tripal/tripal_chado/tripal_chado.install

<?php

function tripal_chado_install() {
  // The foreign key specification doesn't really add one to the
  // Drupal schema, it is just used internally, but we want one.
  db_query('
      ALTER TABLE {tripal_custom_tables}
      ADD CONSTRAINT tripal_custom_tables_fk1
      FOREIGN KEY (mview_id) REFERENCES {tripal_mviews} (mview_id)
      ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
  ');
}


/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal
 */
function tripal_chado_uninstall() {

  // Drop the foreign key between tripal_custom_tables and tripal_mviews
  // so that Drupal can then drop the tables
  db_query('
    ALTER TABLE {tripal_custom_tables}
    DROP CONSTRAINT tripal_custom_tables_fk1 CASCADE
  ');
}

/**
 * Table definition for the tripal_cv_obo table
 * @param $schema
 */
function tripal_chado_tripal_cv_obo_schema() {
  return array(
    'fields' => array(
      'obo_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255
      ),
      'path'  => array(
        'type' => 'varchar',
        'length' => 1024
      ),
    ),
    'indexes' => array(
      'tripal_cv_obo_idx1' => array('obo_id'),
    ),
    'primary key' => array('obo_id'),
  );
}

/**
 * * Table definition for the tripal_cv_defaults table
 * @param unknown $schema
 */
function tripal_chado_tripal_cv_defaults_schema() {
  return array(
    'fields' => array(
      'cv_default_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE
      ),
      'table_name' => array(
        'type' => 'varchar',
        'length' => 128,
        'not null' => TRUE,
      ),
      'field_name' => array(
        'type' => 'varchar',
        'length' => 128,
        'not null' => TRUE,
      ),
      'cv_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      )
    ),
    'indexes' => array(
      'tripal_cv_defaults_idx1' => array('table_name', 'field_name'),
    ),
    'unique keys' => array(
      'tripal_cv_defaults_unq1' => array('table_name', 'field_name', 'cv_id'),
    ),
    'primary key' => array('cv_default_id')
  );
}



/**
 * Add's defaults to the tripal_cv_obo table
 *
 * @ingroup tripal_cv
 */
function tripal_cv_add_obo_defaults() {

  // Insert commonly used ontologies into the tables.
  $ontologies = array(
    array('Relationship Ontology', 'http://purl.obolibrary.org/obo/ro.obo'),
    //    array('Relationship Ontology (older deprecated version)', 'http://www.obofoundry.org/ro/ro.obo'),
    array('Sequence Ontology', 'https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo'),
    array('Gene Ontology', 'http://www.geneontology.org/ontology/gene_ontology.obo'),
    //    array('Cell Ontology', 'https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl.obo'),
  //    array('Plant Structure Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co'),
  //    array('Plant Growth and Development Stages Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co')
  );
  foreach ($ontologies as $o) {
    db_query("INSERT INTO {tripal_cv_obo} (name,path) VALUES (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
  }
}


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

  // Links TripalEntity entities to the chado record.
  $schema['chado_entity'] = tripal_chado_chado_entity_schema();
  $schema['tripal_mviews'] = tripal_chado_tripal_mviews_schema();
  $schema['tripal_custom_tables'] = tripal_chado_tripal_custom_tables_schema();

  $schema['tripal_cv_obo'] = tripal_chado_tripal_cv_obo_schema();
  $schema['tripal_cv_defaults'] = tripal_chado_tripal_cv_defaults_schema();
  $schema['tripal_pub_import'] = tripal_chado_tripal_pub_import_schema();

  // if this module is already installed and enabled, then we want to provide
  // the schemas for all of the custom tables.  This will allow Views to
  // see the schemas.  We check if the module is installed because during
  // installation we don't want to make these custom tables available as we don't
  // want them created in the Drupal database.  The custom tables go in the
  // Chado database.
  if (db_table_exists('tripal_custom_tables')) {
    $sql = 'SELECT * FROM {tripal_custom_tables}';
    $results = db_query($sql);
    foreach ($results as $custom) {
      $schema[$custom->table_name] = unserialize($custom->schema);
    }
  }

  return $schema;
}

/**
 * @section
 * Schema Definitions.
 */
/**
 * Describes the Tripal Custom Tables (tripal_custom_tables) table
 * This keeps track of tables created by Tripal and stored in chado that may or may not
 * also be materialized views.
 *
 * @ingroup tripal
 */
function tripal_chado_tripal_custom_tables_schema() {
  return array(
    'fields' => array(
      'table_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not NULL' => TRUE
      ),
      'table_name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not NULL' => TRUE
      ),
      'schema' => array(
        'type' => 'text',
        'not NULL' => TRUE
      ),
      'mview_id' => array(
        'type' => 'int',
        'not NULL' => FALSE
      )
    ),
    'indexes' => array(
      'table_id' => array('table_id'),
    ),
    'primary key' => array('table_id'),
    'foreign keys' => array(
      'tripal_mviews' => array(
        'table' => 'tripal_mviews',
        'columns' => array(
          'mview_id' => 'mview_id'
        ),
      ),
    ),
  );
}
/**
 * Describes the Tripal Materialized View (tripal_mviews) table
 * This table keeps track of all materialized views created by Tripal and stored in chado
 *
 * @ingroup tripal
 */
function tripal_chado_tripal_mviews_schema() {
  return array(
    'fields' => array(
      'mview_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not NULL' => TRUE
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not NULL' => TRUE
      ),
      'modulename' => array(
        'type' => 'varchar',
        'length' => 50,
        'not NULL' => TRUE,
        'description' => 'The module name that provides the callback for this job'
      ),
      'mv_table' => array(
        'type' => 'varchar',
        'length' => 128,
        'not NULL' => FALSE
      ),
      'mv_specs' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'mv_schema' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'indexed' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'query' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => TRUE
      ),
      'special_index' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'last_update' => array(
        'type' => 'int',
        'not NULL' => FALSE,
        'description' => 'UNIX integer time'
      ),
      'status'        => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'comment' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
    ),
    'indexes' => array(
      'mview_id' => array('mview_id')
    ),
    'unique keys' => array(
      'mv_table' => array('mv_table'),
      'mv_name' => array('name'),
    ),
    'primary key' => array('mview_id'),
  );
}

/**
 * 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_chado_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;
}