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
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