deleting organisms

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deleting organisms

Sofia Robb-3
Hi,

I get the below error when trying to delete organisms. This is a brand new install. I am running tripal core 7.x-2.0.

$ drush trp-run-jobs --username=drupal --root=/var/www/html
Tripal Job Launcher
Running as user 'drupal'
-------------------
Calling: tripal_organism_delete_organisms(Array, 11)

NOTE: Deleting organisms is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
deletions is rolled back and will not be found in the database

Deleting 12 organisms
Removing orphaned organism pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_organism: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error [error]
at end of input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).

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Re: deleting organisms

Kucheran, Lacey Sanderson
Hi Sofia,

I can confirm that this error is reproducible. I’m working on fixing it now.

Thanks for reporting it!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On March 3, 2016 at 9:59:53 AM, Sofia Robb ([hidden email]) wrote:

Hi,

I get the below error when trying to delete organisms. This is a brand new install. I am running tripal core 7.x-2.0.

$ drush trp-run-jobs --username=drupal --root=/var/www/html
Tripal Job Launcher
Running as user 'drupal'
-------------------
Calling: tripal_organism_delete_organisms(Array, 11)

NOTE: Deleting organisms is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
deletions is rolled back and will not be found in the database

Deleting 12 organisms
Removing orphaned organism pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_organism: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error [error]
at end of input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).
------------------------------------------------------------------------------
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Re: deleting organisms

Sofia Robb-3
Hi Lacey,

I just installed the dev version. It works perfectly. 

Sofia

On Thu, Mar 3, 2016 at 10:01 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Sofia,

I can confirm that this error is reproducible. I’m working on fixing it now.

Thanks for reporting it!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On March 3, 2016 at 9:59:53 AM, Sofia Robb ([hidden email]) wrote:

Hi,

I get the below error when trying to delete organisms. This is a brand new install. I am running tripal core 7.x-2.0.

$ drush trp-run-jobs --username=drupal --root=/var/www/html
Tripal Job Launcher
Running as user 'drupal'
-------------------
Calling: tripal_organism_delete_organisms(Array, 11)

NOTE: Deleting organisms is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
deletions is rolled back and will not be found in the database

Deleting 12 organisms
Removing orphaned organism pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_organism: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error [error]
at end of input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).
------------------------------------------------------------------------------
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Troubleshoot faster and improve end-user experience. Signup Now!
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------------------------------------------------------------------------------
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APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
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Re: deleting organisms

Kucheran, Lacey Sanderson
Great :-) I was just sending an email to that effect.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On March 3, 2016 at 10:05:09 AM, Sofia Robb ([hidden email]) wrote:

Hi Lacey,

I just installed the dev version. It works perfectly. 

Sofia

On Thu, Mar 3, 2016 at 10:01 AM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Sofia,

I can confirm that this error is reproducible. I’m working on fixing it now.

Thanks for reporting it!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On March 3, 2016 at 9:59:53 AM, Sofia Robb ([hidden email]) wrote:

Hi,

I get the below error when trying to delete organisms. This is a brand new install. I am running tripal core 7.x-2.0.

$ drush trp-run-jobs --username=drupal --root=/var/www/html
Tripal Job Launcher
Running as user 'drupal'
-------------------
Calling: tripal_organism_delete_organisms(Array, 11)

NOTE: Deleting organisms is performed using a database transaction.
If the load fails or is terminated prematurely then the entire set of
deletions is rolled back and will not be found in the database

Deleting 12 organisms
Removing orphaned organism pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                        [warning]
/var/www/html/sites/all/modules/tripal/tripal_organism/includes/tripal_organism.delete.inc
on line 107 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_organism: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error [error]
at end of input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
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[hidden email]
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------------------------------------------------------------------------------
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APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
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_______________________________________________
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[hidden email]
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