[Gmod-tripal-devel] Error when using OBO loader

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] Error when using OBO loader

Mara Kim-2
Hello,

I get the following error when I use the OBO File loader to load a remote URL:

Name: Flybase CV
Remote URL: http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo:

Submitting the job is successful and gives the following error:
Notice: Undefined variable: obo_name in tripal_submit_obo_job() (line
797 of /var/www/html/sites/all/modules/tripal/tripal_cv/api/tripal_cv.api.inc).

I have attached the trp-job output

--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

oboload.log (1K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Error when using OBO loader

Stephen Ficklin-2
Hi Mara,

Thanks for pointing out this issue. I have committed a fix to the development branch which should fix the error message you saw when submitting the OBO.  However, it looks like you encountered a second problem when trying to load the flybase_controlled_vocabulary.obo.  I believe this is related to another problem reported to the mailing list a few weeks ago regarding  loading of plant ontology OBOs.  That problem was fixed earlier this week.  So, if you pull the most recent code I believe you should now be able to load that ontology without any problems.

Stephen

On 5/8/2014 4:39 PM, Mara Kim wrote:
Hello,

I get the following error when I use the OBO File loader to load a remote URL:

Name: Flybase CV
Remote URL: http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo:

Submitting the job is successful and gives the following error:
Notice: Undefined variable: obo_name in tripal_submit_obo_job() (line
797 of /var/www/html/sites/all/modules/tripal/tripal_cv/api/tripal_cv.api.inc).

I have attached the trp-job output



------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Error when using OBO loader

Mara Kim-2
Hi Stephen,

I get an undefined table error now when I run the OBO loader job.  I
believe that either the chado.tripal_obo_temp table is not being
correctly generated or there needs to be some sort of existence check
before the DELETE statement referencing the table.

In addition, after pulling the newest development code, I keep getting
the following error on pages and when I clear the drupal cache:
Invalid argument supplied for foreach() common.inc:7036

Here is the trp-job error:

BEGIN EXECUTION TRACE
Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_cv_load_obo_v1_2_url(Flybase,
http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo,
358)
Downloading URL
http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo,
saving to /tmp/obo_e1FAv6

NOTE: Loading of this OBO file is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
insertions/updates is rolled back and will not be found in the database


FAILED. Rolling back database changes...
WD T_obo_loader: PDOException: SQLSTATE[42P01]: Undefined table: 7   [error]
ERROR:  relation "chado.tripal_obo_temp" does not exist
LINE 1: DELETE FROM chado.tripal_obo_temp
                    ^: DELETE FROM chado.tripal_obo_temp; Array
(
)
 in chado_query() (line 1328 of
/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).
END EXECUTION TRACE

status  0
real    0m1.620s
user    0m0.823s
sys     0m0.103s


On Thu, May 15, 2014 at 1:12 PM, Stephen Ficklin <[hidden email]> wrote:

> Hi Mara,
>
> Thanks for pointing out this issue. I have committed a fix to the
> development branch which should fix the error message you saw when
> submitting the OBO.  However, it looks like you encountered a second problem
> when trying to load the flybase_controlled_vocabulary.obo.  I believe this
> is related to another problem reported to the mailing list a few weeks ago
> regarding  loading of plant ontology OBOs.  That problem was fixed earlier
> this week.  So, if you pull the most recent code I believe you should now be
> able to load that ontology without any problems.
>
> Stephen
>
>
> On 5/8/2014 4:39 PM, Mara Kim wrote:
>
> Hello,
>
> I get the following error when I use the OBO File loader to load a remote
> URL:
>
> Name: Flybase CV
> Remote URL:
> http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo:
>
> Submitting the job is successful and gives the following error:
> Notice: Undefined variable: obo_name in tripal_submit_obo_job() (line
> 797 of
> /var/www/html/sites/all/modules/tripal/tripal_cv/api/tripal_cv.api.inc).
>
> I have attached the trp-job output
>
>
>
> ------------------------------------------------------------------------------
> Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
> &#149; 3 signs your SCM is hindering your productivity
> &#149; Requirements for releasing software faster
> &#149; Expert tips and advice for migrating your SCM now
> http://p.sf.net/sfu/perforce
>
>
>
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform
> available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] Error when using OBO loader

