Hi Isabelle, It could be that these additions are no longer required, depending on which adapter you are using to talk to Chado (which Ed or I should have asked in the first place). Honestly, I'm not sure how you tell --but there are two and the older one is what needed much of that "stuff" in the apollo-inserts file. Most people would probably want to be using the newer one.
Scott On Thu, Oct 2, 2008 at 5:51 PM, Isabelle Phan <[EMAIL PROTECTED]> wrote: > 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 >> > >> >> > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. [EMAIL PROTECTED] GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
