Chado Group Module: Release Candidate 3

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Chado Group Module: Release Candidate 3

Mara Kim-2

Hello gmod-ers,

I am pleased to announce the release of the Chado Group Module v0.9, Release Candidate 3.

You may download the new release here: https://github.com/autochthe/Chado-group-module/releases/tag/v0.9RC3

Change log:

Added grp_contact table

Added linking_table column in grpmember, and UNIQUE(grpmember_id, linking_table)

Added linking_table column to FOO_grpmember tables, DEFAULT 'FOO' CHECK (linking_table = 'FOO')

Dropped previous faulty UNIQUE constraint FOO_grpmember(FOO_id, grpmember_id)

  Replaced with UNIQUE(grpmember_id) in all FOO_grpmember tables

Added FOREIGN KEY(grpmember_id, linking_table) in all FOO_grpmember tables.

To install from scratch, simply execute `groups.sql`.  If you are upgrading from RC2, run the commands in `upgrade/0.9RC2.sql`, but read the warning below first.

ALERT: this update will break lots of things.  If you are upgrading with previous data, first make sure to backup all data.  Furthermore, the included upgrade script will not work if there are entries in the grpmember table.  I would first copy the data in the grpmember_* tables, as well as any linker tables you have into temporary tables, then truncate those tables.  After you update the schema, you may copy the rows back, defining a value for linking_table.

Any scripts you have that insert into grpmember will now need to define values for the linking_table column.  Furthermore, if you define your own linking tables, look at the included `linker_template.sql` for help structuring your custom tables.


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Re: Chado Group Module: Release Candidate 3

Cannon, Ethalinda K [COM S]

​Hi Mara,


There might be an error in the sample and template X_grpmember tables:

CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grp
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

I think it should be:
CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grpmember
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

​Also, remind me the purpose of the 'linking_table' fields? I read back over the discussion concerning this field, but didn't quite understand. Should linking_table be set to the same table name ("X") in both grpmember records and their X_grpmember linker table records?

I have worked through the Group Module release candidate with our proposed method for saving EQ phenotype statements. The result is pretty frightening, but with loaders and views, should be manageable. You can see the results here: http://gmod.org/wiki/Chado_Post-Composed_Phenotypes#Option_2:_Group_Module_is_decoupled_from_the_phenotype_cvterm_table​


Ethy



From: Mara Kim <[hidden email]>
Sent: Tuesday, February 10, 2015 10:48 AM
To: [hidden email]; gmod-devel; [hidden email]
Subject: [Gmod-schema] Chado Group Module: Release Candidate 3
 

Hello gmod-ers,

I am pleased to announce the release of the Chado Group Module v0.9, Release Candidate 3.

You may download the new release here: https://github.com/autochthe/Chado-group-module/releases/tag/v0.9RC3

Change log:

Added grp_contact table

Added linking_table column in grpmember, and UNIQUE(grpmember_id, linking_table)

Added linking_table column to FOO_grpmember tables, DEFAULT 'FOO' CHECK (linking_table = 'FOO')

Dropped previous faulty UNIQUE constraint FOO_grpmember(FOO_id, grpmember_id)

  Replaced with UNIQUE(grpmember_id) in all FOO_grpmember tables

Added FOREIGN KEY(grpmember_id, linking_table) in all FOO_grpmember tables.

To install from scratch, simply execute `groups.sql`.  If you are upgrading from RC2, run the commands in `upgrade/0.9RC2.sql`, but read the warning below first.

ALERT: this update will break lots of things.  If you are upgrading with previous data, first make sure to backup all data.  Furthermore, the included upgrade script will not work if there are entries in the grpmember table.  I would first copy the data in the grpmember_* tables, as well as any linker tables you have into temporary tables, then truncate those tables.  After you update the schema, you may copy the rows back, defining a value for linking_table.

Any scripts you have that insert into grpmember will now need to define values for the linking_table column.  Furthermore, if you define your own linking tables, look at the included `linker_template.sql` for help structuring your custom tables.


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Re: Chado Group Module: Release Candidate 3

Mara Kim-2
Oh. My. GOD.  Thank you.

On Wed, Feb 18, 2015 at 4:37 PM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

​Hi Mara,


There might be an error in the sample and template X_grpmember tables:

CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grp
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

I think it should be:
CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grpmember
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

​Also, remind me the purpose of the 'linking_table' fields? I read back over the discussion concerning this field, but didn't quite understand. Should linking_table be set to the same table name ("X") in both grpmember records and their X_grpmember linker table records?

I have worked through the Group Module release candidate with our proposed method for saving EQ phenotype statements. The result is pretty frightening, but with loaders and views, should be manageable. You can see the results here: http://gmod.org/wiki/Chado_Post-Composed_Phenotypes#Option_2:_Group_Module_is_decoupled_from_the_phenotype_cvterm_table


Ethy



From: Mara Kim <[hidden email]>
Sent: Tuesday, February 10, 2015 10:48 AM
To: [hidden email]; gmod-devel; [hidden email]
Subject: [Gmod-schema] Chado Group Module: Release Candidate 3
 

Hello gmod-ers,

I am pleased to announce the release of the Chado Group Module v0.9, Release Candidate 3.

You may download the new release here: https://github.com/autochthe/Chado-group-module/releases/tag/v0.9RC3

Change log:

Added grp_contact table

Added linking_table column in grpmember, and UNIQUE(grpmember_id, linking_table)

Added linking_table column to FOO_grpmember tables, DEFAULT 'FOO' CHECK (linking_table = 'FOO')

Dropped previous faulty UNIQUE constraint FOO_grpmember(FOO_id, grpmember_id)

  Replaced with UNIQUE(grpmember_id) in all FOO_grpmember tables

Added FOREIGN KEY(grpmember_id, linking_table) in all FOO_grpmember tables.

To install from scratch, simply execute `groups.sql`.  If you are upgrading from RC2, run the commands in `upgrade/0.9RC2.sql`, but read the warning below first.

ALERT: this update will break lots of things.  If you are upgrading with previous data, first make sure to backup all data.  Furthermore, the included upgrade script will not work if there are entries in the grpmember table.  I would first copy the data in the grpmember_* tables, as well as any linker tables you have into temporary tables, then truncate those tables.  After you update the schema, you may copy the rows back, defining a value for linking_table.

Any scripts you have that insert into grpmember will now need to define values for the linking_table column.  Furthermore, if you define your own linking tables, look at the included `linker_template.sql` for help structuring your custom tables.


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--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: Chado Group Module: Release Candidate 3

Mara Kim-2
I have created a new Release Candidate, RC4. https://github.com/autochthe/Chado-group-module/releases/tag/v0.9RC4


To update, run the appropriate script in the upgrade directory corresponding to the currently installed version.

On Wed, Feb 18, 2015 at 5:20 PM, Mara Kim <[hidden email]> wrote:
Oh. My. GOD.  Thank you.

On Wed, Feb 18, 2015 at 4:37 PM, Cannon, Ethalinda K [E CPE] <[hidden email]> wrote:

​Hi Mara,


There might be an error in the sample and template X_grpmember tables:

CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grp
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

I think it should be:
CREATE TABLE organism_grpmember (
    organism_grpmember_id serial PRIMARY KEY,
    grpmember_id integer NOT NULL REFERENCES grpmember
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    organism_id integer NOT NULL REFERENCES organism
      ON UPDATE CASCADE ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
    linking_table information_schema.sql_identifier
      DEFAULT 'organism' CHECK (linking_table = 'organism'),
    FOREIGN KEY(grpmember_id, linking_table)
      REFERENCES grpmember(grpmember_id, linking_table),
    UNIQUE(grpmember_id)
);

​Also, remind me the purpose of the 'linking_table' fields? I read back over the discussion concerning this field, but didn't quite understand. Should linking_table be set to the same table name ("X") in both grpmember records and their X_grpmember linker table records?

I have worked through the Group Module release candidate with our proposed method for saving EQ phenotype statements. The result is pretty frightening, but with loaders and views, should be manageable. You can see the results here: http://gmod.org/wiki/Chado_Post-Composed_Phenotypes#Option_2:_Group_Module_is_decoupled_from_the_phenotype_cvterm_table


Ethy



From: Mara Kim <[hidden email]>
Sent: Tuesday, February 10, 2015 10:48 AM
To: [hidden email]; gmod-devel; [hidden email]
Subject: [Gmod-schema] Chado Group Module: Release Candidate 3
 

Hello gmod-ers,

I am pleased to announce the release of the Chado Group Module v0.9, Release Candidate 3.

You may download the new release here: https://github.com/autochthe/Chado-group-module/releases/tag/v0.9RC3

Change log:

Added grp_contact table

Added linking_table column in grpmember, and UNIQUE(grpmember_id, linking_table)

Added linking_table column to FOO_grpmember tables, DEFAULT 'FOO' CHECK (linking_table = 'FOO')

Dropped previous faulty UNIQUE constraint FOO_grpmember(FOO_id, grpmember_id)

  Replaced with UNIQUE(grpmember_id) in all FOO_grpmember tables

Added FOREIGN KEY(grpmember_id, linking_table) in all FOO_grpmember tables.

To install from scratch, simply execute `groups.sql`.  If you are upgrading from RC2, run the commands in `upgrade/0.9RC2.sql`, but read the warning below first.

ALERT: this update will break lots of things.  If you are upgrading with previous data, first make sure to backup all data.  Furthermore, the included upgrade script will not work if there are entries in the grpmember table.  I would first copy the data in the grpmember_* tables, as well as any linker tables you have into temporary tables, then truncate those tables.  After you update the schema, you may copy the rows back, defining a value for linking_table.

Any scripts you have that insert into grpmember will now need to define values for the linking_table column.  Furthermore, if you define your own linking tables, look at the included `linker_template.sql` for help structuring your custom tables.


------------------------------------------------------------------------------
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with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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_______________________________________________
Gmod-schema mailing list
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--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema