tripal/tripal_library/tripal_library.install

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

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

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

}

/**
 * Implementation of hook_requirements().
 *
 * @ingroup tripal_library
 */
function tripal_library_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!$GLOBALS["chado_is_installed"]) {
      $requirements ['tripal_library'] = array(
        'title' => "tripal_library",
        'value' => "ERROR: Chado must be installed before this module can be enabled",
        'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_library
 */
function tripal_library_install() {

  // add the materialized view
  tripal_library_add_mview_library_feature_count();

  // add cvterms
  tripal_library_add_cvs();
  tripal_library_add_cvterms();

  // set the default vocabularies
  tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
  tripal_set_default_cv('library', 'type_id', 'library_type');
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_library
 */
function tripal_library_uninstall() {

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_library
 */
function tripal_library_schema() {
  $schema['chado_library'] = 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
      ),
      'library_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
      )
    ),
    'indexes' => array(
      'chado_library_idx1' => array('library_id')
    ),
    'unique keys' => array(
      'chado_library_uq1' => array('nid', 'vid'),
      'chado_library_uq2' => array('vid')
    ),
    'primary key' => array('nid'),
  );
  return $schema;
}

/**
 * Adds a materialized view keeping track of the type of features associated with each library
 *
 * @ingroup tripal_library
 */
function tripal_library_add_mview_library_feature_count(){
  $view_name = 'library_feature_count';
  $comment = 'Provides count of feature by type that are associated with all libraries';

  $schema = array(
    'table' => $view_name,
    'description' => $comment,
    'fields' => array(
      'library_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'num_features' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'feature_type' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'library_feature_count_idx1' => array('library_id'),
    ),
  );

  $sql = "
    SELECT
      L.library_id, L.name,
      count(F.feature_id) as num_features,
      CVT.name as feature_type
    FROM library L
      INNER JOIN library_feature LF  ON LF.library_id = L.library_id
      INNER JOIN feature F           ON LF.feature_id = F.feature_id
      INNER JOIN cvterm CVT          ON F.type_id     = CVT.cvterm_id
    GROUP BY L.library_id, L.name, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
}

/**
 * Adds new CV's used by this module
 *
 * @ingroup tripal_library
 */
function tripal_library_add_cvs(){
  tripal_insert_cv(
    'library_property',
    'Contains properties for libraries.'
  );
  tripal_insert_cv(
    'library_type',
    'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).'
  );
}

/**
 * Adds cvterms needed for the library module
 *
 * @ingroup tripal_library
 */
function tripal_library_add_cvterms() {

  // Insert cvterm 'library_description' into cvterm table of chado
  // database. This CV term is used to keep track of the library
  // description in the libraryprop table.
  tripal_insert_cvterm(
     array(
       'name' => 'Library Description',
       'definition' => 'Description of a library',
       'cv_name' => 'library_property',
       'is_relationship' => 0,
       'db_name' => 'tripal'
      ),
      array('update_existing' => TRUE)
   );

  // add cvterms for the map unit types
  tripal_insert_cvterm(
    array(
      'name' => 'cdna_library',
      'definition' => 'cDNA library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
    array(
      'name' => 'bac_library',
      'definition' => 'Bacterial Artifical Chromsome (BAC) library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
    array(
      'name' => 'fosmid_library',
      'definition' => 'Fosmid library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
    array(
      'name' => 'cosmid_library',
      'definition' => 'Cosmid library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
    array(
      'name' => 'yac_library',
      'definition' => 'Yeast Artificial Chromosome (YAC) library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
    array(
      'name' => 'genomic_library',
      'definition' => 'Genomic Library',
      'cv_name' => 'library_type',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    ),
    array('update_existing' => TRUE)
  );
}

/**
 * This is the required update for tripal_library when upgrading from Drupal core API 6.x.
 *
 */
function tripal_library_update_7200() {
  // Make sure we have the full API loaded this will help during a
  // site upgrade when the tripal_core module is disabled.
  module_load_include('module', 'tripal_core', 'tripal_core');
  tripal_core_import_api();

