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questions on organism page

stacy xu
Hi, everyone,

I am not sure this is the right mailing list to send the questions to as it seems to be more of a "Drupal" question other than "Tripal" question. But I had some very good experience with this mailing list and some errors do appear to be Tripal warnings. I am now half way through Tripal tutorial at page http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b). And I created one of my own organism following the instructions. Everything looks right until I went to the "organism" tab and click any of the specific organisms (human, for example). A bunch of warnings appeared before the organism page:

  • warning: pg_query(): Query failed: ERROR: relation "organism_feature_count" does not exist at character 75 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM organism_feature_count OFC INNER JOIN cvterm CVT on OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = 2 ORDER BY num_features desc in /srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_feature.module on line 1338.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 38 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT A.analysis_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 327.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 72 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 258.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 36 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT analysis_id FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1019.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 26 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1188.
  • warning: pg_query(): Query failed: ERROR: relation "organism_unigene_mview" does not exist at character 15 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM organism_unigene_mview OUM INNER JOIN analysis A ON A.analysis_id = OUM.analysis_id WHERE OUM.organism_id = 2 ORDER BY A.timeexecuted DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_unigene-6.x-0.3.1b-0.1/tripal_analysis_unigene.module on line 807.

I searched extensively on google finding it might be the Drupal problem, I committed the Drupal patch to my database.pgsql.inc from this website http://drupal.org/node/256001, however, nothing has changed. I am using Drupal 6.22 and postgresql 9.0.4. And line 138 in database.postgresql.inc is "  $last_result = pg_query($active_db, $query);". Does anyone ever encountered similar problem and can give me a hint of what to do with it? Thanks!

Thanks,
Stacy

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threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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Re: questions on organism page

Lacey-Anne Sanderson
Hi Stacy,

These errors seem to be suggesting that a number of Tripal materialized views are not initialized. If you go to Administer -> Tripal Management -> Materialized Views and update the organism_feature_count the first error should go away. Remember these register Tripal jobs so you won't see an effect until after the job is run. The others appear to be the same thing -a materialized view isn't initialized. I'm pretty sure they are associated with the analysis modules though and since I don't use any of those, I can't help you much. If you look in the materialized view page do you see any of these listing (
  • go_count_analysis, go_count_analysis, kegg_by_organism, organism_unigene_mview
  • )? If not maybe look on the configuration pages for the analysis modules.

Hope this helps,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-10-03, at 9:16 PM, stacy xu wrote:

Hi, everyone,

I am not sure this is the right mailing list to send the questions to as it seems to be more of a "Drupal" question other than "Tripal" question. But I had some very good experience with this mailing list and some errors do appear to be Tripal warnings. I am now half way through Tripal tutorial at page http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b). And I created one of my own organism following the instructions. Everything looks right until I went to the "organism" tab and click any of the specific organisms (human, for example). A bunch of warnings appeared before the organism page:

  • warning: pg_query(): Query failed: ERROR: relation "organism_feature_count" does not exist at character 75 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM organism_feature_count OFC INNER JOIN cvterm CVT on OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = 2 ORDER BY num_features desc in /srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_feature.module on line 1338.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 38 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT A.analysis_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 327.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 72 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 258.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 36 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT analysis_id FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1019.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 26 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1188.
  • warning: pg_query(): Query failed: ERROR: relation "organism_unigene_mview" does not exist at character 15 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM organism_unigene_mview OUM INNER JOIN analysis A ON A.analysis_id = OUM.analysis_id WHERE OUM.organism_id = 2 ORDER BY A.timeexecuted DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_unigene-6.x-0.3.1b-0.1/tripal_analysis_unigene.module on line 807.

I searched extensively on google finding it might be the Drupal problem, I committed the Drupal patch to my database.pgsql.inc from this website http://drupal.org/node/256001, however, nothing has changed. I am using Drupal 6.22 and postgresql 9.0.4. And line 138 in database.postgresql.inc is "  $last_result = pg_query($active_db, $query);". Does anyone ever encountered similar problem and can give me a hint of what to do with it? Thanks!

Thanks,
Stacy
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: questions on organism page

stacy xu
Opps, I forgot to CC the mailing list again! Sorry for that. I also went to "Materialized view" page under tripal management again to find out that although I launched the command to update all views, only the "organism_feature_count" and "organism_unigene_mview" appeared to be updated. 

