[nativ] [svn] moved project to its own module

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[nativ] [svn] moved project to its own module

Bob MacCallum
Thanks Scott.

I have made the modifications (moved project to its own module) and
have fixed up all the inline makedep.pl and chado-build-schema.pl XML
dependencies.  I can now do a "make load_schema" with SQL from either
of those two approaches with no errors.

The only thing is that I have put rather lame descriptions for project
and natural-diversity in chado-module-metadata.xml

Please "svn update" and let me know if you find any more bugs that need fixing.

cheers,
Bob.

Sending        bin/chado-build-schema.pl
Sending        chado-module-metadata.xml
Sending        modules/mage/mage.sql
Sending        modules/natural_diversity/natural_diversity.sql
Adding         modules/project
Adding         modules/project/project.sql
Sending        modules/www/www.sql
Transmitting file data ......
Committed revision 23417.



On Thu, Jun 17, 2010 at 2:26 PM, Scott Cain <[hidden email]> wrote:

> Hi Bob,
>
> I added you as a developer, so you should have write access to svn now.
>
> I have a request related to what you want to do, though: while I
> appreciate Hilmar's work in writing makedep.pl, I don't use that for
> building the default schema for releases.  I use
> schema/chado/chado-module-metadata.xml, which has a fairly simple xml
> structure.  The script schema/chado/bin/chado-build-schema.pl is a Tk
> script that uses that xml file to build the schema interactively.
> Could you please also update that xml file?
>
> Thanks,
> Scott
>
>
> On Thu, Jun 17, 2010 at 8:31 AM, Bob MacCallum
> <[hidden email]> wrote:
>> Hi,
>>
>> (Note: this is an old email I am resurrecting)
>>
>>> Good catches, I fixed these things in revs 23139 and 23140.  Do have /
>>> do you want a commit bit?
>>>
>>>>     * Dependency problem using makedep.pl since
>>>>       general.sql now uses cvterm in projectprop and
>>>>       project_relationship but cv.sql imports dbxref from general.sql.
>>>>        I tried adding the dependency on cvterm to general.sql but that
>>>>       of course creates a circular dependency.  Can the project tables
>>>>       be moved to another module which imports cvterm?
>>>
>>> I think there's probably a good case for moving these tables to their
>>> own 'Project' module that would depend on General.  Thoughts on this
>>> anyone?  If nobody says anything, I'll just do it.
>>
>> I have just run into this exact same problem with makedep.pl - I can
>> do the move to project/project.sql also.
>> My SF username is 'bobular', please could you give me commit rights?
>>
>> cheers,
>> Bob.
>>
>>>
>>> Rob
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> 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
>

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: [nativ] [svn] moved project to its own module

Scott Cain
Hi Bob,

I think the reason you were able to do "make load_schema" is that it
uses the file modules/default_schema.sql which hasn't been changed
yet.  I rebuilt both default_schema.sql and default_nofuncs.sql (which
is used to autogenerate code, documentation and diagrams) and tried to
load it, and got these errors:

ERROR:  relation "cvterm" does not exist
ERROR:  relation "cvterm" does not exist
ERROR:  relation "project_relationship" does not exist
ERROR:  relation "project_relationship" does not exist
ERROR:  relation "pub" does not exist
ERROR:  relation "project_pub" does not exist
ERROR:  relation "project_pub" does not exist
ERROR:  relation "project_pub" does not exist
ERROR:  relation "contact" does not exist
ERROR:  relation "project_contact" does not exist
ERROR:  relation "project_contact" does not exist
ERROR:  relation "project_contact" does not exist
ERROR:  relation "project" already exists

so things aren't getting assembled in the right order.  I won't have a
chance to look at why that is today; depending on what my Friday is
like, I might get to it tomorrow.  I committed the broken schema files
if anybody wants to take a look in the meantime.

