[hidden email]> wrote:

> Dan.
>
> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>
> chris
>
> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>
>> Seems I still can't log bugs here:
>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>>
>> Error:
>>        Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>>
>>
>> Here I my bug report:
>>
>> I'm following the tutorial here:
>>
>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>>
>>
>> I successfully set up and browsed the first database (going no further
>> than #data_file). I decided to try switching from an in memory
>> (file-based) database to a DBI::mysql database. After taking the
>> appropriate steps (see below), I get the following error when viewing
>> the database in GB:
>>
>>        The landmark named ctgA is not recognized. See the help pages
>> for suggestions.
>>
>>
>> I'm not sure why the landmark is found using a memory (file-based)
>> database, but not found when using the same GFF loaded into mysql.
>>
>> This is the latest bioperl-live (although I'm still struggling with git).
>>
>> Any hints on what might be going wrong? I've a feeling I should
>> perhaps roll back a few versions, as I noticed some SQL errors coming
>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>>
>>
>> Cheers,
>> Dan.
>>
>>
>>
>> 1) I loaded the GFF:
>>
>> bp_seqfeature_load.pl -v -v -f -c -z \
>>  --dsn dbi:mysql:mydb:myhost \
>>  --namespace volvox \
>> --summary \
>>  -u me -p secret \
>> databases/volvox/volvox_remarks.gff3
>>
>>
>> 2) I changed the volvox.conf file:
>>
>> #db_args       = -adaptor memory
>> #               -dir '$HTDOCS/databases/volvox'
>>
>> db_args       = -adaptor DBI::mysql
>>                -dsn mydb:myhost
>>                -namespace volvox
>>                -user me
>>                -pass secret
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Jason Stajich-2
Dan -
I'm not convinced that contig:example is proper type/source for the landmarks & scaffold - i use 'scaffold:chromosome' in my data:

What happens if you change the GFF3 file line from
ctgA example contig 1 50000 . . . Name=ctgA
to
ctgA chromosome scaffold 1 50000 . . . Name=ctgA


I think this can be tweaked in the config but there may be different defaults for the in memory and DBI::mysql implementation.

-jason
Dan Bolser wrote, On 7/13/10 12:49 AM:
Cheers Chris,

Is there a known good version of
"perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
I believe that this is one of the more common databases, so I'm
surprised to find it broken.

What would be the git command to roll back to a stable BioPerl / GBrowse?


Sorry for the basic questions,
Dan.

On 12 July 2010 17:56, Chris Fields [hidden email] wrote:
  
Dan.

Is this maybe something for the GBrowse list? (cc'ing there JIC)

chris

On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:

    
Seems I still can't log bugs here:
https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474

Error:
       Artifact: Only Artifact Admins Can Modify Private ArtifactTypes


Here I my bug report:

I'm following the tutorial here:

http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html


I successfully set up and browsed the first database (going no further
than #data_file). I decided to try switching from an in memory
(file-based) database to a DBI::mysql database. After taking the
appropriate steps (see below), I get the following error when viewing
the database in GB:

       The landmark named ctgA is not recognized. See the help pages
for suggestions.


I'm not sure why the landmark is found using a memory (file-based)
database, but not found when using the same GFF loaded into mysql.

This is the latest bioperl-live (although I'm still struggling with git).

Any hints on what might be going wrong? I've a feeling I should
perhaps roll back a few versions, as I noticed some SQL errors coming
from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".


Cheers,
Dan.



1) I loaded the GFF:

bp_seqfeature_load.pl -v -v -f -c -z \
 --dsn dbi:mysql:mydb:myhost \
 --namespace volvox \
--summary \
 -u me -p secret \
databases/volvox/volvox_remarks.gff3


2) I changed the volvox.conf file:

#db_args       = -adaptor memory
#               -dir '$HTDOCS/databases/volvox'

db_args       = -adaptor DBI::mysql
               -dsn mydb:myhost
               -namespace volvox
               -user me
               -pass secret
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
      
    

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Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Dan Bolser-3
Hi Jason,

Thanks for the suggestion (see below).

On 13 July 2010 23:48, Jason Stajich <[hidden email]> wrote:

> Dan -
> I'm not convinced that contig:example is proper type/source for the
> landmarks & scaffold - i use 'scaffold:chromosome' in my data:
>
> What happens if you change the GFF3 file line from
> ctgA example contig 1 50000 . . . Name=ctgA
> to
> ctgA chromosome scaffold 1 50000 . . . Name=ctgA
>
>
> I think this can be tweaked in the config but there may be different
> defaults for the in memory and DBI::mysql implementation.

I found that this doesn't make any difference, however, I have found
more information about what causes the bug.

>From my previous email you see that I use bp_seqfeature_load.pl with
the "--namespace volvox" option (I should have guessed it was
something to do with this). Looking closely at the resulting tables I
see that the following tables are empty

volvox_attribute
volvox_parent2child
volvox_feature
volvox_interval_stats
volvox_name
volvox_parent2child


they are not empty when created without the "--namespace x" prefix,
which is why DBI::mysql 'normally' works.

All the other tables:

volvox_attributelist
volvox_locationlist
volvox_meta
volvox_sequence
volvox_typelist


appear to be created correctly, with or without the "--namespace x" prefix.


Cheers,
Dan.

