tripal/tripal_example/tripal_example.module

<?php

/**
 * @file
 * This file contains all Drupal hooks for the module other than any node hooks
 * and block hooks. Those go in the [module name].chado_node.inc file and
 * [module_name].blocks.inc respectively
 *
 */

// EXPLANATION: include any files needed for this module. That includes any API
// file, the theme file, or include files.
require('api/tripal_example.api.inc');
require('theme/tripal_example.theme.inc');
require('includes/tripal_example.admin.inc');
require('includes/tripal_example.chado_node.inc');


/**
 * Implementation of hook_permissions()
 *
 * Set the permission types that this module uses.
 *
 * @ingroup tripal_example
 */
function tripal_example_permission() {

  // EXPLANATION:  here we want to setup any of the permission types that this
  // module needs. Our example module creates a new chado node type called
  // 'chado_example'. Therefore, we need permissions to view, edit, delete,
  // create our new node type. Additionally, we want to add a permission that
  // allows for administration of this module. These permissions will appear in
  // the 'People' -> 'Permissions' configuration page and allow the site admin
  // to specify which user roles are allowed to perform specific actions.
  return array(
    'access chado_example content' => array(
      'title' => t('View Examples'),
      'description' => t('Allow users to view example pages.'),
    ),
    'create chado_example content' => array(
      'title' => t('Create Examples'),
      'description' => t('Allow users to create new example pages.'),
    ),
    'delete chado_example content' => array(
      'title' => t('Delete Examples'),
      'description' => t('Allow users to delete example pages.'),
    ),
    'edit chado_example content' => array(
      'title' => t('Edit Examples'),
      'description' => t('Allow users to edit example pages.'),
    ),
    'administer tripal example' => array(
      'title' => t('Administer Examples'),
      'description' => t('Allow users to administer all examples.'),
    ),
  );
}

/**
 * Implements hook_menu()
 *
 * Specifies menu items and URLs used by this module.
 *
 * @ingroup tripal_example
 */
function tripal_example_menu() {
  $items = array();

  // EXPLANATION:  the $items array should be populated to contain a list of
  // menu items or URL callbacks that our module needs.
  // all Tripal Extension modules should provide at least these menu items:
  //  * A menu item for an administrative home page
  //  * A menu item for 'Help' documentation
  //  * A menu item for a module configuration page
  //
  // Additionally, if your module defines a custom node type that is linked
  // to a record in Chado:
  //  * A menu item for syncing drupal nodes with Chado records.
  //

  // EXPLANATION:  all extension modules should have an administrative menu item
  // with the path set to 'admin/tripal/extension/[module name]'. This will
  // place the menu item in the 'Tripal' -> 'Extension Modules' page. Because
  // this is an administrative menu item we must be sure to set the
  // 'access arguments' to be 'administer tripal example' which is a permission
  // type we created in the tripal_example_permissions() function above.
  $items['admin/tripal/extension/tripal_example'] = array(
    'title' => 'Examples',
    'description' => 'Example module for help with development of new extension modules.',
    'page callback' => 'tripal_example_admin_examples_listing',
    'access arguments' => array('administer tripal example'),
    'type' => MENU_NORMAL_ITEM,
  );

  // EXPLANATION: all extension modules should provide help documentation to
  // describe the functionality of the module and any installation or setup
  // tasks that may be required. The menu 'type' is MENU_LOCAL_TASK so that the
  // link appears in a tab on the extension module's administrative page.
  // Here the 'page callback' specifies that we are using Drupal's theme
  // function and the 'page_arguments' indicate the name of the template file
  // Thus, all help documentation should be provided in the
  // [module name]/theme/tripal_example_help.tpl.php file.
  $items['admin/tripal/extension/tripal_example/help'] = array(
    'title' => 'Help',
    'description' => 'Basic Description of Tripal Library Module Functionality',
    'page callback' => 'theme',
    'page arguments' => array('tripal_example_help'),
    'access arguments' => array('administer tripal example'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  // EXPLANATION: all extension modules should provide a configuration page.
  // Even if your module does not need configuration the menu item and page
  // should be created. This helps users recognize that the module is installed
  // and working. The configuration page can simply state that no configuration
  // settings are available. Typically a form is provided for the module's
  // configuration settings. Therefore the 'page callback' uses the
  // drupal_get_form() function and the 'page argument' indicates the form
  // to call is named 'tripal_eample_admin'. The function that describes
  // to form is in the includes/tripal_example.admin.inc file.
  $items['admin/tripal/extension/tripal_example/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Library module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_example_admin'),
    'access arguments' => array('administer tripal example'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  // EXPLANATION: If your module defines a new chado node type and that node
  // type directly links to a record in Chado, then you can use the Tripal API
  // to quickly provide syncing functionality. See the API documentation here
  // for more information on how that is setup:
  // http://api.tripal.info/api/tripal/tripal_core%21api%21tripal_core.chado_nodes.api.inc/function/chado_node_sync_form/2.x
  $items['admin/tripal/extension/tripal_example/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for examples stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_node_sync_form', 'tripal_example', 'chado_example'),
    'access arguments' => array('administer tripal example'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  // EXPLANATION: If your module defines a new node type that uses the default
  // table of contents (left-side bar of content panes on a page). Then a 'TOC'
  // link will automatically appear on the node page to allow for customization
  // of the TOC. However those customizations are only node specific. To provide
  // a tab in the module's administrative pages add the following menu item.
  // This menu will provide a form similar to the one found on the node that
  // allows the user to set global TOC settings for the content type. Be sure to
  // always use a menu path of the form:
  //   admin/tripal/chado/[module name]/[content type name]_toc
  // this allows for a module to support TOC management when there are multiple
  // content types provided by the module, as the content type is specified
  // in the menu path.
  $items['admin/tripal/chado/tripal_example/chado_example_toc'] = array(
    'title' => ' TOC',
    'description' => 'Manage the table of contents for example nodes.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_content_type_toc_form', 'chado_example'),
    'access arguments' => array('administer tripal example'),
    'type' => MENU_LOCAL_TASK,
    'file' =>  'includes/tripal_core.toc.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'weight' => 3
  );

  return $items;
}

/**
 * Implements hook_views_api()
 *
 * This hook tells Drupal that there is views support for this module which then
 * automatically includes the tripal_db.views.inc where all the views
 * integration code is found.
 *
 * @ingroup tripal_example
 */
function tripal_example_views_api() {
  return array(
    'api' => 3.0,
  );
}


/**
 * 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_example
 */
function tripal_example_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  // EXPLANATION: this function defines all of the functions and templates that
  // this module needs to provide content. These details are provided in the
  // form of an array the indicates which functions or templates provide
  // content. Please see the Drupal theming guide for an in-depth description
  // for how theming works in Drupal:
  // https://drupal.org/documentation/theme

  $items = array(

    // EXPLANATION:  If this module defines a new node type that displays Chado
    // data then we should use Tripal's default node template. This template
    // ensures that all content provided by Tripal and Tripal extension modules
    // has the same look and feel. It is designed to be generic such that it
    // won't interfere with the look-and-feel of the default theme. This generic
    // template will organize the node into a table of contents found on the
    // left-side of the page and place the content in the center of the page.
    // User's will cycle through content on the page by clicking the links in
    // the table of contents. If you do not want to use the default Tripal
    // template you can change this array to your liking.
    'node__chado_example' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),

    // EXPLANATION: the following defines all of the template files used for
    // this module. Templates are named with underscores separating words, and
    // correspond directly to a file with the extension '.tpl.php'. For example
    // the 'tripal_example_base' template will have a corresponding
    // tripal_example_base.tpl.php file where the display code is housed.
    // The only required templates are the 'base',  'help' and 'teaser'
    // templates. The base template provides the basic information about the
    // record in Chado. The 'help' template provides the administrative help
    // documentation, and the teaser provides a brief summary of the record that
    // can be used as short description of the record in aggregated lists.

    // the base template
    'tripal_example_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_example_base',
      'path' => "$path/theme/templates",
    ),
    // the help template
    'tripal_example_help' => array(
      'template' => 'tripal_example_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme/templates",
    ),
    // the teaser template.
    'tripal_example_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_example_teaser',
      'path' => "$path/theme/templates",
    ),


    // EXPLANATION: Typically, a different template is created for each subset
    // of data.
    // For example, most Chado tables have a 'XXXXprop', 'XXXX_cvterm',
    // 'XXXX_dbxref', 'XXXX_synonyms', 'XXXX_relationships' tables. Therefore,
    // a template is created to display data from each of these tables.

    'tripal_example_properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_example_properties',
      'path' => "$path/theme/templates",
    ),
    'tripal_example_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_example_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_example_relationships' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_example_relationships',
      'path' => "$path/theme/templates",
    ),

    // EXPLANATION: sometimes a module may want to add content to another
    // modules' node types. For example, the feature module does this by
    // adding a 'feature summary' data to an organism. To add data to another
    // module's node, the templates belong to this module and are specified in
    // the same way as above. However, the naming of the template is changed to
    // include the name of the module that supplies the node type followed by
    // our record name:

    // tripal_organism templates
    'tripal_organism_examples' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_examples',
      'path' => "$path/theme/templates",
    ),
  );

  return $items;
}

/**
 * Implements hook_help()
 *
 * Adds a help page to the module list
 */
function tripal_example_help ($path, $arg) {

  // EXPLANATION: in the tripal_example_menu() function above we created a menu
  // item for the help documentation. The menu item specified a function that
  // should be called when the menu item is clicked. This is that function. But,
  // rather than place HTML code in this function we want to have our help
  // documentation in a template file. We specified in the
  // tripal_example_theme() function that we have a template file so now we want
  // to use get the contents of that template file and return it.
  if ($path == 'admin/help#tripal_example') {
    return theme('tripal_example_help', array());
  }
}


/**
 * Implements hook_cron()
 *
 * @ingroup tripal_example
 */
function tripal_example_cron() {

  // EXPLANATION: here we can add any code that needs to be executed when the
  // Drupal cron is run.
}


/**
 * Implementation of hook_form_alter()
 *
 * Allows a module to alter any form prior to it being rendered. For more
 * details about Drupal's Form API see this page:
 *
 * https://api.drupal.org/api/drupal/includes!form.inc/group/form_api/7
 *
 */
function tripal_example_form_alter(&$form, &$form_state, $form_id) {

  if ($form_id == "chado_example_node_form") {

    // EXPLANATION:  The hook_form_alter() Drupal hook is used to alter a form
    // before it is displayed. This allows any module to provide new form
    // elements or change the form that another module creates. We do not need
    // to alter a form created by another module, but we do want to alter the
    // form for our new node type. For example, all node types will
    // automatically have a 'Preview' button. For inserting or updating data
    // for Chado we don't really need a Preview button and it complicates the
    // form. So, we use the following code to disable the Preview button. If
    // you want to keep the preview button then remove this code. turn of
    // preview button for insert/updates
    $form['actions']['preview']['#access'] = FALSE;

    // EXPLANATION: Drupal always adds a 'body' field to all node types.
    // Our node type doesn't use the 'body' field so we remove it from the form.
    unset($form['body']);
  }
}