I then updated "cv_root_mview" and went into server terminal again to launch "tripal_launch_jobs.php" to see "Calling: tripal_update_mview(1, 38)" to appear from my terminal, however, when going back to the materialized views tab, the "cv_root_mview" still shows that it is not yet populated. So I think Lacey is right  that my materialized view is having the problem, somehow I could have those updated from the web interface. I will take a look to see whether it is my other configuration is causing the problem.


Thanks,
Stacy

On Wed, Oct 5, 2011 at 10:37 AM, stacy xu <[hidden email]> wrote:
Hi, Lacey,

Thanks for getting back to me! I went to the materialized view page under Tripal Management and updated all of those views and run the tripal_launch_jobs.php command from my server's terminal. However, when I went back to specific organism page (human, for example), the warnings and errors remained...

Thanks,
Stacy


On Tue, Oct 4, 2011 at 11:26 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Stacy,

These errors seem to be suggesting that a number of Tripal materialized views are not initialized. If you go to Administer -> Tripal Management -> Materialized Views and update the organism_feature_count the first error should go away. Remember these register Tripal jobs so you won't see an effect until after the job is run. The others appear to be the same thing -a materialized view isn't initialized. I'm pretty sure they are associated with the analysis modules though and since I don't use any of those, I can't help you much. If you look in the materialized view page do you see any of these listing (
  • go_count_analysis, go_count_analysis, kegg_by_organism, organism_unigene_mview
  • )? If not maybe look on the configuration pages for the analysis modules.

Hope this helps,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-10-03, at 9:16 PM, stacy xu wrote:

Hi, everyone,

I am not sure this is the right mailing list to send the questions to as it seems to be more of a "Drupal" question other than "Tripal" question. But I had some very good experience with this mailing list and some errors do appear to be Tripal warnings. I am now half way through Tripal tutorial at page http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b). And I created one of my own organism following the instructions. Everything looks right until I went to the "organism" tab and click any of the specific organisms (human, for example). A bunch of warnings appeared before the organism page:

  • warning: pg_query(): Query failed: ERROR: relation "organism_feature_count" does not exist at character 75 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM organism_feature_count OFC INNER JOIN cvterm CVT on OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = 2 ORDER BY num_features desc in /srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_feature.module on line 1338.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 38 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT A.analysis_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 327.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 72 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 258.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 36 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT analysis_id FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1019.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 26 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1188.
  • warning: pg_query(): Query failed: ERROR: relation "organism_unigene_mview" does not exist at character 15 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM organism_unigene_mview OUM INNER JOIN analysis A ON A.analysis_id = OUM.analysis_id WHERE OUM.organism_id = 2 ORDER BY A.timeexecuted DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_unigene-6.x-0.3.1b-0.1/tripal_analysis_unigene.module on line 807.

I searched extensively on google finding it might be the Drupal problem, I committed the Drupal patch to my database.pgsql.inc from this website http://drupal.org/node/256001, however, nothing has changed. I am using Drupal 6.22 and postgresql 9.0.4. And line 138 in database.postgresql.inc is "  $last_result = pg_query($active_db, $query);". Does anyone ever encountered similar problem and can give me a hint of what to do with it? Thanks!

Thanks,
Stacy
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Re: questions on organism page

Stephen Ficklin-2
Hi Stacy,

Lacey is correct, the problem is with the materialized views.  The error messages state that the 'relation "organism_feature_count" does not exist'.   So this could be one of two problems

1.  The modules did not properly install. 
2.  There is an internal problem with the code that isn't setting the schema path correctly in your case.

Could you use phpPgAdmin to check inside the 'chado' schema of your database and see if the table "organism_feature_count" exists (or any of the other materialized views listed in the errors).  If not, then the the tripal_feature module must not have properly installed.  If this is the problem then you'll have to completely uninstall the feature module (not just disable it).  There is a tab on the Tripal modules page for uninstalling a module after you have disabled it.  After uninstalling, then reinstall and look for any error messages.

If the table "organism_feature_count" does exist in your database then something else is wrong and we'll have to dig a bit deeper.

Stephen

On 10/4/2011 10:46 PM, stacy xu wrote:
Opps, I forgot to CC the mailing list again! Sorry for that. I also went to "Materialized view" page under tripal management again to find out that although I launched the command to update all views, only the "organism_feature_count" and "organism_unigene_mview" appeared to be updated. 

