Contributing to chado

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Contributing to chado

Karl O. Pinc
Hi,

What's the right way to contribute to chado?

I've already sent a patch in to this list,
should I be sending to the gmod-devel list instead?

Is there something better than svn in play?
I'm thinking something distributed so I can
track all my patches.  (The install document
says Chado hasn't been tested on PG 9+
and we're running 9.1 so....)

Thanks.


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

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Re: Contributing to chado

Siddhartha Basu
Hi Karl,
Would you be interested in migrating it to git from svn.
I would like to volunteer some of my time to do the migration. But my
git foo is not so high, so i might need some hand there.

thanks,
-sidd

On Fri, 14 Feb 2014, Karl O. Pinc wrote:

> Hi,
>
> What's the right way to contribute to chado?
>
> I've already sent a patch in to this list,
> should I be sending to the gmod-devel list instead?
>
> Is there something better than svn in play?
> I'm thinking something distributed so I can
> track all my patches.  (The install document
> says Chado hasn't been tested on PG 9+
> and we're running 9.1 so....)
>
> Thanks.
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> Android apps run on BlackBerry 10
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Re: Contributing to chado

Karl O. Pinc
On 02/14/2014 11:53:33 AM, Siddhartha Basu wrote:
> Hi Karl,
> Would you be interested in migrating it to git from svn.
> I would like to volunteer some of my time to do the migration. But my
> git foo is not so high, so i might need some hand there.

Possibly.  Where would we put it?  Github?
Github has the advantage of also supporting svn.

There's also gitlab.com and gitorious.org, both
of which, so I gather, have "better" code review
facilities.

I don't think I could be "it" to run the official
repo but might be able to do the migration.
Does gmod or chado have a organization account
on github or anywhere?


My git-fu waxes and wanes.  I prefer darcs, which is
dirt simple, but git is surely the way to go for this.


There is, by the by, a temptation to incorporate
a schema revision control system.  This might help
manage upgrades.  I hear that sqitch (http://sqitch.org/)
is "the choice" these days, but that's rumor.

See also:
http://petereisentraut.blogspot.com/2012/05/my-anti-take-on-database-
schema-version.html

Regards,

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

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Re: Contributing to chado

Siddhartha Basu
Hi Karl,

On Fri, 14 Feb 2014, Karl O. Pinc wrote:

> On 02/14/2014 11:53:33 AM, Siddhartha Basu wrote:
> > Hi Karl,
> > Would you be interested in migrating it to git from svn.
> > I would like to volunteer some of my time to do the migration. But my
> > git foo is not so high, so i might need some hand there.
>
> Possibly.  Where would we put it?  Github?
> Github has the advantage of also supporting svn.
Github should be very good to start with and definitely have a
higher visibility.

>
> There's also gitlab.com and gitorious.org, both
> of which, so I gather, have "better" code review
> facilities.
>
> I don't think I could be "it" to run the official
> repo but might be able to do the migration.
> Does gmod or chado have a organization account
> on github or anywhere?
Agreed, try this as experiment and if it works then provide a clear
migration plan.
Yes there is an github organization https://github.com/GMOD
and there is an empty chado one.
https://github.com/GMOD/Chado
I believe there  was an effort before for migration.

>
>
> My git-fu waxes and wanes.  I prefer darcs, which is
> dirt simple, but git is surely the way to go for this.
>
>
> There is, by the by, a temptation to incorporate
> a schema revision control system.  This might help
> manage upgrades.  I hear that sqitch (http://sqitch.org/)
> is "the choice" these days, but that's rumor.
>
> See also:
> http://petereisentraut.blogspot.com/2012/05/my-anti-take-on-database-
> schema-version.html
I agree that chado should have some sort schema versioning system. It
does have a folder based diffs to manage schema changes. However, i am
not aware how it works though.
With sqitch its really a coincidence indeed. At dictybase, we are
already using sqitch for schema versioning with chado. The idea is a
sane to manage our custom changes while keeping as much as in sync with
upstream chado changes. Sqitch is highly recommended.
https://github.com/dictyBase/Chado-Sqitch

thanks,
-siddhartha



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

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Re: Contributing to chado

Karl O. Pinc
On 02/15/2014 10:08:27 AM, Siddhartha Basu wrote:

> Hi Karl,
>
> On Fri, 14 Feb 2014, Karl O. Pinc wrote:
>
> > On 02/14/2014 11:53:33 AM, Siddhartha Basu wrote:
> > > Hi Karl,
> > > Would you be interested in migrating it to git from svn.
> > > I would like to volunteer some of my time to do the migration.
> But
> my
> > > git foo is not so high, so i might need some hand there.
> >
> > Possibly.  Where would we put it?  Github?
> > Github has the advantage of also supporting svn.
> Github should be very good to start with and definitely have a
> higher visibility.

