tripal/tripal_library/tripal_library.module

<?php

/**
 * @defgroup tripal_library Library Module
 * @ingroup tripal_modules
 * @{
 * Provides functions for managing chado libraries including creating details pages for each library
 * @}
 */

require('api/tripal_library.api.inc');
require('theme/tripal_library.theme.inc');
require('includes/tripal_library.admin.inc');
require('includes/tripal_library.chado_node.inc');

/**
 * Provide information to drupal about the node types that we're creating
 * in this module
 *
 * @ingroup tripal_library
 */
function tripal_library_node_info() {
  $nodes = array();
  $nodes['chado_library'] = array(
    'name' => t('Library'),
    'base' => 'chado_library',
    'description' => t('A library from the chado database'),
    'has_title' => FALSE,
    'title_label' => t('Library'),
    'has_body' => FALSE,
    'locked' => TRUE,
    'chado_node_api' => array(
      'base_table' => 'library',
      'hook_prefix' => 'chado_library',
      'record_type_title' => array(
        'singular' => t('Library'),
        'plural' => t('Libraries')
      ),
      'sync_filters' => array(
        'type_id' => TRUE,
        'organism_id' => TRUE
      ),
    )
  );
  return $nodes;
}


/**
 * Set the permission types that the chado module uses.  Essentially we
 * want permissionis that protect creation, editing and deleting of chado
 * data objects
 *
 * @ingroup tripal_library
 */
function tripal_library_permisssions() {
  return array(
    'access chado_library content' => array(
      'title' => t('View Libraries'),
      'description' => t('Allow users to view library pages.'),
    ),
    'create chado_library content' => array(
      'title' => t('Create Libraries'),
      'description' => t('Allow users to create new library pages.'),
    ),
    'delete chado_library content' => array(
      'title' => t('Delete Libraries'),
      'description' => t('Allow users to delete library pages.'),
    ),
    'edit chado_library content' => array(
      'title' => t('Edit Libraries'),
      'description' => t('Allow users to edit library pages.'),
    ),
    'adminster tripal library' => array(
      'title' => t('Administer Libraries'),
      'description' => t('Allow users to administer all libraries.'),
    ),
  );
}
/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_library
 */
function chado_library_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_library content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_library content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_library content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_library content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}
/**
 * Menu items are automatically added for the new node types created
 * by this module to the 'Create Content' Navigation menu item.  This function
 * adds more menu items needed for this module.
 *
 * @ingroup tripal_library
 */
function tripal_library_menu() {
  $items = array();
  // The administative settings menu
  $items['admin/tripal/chado/tripal_library'] = array(
    'title' => 'Libraries',
    'description' => 'Any biological library. Examples of genomic libraries include BAC, cDNA, FOSMID, etc.',
    'page callback' => 'tripal_library_admin_libraries_listing',
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_library/help'] = array(
    'title' => 'Help',
    'description' => 'Basic Description of Tripal Library Module Functionality',
    'page callback' => 'theme',
    'page arguments' => array('tripal_library.help'),
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_library/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Library module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_library_admin'),
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );
  $items['admin/tripal/chado/tripal_library/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for libraries stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_library', 'chado_library'),
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );
  return $items;

  // Synchronizing libraries from Chado to Drupal
  $items['chado_sync_libraries'] = array(
    'title' => 'Sync Library Data',
    'page callback' => 'tripal_library_sync_libraries',
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_CALLBACK
  );

  $items['admin/tripal/chado/tripal_library/views/libraries/enable'] = array(
    'title' => 'Enable Library Administrative View',
    'page callback' => 'tripal_views_admin_enable_view',
    'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/chado/tripal_library'),
    'access arguments' => array('administer tripal libraries'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_library
 */
function tripal_library_views_api() {
  return array(
    'api' => 2.0,
  );
}

/**
 * @ingroup tripal_library
 */
function tripal_library_node_view($node, $view_mode, $langcode) {

  switch ($node->type) {
    case 'chado_library':
      if ($view_mode == 'full') {
        $node->content['tripal_library.base'] = array(
          '#value' => theme('tripal_library.base', array('node' => $node)),
        );      
        $node->content['tripal_library.properties'] = array(
          '#value' => theme('tripal_library.properties', array('node' => $node)),
        );
        
        $node->content['tripal_library.references'] = array(
          '#value' => theme('tripal_library.references', array('node' => $node)),
        );      
        $node->content['tripal_library.synonyms'] = array(
          '#value' => theme('tripal_library.synonyms', array('node' => $node)),
        );
        $node->content['tripal_library.terms'] = array(
          '#value' => theme('tripal_library.terms', array('node' => $node)),
        );
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_library.teaser'] = array(
          '#value' => theme('tripal_library.teaser', array('node' => $node)),
        );
      }
      break;
    case 'chado_organism':
      if ($view_mode == 'full') {
        $node->content['tripal_organism.libraries'] = array(
          '#value' => theme('tripal_organism.libraries', array('node' => $node)),
        );
      }
      break;
    case 'chado_feature':
      if ($view_mode == 'full') {
        $node->content['tripal_feature.libraries'] = array(
          '#value' => theme('tripal_feature.libraries', array('node' => $node)),
        );
      }
      break;
  }
}
/**
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_library
 */
function tripal_library_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');
  
  $items = array(
    'node__chado_library' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),

    // tripal_library templates
    'tripal_library.base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.base',
      'path' => "$path/theme/tripal_library",
    ),
    'tripal_library.properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.properties',
      'path' => "$path/theme/tripal_library",
    ),
    'tripal_library.references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.references',
      'path' => "$path/theme/tripal_library",
    ),
    'tripal_library.synonyms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.synonyms',
      'path' => "$path/theme/tripal_library",
    ),
    'tripal_library.terms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.terms',
      'path' => "$path/theme/tripal_library",
    ),
    'tripal_library.help' => array(
      'template' => 'tripal_library.help',
      'variables' =>  array(NULL),
      'path' => "$path/theme",
    ),
    
    // teaser
    'tripal_library.teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library.teaser',
      'path' => "$path/theme/tripal_library",
    ),
    
    // tripal_organism templates
    'tripal_organism.libraries' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism.libraries',
      'path' => "$path/theme/tripal_organism",
    ),
    
    // tripal_feature templates
    'tripal_feature.libraries' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature.libraries',
      'path' => "$path/theme/tripal_feature",
    ),
    
  );
  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_library_help ($path, $arg) {
  if ($path == 'admin/help#tripal_library') {
    return theme('tripal_library_help', array());
  }
}
/**
 * @ingroup tripal_library
 */
function tripal_library_block_info() {

  $blocks['libreferences']['info'] = t('Tripal Library Cross References');
  $blocks['libreferences']['cache'] = DRUPAL_NO_CACHE;

  $blocks['libbase']['info'] = t('Tripal Library Details');
  $blocks['libbase']['cache'] = DRUPAL_NO_CACHE;

  $blocks['libterms']['info'] = t('Tripal Library Terms');
  $blocks['libterms']['cache'] = DRUPAL_NO_CACHE;

  $blocks['libsynonyms']['info'] = t('Tripal Library Synonyms');
  $blocks['libsynonyms']['cache'] = DRUPAL_NO_CACHE;

  $blocks['libproperties']['info'] = t('Tripal Library Properties');
  $blocks['libproperties']['cache'] = DRUPAL_NO_CACHE;

  $blocks['featurelibs']['info'] = t('Tripal Feature Libraries');
  $blocks['featurelibs']['cache'] = DRUPAL_NO_CACHE;

  $blocks['orglibs']['info'] = t('Tripal Organism Libraries');
  $blocks['orglibs']['cache'] = DRUPAL_NO_CACHE;

  return $blocks;
}
/**
 * @ingroup tripal_library
 */
function tripal_library_block_view($delta = '') {

  if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
    $nid = arg(1);
    $node = node_load($nid);

    $block = array();
    switch ($delta) {
      case 'libreferences':
        $block['subject'] = t('Cross References');
        $block['content'] = theme('tripal_library_references', $node);
        break;
      case 'libbase':
        $block['subject'] = t('Library Details');
        $block['content'] = theme('tripal_library_base', $node);
        break;
      case 'libsynonyms':
        $block['subject'] = t('Synonyms');
        $block['content'] = theme('tripal_library_synonyms', $node);
        break;
      case 'libproperties':
        $block['subject'] = t('Properties');
        $block['content'] = theme('tripal_library_properties', $node);
        break;
      case 'libterms':
        $block['subject'] = t('Library Terms');
        $block['content'] = theme('tripal_library_terms', $node);
        break;
      case 'featurelibs':
        $block['subject'] = t('Libraries');
        $block['content'] = theme('tripal_feature_libraries', $node);
        break;
      case 'orglibs':
        $block['subject'] = t('Libraries');
        $block['content'] = theme('tripal_organism_libraries', $node);
        break;
      default :
    }
    return $block;
  }
}

/**
 *
 * @ingroup tripal_library
 */
function tripal_library_cron() {

}


/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_library_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_library_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
}