Stephen Ficklin-2
Hi Mara,

The chado.tripal_obo_temp  is created when the tripal_cv module is
installed.  It seems to be missing from your installation.  This would
occur if the installation did not properly complete.  Or there may have
been some sort of earlier bug when you first installed that module.   I
will test the installation.  If you uninstall and re-install the
tripal_cv module it should solve the problem for you.  But, you may not
want to do that as you will loose all of your synced pages as you'd have
to also uninstall the tripal_feature, tripal_organism and other
modules.  So, the quick fix is to just manually create the table.  
Here's some SQL to do that:

CREATE TABLE chado.tripal_obo_temp (
   id character varying(255) NOT NULL,
   stanza text NOT NULL,
   type character varying(50) NOT NULL,
   CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id);
CREATE INDEX tripal_obo_temp_idx0 ON chado.tripal_obo_temp USING btree (id);
CREATE INDEX tripal_obo_temp_idx1 ON chado.tripal_obo_temp USING btree
(type);

Hope that helps,
Stephen

On 5/17/2014 2:21 PM, Mara Kim wrote:

> Hi Stephen,
>
> I get an undefined table error now when I run the OBO loader job.  I
> believe that either the chado.tripal_obo_temp table is not being
> correctly generated or there needs to be some sort of existence check
> before the DELETE statement referencing the table.
>
> In addition, after pulling the newest development code, I keep getting
> the following error on pages and when I clear the drupal cache:
> Invalid argument supplied for foreach() common.inc:7036
>
> Here is the trp-job error:
>
> BEGIN EXECUTION TRACE
> Tripal Job Launcher
> Running as user 'administrator'
> -------------------
> Calling: tripal_cv_load_obo_v1_2_url(Flybase,
> http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo,
> 358)
> Downloading URL
> http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo,
> saving to /tmp/obo_e1FAv6
>
> NOTE: Loading of this OBO file is performed using a database transaction.
> If the load fails or is terminated prematurely then the entire set of
> insertions/updates is rolled back and will not be found in the database
>
>
> FAILED. Rolling back database changes...
> WD T_obo_loader: PDOException: SQLSTATE[42P01]: Undefined table: 7   [error]
> ERROR:  relation "chado.tripal_obo_temp" does not exist
> LINE 1: DELETE FROM chado.tripal_obo_temp
>                      ^: DELETE FROM chado.tripal_obo_temp; Array
> (
> )
>   in chado_query() (line 1328 of
> /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).
> END EXECUTION TRACE
>
> status  0
> real    0m1.620s
> user    0m0.823s
> sys     0m0.103s
>
>
> On Thu, May 15, 2014 at 1:12 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Mara,
>>
>> Thanks for pointing out this issue. I have committed a fix to the
>> development branch which should fix the error message you saw when
>> submitting the OBO.  However, it looks like you encountered a second problem
>> when trying to load the flybase_controlled_vocabulary.obo.  I believe this
>> is related to another problem reported to the mailing list a few weeks ago
>> regarding  loading of plant ontology OBOs.  That problem was fixed earlier
>> this week.  So, if you pull the most recent code I believe you should now be
>> able to load that ontology without any problems.
>>
>> Stephen
>>
>>
>> On 5/8/2014 4:39 PM, Mara Kim wrote:
>>
>> Hello,
>>
>> I get the following error when I use the OBO File loader to load a remote
>> URL:
>>
>> Name: Flybase CV
>> Remote URL:
>> http://obo.cvs.sourceforge.net/obo/obo/ontology/vocabularies/flybase_controlled_vocabulary.obo:
>>
>> Submitting the job is successful and gives the following error:
>> Notice: Undefined variable: obo_name in tripal_submit_obo_job() (line
>> 797 of
>> /var/www/html/sites/all/modules/tripal/tripal_cv/api/tripal_cv.api.inc).
>>
>> I have attached the trp-job output
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
>> &#149; 3 signs your SCM is hindering your productivity
>> &#149; Requirements for releasing software faster
>> &#149; Expert tips and advice for migrating your SCM now
>> http://p.sf.net/sfu/perforce
>>
>>
>>
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.
>> Get unparalleled scalability from the best Selenium testing platform
>> available
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>
>


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel