[Bioperl-l] Biosql documentation request

[Hilmar Lapp]

The kudos w.r.t. to the INSTALL document should go to Ewan who I 
believe wrote (and tested) that heroically during the Singapore 
hackathon.

Great though that it proved useful.

	-hilmar

On Jun 4, 2004, at 6:15 PM, Brian Osborne wrote:

> Hilmar,
>
> I went ahead and installed postgres as well as the biosql schema when I
> found out that Cygwin would install postgres. Kudos to you: the 
> installation
> of postgres, postgres initialization, and biosql database creation took
> about 10 minutes and I've never used postgres before. I was basically
> following the INSTALL instructions. The new biosql.html has been 
> commited.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: Friday, June 04, 2004 2:16 PM
> To: Brian Osborne
> Cc: Hilmar Lapp; BioPerl; Biosql
> Subject: Re: [Bioperl-l] Biosql documentation request
>
> It pretty much is the latest. Amazing, isn't it? The schema is *very*
> stable.
>
> There are a few additions in the Oracle version which aren't really
> officially blessed yet (meaning, they're not in the MySQL/Pg versions
> but will be soon), and none of which breaks backwards compatibility.
>
> I'll try and see whether I can get postgres_autodoc installed over the
> weekend.
>
> Or maybe somebody on the biosql list has this setup already?
>
>         -hilmar
>
> On Jun 4, 2004, at 4:38 AM, Brian Osborne wrote:
>
>> Hilmar,
>>
>> Neither does the ERD show nullability. The ERD is good but some useful
>> information is missing, yes.
>>
>> The ERD is dated 6/4/2003, is this the latest version? Pardon my
>> ignorance.
>>
>> Brian O.
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
>> Sent: Friday, June 04, 2004 2:20 AM
>> To: Brian Osborne
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Biosql documentation request
>>
>> Brian, if I understand the output correctly it only documents the
>> schema elements. Do you feel that the ERD (doc/biosql-ERD.pdf) does 
>> not
>> fulfill this purpose well enough?
>>
>> The ERD diagram actually doesn't show the unique key constraints, so
>> that would be a difference indeed.
>>
>>         -hilmar
>>
>> On Thursday, June 3, 2004, at 05:56  AM, Brian Osborne wrote:
>>
>>> Bioperl-l,
>>>
>>> Dave Howorth has provided a detailed critique of the 
>>> bioperl-db/biosql
>>> documentation which I'm working through. One thing that he noticed 
>>> was
>>> that
>>> the Biosql file doc/biosql.html was out-of-date. This file was 
>>> created
>>> by
>>> running a script called postgres_autodoc.pl on a Postgres instance of
>>> the
>>> biosql schema. Can anyone provide me with a current version of this
>>> file? I
>>> run biosql on Mysql myself and I haven't found a script or utility
>>> equivalent to postgres_autodoc.pl. postgres_autodoc.pl is available 
>>> at
>>> http://www.rbt.ca/autodoc/.
>>>
>>> Brian O.
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------