Hi Ed, I think Jared's instance of Apollo is misconfigured to look for an old version of Chado, no?
Scott On Tue, Jun 8, 2010 at 3:03 PM, Becksfort, Jared <jared.becksf...@stjude.org> wrote: > Ed, > > Thank you for replying. I suppose I wasn't as clear as I could have been. > The Chado schema (gmod-1.1) that I am using definitely has the cvterm table, > and I can access it from the command line and from a remote system using > PgAdmin III. It has about 36k rows in it, probably from loading ontologies > during setup. > > My guess initial guess was that it is something that I didn't do correctly in > the XML files, and this is still a possibility. I've attached it in case > anyone was curious enough to take a stab at it (search for 'pcgp'). I also > thought that perhaps Apollo was not able to use the newer version of the > Chado schema. I don't think that the schema is faulty because I have used a > lot of gmod tools to load it with data. > > My concern about the query: > SELECT cv.cvterm_id, cv.name FROM cvterm cv, cv c WHERE c.cv_id = > cv.cv_id AND c.cvname='sequence' > > Comes from when I run it using PgAdmin rather than Apollo. I get this error: > > ERROR: column c.cvname does not exist > LINE 1: ...FROM cvterm cv, cv c WHERE c.cv_id = cv.cv_id AND > c.cvname='... > ^ > ********** Error ********** > > ERROR: column c.cvname does not exist > SQL state: 42703 > Character: 80 > > My version of Chado has cv.name instead of cv.cvname (notice the table > aliases in the query). Granted, this could be the next problem that I > encounter rather than the one I am encountering now. I just wondered if they > were in the same try-catch block or whatever Java uses (not a Java guy, > sorry), then maybe the error message was giving the wrong impression. It > could be an error that is preventing DB connectivity, but in that case, I > would have expected a different error, after: > > INFO : connecting to database pcgp as user postgres at > jdbc:postgresql://ergatisvm:5432 > > Thanks for your help! > Jared > > -----Original Message----- > From: Ed Lee [mailto:e...@berkeleybop.org] > Sent: Tuesday, June 08, 2010 12:31 PM > To: Becksfort, Jared > Cc: 'apollo@fruitfly.org' > Subject: Re: [apollo] Apollo hanging at 50% > > Hi Jared, > > Sounds like your schema might be faulty somehow. "cv.cvname" comes from > an older, pre-Flybase migration build of Chado. The current schema > should have it as "cv.name". Apollo supports both schemas and it > figures out which schema to use by querying the "db" table, which > the pre-FMB version lacks. So it sounds like you're missing that > table. Also, the PostgreSQL exception is complaining about the > "cvterm" table not existing. I wouldn't expect PostgreSQL to > complain about a table not existing when it's due to a non existing > column. > > Cheers, > Ed > > On Mon, 7 Jun 2010, Becksfort, Jared wrote: > >> >> Hello, >> >> >> >> I am trying to view a Chado installation using Apollo. After I have >> selected the database to view, Apollo will start to load it but then hang at >> the 50% mark. >> >> >> >> I have installed GMOD-1.1 with all of the ontologies. >> >> >> >> Here is the relevant output in the logs: >> >> >> >> INFO : APOLLO_ROOT: >> /nfs_exports/apps/gnu-apps/ergatis/software/apollo-1.11.5/Apollo >> >> INFO : OS name: Linux >> >> INFO : OS arch: amd64 >> >> INFO : Java version: 1.6.0_15 >> >> INFO : reading config >> file/nfs_exports/apps/gnu-apps/ergatis/software/apollo-1.11.5/Apollo/conf/apoll >> o.cfg >> >> INFO : using history file /home/ergatis/.apollo/apollo.history >> >> INFO : using backup file /home/ergatis/.apollo/apollo.backup >> >> INFO : this is Apollo Genome Annotation and Curation Tool, version 1.11.5, >> last updated Mar 16 2010 >> >> INFO : connecting to database pcgp as user postgres at >> jdbc:postgresql://ergatisvm:5432 >> >> ERROR: SQLException running SELECT cv.cvterm_id, cv.name FROM cvterm cv, cv >> c WHERE c.cv_id = cv.cv_id AND c.cvname='sequence' >> >> org.postgresql.util.PSQLException: ERROR: relation "cvterm" does not exist >> >> >> >> at >> org.postgresql.util.PSQLException.parseServerError(PSQLException.java:139) >> >> >> >> I can connect to the database from the command line. I also notice that >> even if the database were properly connected, this query will fail in >> gmod-1.1 because “cvname” does not exist in the cvterm table – it should >> just be name. It makes me wonder if that is the actual error but it is >> being caught by an exception to the whole query. >> >> >> >> Any help will be appreciated. Please let me know if you need anything else >> from me. >> >> >> >> Thanks! >> >> Jared Becksfort >> >> >> ____________________________________________________________________________ >> Email Disclaimer: www.stjude.org/emaildisclaimer >> >> > > _______________________________________________ > apollo mailing list > apollo@fruitfly.org > http://mail.fruitfly.org/mailman/listinfo/apollo > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ apollo mailing list apollo@fruitfly.org http://mail.fruitfly.org/mailman/listinfo/apollo