I then updated "cv_root_mview" and went into server terminal again to launch "tripal_launch_jobs.php" to see "Calling: tripal_update_mview(1, 38)" to appear from my terminal, however, when going back to the materialized views tab, the "cv_root_mview" still shows that it is not yet populated. So I think Lacey is right  that my materialized view is having the problem, somehow I could have those updated from the web interface. I will take a look to see whether it is my other configuration is causing the problem.


Thanks,
Stacy

On Wed, Oct 5, 2011 at 10:37 AM, stacy xu <[hidden email]> wrote:
Hi, Lacey,

Thanks for getting back to me! I went to the materialized view page under Tripal Management and updated all of those views and run the tripal_launch_jobs.php command from my server's terminal. However, when I went back to specific organism page (human, for example), the warnings and errors remained...

Thanks,
Stacy


On Tue, Oct 4, 2011 at 11:26 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Stacy,

These errors seem to be suggesting that a number of Tripal materialized views are not initialized. If you go to Administer -> Tripal Management -> Materialized Views and update the organism_feature_count the first error should go away. Remember these register Tripal jobs so you won't see an effect until after the job is run. The others appear to be the same thing -a materialized view isn't initialized. I'm pretty sure they are associated with the analysis modules though and since I don't use any of those, I can't help you much. If you look in the materialized view page do you see any of these listing (
  • go_count_analysis, go_count_analysis, kegg_by_organism, organism_unigene_mview
  • )? If not maybe look on the configuration pages for the analysis modules.

Hope this helps,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a moz-do-not-send="true" href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-10-03, at 9:16 PM, stacy xu wrote:

Hi, everyone,

I am not sure this is the right mailing list to send the questions to as it seems to be more of a "Drupal" question other than "Tripal" question. But I had some very good experience with this mailing list and some errors do appear to be Tripal warnings. I am now half way through Tripal tutorial at page http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b). And I created one of my own organism following the instructions. Everything looks right until I went to the "organism" tab and click any of the specific organisms (human, for example). A bunch of warnings appeared before the organism page:

  • warning: pg_query(): Query failed: ERROR: relation "organism_feature_count" does not exist at character 75 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM organism_feature_count OFC INNER JOIN cvterm CVT on OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = 2 ORDER BY num_features desc in /srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_feature.module on line 1338.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 38 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT A.analysis_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 327.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 72 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 258.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 36 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT analysis_id FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1019.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 26 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1188.
  • warning: pg_query(): Query failed: ERROR: relation "organism_unigene_mview" does not exist at character 15 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM organism_unigene_mview OUM INNER JOIN analysis A ON A.analysis_id = OUM.analysis_id WHERE OUM.organism_id = 2 ORDER BY A.timeexecuted DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_unigene-6.x-0.3.1b-0.1/tripal_analysis_unigene.module on line 807.

I searched extensively on google finding it might be the Drupal problem, I committed the Drupal patch to my database.pgsql.inc from this website http://drupal.org/node/256001, however, nothing has changed. I am using Drupal 6.22 and postgresql 9.0.4. And line 138 in database.postgresql.inc is "  $last_result = pg_query($active_db, $query);". Does anyone ever encountered similar problem and can give me a hint of what to do with it? Thanks!

Thanks,
Stacy
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal





------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
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------------------------------------------------------------------------------
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: questions on organism page

stacy xu
Hi, Stephen,

Thanks very much for clear instructions! It all worked out now! The trick is, to go to materialized tab and click on "view" in each specific view to find out which module that is causing the problem and disable/uninstall/cron/install/cron the module. And all materialized view are back to life now. My problem is that the materialized view for my tripal_cv was not installed properly at the beginning and it is causing all other dependent modules having problem on materialized views.

Thanks,
Stacy

On Wed, Oct 5, 2011 at 11:25 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Lacey is correct, the problem is with the materialized views.  The error messages state that the 'relation "organism_feature_count" does not exist'.   So this could be one of two problems

1.  The modules did not properly install. 
2.  There is an internal problem with the code that isn't setting the schema path correctly in your case.

Could you use phpPgAdmin to check inside the 'chado' schema of your database and see if the table "organism_feature_count" exists (or any of the other materialized views listed in the errors).  If not, then the the tripal_feature module must not have properly installed.  If this is the problem then you'll have to completely uninstall the feature module (not just disable it).  There is a tab on the Tripal modules page for uninstalling a module after you have disabled it.  After uninstalling, then reinstall and look for any error messages.

If the table "organism_feature_count" does exist in your database then something else is wrong and we'll have to dig a bit deeper.

Stephen


On 10/4/2011 10:46 PM, stacy xu wrote:
Opps, I forgot to CC the mailing list again! Sorry for that. I also went to "Materialized view" page under tripal management again to find out that although I launched the command to update all views, only the "organism_feature_count" and "organism_unigene_mview" appeared to be updated. 

I then updated "cv_root_mview" and went into server terminal again to launch "tripal_launch_jobs.php" to see "Calling: tripal_update_mview(1, 38)" to appear from my terminal, however, when going back to the materialized views tab, the "cv_root_mview" still shows that it is not yet populated. So I think Lacey is right  that my materialized view is having the problem, somehow I could have those updated from the web interface. I will take a look to see whether it is my other configuration is causing the problem.


Thanks,
Stacy

On Wed, Oct 5, 2011 at 10:37 AM, stacy xu <[hidden email]> wrote:
Hi, Lacey,

Thanks for getting back to me! I went to the materialized view page under Tripal Management and updated all of those views and run the tripal_launch_jobs.php command from my server's terminal. However, when I went back to specific organism page (human, for example), the warnings and errors remained...

Thanks,
Stacy


On Tue, Oct 4, 2011 at 11:26 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Stacy,

These errors seem to be suggesting that a number of Tripal materialized views are not initialized. If you go to Administer -> Tripal Management -> Materialized Views and update the organism_feature_count the first error should go away. Remember these register Tripal jobs so you won't see an effect until after the job is run. The others appear to be the same thing -a materialized view isn't initialized. I'm pretty sure they are associated with the analysis modules though and since I don't use any of those, I can't help you much. If you look in the materialized view page do you see any of these listing (
  • go_count_analysis, go_count_analysis, kegg_by_organism, organism_unigene_mview
  • )? If not maybe look on the configuration pages for the analysis modules.

Hope this helps,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-2430" value="+13069662430" target="_blank">(306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2011-10-03, at 9:16 PM, stacy xu wrote:

Hi, everyone,

I am not sure this is the right mailing list to send the questions to as it seems to be more of a "Drupal" question other than "Tripal" question. But I had some very good experience with this mailing list and some errors do appear to be Tripal warnings. I am now half way through Tripal tutorial at page http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b). And I created one of my own organism following the instructions. Everything looks right until I went to the "organism" tab and click any of the specific organisms (human, for example). A bunch of warnings appeared before the organism page:

  • warning: pg_query(): Query failed: ERROR: relation "organism_feature_count" does not exist at character 75 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT OFC.num_features,OFC.feature_type,CVT.definition FROM organism_feature_count OFC INNER JOIN cvterm CVT on OFC.cvterm_id = CVT.cvterm_id WHERE organism_id = 2 ORDER BY num_features desc in /srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_feature/tripal_feature.module on line 1338.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 38 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT A.analysis_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 327.
  • warning: pg_query(): Query failed: ERROR: relation "go_count_analysis" does not exist at character 72 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id FROM go_count_analysis GCA INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_go-6.x-0.3.1b-0.1/tripal_analysis_go.module on line 258.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 36 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT analysis_id FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1019.
  • warning: pg_query(): Query failed: ERROR: relation "kegg_by_organism" does not exist at character 26 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM kegg_by_organism KBO WHERE organism_id = 2 ORDER BY analysis_id DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_kegg-6.x-0.3.1b-0.1/tripal_analysis_kegg.module on line 1188.
  • warning: pg_query(): Query failed: ERROR: relation "organism_unigene_mview" does not exist at character 15 in /srv/www/htdocs/drupal6/includes/database.pgsql.inc on line 138.
  • user warning: query: SELECT * FROM organism_unigene_mview OUM INNER JOIN analysis A ON A.analysis_id = OUM.analysis_id WHERE OUM.organism_id = 2 ORDER BY A.timeexecuted DESC in /srv/www/htdocs/drupal6/sites/all/modules/tripal_analysis_unigene-6.x-0.3.1b-0.1/tripal_analysis_unigene.module on line 807.

I searched extensively on google finding it might be the Drupal problem, I committed the Drupal patch to my database.pgsql.inc from this website http://drupal.org/node/256001, however, nothing has changed. I am using Drupal 6.22 and postgresql 9.0.4. And line 138 in database.postgresql.inc is "  $last_result = pg_query($active_db, $query);". Does anyone ever encountered similar problem and can give me a hint of what to do with it? Thanks!

Thanks,
Stacy
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal