tripal/tripal_entities/tripal_entities.install

<?php
/**
 * @file
 * Install for a tripal data entity - creates the base table for our entity.
 */

/**
 * Implements hook_install().
 */
function tripal_entities_install() {

  // Unfortunately, some Chado base tables do not have a type_id, so we must
  // take special action for those tables.  These include: organism and
  // analysis. Until we can find an appropriate controlled vocabulary
  // that is well supported by the community with types for these tables we
  // will have to use in-house terms.

  // Add a term to be used for an inherent 'type_id' for the organism table.
  tripal_insert_cvterm(array(
    'id' => 'local:organism',
    'name' => 'organism',
    'definition' => 'An individual form of life, such as a bacterium, protist, ' .
      'fungus, plant, or animal, composed of a single cell or a complex of cells  ' .
      'in which organelles or organs work together to carry out the various  ' .
      'processes of life. (American Heritage® Dictionary of the English ' .
      'Language, Fifth Edition. Copyright © 2011 by Houghton Mifflin ' .
      'Harcourt Publishing Company).',
    'cv_name' => 'local',
  ));

  // Add a term to be used for an inherent 'type_id' for the organism table.
  tripal_insert_cvterm(array(
    'id' => 'local:analysis',
    'name' => 'analysis',
    'definition' => 'A process as a method of studying the nature of something ' .
      'or of determining its essential features and their relations. ' .
      '(Random House Kernerman Webster\'s College Dictionary, © 2010 K ' .
      'Dictionaries Ltd).',
    'cv_name' => 'local',
  ));

  tripal_insert_cvterm(array(
    'id' => 'local:project',
    'name' => 'project',
    'definition' => 'A plan or proposal for accomplishing something. ' .
      '(American Heritage® Dictionary of the English Language, Fifth Edition. ' .
      'Copyright © 2011 by Houghton Mifflin Harcourt Publishing Company).',
    'cv_name' => 'local',
  ));

  // We want to provide a set of commonly used entity types by default. This
  // way when a user first installs Tripal there are some commonly used
  // formats.
  module_load_include('inc', 'tripal_entities', 'api/tripal_entities.api');
  module_load_include('inc', 'tripal_entities', 'includes/tripal_entities.admin');

  // Create the 'Organism' entity type. This uses the local:organism term.
  $error = '';
  $term = array('name' => 'organism', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_entity_type($cvterm, $error)) {
    throw new Exception($error);
  }

  // Create the 'Analysis' entity type. This uses the local:analysis term.
  $error = '';
  $term = array('name' => 'analysis', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_entity_type($cvterm, $error)) {
    throw new Exception($error);
  }

  // Create the 'Project' entity type. This uses the local:project term.
  $error = '';
  $term = array('name' => 'project', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_entity_type($cvterm, $error)) {
    throw new Exception($error);
  }
}

/**
 * Implements hook_schema().
 */
function tripal_entities_schema() {

  // Adds a table for managing TripalEntity entities.
  $schema['tripal_entity'] = tripal_entities_tripal_entity_schema();

  // Adds a table for managing the TripalEntity entity types (bundles).
  $schema['tripal_bundle'] = tripal_entities_tripal_bundle_schema();
  
  // Adds a table for additional information related to bundles.
  $schema['tripal_bundle_variables'] = tripal_entities_tripal_bundle_variables_schema();

  // Links TripalEntity entities to the chado record.
  $schema['chado_entity'] = tripal_entities_chado_entity_schema();

  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() {
//   $terms = chado_generate_var('tripal_term', array('publish' => 1), array('return_array' => 1));
//   foreach ($terms as $term) {
//     $bundle_id = 'bio-data_' . $term->cvterm_id;
//     field_attach_delete_bundle('TripalEntity', $bundle_id);
//   }
}

/**
 * @section
 * Schema Definitions.
 */

/**
 * The base table for Biological Data Entities.
 *
 * This contains the actual data. For example, if you have a 5 genes and 10 mRNA then
 * this table will have 15 records and include both genes and mRNA's.
 */
function tripal_entities_tripal_entity_schema() {

  $schema = 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'),
  );
  return $schema;
}

/**
 * The base table for Biological Data Type Entites.
 * This table contains a list of Biological Data Types.
 * For the example above (5 genes and 10 mRNAs), there would only be two records in
 * this table one for "gene" and another for "mRNA".
 */
function tripal_entities_tripal_bundle_schema() {

  $schema = 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'),
    ),
  );
  return $schema;
}

/**
 * Additional Tripal Bundle Information.
 *
 * This table is used for storing any additonal information describing
 * a tripal bundle. For example, this is a good place to store title/url formats.
 */
function tripal_entities_tripal_bundle_variables_schema() {

  $schema = array(
    'description' => 'This table is used for storing any additonal information describing
      a tripal bundle. For example, this is a good place to store title/url formats.',
    'fields' => array (
      'bundle_variable_id' => array (
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'bundle_id' => array (
        'type' => 'int',
        'not null' => TRUE,
      ),
      'variable_id' => array (
        'type' => 'int',
        'not null' => TRUE,
      ),
      'value' => array (
        'type' => 'text',
        'not null' => FALSE,
      ),
      'rank' => array (
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
    ),
    'primary key' => array (
      0 => 'bundle_variable_id',
    ),
    'unique keys' => array (
      'tripal_bundle_variables_c1' => array (
        0 => 'bundle_id',
        1 => 'variable_id',
        2 => 'rank',
      ),
    ),
    'indexes' => array (
      'tripal_bundle_variables_idx1' => array (
        0 => 'variable_id',
      ),
    ),
    'foreign keys' => array (
      'tripal_variables' => array (
        'table' => 'tripal_variables',
        'columns' => array (
          'variable_id' => 'variable_id',
        ),
      ),
    ),
  );
  
  return $schema;
}

/**
 * Links Biological Data Entities to the chado "base" table the data is stored in.
 * This is where we would specify that a particular gene maps to the record in the
 * chado.feature table with a feature_id=2432;
 */
function tripal_entities_chado_entity_schema() {

  $schema = 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;
}