tripal/tripal/tripal.install

<?php
/**
 * @file
 * Contains functions used to install/uninstall tripal.
 */

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal
 */
function tripal_install() {

  // Add tripal bundle variables needed for storing additional settings for
  // Tripal Bundles.
  tripal_insert_variable(
    'title_format',
    'A pattern including tokens that can be used to generate tripal entity titles.'
  );
  tripal_insert_variable(
    'url_format',
    'A pattern including tokens that can be used to generate tripal entity url aliases.'
  );
  tripal_insert_variable(
    'description',
    'The description of a Tripal Entity type/bundle.'
  );


}



/**
 *
 */
function tripal_uninstall() {
  /*
   // So somehow I was able to uninstall this module without deleting the bundles. This
   // caused aweful errors because fields weren't deleted so when I re-installed, the code
   // tried to create fields that were inactive (despite checking if the field exists
   // before creating). The following code was meant to ensure that all content was deleted
   // before uninstall so these errors would not occur. Unfortunatly I am now unable to
   // test this because the Field API module is disabling uninstall of Tripal Chado until
   // all the content is deleted. Thus ensuring the errors described above don't occur.
   // But I'm Sure I was able to uninstall with content before...
   // **I am slowly going crazy; Crazy going slowly am I**
   // Anyway, I'll leaving the solution code here in case I am able to repeat it in
   // the future.
   // @see https://www.drupal.org/node/1262092
   // @see https://www.drupal.org/node/1861710

   // First delete all TripalEntities.
   $entity_ids = (new EntityFieldQuery)->entityCondition("entity_type", "TripalEntity")->execute();
   $entity_ids = reset($entity_ids);
   entity_delete_multiple("TripalEntity", array_keys($entity_ids));

   // Then delete all TripalBundles.
   $bundle_ids = (new EntityFieldQuery)->entityCondition("entity_type", "TripalBundle")->execute();
   $bundle_ids = reset($bundle_ids);
   entity_delete_multiple("TripalBundle", array_keys($bundle_ids));

   // @TODO: Should we delete all TripalVocabularies and TripalTerms?

   // Finally purge all fields that are no longer used.
   field_purge_batch(100);
   */
}

/**
 *
 */
function tripal_enable() {
  // If Tripal v2 is already installed, the installation of this module
  // will try and recreate some of the tables created with tripal_core and the
  // installation will fail.  Therefore, in the install we renamed it. Now
  // we want to move it back.
  if (db_table_exists('tripal_jobs2')) {
    $sql = "DROP TABLE tripal_jobs";
    db_query($sql);
    $sql = "ALTER TABLE tripal_jobs2 RENAME to tripal_jobs";
    db_query($sql);
    $sql = "ALTER INDEX tripal_jobs_job_id_idx2 RENAME TO tripal_jobs_job_id_idx";
    db_query($sql);
    $sql = "ALTER INDEX tripal_jobs_job_name_idx2 RENAME TO tripal_jobs_job_name_idx";
    db_query($sql);
    $sql = "ALTER INDEX tripal_jobs_pkey2 RENAME TO tripal_jobs_pkey";
    db_query($sql);
    // schema change
    $sql = "ALTER TABLE tripal_jobs ADD COLUMN includes text";
    db_query($sql);
  }

  if (db_table_exists('tripal_token_formats2')) {
    $sql = "DROP TABLE tripal_token_formats";
    db_query($sql);
    $sql = "ALTER TABLE tripal_token_formats2 RENAME TO tripal_token_formats";
    db_query($sql);
    $sql = "ALTER INDEX tripal_token_formats_pkey2 RENAME TO tripal_token_formats_pkey";
    db_query($sql);
    $sql = "ALTER INDEX tripal_token_formats_type_application_key2 RENAME TO tripal_token_formats_type_application_key";
    db_query($sql);
  }

  if (db_table_exists('tripal_variables2')) {
    $sql = "DROP TABLE tripal_variables";
    db_query($sql);
    $sql = "ALTER TABLE tripal_variables2 RENAME TO tripal_variables";
    db_query($sql);
    $sql = "ALTER INDEX tripal_variables_pkey2 RENAME TO tripal_variables_pkey";
    db_query($sql);
    $sql = "ALTER INDEX tripal_variables_tripal_variable_names_idx1_idx2 RENAME TO tripal_variables_tripal_variable_names_idx1_idx";
    db_query($sql);
    $sql = "ALTER INDEX tripal_variables_tripal_variables_c1_key2 RENAME TO tripal_variables_tripal_variables_c1_key";
    db_query($sql);
  }
}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal
 */
function tripal_schema() {

