Chado 1.31 released

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Chado 1.31 released

Scott Cain
Hello,

You have no idea how happy it makes me to announce the release of Chado 1.31:

https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/

This release marks the first schema change in Chado in 5 years, and incorporates several changes, including

* Converting all primary and foreign keys from integers to BigInts
* Converting feature.seqlen and featureloc.fmin and fmax from integers to BigInts (darn pine trees!)
* Several added linking tables.
* Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not found (thanks Eric Rasche).
* Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks Naama Menda).
* Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl (thanks Alexie Papanicolaou).
* Removed much of the initialization data included with Chado that is considered out of date.

For details on what changed in the schema, you can find the sql diff in chado/schemas/1.23-1.31/diff.sql or at 


(note that this file is fairly large, due to the large number of statements required to convert all of the primary keys to BigInts.)

Note that if you are a Tripal user, you will want to wait until Tripal has been updated to support the new schema.  

Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and Lacey Sanderson, without whom I never would have gotten this release out.

Thanks,
Scott




--
------------------------------------------------------------------------
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: Chado 1.31 released

Siddhartha Basu
Congrats to Scott and to all the chado contributors, seems like the pine tree
is a good motivation.

Quick question though, is it available through a github checkout or
through any tag/branch. It's also possible to tarball the chado release
and make it available through release page.

thanks,
-sidd

On Thu, 21 Jan 2016, Scott Cain wrote:

>    Hello,
>
>    You have no idea how happy it makes me to announce the release of Chado
>    1.31:
>
>    https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
>
>    This release marks the first schema change in Chado in 5 years, and
>    incorporates several changes, including
>
>    * Converting all primary and foreign keys from integers to BigInts
>    * Converting feature.seqlen and featureloc.fmin and fmax from integers to
>    BigInts (darn pine trees!)
>    * Several added linking tables.
>    * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
>    found (thanks Eric Rasche).
>    * Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
>    Naama Menda).
>    * Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
>    (thanks Alexie Papanicolaou).
>    * Removed much of the initialization data included with Chado that is
>    considered out of date.
>
>    For details on what changed in the schema, you can find the sql diff in
>    chado/schemas/1.23-1.31/diff.sql or atA
>    https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>    (note that this file is fairly large, due to the large number of
>    statements required to convert all of the primary keys to BigInts.)
>    Note that if you are a Tripal user, you will want to wait until Tripal has
>    been updated to support the new schema. A
>    Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
>    Lacey Sanderson, without whom I never would have gotten this release out.
>    Thanks,
>    Scott
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D. A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A
>    scott at scottcain dot net
>    GMOD Coordinator (http://gmod.org/) A  A  A  A  A  A  A  A  A  A
>    216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: Chado 1.31 released

Scott Cain
Hi Sid,

Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:


Though I suppose I should tag it in someway now that I've released it.  Time to read about how to do that in git :-)

Scott


On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <[hidden email]> wrote:
Congrats to Scott and to all the chado contributors, seems like the pine tree
is a good motivation.

Quick question though, is it available through a github checkout or
through any tag/branch. It's also possible to tarball the chado release
and make it available through release page.

thanks,
-sidd

On Thu, 21 Jan 2016, Scott Cain wrote:

>    Hello,
>
>    You have no idea how happy it makes me to announce the release of Chado
>    1.31:
>
>    https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
>
>    This release marks the first schema change in Chado in 5 years, and
>    incorporates several changes, including
>
>    * Converting all primary and foreign keys from integers to BigInts
>    * Converting feature.seqlen and featureloc.fmin and fmax from integers to
>    BigInts (darn pine trees!)
>    * Several added linking tables.
>    * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
>    found (thanks Eric Rasche).
>    * Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
>    Naama Menda).
>    * Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
>    (thanks Alexie Papanicolaou).
>    * Removed much of the initialization data included with Chado that is
>    considered out of date.
>
>    For details on what changed in the schema, you can find the sql diff in
>    chado/schemas/1.23-1.31/diff.sql or atA
>    https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>    (note that this file is fairly large, due to the large number of
>    statements required to convert all of the primary keys to BigInts.)
>    Note that if you are a Tripal user, you will want to wait until Tripal has
>    been updated to support the new schema. A
>    Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
>    Lacey Sanderson, without whom I never would have gotten this release out.
>    Thanks,
>    Scott
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D. A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A
>    scott at scottcain dot net
>    GMOD Coordinator (http://gmod.org/) A  A  A  A  A  A  A  A  A  A
>    <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140

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


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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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Re: Chado 1.31 released

Scott Cain
OK, now it's available via the the 1.31-release tag:


(Thanks Joe Carlson!)


On Fri, Jan 22, 2016 at 10:54 AM, Scott Cain <[hidden email]> wrote:
Hi Sid,

Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:


Though I suppose I should tag it in someway now that I've released it.  Time to read about how to do that in git :-)

Scott


On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <[hidden email]> wrote:
Congrats to Scott and to all the chado contributors, seems like the pine tree
is a good motivation.

Quick question though, is it available through a github checkout or
through any tag/branch. It's also possible to tarball the chado release
and make it available through release page.

thanks,
-sidd

On Thu, 21 Jan 2016, Scott Cain wrote:

>    Hello,
>
>    You have no idea how happy it makes me to announce the release of Chado
>    1.31:
>
>    https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
>
>    This release marks the first schema change in Chado in 5 years, and
>    incorporates several changes, including
>
>    * Converting all primary and foreign keys from integers to BigInts
>    * Converting feature.seqlen and featureloc.fmin and fmax from integers to
>    BigInts (darn pine trees!)
>    * Several added linking tables.
>    * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
>    found (thanks Eric Rasche).
>    * Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
>    Naama Menda).
>    * Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
>    (thanks Alexie Papanicolaou).
>    * Removed much of the initialization data included with Chado that is
>    considered out of date.
>
>    For details on what changed in the schema, you can find the sql diff in
>    chado/schemas/1.23-1.31/diff.sql or atA
>    https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>    (note that this file is fairly large, due to the large number of
>    statements required to convert all of the primary keys to BigInts.)
>    Note that if you are a Tripal user, you will want to wait until Tripal has
>    been updated to support the new schema. A
>    Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
>    Lacey Sanderson, without whom I never would have gotten this release out.
>    Thanks,
>    Scott
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D. A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A
>    scott at scottcain dot net
>    GMOD Coordinator (http://gmod.org/) A  A  A  A  A  A  A  A  A  A
>    <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140

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


------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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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Re: Chado 1.31 released

Siddhartha Basu
Scott (and Joe), you are awesome :-)

-sidd

On Fri, 22 Jan 2016, Scott Cain wrote:

>    OK, now it's available via the the 1.31-release tag:
>    https://github.com/GMOD/Chado/releases/tag/1.31-release
>    (Thanks Joe Carlson!)
>    On Fri, Jan 22, 2016 at 10:54 AM, Scott Cain <[hidden email]> wrote:
>
>      Hi Sid,
>      Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:
>      https://github.com/GMOD/Chado/tree/1.31
>      Though I suppose I should tag it in someway now that I've released it.A
>      Time to read about how to do that in git :-)
>      Scott
>      On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <[hidden email]>
>      wrote:
>
>        Congrats to Scott and to all the chado contributors, seems like the
>        pine tree
>        is a good motivation.
>
>        Quick question though, is it available through a github checkout or
>        through any tag/branch. It's also possible to tarball the chado
>        release
>        and make it available through release page.
>
>        thanks,
>        -sidd
>        On Thu, 21 Jan 2016, Scott Cain wrote:
>
>        >A  A  Hello,
>        >
>        >A  A  You have no idea how happy it makes me to announce the release
>        of Chado
>        >A  A  1.31:
>        >
>        >A  A  https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
>        >
>        >A  A  This release marks the first schema change in Chado in 5 years,
>        and
>        >A  A  incorporates several changes, including
>        >
>        >A  A  * Converting all primary and foreign keys from integers to
>        BigInts
>        >A  A  * Converting feature.seqlen and featureloc.fmin and fmax from
>        integers to
>        >A  A  BigInts (darn pine trees!)
>        >A  A  * Several added linking tables.
>        >A  A  * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of"
>        term is not
>        >A  A  found (thanks Eric Rasche).
>        >A  A  * Fixed the ncbi_taxonomy loader to load the entire NCBI
>        taxonomy (thanks
>        >A  A  Naama Menda).
>        >A  A  * Fixed the "organism by data" functionality of
>        gmod_bulk_load_gff3.pl
>        >A  A  (thanks Alexie Papanicolaou).
>        >A  A  * Removed much of the initialization data included with Chado
>        that is
>        >A  A  considered out of date.
>        >
>        >A  A  For details on what changed in the schema, you can find the sql
>        diff in
>        >A  A  chado/schemas/1.23-1.31/diff.sql or atA
>        >A  A
>        https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>        >A  A  (note that this file is fairly large, due to the large number
>        of
>        >A  A  statements required to convert all of the primary keys to
>        BigInts.)
>        >A  A  Note that if you are a Tripal user, you will want to wait until
>        Tripal has
>        >A  A  been updated to support the new schema. A
>        >A  A  Finally, I want to give a very big "THANK YOU!!" to Stephen
>        Ficklin and
>        >A  A  Lacey Sanderson, without whom I never would have gotten this
>        release out.
>        >A  A  Thanks,
>        >A  A  Scott
>        >
>        >A  A  --
>        >A  A
>        ------------------------------------------------------------------------
>        >A  A  Scott Cain, Ph. D. AA  AA  AA  AA  AA  AA  AA  AA  AA  AA  AA
>        AA  AA  AA  AA  AA  A
>        >A  A  scott at scottcain dot net
>        >A  A  GMOD Coordinator (http://gmod.org/) AA  AA  AA  AA  AA  AA  AA
>        AA  AA  A
>        >A  A  216-392-3087
>        >A  A  Ontario Institute for Cancer Research
>
>        >
>        ------------------------------------------------------------------------------
>        > Site24x7 APM Insight: Get Deep Visibility into Application
>        Performance
>        > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>        > Monitor end-to-end web transactions and take corrective actions now
>        > Troubleshoot faster and improve end-user experience. Signup Now!
>        > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>
>        > _______________________________________________
>        > Gmod-schema mailing list
>        > [hidden email]
>        > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>        ------------------------------------------------------------------------------
>        Site24x7 APM Insight: Get Deep Visibility into Application Performance
>        APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>        Monitor end-to-end web transactions and take corrective actions now
>        Troubleshoot faster and improve end-user experience. Signup Now!
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>        _______________________________________________
>        Gmod-schema mailing list
>        [hidden email]
>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A A
>      scott at scottcain dot net
>      GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A A
>      216-392-3087
>      Ontario Institute for Cancer Research
>
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A A
>    scott at scottcain dot net
>    GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A A
>    216-392-3087
>    Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
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> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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