Bug in DBIx::DBStag Makefile.PL?

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Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
Hi,

FYI.  Got this output:

[kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
Use of uninitialized value $TESTDSN in concatenation (.) or string at
Makefile.PL line 236.
Use of uninitialized value $TESTDRIVER in concatenation (.) or string
at Makefile.PL line 236.
Usage: perl Makefile.PL [options]

Possible options are:


  --testhost=<host>      Use the DBMS on <host> for testing
                         defaults to empty (localhost)

  --testdsn=<db>         Use the DBI datasource <dsn> for running the
test suite
                         defaults to

  --testdriver=<dbms>    Use the DBD driver <db> for running the test
suite
                         defaults to
                         (you may also need to change testrecreate)

  --testuser=<user>      Use the username <user> for running the test
suite;
                         defaults to no username

  --testpassword=<pwd>   Use the password <pwd> for running the test
suite;
                         defaults to no password

  --testrecreate=<cmd>   Unix command string for dropping and creating
the db

  --help                 Print this message and exit

Examples:

perl Makefile.PL

  uses the postgresql database 'test' on localhost

perl Makefile.PL --testhost mydbserver

  uses the postgresql database 'test' on host mydbserver

perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h mydbserver
mytestdb'

  uses the postgresql database 'mytestdb' on host mydbserver

Note: the options are only important for running the test suite - if
you are willing to risk an install without running the test suite,
just do this:

perl Makefile.PL
make install


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Scott Cain
Hi Karl,

I'm back at my computer, and it looks like I'm going to be spending the afternoon catching up with your emails :-)

I fixed this in git--the problem was just unescaped dollar signs in the documentation.  It doesn't affect the performance of Makefile.PL.

Scott



On Mon, Feb 17, 2014 at 9:54 AM, Karl O. Pinc <[hidden email]> wrote:
Hi,

FYI.  Got this output:

[kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
Use of uninitialized value $TESTDSN in concatenation (.) or string at
Makefile.PL line 236.
Use of uninitialized value $TESTDRIVER in concatenation (.) or string
at Makefile.PL line 236.
Usage: perl Makefile.PL [options]

Possible options are:


  --testhost=<host>      Use the DBMS on <host> for testing
                         defaults to empty (localhost)

  --testdsn=<db>         Use the DBI datasource <dsn> for running the
test suite
                         defaults to

  --testdriver=<dbms>    Use the DBD driver <db> for running the test
suite
                         defaults to
                         (you may also need to change testrecreate)

  --testuser=<user>      Use the username <user> for running the test
suite;
                         defaults to no username

  --testpassword=<pwd>   Use the password <pwd> for running the test
suite;
                         defaults to no password

  --testrecreate=<cmd>   Unix command string for dropping and creating
the db

  --help                 Print this message and exit

Examples:

perl Makefile.PL

  uses the postgresql database 'test' on localhost

perl Makefile.PL --testhost mydbserver

  uses the postgresql database 'test' on host mydbserver

perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h mydbserver
mytestdb'

  uses the postgresql database 'mytestdb' on host mydbserver

Note: the options are only important for running the test suite - if
you are willing to risk an install without running the test suite,
just do this:

perl Makefile.PL
make install


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

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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Karl O. Pinc
There are some other issues, of varying severity.


On 02/17/2014 11:54:21 AM, Karl O. Pinc wrote:

> Hi,
>
> FYI.  Got this output:
>
> [kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
> Use of uninitialized value $TESTDSN in concatenation (.) or string at
> Makefile.PL line 236.
> Use of uninitialized value $TESTDRIVER in concatenation (.) or string
> at Makefile.PL line 236.
> Usage: perl Makefile.PL [options]

<snip>

> perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
> mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h
> mydbserver
> mytestdb'

The above should be '-testrecreate' not '-mytestdbrecreate'.



However, this does not work.  The test db must be created
manually _before_ running the above.  After that it works.

