tripal/tripal_stock/tripal_stock.module

<?php
// $Id$

require("tripal_stock-administration.inc");
require("tripal_stock-api_functions.inc");
require("other_module_api_functions.inc");

/*************************************************************************
 * Implementation of hook_menu()
 * Purpose: Add menu items for this module
 * Note: A Menu item for the Create chado_stock form is automatically
 *   added to the 'Create Content' Navigation menu
 *
 * @return and array for menu descriptions
 */
function tripal_stock_menu() {
  $items = array();

  //Administrative settings menu
  $items['admin/tripal/tripal_stock'] = array(
    'title' => t('Stocks'),
    'description' => t('Settings for Chado Stocks'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_stock_admin'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  //Displaying stocks
  $items['stocks'] = array(
  	'menu_name' => ('primary-links'),
    'title' => t('Stocks'),
    'page callback' => 'tripal_stock_show_stocks',
    'access arguments' => array('access chado_stock content'),
    'type' => MENU_NORMAL_ITEM,  
  );

  return $items;
}


/*************************************************************************
 * Implementation of hook_perm()
 * Purpose: Set the permission types that the chado stock module uses
 *
 * @return an array listing the possible permission catagories
 */
function tripal_stock_perm() {
  return array(
    'access chado_stock content',
    'create chado_stock content',
    'edit chado_stock content',
    'delete chado_stock content'
  );
}

/*************************************************************************
 * Implements hook_access()
 * Purpose: Maps permission catagories to actions; 
 *   TRUE grants access; FALSE denies it
 */
function tripal_stock_access($op, $node, $account) {
   if ($op == 'create') {
      return user_access('create chado_stock content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_stock content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_stock content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_stock content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}

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

/*************************************************************************
 * Implements hook_theme()
 * Purpose: Register themeing functions for this module
 *
 * @return an array of themeing functions to register
 */
function tripal_stock_theme() {
	return array(
		'tripal_stock_stock_table' => array (
			'arguments' => array('stocks'),
		),
	);
}

/*************************************************************************
 * Purpose: show stocks stored in drupals chado_stock table
 */
function tripal_stock_show_stocks () {
	$sql = "SELECT COUNT(stock_id) FROM {chado_stock}";
   $no_stocks = db_result(db_query($sql));
   if($no_stocks != 0) {
      $stocks = get_chado_stocks();
      if($no_stocks != count($stocks)) {
         drupal_set_message("Synchronization needed.");
      }
      return theme('tripal_stock_stock_table',&$stocks);
   } else {
      return t("No Stocks exists. Please contact administrators to ".
               "synchronize stocks.");
   }
}

function theme_tripal_stock_stock_table (&$stocks) {

	// cycle through the stocks and build the stocks page
	$output = "<div id=\"stocks\">";
	$output .= '<table>';
  $output .= "<tr>";
  $output .= "<th>Name</th>";
  $output .= "<th>Type</th>";
  $output .= "<th>Organism</th>";
  $output .= "<th>Description</th>";
  $output .= "</tr>";

  foreach($stocks as $stock){
		$output .= "<tr>";
		$output .= "<td>".l($stock->stock_name, "node/".$stock->nid)."</td>";
		$output .= "<td>".$stock->stock_type."</td>";
		$output .= "<td nowrap>".$stock->organism->common_name."</td>";
		$output .= "<td>".$stock->description."</td>";
		$output .= "</tr>";
	}
	$output .= "</table>";
	$output .= "</div>";

   return $output;
}

/*************************************************************************
 * @section Implementation of stock Node
 * including node_load, form, insert, update, delete(by nid and vid)
 *************************************************************************/

/*************************************************************************
 * Implements hook_node_info() 
 */
function tripal_stock_node_info() {
  return array(
    'chado_stock' => array(
      'name' => t('Stock'),
      'module' => 'chado_stock',
      'description' => t('A Chado Stock is a collection of material that can be sampled and have experiments performed on it.'),
      'has_title' => TRUE,
      'has_body' => FALSE,
    ),
  );
}

/*************************************************************************
 * Implements hook_load()
 * Everytime a chado_stock node is viewed or manipulated this hook is called first to prepare the data
 */
function chado_stock_load($node) {

  // Gets the stock_id from the drupal chado_stock table---------------------------------------
  $map = db_fetch_object(db_query(
    "SELECT stock_id as stock_id FROM {chado_stock} WHERE vid=%d",
    $node->vid
  ));
  $node->stock_id = $map->stock_id;  
  
  //Get the main stock information from the chado stock table-----------------------------------
  $previous_db = tripal_db_set_active('chado');
  $chado_stock = db_fetch_object(db_query(
    "SELECT s.name, s.uniquename, s.description, c.name as type, c.cvterm_id as type_id, s.is_obsolete, s.organism_id "
    ."FROM stock s, cvterm c WHERE s.type_id=c.cvterm_id AND stock_id=%d",
    $map->stock_id
  ));
  tripal_db_set_active($previous_db);
  //add to node
  $node->stock_name = $chado_stock->name;
  $node->uniquename = $chado_stock->uniquename;
  $node->description = $chado_stock->description;
  $node->stock_type = $chado_stock->type;
  $node->stock_type_id = $chado_stock->type_id;
  $node->is_obsolete = $chado_stock->is_obsolete;

  // Get organism details from chado & add to node-----------------------------------------------
  // get organism if for current stock
  // pull all data from chado for the organism and assign it to the current node
  $node->organism = get_chado_organism(NULL,$chado_stock->organism_id);

  // Add Synonyms for stock----------------------------------------------------------------------
  // These are a special case of property (stockprop table) where cvterm='synonym'
  $previous_db = tripal_db_set_active('chado');
  $results = db_query(
    "SELECT sp.stockprop_id, sp.value as value, sp.type_id, 'synonym' as type FROM stockprop sp, cvterm c "
    ."WHERE sp.stock_id=%d AND sp.type_id=c.cvterm_id AND c.name='synonym'",
    $map->stock_id
  );
  tripal_db_set_active($previous_db);
  $i=0;
  // Node->synonyms is an array of synonyms(strings)
  while ($r = db_fetch_object($results) ) {
    $synonyms[$i++] = $r;
  }
  $node->synonyms = $synonyms;

  // Add properties for stock (not including synonyms)-------------------------------------------
  // $node->properties is an array of objects where each object describes a single property and has a type and value
  $previous_db = tripal_db_set_active('chado');
  $results = db_query(
    "SELECT sp.stockprop_id, c.name as type, sp.value as value FROM stockprop sp, cvterm c "
    ."WHERE sp.stock_id=%d AND sp.type_id=c.cvterm_id AND c.name != 'synonym'",
    $map->stock_id
  );
  tripal_db_set_active($previous_db);
  $i=0;
  while ($r = db_fetch_object($results) ) {
    $properties[$i++] = $r;
  }
  $node->properties = $properties;

  // Add in main db reference-----------------------------------------------------------------------
  // this is the dbxref_id in the stock table
  //$node->main_db_reference is an object describing the dbxref and has an accession, version, description, db_name, db_description, & urlprefix
  $previous_db = tripal_db_set_active('chado');
  $db_reference = db_fetch_object(db_query(
    "SELECT dbx.dbxref_id, dbx.accession, dbx.version, dbx.description, db.db_id, db.name as db_name, db.description as db_description, db.urlprefix as db_urlprefix "
    ."FROM dbxref dbx, db db, stock s WHERE stock_id=%d AND s.dbxref_id=dbx.dbxref_id AND dbx.db_id=db.db_id",
    $map->stock_id
  ));
  tripal_db_set_active($previous_db);
  $node->main_db_reference = $db_reference;

  // Add in extra references to external databases---------------------------------------------------
  // this includes all the dbxref entries in stock_dbxref
  // $node->db_referencesi s an array of objects where each object describes a given dbxref and has the same fields as the main db references
  $previous_db = tripal_db_set_active('chado');
  $results = db_query(
    "SELECT dbx.dbxref_id, dbx.accession, dbx.version,	dbx.description, db.db_id, db.name as db_name, db.description as db_description, db.urlprefix as db_urlprefix "
    ."FROM dbxref dbx, db db, stock_dbxref s WHERE stock_id=%d AND s.dbxref_id=dbx.dbxref_id AND dbx.db_id=db.db_id",
    $map->stock_id
  );
  tripal_db_set_active($previous_db);
    $i=0;
  while ($r = db_fetch_object($results) ) {
    $db_references[$i++] = $r;
  }
  $node->db_references = $db_references;

  // Add relationships for stock---------------------------------------------------------------------
  // Relationships are broken down into those where the current stock is the subject (other details stored in $node->object_relationships)
  // and those where the current stock is the object (other details stored in $node->subject_relationships)
  // fields available to each include object/subject_name, object/subject_id (stock_id in chado) and object/subject_nid (node id in drupal)
     // where current is subject.............................
     $previous_db = tripal_db_set_active('chado');
     $result = db_query(
       "SELECT sr.stock_relationship_id, c.name as relationship_type, sr.type_id as relationship_type_id, s.uniquename as object_uniquename, s.name as object_name, s.stock_id as object_id "
       . "FROM stock_relationship sr, stock s, cvterm c "
       . "WHERE sr.subject_id=%d AND sr.object_id=s.stock_id AND sr.type_id=c.cvterm_id",
       $map->stock_id
     );
     tripal_db_set_active($previous_db);
     $i=0;
     $relationships= array();
     while ($r = db_fetch_object($result) ) {

