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/cvtermpath'] = array(
     'title' => 'Update Chado cvtermpath table for GO terms',
     'description' => 'Manage integration of Chado controlled vocabularies',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_cv_cvtermpath_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/tripal_cv'] = array(
     'title' => 'Controlled Vocabulary Management',
     'description' => 'Manage controlled vocabularies/ontolgoies in Chado ',
     'page callback' => 'tripal_cv_admin_page',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/tripal_cv/new'] = array(
     'title' => 'Add a Controlled Vocabulary',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_cv_form'),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_cv/edit/js'] = array(
     'title' => 'Edit Controlled Vocabularies',
     'page callback' => 'tripal_ajax_cv_edit',
     'access arguments' => array('access administration pages'),
     '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_page(){
   $add_url = url("admin/tripal/tripal_cv/new");
   $cvtermpath_url = url("admin/tripal/tripal_cv/cvtermpath");
   $output = "<a href=\"$add_url\">Add a new controlled vocabulary</a> | ";
   $output .= "<a href=\"$cvtermpath_url\">Update the cvtermpath table</a> ";  
   $output .= drupal_get_form('tripal_cv_select_form');
   $output .= '<div id="db-edit-div">Please select a database above to view or edit</div>';
   return $output;
}
/*************************************************************************
*
*/
function tripal_cv_select_form(){

	$previous_db = db_set_active('chado');  // use chado database
	// get a list of db from chado for user to choose
	$sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
	$results = db_query ($sql);
	db_set_active($previous_db); // use drupal database

	$cvs = array();
   $cvs[] = '';
	while ($cv = db_fetch_object($results)){
		$cvs[$cv->cv_id] = $cv->name;
	}

	$form['cvid'] = array(
      '#title' => t('Controlled Vocabulary/Ontology Name'),
      '#type' => 'select',
      '#options' => $cvs,
      '#ahah' => array(
         'path' => 'admin/tripal/tripal_cv/edit/js',
         'wrapper' => 'db-edit-div',
         'effect' => 'fade',
         'event' => 'change',
         'method' => 'replace',
      ),
	);

   return $form;
}
/*************************************************************************
*
*/
function tripal_ajax_cv_edit (){ 
   // get the database id, build the form and then return the JSON object
   $cvid = $_POST['cvid'];
   $form = drupal_get_form('tripal_cv_form',$cvid);
   drupal_json(array('status' => TRUE, 'data' => $form));
}
/*************************************************************************
*
*/
function tripal_cv_form(&$form_state = NULL,$cvid = NULL){

   // get this requested database
   if($cvid){
      $sql = "SELECT * FROM {cv} WHERE cv_id = %d ";
      $previous_db = db_set_active('chado');
      $cv = db_fetch_object(db_query($sql,$cvid));
      db_set_active($previous_db);


      # set the default values.  If there is a value set in the 
      # form_state then let's use that, otherwise, we'll pull 
      # the values from the database 
      $default_db = $form_state['values']['name'];
      $default_desc = $form_state['values']['description'];
      $default_url = $form_state['values']['url'];
      $default_urlprefix = $form_state['values']['urlprefix'];
      if(!$default_db){
         $default_cv = $cv->name;
      }
      if(!$default_desc){
         $default_desc = $cv->definition;
      }
      $action = 'Update';
   } else {
      $action = 'Add';
   }

   $form['cvid'] = array(
      '#type' => 'hidden',
      '#value' => $cvid
   );

   $form['name']= array(
      '#type'          => 'textfield',
      '#title'         => t("Controlled Vocabulary name"),
      '#description'   => t('Please enter the name for this vocabulary.'),
      '#required'      => TRUE,
      '#default_value' => $default_cv,
      '#weight'        => 1
   );

   $form['definition']= array(
      '#type'          => 'textarea',
      '#title'         => t('Description'),
      '#description'   => t('Please enter a description for this vocabulary'),
      '#default_value' => $default_desc,
      '#weight'        => 2
   );

   if(strcmp($action,'Update')==0){
      $form['update'] = array (
        '#type'         => 'submit',
        '#value'        => t('Update'),
        '#weight'       => 5,
        '#executes_submit_callback' => TRUE,
      );
      $form['delete'] = array (
        '#type'         => 'submit',
        '#value'        => t('Delete'),
        '#weight'       => 6,
        '#executes_submit_callback' => TRUE,
      );
   } else {
      $form['add'] = array (
        '#type'         => 'submit',
        '#value'        => t('Add'),
        '#weight'       => 5,
        '#executes_submit_callback' => TRUE,
      );
   }
   $form['#redirect'] = 'admin/tripal/tripal_cv';


   return $form;
}
/************************************************************************
*
*/
function tripal_cv_form_submit($form, &$form_state){

   $name =  $form_state['values']['name'];
   $desc =  $form_state['values']['definition'];
   $cvid =  $form_state['values']['cvid'];
   $op   =  $form_state['values']['op'];

   if($cvid){ 
      if(strcmp($op,'Update')==0){
         $sql = "
            UPDATE {cv} SET 
              name = '%s',
              definition = '%s'
            WHERE cv_id = %d
         ";
         $previous_db = db_set_active('chado');
         $db = db_query($sql,$name,$desc,$cvid);
         db_set_active($previous_db);
         if($db){
           drupal_set_message("Controlled vocabulary updated");
         } else {
           drupal_set_message("Failed to update controlled vocabulary.");
         }
      } 
      if(strcmp($op,'Delete')==0){
         $sql = "
            DELETE FROM {cv}
            WHERE cv_id = %d
         ";
         $previous_db = db_set_active('chado');
         $db = db_query($sql,$cvid);
         db_set_active($previous_db);
         if($db){
           drupal_set_message("Controlled vocabulary deleted");
         } else {
           drupal_set_message("Failed to delete controlled vocabulary.");
         }
      }
   } 
   else { 
      $sql = "
         INSERT INTO {cv}
          (name,definition)
         VALUES 
          ('%s','%s')
      ";
      $previous_db = db_set_active('chado');
      $db = db_query($sql,$name,$desc);
      db_set_active($previous_db);
      if($db){
        drupal_set_message("External database added");
      } else {
        drupal_set_message("Failed to add external database.");
      }
   } 

   return '';
}
/*************************************************************************
*
*/
function tripal_cv_cvtermpath_form () {

	$previous_db = db_set_active('chado');  // use chado database
	// get a list of db from chado for user to choose
	$sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
	$results = db_query ($sql);
	db_set_active($previous_db); // use drupal database

	$cvs = array();
   $cvs[] = '';
	while ($cv = db_fetch_object($results)){
		$cvs[$cv->cv_id] = $cv->name;
	}

	$form['cvid'] = array(
      '#title' => t('Controlled Vocabulary/Ontology Name'),
      '#type' => 'select',
      '#options' => $cvs,
      '#description' => t('Select a controlled vocabulary for which you would like to upate the cvtermpath.'),
	);

   $form['description'] = array(
       '#type' => 'item',
       '#value' => t("Submit a job to update chado cvtermpath table."),
       '#weight' => 1,
   );
   $form['button'] = array(
      '#type' => 'submit',
      '#value' => t('Update cvtermpath'),
      '#weight' => 2,
   );
   return $form;
}
/*************************************************************************
*
*/
function tripal_cv_cvtermpath_form_validate($form, &$form_state) {
   global $user;

   $cvid =  $form_state['values']['cvid'];

   // first get the controlled vocabulary name:
   $previous_db = db_set_active('chado');
   $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE cv_id = %d",$cvid));
   db_set_active($previous_db);

   // Submit a job to update cvtermpath
   $job_args = array($cvid);
   if ($form_state['values']['op'] == t('Update cvtermpath')) {
      tripal_add_job("Update cvtermpath: $cv->name",'tripal_cv',
         'tripal_cv_update_cvtermpath',$job_args,$user->uid);
   }
}

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

   // first get the controlled vocabulary name:
   $previous_db = db_set_active('chado');
   $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE cv_id = %d",$cvid));
   print "\nUpdating cvtermpath for $cv->name...\n";

   // now fill the cvtermpath table
   $sql = "SELECT * FROM fill_cvtermpath('%s')";
   db_query($sql,$cv->name);         
   db_set_active($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;
}