Hello Ed
I can now save and delete synonyms, thanks a lot for fixing this so
quickly!
However I haven't managed to fix my configuration file to log in into my
chado database without doing all sorts of convoluted actions. I'm
filling the form with my DB username and hit return.
This produces a stack strace:
INFO : checking that the database contains a sequence of type chromosome
with name=No database connection
ERROR: cannot find seq
java.lang.Throwable
at
apollo.dataadapter.chado.jdbc.JdbcChadoAdapter.validateConnectionAndSequ
ence(JdbcChadoAdapter.java:478)
at
apollo.dataadapter.chado.ChadoAdapter.getCurationSet(ChadoAdapter.java:2
34)
at
apollo.dataadapter.chado.ChadoAdapterGUI.doOperation(ChadoAdapterGUI.jav
a:298)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdap
terChooser.java:361)
at
apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:740
)
at
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterC
hooser.java:136)
at java.lang.Thread.run(Thread.java:595)
I then switch to 'gene' instead of 'chromosome' (I know it does not make
sense, but I figured out this is the only way to see my data!)
This produces another stack trace:
INFO : checking that the database contains a sequence of type gene with
name=NC_001905
ERROR: cannot find seq
etc...
If I now switch back to 'chromosome', I can log in!
This is my chado-adapter.xml configuration:
<chadodb>
<name>chado_dev</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://localhost:5432/chado_dev</url>
<dbName>chado_dev</dbName>
<dbUser>chado</dbUser>
<dbInstance>riceInstance</dbInstance>
<style>rice.style</style>
<!-- default database to use for loading and saving from -->
<!-- command line if none is specified -->
<default-command-line-db>true</default-command-line-db>
</chadodb>
What property should I set to be able to login cleanly? I've tried to
set DbPassword, but that didn't work.
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
> > >
> >
> >
> >
>
>
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