Re: [mart-dev] MartBuilder question
Richard, I certainly did not set out with Biomart with the idea of learning more about Postgres but that seems to be what's happening. That's life. I've added a few lines to Biosql's Postgres script that allows you to create Biosql in a specified schema, and I've modified that load_taxonomy.pl script to load using a given database and schema. This all seems to work. Last step, modify bioperl-db's load_seqdatabase.pl script to do the same... BIO On 5/25/07 6:08 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > Let me know how you get on with trying to do this within a non-public > schema.
Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hmmm interesting idea. I'll certainly think about it. cheers, Richard Guðmundur Árni Þórisson wrote: > Of course, of course (silly me!). However, it may prove useful to have > MBuilder optionally produce the table-definition SQL + SQL-script to > dump out the data to textfiles, to support heterogenous db-engine > setups. The tables could then be created in the target database and > textfiles subsequently loaded. > > >Mummi > > On 24 May 2007, at 16:59, Richard Holland wrote: > > Hello. > > The quick answer is 'no'. > > The slightly longer answer is because it builds marts by executing > 'create X as select Y from Z' statements against a single database - and > so both source and target schemas need to be living in the database for > this to work. > > cheers, > Richard > > Guðmundur Árni Þórisson wrote: Richard, if I may pitch in a question: can one use MartBuilder to pull data out of say PostgreSQL and create + load into a mart in MySQL? The answer might be in the manual somewhere but I'm sure you have the quick answer! It's possible I might for my project end up having the master database in PostgreSQL (for various reasons), but then have the corresponding Mart in MySQL + read-only MyISAM tables for speed. Mummi --- Gudmundur A. Thorisson, PhD student, Brookes lab Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK E-mail: [EMAIL PROTECTED] Tel: +44 (0)116 252-3055 On 24 May 2007, at 16:34, Richard Holland wrote: The public thing is interesting. When you originally connected MartBuilder to your source schema, I'm assuming you used database=postgres and schema=bioseqdb? What target schema did you give it when you asked it to generate the SQL? Was is bioseqdbmart? Are both the bioseqdb and bioseqdbmart schemas in the same database, ie. postgres? cheers, Richard Brian Osborne wrote: >>> Richard, >>> >>> So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb >>> and the >>> mart or target is bioseqdbmart. OK, so: >>> >>> psql bioseqdbmart postgres < bioseqdbmart.sql >>> >>> might not work, I should be logged in. Let's log in... >>> >>> Hmm. I see: >>> >>> bioseqdbmart=# \i bioseqdbmart.sql >>> psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists >>> SET >>> psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not >>> exist >>> SET >>> psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does >>> not >>> exist >>> SET >>> >>> ...and more errors. >>> >>> "public.bioentry" is troubling, it should be >>> "public.bioseqdb.bioentry" or >>> "bioseqdb.bioentry", I think. That error comes from this: >>> >>> bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select >>> a.accession as >>> accession,a.biodatabase_id as biodatabase_id, >>> bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as >>> description,a.division as division,a.identifier as >>> bioseqdbmart-# identifier,a.name as name,a.taxon_id as >>> taxon_id,a.version as >>> version,b.authority as authority, >>> bioseqdbmart-# b.description as description_biodatabase,b.name as >>> name_biodatabase from public.bioentry as a left join >>> bioseqdbmart-# public.biodatabase as b on >>> a.biodatabase_id=b.biodatabase_id; >>> ERROR: relation "public.bioentry" does not exist >>> bioseqdbmart=# >>> >>> >>> Brian O. >>> >>> >>> On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: >>> run whilst logged in as the target schema owner. >>> >>> -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVurZ4C5LeMEKA/QRAu0rAJ9dtmWc0L3424M/kQUARy0uB9ZLWgCdHd+H YYHMaAxBpruQm1Nv8Q2PZz4= =+PJW -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
Richard, You may be right, but it appears that there is more than one way to solve this. Now I can build the Biosql database with a specific schema and connect to it in MartBuilder (e.g. "bioseqdb" and "biosql", no need to use the "public" schema). The mart SQL script that's created by MartBuilder works now, and I don't have to change any permissions. No data yet... BIO On 5/25/07 9:16 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > I think it might actually just boil down to permissions. Whilst logged > in as the bioseqdbmart user can you do a select against any table in the > public schema? If not, then there lies the problem.
Re: [mart-dev] MartBuilder question
Of course, of course (silly me!). However, it may prove useful to have MBuilder optionally produce the table-definition SQL + SQL- script to dump out the data to textfiles, to support heterogenous db- engine setups. The tables could then be created in the target database and textfiles subsequently loaded. Mummi On 24 May 2007, at 16:59, Richard Holland wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello. The quick answer is 'no'. The slightly longer answer is because it builds marts by executing 'create X as select Y from Z' statements against a single database - and so both source and target schemas need to be living in the database for this to work. cheers, Richard Guðmundur Árni Þórisson wrote: Richard, if I may pitch in a question: can one use MartBuilder to pull data out of say PostgreSQL and create + load into a mart in MySQL? The answer might be in the manual somewhere but I'm sure you have the quick answer! It's possible I might for my project end up having the master database in PostgreSQL (for various reasons), but then have the corresponding Mart in MySQL + read-only MyISAM tables for speed. Mummi --- Gudmundur A. Thorisson, PhD student, Brookes lab Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK E-mail: [EMAIL PROTECTED] Tel: +44 (0)116 252-3055 On 24 May 2007, at 16:34, Richard Holland wrote: The public thing is interesting. When you originally connected MartBuilder to your source schema, I'm assuming you used database=postgres and schema=bioseqdb? What target schema did you give it when you asked it to generate the SQL? Was is bioseqdbmart? Are both the bioseqdb and bioseqdbmart schemas in the same database, ie. postgres? cheers, Richard Brian Osborne wrote: Richard, So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb and the mart or target is bioseqdbmart. OK, so: psql bioseqdbmart postgres < bioseqdbmart.sql might not work, I should be logged in. Let's log in... Hmm. I see: bioseqdbmart=# \i bioseqdbmart.sql psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists SET psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not exist SET psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does not exist SET ...and more errors. "public.bioentry" is troubling, it should be "public.bioseqdb.bioentry" or "bioseqdb.bioentry", I think. That error comes from this: bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select a.accession as accession,a.biodatabase_id as biodatabase_id, bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as description,a.division as division,a.identifier as bioseqdbmart-# identifier,a.name as name,a.taxon_id as taxon_id,a.version as version,b.authority as authority, bioseqdbmart-# b.description as description_biodatabase,b.name as name_biodatabase from public.bioentry as a left join bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; ERROR: relation "public.bioentry" does not exist bioseqdbmart=# Brian O. On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: run whilst logged in as the target schema owner. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVbZe4C5LeMEKA/QRAioZAJ93gc2kLvyRHoj16iVIe+gE/bTszQCbBOYe OYGNosThAaDoIBJ7b7pd2yo= =ryuw -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I think it might actually just boil down to permissions. Whilst logged in as the bioseqdbmart user can you do a select against any table in the public schema? If not, then there lies the problem. (Certainly in Oracle permissions need to be granted on the source schema to allow the target schema owner to access it - not sure how this works in Postgres with the public schema.) cheers, Richard Brian Osborne wrote: > Richard, > > I certainly did not set out with Biomart with the idea of learning more > about Postgres but that seems to be what's happening. That's life. > > I've added a few lines to Biosql's Postgres script that allows you to create > Biosql in a specified schema, and I've modified that load_taxonomy.pl script > to load using a given database and schema. This all seems to work. Last > step, modify bioperl-db's load_seqdatabase.pl script to do the same... > > BIO > > > On 5/25/07 6:08 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > >> Let me know how you get on with trying to do this within a non-public >> schema. > > -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVuGc4C5LeMEKA/QRAt4BAJwLrr59quFd4A4YuvbW5yiHxOociQCdF884 t5mYUi29m6BT8IQAtMm2Q90= =CVSO -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
On 25 May 2007, at 11:08, Richard Holland wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
To be honest I'm not a Postgres expert. From what I understand 'public'
is some kind of special schema that shouldn't normally be used, but I
might be wrong!
'public' is just a default postgress schema. If you setup
a new database and you do not specify otherwise, your tables will
go by default to a public schema. Assuming that your source schema
is in public, it would be probably best to set target schema in MBuilder
as other than public to keep mart and source schema separated
(as we normally do anyway)
a.
Let me know how you get on with trying to do this within a non-public
schema.
cheers,
Richard
Brian Osborne wrote:
Richard,
I think I see the problem, not a surprising one. Biosql's Postgres
script
does not create a schema within the Biosql database, you're just
populating
the db with tables. Within MartBuilder you must specify a schema,
entering
database as 'bioseqdb' and schema as 'bioseqdb' does not work ('schema
connection failed'). So I tried other possibilities and 'public'
worked for
some reason. Perhaps it shouldn't have?
However, since 'public.bioentry' doesn't exist the mart is not built.
Looks
like I have to modify the Biosql Postgres script to create a schema,
not
just a database (it's based on Mysql).
BIO
On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote:
Yes, I know BioSQL well! :)
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---
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
---
Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
To be honest I'm not a Postgres expert. From what I understand 'public'
is some kind of special schema that shouldn't normally be used, but I
might be wrong!
Let me know how you get on with trying to do this within a non-public
schema.
cheers,
Richard
Brian Osborne wrote:
> Richard,
>
> I think I see the problem, not a surprising one. Biosql's Postgres script
> does not create a schema within the Biosql database, you're just populating
> the db with tables. Within MartBuilder you must specify a schema, entering
> database as 'bioseqdb' and schema as 'bioseqdb' does not work ('schema
> connection failed'). So I tried other possibilities and 'public' worked for
> some reason. Perhaps it shouldn't have?
>
> However, since 'public.bioentry' doesn't exist the mart is not built. Looks
> like I have to modify the Biosql Postgres script to create a schema, not
> just a database (it's based on Mysql).
>
>
> BIO
>
>
> On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote:
>
>> Yes, I know BioSQL well! :)
>
>
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ENmJDju5IJkaFLKbwtVkRoo=
=O74g
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Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello. The quick answer is 'no'. The slightly longer answer is because it builds marts by executing 'create X as select Y from Z' statements against a single database - and so both source and target schemas need to be living in the database for this to work. cheers, Richard Guðmundur Árni Þórisson wrote: > Richard, if I may pitch in a question: can one use MartBuilder to pull > data out of say PostgreSQL and create + load into a mart in MySQL? The > answer might be in the manual somewhere but I'm sure you have the quick > answer! >It's possible I might for my project end up having the master > database in PostgreSQL (for various reasons), but then have the > corresponding Mart in MySQL + read-only MyISAM tables for speed. > > > Mummi > > --- > Gudmundur A. Thorisson, PhD student, Brookes lab > Department of Genetics > University of Leicester > University Road > Leicester, LE1 7RH, UK > E-mail: [EMAIL PROTECTED] > Tel: +44 (0)116 252-3055 > > On 24 May 2007, at 16:34, Richard Holland wrote: > > The public thing is interesting. > > When you originally connected MartBuilder to your source schema, I'm > assuming you used database=postgres and schema=bioseqdb? > > What target schema did you give it when you asked it to generate the > SQL? Was is bioseqdbmart? > > Are both the bioseqdb and bioseqdbmart schemas in the same database, ie. > postgres? > > cheers, > Richard > > Brian Osborne wrote: Richard, So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb and the mart or target is bioseqdbmart. OK, so: psql bioseqdbmart postgres < bioseqdbmart.sql might not work, I should be logged in. Let's log in... Hmm. I see: bioseqdbmart=# \i bioseqdbmart.sql psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists SET psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not exist SET psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does not exist SET ...and more errors. "public.bioentry" is troubling, it should be "public.bioseqdb.bioentry" or "bioseqdb.bioentry", I think. That error comes from this: bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select a.accession as accession,a.biodatabase_id as biodatabase_id, bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as description,a.division as division,a.identifier as bioseqdbmart-# identifier,a.name as name,a.taxon_id as taxon_id,a.version as version,b.authority as authority, bioseqdbmart-# b.description as description_biodatabase,b.name as name_biodatabase from public.bioentry as a left join bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; ERROR: relation "public.bioentry" does not exist bioseqdbmart=# Brian O. On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > run whilst logged in as the target schema owner. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVbZe4C5LeMEKA/QRAioZAJ93gc2kLvyRHoj16iVIe+gE/bTszQCbBOYe OYGNosThAaDoIBJ7b7pd2yo= =ryuw -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
Richard, if I may pitch in a question: can one use MartBuilder to pull data out of say PostgreSQL and create + load into a mart in MySQL? The answer might be in the manual somewhere but I'm sure you have the quick answer! It's possible I might for my project end up having the master database in PostgreSQL (for various reasons), but then have the corresponding Mart in MySQL + read-only MyISAM tables for speed. Mummi --- Gudmundur A. Thorisson, PhD student, Brookes lab Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK E-mail: [EMAIL PROTECTED] Tel: +44 (0)116 252-3055 On 24 May 2007, at 16:34, Richard Holland wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The public thing is interesting. When you originally connected MartBuilder to your source schema, I'm assuming you used database=postgres and schema=bioseqdb? What target schema did you give it when you asked it to generate the SQL? Was is bioseqdbmart? Are both the bioseqdb and bioseqdbmart schemas in the same database, ie. postgres? cheers, Richard Brian Osborne wrote: Richard, So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb and the mart or target is bioseqdbmart. OK, so: psql bioseqdbmart postgres < bioseqdbmart.sql might not work, I should be logged in. Let's log in... Hmm. I see: bioseqdbmart=# \i bioseqdbmart.sql psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists SET psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not exist SET psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does not exist SET ...and more errors. "public.bioentry" is troubling, it should be "public.bioseqdb.bioentry" or "bioseqdb.bioentry", I think. That error comes from this: bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select a.accession as accession,a.biodatabase_id as biodatabase_id, bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as description,a.division as division,a.identifier as bioseqdbmart-# identifier,a.name as name,a.taxon_id as taxon_id,a.version as version,b.authority as authority, bioseqdbmart-# b.description as description_biodatabase,b.name as name_biodatabase from public.bioentry as a left join bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; ERROR: relation "public.bioentry" does not exist bioseqdbmart=# Brian O. On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: run whilst logged in as the target schema owner. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVbCJ4C5LeMEKA/QRAr1lAKCfLBi6HpDwCo1liCikscGmVxxdjQCeKljT zHNwNkyL8Y8DDVlSjGaKJeY= =6VHt -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The public thing is interesting. When you originally connected MartBuilder to your source schema, I'm assuming you used database=postgres and schema=bioseqdb? What target schema did you give it when you asked it to generate the SQL? Was is bioseqdbmart? Are both the bioseqdb and bioseqdbmart schemas in the same database, ie. postgres? cheers, Richard Brian Osborne wrote: > Richard, > > So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb and the > mart or target is bioseqdbmart. OK, so: > > psql bioseqdbmart postgres < bioseqdbmart.sql > > might not work, I should be logged in. Let's log in... > > Hmm. I see: > > bioseqdbmart=# \i bioseqdbmart.sql > psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists > SET > psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not exist > SET > psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does not > exist > SET > > ...and more errors. > > "public.bioentry" is troubling, it should be "public.bioseqdb.bioentry" or > "bioseqdb.bioentry", I think. That error comes from this: > > bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select a.accession as > accession,a.biodatabase_id as biodatabase_id, > bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as > description,a.division as division,a.identifier as > bioseqdbmart-# identifier,a.name as name,a.taxon_id as taxon_id,a.version as > version,b.authority as authority, > bioseqdbmart-# b.description as description_biodatabase,b.name as > name_biodatabase from public.bioentry as a left join > bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; > ERROR: relation "public.bioentry" does not exist > bioseqdbmart=# > > > Brian O. > > > On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > >> run whilst logged in as the target schema owner. > > -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVbCJ4C5LeMEKA/QRAr1lAKCfLBi6HpDwCo1liCikscGmVxxdjQCeKljT zHNwNkyL8Y8DDVlSjGaKJeY= =6VHt -END PGP SIGNATURE-
Re: [mart-dev] MartBuilder question
Richard,
I think I see the problem, not a surprising one. Biosql's Postgres script
does not create a schema within the Biosql database, you're just populating
the db with tables. Within MartBuilder you must specify a schema, entering
database as 'bioseqdb' and schema as 'bioseqdb' does not work ('schema
connection failed'). So I tried other possibilities and 'public' worked for
some reason. Perhaps it shouldn't have?
However, since 'public.bioentry' doesn't exist the mart is not built. Looks
like I have to modify the Biosql Postgres script to create a schema, not
just a database (it's based on Mysql).
BIO
On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote:
> Yes, I know BioSQL well! :)
Re: [mart-dev] MartBuilder question
Richard, So the SQL file's name is bioseqdbmart.sql, the source is bioseqdb and the mart or target is bioseqdbmart. OK, so: psql bioseqdbmart postgres < bioseqdbmart.sql might not work, I should be logged in. Let's log in... Hmm. I see: bioseqdbmart=# \i bioseqdbmart.sql psql:bioseqdbmart.sql:1: ERROR: schema "bioseqdbmart" already exists SET psql:bioseqdbmart.sql:6: ERROR: relation "public.bioentry" does not exist SET psql:bioseqdbmart.sql:9: ERROR: relation "bioseqdbmart.temp__1" does not exist SET ...and more errors. "public.bioentry" is troubling, it should be "public.bioseqdb.bioentry" or "bioseqdb.bioentry", I think. That error comes from this: bioseqdbmart=# create table bioseqdbmart.TEMP__1 as select a.accession as accession,a.biodatabase_id as biodatabase_id, bioseqdbmart-# a.bioentry_id as bioentry_id_key,a.description as description,a.division as division,a.identifier as bioseqdbmart-# identifier,a.name as name,a.taxon_id as taxon_id,a.version as version,b.authority as authority, bioseqdbmart-# b.description as description_biodatabase,b.name as name_biodatabase from public.bioentry as a left join bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; ERROR: relation "public.bioentry" does not exist bioseqdbmart=# Brian O. On 5/24/07 10:36 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote: > run whilst logged in as the target schema owner.
Re: [mart-dev] MartBuilder question
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello. Yes, I know BioSQL well! :) The script 'create' statements are of the form: create X as select Y from Z; These statements will therefore create tables and simultaneously populate them. In order to do this, the script requires full read permissions on the source schema, and full write permissions on the target schema, and needs to be run whilst logged in as the target schema owner. cheers, Richard Brian Osborne wrote: > mart-dev, > > I?m just starting to use BioMart 0.5, my aim is to build new marts from > various bio-schemas and see if I can contribute to the documentation. My > first target schema is Biosql (biosql.org), I?m using their latest > schema from their CVS and have created my database in Postgres and > loaded it with a small number of sequence records, ~2000. I don?t know > if you know Biosql, it?s a small-ish schema dealing with sequence, > sequence annotation, and taxonomy. There is a central bioentry table > with identifiers and descriptive information on sequences. > > My question: I?m on page 17 of the manual (nice manual, by the way) > which describes how to use MartBuilder. I?ve created an SQL script from > my Biosql database that should make a new mart but I?m a bit puzzled ? > shouldn?t this script contain data? That?s what page 17 seems to be > saying. The SQL script I?ve created has create and alter and drop > statements but not much more. I?m also having trouble executing this > script but let?s take this one step at a time... > > Thanks again, > > Brian O. > -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGVaL04C5LeMEKA/QRAuABAJ9KxlvbF3H5iQotiH5GC27QeCI/rACeJt4v 0OiuCFNL0hF2IWN7n7VQF2w= =dxRe -END PGP SIGNATURE-
