Installing Chado into a DBMS schema

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Installing Chado into a DBMS schema

Karl O. Pinc
Hi,

I'd like to patch Chado so that the installation
process will install into a DBMS schema, since it
does not seem to do this.  And I want to get whatever
patches I come up with incorporated into chado.

The approach I'm thinking of is to use m4 to substitute
the name of the schema into the appropriate places
in the .sql files, textual substitution being what
m4 is designed to do.  Is this an appropriate
approach?  If not, what would be acceptable?

Please advise.


Karl <[hidden email]>
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Re: Installing Chado into a DBMS schema

Scott Cain
Hi Karl,

I think the Makefile-based installation already does this (the Tripal-based install puts it in a schema called "chado").  If you proved a name of a schema in interrogation when running "perl Makefile.PL", it should use that schema when installing.  Does it not do this (admittedly, I haven't done Chado installation this way in quite a while)?  If not, sorry, I didn't realize that was buggy or unimplemented.  Your approach does make sense if we still need to do it.

Thanks,
Scott



On Fri, Mar 14, 2014 at 11:20 AM, Karl O. Pinc <[hidden email]> wrote:
Hi,

I'd like to patch Chado so that the installation
process will install into a DBMS schema, since it
does not seem to do this.  And I want to get whatever
patches I come up with incorporated into chado.

The approach I'm thinking of is to use m4 to substitute
the name of the schema into the appropriate places
in the .sql files, textual substitution being what
m4 is designed to do.  Is this an appropriate
approach?  If not, what would be acceptable?

Please advise.


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Ontario Institute for Cancer Research

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Re: Installing Chado into a DBMS schema

Karl O. Pinc
On 03/17/2014 01:16:56 PM, Scott Cain wrote:

> Hi Karl,
>
> I think the Makefile-based installation already does this (the
> Tripal-based
> install puts it in a schema called "chado").  If you proved a name of
> a
> schema in interrogation when running "perl Makefile.PL", it should
> use
> that
> schema when installing.  Does it not do this (admittedly, I haven't
> done
> Chado installation this way in quite a while)?  If not, sorry, I
> didn't
> realize that was buggy or unimplemented.  Your approach does make
> sense if
> we still need to do it.

I'm working off CVS head (converted to git) and near as I can tell,
no, the perl install does not do this.  It does ask the question
regards what (dbms) schema should be used but that's all that seems
to happen.

Grepping through the *.sql files (I've forgotten just where at
this point) the "public" schema is hardcoded in a number of
places.

Also, can you enlighten me?  Is there an actual packaging system
for the modules or is there just some hardcoded logic somewhere?
I'm thinking about making custom installs "easy" and don't want
to break anything -- and am now thinking that maybe Tripal and
Makefile.PL are doing something different?

Prior discussion of "linking tables", those tables that
provide relationships between modules, and which module
they belong in makes me think about module packaging.
Seems to me that "linking tables" belong in neither,
but instead should be pulled in by the module
package management when needed.

If I'm going to stick my finger in then I may wind up going
all the way and whacking out some simple package management.
But this is obviously core to Chado, in at least some
sense, and I sure don't want to meddle unless chado-the-group
is interested.

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Installing Chado into a DBMS schema

Karl O. Pinc
On 03/17/2014 03:30:57 PM, Karl O. Pinc wrote:

> On 03/17/2014 01:16:56 PM, Scott Cain wrote:
> > Hi Karl,
> >
> > I think the Makefile-based installation already does this (the
> > Tripal-based
> > install puts it in a schema called "chado").  If you proved a name
> of
> > a
> > schema in interrogation when running "perl Makefile.PL", it should
> > use
> > that
> > schema when installing.  Does it not do this (admittedly, I haven't
> > done
> > Chado installation this way in quite a while)?  If not, sorry, I
> > didn't
> > realize that was buggy or unimplemented.  Your approach does make
> > sense if
> > we still need to do it.
>
> I'm working off CVS head (converted to git) and near as I can tell,
> no, the perl install does not do this.  It does ask the question
> regards what (dbms) schema should be used but that's all that seems
> to happen.

It's remotely possible that this is an artifact of the build
process, since I tried the build several times in different
databases, etc.  I'm pretty sure though that I did a "make clean"
in between.


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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