Hello Ed and Scott,
first I discovered:
http://gmod.org/wiki/Apollo-Chado
perhaps this link could be added to the Apollo documentation?
So I added the cv terms, but apollo-inserts (.sql??) fails:
ERROR: null value in column "cv_id" violates not-null constraint
-> this is caused by bug in SQL statement:
insert into cvterm (name, cv_id, dbxref_id, is_relationshiptype) values
('producedby',(select cv_id from cv where name='Relationship
Ontology'),(select dbxref_id from dbxref where accession = 'Relationship
Ontology:producedby'),1);
I kind of guess it should be:
....select cv_id from cv where name='relationship'...
NOTICE: CREATE TABLE will create implicit sequence
"feature_namegenerator_feature_namegenerator_id_seq" for serial column
"feature_namegenerator.feature_namegenerator_id"
NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index
"feature_namegenerator_pkey" for table "feature_namegenerator"
CREATE TABLE
INSERT 0 0
INSERT 0 0
ERROR: aggregates not allowed in WHERE clause
These statements are invalid:
INSERT INTO feature_namegenerator (name,type_id,count)
SELECT substr(name, 0 , (position('-' in name))),
(select cvterm_id from cvterm where cv_id=7 and
name='transcript'),
to_number(max(substring(name from 21)), '99999')
FROM feature WHERE name like 'RICE%-transcript%' group by name;
INSERT INTO feature_namegenerator (name,type_id,count)
SELECT substr(name, 0 , (position('-' in name))),
(select cvterm_id from cvterm where cv_id=14 and name='protein'),
to_number(max(substring(name from 19)), '99999')
FROM feature WHERE name like 'RICE%-protein%' group by name;
I am not sure what the correct statements should be, apart that the
cvterm_id is null and so even if the SQL syntax was correct, the inserts
would fail.
any hints?
Isabelle
> -----Original Message-----
> From: Ed Lee [mailto:[EMAIL PROTECTED]
> Sent: Thursday, October 02, 2008 1:25 PM
> To: Isabelle Phan
> Cc: [email protected]; Gowthaman Ramasamy
> Subject: Re: [apollo] saving to chado DB
>
> Hi Isabelle,
>
> I'll take a look at the mentioned issues. Unfortunately SourceForge's
> CVS is down (again...) so I'll need for it to come back up
> before I can
> commit any changes. I'll let you know what I find.
>
> Cheers,
> Ed
>
> On Thu, 2008-10-02 at 12:29 -0700, Isabelle Phan wrote:
> > Hello
> >
> > I am running Apollo 1.9.5 on a chado database and having
> trouble editing
> > data with the Annotation editor:
> >
> > 1) add synonym to gene name seems to work, data is saved in tables
> > feature_synonym and synonym in but error logs returns:
> > lookup failed for cvterm_id for cvterm with name ='synonym'
> > database has no 'synonym' cvterm;
> >
> > I checked that an entry exists in table cvterm with name = 'synonym'
> > (cvterm_id=28874), so I don't quite understand that message.
> >
> > 2) delete synonym from gene name fails. The interface shows no error
> > upon saving, but the records are still there in feature_synonym and
> > synonym, and the error logs show the same messages as above
> after the
> > DELETE statement.
> >
> >
> >
> > Isabelle
> > _______________________________________________
> > apollo mailing list
> > [email protected]
> > http://mail.fruitfly.org/mailman/listinfo/apollo
> >
>
>
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