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
>
>
> ____________________________________________________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer
>
>
<?xml version="1.0" encoding="UTF-8"?>
<!-- This file is used to config chado database adapter -->
<chado-adapter>
<chadoInstance id="referenceInstance" default="true">
<writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemplateFile>
<featureCV>sequence</featureCV>
<polypeptideType>polypeptide</polypeptideType>
<relationshipCV>relationship</relationshipCV>
<propertyTypeCV>feature_property</propertyTypeCV>
<!-- default is part_of -->
<partOfCvTerm>part_of</partOfCvTerm>
<transProtRelationTerm>derives_from</transProtRelationTerm>
<searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
<clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
<oneLevelAnnotTypes>
<type>promoter</type>
<type>insertion site</type>
<type>transposable_element</type>
<type>transposable_element_insertion_site</type>
<type>remark</type>
<type>repeat_region</type>
</oneLevelAnnotTypes>
<threeLevelAnnotTypes>
<type>gene</type>
<type>pseudogene</type>
<type>tRNA</type>
<type>snRNA</type>
<type>snoRNA</type>
<type>ncRNA</type>
<type>rRNA</type>
<type>miRNA</type>
</threeLevelAnnotTypes>
</chadoInstance>
<chadoInstance id="riceInstance" default="true">
<inheritsInstance>referenceInstance</inheritsInstance>
<partOfCvTerm>part_of</partOfCvTerm>
<inheritsInstance>referenceInstance</inheritsInstance>
<featureCV>sequence</featureCV>
<relationshipCV>relationship</relationshipCV>
<propertyTypeCV>feature_property</propertyTypeCV>
<writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile>
<sequenceTypes>
<type>gene</type>
<!-- bacs are not in rice yet <type>BAC</type> -->
<!-- useStartAndEnd specifies this is a range so that different GUI
can be used, queryForValue -> query db for chroms/seqIds -->
<type>
<name>chromosome</name>
<useStartAndEnd>true</useStartAndEnd>
<queryForValueList>true</queryForValueList>
<isTopLevel>true</isTopLevel>
</type>
</sequenceTypes>
<genePredictionPrograms>
<program>FgenesH</program>
</genePredictionPrograms>
<searchHitPrograms>
<program>blat</program>
</searchHitPrograms>
<searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
<clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
<oneLevelAnnotTypes>
<type>promoter</type>
<type>transposable_element</type>
<type>remark</type>
<type>repeat_region</type>
</oneLevelAnnotTypes>
<threeLevelAnnotTypes>
<type>gene</type>
<type>pseudogene</type>
<type>tRNA</type>
<type>snRNA</type>
<type>snoRNA</type>
<type>ncRNA</type>
<type>rRNA</type>
<type>miRNA</type>
</threeLevelAnnotTypes>
</chadoInstance>
<chadoInstance id="riceInstance-no-hits">
<genePredictionPrograms>
<program>FgenesH</program>
</genePredictionPrograms>
<searchHitPrograms>
</searchHitPrograms>
<searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
<clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
<oneLevelAnnotTypes>
<type>promoter</type>
<type>transposable_element</type>
<type>remark</type>
<type>repeat_region</type>
</oneLevelAnnotTypes>
<threeLevelAnnotTypes>
<type>gene</type>
<type>pseudogene</type>
<type>tRNA</type>
<type>snRNA</type>
<type>snoRNA</type>
<type>ncRNA</type>
<type>rRNA</type>
<type>miRNA</type>
</threeLevelAnnotTypes>
</chadoInstance>
<chadoInstance id="ricePure">
<inheritsInstance>riceInstance</inheritsInstance>
<pureJDBCWriteMode>true</pureJDBCWriteMode>
<pureJDBCCopyOnWrite>false</pureJDBCCopyOnWrite>
<pureJDBCNoCommit>false</pureJDBCNoCommit>
<!-- logDirectory>/Users/mgibson/.apollo</logDirectory -->
<queryFeatureIdWithUniquename>true</queryFeatureIdWithUniquename>
<queryFeatureIdWithName>true</queryFeatureIdWithName>
</chadoInstance>
<chadodb>
<name>PCGP</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://ergatisvm:5432</url>
<dbName>pcgp</dbName>
<dbUser>postgres</dbUser>
<dbInstance>ricePure</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>
<!-- Marks Test rice database at brebiou.cshl.org -->
<chadodb>
<name>RiceDB test server at brebiou(Tunneling)</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://localhost:15432/rice</url>
<dbName>rice</dbName>
<dbUser>mgibson</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>false</default-command-line-db>
</chadodb>
<chadodb>
<name>RiceDB test server at brebiou(Tunneling,no hits)</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://localhost:15432/rice</url>
<dbName>rice</dbName>
<dbUser>mgibson</dbUser>
<dbInstance>riceInstance-no-hits</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>
<!-- Scotts Test rice database at gmod.cshl.org - works with ssh
tunnel on local host
ssh -L15432:gmod.cshl.edu:5432 -l cain -N gmod.cshl.edu -->
<chadodb>
<name>RiceDB test server at gmod.cshl.edu(Tunneling)</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://localhost:15432/rice</url>
<dbName>rice</dbName>
<dbUser>cain</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>
<chadodb>
<name>dicty hack</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://gmod.genetics.northwestern.edu:5432/ubuntu</url>
<dbName>ubuntu</dbName>
<dbUser>mark</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>
<chadodb>
<name>dicty pure</name>
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
<url>jdbc:postgresql://gmod.genetics.northwestern.edu:5432/ubuntu</url>
<dbName>ubuntu</dbName>
<dbUser>mark</dbUser>
<dbInstance>ricePure</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>
</chado-adapter>
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