  // the library types were formerly in a vocabulary named 'tripal_library_types'.
  // rename that to just be 'library_type'. We cannot use the Tripal API calls
  // because during upgrade the tripal_core should also be disabled
  try {
    $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_type'")->fetchObject();
    if (!$check->cv_id) {
      $sql = "UPDATE chado.cv SET name = 'library_type' WHERE name = 'tripal_library_types'";
      db_query($sql);
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to change the vocabulary from tripal_library_types to library_type: '. $error);
  }

  // add the library_property CV
  try {
    $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_property'")->fetchObject();
    if (!$check->cv_id) {
      $sql = "INSERT INTO chado.cv (name, definition) VALUES (
        'library_property',
        'Contains properties for libraries.')
      ";
      db_query($sql);
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add library_property vocabulary: '. $error);
  }

  // add the library_type CV
  try {
    $check = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_type'")->fetchObject();
    if (!$check->cv_id) {
      $sql = "INSERT INTO chado.cv (name, definition) VALUES (
        'library_type',
        'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).')
      ";
      db_query($sql);
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add library_type vocabulary: '. $error);
  }

  // For Tripal in Drupal 6 the library_description cvterm was stored in the
  // 'tripal' CV.  It should be stored in the new library_property CV that
  // is added by this module for Tripal 2.0 and Drupal 7.  So, we need to
  // reset the CV ID for that term and rename the term to 'Library Description'
  // We cannot use the Tripal API calls in the 7000 update
  // because during upgrade the tripal_core should also be disabled
  $sql = "
    UPDATE chado.cvterm
    SET
      name = 'Library Description',
      cv_id = (SELECT cv_id FROM chado.cv WHERE name = 'library_property')
    WHERE
      name = 'library_description' AND
      cv_id = (SELECT cv_id FROM chado.cv WHERE name = 'tripal')
  ";
  try {
    db_query($sql);
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to change library_description property type to the library_property CV and update the name: '. $error);
  }

  // During the upgrade from D6 to D7 the vocabulary terms assigned to libraries were
  // copied to the field_data_taxonomyextra table rather than to the correct
  // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
  $vid = db_query("SELECT vid FROM {taxonomy_vocabulary} WHERE name = 'Library'")->fetchField();
  if ($vid) {
    try {
      if (db_table_exists('field_data_taxonomyextra')) {
        // 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);
        $sql = "DELETE FROM field_data_taxonomyextra WHERE bundle = 'chado_library'";
        db_query($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);
        $sql = "DELETE FROM field_revision_taxonomyextra WHERE bundle = 'chado_library'";
        db_query($sql);
      }
    }
    catch (\PDOException $e) {
      $error = $e->getMessage();
      throw new DrupalUpdateException('Could not move library taxonomy terms: '. $error);
    }
  }

  // set the default vocabularies
  // library_type
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_type'")->fetchField();
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'library')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
          'table_name' => 'library',
          'field_name' => 'type_id',
          'cv_id' => $cv_id
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to set library_type vocabulary as default: '. $error);
  }
  // library_property
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'library_property'")->fetchField();
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'libraryprop')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
          'table_name' => 'libraryprop',
          'field_name' => 'type_id',
          'cv_id' => $cv_id
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to set the library_property vocabulary as default: '. $error);
  }

}

/**
 * Implementation of hook_update_dependencies().
 *
 * It specifies a list of other modules whose updates must be run prior to
 * this one.  It also ensures the the Tripal API is in scope for site
 * upgrades when tripal_core is disabled.
 */
function tripal_library_update_dependencies() {

  $dependencies = array();

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

  return $dependencies;
}

/**
 * Fixes an error with the materialized view installation
 *
 */
function tripal_library_update_7201() {
  // Make sure we have the full API loaded this will help during a
  // site upgrade when the tripal_core module is disabled.
  module_load_include('module', 'tripal_core', 'tripal_core');
  tripal_core_import_api();

  // 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 = 'library_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();
  }
}