<?php
/**
* @file
* Install for a tripal data entity - creates the base table for our entity.
*/
function tripal_entities_install() {
// add any external databases used by the file module.
// tripal_entities_add_dbs();
// add any controlled vocabularies used by the file module.
// tripal_entities_add_cvs();
// add any controlled vocabulary terms
// tripal_entities_add_cvterms();
// add any custom tables. For this case we will add an 'file' table to the
// chado schema
tripal_entities_add_custom_tables();
}
/**
*
*/
function tripal_entities_add_custom_tables() {
tripal_entities_add_tripal_vocabulary_table();
tripal_entities_add_tripal_vocabulary_usage_table();
tripal_entities_add_tripal_term_table();
tripal_entities_add_tripal_term_usage_table();
tripal_entities_add_tripal_term_relationship_table();
}
/**The current Entity Example (Genes) requires the Sequence Ontology. [warning]
*
*/
function tripal_entities_add_tripal_vocabulary_table() {
$schema = array (
'table' => 'tripal_vocabulary',
'fields' => array (
'vocabulary_id' => array(
'type' => 'serial',
'not null' => TRUE
),
'cv_id' => array (
'type' => 'int',
'not null' => TRUE
),
'db_id' => array (
'type' => 'int',
'not null' => TRUE
),
'publish' => array (
'type' => 'int',
'not null' => TRUE,
'default' => 0
),
),
'primary key' => array (
0 => 'vocabulary_id'
),
'foreign keys' => array (
'cv' => array (
'table' => 'cv',
'columns' => array (
'cv_id' => 'cv_id'
)
),
'db' => array (
'table' => 'db',
'columns' => array (
'db_id' => 'db_id'
)
),
),
'unique keys' => array (
'tripal_vocabulary_cvdb' => array (
'cv_id', 'db_id'
),
),
'indexes' => array(
'tripal_vocabulary_cv_id' => array('cv_id'),
'tripal_vocabulary_db_id' => array('db_id'),
)
);
chado_create_custom_table('tripal_vocabulary', $schema, TRUE);
}
/**
*
*/
function tripal_entities_add_tripal_term_table() {
$schema = array (
'table' => 'tripal_term',
'fields' => array (
'term_id' => array(
'type' => 'serial',
'not null' => TRUE
),
'vocabulary_id' => array (
'type' => 'int',
'not null' => TRUE
),
'cvterm_id' => array (
'type' => 'int',
'not null' => TRUE
),
'publish' => array (
'type' => 'int',
'not null' => TRUE,
'default' => 0
),
),
'primary key' => array (
0 => 'term_id'
),
'foreign keys' => array (
'cvterm' => array (
'table' => 'cvterm',
'columns' => array (
'cvterm_id' => 'cvterm_id'
)
),
'tripal_vocabulary' => array (
'table' => 'tripal_vocabulary',
'columns' => array (
'vocabulary_id' => 'vocabulary_id'
)
),
),
'unique keys' => array (
'tripal_term_unq' => array (
'vocabulary_id', 'cvterm_id'
),
),
'indexes' => array(
'tripal_term_vocabulary_id' => array('vocabulary_id'),
'tripal_term_cvterm_id' => array('cvterm_id'),
),
);
chado_create_custom_table('tripal_term', $schema, TRUE);
}
/**
*
*/
function tripal_entities_add_tripal_vocabulary_usage_table(){
$schema = array (
'table' => 'tripal_vocabulary_usage',
'fields' => array (
'vocabulary_usage_id' => array(
'type' => 'serial',
'not null' => TRUE
),
'vocabulary_id' => array (
'type' => 'int',
'not null' => TRUE
),
'data_table' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
'type_table' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
'field' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
),
'primary key' => array (
0 => 'vocabulary_usage_id'
),
'foreign keys' => array (
'tripal_vocabulary' => array (
'table' => 'tripal_vocabulary',
'columns' => array (
'vocabulary_id' => 'vocabulary_id'
),
),
),
'unique keys' => array (
'tripal_vocabulary_ridbase' => array (
'vocabulary_id', 'data_table'
),
),
'indexes' => array(
'tripal_vocabulary_vocabulary_id' => array('vocabulary_id'),
'tripal_vocabulary_data_table' => array('data_table'),
'tripal_vocabulary_type_table' => array('type_table'),
),
);
chado_create_custom_table('tripal_vocabulary_usage', $schema, TRUE);
}
/**
*
*/
function tripal_entities_add_tripal_term_usage_table(){
$schema = array (
'table' => 'tripal_term_usage',
'fields' => array (
'term_usage_id' => array(
'type' => 'serial',
'not null' => TRUE
),
'term_id' => array (
'type' => 'int',
'not null' => TRUE
),
'data_table' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
'type_table' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
'field' => array (
'type' => 'varchar',
'length' => 128,
'not null' => TRUE
),
),
'primary key' => array (
0 => 'term_usage_id'
),
'foreign keys' => array (
'tripal_term' => array (
'table' => 'tripal_term',
'columns' => array (
'term_id' => 'term_id'
),
),
),
'unique keys' => array (
'tripal_term_usage_ridbase' => array (
'term_id', 'type_table', 'field'
),
),
'indexes' => array(
'tripal_term_usage_term_id' => array('term_id'),
),
);
chado_create_custom_table('tripal_term_usage', $schema, TRUE);
}
/**
*
*/
function tripal_entities_add_tripal_term_relationship_table(){
$schema = array (
'table' => 'tripal_term_relationship',
'fields' => array (
'relationship_id' => array(
'type' => 'serial',
'not null' => TRUE
),
'subject_id' => array (
'type' => 'int',
'not null' => TRUE
),
'type_id' => array (
'type' => 'int',
'not null' => TRUE
),
'object_id' => array (
'type' => 'int',
'not null' => FALSE
),
'fieldname' => array(
'type' => 'varchar',
'length' => 128,
'not null' => FALSE,
)
),
'primary key' => array (
0 => 'relationship_id'
),
'foreign keys' => array (
'tripal_term' => array (
'table' => 'tripal_term',
'columns' => array (
'subject_id' => 'term_id',
'object_id' => 'term_id',
),
),
),
'unique keys' => array (
'tripal_term_relationship_unq' => array (
'subject_id', 'type_id', 'object_id'
),
),
'indexes' => array(
'tripal_term_relationship_subject_id' => array('subject_id'),
'tripal_term_relationship_object_id' => array('object_id'),
'tripal_term_relationship_type_id' => array('type_id'),
),
);
chado_create_custom_table('tripal_term_relationship', $schema, TRUE);
}
/**
* Implements hook_schema().
*
* @ingroup entity_example
*/
function tripal_entities_schema() {
$schema['tripal_entity'] = array(
'description' => 'The base table for Tripal Vocabulary-based entities.',
'fields' => array(
'id' => array(
'description' => 'The primary identifier for a vocabulary entity.',
'type' => 'serial',
'unsigned' => TRUE,
'not null' => TRUE,
),
'type' => array(
'description' => 'The type of entity. This should be an official vocabulary ID (e.g. SO, RO, GO).',
'type' => 'varchar',
'length' => 64,
'not null' => TRUE,
'default' => '',
),
'bundle' => array(
'description' => 'The type of bundle. This should be an official vocabulary ID (e.g. SO, RO, GO) followed by an underscore and the term accession.',
'type' => 'varchar',
'length' => 1024,
'not null' => TRUE,
'default' => '',
),
'cvterm_id' => array(
'description' => 'The cvterm_id for the type of entity. This cvterm_id should match a record in the Chado cvterm table.',
'type' => 'int',
'not null' => TRUE,
),
'title' => array(
'description' => 'The title of this node, always treated as non-markup plain text.',
'type' => 'text',
'not null' => TRUE,
'default' => '',
),
'uid' => array(
'description' => 'The {users}.uid that owns this node; initially, this is the user that created it.',
'type' => 'int',
'not null' => TRUE,
'default' => 0,
),
'status' => array(
'description' => 'Boolean indicating whether the node is published (visible to non-administrators).',
'type' => 'int',
'not null' => TRUE,
'default' => 1,
),
'created' => array(
'description' => 'The Unix timestamp when the node was created.',
'type' => 'int',
'not null' => TRUE,
'default' => 0,
),
'changed' => array(
'description' => 'The Unix timestamp when the node was most recently saved.',
'type' => 'int',
'not null' => TRUE,
'default' => 0,
),
),
'indexes' => array(
'cvterm_id' => array('cvterm_id'),
'entity_changed' => array('changed'),
'entity_created' => array('created'),
'type' => array('type'),
'uid' => array('uid'),
),
'unique keys' => array(
),
'primary key' => array('id'),
);
$schema['tripal_bundle'] = array(
'description' => 'Stores information about defined tripal data types.',
'fields' => array(
'id' => array(
'type' => 'serial',
'not null' => TRUE,
'description' => 'Primary Key: Unique Chado data type identifier.',
),
'type' => array(
'description' => 'The type of entity. This should be an official vocabulary ID (e.g. SO, RO, GO).',
'type' => 'varchar',
'length' => 64,
'not null' => TRUE,
'default' => '',
),
'bundle' => array(
'description' => 'The type of bundle. This should be an official vocabulary ID (e.g. SO, RO, GO) followed by an underscore and the term accession.',
'type' => 'varchar',
'length' => 1024,
'not null' => TRUE,
'default' => '',
),
'label' => array(
'description' => 'The human-readable name of this bundle.',
'type' => 'varchar',
'length' => 255,
'not null' => TRUE,
'default' => '',
),
'weight' => array(
'type' => 'int',
'not null' => TRUE,
'default' => 0,
'size' => 'tiny',
'description' => 'The weight of this tripal data type in relation to others.',
),
'data' => array(
'type' => 'text',
'not null' => FALSE,
'size' => 'big',
'serialize' => TRUE,
'description' => 'A serialized array of additional data related to this tripal data type.',
),
) + entity_exportable_schema_fields(),
'primary key' => array('id'),
'unique keys' => array(
'bundle' => array('bundle'),
),
);
$schema['chado_entity'] = array(
'description' => 'The linker table that associates an enitity from the public.tripal_entity table with a "base" record in Chado',
'fields' => array(
'chado_entity_id' => array(
'description' => 'The primary identifier for this table.',
'type' => 'serial',
'unsigned' => TRUE,
'not null' => TRUE,
),
'entity_id' => array(
'description' => 'The unique entity id.',
'type' => 'int',
'not null' => TRUE,
),
'record_id' => array(
'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
'type' => 'int',
'not null' => TRUE,
),
'data_table' => array(
'description' => 'Indicates the table in Chado that this term services (e.g. feature, stock, library, etc.)',
'type' => 'varchar',
'length' => 128,
'not null' => TRUE,
'default' => '',
),
'type_table' => array(
'description' => 'Sometimes the record in the data table doesn’t have a field that specifies the record type. For example, an analysis type is stored in the analysisprop table. If the data_table does have a type field then this value will be the same as the data_table.',
'type' => 'varchar',
'length' => 128,
'not null' => TRUE,
'default' => '',
),
'field' => array(
'description' => 'The name of the field in the typetable that contains the cvterm record.',
'type' => 'varchar',
'length' => 128,
'not null' => FALSE,
'default' => ''
),
),
'indexes' => array(
'record_id' => array('record_id'),
'entity_id' => array('entity_id'),
'data_table' => array('data_table'),
),
'unique keys' => array(
'record' => array('data_table', 'record_id'),
'entity_id' => array('entity_id'),
),
'primary key' => array('chado_entity_id'),
);
return $schema;
}
/**
* Implements hook_uninstall().
*
* At uninstall time we'll notify field.module that the entity was deleted
* so that attached fields can be cleaned up.
*/
function tripal_entities_uninstall() {
// TODO: make this dynamic (not hardcoded bundle).
$terms = chado_generate_var('tripal_term', array('publish' => 1), array('return_array' => 1));
foreach ($terms as $term) {
$entity_type = $term->vocab_id->db_id->name;
$bundle_id = $term->cvterm_id->dbxref_id->db_id->name . '_' . $term->cvterm_id->dbxref_id->accession;
print "$entity_type : $bundle_id\n";
field_attach_delete_bundle($entity_type, $bundle_id);
}
}