> -jason
> Dan Bolser wrote, On 7/13/10 12:49 AM:
>
> Cheers Chris,
>
> Is there a known good version of
> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
> I believe that this is one of the more common databases, so I'm
> surprised to find it broken.
>
> What would be the git command to roll back to a stable BioPerl / GBrowse?
>
>
> Sorry for the basic questions,
> Dan.
>
> On 12 July 2010 17:56, Chris Fields <[hidden email]> wrote:
>
>
> Dan.
>
> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>
> chris
>
> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>
>
>
> Seems I still can't log bugs here:
> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>
> Error:
>        Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>
>
> Here I my bug report:
>
> I'm following the tutorial here:
>
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>
>
> I successfully set up and browsed the first database (going no further
> than #data_file). I decided to try switching from an in memory
> (file-based) database to a DBI::mysql database. After taking the
> appropriate steps (see below), I get the following error when viewing
> the database in GB:
>
>        The landmark named ctgA is not recognized. See the help pages
> for suggestions.
>
>
> I'm not sure why the landmark is found using a memory (file-based)
> database, but not found when using the same GFF loaded into mysql.
>
> This is the latest bioperl-live (although I'm still struggling with git).
>
> Any hints on what might be going wrong? I've a feeling I should
> perhaps roll back a few versions, as I noticed some SQL errors coming
> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>
>
> Cheers,
> Dan.
>
>
>
> 1) I loaded the GFF:
>
> bp_seqfeature_load.pl -v -v -f -c -z \
>  --dsn dbi:mysql:mydb:myhost \
>  --namespace volvox \
> --summary \
>  -u me -p secret \
> databases/volvox/volvox_remarks.gff3
>
>
> 2) I changed the volvox.conf file:
>
> #db_args       = -adaptor memory
> #               -dir '$HTDOCS/databases/volvox'
>
> db_args       = -adaptor DBI::mysql
>                -dsn mydb:myhost
>                -namespace volvox
>                -user me
>                -pass secret
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql"

Dan Bolser-3
On 14 July 2010 11:27, Dan Bolser <[hidden email]> wrote:

> Hi Jason,
>
> Thanks for the suggestion (see below).
>
> On 13 July 2010 23:48, Jason Stajich <[hidden email]> wrote:
>> Dan -
>> I'm not convinced that contig:example is proper type/source for the
>> landmarks & scaffold - i use 'scaffold:chromosome' in my data:
>>
>> What happens if you change the GFF3 file line from
>> ctgA example contig 1 50000 . . . Name=ctgA
>> to
>> ctgA chromosome scaffold 1 50000 . . . Name=ctgA
>>
>>
>> I think this can be tweaked in the config but there may be different
>> defaults for the in memory and DBI::mysql implementation.
>
> I found that this doesn't make any difference, however, I have found
> more information about what causes the bug.
>
> From my previous email you see that I use bp_seqfeature_load.pl with
> the "--namespace volvox" option (I should have guessed it was
> something to do with this). Looking closely at the resulting tables I
> see that the following tables are empty
>
> volvox_attribute
> volvox_parent2child
> volvox_feature
> volvox_interval_stats
> volvox_name
> volvox_parent2child
>
>
> they are not empty when created without the "--namespace x" prefix,
> which is why DBI::mysql 'normally' works.
>
> All the other tables:
>
> volvox_attributelist
> volvox_locationlist
> volvox_meta
> volvox_sequence
> volvox_typelist
>
>
> appear to be created correctly, with or without the "--namespace x" prefix.

It might be worth mentioning that this issue can be 'resolved' by not
using the -f (fast load) option. i.e. its the specific combination of
--namespace and -f that causes the bug.

http://bugzilla.open-bio.org/show_bug.cgi?id=3110


> Cheers,
> Dan.
>
>> -jason
>> Dan Bolser wrote, On 7/13/10 12:49 AM:
>>
>> Cheers Chris,
>>
>> Is there a known good version of
>> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to?
>> I believe that this is one of the more common databases, so I'm
>> surprised to find it broken.
>>
>> What would be the git command to roll back to a stable BioPerl / GBrowse?
>>
>>
>> Sorry for the basic questions,
>> Dan.
>>
>> On 12 July 2010 17:56, Chris Fields <[hidden email]> wrote:
>>
>>
>> Dan.
>>
>> Is this maybe something for the GBrowse list? (cc'ing there JIC)
>>
>> chris
>>
>> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote:
>>
>>
>>
>> Seems I still can't log bugs here:
>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474
>>
>> Error:
>>        Artifact: Only Artifact Admins Can Modify Private ArtifactTypes
>>
>>
>> Here I my bug report:
>>
>> I'm following the tutorial here:
>>
>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html
>>
>>
>> I successfully set up and browsed the first database (going no further
>> than #data_file). I decided to try switching from an in memory
>> (file-based) database to a DBI::mysql database. After taking the
>> appropriate steps (see below), I get the following error when viewing
>> the database in GB:
>>
>>        The landmark named ctgA is not recognized. See the help pages
>> for suggestions.
>>
>>
>> I'm not sure why the landmark is found using a memory (file-based)
>> database, but not found when using the same GFF loaded into mysql.
>>
>> This is the latest bioperl-live (although I'm still struggling with git).
>>
>> Any hints on what might be going wrong? I've a feeling I should
>> perhaps roll back a few versions, as I noticed some SQL errors coming
>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm".
>>
>>
>> Cheers,
>> Dan.
>>
>>
>>
>> 1) I loaded the GFF:
>>
>> bp_seqfeature_load.pl -v -v -f -c -z \
>>  --dsn dbi:mysql:mydb:myhost \
>>  --namespace volvox \
>> --summary \
>>  -u me -p secret \
>> databases/volvox/volvox_remarks.gff3
>>
>>
>> 2) I changed the volvox.conf file:
>>
>> #db_args       = -adaptor memory
>> #               -dir '$HTDOCS/databases/volvox'
>>
>> db_args       = -adaptor DBI::mysql
>>                -dsn mydb:myhost
>>                -namespace volvox
>>                -user me
>>                -pass secret
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>

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