[Gmod-tripal-devel] When, where and how are custom tripal tables generated?

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

[Gmod-tripal-devel] When, where and how are custom tripal tables generated?

Michael Dondrup
Hi,

I am trying to get a better understanding of the process that creates the custom tripal tables in the
public schema.  After trying a fresh start (I did 'drop schema cascade',  which is not a good idea), I
had possibly lost some of the tables outside of the chado schema itself. It is totally
possible that I have made a mess here, but on the other hand, I haven't been able to restore some of these
tables. Among the tables that are missing are:

tripal_custom_tables, tripal_jobs, tripal_mviews*

In my understanding, for non-tripal modules, applying deactivate->uninstall->activate to the module
will most likely restore their auxilliary tables. I tried this as well, but could not recover the tables.

Is there an SQLfile somewhere? or when and how are these tables created,or would it be possible to
trigger table create in module activation after uninstall or during chado installation?

* I checked in psql, they are really missing. In another database using tripal v0.3 I was able to
find table definitions tripal_jobs and tripal_mviews, but not tripal_custom_tables

I searched the tripal code base and found:

grep -B20 -rie "db_create_table.*tripal_custom_tables" *


*  Update for Drupal 6.x, Tripal 0.4
tripal_core.install- *  This update
tripal_core.install- *   - adjusts the materialized view by adding status, comment and mv_schema columns
tripal_core.install- *   - changes the specs of mv_table, mv_specs and indexed
tripal_core.install- *   - creates the tripal_custom_tables table
tripal_core.install- *
tripal_core.install- * @ingroup tripal_feature
tripal_core.install- */
tripal_core.install-function tripal_core_update_6000() {
tripal_core.install-  // add additional columsn to the tripal_mviews table
tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'status', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'comment', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'mv_schema', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_table', 'mv_table', array('type' => 'varchar', 'length' => 128, 'not NULL' => FALSE));
tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_specs', 'mv_specs', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'indexed', 'indexed', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
tripal_core.install-
tripal_core.install-  // create the custom tables table
tripal_core.install-  $ret = array();
tripal_core.install-  $schema = tripal_core_custom_tables_schema();
tripal_core.install:  db_create_table($ret, 'tripal_custom_tables', $schema['tripal_custom_tables']);

as the only occurrence. Does this mean that one will get this definition only during an update from 0.3?

Best Michael


---------------------------------------------------------------------------------------------------------------------------------------


The process in detail:

0.
Deactivated all Tripal modules and Views and ahah helper modules, unistalled all these modules.


updated to latest tripal dev-version:
commit c2c9fbbd0ce3301f5915d602d30205e181cc6078
Author: spficklin <[hidden email]>
Date:   Thu Jan 24 22:57:17 2013 -0500


1. Only Tripal Core 6.x-1.0 is active:

/?q=admin/tripal/custom_tables:
• warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
• user warning: query: SELECT * FROM tripal_custom_tables ORDER BY table_name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 270.


/?q=admin/tripal/tripal_jobs:
• warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 217 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
• user warning: query: SELECT count(*) FROM ( SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC) as t1 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.
• warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 195 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
• user warning: ERROR: relation "tripal_jobs" does not exist at character 195 query: SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC LIMIT 25 OFFSET 0 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.


/?q=admin/tripal/mviews:
• warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
• user warning: query: SELECT * FROM tripal_mviews ORDER BY name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/mviews.php on line 462.

2. Run: New Install of Chado v.1.2,
no errors, checked that the schema exists


3. Activated Tripal DB 6.x-1.0:
no additional warnings (in Databases)

4. Activated Tripal CV:
no further warnings

5.  Tripal Organism:
6.  Tripal Analysis
7.  Tripal Feature:
/?q=admin/build/modules
• warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
• user warning: query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_feature_count', 'tripal_feature', 'organism_feature_count', 'organism_id integer, genus character varying(255), species character varying(255), common_name character varying(255), num_features integer, cvterm_id integer, feature_type character varying(255)', 'organism_id,cvterm_id,feature_type', 'SELECT O.organism_id, O.genus, O.species, O.common_name, count(F.feature_id) as num_features, CVT.cvterm_id, CVT.name as feature_type FROM {Organism} O INNER JOIN Feature F ON O.Organism_id = F.organism_id INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id GROUP BY O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.