But, "make test" still does not work unless
PGHOST is set to the same thing as
--testuser=<user>.

And then after that the test db must still be
manually dropped.


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Scott Cain
Ah, I hate it when people only read the first paragraph of an email :-)

I'll look at the other things, though I don't think I'll take the time to let Makefile.PL create and destroy databases on it's own, at least not this week :-)

Scott



On Mon, Feb 17, 2014 at 10:17 AM, Karl O. Pinc <[hidden email]> wrote:
There are some other issues, of varying severity.


On 02/17/2014 11:54:21 AM, Karl O. Pinc wrote:
> Hi,
>
> FYI.  Got this output:
>
> [kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
> Use of uninitialized value $TESTDSN in concatenation (.) or string at
> Makefile.PL line 236.
> Use of uninitialized value $TESTDRIVER in concatenation (.) or string
> at Makefile.PL line 236.
> Usage: perl Makefile.PL [options]

<snip>

> perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
> mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h
> mydbserver
> mytestdb'

The above should be '-testrecreate' not '-mytestdbrecreate'.



However, this does not work.  The test db must be created
manually _before_ running the above.  After that it works.

But, "make test" still does not work unless
PGHOST is set to the same thing as
--testuser=<user>.

And then after that the test db must still be
manually dropped.


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

------------------------------------------------------------------------------
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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: Bug in DBIx::DBStag Makefile.PL?

Scott Cain
Karl,

I cleaned up the doc stuff, but the rest I'm going to put off for the moment. I created an issue so that I hopefully won't forget about it:


Scott



On Mon, Feb 17, 2014 at 10:21 AM, Scott Cain <[hidden email]> wrote:
Ah, I hate it when people only read the first paragraph of an email :-)

I'll look at the other things, though I don't think I'll take the time to let Makefile.PL create and destroy databases on it's own, at least not this week :-)

Scott



On Mon, Feb 17, 2014 at 10:17 AM, Karl O. Pinc <[hidden email]> wrote:
There are some other issues, of varying severity.


On 02/17/2014 11:54:21 AM, Karl O. Pinc wrote:
> Hi,
>
> FYI.  Got this output:
>
> [kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
> Use of uninitialized value $TESTDSN in concatenation (.) or string at
> Makefile.PL line 236.
> Use of uninitialized value $TESTDRIVER in concatenation (.) or string
> at Makefile.PL line 236.
> Usage: perl Makefile.PL [options]

<snip>

> perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
> mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h
> mydbserver
> mytestdb'

The above should be '-testrecreate' not '-mytestdbrecreate'.



However, this does not work.  The test db must be created
manually _before_ running the above.  After that it works.

But, "make test" still does not work unless
PGHOST is set to the same thing as
--testuser=<user>.

And then after that the test db must still be
manually dropped.


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

------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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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: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Scott Cain
On 02/17/2014 12:21:58 PM, Scott Cain wrote:

> Ah, I hate it when people only read the first paragraph of an email
> :-)
>
> I'll look at the other things, though I don't think I'll take the
> time
> to
> let Makefile.PL create and destroy databases on it's own, at least
> not
> this
> week :-)

It should be pretty painless sh to:
  Test that test db does not exist
  Create test db before start
  Destroy test db after finish

Of course it's still more shaving yaks, but
might be worth it rather than have to
spend time documenting the oddities.


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Scott Cain
On 02/17/2014 12:29:59 PM, Scott Cain wrote:
> Karl,
>
> I cleaned up the doc stuff, but the rest I'm going to put off for the
> moment. I created an issue so that I hopefully won't forget about it:
>
>   https://github.com/cmungall/DBIx-DBStag/issues/1


No worries.


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Karl O. Pinc
On 02/17/2014 12:33:22 PM, Karl O. Pinc wrote:

> On 02/17/2014 12:21:58 PM, Scott Cain wrote:
> > Ah, I hate it when people only read the first paragraph of an email
> > :-)
> >
> > I'll look at the other things, though I don't think I'll take the
> > time
> > to
> > let Makefile.PL create and destroy databases on it's own, at least
> > not
> > this
> > week :-)
>
> It should be pretty painless sh to:
>   Test that test db does not exist
>   Create test db before start
>   Destroy test db after finish
>
> Of course it's still more shaving yaks, but
> might be worth it rather than have to
> spend time documenting the oddities.

I relish whatever I can avoid learning about
perl, but won't the cpan install always fail
if the DBStag tests fail?  Rhetorical question,
just a thought.



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

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Re: Bug in DBIx::DBStag Makefile.PL?

Scott Cain
Yes, if the DBStag tests fail, cpan won't install without a force, as in "force install DBIx::DBStag".


On Mon, Feb 17, 2014 at 10:40 AM, Karl O. Pinc <[hidden email]> wrote:
On 02/17/2014 12:33:22 PM, Karl O. Pinc wrote:
> On 02/17/2014 12:21:58 PM, Scott Cain wrote:
> > Ah, I hate it when people only read the first paragraph of an email
> > :-)
> >
> > I'll look at the other things, though I don't think I'll take the
> > time
> > to
> > let Makefile.PL create and destroy databases on it's own, at least
> > not
> > this
> > week :-)
>
> It should be pretty painless sh to:
>   Test that test db does not exist
>   Create test db before start
>   Destroy test db after finish
>
> Of course it's still more shaving yaks, but
> might be worth it rather than have to
> spend time documenting the oddities.

I relish whatever I can avoid learning about
perl, but won't the cpan install always fail
if the DBStag tests fail?  Rhetorical question,
just a thought.



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



--
------------------------------------------------------------------------
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: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Scott Cain
On 02/17/2014 12:16:50 PM, Scott Cain wrote:
> Hi Karl,
>
> I'm back at my computer, and it looks like I'm going to be spending
> the
> afternoon catching up with your emails :-)

You want me to poke porting chado from svn to git
with a stick and send the script to the list
if I can get something to work?  Or is this
something you'd rather get to yourself?

I'm accumulating bits of patches as I go
through the installation process, sorta.
It'd be nice to have a good tool to keep
track of these.


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Karl O. Pinc
In reply to this post by Scott Cain
On 02/17/2014 12:45:30 PM, Scott Cain wrote:
> Yes, if the DBStag tests fail, cpan won't install without a force, as
> in
> "force install DBIx::DBStag".

Yah.  I thought about that.  But since I don't know
what I'm doing I figured I'd be better off
digging through the errors now rather than
get some random wrong result out of chado
for an unknown reason later.


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

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Re: Bug in DBIx::DBStag Makefile.PL?

Chris Mungall
In reply to this post by Scott Cain

What's standard for test harnesses for perl modules that read/write to
rdbmss these days?

Should I just migrate DBStag to the GMOD org on github?

Of course, you should remove all dependencies on this module. AFAIK the
only place it is used is ontology loading?


On 17 Feb 2014, at 10:29, Scott Cain wrote:

