mcl.install

<?php
/**
 * @file
 * Contains functions used to install/uninstall MCL module
 */
/**
 * Implementation of hook_install().
 *
 * @ingroup
 */
function mcl_install() {

  // Populates table with default values.
  mcl_populate_table_defaults();
}

/**
 * Implementation of hook_uninstall().
 *
 */
function mcl_uninstall() {
  // Remove MCL directory and its sub-directories.
}

/**
 * Implementation of hook_schema().
 *
 */
function mcl_schema() {
  $schema = array();
  mcl_add_table_mcl_var($schema);
  mcl_add_table_mcl_user($schema);
  mcl_add_table_mcl_file($schema);
  mcl_add_table_mcl_job($schema);
  mcl_add_table_mcl_template($schema);
  mcl_add_table_mcl_template_type($schema);
  return $schema;
}

/**
 * Adds mcl_var table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_var(&$schema) {
  $schema['mcl_var'] = array(
    'fields' => array(
      'var_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'value' => array(
        'type' => 'varchar',
        'length' => '1024',
      ),
      'description' => array(
        'type' => 'text',
      ),
    ),
    'primary key' => array('var_id'),
    'unique keys' => array(
      'ukey_mcl_var_name' => array('name')
    ),
  );
}

/**
 * Adds mcl_user table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_user(&$schema) {
  $schema['mcl_user'] = array(
    'fields' => array(
      'user_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'uid' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'mail' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'prop' => array(
        'type' => 'text',
        'not null' => FALSE,
      ),
    ),
    'primary key' => array('user_id'),
  );
}

/**
 * Adds mcl_template table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_template(&$schema) {
  $schema['mcl_template'] = array(
    'fields' => array(
      'template_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'template' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'template_type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'public' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 1,
      ),
    ),
    'primary key' => array('template_id'),
    'unique keys' => array(
      'ukey_mcl_template_template' => array('template')
    ),
  );
}

/**
 * Adds template_type table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_template_type(&$schema) {
  $schema['mcl_template_type'] = array(
    'fields' => array(
      'template_type_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'rank' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('template_type_id'),
    'unique keys' => array(
      'ukey_mcl_template_type' => array('type')
    ),
  );
}

/**
 * Adds mcl_file table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_file(&$schema) {
  $schema['mcl_file'] = array(
    'fields' => array(
      'file_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'filename' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'filepath' => array(
        'type' => 'varchar',
        'length' => '512',
        'not null' => TRUE,
      ),
      'filesize' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0,
      ),
      'uri' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'user_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'job_id' => array(
        'type' => 'int',
      ),
      'submit_date' => array(
        'type' => 'datetime',
        'mysql_type' => 'datetime',                     // The equivalent MySQL data type
        'pgsql_type' => 'timestamp without time zone',  // The equivalent PostgreSQL data type
        'not null' => TRUE,
      ),
    'prop' => array(
        'type' => 'text',
      ),
    ),
    'primary key' => array('file_id'),
  );
}

/**
 * Adds mcl_job table.
 *
 * @param  $schema
 */
function mcl_add_table_mcl_job(&$schema) {
  $schema['mcl_job'] = array(
    'fields' => array(
      'job_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'class_name' => array(
        'type' => 'varchar',
        'length' => '255',
      ),
      'status' => array(
        'type' => 'int',
      ),
      'param' => array(
        'type' => 'text',
      ),
      'prop' => array(
        'type' => 'text',
      ),
      'user_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'submit_date' => array(
        'type' => 'datetime',
        'mysql_type' => 'datetime',                     // The equivalent MySQL data type
        'pgsql_type' => 'timestamp without time zone',  // The equivalent PostgreSQL data type
        'not null' => TRUE,
      ),
      'complete_date' => array(
        'type' => 'datetime',
        'mysql_type' => 'datetime',                     // The equivalent MySQL data type
        'pgsql_type' => 'timestamp without time zone',  // The equivalent PostgreSQL data type
      ),
    ),
    'primary key' => array('job_id'),
  );
}

/**
 * Populates table with default values.
 *
 */
function mcl_populate_table_defaults() {
  $module_path = drupal_get_path('module', 'mcl');

  // Includes .inc file.
  require_once("$module_path/includes/mcl.inc");

  // Registers autoloader.
  require_once "$module_path/includes/class/mcl_class_loader.class.inc";
  $bims_autoloader = new MCL_CLASS_LOADER($module_path);
  $bims_autoloader->register();

  // Populates mcl_var table.
  mcl_populate_mcl_var();

  // Populates mcl_template and mcl_template_type tables.
  mcl_populate_mcl_templates();
}

/**
 * Populates mcl_var table.
 *
 */
function mcl_populate_mcl_var() {

  // Gets null/default value.
  $null_cvterm  = MCL_CHADO_CVTERM::addNull();
  $null_pub     = MCL_CHADO_PUB::addNull();
  $na_organism  = MCL_CHADO_ORGANISM::addNA();
  $na_location  = MCL_CHADO_LOCATION::addNA();

  // Adds MCL global variables.
  $mcl_vars = array(
    'SITE_DB'               => array('type' => 'SITE',    'value' => 'MAIN',                             'desc' => 'The name of the site specific DB'),
    'SITE_CV'               => array('type' => 'SITE',    'value' => 'MAIN',                             'desc' => 'The name of the site specific CV'),
    'SITE_TRAIT_ONTOLOGY'   => array('type' => 'SITE',    'value' => 'rosaceae_trait_ontology',          'desc' => 'CV.name for site specific trait ontology'),
    'CVTERM_ID'             => array('type' => 'DEFAULT', 'value' => $null_cvterm->getCvtermID(),        'desc' => 'dummy cvterm ID. It is used for type_id of NULL pub.'),
    'PUB_ID'                => array('type' => 'DEFAULT', 'value' => $null_pub->getPubID(),              'desc' => 'dummy pub ID. It is used for chado.cvterm_feature.pub_id.'),
    'ORGANISM_ID'           => array('type' => 'DEFAULT', 'value' => $na_organism->getOrganismID(),      'desc' => 'dummy organism ID. It is used for organims ID of a linkage group.'),
    'ND_GEOLOCATION_ID'     => array('type' => 'DEFAULT', 'value' => $na_location->getNdGeolocationID(), 'desc' => 'chado.nd_geolocation.nd_geolocation_id for "Not Available"'),
  );

  // Adds variables.
  foreach ($mcl_vars as $name => $prop) {
    if (!MCL_VAR::addVar($prop['type'], $name, $prop['value'], $prop['desc'])) {
      print "\nError : Failed to add a variable.\n\n";
      exit;
    }
  }
}

/**
 * Populates mcl_template and mcl_template_type tables.
 *
 */
function mcl_populate_mcl_templates() {

  // Default template types.
  $template_types = array(
    'DB',
    'CV',
    'CVTERM',
    'LIBRARY',
    'TRAIT',
    'CONTACT',
    'DATASET',
    'IMAGE',
    'DESCRIPTOR',
    'SITE',
    'STOCK',
    'CROSS',
    'PROGENY',
    'MARKER',
    'MTL',
    'QTL',
    'PROGENY',
    'MAP',
    'MAP_POSITION',
    'FIELD_BOOK',
    'PHENOTYPE',
    'GENOTYPE',
  );

  // Adds template types.
  $rank = 20;
  foreach ($template_types as $template_type) {
    $details = array(
      'type' => $template_type,
    );
    $mcl_template_type = MCL_TEMPLATE_TYPE::byKey($details);
    if ($mcl_template_type) {
      print "\n$template_type already existed.\n\n";
    }
    else {
      $details['rank'] = $rank;
      $mcl_template_type = new MCL_TEMPLATE_TYPE($details);
      if (!$mcl_template_type->insert()) {
        print "\nError : Failed to add a template type\n\n";
        exit;
      }
      $rank += 10;
    }
  }

  // Adds templates.
  MCL_TEMPLATE::updateTemplates();
}

/**
 * Update function defined below.
 */
/**
 * .....
 */
function mcl_update_7007() {
  $transaction = db_transaction();
  try {
    mcl_populate_table_defaults();
  }
  catch (\PDOException $e) {
    $transaction->rollback();
    $error = $e->getMessage();
    throw new DrupalUpdateException($error);
  }
}