Scott


On Thu, Jun 17, 2010 at 12:33 PM, Bob MacCallum
<[hidden email]> wrote:

> Thanks Scott.
>
> I have made the modifications (moved project to its own module) and
> have fixed up all the inline makedep.pl and chado-build-schema.pl XML
> dependencies.  I can now do a "make load_schema" with SQL from either
> of those two approaches with no errors.
>
> The only thing is that I have put rather lame descriptions for project
> and natural-diversity in chado-module-metadata.xml
>
> Please "svn update" and let me know if you find any more bugs that need fixing.
>
> cheers,
> Bob.
>
> Sending        bin/chado-build-schema.pl
> Sending        chado-module-metadata.xml
> Sending        modules/mage/mage.sql
> Sending        modules/natural_diversity/natural_diversity.sql
> Adding         modules/project
> Adding         modules/project/project.sql
> Sending        modules/www/www.sql
> Transmitting file data ......
> Committed revision 23417.
>
>
>
> On Thu, Jun 17, 2010 at 2:26 PM, Scott Cain <[hidden email]> wrote:
>> Hi Bob,
>>
>> I added you as a developer, so you should have write access to svn now.
>>
>> I have a request related to what you want to do, though: while I
>> appreciate Hilmar's work in writing makedep.pl, I don't use that for
>> building the default schema for releases.  I use
>> schema/chado/chado-module-metadata.xml, which has a fairly simple xml
>> structure.  The script schema/chado/bin/chado-build-schema.pl is a Tk
>> script that uses that xml file to build the schema interactively.
>> Could you please also update that xml file?
>>
>> Thanks,
>> Scott
>>
>>
>> On Thu, Jun 17, 2010 at 8:31 AM, Bob MacCallum
>> <[hidden email]> wrote:
>>> Hi,
>>>
>>> (Note: this is an old email I am resurrecting)
>>>
>>>> Good catches, I fixed these things in revs 23139 and 23140.  Do have /
>>>> do you want a commit bit?
>>>>
>>>>>     * Dependency problem using makedep.pl since
>>>>>       general.sql now uses cvterm in projectprop and
>>>>>       project_relationship but cv.sql imports dbxref from general.sql.
>>>>>        I tried adding the dependency on cvterm to general.sql but that
>>>>>       of course creates a circular dependency.  Can the project tables
>>>>>       be moved to another module which imports cvterm?
>>>>
>>>> I think there's probably a good case for moving these tables to their
>>>> own 'Project' module that would depend on General.  Thoughts on this
>>>> anyone?  If nobody says anything, I'll just do it.
>>>
>>> I have just run into this exact same problem with makedep.pl - I can
>>> do the move to project/project.sql also.
>>> My SF username is 'bobular', please could you give me commit rights?
>>>
>>> cheers,
>>> Bob.
>>>
>>>>
>>>> Rob
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> 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
>>
>



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
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Re: [nativ] [svn] moved project to its own module

Bob MacCallum
It looks like I forgot to commit the trimmed down "general/general.sql" sorry!
I also had a typo in the XML, (project depends on project, oops!)

I assume the default schema is the one which the GUI generates without
any changes to the default checkboxes, so I have done this and
committed the default_*.sql files too.

Sending        chado-module-metadata.xml
Sending        modules/default_nofuncs.sql
Sending        modules/default_schema.sql
Sending        modules/general/general.sql
Transmitting file data ....
Committed revision 23422.

Sorry for the confusion.  Please let me know of any other problems.

cheers,
Bob.


