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Tripal
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Functions | |
| tripal_chado_prepare_form ($form, $form_state) | |
| tripal_chado_prepare_form_submit ($form, $form_state) | |
| tripal_chado_prepare_drush_submit () | |
| tripal_chado_load_ontologies () | |
| tripal_chado_prepare_chado ($job=NULL) | |
| tripal_chado_prepare_general_types ($job) | |
| tripal_chado_prepare_genomic_types ($job) | |
| tripal_chado_prepare_expression_types ($job) | |
| tripal_chado_prepare_germplasm_types ($job) | |
| tripal_chado_prepare_genetic_types ($job) | |
| _tripal_chado_prepare_create_bundle ($args, $job) | |
| tripal_chado_add_v1_1_custom_tables () | |
| tripal_chado_add_v1_2_custom_tables () | |
| tripal_chado_add_vx_x_custom_tables () | |
| tripal_chado_fix_v1_3_custom_tables () | |
Functions to install chado schema through Drupal
| _tripal_chado_prepare_create_bundle | ( | $args, | |
| $job | |||
| ) |
A helper function to consolidate the code used to create a bundle.
| tripal_chado_add_v1_1_custom_tables | ( | ) |
For Chado v1.1 Tripal provides some new custom tables.
For Chado v1.2 or greater these tables are not needed as they are part of the schema update.
| tripal_chado_add_v1_2_custom_tables | ( | ) |
For Chado v1.2 Tripal provides some new custom tables.
For Chado v1.3 these tables are not needed as they are part of the schema update.
| tripal_chado_add_vx_x_custom_tables | ( | ) |
Add custom tables for any version of Chado.
These are tables that Chado uses to manage the site (i.e. temporary loading tables) and not for primary data storage.
| tripal_chado_fix_v1_3_custom_tables | ( | ) |
Many of the custom tables created for Chado v1.2 are now in Chado v1.3.
These tables need not be tracked by Tripal anymore as custom tables and in some cases the Chado version has different columns so we need to adjust them.
| tripal_chado_prepare_chado | ( | $job = NULL | ) |
Prepares Chado for use by Tripal.
| tripal_chado_prepare_drush_submit | ( | ) |
Submit function for the tripal_chado_prepare_form().
| $form | |
| $form_state |
| tripal_chado_prepare_expression_types | ( | $job | ) |
Creates the "Expression" category of content types.
| tripal_chado_prepare_form | ( | $form, | |
| $form_state | |||
| ) |
Prepares Chado for Tripal use
| tripal_chado_prepare_form_submit | ( | $form, | |
| $form_state | |||
| ) |
Submit function for the tripal_chado_prepare_form().
| $form | |
| $form_state |
| tripal_chado_prepare_general_types | ( | $job | ) |
Creates the "General" category of content types.
| tripal_chado_prepare_genetic_types | ( | $job | ) |
Creates the "Genetic" category of content types.
| tripal_chado_prepare_genomic_types | ( | $job | ) |
Creates the "Genomic" category of content types.
| tripal_chado_prepare_germplasm_types | ( | $job | ) |
Creates the "Germplasm/Breeding" category of content types.
SPF: We need a bit more testing before we add this conteont type as it resolves to the cvterm table. Currently, it can't be created. $args = array( 'vocabulary' => 'NCIT', 'accession' => 'C85496', 'term_name' => 'Phenotypic Trait', 'storage_args' => array( 'data_table' => 'cvterm', 'type_column' => 'type_id', ), 'category' => 'Germplasm/Breeding', ); _tripal_chado_prepare_create_bundle($args, $job);
1.9.1