column "type_id" violates not-null constraint

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column "type_id" violates not-null constraint

Sofia Robb
Hi,

I have a new fresh install of tripal and drupal. I was unable to load the relationship ontology, but I saw in a post in the mailing list that it might not be necessary, so I moved on. I am now trying to load a gff with source features of type contig. i get this error, is this due to the missing ro.obo? Or is this something different?

Thanks,
Sofia

Tripal Job Launcher
Running as user 'administrator'
-------------------
bash-4.2$ ~/.composer/vendor/bin/drush trp-run-jobs --username=administrator --root=/var/www/html
Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_load_gff3(/var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff, 13, 11, 0, 1, 0, 0, 1, , , 0, , contig, , 0, 18)

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

Opening /var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff
Parsing Line 0 (0.00%). Memory: 26,552,560 bytes
FAILED: Rolling back database changes...
WD tripal_feature: PDOException: SQLSTATE[23502]: Not null violation: 7 ERROR:  null value in column "type_id" violates not-null constraint      [error]
DETAIL:  Failing row contains (4, 43297, 43296, null, null, 0).: INSERT INTO chado.feature_relationship (subject_id, object_id, type_id) VALUES
(:subject_id, :object_id, :type_id); Array
(
    [:subject_id] => 43297
    [:object_id] => 43296
    [:type_id] =>
)
 in chado_query() (line 1505 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).

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Re: column "type_id" violates not-null constraint

Stephen Ficklin-2
Hi Sofia,

The most recent version of Tripal uses the relationship terms from the sequence ontology rather than the relationship ontology.   It seems the failure is due to an insert in the feature_relationship record.  Are you using the most recent development version of Tripal?  Did you have any problems when loading the sequence ontology?

Stephen

On 12/21/2015 2:33 PM, Sofia Robb wrote:
Hi,

I have a new fresh install of tripal and drupal. I was unable to load the relationship ontology, but I saw in a post in the mailing list that it might not be necessary, so I moved on. I am now trying to load a gff with source features of type contig. i get this error, is this due to the missing ro.obo? Or is this something different?

Thanks,
Sofia

Tripal Job Launcher
Running as user 'administrator'
-------------------
bash-4.2$ ~/.composer/vendor/bin/drush trp-run-jobs --username=administrator --root=/var/www/html
Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_load_gff3(/var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff, 13, 11, 0, 1, 0, 0, 1, , , 0, , contig, , 0, 18)

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

Opening /var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff
Parsing Line 0 (0.00%). Memory: 26,552,560 bytes
FAILED: Rolling back database changes...
WD tripal_feature: PDOException: SQLSTATE[23502]: Not null violation: 7 ERROR:  null value in column "type_id" violates not-null constraint      [error]
DETAIL:  Failing row contains (4, 43297, 43296, null, null, 0).: INSERT INTO chado.feature_relationship (subject_id, object_id, type_id) VALUES
(:subject_id, :object_id, :type_id); Array
(
    [:subject_id] => 43297
    [:object_id] => 43296
    [:type_id] =>
)
 in chado_query() (line 1505 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).


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Re: column "type_id" violates not-null constraint

Sofia Robb
Hi Stephen,

I was running the most current stable, I forgot to install the dev version. Seems to be working!!

Thanks Again!!!
Sofia

On Tue, Dec 22, 2015 at 1:28 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Sofia,

The most recent version of Tripal uses the relationship terms from the sequence ontology rather than the relationship ontology.   It seems the failure is due to an insert in the feature_relationship record.  Are you using the most recent development version of Tripal?  Did you have any problems when loading the sequence ontology?

Stephen


On 12/21/2015 2:33 PM, Sofia Robb wrote:
Hi,

I have a new fresh install of tripal and drupal. I was unable to load the relationship ontology, but I saw in a post in the mailing list that it might not be necessary, so I moved on. I am now trying to load a gff with source features of type contig. i get this error, is this due to the missing ro.obo? Or is this something different?

Thanks,
Sofia

Tripal Job Launcher
Running as user 'administrator'
-------------------
bash-4.2$ ~/.composer/vendor/bin/drush trp-run-jobs --username=administrator --root=/var/www/html
Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_load_gff3(/var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff, 13, 11, 0, 1, 0, 0, 1, , , 0, , contig, , 0, 18)

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

Opening /var/other_data/organisms/planaria/Smed/SmedSxl/genomes/SmedSxl_v3.1/analysis/MAKER_082015/SmedSxl_genome_v3.1.maker.renamed.gff
Parsing Line 0 (0.00%). Memory: 26,552,560 bytes
FAILED: Rolling back database changes...
WD tripal_feature: PDOException: SQLSTATE[23502]: Not null violation: 7 ERROR:  null value in column "type_id" violates not-null constraint      [error]
DETAIL:  Failing row contains (4, 43297, 43296, null, null, 0).: INSERT INTO chado.feature_relationship (subject_id, object_id, type_id) VALUES
(:subject_id, :object_id, :type_id); Array
(
    [:subject_id] => 43297
    [:object_id] => 43296
    [:type_id] =>
)
 in chado_query() (line 1505 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).


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