On Thu, Jun 17, 2010 at 9:09 PM, Scott Cain <[hidden email]> wrote:

> Hi Bob,
>
> I think the reason you were able to do "make load_schema" is that it
> uses the file modules/default_schema.sql which hasn't been changed
> yet.  I rebuilt both default_schema.sql and default_nofuncs.sql (which
> is used to autogenerate code, documentation and diagrams) and tried to
> load it, and got these errors:
>
> ERROR:  relation "cvterm" does not exist
> ERROR:  relation "cvterm" does not exist
> ERROR:  relation "project_relationship" does not exist
> ERROR:  relation "project_relationship" does not exist
> ERROR:  relation "pub" does not exist
> ERROR:  relation "project_pub" does not exist
> ERROR:  relation "project_pub" does not exist
> ERROR:  relation "project_pub" does not exist
> ERROR:  relation "contact" does not exist
> ERROR:  relation "project_contact" does not exist
> ERROR:  relation "project_contact" does not exist
> ERROR:  relation "project_contact" does not exist
> ERROR:  relation "project" already exists
>
> so things aren't getting assembled in the right order.  I won't have a
> chance to look at why that is today; depending on what my Friday is
> like, I might get to it tomorrow.  I committed the broken schema files
> if anybody wants to take a look in the meantime.
>
> Scott
>
>
> On Thu, Jun 17, 2010 at 12:33 PM, Bob MacCallum
> <[hidden email]> wrote:
>> Thanks Scott.
>>
>> I have made the modifications (moved project to its own module) and
>> have fixed up all the inline makedep.pl and chado-build-schema.pl XML
>> dependencies.  I can now do a "make load_schema" with SQL from either
>> of those two approaches with no errors.
>>
>> The only thing is that I have put rather lame descriptions for project
>> and natural-diversity in chado-module-metadata.xml
>>
>> Please "svn update" and let me know if you find any more bugs that need fixing.
>>
>> cheers,
>> Bob.
>>
>> Sending        bin/chado-build-schema.pl
>> Sending        chado-module-metadata.xml
>> Sending        modules/mage/mage.sql
>> Sending        modules/natural_diversity/natural_diversity.sql
>> Adding         modules/project
>> Adding         modules/project/project.sql
>> Sending        modules/www/www.sql
>> Transmitting file data ......
>> Committed revision 23417.
>>
>>
>>
>> On Thu, Jun 17, 2010 at 2:26 PM, Scott Cain <[hidden email]> wrote:
>>> Hi Bob,
>>>
>>> I added you as a developer, so you should have write access to svn now.
>>>
>>> I have a request related to what you want to do, though: while I
>>> appreciate Hilmar's work in writing makedep.pl, I don't use that for
>>> building the default schema for releases.  I use
>>> schema/chado/chado-module-metadata.xml, which has a fairly simple xml
>>> structure.  The script schema/chado/bin/chado-build-schema.pl is a Tk
>>> script that uses that xml file to build the schema interactively.
>>> Could you please also update that xml file?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> On Thu, Jun 17, 2010 at 8:31 AM, Bob MacCallum
>>> <[hidden email]> wrote:
>>>> Hi,
>>>>
>>>> (Note: this is an old email I am resurrecting)
>>>>
>>>>> Good catches, I fixed these things in revs 23139 and 23140.  Do have /
>>>>> do you want a commit bit?
>>>>>
>>>>>>     * Dependency problem using makedep.pl since
>>>>>>       general.sql now uses cvterm in projectprop and
>>>>>>       project_relationship but cv.sql imports dbxref from general.sql.
>>>>>>        I tried adding the dependency on cvterm to general.sql but that
>>>>>>       of course creates a circular dependency.  Can the project tables
>>>>>>       be moved to another module which imports cvterm?
>>>>>
>>>>> I think there's probably a good case for moving these tables to their
>>>>> own 'Project' module that would depend on General.  Thoughts on this
>>>>> anyone?  If nobody says anything, I'll just do it.
>>>>
>>>> I have just run into this exact same problem with makedep.pl - I can
>>>> do the move to project/project.sql also.
>>>> My SF username is 'bobular', please could you give me commit rights?
>>>>
>>>> cheers,
>>>> Bob.
>>>>
>>>>>
>>>>> Rob
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>> lucky parental unit.  See the prize list and enter to win:
>>>> http://p.sf.net/sfu/thinkgeek-promo
>>>> _______________________________________________
>>>> 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
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema