I am using apollo.dataadapter.chado.jdbc.PostgresChadoAdapter Isabelle
> -----Original Message----- > From: Scott Cain [mailto:[EMAIL PROTECTED] > Sent: Thursday, October 02, 2008 3:01 PM > To: Isabelle Phan > Cc: Ed Lee; [email protected]; Gowthaman Ramasamy > Subject: Re: [apollo] saving to chado DB > > 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