  // If Tripal v2 is already installed, the installation of this module
  // will try and recreate some of the tables created with tripal_core and the
  // installation will fail.  Therefore, we need to temporarily move those
  // tables out of the way, let the module install and then move them back.
  $migrated = variable_get ('tripal_v2_upgrade_v3_check', FALSE);
  if (!$migrated) {
    if (db_table_exists('tripal_jobs')) {
      // Move the tripal_jobs table out of the way.
      $sql = "ALTER TABLE tripal_jobs RENAME TO tripal_jobs2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_jobs_job_id_idx RENAME TO tripal_jobs_job_id_idx2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_jobs_job_name_idx RENAME TO tripal_jobs_job_name_idx2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_jobs_pkey RENAME TO tripal_jobs_pkey2";
      db_query($sql);
    }

    if (db_table_exists('tripal_token_formats')) {
      // Move the tripal_token_formats table out of the way.
      $sql = "ALTER TABLE tripal_token_formats RENAME TO tripal_token_formats2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_token_formats_pkey RENAME TO tripal_token_formats_pkey2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_token_formats_type_application_key RENAME TO tripal_token_formats_type_application_key2";
      db_query($sql);
    }

    if (db_table_exists('tripal_variables')) {
      // Move the tripal_variables table out of the way.
      $sql = "ALTER TABLE tripal_variables RENAME TO tripal_variables2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_variables_pkey RENAME TO tripal_variables_pkey2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_variables_tripal_variable_names_idx1_idx RENAME TO tripal_variables_tripal_variable_names_idx1_idx2";
      db_query($sql);
      $sql = "ALTER INDEX tripal_variables_tripal_variables_c1_key RENAME TO tripal_variables_tripal_variables_c1_key2";
      db_query($sql);
    }
    variable_set ('tripal_v2_upgrade_v3_check', TRUE);
  }
  $schema = array();

  $schema['tripal_jobs'] = tripal_tripal_jobs_schema();
  $schema['tripal_token_formats'] = tripal_tripal_token_formats_schema();
  $schema['tripal_variables'] = tripal_tripal_variables_schema();


  // Adds a table for managing TripalEntity entities.
  $schema['tripal_vocab'] = tripal_tripal_vocab_schema();
  $schema['tripal_term'] = tripal_tripal_term_schema();
  $schema['tripal_entity'] = tripal_tripal_entity_schema();
  $schema['tripal_bundle'] = tripal_tripal_bundle_schema();

  // Adds a table for additional information related to bundles.
  $schema['tripal_bundle_variables'] = tripal_tripal_bundle_variables_schema();

  return $schema;
}
function tripal_tripal_jobs_schema() {
  return array(
    'fields' => array(
      'job_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not NULL' => TRUE
      ),
      'uid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => TRUE,
        'description' => 'The Drupal userid of the submitee'
      ),
      'job_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'
      ),
      'callback' => array(
        'type' => 'varchar',
        'length' => 255,
        'not NULL' => TRUE
      ),
      'arguments' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'progress' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'default' => 0,
        'not NULL' => FALSE,
        'description' => 'a value from 0 to 100 indicating percent complete'
      ),
      'status' => array(
        'type' => 'varchar',
        'length' => 50,
        'not NULL' => TRUE
      ),
      'submit_date' => array(
        'type' => 'int',
        'not NULL' => TRUE,
        'description' => 'UNIX integer submit time'
      ),
      'start_time' => array(
        'type' => 'int',
        'not NULL' => FALSE,
        'description' => 'UNIX integer start time'
      ),
      'end_time' => array(
        'type' => 'int',
        'not NULL' => FALSE,
        'description' => 'UNIX integer end time'
      ),
      'error_msg' => array(
        'type' => 'text',
        'size' => 'normal',
        'not NULL' => FALSE
      ),
      'pid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => FALSE,
        'description' => 'The process id for the job'
      ),
      'priority' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => TRUE,
        'default' => '0',
        'description' => 'The job priority'
      ),
      'mlock' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => FALSE,
        'description' => 'If set to 1 then all jobs for the module are held until this one finishes'
      ),
      'lock' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not NULL' => FALSE,
        'description' => 'If set to 1 then all jobs are held until this one finishes'
      ),
      'includes' => array(
        'type' => 'text',
        'description' => 'A serialized array of file paths that should be included prior to executing the job.',
        'not NULL' => FALSE,
      )
    ),
    'indexes' => array(
      'job_id' => array('job_id'),
      'job_name' => array('job_name')
    ),
    'primary key' => array('job_id'),
  );
}
/**
 *
 * @return
 */
function tripal_tripal_token_formats_schema() {
  return array(
    'fields' => array(
      'tripal_format_id' => array(
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE
      ),
      'content_type' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE
      ),
      'application' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE
      ),
      'format' => array(
        'type' => 'text',
        'not null' => TRUE
      ),
      'tokens' => array(
        'type' => 'text',
        'not null' => TRUE
      ),
    ),
    'unique keys' => array(
      'type_application' => array('content_type', 'application'),
    ),
    'primary key' => array('tripal_format_id'),
  );
}
function tripal_tripal_variables_schema() {