7. Activated Views and ahah-helper module
tried to apply the patches before, but I got:

patch -p1 < ../tripal/tripal_views/patches/views_data_export-postgresql-1293788-2.patch
patching file plugins/views_data_export_plugin_display_export.inc
Reversed (or previously applied) patch detected!  Assume -R? [n]
Apply anyway? [n]
Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file plugins/views_data_export_plugin_display_export.inc.rej

So, I assume I had applied the patch already



8. Activated: Analysis Blast, Kegg, GO, Interpro, Unigene (all at once):

        • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_organisms' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_organisms', 'a:5:{s:5:"table";s:15:"blast_organisms";s:6:"fields";a:2:{s:12:"blast_org_id";a:2:{s:4:"type";s:6:"serial";s:8:"not null";b:1;}s:14:"blast_org_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}}s:11:"primary key";a:1:{i:0;s:12:"blast_org_id";}s:7:"indexes";a:1:{s:18:"blast_org_name_idx";a:1:{i:0;s:14:"blast_org_name";}}s:11:"unique keys";a:1:{s:17:"blast_org_name_uq";a:1:{i:0;s:14:"blast_org_name";}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
        • Could not add custom table blast_organisms. Please check the schema array.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 15 query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_hit_data' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_hit_data', 'a:4:{s:5:"table";s:14:"blast_hit_data";s:6:"fields";a:14:{s:18:"analysisfeature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:11:"analysis_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:10:"feature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:5:"db_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:7:"hit_num";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:8:"hit_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:7:"hit_url";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:15:"hit_description";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:12:"hit_organism";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:12:"blast_org_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:0;}s:13:"hit_accession";a:3:{s:4:"type";s:7:"varchar";s:6:"length";s:3:"255";s:8:"not null";b:0;}s:13:"hit_best_eval";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:14:"hit_best_score";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:7:"hit_pid";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}}s:7:"indexes";a:9:{s:18:"analysisfeature_id";a:1:{i:0;s:18:"analysisfeature_id";}s:10:"feature_id";a:1:{i:0;s:10:"feature_id";}s:11:"analysis_id";a:1:{i:0;s:11:"analysis_id";}s:12:"blast_org_id";a:1:{i:0;s:12:"blast_org_id";}s:5:"db_id";a:1:{i:0;s:5:"db_id";}s:12:"hit_organism";a:1:{i:0;s:12:"hit_organism";}s:8:"hit_name";a:1:{i:0;s:12:"hit_organism";}s:13:"hit_accession";a:1:{i:0;s:13:"hit_accession";}s:13:"hit_best_eval";a:1:{i:0;s:13:"hit_best_eval";}}s:12:"foreign keys";a:5:{s:2:"db";a:2:{s:5:"table";s:2:"db";s:7:"columns";a:1:{s:5:"db_id";s:5:"db_id";}}s:15:"analysisfeature";a:2:{s:5:"table";s:15:"analysisfeature";s:7:"columns";a:1:{s:18:"analysisfeature_id";s:18:"analysisfeature_id";}}s:8:"analysis";a:2:{s:5:"table";s:8:"analysis";s:7:"columns";a:1:{s:11:"analysis_id";s:11:"analysis_id";}}s:7:"feature";a:2:{s:5:"table";s:7:"feature";s:7:"columns";a:1:{s:10:"feature_id";s:10:"feature_id";}}s:15:"blast_organisms";a:2:{s:5:"table";s:15:"blast_organisms";s:7:"columns";a:1:{s:12:"blast_org_id";s:12:"blast_org_id";}}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
        • Could not add custom table blast_hit_data. Please check the schema array.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_organism', 'tripal_analysis_go', 'go_count_organism', 'cvname character varying(255), cvterm_id integer, organism_id integer, feature_count integer', 'cvterm_id,organism_id', 'SELECT T1.cvname, T1.object_id, T1.organism_id, count(T1.feature_id) FROM (SELECT DISTINCT CVT3.name as cvname, CVTP.object_id, O.organism_id, F.feature_id FROM cvtermpath CVTP INNER JOIN CVTerm CVT ON CVTP.subject_id = CVT.cvterm_id INNER JOIN CVTerm CVT2 ON CVTP.type_id = CVT2.cvterm_id INNER JOIN CVTerm CVT3 ON CVTP.object_id = CVT3.cvterm_id INNER JOIN Feature_cvterm FCVT ON FCVT.cvterm_id = CVT.cvterm_id INNER JOIN Feature F ON FCVT.feature_id = F.feature_id INNER JOIN CV ON CV.cv_id = CVT.cv_id INNER JOIN Organism O ON O.organism_id = F.organism_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'') ) as T1 GROUP BY T1.cvname,T1.object_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_analysis', 'tripal_analysis_go', 'go_count_analysis', 'cvname character varying(255), cvterm_id integer, analysis_id integer, organism_id integer, feature_count integer', 'cvterm_id,analysis_id,organism_id', 'SELECT T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id,count(*) as feature_count FROM (SELECT DISTINCT AF.analysis_id, AF.feature_id,CVT.name as cvname, CVT.cvterm_id,CVTP.object_id,CV.name, F.organism_id FROM analysisfeatureprop AFP INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN cvtermpath CVTP ON CVTP.subject_id = AFP.type_id INNER JOIN cvterm CVT ON CVTP.object_id = CVT.cvterm_id INNER JOIN CV ON CV.cv_id = CVT.cv_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'')) as T1 GROUP BY T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('kegg_by_organism', 'kegg_by_organism', 'kegg_by_organism', 'analysis_name character varying(255), analysis_id integer, organism_id integer', 'analysis_id,organism_id', 'SELECT DISTINCT A.name,A.analysis_id,F.organism_id FROM analysisprop AP INNER JOIN analysis A on A.analysis_id = AP.analysis_id INNER JOIN cvterm CVT on CVT.cvterm_id = AP.type_id INNER JOIN analysisfeature AF on AF.analysis_id = A.analysis_id INNER JOIN feature F on F.feature_id = AF.feature_id WHERE CVT.name = ''analysis_kegg_settings''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
        • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
        • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_unigene_mview', 'tripal_analysis_unigene', 'organism_unigene_mview', 'analysis_id integer, organism_id integer', 'analysis_id, organism_id', 'SELECT DISTINCT A.analysis_id, O.organism_id FROM {Analysis} A INNER JOIN analysisprop AP ON AP.analysis_id = A.analysis_id INNER JOIN cvterm CVT ON AP.type_id = CVT.cvterm_id INNER JOIN cv CV ON CV.cv_id = CVT.cv_id INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN organism O ON F.organism_id = O.organism_id WHERE CV.name = ''tripal'' AND CVT.name=''analysis_unigene_name''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.









------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
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] When, where and how are custom tripal tables generated?

Stephen Ficklin-2
Hi Michael,

Those tables are added automatically in the install of the tripal_core
module.  You would have to uninstall all of the tripal modules to be
able to uninstall and re-enable the tripal_core module.  But, if you
have features, organisms, etc. synced you will lose all of those synced
nodes, and you'll have to resync everything.  You shouldn't lose any
data in Chado tables (although it sounds like you dropped your Chado
schema anyway).  If you disable tripal_core and then uninstall it and
then re-enable it should recreate those tables for you.  Drush commands:

(first uninstall all other tripal modules)
drush pm-disable tripal_core
drush pm-uninstall tripal_core
drush pm-enable tripal_core
(now re-enable all other tripal modules)

The update functions you see in the tripal_core.install file are for
incremental updates to the schema,  but if you install fresh after a
complete uninstall you get all of the updates to the tables.

Hope that helps,

Stephen

On 1/30/2013 9:30 AM, Michael Dondrup wrote:

> Hi,
>
> I am trying to get a better understanding of the process that creates the custom tripal tables in the
> public schema.  After trying a fresh start (I did 'drop schema cascade',  which is not a good idea), I
> had possibly lost some of the tables outside of the chado schema itself. It is totally
> possible that I have made a mess here, but on the other hand, I haven't been able to restore some of these
> tables. Among the tables that are missing are:
>
> tripal_custom_tables, tripal_jobs, tripal_mviews*
>
> In my understanding, for non-tripal modules, applying deactivate->uninstall->activate to the module
> will most likely restore their auxilliary tables. I tried this as well, but could not recover the tables.
>
> Is there an SQLfile somewhere? or when and how are these tables created,or would it be possible to
> trigger table create in module activation after uninstall or during chado installation?
>
> * I checked in psql, they are really missing. In another database using tripal v0.3 I was able to
> find table definitions tripal_jobs and tripal_mviews, but not tripal_custom_tables
>
> I searched the tripal code base and found:
>
> grep -B20 -rie "db_create_table.*tripal_custom_tables" *
>
>
> *  Update for Drupal 6.x, Tripal 0.4
> tripal_core.install- *  This update
> tripal_core.install- *   - adjusts the materialized view by adding status, comment and mv_schema columns
> tripal_core.install- *   - changes the specs of mv_table, mv_specs and indexed
> tripal_core.install- *   - creates the tripal_custom_tables table
> tripal_core.install- *
> tripal_core.install- * @ingroup tripal_feature
> tripal_core.install- */
> tripal_core.install-function tripal_core_update_6000() {
> tripal_core.install-  // add additional columsn to the tripal_mviews table
> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'status', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'comment', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'mv_schema', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_table', 'mv_table', array('type' => 'varchar', 'length' => 128, 'not NULL' => FALSE));
> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_specs', 'mv_specs', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'indexed', 'indexed', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
> tripal_core.install-
> tripal_core.install-  // create the custom tables table
> tripal_core.install-  $ret = array();
> tripal_core.install-  $schema = tripal_core_custom_tables_schema();
> tripal_core.install:  db_create_table($ret, 'tripal_custom_tables', $schema['tripal_custom_tables']);
>
> as the only occurrence. Does this mean that one will get this definition only during an update from 0.3?
>
> Best Michael
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------
>
>
> The process in detail:
>
> 0.
> Deactivated all Tripal modules and Views and ahah helper modules, unistalled all these modules.
>
>
> updated to latest tripal dev-version:
> commit c2c9fbbd0ce3301f5915d602d30205e181cc6078
> Author: spficklin <[hidden email]>
> Date:   Thu Jan 24 22:57:17 2013 -0500
>
>
> 1. Only Tripal Core 6.x-1.0 is active:
>
> /?q=admin/tripal/custom_tables:
> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: query: SELECT * FROM tripal_custom_tables ORDER BY table_name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 270.
>
>
> /?q=admin/tripal/tripal_jobs:
> • warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 217 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: query: SELECT count(*) FROM ( SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC) as t1 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 195 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_jobs" does not exist at character 195 query: SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC LIMIT 25 OFFSET 0 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.
>
>
> /?q=admin/tripal/mviews:
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: query: SELECT * FROM tripal_mviews ORDER BY name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/mviews.php on line 462.
>
> 2. Run: New Install of Chado v.1.2,
> no errors, checked that the schema exists
>
>
> 3. Activated Tripal DB 6.x-1.0:
> no additional warnings (in Databases)
>
> 4. Activated Tripal CV:
> no further warnings
>
> 5.  Tripal Organism:
> 6.  Tripal Analysis
> 7.  Tripal Feature:
> /?q=admin/build/modules
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_feature_count', 'tripal_feature', 'organism_feature_count', 'organism_id integer, genus character varying(255), species character varying(255), common_name character varying(255), num_features integer, cvterm_id integer, feature_type character varying(255)', 'organism_id,cvterm_id,feature_type', 'SELECT O.organism_id, O.genus, O.species, O.common_name, count(F.feature_id) as num_features, CVT.cvterm_id, CVT.name as feature_type FROM {Organism} O INNER JOIN Feature F ON O.Organism_id = F.organism_id INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id GROUP BY O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>
> 7. Activated Views and ahah-helper module
> tried to apply the patches before, but I got:
>
> patch -p1 < ../tripal/tripal_views/patches/views_data_export-postgresql-1293788-2.patch
> patching file plugins/views_data_export_plugin_display_export.inc
> Reversed (or previously applied) patch detected!  Assume -R? [n]
> Apply anyway? [n]
> Skipping patch.
> 3 out of 3 hunks ignored -- saving rejects to file plugins/views_data_export_plugin_display_export.inc.rej
>
> So, I assume I had applied the patch already
>
>
>
> 8. Activated: Analysis Blast, Kegg, GO, Interpro, Unigene (all at once):
>
> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_organisms' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_organisms', 'a:5:{s:5:"table";s:15:"blast_organisms";s:6:"fields";a:2:{s:12:"blast_org_id";a:2:{s:4:"type";s:6:"serial";s:8:"not null";b:1;}s:14:"blast_org_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}}s:11:"primary key";a:1:{i:0;s:12:"blast_org_id";}s:7:"indexes";a:1:{s:18:"blast_org_name_idx";a:1:{i:0;s:14:"blast_org_name";}}s:11:"unique keys";a:1:{s:17:"blast_org_name_uq";a:1:{i:0;s:14:"blast_org_name";}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
> • Could not add custom table blast_organisms. Please check the schema array.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 15 query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_hit_data' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_hit_data', 'a:4:{s:5:"table";s:14:"blast_hit_data";s:6:"fields";a:14:{s:18:"analysisfeature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:11:"analysis_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:10:"feature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:5:"db_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:7:"hit_num";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:8:"hit_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:7:"hit_url";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:15:"hit_description";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:12:"hit_organism";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:12:"blast_org_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:0;}s:13:"hit_accession";a:3:{s:4:"type";s:7:"varchar";s:6:"length";s:3:"255";s:8:"not null";b:0;}s:13:"hit_best_eval";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:14:"hit_best_score";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:7:"hit_pid";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}}s:7:"indexes";a:9:{s:18:"analysisfeature_id";a:1:{i:0;s:18:"analysisfeature_id";}s:10:"feature_id";a:1:{i:0;s:10:"feature_id";}s:11:"analysis_id";a:1:{i:0;s:11:"analysis_id";}s:12:"blast_org_id";a:1:{i:0;s:12:"blast_org_id";}s:5:"db_id";a:1:{i:0;s:5:"db_id";}s:12:"hit_organism";a:1:{i:0;s:12:"hit_organism";}s:8:"hit_name";a:1:{i:0;s:12:"hit_organism";}s:13:"hit_accession";a:1:{i:0;s:13:"hit_accession";}s:13:"hit_best_eval";a:1:{i:0;s:13:"hit_best_eval";}}s:12:"foreign keys";a:5:{s:2:"db";a:2:{s:5:"table";s:2:"db";s:7:"columns";a:1:{s:5:"db_id";s:5:"db_id";}}s:15:"analysisfeature";a:2:{s:5:"table";s:15:"analysisfeature";s:7:"columns";a:1:{s:18:"analysisfeature_id";s:18:"analysisfeature_id";}}s:8:"analysis";a:2:{s:5:"table";s:8:"analysis";s:7:"columns";a:1:{s:11:"analysis_id";s:11:"analysis_id";}}s:7:"feature";a:2:{s:5:"table";s:7:"feature";s:7:"columns";a:1:{s:10:"feature_id";s:10:"feature_id";}}s:15:"blast_organisms";a:2:{s:5:"table";s:15:"blast_organisms";s:7:"columns";a:1:{s:12:"blast_org_id";s:12:"blast_org_id";}}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
> • Could not add custom table blast_hit_data. Please check the schema array.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_organism', 'tripal_analysis_go', 'go_count_organism', 'cvname character varying(255), cvterm_id integer, organism_id integer, feature_count integer', 'cvterm_id,organism_id', 'SELECT T1.cvname, T1.object_id, T1.organism_id, count(T1.feature_id) FROM (SELECT DISTINCT CVT3.name as cvname, CVTP.object_id, O.organism_id, F.feature_id FROM cvtermpath CVTP INNER JOIN CVTerm CVT ON CVTP.subject_id = CVT.cvterm_id INNER JOIN CVTerm CVT2 ON CVTP.type_id = CVT2.cvterm_id INNER JOIN CVTerm CVT3 ON CVTP.object_id = CVT3.cvterm_id INNER JOIN Feature_cvterm FCVT ON FCVT.cvterm_id = CVT.cvterm_id INNER JOIN Feature F ON FCVT.feature_id = F.feature_id INNER JOIN CV ON CV.cv_id = CVT.cv_id INNER JOIN Organism O ON O.organism_id = F.organism_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'') ) as T1 GROUP BY T1.cvname,T1.object_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_analysis', 'tripal_analysis_go', 'go_count_analysis', 'cvname character varying(255), cvterm_id integer, analysis_id integer, organism_id integer, feature_count integer', 'cvterm_id,analysis_id,organism_id', 'SELECT T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id,count(*) as feature_count FROM (SELECT DISTINCT AF.analysis_id, AF.feature_id,CVT.name as cvname, CVT.cvterm_id,CVTP.object_id,CV.name, F.organism_id FROM analysisfeatureprop AFP INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN cvtermpath CVTP ON CVTP.subject_id = AFP.type_id INNER JOIN cvterm CVT ON CVTP.object_id = CVT.cvterm_id INNER JOIN CV ON CV.cv_id = CVT.cv_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'')) as T1 GROUP BY T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('kegg_by_organism', 'kegg_by_organism', 'kegg_by_organism', 'analysis_name character varying(255), analysis_id integer, organism_id integer', 'analysis_id,organism_id', 'SELECT DISTINCT A.name,A.analysis_id,F.organism_id FROM analysisprop AP INNER JOIN analysis A on A.analysis_id = AP.analysis_id INNER JOIN cvterm CVT on CVT.cvterm_id = AP.type_id INNER JOIN analysisfeature AF on AF.analysis_id = A.analysis_id INNER JOIN feature F on F.feature_id = AF.feature_id WHERE CVT.name = ''analysis_kegg_settings''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_unigene_mview', 'tripal_analysis_unigene', 'organism_unigene_mview', 'analysis_id integer, organism_id integer', 'analysis_id, organism_id', 'SELECT DISTINCT A.analysis_id, O.organism_id FROM {Analysis} A INNER JOIN analysisprop AP ON AP.analysis_id = A.analysis_id INNER JOIN cvterm CVT ON AP.type_id = CVT.cvterm_id INNER JOIN cv CV ON CV.cv_id = CVT.cv_id INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN organism O ON F.organism_id = O.organism_id WHERE CV.name = ''tripal'' AND CVT.name=''analysis_unigene_name''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_jan
> _______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel



------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
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] When, where and how are custom tripal tables generated?

Michael Dondrup
Hi Stephen,

Thank you very much, doing it the way you described using drush worked.
I had tried deactivating and
uninstalling the same modules using the web-interface several times,
but that didn't have the desired effect.
Maybe I didn't do that correctly. Whatever, I will use only drush from now on.

Best
Michael

On Jan 30, 2013, at 8:06 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Those tables are added automatically in the install of the tripal_core module.  You would have to uninstall all of the tripal modules to be able to uninstall and re-enable the tripal_core module.  But, if you have features, organisms, etc. synced you will lose all of those synced nodes, and you'll have to resync everything.  You shouldn't lose any data in Chado tables (although it sounds like you dropped your Chado schema anyway).  If you disable tripal_core and then uninstall it and then re-enable it should recreate those tables for you.  Drush commands:
>
> (first uninstall all other tripal modules)
> drush pm-disable tripal_core
> drush pm-uninstall tripal_core
> drush pm-enable tripal_core
> (now re-enable all other tripal modules)
>
> The update functions you see in the tripal_core.install file are for incremental updates to the schema,  but if you install fresh after a complete uninstall you get all of the updates to the tables.
>
> Hope that helps,
>
> Stephen
>
> On 1/30/2013 9:30 AM, Michael Dondrup wrote:
>> Hi,
>>
>> I am trying to get a better understanding of the process that creates the custom tripal tables in the
>> public schema.  After trying a fresh start (I did 'drop schema cascade',  which is not a good idea), I
>> had possibly lost some of the tables outside of the chado schema itself. It is totally
>> possible that I have made a mess here, but on the other hand, I haven't been able to restore some of these
>> tables. Among the tables that are missing are:
>>
>> tripal_custom_tables, tripal_jobs, tripal_mviews*
>>
>> In my understanding, for non-tripal modules, applying deactivate->uninstall->activate to the module
>> will most likely restore their auxilliary tables. I tried this as well, but could not recover the tables.
>>
>> Is there an SQLfile somewhere? or when and how are these tables created,or would it be possible to
>> trigger table create in module activation after uninstall or during chado installation?
>>
>> * I checked in psql, they are really missing. In another database using tripal v0.3 I was able to
>> find table definitions tripal_jobs and tripal_mviews, but not tripal_custom_tables
>>
>> I searched the tripal code base and found:
>>
>> grep -B20 -rie "db_create_table.*tripal_custom_tables" *
>>
>>
>> *  Update for Drupal 6.x, Tripal 0.4
>> tripal_core.install- *  This update
>> tripal_core.install- *   - adjusts the materialized view by adding status, comment and mv_schema columns
>> tripal_core.install- *   - changes the specs of mv_table, mv_specs and indexed
>> tripal_core.install- *   - creates the tripal_custom_tables table
>> tripal_core.install- *
>> tripal_core.install- * @ingroup tripal_feature
>> tripal_core.install- */
>> tripal_core.install-function tripal_core_update_6000() {
>> tripal_core.install-  // add additional columsn to the tripal_mviews table
>> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'status', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
>> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'comment', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
>> tripal_core.install-  db_add_field($ret, 'tripal_mviews', 'mv_schema', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
>> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_table', 'mv_table', array('type' => 'varchar', 'length' => 128, 'not NULL' => FALSE));
>> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'mv_specs', 'mv_specs', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
>> tripal_core.install-  db_change_field($ret, 'tripal_mviews', 'indexed', 'indexed', array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE));
>> tripal_core.install-
>> tripal_core.install-  // create the custom tables table
>> tripal_core.install-  $ret = array();
>> tripal_core.install-  $schema = tripal_core_custom_tables_schema();
>> tripal_core.install:  db_create_table($ret, 'tripal_custom_tables', $schema['tripal_custom_tables']);
>>
>> as the only occurrence. Does this mean that one will get this definition only during an update from 0.3?
>>
>> Best Michael
>>
>>
>> ---------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>> The process in detail:
>>
>> 0.
>> Deactivated all Tripal modules and Views and ahah helper modules, unistalled all these modules.
>>
>>
>> updated to latest tripal dev-version:
>> commit c2c9fbbd0ce3301f5915d602d30205e181cc6078
>> Author: spficklin <[hidden email]>
>> Date:   Thu Jan 24 22:57:17 2013 -0500
>>
>>
>> 1. Only Tripal Core 6.x-1.0 is active:
>>
>> /?q=admin/tripal/custom_tables:
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: query: SELECT * FROM tripal_custom_tables ORDER BY table_name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 270.
>>
>>
>> /?q=admin/tripal/tripal_jobs:
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 217 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: query: SELECT count(*) FROM ( SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC) as t1 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_jobs" does not exist at character 195 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_jobs" does not exist at character 195 query: SELECT TJ.job_id,TJ.uid,TJ.job_name,TJ.modulename,TJ.progress, TJ.status as job_status, TJ,submit_date,TJ.start_time, TJ.end_time,TJ.priority,U.name as username FROM tripal_jobs TJ INNER JOIN users U on TJ.uid = U.uid ORDER BY job_id DESC LIMIT 25 OFFSET 0 in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/jobs.php on line 200.
>>
>>
>> /?q=admin/tripal/mviews:
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: query: SELECT * FROM tripal_mviews ORDER BY name in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/mviews.php on line 462.
>>
>> 2. Run: New Install of Chado v.1.2,
>> no errors, checked that the schema exists
>>
>>
>> 3. Activated Tripal DB 6.x-1.0:
>> no additional warnings (in Databases)
>>
>> 4. Activated Tripal CV:
>> no further warnings
>>
>> 5.  Tripal Organism:
>> 6.  Tripal Analysis
>> 7.  Tripal Feature:
>> /?q=admin/build/modules
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_feature_count', 'tripal_feature', 'organism_feature_count', 'organism_id integer, genus character varying(255), species character varying(255), common_name character varying(255), num_features integer, cvterm_id integer, feature_type character varying(255)', 'organism_id,cvterm_id,feature_type', 'SELECT O.organism_id, O.genus, O.species, O.common_name, count(F.feature_id) as num_features, CVT.cvterm_id, CVT.name as feature_type FROM {Organism} O INNER JOIN Feature F ON O.Organism_id = F.organism_id INNER JOIN Cvterm CVT ON F.type_id = CVT.cvterm_id GROUP BY O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>>
>> 7. Activated Views and ahah-helper module
>> tried to apply the patches before, but I got:
>>
>> patch -p1 < ../tripal/tripal_views/patches/views_data_export-postgresql-1293788-2.patch
>> patching file plugins/views_data_export_plugin_display_export.inc
>> Reversed (or previously applied) patch detected!  Assume -R? [n]
>> Apply anyway? [n]
>> Skipping patch.
>> 3 out of 3 hunks ignored -- saving rejects to file plugins/views_data_export_plugin_display_export.inc.rej
>>
>> So, I assume I had applied the patch already
>>
>>
>>
>> 8. Activated: Analysis Blast, Kegg, GO, Interpro, Unigene (all at once):
>>
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_organisms' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_organisms', 'a:5:{s:5:"table";s:15:"blast_organisms";s:6:"fields";a:2:{s:12:"blast_org_id";a:2:{s:4:"type";s:6:"serial";s:8:"not null";b:1;}s:14:"blast_org_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}}s:11:"primary key";a:1:{i:0;s:12:"blast_org_id";}s:7:"indexes";a:1:{s:18:"blast_org_name_idx";a:1:{i:0;s:14:"blast_org_name";}}s:11:"unique keys";a:1:{s:17:"blast_org_name_uq";a:1:{i:0;s:14:"blast_org_name";}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>> • Could not add custom table blast_organisms. Please check the schema array.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 15 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 15 query: SELECT * FROM tripal_custom_tables WHERE table_name = 'blast_hit_data' in /export/home/licebase/drupal/sites/all/modules/tripal/tripal_core/includes/custom_tables.php on line 106.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_custom_tables" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_custom_tables" does not exist at character 13 query: INSERT INTO tripal_custom_tables (table_name, schema) VALUES ('blast_hit_data', 'a:4:{s:5:"table";s:14:"blast_hit_data";s:6:"fields";a:14:{s:18:"analysisfeature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:11:"analysis_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:10:"feature_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:5:"db_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:7:"hit_num";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:1;}s:8:"hit_name";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:7:"hit_url";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:15:"hit_description";a:2:{s:4:"type";s:4:"text";s:8:"not null";b:0;}s:12:"hit_organism";a:3:{s:4:"type";s:7:"varchar";s:6:"length";i:1025;s:8:"not null";b:0;}s:12:"blast_org_id";a:2:{s:4:"type";s:3:"int";s:8:"not null";b:0;}s:13:"hit_accession";a:3:{s:4:"type";s:7:"varchar";s:6:"length";s:3:"255";s:8:"not