tripal/tripal_cv/tripal_cv.module

<?php

require_once "charts.php";
require_once "trees.php";

//
// Copyright 2009 Clemson University
//
/*************************************************************************
*
*/
function tripal_cv_init(){

   // add the tripal_cv JS and CSS
   drupal_add_css(drupal_get_path('theme', 'tripal').
                                  '/css/tripal_cv.css');
   drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_cv.js');

   // add the jsTree JS and CSS
   drupal_add_css(drupal_get_path('theme', 'tripal').'/js/jsTree/source/tree_component.css');
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jsTree/source/_lib.js');
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jsTree/source/tree_component.js');
}
/*************************************************************************
*
*/
function tripal_cv_menu() {
   $items = array();

   $items['admin/tripal/tripal_cv'] = array(
     'title' => 'CV',
     'description' => 'Manage integration of Chado controlled vocabularies',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_cv_admin'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['tripal_cv_chart'] = array(
      'path' => 'tripal_cv_chart',
      'title' => t('CV Chart'),
      'page callback' => 'tripal_cv_chart',
      'page arguments' => array(1),
      'access arguments' => array('access content'),
      'type' => MENU_CALLBACK
   );

   $items['tripal_cv_tree'] = array(
      'path' => 'tripal_cv_tree',
      'title' => t('CV Term Viewer'),
      'page callback' => 'tripal_cv_tree',
      'page arguments' => array(1),
      'access arguments' => array('access content'),
      'type' => MENU_CALLBACK
   );
   // menu items for working with the CV module tree browser
   /*
   $items['cv_browser'] = array(
      'title' => t('CV Relationship Browser'),
      'page callback' => 'tripal_cv_show_browser',
      'access arguments' => array('access chado_cv content'),
      'type' => MENU_NORMAL_ITEM
   );
   */
   $items['tripal_cv_init_browser'] = array(
      'path' => 'tripal_cv_init_browser',
      'title' => t('CV Browser'),
      'page callback' => 'tripal_cv_init_browser',
      'page arguments' => array(1),
      'access arguments' => array('access content'),
      'type' => MENU_CALLBACK
   );
   // menu item for interaction with the tree
   $items['tripal_cv_update_tree'] = array(
      'path' => 'tripal_cv_update_tree',
      'title' => t('CV Tree'),
      'page callback' => 'tripal_cv_update_tree',
      'page arguments' => array(2,3),
      'access arguments' => array('access content'),
      'type' => MENU_CALLBACK
   );

   // menu items for working with terms
   $items['tripal_cv_cvterm_info'] = array(
      'path' => 'tripal_cv_cvterm_info',
      'title' => t('CV Term Viewer'),
      'page callback' => 'tripal_cv_cvterm_info',
      'page arguments' => array(1),
      'access arguments' => array('access content'),
      'type' => MENU_CALLBACK
   );

   $items['tripal_cv_cvterm_edit'] = array(
      'path' => 'tripal_cv_edit',
      'title' => t('CV Term Editor'),
      'page callback' => 'tripal_cv_cvterm_edit',
      'page arguments' => array(1),
      'access arguments' => array('edit chado_cv content'),
      'type' => MENU_CALLBACK
   );

   return $items;
}
/*******************************************************************************
 *  The following function proves access control for users trying to
 *  perform actions on data managed by this module
 */
function chado_cv_access($op, $node, $account){
  if ($op == 'create') {
      return user_access('create chado_cv content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_cv content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_cv content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_cv content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}
/*******************************************************************************
*  Set the permission types that the chado module uses.  Essentially we
*  want permissionis that protect creation, editing and deleting of chado
*  data objects
*/
function tripal_cv_perm(){
   return array(
      'access chado_cv content',
      'create chado_cv content',
      'delete chado_cv content',
      'edit chado_cv content',
   );
}

/*************************************************************************
*
*/
function tripal_cv_admin () {
	$form['update_cvtermpath'] = array(
      '#type' => 'fieldset',
      '#title' => t('Chado cvtermpath')
   );
   $form['update_cvtermpath']['description'] = array(
       '#type' => 'item',
       '#value' => t("Submit a job to update chado cvtermpath table."),
       '#weight' => 1,
   );
   $form['update_cvtermpath']['button'] = array(
      '#type' => 'submit',
      '#value' => t('Update cvtermpath'),
      '#weight' => 2,
   );
   return system_settings_form($form);
}

/*************************************************************************
*
*/
function tripal_cv_admin_validate($form, &$form_state) {
   global $user;
	// -------------------------------------
   // Submit a job to update cvtermpath
   $job_args = array();
   if ($form_state['values']['op'] == t('Update cvtermpath')) {
      tripal_add_job('Update cvtermpath','tripal_cv',
         'tripal_cv_update_cvtermpath',$job_args,$user->uid);
   }
}

/***********************************************************
 * Update the cvtermpath table
 */
function tripal_cv_update_cvtermpath($dummy = NULL, $job_id = NULL) {

   print "\nUpdating cvtermpath...\n";

   $previous_db = db_set_active('chado');
   $sql = "SELECT * FROM fill_cvtermpath('biological_process')";
   db_query($sql);         
   $sql = "SELECT * FROM fill_cvtermpath('molecular_function')";
   db_query($sql);
   $sql = "SELECT * FROM fill_cvtermpath('cellular_component')";
   db_query($sql);
   db_set_active($previous_db);
   return;

}

/*******************************************************************************
 *  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
 */
function tripal_cv_theme () {
   return array(
      'tripal_cv_cvterm_edit' => array (
         'arguments' => array('cvterm'),
      ),
   );
}

/*************************************************************************
*/
function tripal_cv_get_cv_id($cv_name){

   $sql = "
      SELECT cv_id FROM {cv} WHERE name = '%s'
   ";
   $previous_db = db_set_active('chado');
   $cv = db_fetch_object(db_query($sql,$cv_name));
   db_set_active($previous_db);
   return $cv->cv_id;
}
/*************************************************************************
*
*/
function tripal_cv_cvterm_edit($cvterm_id){
   $sql = "
      SELECT CVT.name as cvtermname, CVT.definition, CV.name as cvname
      FROM {CVTerm} CVT
        INNER JOIN CV on CVT.cv_id = CV.cv_id
      WHERE CVT.cvterm_id = %d
   ";
   $previous_db = db_set_active('chado');
   $cvterm = db_fetch_object(db_query($sql,$cvterm_id));
   db_set_active($previous_db);
   return theme('tripal_cv_cvterm_edit',$cvterm);
}
/*************************************************************************
*
*/
function theme_tripal_cv_cvterm_edit(&$cvterm){
   $output = "
      <div id=\"cvterm\">
      <table>
        <tr><th>Term</th><td>$cvterm->cvtermname</td></tr>
        <tr><th>Vocabulary</th><td>$cvterm->cvname</td></tr>
        <tr><th>Definition</th><td>$cvterm->definition</td></tr>
      </table>
      </div>
   ";
   return $output;
}