   return array(
    'description' => 'This table houses a list of unique variable names that ' .
      'can be used in the tripal_node_variables table.',
    'fields' => array(
      'variable_id' => array (
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'description' => array(
        'type' => 'text',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array (
        0 => 'variable_id',
    ),
    'unique keys' => array (
      'tripal_variables_c1' => array (
        0 => 'name',
      ),
    ),
    'indexes' => array (
      'tripal_variable_names_idx1' => array (
        0 => 'variable_id',
      ),
    ),
  );

  return $schema;
}
/**
 * @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_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' => '',
      ),
      'term_id' => array(
        'description' => 'The term_id for the type of entity. This term_id corresponds to a TripalTerm record.',
        '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(
      'term_id' => array('term_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 TripalVocab schema.
 *
 * 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_tripal_vocab_schema() {

  // This schema only provides enough information to assign a unique ID
  // to the vocabulary. Any additonal information is added to the Entity object
  // by the selected database back-end.
  $schema = array(
    'description' => 'The base table for TripalVocab entities.',
    'fields' => array(
      'id' => array(
        'description' => 'The primary identifier for a vocab entity.',
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'namespace' => array(
        'description' => 'The namespace for the vocabulary (e.g. SO, PATO, etc.).',
        'type' => 'varchar',
        'length' => 10,
        'not null' => TRUE,
      ),
      'created' => array(
        'description' => 'The Unix timestamp when the entity was created.',
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
      'changed' => array(
        'description' => 'The Unix timestamp when the entity was most recently saved.',
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
    ),
    'indexes' => array(
      'namespace' => array('namespace'),
      'entity_changed' => array('changed'),
      'entity_created' => array('created'),
    ),
    'unique keys' => array('namespace' => array('namespace')),
    'primary key' => array('id'),
  );
  return $schema;
}

/**
 * The base table for TripalTerm 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_tripal_term_schema() {

  // This schema only provides enough information to assign a unique ID
  // to the term and associate it to it's vocabulary. Any additonal information
  // is added to the Entity object by the selected database back-end.
  $schema = array(
    'description' => 'The base table for TripalTerm entities.',
    'fields' => array(
      'id' => array(
        'description' => 'The primary identifier for a term entity.',
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'vocab_id' => array(
        'description' => 'The vocabulary_id of the TripalVocab entity to which this term belongs.',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'accession' => array(
        'description' => 'The id (or accession) of this term in the vocabulary.',
        'type' => 'varchar',
        'length' => 1024,
        'not null' => TRUE,
        'default' => '',
      ),
      'name' => array(
        'description' => 'The human readable name for this term.',
        'type' => 'varchar',
        'length' => 1024,
        'not null' => TRUE,
        'default' => '',
      ),
      'created' => array(
        'description' => 'The Unix timestamp when the entity was created.',
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
      'changed' => array(
        'description' => 'The Unix timestamp when the entity was most recently saved.',
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
    ),
    'indexes' => array(
      'vocab_id' => array('vocab_id'),
      'accession' => array('accession'),
      'entity_changed' => array('changed'),
      'entity_created' => array('created'),
    ),
    'foreign keys' => array(
      'tripal_vocab' => array(
        'table' => 'tripal_vocab',
        'columns' => array(
          'vocab_id' => 'vocab_id',
        ),
      ),
    ),
    'unique keys' => array('vocab_term' => array('vocab_id', 'accession')),
    'primary key' => array('id'),
  );
  return $schema;
}

/**
 * The base table for TripalEntity entities.
 *
 * 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_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 numeric ID.',
      ),
      'type' => array(
        'description' => 'The type of entity (e.g. TripalEntity).',
        'type' => 'varchar',
        'length' => 64,
        'not null' => TRUE,
        'default' => '',
      ),
      'term_id' => array(
        'description' => 'The term_id for the type of entity. This term_id corresponds to a TripalTerm record.',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'name' => array(
        'description' => 'The name of the 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' => '',
      ),
    ),
    'indexes' => array(
      'name' => array('name'),
      'term_id' => array('term_id'),
    ),
    'primary key' => array('id'),
    'unique keys' => array(
      'name' => array('name'),
    ),
  );
  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_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;
}

/**
 * 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_update_7300() {
  try {
    if (!db_field_exists('tripal_jobs', 'includes')) {
      db_add_field('tripal_jobs', 'includes', array(
        'type' => 'text',
        'description' => 'A serialized array of file paths that should be included prior to executing the job.',
        'not NULL' => FALSE,
      ));
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to complete update' . $error);
  }
}