Hi Jared,
I don't think that using the FlybaseChadoInstance would give you the
pre-FMB schema I mentioned. But yes, you're better off using the
RiceChadoInstance, which will use the standard Chado install (unless
you're actually using a FB dump or derivative). You'll want to
change the <clsName> element to:
<clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
rather than
<clsName>apollo.dataadapter.chado.jdbc.RiceInstance</clsName>
(note the "Chado" in RiceChadoInstance).
Can you check that your database contains the "db" table? As
I mentioned, it's used to determine the version of Chado, as the
pre-FMB version did not contain that table.
Cheers,
Ed
On Wed, 9 Jun 2010, Becksfort, Jared wrote:
Thanks, that is helpful. I'm sorry if I'm being dense, but how should I configure it to
look for the newer version? After looking at the Apollo website, I tried changing in
"referenceInstance":
<clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
To:
<clsName>apollo.dataadapter.chado.jdbc.RiceInstance</clsName>
But this resulted in:
ERROR: ChadoAdapter.generateChadoInstance(): java.lang.ClassNotFoundException:
apollo.dataadapter.chado.jdbc.RiceInstance
Which must mean that I am entering the wrong thing here or need to get this
file.
Thanks,
Jared
-----Original Message-----
From: Scott Cain [mailto:[email protected]]
Sent: Tuesday, June 08, 2010 2:42 PM
To: Becksfort, Jared
Cc: Ed Lee; [email protected]
Subject: Re: [apollo] Apollo hanging at 50%
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
<[email protected]> 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:[email protected]]
Sent: Tuesday, June 08, 2010 12:31 PM
To: Becksfort, Jared
Cc: '[email protected]'
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
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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