tripal/tripal_pub/tripal_pub.module

<?php

/**
 *  @file
 * This file contains the basic functions needed for this drupal module.
 * The drupal tripal_pub module maps directly to the chado X module. 
 *
 * For documentation regarding the Chado X module: 
 * @see http://gmod.org/wiki/Chado_General_Module
 */


//-----------------------------------------------------------------------------
//  SECTION: Main Section for Tripal Publication Module
//-----------------------------------------------------------------------------

/**
 * Implements hook_pub_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_project.views.inc where all the
 *  views integration code is located.
 */ 
function tripal_pub_views_api() {

   return array(
      'api' => 2.0,
   );
}


/**
* Implementation of hook_node_info()
*
* This tripal_pub_node_info, is a simple node that describes the functionallity of the module. It specifies
* that the title (Project Name) and body (Description) are set to true so the information can be
* entered
*
*/
function tripal_pub_node_info() {
  return array(
    'tripal_pub' => array(
      'name' => t('Publication'),
      'module' => 'tripal_pub',
      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
    	'has_title' => TRUE,
    	'title_label' =>t('Title'),
    	'had_body' => FALSE,
    )
  );
}


/**
* Implementation of tripal_pub_form().
*
*  This form takes the following information:A Publication Title,Volume title,Volume,Series Name,
*  Issue,Publication Year,Pages where the Article is located, Miniref,Type-Id, if the article is Obsolete,
*  Publishing company,Pubplication Place and a Uniquename for the the instance. It then puts the 
*  infromation into the Chado_project database table based on its 'pub_id'.
*
*  @parm &$node
*    The node that is created when the database is initialized
*
*  @parm $form_state
*    The state of the form, that has the user entered information that is neccessary for, setting
*    up the database of the project
*
*  @return $form
*    The information that was enterd allong with   
*
*/
function tripal_pub_form(&$node, $form_state) {
  
	$type = node_get_types('type', $node);
	
	//define form elements for the node's title and body.
	$form['title'] = array(
		'#type' => 'textfield',
		'#title' => t('Article Title'),
		'#description' => t('Title Heading'),
		'#required' => TRUE,
		'#default_value' => $node->title
	);
	
	$form['volumetitle'] = array(
	  '#type' => 'textfield',
		'#title' => t('Volume Title'),
		'#description' => t('Title of part if one of a series.'),
		'#required' => TRUE,
		'#default_value' => isset($node->pub_id->volumetitle) ? $node->pub_id->volumetitle : ''
	);
	
	$form['volume'] = array(
		'#type' => 'textfield',
		'#title' => t('Volume'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->volume) ? $node->pub_id->volume : ''
	);
	
	$form['series_name'] = array(
		'#type' => 'textfield',
		'#title' => t('Series Name'),
		'#required' => TRUE,
		'#default_value' => isset($node->pub_id->series_name) ? $node->pub_id->series_name : ''
	);
	
	$form['issue'] = array(
		'#type' => 'textfield',
		'#title' => t('Issue'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->issue) ? $node->pub_id->issue : ''
	);
	
	$form['pyear'] = array(
		'#type' => 'textfield',
		'#title' => t('Publication Year'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->pyear) ? $node->pub_id->pyear : ''
	);
	
	$form['pages'] = array(
		'#type' => 'textfield',
		'#title' => t('Pages'),
		'#description' => t('Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'),
		'#required' => TRUE,
		'#default_value' => isset($node->pub_id->pages) ? $node->pub_id->pages : ''
	);
	
	$form['miniref'] = array(
		'#type' => 'textfield',
		'#title' => t('Mini-Ref'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->miniref) ? $node->pub_id->miniref : ''
	);
	
	$form['uniquename'] = array(
		'#type' => 'textfield',
		'#title' => t('Unique Name'),
		'#required' => TRUE,
		'#default_value' => isset($node->pub_id->uniquename) ? $node->pub_id->uniquename : ''
	);
	
	$values= array(
	  'cv_id'=>array(
	  'name'=>'publication'),
	);
	
	//population select list with 'cvterm' names
	$result = tripal_core_chado_select ('cvterm', array('cvterm_id', 'name'), $values);
	
	foreach ($result as $value) {
	  $newArray[$value->cvterm_id]=$value->name;     //options for the select list
	}
	
	$form['type_id'] = array(
		'#type' => 'select',
		'#title' => t('Publication Type'),
		'#options' => $newArray,
		'#description' => t('Type of publication (book, journal, poem, graffiti, etc). Uses pub cv.'),
		'#required' => TRUE,
		'#default_value'=>isset($node->pub_id->type_id) ? $node->pub_id->type_id : ''
	);
	
	$form['is_obsolete'] = array(
		'#type' => 'checkbox',
		'#title' => t('Is Obsolete?(Check for Yes)'),
		'#required' => TRUE,
		'#default_value'=>isset($node->pub_id->is_obsolete) ? $node->pub_id->is_obsolete : FALSE
	);
	
	$form['publisher'] = array(
		'#type' => 'textfield',
		'#title' => t('Publisher Name'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->publisher) ? $node->pub_id->publisher : ''
	);
	
	$form['pubplace'] = array(
		'#type' => 'textfield',
		'#title' => t('Place of Publication'),
		'#required' => FALSE,
		'#default_value' => isset($node->pub_id->pubplace) ? $node->pub_id->pubplace  : ''
	);
	
	return $form;
}


/**
 *  Implements tripal_pub_help()
 *
 *  This function simply states, in HTML tags, the creator of the the module and the contact	
 *  for the programmer
 *
 *  @parm $path
 *    The absolute path of the module and help information
 *
 *  @parm $arg
 *    The argument
 */
function tripal_pub_help($path, $arg) {
  switch ($path) {
  
    case 'admin/help#tripal_pub':
      
      return '<p>'. t('Module Created By:Chad Krilow (e-mail:cnk046@mail.usask.ca)') .'</p>';
			
			break;
  
  }
}


/**
 * Implements hook_pub_perm()
 *
 *  This function sets the permission for the user to access the information in the database.
 *  This includes creating, inserting, deleting and updating of information in the database
 *
 */
function tripal_pub_perm() {

  return array('create tripal_pub', 'edit own tripal_pub');
  
}


/**
 * Implements tripal_project_access()
 *
 *  This function sets the access permission for database operations.
 *  
 *  @parm $op
 *    The operation that is to be performed
 *
 *  @parm $node
 *    The specific node which is to have the operation performed  
 *
 *  @parm $account
 *    The account of the user that is performing the operations  
 *
 *  @return
 *    True if a operation was performed, else False
 *
 */
function tripal_pub_access($op, $node, $account) {

  if ($op == 'create') {
    // Only users with permission to do so may create this node type.
    if(!user_access('create tripal_pub', $account){
      return FALSE;
    }
  }

  // Users who create a node may edit or delete it later, assuming they have the
  // necessary permissions.
  if ($op == 'update' || $op == 'delete') {
    if (!user_access('edit own tripal_pub',$account)) {
      return FALSE;
    }
    if (user_access('edit own tripal_pub',$account) && ($account->uid != $node->uid)) {
      return FALSE;
    }
  }
  return NULL;
}


/**
* Implementation of tripal_pub_insert()
*
*  This function takes the user entered information and inserts it into the database
*
*  @parm $node
*    Then node which has the information stored within the node-ID
*
*/
function tripal_pub_insert($node) {

  $values =  array(
    'title' => $node->title,
    'volumetitle' => $node->volumetitle,
    'volume'=>$node->volume,
    'series_name'=>$node->series_name,
    'issue'=>$node->issue,
    'pyear'=>$node->pyear,
    'pages'=>$node->pages,
    'miniref'=>$node->miniref,
    'type_id'=>$node->type_id,
    'is_obsolete'=>$node->is_obsolete,
    'publisher'=>$node->publisher,
    'pubplace'=>$node->pubplace,
    'uniquename' => $node->uniquename
  );
  
  //inserts info into chado table.
  $result = tripal_core_chado_insert('pub',$values);

	//inserts the row of vid,nid,project_id into the chado_project table
  db_query("INSERT INTO {chado_pub} (nid, vid, pub_id) VALUES (%d, %d, %d)", 
    $node->nid, 
    $node->vid,
    $result['pub_id']
  );
}


/**
* Implementation of tripal_pub_delete().
*
* This function takes a node that is linked to a publication-Id, and if 'Delete' is selected 
* in the 'Edit' section of the page, the Selected publication is deleted from the database.
*
* @param $node
*   The node that is to be deleted
*/
function tripal_pub_delete($node) {
  
  // Matching all revision, by using the node's pub_id.
  $values =  array(
	  'pub_id' => $node->pub_id->pub_id,
  );
  
  //deleting row in chado table
  tripal_core_chado_delete('pub',$values);
  
  //deleteing in drupal chado_project table
  db_query('DELETE FROM {chado_pub} WHERE nid = %d', $node->nid);
	
}


/**
*Implementation of tripal_pub_update().
*
*  This function updates the node that is to be modified. All the modified aspects of the 
*  database are updated as they are edited in the 'Edit' form.
*
* @param $node
*	  the node that is to be modified, all of the modified sections of the chado table are updated
*
*/
function tripal_pub_update($node){
	
  $values =  array(
    'title' => $node->title,
    'volumetitle' => $node->volumetitle,
    'volume'=>$node->volume,
    'series_name'=>$node->series_name,
    'issue'=>$node->issue,
    'pyear'=>$node->pyear,
    'pages'=>$node->pages,
    'miniref'=>$node->miniref,
    'uniquename'=>$node->uniquename,
    'type_id'=>$node->type_id,
    'is_obsolete'=>$node->is_obsolete,
    'publisher'=>$node->publisher,
    'pubplace'=>$node->pubplace,
  );
   
  $result = db_fetch_object(db_query('SELECT pub_id FROM {chado_pub} WHERE nid=%d AND vid=%d ',$node->nid, $node->vid));
   
  //extract pub_id from the chad table for update function
  $match = array( 'pub_id' => $result->pub_id ) ;
   
  //$table to be updated, $match is the 'pub_id', $value are the values that are to be updated
  $update_result = tripal_core_chado_update('pub',$match,$values);
  
}


/**
* Implementation of tripal_pub_load().
*
* This function is used to load the information, based on the 'pub_id', into the database
*
*  @param $node
*    The node that contains the information which  is to be loaded into the database, contains the 
*    user entered information
*
*  @return $node
*    The node containing the information which is to loaded in the database
*/
function tripal_pub_load($node) {

	$result = db_fetch_object(db_query('SELECT * FROM {chado_pub} WHERE nid=%d AND vid=%d ',$node->nid, $node->vid));
	
	$values = array(
	  'pub_id' => $result->pub_id,
	);
	
	if(empty($result->pub_id)){
		drupal_set_message("Unable to find publication", 'error');
	}else{
  	$node->pub_id = tripal_core_generate_chado_var('pub',$values);
  }

  return $node;
}


//-----------------------------------------------------------------------------
//  END OF SOFTWARE
//-----------------------------------------------------------------------------