Small modification to DBIx::DBStag

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Small modification to DBIx::DBStag

Scott Cain
Hi Chris,

I know you'd probably like for DBIx::DBStag to die a quiet death, but until it does, I'd like to implement a small change to it and stag-storenode.pl.  The problem is when Chado is installed in a non-public schema (like as is the default thing to do when using Tripal).  DBIx::DBSchema assumes that the default schema is public, and forces qualifying tables with the schema when constructing queries (though it may be possible to set the default schema to an empty string, which would be ideal). 

My plan is to work on getting around this "design flaw" by adding options to stag-storenode.pl and the constructor of DBIx::DBStag, unless you have suggestions for a better approach.

Thanks,
Scott


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

------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
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Re: Small modification to DBIx::DBStag

Chris Mungall

Hi Scott

That sounds fine to me I made you a collaborator on


(or you can fork and push changes to me if you prefer)

I should probably give you PAUSE rights too. I'm not quite sure how that's done.

On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:

Hi Chris,

I know you'd probably like for DBIx::DBStag to die a quiet death, but until it does, I'd like to implement a small change to it and stag-storenode.pl.  The problem is when Chado is installed in a non-public schema (like as is the default thing to do when using Tripal).  DBIx::DBSchema assumes that the default schema is public, and forces qualifying tables with the schema when constructing queries (though it may be possible to set the default schema to an empty string, which would be ideal). 

My plan is to work on getting around this "design flaw" by adding options to stag-storenode.pl and the constructor of DBIx::DBStag, unless you have suggestions for a better approach.

Thanks,
Scott


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


------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
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Re: Small modification to DBIx::DBStag

Siddhartha Basu
Hi Chris,
You could try the co-maintainership system in PAUSE.

thanks,
-siddhartha

On Mon, 03 Jun 2013, Chris Mungall wrote:

>    Hi Scott
>    That sounds fine to me I made you a collaborator on
>    https://github.com/cmungall/DBIx-DBStag
>    (or you can fork and push changes to me if you prefer)
>    I should probably give you PAUSE rights too. I'm not quite sure how that's
>    done.
>    On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:
>
>      Hi Chris,
>
>      I know you'd probably like for DBIx::DBStag to die a quiet death, but
>      until it does, I'd like to implement a small change to it and
>      stag-storenode.pl.  The problem is when Chado is installed in a
>      non-public schema (like as is the default thing to do when using
>      Tripal).  DBIx::DBSchema assumes that the default schema is public, and
>      forces qualifying tables with the schema when constructing queries
>      (though it may be possible to set the default schema to an empty string,
>      which would be ideal).
>
>      My plan is to work on getting around this "design flaw" by adding
>      options to stag-storenode.pl and the constructor of DBIx::DBStag, unless
>      you have suggestions for a better approach.
>
>      Thanks,
>      Scott
>
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.                                   scott at scottcain
>      dot net
>      GMOD Coordinator (http://gmod.org/)                     216-392-3087
>      Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
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Re: Small modification to DBIx::DBStag

Scott Cain
Hi Chris and Siddhartha,

I'm pretty sure I'm already a co-maintainer (in fact, if you look at search.cpan.org you'll see me as the owner, since I built the last release).  What I didn't have was commit privs on Chris's github repo.

Also, as it turns out, the problem is deeper than just a "simple fix" to DBIx::DBStag: DBIx::DBSchema needs fixed too, and I'm not even sure of the best way to do it.  I've contacted the author for suggestions and help.

Thanks,
Scott



On Tue, Jun 4, 2013 at 10:49 AM, Siddhartha Basu <[hidden email]> wrote:
Hi Chris,
You could try the co-maintainership system in PAUSE.

thanks,
-siddhartha

On Mon, 03 Jun 2013, Chris Mungall wrote:

>    Hi Scott
>    That sounds fine to me I made you a collaborator on
>    https://github.com/cmungall/DBIx-DBStag
>    (or you can fork and push changes to me if you prefer)
>    I should probably give you PAUSE rights too. I'm not quite sure how that's
>    done.
>    On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:
>
>      Hi Chris,
>
>      I know you'd probably like for DBIx::DBStag to die a quiet death, but
>      until it does, I'd like to implement a small change to it and
>      stag-storenode.pl.  The problem is when Chado is installed in a
>      non-public schema (like as is the default thing to do when using
>      Tripal).  DBIx::DBSchema assumes that the default schema is public, and
>      forces qualifying tables with the schema when constructing queries
>      (though it may be possible to set the default schema to an empty string,
>      which would be ideal).
>
>      My plan is to work on getting around this "design flaw" by adding
>      options to stag-storenode.pl and the constructor of DBIx::DBStag, unless
>      you have suggestions for a better approach.
>
>      Thanks,
>      Scott
>
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.                                   scott at scottcain
>      dot net
>      GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>      Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
_______________________________________________
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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

------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
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Re: Small modification to DBIx::DBStag

Siddhartha Basu
Hi Scott,

On Tue, 04 Jun 2013, Scott Cain wrote:

>    Hi Chris and Siddhartha,
>
>    I'm pretty sure I'm already a co-maintainer (in fact, if you look at
>    search.cpan.org you'll see me as the owner, since I built the last
>    release).  What I didn't have was commit privs on Chris's github repo.
I should have checked the CPAN before i posted, sorry for any
confusion.

>
>    Also, as it turns out, the problem is deeper than just a "simple fix" to
>    DBIx::DBStag: DBIx::DBSchema needs fixed too, and I'm not even sure of the
>    best way to do it.  I've contacted the author for suggestions and help.
Just wondering, whether its time to consider another ontology loader for
replacement, for instance, the one maintained/written by Naama Menda.
I haven't used it seriously though(still in Oracle), just throwing out
and idea.

thanks,
-siddhartha




>
>    Thanks,
>    Scott
>
>    On Tue, Jun 4, 2013 at 10:49 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Chris,
>      You could try the co-maintainership system in PAUSE.
>
>      thanks,
>      -siddhartha
>      On Mon, 03 Jun 2013, Chris Mungall wrote:
>
>      >    Hi Scott
>      >    That sounds fine to me I made you a collaborator on
>      >    https://github.com/cmungall/DBIx-DBStag
>      >    (or you can fork and push changes to me if you prefer)
>      >    I should probably give you PAUSE rights too. I'm not quite sure how
>      that's
>      >    done.
>      >    On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:
>      >
>      >      Hi Chris,
>      >
>      >      I know you'd probably like for DBIx::DBStag to die a quiet death,
>      but
>      >      until it does, I'd like to implement a small change to it and
>      >      stag-storenode.pl.  The problem is when Chado is installed in a
>      >      non-public schema (like as is the default thing to do when using
>      >      Tripal).  DBIx::DBSchema assumes that the default schema is
>      public, and
>      >      forces qualifying tables with the schema when constructing
>      queries
>      >      (though it may be possible to set the default schema to an empty
>      string,
>      >      which would be ideal).
>      >
>      >      My plan is to work on getting around this "design flaw" by adding
>      >      options to stag-storenode.pl and the constructor of DBIx::DBStag,
>      unless
>      >      you have suggestions for a better approach.
>      >
>      >      Thanks,
>      >      Scott
>      >
>      >      --
>      >    
>       ------------------------------------------------------------------------
>      >      Scott Cain, Ph. D.                                   scott at
>      scottcain
>      >      dot net
>      >      GMOD Coordinator (http://gmod.org/)                    
>      216-392-3087
>      >      Ontario Institute for Cancer Research
>
>      >
>      ------------------------------------------------------------------------------
>      > How ServiceNow helps IT people transform IT departments:
>      > 1. A cloud service to automate IT design, transition and operations
>      > 2. Dashboards that offer high-level views of enterprise services
>      > 3. A single system of record for all IT processes
>      > http://p.sf.net/sfu/servicenow-d2d-j
>
>      > _______________________________________________
>      > Gmod-schema mailing list
>      > [hidden email]
>      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      ------------------------------------------------------------------------------
>      How ServiceNow helps IT people transform IT departments:
>      1. A cloud service to automate IT design, transition and operations
>      2. Dashboards that offer high-level views of enterprise services
>      3. A single system of record for all IT processes
>      http://p.sf.net/sfu/servicenow-d2d-j
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.                                   scott at scottcain
>    dot net
>    GMOD Coordinator (http://gmod.org/)                     216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
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Re: Small modification to DBIx::DBStag

Scott Cain
Yep, I was thinking the same thing--I was just talking with Rob Buels about it in fact.  I suspect that will happen with the next release of Chado.

Scott



On Tue, Jun 4, 2013 at 12:55 PM, Siddhartha Basu <[hidden email]> wrote:
Hi Scott,

On Tue, 04 Jun 2013, Scott Cain wrote:

>    Hi Chris and Siddhartha,
>
>    I'm pretty sure I'm already a co-maintainer (in fact, if you look at
>    search.cpan.org you'll see me as the owner, since I built the last
>    release).  What I didn't have was commit privs on Chris's github repo.
I should have checked the CPAN before i posted, sorry for any
confusion.

>
>    Also, as it turns out, the problem is deeper than just a "simple fix" to
>    DBIx::DBStag: DBIx::DBSchema needs fixed too, and I'm not even sure of the
>    best way to do it.  I've contacted the author for suggestions and help.
Just wondering, whether its time to consider another ontology loader for
replacement, for instance, the one maintained/written by Naama Menda.
I haven't used it seriously though(still in Oracle), just throwing out
and idea.

thanks,
-siddhartha




>
>    Thanks,
>    Scott
>
>    On Tue, Jun 4, 2013 at 10:49 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Chris,
>      You could try the co-maintainership system in PAUSE.
>
>      thanks,
>      -siddhartha
>      On Mon, 03 Jun 2013, Chris Mungall wrote:
>
>      >    Hi Scott
>      >    That sounds fine to me I made you a collaborator on
>      >    https://github.com/cmungall/DBIx-DBStag
>      >    (or you can fork and push changes to me if you prefer)
>      >    I should probably give you PAUSE rights too. I'm not quite sure how
>      that's
>      >    done.
>      >    On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:
>      >
>      >      Hi Chris,
>      >
>      >      I know you'd probably like for DBIx::DBStag to die a quiet death,
>      but
>      >      until it does, I'd like to implement a small change to it and
>      >      stag-storenode.pl.  The problem is when Chado is installed in a
>      >      non-public schema (like as is the default thing to do when using
>      >      Tripal).  DBIx::DBSchema assumes that the default schema is
>      public, and
>      >      forces qualifying tables with the schema when constructing
>      queries
>      >      (though it may be possible to set the default schema to an empty
>      string,
>      >      which would be ideal).
>      >
>      >      My plan is to work on getting around this "design flaw" by adding
>      >      options to stag-storenode.pl and the constructor of DBIx::DBStag,
>      unless
>      >      you have suggestions for a better approach.
>      >
>      >      Thanks,
>      >      Scott
>      >
>      >      --
>      >
>       ------------------------------------------------------------------------
>      >      Scott Cain, Ph. D.                                   scott at
>      scottcain
>      >      dot net
>      >      GMOD Coordinator (http://gmod.org/)
>      <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>      >      Ontario Institute for Cancer Research
>
>      >
>      ------------------------------------------------------------------------------
>      > How ServiceNow helps IT people transform IT departments:
>      > 1. A cloud service to automate IT design, transition and operations
>      > 2. Dashboards that offer high-level views of enterprise services
>      > 3. A single system of record for all IT processes
>      > http://p.sf.net/sfu/servicenow-d2d-j
>
>      > _______________________________________________
>      > Gmod-schema mailing list
>      > [hidden email]
>      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      ------------------------------------------------------------------------------
>      How ServiceNow helps IT people transform IT departments:
>      1. A cloud service to automate IT design, transition and operations
>      2. Dashboards that offer high-level views of enterprise services
>      3. A single system of record for all IT processes
>      http://p.sf.net/sfu/servicenow-d2d-j
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.                                   scott at scottcain
>    dot net
>    GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
_______________________________________________
Gmod-schema mailing list
[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

------------------------------------------------------------------------------
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j
_______________________________________________
Gmod-schema mailing list
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