> Karl,
>
> I cleaned up the doc stuff, but the rest I'm going to put off for the
> moment. I created an issue so that I hopefully won't forget about it:
>
> https://github.com/cmungall/DBIx-DBStag/issues/1
>
> Scott
>
>
>
> On Mon, Feb 17, 2014 at 10:21 AM, Scott Cain <[hidden email]>
> wrote:
>
>> Ah, I hate it when people only read the first paragraph of an email
>> :-)
>>
>> I'll look at the other things, though I don't think I'll take the
>> time to
>> let Makefile.PL create and destroy databases on it's own, at least
>> not this
>> week :-)
>>
>> Scott
>>
>>
>>
>> On Mon, Feb 17, 2014 at 10:17 AM, Karl O. Pinc <[hidden email]> wrote:
>>
>>> There are some other issues, of varying severity.
>>>
>>>
>>> On 02/17/2014 11:54:21 AM, Karl O. Pinc wrote:
>>>> Hi,
>>>>
>>>> FYI.  Got this output:
>>>>
>>>> [kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
>>>> Use of uninitialized value $TESTDSN in concatenation (.) or string
>>>> at
>>>> Makefile.PL line 236.
>>>> Use of uninitialized value $TESTDRIVER in concatenation (.) or
>>>> string
>>>> at Makefile.PL line 236.
>>>> Usage: perl Makefile.PL [options]
>>>
>>> <snip>
>>>
>>>> perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver'
>>>> -
>>>> mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h
>>>> mydbserver
>>>> mytestdb'
>>>
>>> The above should be '-testrecreate' not '-mytestdbrecreate'.
>>>
>>>
>>>
>>> However, this does not work.  The test db must be created
>>> manually _before_ running the above.  After that it works.
>>>
>>> But, "make test" still does not work unless
>>> PGHOST is set to the same thing as
>>> --testuser=<user>.
>>>
>>> And then after that the test db must still be
>>> manually dropped.
>>>
>>>
>>> Karl <[hidden email]>
>>> Free Software:  "You don't pay back, you pay forward."
>>>               -- Robert A. Heinlein
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Managing the Performance of Cloud-Based Applications
>>> Take advantage of what the Cloud has to offer - Avoid Common
>>> Pitfalls.
>>> Read the Whitepaper.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> 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
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-schema mailing list
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Re: Bug in DBIx::DBStag Makefile.PL?

Scott Cain
Hi Chris,

That's correct--DBStag is only used for ontology loading.  When a better option comes along, I'll dump it :-)

It doesn't matter much to me where it sits; I think own it on cpan, so if I need to make a new release I can.

Scott



On Mon, Feb 17, 2014 at 11:00 AM, Chris Mungall <[hidden email]> wrote:

What's standard for test harnesses for perl modules that read/write to rdbmss these days?

Should I just migrate DBStag to the GMOD org on github?

Of course, you should remove all dependencies on this module. AFAIK the only place it is used is ontology loading?



On 17 Feb 2014, at 10:29, Scott Cain wrote:

Karl,

I cleaned up the doc stuff, but the rest I'm going to put off for the
moment. I created an issue so that I hopefully won't forget about it:

https://github.com/cmungall/DBIx-DBStag/issues/1

Scott



On Mon, Feb 17, 2014 at 10:21 AM, Scott Cain <[hidden email]> wrote:

Ah, I hate it when people only read the first paragraph of an email :-)

I'll look at the other things, though I don't think I'll take the time to
let Makefile.PL create and destroy databases on it's own, at least not this
week :-)

Scott



On Mon, Feb 17, 2014 at 10:17 AM, Karl O. Pinc <[hidden email]> wrote:

There are some other issues, of varying severity.


On 02/17/2014 11:54:21 AM, Karl O. Pinc wrote:
Hi,

FYI.  Got this output:

[kop@papio DBIx-DBStag-0.12]$ perl Makefile.PL --help
Use of uninitialized value $TESTDSN in concatenation (.) or string at
Makefile.PL line 236.
Use of uninitialized value $TESTDRIVER in concatenation (.) or string
at Makefile.PL line 236.
Usage: perl Makefile.PL [options]

<snip>

perl Makefile.PL -testdsn 'dbi:Pg:dbname=mytestdb;host=mydbserver' -
mytestdbrecreate 'dropdb -h mydbserver mytestdb; createdb -h
mydbserver
mytestdb'

The above should be '-testrecreate' not '-mytestdbrecreate'.



However, this does not work.  The test db must be created
manually _before_ running the above.  After that it works.

But, "make test" still does not work unless
PGHOST is set to the same thing as
--testuser=<user>.

And then after that the test db must still be
manually dropped.


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


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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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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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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