null";b:0;}s:13:"hit_best_eval";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:14:"hit_best_score";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}s:7:"hit_pid";a:3:{s:4:"type";s:5:"float";s:4:"size";s:3:"big";s:8:"not null";b:0;}}s:7:"indexes";a:9:{s:18:"analysisfeature_id";a:1:{i:0;s:18:"analysisfeature_id";}s:10:"feature_id";a:1:{i:0;s:10:"feature_id";}s:11:"analysis_id";a:1:{i:0;s:11:"analysis_id";}s:12:"blast_org_id";a:1:{i:0;s:12:"blast_org_id";}s:5:"db_id";a:1:{i:0;s:5:"db_id";}s:12:"hit_organism";a:1:{i:0;s:12:"hit_organism";}s:8:"hit_name";a:1:{i:0;s:12:"hit_organism";}s:13:"hit_accession";a:1:{i:0;s:13:"hit_accession";}s:13:"hit_best_eval";a:1:{i:0;s:13:"hit_best_eval";}}s:12:"foreign keys";a:5:{s:2:"db";a:2:{s:5:"table";s:2:"db";s:7:"columns";a:1:{s:5:"db_id";s:5:"db_id";}}s:15:"analysisfeature";a:2:{s:5:"table";s:15:"analysisfeature";s:7:"columns";a:1:{s:18:"analysisfeature_id";s:18:"analysisfeature_id";}}s:8:"analysis";a:2:{s:5:"table";s:8:"analysis";s:7:"columns";a:1:{s:11:"analysis_id";s:11:"analysis_id";}}s:7:"feature";a:2:{s:5:"table";s:7:"feature";s:7:"columns";a:1:{s:10:"feature_id";s:10:"feature_id";}}s:15:"blast_organisms";a:2:{s:5:"table";s:15:"blast_organisms";s:7:"columns";a:1:{s:12:"blast_org_id";s:12:"blast_org_id";}}}}') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>> • Could not add custom table blast_hit_data. Please check the schema array.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_organism', 'tripal_analysis_go', 'go_count_organism', 'cvname character varying(255), cvterm_id integer, organism_id integer, feature_count integer', 'cvterm_id,organism_id', 'SELECT T1.cvname, T1.object_id, T1.organism_id, count(T1.feature_id) FROM (SELECT DISTINCT CVT3.name as cvname, CVTP.object_id, O.organism_id, F.feature_id FROM cvtermpath CVTP INNER JOIN CVTerm CVT ON CVTP.subject_id = CVT.cvterm_id INNER JOIN CVTerm CVT2 ON CVTP.type_id = CVT2.cvterm_id INNER JOIN CVTerm CVT3 ON CVTP.object_id = CVT3.cvterm_id INNER JOIN Feature_cvterm FCVT ON FCVT.cvterm_id = CVT.cvterm_id INNER JOIN Feature F ON FCVT.feature_id = F.feature_id INNER JOIN CV ON CV.cv_id = CVT.cv_id INNER JOIN Organism O ON O.organism_id = F.organism_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'') ) as T1 GROUP BY T1.cvname,T1.object_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('go_count_analysis', 'tripal_analysis_go', 'go_count_analysis', 'cvname character varying(255), cvterm_id integer, analysis_id integer, organism_id integer, feature_count integer', 'cvterm_id,analysis_id,organism_id', 'SELECT T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id,count(*) as feature_count FROM (SELECT DISTINCT AF.analysis_id, AF.feature_id,CVT.name as cvname, CVT.cvterm_id,CVTP.object_id,CV.name, F.organism_id FROM analysisfeatureprop AFP INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN cvtermpath CVTP ON CVTP.subject_id = AFP.type_id INNER JOIN cvterm CVT ON CVTP.object_id = CVT.cvterm_id INNER JOIN CV ON CV.cv_id = CVT.cv_id WHERE (CV.name = ''biological_process'' or CV.name = ''molecular_function'' or CV.name = ''cellular_component'')) as T1 GROUP BY T1.cvname,T1.cvterm_id,T1.analysis_id,T1.organism_id', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('kegg_by_organism', 'kegg_by_organism', 'kegg_by_organism', 'analysis_name character varying(255), analysis_id integer, organism_id integer', 'analysis_id,organism_id', 'SELECT DISTINCT A.name,A.analysis_id,F.organism_id FROM analysisprop AP INNER JOIN analysis A on A.analysis_id = AP.analysis_id INNER JOIN cvterm CVT on CVT.cvterm_id = AP.type_id INNER JOIN analysisfeature AF on AF.analysis_id = A.analysis_id INNER JOIN feature F on F.feature_id = AF.feature_id WHERE CVT.name = ''analysis_kegg_settings''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>> • warning: pg_query(): Query failed: ERROR: relation "tripal_mviews" does not exist at character 13 in /export/home/licebase/drupal/includes/database.pgsql.inc on line 138.
>> • user warning: ERROR: relation "tripal_mviews" does not exist at character 13 query: INSERT INTO tripal_mviews (name, modulename, mv_table, mv_specs, indexed, query, special_index) VALUES ('organism_unigene_mview', 'tripal_analysis_unigene', 'organism_unigene_mview', 'analysis_id integer, organism_id integer', 'analysis_id, organism_id', 'SELECT DISTINCT A.analysis_id, O.organism_id FROM {Analysis} A INNER JOIN analysisprop AP ON AP.analysis_id = A.analysis_id INNER JOIN cvterm CVT ON AP.type_id = CVT.cvterm_id INNER JOIN cv CV ON CV.cv_id = CVT.cv_id INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id INNER JOIN feature F ON AF.feature_id = F.feature_id INNER JOIN organism O ON F.organism_id = O.organism_id WHERE CV.name = ''tripal'' AND CVT.name=''analysis_unigene_name''', '') in /export/home/licebase/drupal/includes/common.inc on line 3592.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_jan
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel