-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 per
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:
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 ('
-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 bioseqdbma
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
data
-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
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 s
-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,
Richar
-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
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 subseq
-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
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 MartBuild
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 sc
13 matches
Mail list logo
