tripal/tripal_feature/tripal_feature.install

<?php
/**
 * @file
 * Installation of the feature module
 */

/**
 * Implements hook_disable().
 *
 * Disable default views when module is disabled
 *
 * @ingroup tripal_feature
 */
function tripal_feature_disable() {

  // Disable all default views provided by this module
  require_once("tripal_feature.views_default.inc");
  $views = tripal_feature_views_default_views();
  foreach (array_keys($views) as $view_name) {
    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
  }

}

/**
 * Implements hook_requirements().
 *
 * @ingroup tripal_feature
 */
function tripal_feature_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!$GLOBALS["chado_is_installed"]) {
      $requirements ['tripal_feature'] = array(
          'title' => "t ripal_feature",
          'value' => "ERROR: Chado must be installed before this module can be enabled",
          'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/**
 * Implements hook_install().
 *
 * @ingroup tripal_feature
 */
function tripal_feature_install() {

  // Add the feature properties vocabulary provided by Chado.
  $obo_path = '{tripal_feature}/files/feature_property.obo';
  $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
  tripal_submit_obo_job(array('obo_id' => $obo_id));

  // Add the materialized view.
  tripal_feature_add_organism_count_mview();

  // Add the custom tables.
  tripal_feature_add_tripal_gff_temp_table();
  tripal_feature_add_tripal_gffcds_temp_table();
  tripal_feature_add_tripal_gffprotein_temp_table();

  // Add the vocabularies used by the feature module.
  tripal_feature_add_cvs();

  // Set the default vocabularies.
  tripal_set_default_cv('feature', 'type_id', 'sequence');
  tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
  tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
}

/**
 * Implements hook_uninstall().
 *
 * @ingroup tripal_feature
 */
function tripal_feature_uninstall() {

}

function tripal_feature_add_tripal_gff_temp_table() {
  $schema = array(
    'table' => 'tripal_gff_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'uniquename' => array(
        'type' => 'text',
        'not null' => TRUE,
      ),
      'type_name' => array(
        'type' => 'varchar',
        'length' => '1024',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('organism_id'),
      'tripal_gff_temp_idx1' => array('uniquename'),
    ),
    'unique keys' => array(
      'tripal_gff_temp_uq0' => array('feature_id'),
      'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'),
    ),
  );
  chado_create_custom_table('tripal_gff_temp', $schema, TRUE);
}

/**
 *
 */
function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
  $schema = array(
    'table' => 'tripal_gffcds_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'parent_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'phase' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'strand' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmin' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmax' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('parent_id'),
    ),
  );
  chado_create_custom_table('tripal_gffcds_temp', $schema, $skip_recreate);
}

/**
 *
 */
function tripal_feature_add_tripal_gffprotein_temp_table() {
  $schema = array(
    'table' => 'tripal_gffprotein_temp',
    'fields' => array(
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'parent_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmin' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'fmax' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'tripal_gff_temp_idx0' => array('feature_id'),
      'tripal_gff_temp_idx0' => array('parent_id'),
    ),
    'unique keys' => array(
      'tripal_gff_temp_uq0' => array('feature_id'),
    ),
  );
  chado_create_custom_table('tripal_gffprotein_temp', $schema, TRUE);
}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_feature
 */
function tripal_feature_schema() {

  $schema['chado_feature'] = array(
    'fields' => array(
      'vid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not null' => TRUE,
        'default' => 0
       ),
      'nid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not null' => TRUE,
        'default' => 0
       ),
      'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
      ),
      'sync_date' => array(
        'type' => 'int',
        'not null' => FALSE,
        'description' => 'UNIX integer sync date/time'
      ),
    ),
    'indexes' => array(
      'chado_feature_idx1' => array('feature_id')
    ),
    'unique keys' => array(
      'chado_feature_uq1' => array('nid', 'vid'),
      'chado_feature_uq2' => array('vid')
    ),
    'primary key' => array('nid'),
  );

  return $schema;
};

/**
 * Creates a materialized view that stores the type & number of features per organism
 *
 * @ingroup tripal_feature
 */
function tripal_feature_add_organism_count_mview() {
  $view_name = 'organism_feature_count';
  $comment = 'Stores the type and number of features per organism';

  $schema = array(
    'description' => $comment,
    'table' => $view_name,
    'fields' => array(
      'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'genus' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'species' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'common_name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
      ),
      'num_features' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'feature_type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'organism_feature_count_idx1' => array('organism_id'),
      'organism_feature_count_idx2' => array('cvterm_id'),
      'organism_feature_count_idx3' => array('feature_type'),
    ),
  );

  $sql = "
    SELECT
        O.organism_id, O.genus, O.species, O.common_name,
        count(F.feature_id) as num_features,
        CVT.cvterm_id, CVT.name as feature_type
     FROM organism O
        INNER JOIN feature F  ON O.Organism_id = F.organism_id
        INNER JOIN cvterm CVT ON F.type_id     = CVT.cvterm_id
     GROUP BY
        O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
}
/**
 * Add cvs related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_feature_add_cvs() {

  // Add cv for relationship types
  tripal_insert_cv(
    'feature_relationship',
    'Contains types of relationships between features.'
  );

  // the feature_property CV already exists... it comes with chado, but we need to
  // add it just in case it doesn't get added before the feature module is installed
  tripal_insert_cv(
    'feature_property',
    'Stores properties about features'
  );

  // the feature type vocabulary should be the sequence ontology, and even though
  // this ontology should get loaded we will create it here just so that we can
  // set the default vocabulary for the feature.type_id field
  tripal_insert_cv(
    'sequence',
    'The Sequence Ontology'
  );
}

/**
 * This is the required update for tripal_feature when upgrading from Drupal core API 6.x.
 * This update may take some time to complete.
 */
function tripal_feature_update_7200() {
  // During the upgrade from D6 to D7 the vocabulary terms assigned to features were
  // copied to the field_data_taxonomyextra table rather than to the correct
  // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
  $vid = db_query("SELECT vid FROM {taxonomy_vocabulary} WHERE name = 'Feature Type'")->fetchField();
  if ($vid) {
    try {
      // first move from the field_data_taxonomyextra table
      $sql = "
        INSERT INTO {field_data_taxonomy_vocabulary_$vid}
          (entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomy_vocabulary_" . $vid. "_tid)
        (SELECT entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomyextra_tid
         FROM field_data_taxonomyextra
         WHERE bundle = 'chado_feature')
      ";
      db_query($sql);
      $sql = "DELETE FROM field_data_taxonomyextra WHERE bundle = 'chado_feature'";
      db_query($sql);

      // next move from the field_revision_taxonomyextra table
      $sql = "
        INSERT INTO {field_revision_taxonomy_vocabulary_$vid}
          (entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomy_vocabulary_" . $vid. "_tid)
        (SELECT entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomyextra_tid
         FROM field_revision_taxonomyextra
         WHERE bundle = 'chado_feature')
      ";
      db_query($sql);
      $sql = "DELETE FROM field_revision_taxonomyextra WHERE bundle = 'chado_feature'";
      db_query($sql);
    }
    catch (\PDOException $e) {
      $error = $e->getMessage();
      throw new DrupalUpdateException('Could not move feature taxonomy terms: '. $error);
    }
  }

  // set the default feature property vocabulary
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'feature_property'")->fetchField();
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'featureprop',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
        ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to set feature_property vocabulary as default: '. $error);
  }

  // add the feature_relationshp CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'feature_relationship'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'feature_relationship',
        'definition' => 'Contains types of relationships between features.'
      ))
      ->execute();
    }
    // use the new feature_relationship CV we just added
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'feature_relationship',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add feature_relationship vocabulary: '. $error);
  }

  // set the feature_type as the 'sequence' ontology
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'sequence'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'sequence',
        'definition' => 'The Sequence Ontology.'
      ))
      ->execute();
    }
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'feature',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add sequence vocabulary which will be used for the sequence ontology: '. $error);
  }


}

/**
 * Implementation of hook_update_dependencies().  It specifies a list of
 * other modules whose updates must be run prior to this one.
 */
function tripal_feature_update_dependencies() {
  $dependencies = array();

  // the tripal_cv update 7200 must run prior to update 7200 of this module
  $dependencies['tripal_feature'][7200] = array(
    'tripal_cv' => 7200
  );

  return $dependencies;
}

/**
 * Fixes an error with the materialized view installation
 *
 */
function tripal_feature_update_7201() {

  try {
    // there is a bug in the Tripal v2.0-alpha release that didn't add the
    // materialized view schema to the mviews table.
    // get the schema for the materialized view from the custom_tables table
    // as there is a copy there, but only if the schema is missing from the
    // materialized view table
    $view_name = 'organism_feature_count';
    $schema = db_select('tripal_mviews', 'tm')
      ->fields('tm', array('mv_schema'))
      ->condition('name', $view_name)
      ->execute()
      ->fetchField();
    if (!$schema or $schema == 'Array') {
      $schema = db_select('tripal_custom_tables', 'tct')
        ->fields('tct', array('schema'))
        ->condition('table_name', $view_name)
        ->execute()
        ->fetchField();
      $schema_str = var_export(unserialize($schema), TRUE);
      $schema_str = preg_replace('/=>\s+\n\s+array/', '=> array', $schema_str);
      db_update('tripal_mviews')
        ->fields(array(
        'mv_schema' => $schema_str
        ))
        ->condition('name', $view_name)
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to complete update' . $error);
  }
}

/**
 * Adds the temporary tables used for loading GFF files.
 */
function tripal_feature_update_7202() {
  try {
    tripal_feature_add_tripal_gff_temp_table();
    tripal_feature_add_tripal_gffcds_temp_table();
    tripal_feature_add_tripal_gffprotein_temp_table();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to complete update' . $error);
  }
}

/**
 * Removes the unique constraint on the tripal_gffcds_temp table.
 */
function tripal_feature_update_7203() {
  try {
    tripal_feature_add_tripal_gffcds_temp_table(FALSE);
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to complete update' . $error);
  }
}