Upgrade older Chado database

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Upgrade older Chado database

Stephen Ficklin-2

Hi all,

 

Sorry to post this if it’s already been answered.  I can’t seem to find the answer.  Is there an easy way to upgrade a Chado database from version 1.0 to 1.1? 

 

Thanks,

Stephen


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Re: Upgrade older Chado database

Robert Buels
Yep, Chado needs migration scripts.  Who's going to implement it?

http://search.cpan.org/perldoc?DBIx::Migration::Directories would
probably be a good thing to use.

Rob

On 03/23/2011 11:08 AM, Stephen Ficklin wrote:

> Hi all,
>
> Sorry to post this if it’s already been answered. I can’t seem to find
> the answer. Is there an easy way to upgrade a Chado database from
> version 1.0 to 1.1?
>
> Thanks,
>
> Stephen
>
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
>
>
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: Upgrade older Chado database

Scott Cain
While Rob is absolutely correct (and I'm curious about the migration module he mentioned), there is at least a "Changes.sql" file that has SQL commands to change the data base.  My recollection is that there probably isn't actual data moving around that needs to happen.  It is all adding tables and a few columns with reasonable defaults.

Scott

Sent from my iPad

On 2011-03-23, at 12:21 PM, Robert Buels <[hidden email]> wrote:

> Yep, Chado needs migration scripts.  Who's going to implement it?
>
> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
> probably be a good thing to use.
>
> Rob
>
> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>> Hi all,
>>
>> Sorry to post this if it’s already been answered. I can’t seem to find
>> the answer. Is there an easy way to upgrade a Chado database from
>> version 1.0 to 1.1?
>>
>> Thanks,
>>
>> Stephen
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>>
>>
>>
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
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Re: Upgrade older Chado database

Jonathan "Duke" Leto
In reply to this post by Robert Buels
Howdy,

As a first step, the Chado schema should probably grow a table that stores the
current Chado schema version. Something like a "chado metadata" table. Any time
any change to the schema is made, even changing a default or changing an index,
should bump the schema version number up.

This will allow software to be smarter and be able to detect incompatible
versions of things trying to be used together, as well as allowing more robust
migration scripts.

Duke

On Wed, Mar 23, 2011 at 12:21 PM, Robert Buels <[hidden email]> wrote:

> Yep, Chado needs migration scripts.  Who's going to implement it?
>
> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
> probably be a good thing to use.
>
> Rob
>
> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>> Hi all,
>>
>> Sorry to post this if it’s already been answered. I can’t seem to find
>> the answer. Is there an easy way to upgrade a Chado database from
>> version 1.0 to 1.1?
>>
>> Thanks,
>>
>> Stephen
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>>
>>
>>
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
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Re: Upgrade older Chado database

Siddhartha Basu
In reply to this post by Scott Cain
As an alternate i am playing around with
DBICDH(DBIx::Class::DeploymentHandler)
http://search.cpan.org/dist/DBIx-Class-DeploymentHandler
The docs are a bit rough though. The schema directory organization is
inspired by DBIx::Migration::Directories. It is expected to play nicely
with BCS. Few links ....
http://www.pythian.com/news/19797/dbixclassdeploymenthandler-is-awesome
http://afoolishmanifesto.com/dbicdh-intro/slideshow.html

-siddhartha

On Wed, 23 Mar 2011, Scott Cain wrote:

> While Rob is absolutely correct (and I'm curious about the migration module he mentioned), there is at least a "Changes.sql" file that has SQL commands to change the data base.  My recollection is that there probably isn't actual data moving around that needs to happen.  It is all adding tables and a few columns with reasonable defaults.
>
> Scott
>
> Sent from my iPad
>
> On 2011-03-23, at 12:21 PM, Robert Buels <[hidden email]> wrote:
>
> > Yep, Chado needs migration scripts.  Who's going to implement it?
> >
> > http://search.cpan.org/perldoc?DBIx::Migration::Directories would
> > probably be a good thing to use.
> >
> > Rob
> >
> > On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
> >> Hi all,
> >>
> >> Sorry to post this if it’s already been answered. I can’t seem to find
> >> the answer. Is there an easy way to upgrade a Chado database from
> >> version 1.0 to 1.1?
> >>
> >> Thanks,
> >>
> >> Stephen
> >>
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Enable your software for Intel(R) Active Management Technology to meet the
> >> growing manageability and security demands of your customers. Businesses
> >> are taking advantage of Intel(R) vPro (TM) technology - will your software
> >> be a part of the solution? Download the Intel(R) Manageability Checker
> >> today! http://p.sf.net/sfu/intel-dev2devmar
> >>
> >>
> >>
> >> _______________________________________________
> >> Gmod-schema mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
> >
> > ------------------------------------------------------------------------------
> > Enable your software for Intel(R) Active Management Technology to meet the
> > growing manageability and security demands of your customers. Businesses
> > are taking advantage of Intel(R) vPro (TM) technology - will your software
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> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
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Re: Upgrade older Chado database

