found it on http://apollo.berkeleybop.org
I've updated the GMOD page I. > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Isabelle Phan > Sent: Monday, October 06, 2008 9:37 AM > To: Ed Lee > Cc: [email protected]; Scott Cain; Gowthaman Ramasamy > Subject: RE: [apollo] saving to chado DB > > Hello Ed > > great, where is it? > > GMOD points me to sourceforge: > > http://sourceforge.net/project/showfiles.php?group_id=27707&pa ckage_id=4 > 3774 > > I can only see version 1.9.3 > > Isabelle > > > -----Original Message----- > > From: Ed Lee [mailto:[EMAIL PROTECTED] > > Sent: Monday, October 06, 2008 9:23 AM > > To: Isabelle Phan > > Cc: Scott Cain; [email protected]; Gowthaman Ramasamy > > Subject: RE: [apollo] saving to chado DB > > > > Hi Isabelle, > > > > I've cut a new release of Apollo (1.9.6) that has the updated Chado > > synonym handling code, along with some other changes as > well. Let me > > know how it works out for you. > > > > Cheers, > > Ed > > > > On Fri, 2008-10-03 at 09:13 -0700, Isabelle Phan wrote: > > > Hello Ed > > > > > > yes, I think the 'null' cv is the problem. Scott's query: > > > > > > SELECT cv.name FROM cv JOIN cvterm USING (cv_id) WHERE > > cvterm.name='synonym'; > > > > > > returns 'feature_property' on my chado database. > > > > > > many thanks for your kind help. Can't wait to test the > > updated version. > > > > > > best, > > > > > > Isabelle > > > > > > -- > > > Isabelle Phan, DPhil > > > Seattle Biomedical Research Institute > > > +1(206)256 7113 > > > > > > > > > > > > -----Original Message----- > > > From: Ed Lee [mailto:[EMAIL PROTECTED] > > > Sent: Thu 10/2/2008 6:18 PM > > > To: Isabelle Phan > > > Cc: Scott Cain; [email protected]; Gowthaman Ramasamy > > > Subject: RE: [apollo] saving to chado DB > > > > > > Hi Isabelle, > > > > > > Scott's gut feeling is probably right about Apollo needing > > the 'synonym' > > > cvterm to belong to a specific cv. For some reason, Apollo > > expects it > > > to belong to the 'null' cv (not an empty cv, but a cv > > called 'null'). > > > I'm not sure the historic reason for this decision and I'm > > guessing your > > > Chado instance has the 'synonym' cvterm that belongs to > another cv. > > > > > > Anyway, I've made modifications to the code to try to use > > the 'null' cv > > > first (as to not break expected behavior) but to fall back > > to whatever > > > other cv if it's not found. > > > > > > I'll cut a new release of Apollo with this bug fix tomorrow > > and you can > > > give it a try and let me know how it works. > > > > > > Out of curiosity, could you run the SQL query that Scott > > mentioned and > > > send the results? > > > > > > Cheers, > > > Ed > > > > > > On Thu, 2008-10-02 at 15:09 -0700, Isabelle Phan wrote: > > > > forgot to say I am still getting the error upon saving > > and I am unable > > > > to delete a synonym. > > > > > > > > What can I try next? > > > > > > > > Isabelle > > > > > > > > > -----Original Message----- > > > > > From: [EMAIL PROTECTED] > > > > > [mailto:[EMAIL PROTECTED] On Behalf Of > Isabelle Phan > > > > > Sent: Thursday, October 02, 2008 3:04 PM > > > > > To: Scott Cain > > > > > Cc: [email protected]; Gowthaman Ramasamy > > > > > Subject: RE: [apollo] saving to chado DB > > > > > > > > > > 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 > > > > > > > > > _______________________________________________ > > > > apollo mailing list > > > > [email protected] > > > > http://mail.fruitfly.org/mailman/listinfo/apollo > > > > > > > > > > > > > > > > > > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo > _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
