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Tripal 0.3b
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Tripal 0.3b
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Functions | |
| tripal_cv_load_obo_v1_2_id ($obo_id, $jobid=NULL) | |
| tripal_cv_load_obo_v1_2_file ($obo_name, $file, $jobid=NULL, $is_new=1) | |
| tripal_cv_load_obo_v1_2_url ($obo_name, $url, $jobid=NULL, $is_new=1) | |
| tripal_cv_load_update_cvtermpath ($newcvs, $jobid) | |
| tripal_cv_load_obo_v1_2 ($file, $jobid=NULL, &$newcvs) | |
| tripal_cv_obo_quiterror ($message) | |
| tripal_cv_obo_loader_done () | |
| tripal_cv_obo_process_terms ($terms, $defaultcv, $obo, $jobid=null, &$newcvs) | |
| tripal_cv_obo_process_term ($term, $defaultcv, $obo, $is_relationship=0, &$newcvs) | |
| tripal_cv_obo_add_db ($dbname) | |
| tripal_cv_obo_add_cv ($name, $comment) | |
| tripal_cv_obo_add_cvterm_prop ($cvterm, $property, $value, $rank) | |
| tripal_cv_obo_add_relationship ($cvterm, $defaultcv, $obo, $rel, $objname, $object_is_relationship=0) | |
| tripal_cv_obo_get_term ($obo, $id) | |
| tripal_cv_obo_add_synonyms ($term, $cvterm) | |
| tripal_cv_obo_add_cv_term ($term, $defaultcv, $is_relationship=0, $update=1) | |
| tripal_cv_obo_add_cvterm_dbxref ($cvterm, $xref) | |
| tripal_cv_obo_add_dbxref ($db_id, $accession, $version='', $description='') | |
| tripal_cv_obo_parse ($obo_file, &$obo, &$header) | |
| tripal_cv_obo_form (&$form_state=NULL) | |
| tripal_cv_obo_form_submit ($form, &$form_state) | |
| tripal_cv_load_obo_v1_2 | ( | $ | file, |
| $ | jobid = NULL, |
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| &$ | newcvs | ||
| ) |
Definition at line 107 of file obo_loader.php.
References tripal_cv_obo_add_cv(), tripal_cv_obo_add_db(), tripal_cv_obo_loader_done(), tripal_cv_obo_parse(), tripal_cv_obo_process_term(), tripal_cv_obo_process_terms(), tripal_cv_obo_quiterror(), and tripal_db_set_active().
Referenced by tripal_cv_load_obo_v1_2_file(), and tripal_cv_load_obo_v1_2_url().
| tripal_cv_load_obo_v1_2_file | ( | $ | obo_name, |
| $ | file, | ||
| $ | jobid = NULL, |
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| $ | is_new = 1 |
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| ) |
Definition at line 40 of file obo_loader.php.
References tripal_cv_load_obo_add_ref(), tripal_cv_load_obo_v1_2(), and tripal_cv_load_update_cvtermpath().
Referenced by tripal_cv_load_obo_v1_2_id().
| tripal_cv_load_obo_v1_2_id | ( | $ | obo_id, |
| $ | jobid = NULL |
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| ) |
Definition at line 12 of file obo_loader.php.
References $_SERVER, tripal_cv_load_obo_v1_2_file(), and tripal_cv_load_obo_v1_2_url().
| tripal_cv_load_obo_v1_2_url | ( | $ | obo_name, |
| $ | url, | ||
| $ | jobid = NULL, |
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| $ | is_new = 1 |
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| ) |
Definition at line 55 of file obo_loader.php.
References tripal_cv_load_obo_add_ref(), tripal_cv_load_obo_v1_2(), and tripal_cv_load_update_cvtermpath().
Referenced by tripal_cv_load_obo_v1_2_id().
| tripal_cv_load_update_cvtermpath | ( | $ | newcvs, |
| $ | jobid | ||
| ) |
Definition at line 89 of file obo_loader.php.
References tripal_cv_update_cvtermpath().
Referenced by tripal_cv_load_obo_v1_2_file(), and tripal_cv_load_obo_v1_2_url().
| tripal_cv_obo_add_cv | ( | $ | name, |
| $ | comment | ||
| ) |
Definition at line 337 of file obo_loader.php.
References tripal_cv_obo_quiterror().
Referenced by tripal_cv_load_obo_v1_2(), tripal_cv_obo_add_cv_term(), and tripal_cv_obo_add_cvterm_prop().
| tripal_cv_obo_add_cv_term | ( | $ | term, |
| $ | defaultcv, | ||
| $ | is_relationship = 0, |
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| $ | update = 1 |
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| ) |
Definition at line 544 of file obo_loader.php.
References tripal_cv_obo_add_cv(), tripal_cv_obo_add_db(), tripal_cv_obo_add_dbxref(), and tripal_cv_obo_quiterror().
Referenced by tripal_core_load_gff3_alias(), tripal_cv_obo_add_cvterm_prop(), tripal_cv_obo_add_relationship(), tripal_cv_obo_add_synonyms(), and tripal_cv_obo_process_term().
| tripal_cv_obo_add_cvterm_dbxref | ( | $ | cvterm, |
| $ | xref | ||
| ) |
Definition at line 662 of file obo_loader.php.
References tripal_cv_obo_add_db(), tripal_cv_obo_add_dbxref(), and tripal_cv_obo_quiterror().
Referenced by tripal_cv_obo_process_term().
| tripal_cv_obo_add_cvterm_prop | ( | $ | cvterm, |
| $ | property, | ||
| $ | value, | ||
| $ | rank | ||
| ) |
Definition at line 365 of file obo_loader.php.
References tripal_cv_obo_add_cv(), tripal_cv_obo_add_cv_term(), and tripal_cv_obo_quiterror().
Referenced by tripal_cv_obo_process_term().
| tripal_cv_obo_add_db | ( | $ | dbname | ) |
Definition at line 321 of file obo_loader.php.
References tripal_cv_obo_quiterror().
Referenced by tripal_cv_load_obo_v1_2(), tripal_cv_obo_add_cv_term(), and tripal_cv_obo_add_cvterm_dbxref().
| tripal_cv_obo_add_dbxref | ( | $ | db_id, |
| $ | accession, | ||
| $ | version = '', |
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| $ | description = '' |
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| ) |
Definition at line 706 of file obo_loader.php.
References tripal_cv_obo_quiterror().
Referenced by tripal_cv_obo_add_cv_term(), and tripal_cv_obo_add_cvterm_dbxref().
| tripal_cv_obo_add_relationship | ( | $ | cvterm, |
| $ | defaultcv, | ||
| $ | obo, | ||
| $ | rel, | ||
| $ | objname, | ||
| $ | object_is_relationship = 0 |
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| ) |
Definition at line 412 of file obo_loader.php.
References tripal_cv_obo_add_cv_term(), tripal_cv_obo_get_term(), and tripal_cv_obo_quiterror().
Referenced by tripal_cv_obo_process_term().
| tripal_cv_obo_add_synonyms | ( | $ | term, |
| $ | cvterm | ||
| ) |
Definition at line 467 of file obo_loader.php.
References tripal_cv_obo_add_cv_term(), and tripal_cv_obo_quiterror().
Referenced by tripal_cv_obo_process_term().
| tripal_cv_obo_form | ( | &$ | form_state = NULL | ) |
Purpose: Provides the form to load an already existing controlled Vocabulary into chado
Definition at line 841 of file tripal_cv.module.
| tripal_cv_obo_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Purpose: The submit function for the load ontology form. It registers a tripal job to run the obo_loader.php script
Definition at line 937 of file tripal_cv.module.
References $args, $user, and tripal_add_job().
| tripal_cv_obo_get_term | ( | $ | obo, |
| $ | id | ||
| ) |
Definition at line 452 of file obo_loader.php.
Referenced by tripal_cv_obo_add_relationship().
| tripal_cv_obo_loader_done | ( | ) |
Definition at line 163 of file obo_loader.php.
References tripal_db_set_active().
Referenced by tripal_cv_load_obo_v1_2().
| tripal_cv_obo_parse | ( | $ | obo_file, |
| &$ | obo, | ||
| &$ | header | ||
| ) |
Definition at line 729 of file obo_loader.php.
Referenced by tripal_cv_load_obo_v1_2().
| tripal_cv_obo_process_term | ( | $ | term, |
| $ | defaultcv, | ||
| $ | obo, | ||
| $ | is_relationship = 0, |
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| &$ | newcvs | ||
| ) |
Definition at line 199 of file obo_loader.php.
References tripal_cv_obo_add_cv_term(), tripal_cv_obo_add_cvterm_dbxref(), tripal_cv_obo_add_cvterm_prop(), tripal_cv_obo_add_relationship(), tripal_cv_obo_add_synonyms(), and tripal_cv_obo_quiterror().
Referenced by tripal_cv_load_obo_v1_2(), and tripal_cv_obo_process_terms().
| tripal_cv_obo_process_terms | ( | $ | terms, |
| $ | defaultcv, | ||
| $ | obo, | ||
| $ | jobid = null, |
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| &$ | newcvs | ||
| ) |
Definition at line 173 of file obo_loader.php.
References tripal_cv_obo_process_term(), tripal_cv_obo_quiterror(), and tripal_job_set_progress().
Referenced by tripal_cv_load_obo_v1_2().
| tripal_cv_obo_quiterror | ( | $ | message | ) |
Definition at line 154 of file obo_loader.php.
Referenced by tripal_core_load_gff3_alias(), tripal_cv_load_obo_v1_2(), tripal_cv_obo_add_cv(), tripal_cv_obo_add_cv_term(), tripal_cv_obo_add_cvterm_dbxref(), tripal_cv_obo_add_cvterm_prop(), tripal_cv_obo_add_db(), tripal_cv_obo_add_dbxref(), tripal_cv_obo_add_relationship(), tripal_cv_obo_add_synonyms(), tripal_cv_obo_process_term(), and tripal_cv_obo_process_terms().
1.7.4 