Robert Buels
In reply to this post by Jonathan "Duke" Leto
Using DBIx::Migration::Directories, the table would by default be called
'migration_schema_version'.  It also has a 'migration_schema_log' table
that logs which migration procedures are done to a given database.

R

On 03/23/2011 11:53 PM, Jonathan "Duke" Leto wrote:

> Howdy,
>
> As a first step, the Chado schema should probably grow a table that stores the
> current Chado schema version. Something like a "chado metadata" table. Any time
> any change to the schema is made, even changing a default or changing an index,
> should bump the schema version number up.
>
> This will allow software to be smarter and be able to detect incompatible
> versions of things trying to be used together, as well as allowing more robust
> migration scripts.
>
> Duke
>
> On Wed, Mar 23, 2011 at 12:21 PM, Robert Buels<[hidden email]>  wrote:
>> Yep, Chado needs migration scripts.  Who's going to implement it?
>>
>> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
>> probably be a good thing to use.
>>
>> Rob
>>
>> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>>> Hi all,
>>>
>>> Sorry to post this if it’s already been answered. I can’t seem to find
>>> the answer. Is there an easy way to upgrade a Chado database from
>>> version 1.0 to 1.1?
>>>
>>> Thanks,
>>>
>>> Stephen
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Enable your software for Intel(R) Active Management Technology to meet the
>>> growing manageability and security demands of your customers. Businesses
>>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>


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Re: Upgrade older Chado database

Jonathan "Duke" Leto
Howdy,

This sounds nice, because we could piggy-back on the hard work that people have
put into database schema migrations, without having to re-invent and maintain
that wheel.

Should we start hacking on something like this in a branch? What would be the
first useful feature to implement using this new database schema
version information?

Duke


On Thu, Mar 24, 2011 at 9:04 AM, Robert Buels <[hidden email]> wrote:

> Using DBIx::Migration::Directories, the table would by default be called
> 'migration_schema_version'.  It also has a 'migration_schema_log' table
> that logs which migration procedures are done to a given database.
>
> R
>
> On 03/23/2011 11:53 PM, Jonathan "Duke" Leto wrote:
>> Howdy,
>>
>> As a first step, the Chado schema should probably grow a table that stores the
>> current Chado schema version. Something like a "chado metadata" table. Any time
>> any change to the schema is made, even changing a default or changing an index,
>> should bump the schema version number up.
>>
>> This will allow software to be smarter and be able to detect incompatible
>> versions of things trying to be used together, as well as allowing more robust
>> migration scripts.
>>
>> Duke
>>
>> On Wed, Mar 23, 2011 at 12:21 PM, Robert Buels<[hidden email]>  wrote:
>>> Yep, Chado needs migration scripts.  Who's going to implement it?
>>>
>>> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
>>> probably be a good thing to use.
>>>
>>> Rob
>>>
>>> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>>>> Hi all,
>>>>
>>>> Sorry to post this if it’s already been answered. I can’t seem to find
>>>> the answer. Is there an easy way to upgrade a Chado database from
>>>> version 1.0 to 1.1?
>>>>
>>>> Thanks,
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Enable your software for Intel(R) Active Management Technology to meet the
>>>> growing manageability and security demands of your customers. Businesses
>>>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Enable your software for Intel(R) Active Management Technology to meet the
>>> growing manageability and security demands of your customers. Businesses
>>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
> _______________________________________________
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>



--
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[hidden email]
http://leto.net

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Re: Upgrade older Chado database

Stephen Ficklin-2
Hi All,

Thanks for the discussion!  It looks like in the short term I can use the
Changes.sql file that Scott mentions to apply changes. Although I did notice
that a rank column was added to the analysisprop table in v1.1 along with it
being added to the unique key constraint.  But this isn't in the Changes.sql
file that comes with version 1.1.

Stephen

-----Original Message-----
From: Jonathan "Duke" Leto [mailto:[hidden email]]
Sent: Friday, March 25, 2011 2:50 PM
To: Robert Buels
Cc: GMOD Schema List
Subject: Re: [Gmod-schema] Upgrade older Chado database

Howdy,

This sounds nice, because we could piggy-back on the hard work that people
have
put into database schema migrations, without having to re-invent and
maintain
that wheel.

Should we start hacking on something like this in a branch? What would be
the
first useful feature to implement using this new database schema
version information?

Duke


On Thu, Mar 24, 2011 at 9:04 AM, Robert Buels <[hidden email]> wrote:

> Using DBIx::Migration::Directories, the table would by default be called
> 'migration_schema_version'.  It also has a 'migration_schema_log' table
> that logs which migration procedures are done to a given database.
>
> R
>
> On 03/23/2011 11:53 PM, Jonathan "Duke" Leto wrote:
>> Howdy,
>>
>> As a first step, the Chado schema should probably grow a table that
stores the
>> current Chado schema version. Something like a "chado metadata" table.
Any time
>> any change to the schema is made, even changing a default or changing an
index,
>> should bump the schema version number up.
>>
>> This will allow software to be smarter and be able to detect incompatible
>> versions of things trying to be used together, as well as allowing more
robust

>> migration scripts.
>>
>> Duke
>>
>> On Wed, Mar 23, 2011 at 12:21 PM, Robert Buels<[hidden email]>  wrote:
>>> Yep, Chado needs migration scripts.  Who's going to implement it?
>>>
>>> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
>>> probably be a good thing to use.
>>>
>>> Rob
>>>
>>> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>>>> Hi all,
>>>>
>>>> Sorry to post this if it’s already been answered. I can’t seem to find
>>>> the answer. Is there an easy way to upgrade a Chado database from
>>>> version 1.0 to 1.1?
>>>>
>>>> Thanks,
>>>>
>>>> Stephen
>>>>
>>>>
>>>>
>>>>
----------------------------------------------------------------------------
--
>>>> Enable your software for Intel(R) Active Management Technology to meet
the
>>>> growing manageability and security demands of your customers.
Businesses
>>>> are taking advantage of Intel(R) vPro (TM) technology - will your
software

>>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>
>>>
----------------------------------------------------------------------------
--
>>> Enable your software for Intel(R) Active Management Technology to meet
the
>>> growing manageability and security demands of your customers. Businesses
>>> are taking advantage of Intel(R) vPro (TM) technology - will your
software

>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>
>
>
----------------------------------------------------------------------------
--

> Enable your software for Intel(R) Active Management Technology to meet the
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> are taking advantage of Intel(R) vPro (TM) technology - will your software
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--
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[hidden email]
http://leto.net

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Re: Upgrade older Chado database

Scott Cain
In reply to this post by Jonathan "Duke" Leto
Hi Duke,

I've been planning on doing exactly this.  I'll probably create a
table called "meta" that will have a cvterm tag and value columns.

Scott


On Thu, Mar 24, 2011 at 2:53 AM, Jonathan "Duke" Leto <[hidden email]> wrote:

> Howdy,
>
> As a first step, the Chado schema should probably grow a table that stores the
> current Chado schema version. Something like a "chado metadata" table. Any time
> any change to the schema is made, even changing a default or changing an index,
> should bump the schema version number up.
>
> This will allow software to be smarter and be able to detect incompatible
> versions of things trying to be used together, as well as allowing more robust
> migration scripts.
>
> Duke
>
> On Wed, Mar 23, 2011 at 12:21 PM, Robert Buels <[hidden email]> wrote:
>> Yep, Chado needs migration scripts.  Who's going to implement it?
>>
>> http://search.cpan.org/perldoc?DBIx::Migration::Directories would
>> probably be a good thing to use.
>>
>> Rob
>>
>> On 03/23/2011 11:08 AM, Stephen Ficklin wrote:
>>> Hi all,
>>>
>>> Sorry to post this if it’s already been answered. I can’t seem to find
>>> the answer. Is there an easy way to upgrade a Chado database from
>>> version 1.0 to 1.1?
>>>
>>> Thanks,
>>>
>>> Stephen
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Enable your software for Intel(R) Active Management Technology to meet the
>>> growing manageability and security demands of your customers. Businesses
>>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>>> be a part of the solution? Download the Intel(R) Manageability Checker
>>> today! http://p.sf.net/sfu/intel-dev2devmar
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>> ------------------------------------------------------------------------------
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> Jonathan "Duke" Leto
> [hidden email]
> http://leto.net
>
> ------------------------------------------------------------------------------
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
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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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