How to delete an old Blast analysis.

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How to delete an old Blast analysis.

Michael Dondrup-3
Hi,
I was trying to delete an old Blast analysis, however, I have been unable to
figure out the proper way of doing that. The aim is to have the old blast results
no longer appear  under the homology tab for each feature. I have tried several
things:
1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
in chado.

Please let me know to fix this.

Michael

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Re: How to delete an old Blast analysis.

Stephen Ficklin-2

Hi Michael,

I think I see where the problem lies.  But one question.  When you tried to delete the node it should have cascade deleted the analysis in Chado.  Did you receive any error messages during either of your two delete attempts?

Thanks,
Stephen


On 3/1/2017 4:22 AM, Michael Dondrup wrote:
Hi,
I was trying to delete an old Blast analysis, however, I have been unable to
figure out the proper way of doing that. The aim is to have the old blast results
no longer appear  under the homology tab for each feature. I have tried several
things:
1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
in chado.

Please let me know to fix this.

Michael


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Re: How to delete an old Blast analysis.

Michael Dondrup-3
Hi, 
There seem to be 3 different ways to delete the analysis out of which only 1.,2. seems to work:

The first approach is from admin/tripal/chado/tripal_analysis -> Search. In the right column there are links to ‘edit’ and ‘delete’ (node/123/delete&destination=admin/tripal/chado/tripal_analysis/analysis%3Fname%3D%26program%3D%26sourcename%3D)
These links are only shown for analyses that are synced. 

The second is to go via content directly: node/123/delete&destination=admin/content . This seems to work now on our test server, on our 
production server, this had only removed the drupal node, maybe because I was not logged in as User 0 or because my other attempts had created a mess. I should say, that I was trying to replace an old Blast analysis with a newer one which were using the same data base (NR).

The third approach would be via the Analysis -> Delete tab (admin/tripal/chado/tripal_analysis/delete). This generates a tripal job. When trying to run this job, the error messages below are generated.




Tripal Job Launcher
Running as user 'lb_admin'
-------------------
Calling: tripal_analysis_delete_analyses(Array, 382)

NOTE: Deleting analyses 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 1 analyses
strcmp() expects parameter 1 to be string, array given tripal_core.chado_query.api.inc:882       [warning]
Removing orphaned analysis pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_analysis: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error at end of[error]
input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/home/licebase/d7/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).


On Mar 2, 2017, at 6:56 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Michael,

I think I see where the problem lies.  But one question.  When you tried to delete the node it should have cascade deleted the analysis in Chado.  Did you receive any error messages during either of your two delete attempts?

Thanks,
Stephen

On 3/1/2017 4:22 AM, Michael Dondrup wrote:
Hi,
I was trying to delete an old Blast analysis, however, I have been unable to
figure out the proper way of doing that. The aim is to have the old blast results
no longer appear  under the homology tab for each feature. I have tried several
things:
1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
in chado.

Please let me know to fix this.

Michael



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Re: How to delete an old Blast analysis.

Stephen Ficklin-2

Okay, we'll add to our testing for Tripal 2.1 to check the analysis delete functionality.   It sounds like the other two methods work as advertised except on your production server.   Tripal doesn't restrict operations to User 0 specifically. It allows you to set who can do what, but is possible there could be a permission problem.  We'll look into it. 

Stephen


On 3/3/2017 9:03 AM, Michael Dondrup wrote:
Hi, 
There seem to be 3 different ways to delete the analysis out of which only 1.,2. seems to work:

The first approach is from admin/tripal/chado/tripal_analysis -> Search. In the right column there are links to ‘edit’ and ‘delete’ (node/123/delete&destination=admin/tripal/chado/tripal_analysis/analysis%3Fname%3D%26program%3D%26sourcename%3D)
These links are only shown for analyses that are synced. 

The second is to go via content directly: node/123/delete&destination=admin/content . This seems to work now on our test server, on our 
production server, this had only removed the drupal node, maybe because I was not logged in as User 0 or because my other attempts had created a mess. I should say, that I was trying to replace an old Blast analysis with a newer one which were using the same data base (NR).

The third approach would be via the Analysis -> Delete tab (admin/tripal/chado/tripal_analysis/delete). This generates a tripal job. When trying to run this job, the error messages below are generated.




Tripal Job Launcher
Running as user 'lb_admin'
-------------------
Calling: tripal_analysis_delete_analyses(Array, 382)

NOTE: Deleting analyses 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 1 analyses
strcmp() expects parameter 1 to be string, array given tripal_core.chado_query.api.inc:882       [warning]
Removing orphaned analysis pages
Missing argument 3 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988
Missing argument 4 for chado_cleanup_orphaned_nodes(), called in                                 [warning]
/home/licebase/d7/sites/all/modules/tripal/tripal_analysis/includes/tripal_analysis.delete.inc on
line 108 and defined tripal_core.chado_nodes.api.inc:988

FAILED: Rolling back database changes...
WD tripal_analysis: PDOException: SQLSTATE[42601]: Syntax error: 7 ERROR:  syntax error at end of[error]
input
LINE 1: SELECT COUNT(*) FROM
                             ^: SELECT COUNT(*) FROM ; Array
(
)
 in chado_cleanup_orphaned_nodes() (line 1000 of
/home/licebase/d7/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_nodes.api.inc).


On Mar 2, 2017, at 6:56 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Michael,

I think I see where the problem lies.  But one question.  When you tried to delete the node it should have cascade deleted the analysis in Chado.  Did you receive any error messages during either of your two delete attempts?

Thanks,
Stephen

On 3/1/2017 4:22 AM, Michael Dondrup wrote:
Hi,
I was trying to delete an old Blast analysis, however, I have been unable to
figure out the proper way of doing that. The aim is to have the old blast results
no longer appear  under the homology tab for each feature. I have tried several
things:
1. delete via tripal/chado/tripal_analysis/delete , run drush, the Analysis is still there
2. Delete drupal node for the analysis and clean up orphans, node is gone but the analysis is still listed
in chado.

Please let me know to fix this.

Michael



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