> > I don't think I could be "it" to run the official
> > repo but might be able to do the migration.
> > Does gmod or chado have a organization account
> > on github or anywhere?
> Agreed, try this as experiment and if it works then provide a clear
> migration plan.
> Yes there is an github organization https://github.com/GMOD
> and there is an empty chado one.
> https://github.com/GMOD/Chado
> I believe there  was an effort before for migration.

Good.  I'll see about taking a stab at conversion
and put the result in my github account.  You (?)
can use that to make an official repo.

I'll send to the list when there's results, or not.



> I agree that chado should have some sort schema versioning system. It
> does have a folder based diffs to manage schema changes. However, i
> am
> not aware how it works though.
> With sqitch its really a coincidence indeed. At dictybase, we are
> already using sqitch for schema versioning with chado. The idea is a
> sane to manage our custom changes while keeping as much as in sync
> with
> upstream chado changes. Sqitch is highly recommended.
> https://github.com/dictyBase/Chado-Sqitch


Sounds like a separate undertaking.



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

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Re: Contributing to chado

Karl O. Pinc
On 02/15/2014 11:21:15 AM, Karl O. Pinc wrote:
> On 02/15/2014 10:08:27 AM, Siddhartha Basu wrote:
> > On Fri, 14 Feb 2014, Karl O. Pinc wrote:
> > > On 02/14/2014 11:53:33 AM, Siddhartha Basu wrote:
> > > > Hi Karl,
> > > > Would you be interested in migrating it to git from svn.


> I'll see about taking a stab at conversion
> and put the result in my github account.

Git requires names and email addresses for all the
authors.  (While there's probably a way to fake
it, git is designed around an email based workflow
and I don't know what headaches trying to fudge
this would cause.)

This means making everybody's email
addresses public, probably starting with me
posting a list of emails here in case there's corrections.

Regardless, email addresses will be in the
public git repo and available for spam harvesting,
etc.

Is there a problem with publicly posting
all the email addresses of all the chado
contributors?  If so how do you
suggest I address it?

Regards,

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

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Re: Contributing to chado

Hilmar Lapp-3

On Sat, Feb 15, 2014 at 10:38 PM, Karl O. Pinc <[hidden email]> wrote:
Git requires names and email addresses for all the
authors. [...] This means making everybody's email
addresses public, probably starting with me
posting a list of emails here in case there's corrections.
[...]
Is there a problem with publicly posting
all the email addresses of all the chado
contributors?

For one, you don't need to post them here on the list. You could also post them as a gist, for example (which would have the added benefit of allowing others to help with adding on or fixing emails).

More generally speaking, we have found this to be a complete non-issue among the Bio* projects when most of them (including the largest ones) migrated over to git (and Github) years ago. I think it's a fair assumption that people who contribute publicly to open-source projects are fine with the email they use for this being publicly retrievable.  

  -hilmar
--
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Re: Contributing to chado

Scott Cain
I'm still planning on moving Chado to git; rob and I both tried and failed once to do the migration, but I think if we work together we'll probably get it right :-)


Sent from my iPhone

On Feb 16, 2014, at 9:44 AM, Hilmar Lapp <[hidden email]> wrote:


On Sat, Feb 15, 2014 at 10:38 PM, Karl O. Pinc <[hidden email]> wrote:
Git requires names and email addresses for all the
authors. [...] This means making everybody's email
addresses public, probably starting with me
posting a list of emails here in case there's corrections.
[...]
Is there a problem with publicly posting
all the email addresses of all the chado
contributors?

For one, you don't need to post them here on the list. You could also post them as a gist, for example (which would have the added benefit of allowing others to help with adding on or fixing emails).

More generally speaking, we have found this to be a complete non-issue among the Bio* projects when most of them (including the largest ones) migrated over to git (and Github) years ago. I think it's a fair assumption that people who contribute publicly to open-source projects are fine with the email they use for this being publicly retrievable.  

  -hilmar
--
Hilmar Lapp -:- lappland.io

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Re: Contributing to chado

Karl O. Pinc
In reply to this post by Hilmar Lapp-3
On 02/16/2014 08:44:30 AM, Hilmar Lapp wrote:
> On Sat, Feb 15, 2014 at 10:38 PM, Karl O. Pinc <[hidden email]> wrote:

> For one, you don't need to post them here on the list. You could also
> post
> them as a gist, for example (which would have the added benefit of
> allowing
> others to help with adding on or fixing emails).

Yup.  Better idea.

>
> More generally speaking, we have found this to be a complete non-
> issue

Good.  (Seemed better to be safe than sorry and ask first.)

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

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Re: Contributing to chado

Karl O. Pinc
In reply to this post by Scott Cain
On 02/16/2014 11:29:49 AM, Scott Cain wrote:
> I'm still planning on moving Chado to git; rob and I both tried and
> failed once to do the migration, but I think if we work together
> we'll
> probably get it right :-)

Is it worth my taking a stab at it?



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

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Re: Contributing to chado

Fields, Christopher J
IIRC the problem with the initial test was that there were files in the history that were very large and caused problems.  Is that right Scott?

If so, might be worth trying a filter-branch to get rid of those.  It's essentially what we do for the BioPerl splits.

http://www.bioperl.org/wiki/Using_Git/Advanced#Split_a_module_from_bioperl-live

Chris

Sent from my iPad

> On Feb 16, 2014, at 12:53 PM, "Karl O. Pinc" <[hidden email]> wrote:
>
>> On 02/16/2014 11:29:49 AM, Scott Cain wrote:
>> I'm still planning on moving Chado to git; rob and I both tried and
>> failed once to do the migration, but I think if we work together
>> we'll
>> probably get it right :-)
>
> Is it worth my taking a stab at it?
>
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                 -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> Android apps run on BlackBerry 10
> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> Now with support for Jelly Bean, Bluetooth, Mapview and more.
> Get your Android app in front of a whole new audience.  Start now.
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> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Re: Contributing to chado

Scott Cain
When I tried to migrate to github (not to the GMOD/Chado repository--that's left over from Rob's attempt; I tried to migrate to a personal repository as a test), the problem I had was that the history wasn't migrated over.  The problem Rob had was that there is a directory in the history (no longer in the main trunk) that is too big to go into github.  The problematic directory had database dumps in it:

schema/trunk/chado/modules/sequence/apollo-bridge/sample_db

It can be removed when migrating.

Ideally, the git home of Chado would be in the GMOD repository that already exists.

Thanks,
Scott




On Sun, Feb 16, 2014 at 11:21 AM, Fields, Christopher J <[hidden email]> wrote:
>
> IIRC the problem with the initial test was that there were files in the history that were very large and caused problems.  Is that right Scott?
>
> If so, might be worth trying a filter-branch to get rid of those.  It's essentially what we do for the BioPerl splits.
>
> http://www.bioperl.org/wiki/Using_Git/Advanced#Split_a_module_from_bioperl-live
>
> Chris
>
> Sent from my iPad
>
> > On Feb 16, 2014, at 12:53 PM, "Karl O. Pinc" <[hidden email]> wrote:
> >
> >> On 02/16/2014 11:29:49 AM, Scott Cain wrote:
> >> I'm still planning on moving Chado to git; rob and I both tried and
> >> failed once to do the migration, but I think if we work together
> >> we'll
> >> probably get it right :-)
> >
> > Is it worth my taking a stab at it?
> >
> >
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                 -- Robert A. Heinlein
> >
> > ------------------------------------------------------------------------------
> > Android apps run on BlackBerry 10
> > Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> > Now with support for Jelly Bean, Bluetooth, Mapview and more.
> > Get your Android app in front of a whole new audience.  Start now.
> > http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema




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

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Re: Contributing to chado

Hilmar Lapp-3
Use the --ignore-paths option to git svn clone. Works well in my hands.

   -hilmar


On Mon, Feb 17, 2014 at 2:04 PM, Scott Cain <[hidden email]> wrote:
When I tried to migrate to github (not to the GMOD/Chado repository--that's left over from Rob's attempt; I tried to migrate to a personal repository as a test), the problem I had was that the history wasn't migrated over.  The problem Rob had was that there is a directory in the history (no longer in the main trunk) that is too big to go into github.  The problematic directory had database dumps in it:

schema/trunk/chado/modules/sequence/apollo-bridge/sample_db

It can be removed when migrating.

Ideally, the git home of Chado would be in the GMOD repository that already exists.

Thanks,
Scott





On Sun, Feb 16, 2014 at 11:21 AM, Fields, Christopher J <[hidden email]> wrote:
>
> IIRC the problem with the initial test was that there were files in the history that were very large and caused problems.  Is that right Scott?
>
> If so, might be worth trying a filter-branch to get rid of those.  It's essentially what we do for the BioPerl splits.
>
> http://www.bioperl.org/wiki/Using_Git/Advanced#Split_a_module_from_bioperl-live
>
> Chris
>
> Sent from my iPad
>
> > On Feb 16, 2014, at 12:53 PM, "Karl O. Pinc" <[hidden email]> wrote:
> >
> >> On 02/16/2014 11:29:49 AM, Scott Cain wrote:
> >> I'm still planning on moving Chado to git; rob and I both tried and
> >> failed once to do the migration, but I think if we work together
> >> we'll
> >> probably get it right :-)
> >
> > Is it worth my taking a stab at it?
> >
> >
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                 -- Robert A. Heinlein
> >
> > ------------------------------------------------------------------------------
> > Android apps run on BlackBerry 10
> > Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> > Now with support for Jelly Bean, Bluetooth, Mapview and more.
> > Get your Android app in front of a whole new audience.  Start now.
> > http://pubads.g.doubleclick.net/gampad/clk?id=124407151&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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Hilmar Lapp -:- lappland.io


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Re: Contributing to chado

Fields, Christopher J
Worth a shot, it would be better than scrubbing the history (though that remains an option).

chris

On Feb 17, 2014, at 1:10 PM, Hilmar Lapp <[hidden email]> wrote:

Use the --ignore-paths option to git svn clone. Works well in my hands.

   -hilmar


On Mon, Feb 17, 2014 at 2:04 PM, Scott Cain <[hidden email]> wrote:
When I tried to migrate to github (not to the GMOD/Chado repository--that's left over from Rob's attempt; I tried to migrate to a personal repository as a test), the problem I had was that the history wasn't migrated over.  The problem Rob had was that there is a directory in the history (no longer in the main trunk) that is too big to go into github.  The problematic directory had database dumps in it:

schema/trunk/chado/modules/sequence/apollo-bridge/sample_db

It can be removed when migrating.

Ideally, the git home of Chado would be in the GMOD repository that already exists.

Thanks,
Scott





On Sun, Feb 16, 2014 at 11:21 AM, Fields, Christopher J <[hidden email]> wrote:
>
> IIRC the problem with the initial test was that there were files in the history that were very large and caused problems.  Is that right Scott?
>
> If so, might be worth trying a filter-branch to get rid of those.  It's essentially what we do for the BioPerl splits.
>
> http://www.bioperl.org/wiki/Using_Git/Advanced#Split_a_module_from_bioperl-live
>
> Chris
>
> Sent from my iPad
>
> > On Feb 16, 2014, at 12:53 PM, "Karl O. Pinc" <[hidden email]> wrote:
> >
> >> On 02/16/2014 11:29:49 AM, Scott Cain wrote:
> >> I'm still planning on moving Chado to git; rob and I both tried and
> >> failed once to do the migration, but I think if we work together
> >> we'll
> >> probably get it right :-)
> >
> > Is it worth my taking a stab at it?
> >
> >
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                 -- Robert A. Heinlein
> >
> > ------------------------------------------------------------------------------
> > Android apps run on BlackBerry 10
> > Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Contributing to chado

Karl O. Pinc
In reply to this post by Hilmar Lapp-3
On 02/17/2014 01:10:54 PM, Hilmar Lapp wrote:
> Use the --ignore-paths option to git svn clone. Works well in my
> hands.

"The tool" seems to be svn2git:

https://github.com/nirvdrum/svn2git

This has useful info, including a section on
creating a good author list.  (svn2git has
a --authors AUTHORSFILE option.)

http://john.albin.net/git/convert-subversion-to-git


Karl <[hidden email]>
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Re: Contributing to chado

Hilmar Lapp-3
svn2git is a great tool, but note that really it is just a wrapper around 'git svn', the svn interface built into git (at least reasonably current versions).

We've been using svn2git a lot, with great success. For a conversion I did recently it threw an uninformative error, and so I was forced to look under the hood, i.e., at git svn. Which in the end wasn't much harder, and worked just fine.

Because svn allows you to keep committing to tags, git svn will put tags from svn under remotes/tags/<tagname> (it can't decide automatically whether a tag was in effect used as a branch). It's trivial to git tag them from there (if you know that your svn tags have been just that, namely tags), and perhaps that step is what svn2git also adds on your behalf. Just wanted to mention it in case you're caught by surprise.

   -hilmar


On Mon, Feb 17, 2014 at 4:20 PM, Karl O. Pinc <[hidden email]> wrote:
On 02/17/2014 01:10:54 PM, Hilmar Lapp wrote:
> Use the --ignore-paths option to git svn clone. Works well in my
> hands.

"The tool" seems to be svn2git:

https://github.com/nirvdrum/svn2git

This has useful info, including a section on
creating a good author list.  (svn2git has
a --authors AUTHORSFILE option.)

http://john.albin.net/git/convert-subversion-to-git


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



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