Apollo hanging at 50%

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Apollo hanging at 50%

Becksfort, Jared

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/apollo.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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Re: Apollo hanging at 50%

Ed Lee
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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RE: Apollo hanging at 50%

Becksfort, Jared
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:[hidden email]]
Sent: Tuesday, June 08, 2010 12:31 PM
To: Becksfort, Jared
Cc: '[hidden email]'
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
[hidden email]
http://mail.fruitfly.org/mailman/listinfo/apollo

chado-adapter-aceview-test.xml (10K) Download Attachment
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Re: Apollo hanging at 50%

Scott Cain
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
<[hidden email]> 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:[hidden email]]
> Sent: Tuesday, June 08, 2010 12:31 PM
> To: Becksfort, Jared
> Cc: '[hidden email]'
> 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
> [hidden email]
> 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
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RE: Apollo hanging at 50%

Becksfort, Jared
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:[hidden email]]
Sent: Tuesday, June 08, 2010 2:42 PM
To: Becksfort, Jared
Cc: Ed Lee; [hidden email]
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
<[hidden email]> 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:[hidden email]]
> Sent: Tuesday, June 08, 2010 12:31 PM
> To: Becksfort, Jared
> Cc: '[hidden email]'
> 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
> [hidden email]
> 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


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RE: Apollo hanging at 50%

Ed Lee
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:[hidden email]]
> Sent: Tuesday, June 08, 2010 2:42 PM
> To: Becksfort, Jared
> Cc: Ed Lee; [hidden email]
> 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
> <[hidden email]> 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:[hidden email]]
>> Sent: Tuesday, June 08, 2010 12:31 PM
>> To: Becksfort, Jared
>> Cc: '[hidden email]'
>> 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
>> [hidden email]
>> 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
>
>
>
>
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RE: Apollo hanging at 50%

Becksfort, Jared
Ed,

I changed the clsName and the error for that problem went away, but the original problem with the query is still happening.

My schema has the db table.  I have attached the data in it.  I do not see Chado or GMOD mentioned anywhere within it, so I cannot say which version of Chado it is trying to use.

Thanks,
Jared

-----Original Message-----
From: Ed Lee [mailto:[hidden email]]
Sent: Wednesday, June 09, 2010 12:48 PM
To: Becksfort, Jared
Cc: 'Scott Cain'; [hidden email]
Subject: RE: [apollo] Apollo hanging at 50%

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:[hidden email]]
> Sent: Tuesday, June 08, 2010 2:42 PM
> To: Becksfort, Jared
> Cc: Ed Lee; [hidden email]
> 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
> <[hidden email]> 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:[hidden email]]
>> Sent: Tuesday, June 08, 2010 12:31 PM
>> To: Becksfort, Jared
>> Cc: '[hidden email]'
>> 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
>> [hidden email]
>> 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
>
>
>
>

_______________________________________________
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chado.db.sql.txt (7K) Download Attachment
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RE: Apollo hanging at 50%

Becksfort, Jared
In reply to this post by Ed Lee
Hi Ed,

I took a look at the code, and I think (as you probably already have figured out) that the function guessSchemaVersion in SchemaVersion.java is not correctly guessing the version.  This may also be messing up the getCVTerms function in JdbcChadoAdapter.java.  I thought that I would rebuild the code to see if I could fix this, but 2 issues appear:

1.  The code to download on sourceforge for gmod-1.1 is Apollo 1.11.1 rather that 1.11.6, the newest version.  Is this code available?
2.  There is no makefile in the src/java directory to rebuild as per the README.

Any thoughts are appreciated.  I will be happy to submit a fix if I figure one out.

Thanks,
Jared

-----Original Message-----
From: Ed Lee [mailto:[hidden email]]
Sent: Wednesday, June 09, 2010 12:48 PM
To: Becksfort, Jared
Cc: 'Scott Cain'; [hidden email]
Subject: RE: [apollo] Apollo hanging at 50%

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:[hidden email]]
> Sent: Tuesday, June 08, 2010 2:42 PM
> To: Becksfort, Jared
> Cc: Ed Lee; [hidden email]
> 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
> <[hidden email]> 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:[hidden email]]
>> Sent: Tuesday, June 08, 2010 12:31 PM
>> To: Becksfort, Jared
>> Cc: '[hidden email]'
>> 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
>> [hidden email]
>> 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
>
>
>
>

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RE: Apollo hanging at 50%

Ed Lee
Hi Jared,

> 1.  The code to download on sourceforge for gmod-1.1 is Apollo 1.11.1 rather that 1.11.6, the newest version.  Is this code available?

To get the most current code, you should checkout the code from SVN:

$ svn co https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk Apollo

> 2.  There is no makefile in the src/java directory to rebuild as per the README.

You should use ant to build Apollo.

$ cd Apollo/src/java  ## assuming your checkout is named Apollo
$ ant jar

> Any thoughts are appreciated.  I will be happy to submit a fix if I figure one out.

If you can provide a database dump (or access to the database), I can also
poke at this problem a bit further to figure out why the Apollo is guessing
the pre-FMB schema.

Cheers,
Ed
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RE: Apollo hanging at 50%

Becksfort, Jared
Ed and Scott,

Thanks so much for your help with this last week.  After checking out the code and adding debug lines throughout, it became clear that although Apollo was able to connect to my PostgreSQL installation, it was not able to find any of the tables.  This included the "db" table, so the PRE_FMB schema was being used to query tables that it could not access.

I changed the line in conf/chado-adapter.xml so that it had the database name on the end of the connection string

        <chadodb>
        <name>pcgp</name>
        <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
        <url>jdbc:postgresql://IPADDRESS:5432/pcgp</url>  THE PCGP ON WAS NOT ON THE END
        <dbName>pcgp</dbName>
        <dbUser>postgres</dbUser>
        <dbInstance>riceInstance</dbInstance>
        <style>rice.style</style>
        <default-command-line-db>false</default-command-line-db>
        </chadodb>

Everything worked after that.  Thanks again.

Jared

-----Original Message-----
From: Ed Lee [mailto:[hidden email]]
Sent: Thursday, June 10, 2010 6:24 PM
To: Becksfort, Jared
Cc: 'Scott Cain'; [hidden email]
Subject: RE: [apollo] Apollo hanging at 50%

Hi Jared,

> 1.  The code to download on sourceforge for gmod-1.1 is Apollo 1.11.1 rather that 1.11.6, the newest version.  Is this code available?

To get the most current code, you should checkout the code from SVN:

$ svn co https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk Apollo

> 2.  There is no makefile in the src/java directory to rebuild as per the README.

You should use ant to build Apollo.

$ cd Apollo/src/java  ## assuming your checkout is named Apollo
$ ant jar

> Any thoughts are appreciated.  I will be happy to submit a fix if I figure one out.

If you can provide a database dump (or access to the database), I can also
poke at this problem a bit further to figure out why the Apollo is guessing
the pre-FMB schema.

Cheers,
Ed


Email Disclaimer:  www.stjude.org/emaildisclaimer

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