Re: load relationship ontology

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Re: load relationship ontology

Stephen Ficklin-2
Hello,

I'm CC'ing my response to the Tripal mailing list in the event others have the same question. Unfortunately, this problem occurs with the current version of the Relationship Ontology (RO).  There are some new constructs to the ro.obo file that are not documented in the OBO v1.3 specification and therefore the Tripal OBO Loader has problems with it.  We're working to fix this and should have something soon.  The RO has also changed quite a bit from when it was first included with Chado.  If you do not have an immediate need for the current terms in the RO you may find that the terms you need may be in the Sequence Ontology (e.g. part_of, derives_from, etc).  Tripal's FASTA and GFF loaders do not use the RO so if you are planning to use those loaders you should be fine without it.

Best,
Stephen

On 12/4/2015 10:18 PM, 黎志 wrote:
HI,
    When I load Relationship ontology,erros following:
    /var/www# drush trp-run-jobs --username=administrator
Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_cv_load_obo_v1_2_id(1, 6)
Downloading URL http://purl.obolibrary.org/obo/ro.obo, saving to /tmp/obo_lZpGyv

NOTE: Loading of this OBO 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

Step 1: Preloading File /tmp/obo_lZpGyv
WD t_obo_loader: This OBO is missing the 'default-namespace' header. [warning]
It is not possible to determine which vocabulary terms without a
'namespace' key should go.  Instead, those terms will be placed in
the 'RO' vocabulary.

Step 2: Loading type defs...
458 of 458 records. (100.00%) Memory: 28,484,760 bytes
Step 3: Loading terms...
WD T_obo_loader: Cannot add cvterm cell part                         [error]
[site http://default] [TRIPAL ERROR] [T_OBO_LOADER] Cannot add cvterm cell part
Drush command terminated abnormally due to an unrecoverable error.   [error]
PHP Fatal error:  Uncaught exception 'PDOException' with message 'SQLSTATE[23503]: Foreign key violation: 7 ERROR:  insert or update on table "cvterm_dbxref" violates foreign key constraint "cvterm_dbxref_cvterm_id_fkey"
DETAIL:  Key (cvterm_id)=(836) is not present in table "cvterm".' in /var/www/includes/database/database.inc:1148
Stack trace:
#0 /var/www/includes/database/database.inc(1148): PDO->commit()
#1 /var/www/includes/database/database.inc(1131): DatabaseConnection->popCommittableTransactions()
#2 /var/www/includes/database/database.inc(1908): DatabaseConnection->popTransaction('drupal_transact...')
#3 [internal function]: DatabaseTransaction->__destruct()
#4 {main}
  thrown in /var/www/includes/database/database.inc on line 1148
Thanks for your answer!


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