tripal/tripal_contact/tripal_contact.install

<?php

/**
 * @file
 * Handles install, uninstall, disable and enable functionality including database tables.
 *
 * @ingroup tripal_contact
 */

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

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

}

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

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_contact
 */
function tripal_contact_install() {

  // Create the module's data directory.
  tripal_create_files_dir('tripal_contact');

  // Add the contactprop table to Chado.
  tripal_contact_add_custom_tables();

  // Add loading of the the tripal contact ontology to the job queue.
  $obo_path = '{tripal_contact}/files/tcontact.obo';
  $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
  tripal_submit_obo_job(array('obo_id' => $obo_id));

  // Add cvterms for relationship types.
  tripal_contact_add_cvs();
  tripal_contact_add_cvterms();

  // Set the default vocabularies.
  tripal_set_default_cv('contact', 'type_id', 'tripal_contact');
  tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
  tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_contact
 */
function tripal_contact_uninstall() {
  /*
  // remove our custom block visibility settings per node type
  db_delete('block_node_type')
    ->condition('module', 'chado_contact')
    ->condition('delta', 'contbase')
    ->execute();
    */
}

/**
 * Adds any cvs needed by this module.
 *
 * @ingroup tripal_contact
 */
function tripal_contact_add_cvs() {

  // Add the cv for contact properties. This is a default vocabulary in the event
  // that a user does not want to use the tripal_contact vocabulary
  tripal_insert_cv(
    'contact_property',
    'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
  );

  // add the cv for the contact type. This is a default vocabulary in the event
  // that a user does not want to use the tripal_contact vocabulary
  tripal_insert_cv(
    'contact_type',
    'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
  );

  // Add the cv for the tripal_contact vocabulary which is loaded via the OBO
  tripal_insert_cv(
   'tripal_contact',
   'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
  );

  // add the cv for contact relationships
  tripal_insert_cv(
    'contact_relationship',
    'Contains types of relationships between contacts.'
  );

}

/**
 * Adds any cvterms needed by this module.
 *
 * @ingroup tripal_contact
 */
function tripal_contact_add_cvterms() {

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_contact
 */
function tripal_contact_schema() {
  $schema['chado_contact'] = 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
      ),
      'contact_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
      )
    ),
    'indexes' => array(
      'contact_id' => array('contact_id')
    ),
    'unique keys' => array(
      'nid_vid' => array('nid', 'vid'),
      'vid' => array('vid')
    ),
    'primary key' => array('nid'),
  );
  return $schema;
}

/**
 * Add any custom tables needed by this module.
 * - Contactprop: keep track of properties of contact
 *
 * @ingroup tripal_contact
 */
function tripal_contact_add_custom_tables(){
  $schema = array (
    'table' => 'contactprop',
    'fields' => array (
      'contactprop_id' => array (
        'type' => 'serial',
        'not null' => true,
      ),
      'contact_id' => array (
        'type' => 'int',
        'not null' => true,
      ),
      'type_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 => 'contactprop_id',
    ),
    'unique keys' => array (
      'contactprop_c1' => array (
        0 => 'contact_id',
        1 => 'type_id',
        2 => 'rank',
      ),
    ),
    'indexes' => array (
      'contactprop_idx1' => array (
        0 => 'contact_id',
      ),
      'contactprop_idx2' => array (
        0 => 'type_id',
      ),
    ),
    'foreign keys' => array (
      'cvterm' => array (
        'table' => 'cvterm',
        'columns' => array (
          'type_id' => 'cvterm_id',
        ),
      ),
      'contact' => array (
        'table' => 'contact',
        'columns' => array (
          'contact_id' => 'contact_id',
        ),
      ),
    ),
  );
  chado_create_custom_table('contactprop', $schema, TRUE);
}

/**
 * This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
 *
 */
function tripal_contact_update_7200() {

  // We cannot use the Tripal API calls in the 7200 update
  // because during upgrade the tripal_core will be disabled

  // add the contact_type CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'tripal_contact'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'tripal_contact',
        'definition' => 'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
      ))
      ->execute();
    }
    // make this CV the defaults for the contact properties and contact types
    db_insert('tripal_cv_defaults')
      ->fields(array(
         'table_name' => 'contact',
         'field_name' => 'type_id',
         'cv_id' => $cv_id
       ))
      ->execute();
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'contactprop',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add tripal_contact vocabulary: '. $error);
  }


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

  // add the contact_type CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_type'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'contact_type',
        'definition' => 'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
      ))
      ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add contact_type vocabulary: '. $error);
  }

  // add the contact_property CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'contact_property'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'contact_property',
        'definition' => 'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
      ))
      ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add contact_property vocabulary: '. $error);
  }
}

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

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

  return $dependencies;
}

/**
 * Adds missing foreign key constraints
 *
 */
function tripal_contact_update_7201() {
  // there was a bug in the function for creating a custom table that
  // kept foreign key constraints from being added.  So, we need to add those
  // to keep from error messages appear, we will drop the FK if it already
  // exists and then re-add it.
  try {
    $fkey_exists = db_query('SELECT TRUE FROM pg_constraint WHERE conname = :constraint', array(':constraint' => 'contactprop_type_id_fkey'))->fetchField();
    if ($fkey_exists) {
      db_query('
        ALTER TABLE chado.contactprop
        DROP CONSTRAINT contactprop_type_id_fkey CASCADE
      ');
      db_query('
        ALTER TABLE chado.contactprop
        DROP CONSTRAINT contactprop_contact_id_fkey CASCADE
      ');
    }
    db_query('
      ALTER TABLE chado.contactprop
      ADD CONSTRAINT contactprop_type_id_fkey
      FOREIGN KEY (type_id) REFERENCES chado.cvterm (cvterm_id)
      ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
    ');
    db_query('
      ALTER TABLE chado.contactprop
      ADD CONSTRAINT contactprop_contact_id_fkey
      FOREIGN KEY (contact_id) REFERENCES chado.contact (contact_id)
      ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
    ');
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to update foriegn key: '. $error);
  }
}
/**
 * Updates path of tripal_contact OBO to be relative.
 */
function tripal_contact_update_7202() {
  try {
    // Remove duplicates.
    db_delete('tripal_cv_obo')
      ->condition('name', 'Tripal Contacts')
      ->execute();
    
    // Add in the updated path.
    $obo_path = '{tripal_contact}/files/tcontact.obo';
    $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to update tripal_contact OBO path: '. $error);
  }
}