treebase-devel

[Treebase-devel] Getting started with TreeeBase development

[Vladimir G. <vga...@ne...>]

Hi everyone,

Just starting on the project, I am trying to figure out my way around,  
so here are a few disjoint questions.  Thanks for any help!


The high-priority items marked with my name in the release plan  
(google doc) are:
- TreeBase: TB1 --> TB2 import
- TreeBase: Password hashing [TB 2797430]
- TreeBase: Reviewer/Referee Access [TB 2826165]
My feeling is that the 1st of them (TB1 --> TB2 import) is the most  
pressing, but that  the other two could be easier to understand.
Which one would make the most sense to start with?

In any case, I'd need 1-on-1 help (Skype?) with someone who can show  
me the ropes as well as explain in some detail what needs to be done.  
Rutger?

So far, I have scanned through all the wiki pages accessible from the  
root.  My next step will be setting up a development environment as  
outlined on https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment 
   Can someone clarify whether I will need to set up a local DB and a  
local web server for development purposes or whether I should use  
those at treebase-dev.nescent.org ?

Do developers have application accounts, with varying privileges, for  
playing and testing?  I did auto-register for an account (vgapeyev),  
which got a "User" role.

Is there a pre-laid DB diagram somewhere, or any other documentation  
on the DB and application design and architecture?

Thanks,

--Vladimir

Re: [Treebase-devel] Getting started with TreeeBase development

[Rutger V. <rut...@gm...>]

Dear Vladimir,

thanks for taking the initiative on this, welcome aboard!

> The high-priority items marked with my name in the release plan
> (google doc) are:
> - TreeBase: TB1 --> TB2 import
> - TreeBase: Password hashing [TB 2797430]
> - TreeBase: Reviewer/Referee Access [TB 2826165]
> My feeling is that the 1st of them (TB1 --> TB2 import) is the most
> pressing, but that  the other two could be easier to understand.
> Which one would make the most sense to start with?

Either Password hashing or referee access. I know that TB1->TB2 import
might seem the most pressing on the surface, but that item is actually
only about 2009 submissions, we have all the data from preceding
years. Besides, doing the last import requires some amount of
pre-processing on the part of Bill Piel.

> In any case, I'd need 1-on-1 help (Skype?) with someone who can show
> me the ropes as well as explain in some detail what needs to be done.
> Rutger?

I'd prefer we make initial contact through gmail chat. I always have a
tab with gmail open in my browser, so you can always ping me that way
(user: rutgeraldo). If you want to hear my voice we can just take it
from there, either through google voice chat or skype or ichat.

> So far, I have scanned through all the wiki pages accessible from the
> root.  My next step will be setting up a development environment as
> outlined on https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment
>   Can someone clarify whether I will need to set up a local DB and a
> local web server for development purposes or whether I should use
> those at treebase-dev.nescent.org ?

You don't need to set up a local DB (I can give you the JDBC
connection credentials for the nescent instance off-list), but it's
probably handy if you do set up a local tomcat, either integrated in
eclipse or to launch using the publish script that we also use for
building and deploying on treebasedb-dev.nescent.org

> Do developers have application accounts, with varying privileges, for
> playing and testing?  I did auto-register for an account (vgapeyev),
> which got a "User" role.

Yes, it's handy to have one of those. You will probably want to be
able to upgrade and downgrade that account once in a while to see the
User view versus the Reviewer or Admin view.

> Is there a pre-laid DB diagram somewhere, or any other documentation
> on the DB and application design and architecture?

Not at this point. There are old ER diagrams of the schema but they
will probably be more confusing than helpful at this point, being out
of date. What you can do is install Aqua Data Studio
(http://www.aquafold.com/) and use that to create new diagrams,
explore the tables in other ways and run queries from your desktop.

Rutger

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Getting started with TreeeBase development

[Hilmar L. <hl...@ne...>]

On Dec 8, 2009, at 4:44 AM, Rutger Vos wrote:

>> The high-priority items marked with my name in the release plan
>> (google doc) are:
>> - TreeBase: TB1 --> TB2 import
>> - TreeBase: Password hashing [TB 2797430]
>> - TreeBase: Reviewer/Referee Access [TB 2826165]
>> My feeling is that the 1st of them (TB1 --> TB2 import) is the most
>> pressing, but that  the other two could be easier to understand.
>> Which one would make the most sense to start with?
>
> Either Password hashing or referee access. I know that TB1->TB2 import
> might seem the most pressing on the surface


It sounds to me like password hashing and reviewer access are best for  
getting your feet (hands?) wet with the code.

We do need a dated plan for the TB1->TB2 data import though, as that's  
I think what will determine when we can go public. Also, my sense is  
that there are unknown factors in that (untested scripts and Java code  
that used to need a lot of post-migration massaging), so the sooner we  
can shed light on that the more confident we can be. Does that sound  
right?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Getting started with TreeeBase development

[youjun g. <you...@ya...>]

Welcome on board Vladimir,

Rutger, I am going through the source code, and will have time working on
the debugging of the TreeBASE code. The question is, do we need to build and
re-deploy the war file to the production server every time we fix a bug?

Youjun

On Tue, Dec 8, 2009 at 4:44 AM, Rutger Vos <rut...@gm...> wrote:

> Dear Vladimir,
>
> thanks for taking the initiative on this, welcome aboard!
>
> > The high-priority items marked with my name in the release plan
> > (google doc) are:
> > - TreeBase: TB1 --> TB2 import
> > - TreeBase: Password hashing [TB 2797430]
> > - TreeBase: Reviewer/Referee Access [TB 2826165]
> > My feeling is that the 1st of them (TB1 --> TB2 import) is the most
> > pressing, but that  the other two could be easier to understand.
> > Which one would make the most sense to start with?
>
> Either Password hashing or referee access. I know that TB1->TB2 import
> might seem the most pressing on the surface, but that item is actually
> only about 2009 submissions, we have all the data from preceding
> years. Besides, doing the last import requires some amount of
> pre-processing on the part of Bill Piel.
>
> > In any case, I'd need 1-on-1 help (Skype?) with someone who can show
> > me the ropes as well as explain in some detail what needs to be done.
> > Rutger?
>
> I'd prefer we make initial contact through gmail chat. I always have a
> tab with gmail open in my browser, so you can always ping me that way
> (user: rutgeraldo). If you want to hear my voice we can just take it
> from there, either through google voice chat or skype or ichat.
>
> > So far, I have scanned through all the wiki pages accessible from the
> > root.  My next step will be setting up a development environment as
> > outlined on
> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment
> >   Can someone clarify whether I will need to set up a local DB and a
> > local web server for development purposes or whether I should use
> > those at treebase-dev.nescent.org ?
>
> You don't need to set up a local DB (I can give you the JDBC
> connection credentials for the nescent instance off-list), but it's
> probably handy if you do set up a local tomcat, either integrated in
> eclipse or to launch using the publish script that we also use for
> building and deploying on treebasedb-dev.nescent.org
>
> > Do developers have application accounts, with varying privileges, for
> > playing and testing?  I did auto-register for an account (vgapeyev),
> > which got a "User" role.
>
> Yes, it's handy to have one of those. You will probably want to be
> able to upgrade and downgrade that account once in a while to see the
> User view versus the Reviewer or Admin view.
>
> > Is there a pre-laid DB diagram somewhere, or any other documentation
> > on the DB and application design and architecture?
>
> Not at this point. There are old ER diagrams of the schema but they
> will probably be more confusing than helpful at this point, being out
> of date. What you can do is install Aqua Data Studio
> (http://www.aquafold.com/) and use that to create new diagrams,
> explore the tables in other ways and run queries from your desktop.
>
> Rutger
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
>
> ------------------------------------------------------------------------------
> Return on Information:
> Google Enterprise Search pays you back
> Get the facts.
> http://p.sf.net/sfu/google-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>

Re: [Treebase-devel] Getting started with TreeeBase development

[Rutger V. <rut...@gm...>]

> Rutger, I am going through the source code, and will have time working on
> the debugging of the TreeBASE code. The question is, do we need to build and
> re-deploy the war file to the production server every time we fix a bug?

In principle that would be handy, so that others can see the
improvement right away when a ticket is closed. It's not that hard to
do though: when you ssh into treebasedb-dev.nescent.org all you have
to do is issue 'publish' on the command line (it's in the $PATH) and
it'll update the source, build the war, copy it into the tomcat
servlet folder and restart tomcat.

> On Tue, Dec 8, 2009 at 4:44 AM, Rutger Vos <rut...@gm...> wrote:
>>
>> Dear Vladimir,
>>
>> thanks for taking the initiative on this, welcome aboard!
>>
>> > The high-priority items marked with my name in the release plan
>> > (google doc) are:
>> > - TreeBase: TB1 --> TB2 import
>> > - TreeBase: Password hashing [TB 2797430]
>> > - TreeBase: Reviewer/Referee Access [TB 2826165]
>> > My feeling is that the 1st of them (TB1 --> TB2 import) is the most
>> > pressing, but that  the other two could be easier to understand.
>> > Which one would make the most sense to start with?
>>
>> Either Password hashing or referee access. I know that TB1->TB2 import
>> might seem the most pressing on the surface, but that item is actually
>> only about 2009 submissions, we have all the data from preceding
>> years. Besides, doing the last import requires some amount of
>> pre-processing on the part of Bill Piel.
>>
>> > In any case, I'd need 1-on-1 help (Skype?) with someone who can show
>> > me the ropes as well as explain in some detail what needs to be done.
>> > Rutger?
>>
>> I'd prefer we make initial contact through gmail chat. I always have a
>> tab with gmail open in my browser, so you can always ping me that way
>> (user: rutgeraldo). If you want to hear my voice we can just take it
>> from there, either through google voice chat or skype or ichat.
>>
>> > So far, I have scanned through all the wiki pages accessible from the
>> > root.  My next step will be setting up a development environment as
>> > outlined on
>> > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment
>> >   Can someone clarify whether I will need to set up a local DB and a
>> > local web server for development purposes or whether I should use
>> > those at treebase-dev.nescent.org ?
>>
>> You don't need to set up a local DB (I can give you the JDBC
>> connection credentials for the nescent instance off-list), but it's
>> probably handy if you do set up a local tomcat, either integrated in
>> eclipse or to launch using the publish script that we also use for
>> building and deploying on treebasedb-dev.nescent.org
>>
>> > Do developers have application accounts, with varying privileges, for
>> > playing and testing?  I did auto-register for an account (vgapeyev),
>> > which got a "User" role.
>>
>> Yes, it's handy to have one of those. You will probably want to be
>> able to upgrade and downgrade that account once in a while to see the
>> User view versus the Reviewer or Admin view.
>>
>> > Is there a pre-laid DB diagram somewhere, or any other documentation
>> > on the DB and application design and architecture?
>>
>> Not at this point. There are old ER diagrams of the schema but they
>> will probably be more confusing than helpful at this point, being out
>> of date. What you can do is install Aqua Data Studio
>> (http://www.aquafold.com/) and use that to create new diagrams,
>> explore the tables in other ways and run queries from your desktop.
>>
>> Rutger
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>> ------------------------------------------------------------------------------
>> Return on Information:
>> Google Enterprise Search pays you back
>> Get the facts.
>> http://p.sf.net/sfu/google-dev2dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Getting started with TreeeBase development

[Hilmar L. <hl...@ne...>]

On Dec 8, 2009, at 10:08 AM, Rutger Vos wrote:

> all you have to do is issue 'publish' on the command line


Can we name that publish-treebase instead please? :-)

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Getting started with TreeeBase development

[youjun g. <you...@ya...>]

That's great.

Based my understand, correct me if I am wrong, the "publish" script will:

1. download the new version of the source code form sourceforge;
2. build the war
3. re-deploy

Youjun

On Tue, Dec 8, 2009 at 10:08 AM, Rutger Vos <rut...@gm...> wrote:

> > Rutger, I am going through the source code, and will have time working on
> > the debugging of the TreeBASE code. The question is, do we need to build
> and
> > re-deploy the war file to the production server every time we fix a bug?
>
> In principle that would be handy, so that others can see the
> improvement right away when a ticket is closed. It's not that hard to
> do though: when you ssh into treebasedb-dev.nescent.org all you have
> to do is issue 'publish' on the command line (it's in the $PATH) and
> it'll update the source, build the war, copy it into the tomcat
> servlet folder and restart tomcat.
>
> > On Tue, Dec 8, 2009 at 4:44 AM, Rutger Vos <rut...@gm...> wrote:
> >>
> >> Dear Vladimir,
> >>
> >> thanks for taking the initiative on this, welcome aboard!
> >>
> >> > The high-priority items marked with my name in the release plan
> >> > (google doc) are:
> >> > - TreeBase: TB1 --> TB2 import
> >> > - TreeBase: Password hashing [TB 2797430]
> >> > - TreeBase: Reviewer/Referee Access [TB 2826165]
> >> > My feeling is that the 1st of them (TB1 --> TB2 import) is the most
> >> > pressing, but that  the other two could be easier to understand.
> >> > Which one would make the most sense to start with?
> >>
> >> Either Password hashing or referee access. I know that TB1->TB2 import
> >> might seem the most pressing on the surface, but that item is actually
> >> only about 2009 submissions, we have all the data from preceding
> >> years. Besides, doing the last import requires some amount of
> >> pre-processing on the part of Bill Piel.
> >>
> >> > In any case, I'd need 1-on-1 help (Skype?) with someone who can show
> >> > me the ropes as well as explain in some detail what needs to be done.
> >> > Rutger?
> >>
> >> I'd prefer we make initial contact through gmail chat. I always have a
> >> tab with gmail open in my browser, so you can always ping me that way
> >> (user: rutgeraldo). If you want to hear my voice we can just take it
> >> from there, either through google voice chat or skype or ichat.
> >>
> >> > So far, I have scanned through all the wiki pages accessible from the
> >> > root.  My next step will be setting up a development environment as
> >> > outlined on
> >> >
> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment
> >> >   Can someone clarify whether I will need to set up a local DB and a
> >> > local web server for development purposes or whether I should use
> >> > those at treebase-dev.nescent.org ?
> >>
> >> You don't need to set up a local DB (I can give you the JDBC
> >> connection credentials for the nescent instance off-list), but it's
> >> probably handy if you do set up a local tomcat, either integrated in
> >> eclipse or to launch using the publish script that we also use for
> >> building and deploying on treebasedb-dev.nescent.org
> >>
> >> > Do developers have application accounts, with varying privileges, for
> >> > playing and testing?  I did auto-register for an account (vgapeyev),
> >> > which got a "User" role.
> >>
> >> Yes, it's handy to have one of those. You will probably want to be
> >> able to upgrade and downgrade that account once in a while to see the
> >> User view versus the Reviewer or Admin view.
> >>
> >> > Is there a pre-laid DB diagram somewhere, or any other documentation
> >> > on the DB and application design and architecture?
> >>
> >> Not at this point. There are old ER diagrams of the schema but they
> >> will probably be more confusing than helpful at this point, being out
> >> of date. What you can do is install Aqua Data Studio
> >> (http://www.aquafold.com/) and use that to create new diagrams,
> >> explore the tables in other ways and run queries from your desktop.
> >>
> >> Rutger
> >>
> >> --
> >> Dr. Rutger A. Vos
> >> School of Biological Sciences
> >> Philip Lyle Building, Level 4
> >> University of Reading
> >> Reading
> >> RG6 6BX
> >> United Kingdom
> >> Tel: +44 (0) 118 378 7535
> >> http://www.nexml.org
> >> http://rutgervos.blogspot.com
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Return on Information:
> >> Google Enterprise Search pays you back
> >> Get the facts.
> >> http://p.sf.net/sfu/google-dev2dev
> >> _______________________________________________
> >> Treebase-devel mailing list
> >> Tre...@li...
> >> https://lists.sourceforge.net/lists/listinfo/treebase-devel
> >
> >
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>

Re: [Treebase-devel] Getting started with TreeeBase development

[Rutger V. <rut...@gm...>]

Yup, that is exactly what it does.

On Tue, Dec 8, 2009 at 3:36 PM, youjun guo <you...@ya...> wrote:
> That's great.
>
> Based my understand, correct me if I am wrong, the "publish" script will:
>
> 1. download the new version of the source code form sourceforge;
> 2. build the war
> 3. re-deploy
>
> Youjun
>
> On Tue, Dec 8, 2009 at 10:08 AM, Rutger Vos <rut...@gm...> wrote:
>>
>> > Rutger, I am going through the source code, and will have time working
>> > on
>> > the debugging of the TreeBASE code. The question is, do we need to build
>> > and
>> > re-deploy the war file to the production server every time we fix a bug?
>>
>> In principle that would be handy, so that others can see the
>> improvement right away when a ticket is closed. It's not that hard to
>> do though: when you ssh into treebasedb-dev.nescent.org all you have
>> to do is issue 'publish' on the command line (it's in the $PATH) and
>> it'll update the source, build the war, copy it into the tomcat
>> servlet folder and restart tomcat.
>>
>> > On Tue, Dec 8, 2009 at 4:44 AM, Rutger Vos <rut...@gm...> wrote:
>> >>
>> >> Dear Vladimir,
>> >>
>> >> thanks for taking the initiative on this, welcome aboard!
>> >>
>> >> > The high-priority items marked with my name in the release plan
>> >> > (google doc) are:
>> >> > - TreeBase: TB1 --> TB2 import
>> >> > - TreeBase: Password hashing [TB 2797430]
>> >> > - TreeBase: Reviewer/Referee Access [TB 2826165]
>> >> > My feeling is that the 1st of them (TB1 --> TB2 import) is the most
>> >> > pressing, but that  the other two could be easier to understand.
>> >> > Which one would make the most sense to start with?
>> >>
>> >> Either Password hashing or referee access. I know that TB1->TB2 import
>> >> might seem the most pressing on the surface, but that item is actually
>> >> only about 2009 submissions, we have all the data from preceding
>> >> years. Besides, doing the last import requires some amount of
>> >> pre-processing on the part of Bill Piel.
>> >>
>> >> > In any case, I'd need 1-on-1 help (Skype?) with someone who can show
>> >> > me the ropes as well as explain in some detail what needs to be done.
>> >> > Rutger?
>> >>
>> >> I'd prefer we make initial contact through gmail chat. I always have a
>> >> tab with gmail open in my browser, so you can always ping me that way
>> >> (user: rutgeraldo). If you want to hear my voice we can just take it
>> >> from there, either through google voice chat or skype or ichat.
>> >>
>> >> > So far, I have scanned through all the wiki pages accessible from the
>> >> > root.  My next step will be setting up a development environment as
>> >> > outlined on
>> >> >
>> >> > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment
>> >> >   Can someone clarify whether I will need to set up a local DB and a
>> >> > local web server for development purposes or whether I should use
>> >> > those at treebase-dev.nescent.org ?
>> >>
>> >> You don't need to set up a local DB (I can give you the JDBC
>> >> connection credentials for the nescent instance off-list), but it's
>> >> probably handy if you do set up a local tomcat, either integrated in
>> >> eclipse or to launch using the publish script that we also use for
>> >> building and deploying on treebasedb-dev.nescent.org
>> >>
>> >> > Do developers have application accounts, with varying privileges, for
>> >> > playing and testing?  I did auto-register for an account (vgapeyev),
>> >> > which got a "User" role.
>> >>
>> >> Yes, it's handy to have one of those. You will probably want to be
>> >> able to upgrade and downgrade that account once in a while to see the
>> >> User view versus the Reviewer or Admin view.
>> >>
>> >> > Is there a pre-laid DB diagram somewhere, or any other documentation
>> >> > on the DB and application design and architecture?
>> >>
>> >> Not at this point. There are old ER diagrams of the schema but they
>> >> will probably be more confusing than helpful at this point, being out
>> >> of date. What you can do is install Aqua Data Studio
>> >> (http://www.aquafold.com/) and use that to create new diagrams,
>> >> explore the tables in other ways and run queries from your desktop.
>> >>
>> >> Rutger
>> >>
>> >> --
>> >> Dr. Rutger A. Vos
>> >> School of Biological Sciences
>> >> Philip Lyle Building, Level 4
>> >> University of Reading
>> >> Reading
>> >> RG6 6BX
>> >> United Kingdom
>> >> Tel: +44 (0) 118 378 7535
>> >> http://www.nexml.org
>> >> http://rutgervos.blogspot.com
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Return on Information:
>> >> Google Enterprise Search pays you back
>> >> Get the facts.
>> >> http://p.sf.net/sfu/google-dev2dev
>> >> _______________________________________________
>> >> Treebase-devel mailing list
>> >> Tre...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>> >
>> >
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading
>> RG6 6BX
>> United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Getting started with TreeeBase development

[Vladimir G. <vga...@ne...>]

On Dec 8, 2009, at 10:08 AM, Rutger Vos wrote:

>> Rutger, I am going through the source code, and will have time  
>> working on
>> the debugging of the TreeBASE code. The question is, do we need to  
>> build and
>> re-deploy the war file to the production server every time we fix a  
>> bug?
>
> In principle that would be handy, so that others can see the
> improvement right away when a ticket is closed. It's not that hard to
> do though: when you ssh into treebasedb-dev.nescent.org all you have
> to do is issue 'publish' on the command line (it's in the $PATH) and
> it'll update the source, build the war, copy it into the tomcat
> servlet folder and restart tomcat.

Rutger, I don't get this yet.  The treebase@treebase-dev account (for  
which I've got the credentials from Jon) does not seem to have any  
setup like this.  Setting up each of our treebase-dev accounts like  
this would be duplication of effort (I am doing that on my Mac  
already). I suspect you had in mind ssh'ing to rvosa@treebase-dev....
--VG

Re: [Treebase-devel] Getting started with TreeeBase development

[Rutger V. <rut...@gm...>]

> Rutger, I don't get this yet.  The treebase@treebase-dev account (for
> which I've got the credentials from Jon) does not seem to have any
> setup like this.  Setting up each of our treebase-dev accounts like
> this would be duplication of effort (I am doing that on my Mac
> already). I suspect you had in mind ssh'ing to rvosa@treebase-dev....

Yeah, I had that in mind. Not ideal because it's tied to my name, but
it'd be easiest for us if we come up with a way for us to share that
setup.

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Getting started with TreeeBase development

[Hilmar L. <hl...@ne...>]

On Dec 8, 2009, at 11:33 AM, Rutger Vos wrote:

> it'd be easiest for us if we come up with a way for us to share that
> setup.

A treebase-env.sh shell script maybe that's somewhere under /etc? Or  
a /home/treebase/treebase-env.sh script?

There's surely ways to do this according to best practices. Jon, do  
you want to advise from sysadmin point here?

	-hilmar

-- 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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Re: [Treebase-devel] Getting started with TreeeBase development

[William P. <wil...@ya...>]

On Dec 8, 2009, at 4:44 AM, Rutger Vos wrote:

> Either Password hashing or referee access.

Either of these would be great. If the latter, let's chat because I'd like to develop a clearer sense of how that will be implemented. 

> Besides, doing the last import requires some amount of pre-processing on the part of Bill Piel.

I've started working on the pre-processing. Since Jan 09, TreeBASE has acquired about 30,000 distinct taxon labels that it hasn't seen before. So the good news is that submissions to TreeBASE have proceeded at a healthy pace. The bad news is that I have to map 30,000 names against uBio -- a procedure that has scripts to assist me, but that still requires inspection of every mapping. So, it will take some time -- hence better for you to start with the password hashing or referee access.

Bill

Re: [Treebase-devel] Getting started with TreeeBase development

[Hilmar L. <hl...@ne...>]

On Dec 8, 2009, at 6:28 PM, William Piel wrote:

> The bad news is that I have to map 30,000 names against uBio -- a  
> procedure that has scripts to assist me, but that still requires  
> inspection of every mapping. So, it will take some time


Bill - do you have a ballpark estimate? It sounds like this has the  
potential to be the rate-limiting factor for pinning down a release  
target date. Is there room for further automation with additional  
scripting? Should we look into possibilities for hiring some help for  
this curation activity? Is there a way we can harness the TB2  
machinery for taxon name resolution?

	-hilmar
-- 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Getting started with TreeeBase development

[William P. <wil...@ya...>]

On Dec 8, 2009, at 8:01 PM, Hilmar Lapp wrote:

> Bill - do you have a ballpark estimate?

That's hard to do -- but I don't think I'll be holding anything up if Vladimir is going to first tackle these one or two other issues first.

> Is there room for further automation with additional  scripting?

I don't think so. 

> Should we look into possibilities for hiring some help for  this curation activity?

I have workers I can solicit if needed -- but seeing as I'm in Santa Barbara this week, that's not realistic. 

Rather, this will just be my evening entertainment... 

bp