       //get nid
       $object = db_fetch_object(db_query("SELECT * FROM {node} n, {chado_stock} c WHERE c.nid=n.nid AND c.vid=n.vid AND c.stock_id=%d", $r->object_id ));
       $r->object_nid = $object->nid;

       $relationships[$i++] = $r;
     }
     $node->object_relationships = $relationships;

     // where current is object.............................
     $previous_db = tripal_db_set_active('chado');
     $result = db_query(
       "SELECT sr.stock_relationship_id, c.name as relationship_type, sr.type_id as relationship_type_id, s.uniquename as subject_uniquename, s.name as subject_name, s.stock_id as subject_id "
       . "FROM stock_relationship sr, stock s, cvterm c "
       . "WHERE	sr.object_id=%d AND sr.subject_id=s.stock_id AND sr.type_id=c.cvterm_id",
       $map->stock_id
     );
     tripal_db_set_active($previous_db);
     $i=0;
     $relationships= array();
     while ($r = db_fetch_object($result) ) {

       //get nid
       $subject = db_fetch_object(db_query("SELECT * FROM {node} n, {chado_stock} c WHERE c.nid=n.nid AND c.vid=n.vid AND c.stock_id=%d", $r->subject_id ));
       $r->subject_nid = $subject->nid;

       $relationships[$i++] = $r;
     }
     $node->subject_relationships = $relationships;

     return $node;
}


/*************************************************************************
 * Implements hook_form()	
 * Creates the main Add/Edit/Delete Form for chado stocks
 *
 * Parts to be added by this form
 *     name, 
 *     uniquename, 
 *     description, 
 *     type => select from cvterm with key cvterm_id,
 *     organism => select from available with key organism_id
 *     main_db_reference => accession, version, description, db_name(select from dropdown) 
 */
function chado_stock_form($node, $form_state) {
  $type = node_get_types('type', $node);

  // This defines the path for the next step in a simulated multipart form
  // NOTE: The %node gets replaced with the nid in insert
  $form['next_step_path'] = array(
    '#type' => 'hidden',
    '#value' => 'node/%node/properties'
  );

  // If you don't want a multipart form set this to false
  // Will then do default redirect (to new node) on submit
  $form['simulate_multipart'] = array(
    '#type' => 'textfield',
    '#attributes'=>array('style'=>"display:none"),
    '#default_value' => TRUE
  );

  if (!isset($node->uniquename)) {
    $form['progress'] = array( 
      '#type' => 'item', 
      '#value' => 'blank', //implement_add_chado_properties_progress('main')
    );
  }

  $form['names'] = array(
    '#type' => 'fieldset',
    '#title' => t('Stock Name')
  );

  $form['names']['title'] = array(
    '#type' => 'textfield',
    '#title' => t('Name'),
    '#default_value' => $node->title,
    '#required'	     => TRUE
  );

  $form['names']['uniquename'] = array(
    '#type' => 'textfield',
    '#title' => t('Unique Name'),
    '#default_value' => $node->uniquename,
    '#required'	     => TRUE
  );

  $form['names']['stock_id'] = array(
    '#type' => 'hidden',
    '#value' => $node->stock_id
  );

  $form['details'] = array(
    '#type' => 'fieldset',
    '#title' =>	t('Stock Details')
  );

  $type_options = get_chado_cvterm_options( variable_get('chado_stock_types_cv', 'null') );
  $type_options[0] = 'Select a Type';
  if ($node->nid == '') { $type_default = 0; } else { $type_default = $node->stock_type_id; }
  $form['details']['type_id'] = array(
    '#type' => 'select',
    '#title' => t('Type of Stock'),
    '#options' => $type_options,
    '#default_value' => $type_default,
    '#required'	  => TRUE,
  );

  $stock_oganism_options = get_chado_organism_options();
  $stock_oganism_options[0] = 'Select An Organism';
  if ($node->nid == '') { $organism_default = 0; } else {  $organism_default = $node->organism->organism_id; }
  $form['details']['organism_id'] = array(
    '#type' => 'select',
    '#title' => t('Source Organism for stock'),
    '#default_value' => $organism_default,
    '#options' => $stock_oganism_options,
    '#required'	  => TRUE
  );

  $form['details']['stock_description'] = array(
    '#type' => 'textarea',
    '#title' => t('Notes'),
    '#default_value' => $node->description,
    '#description' => t('Briefly enter any notes on the above stock. This should not include phenotypes or genotypes.'),
  );

  $form['database_reference'] = array(
    '#type' => 'fieldset',
    '#title' => t('Stock Database Reference')
  );

  $form['database_reference']['accession'] = array(
    '#type' => 'textfield',
    '#title' => t('Accession'),
    '#default_value' => $node->main_db_reference->accession
  );

  $form['database_reference']['db_description'] = array(
    '#type' => 'textarea',
    '#title' => t('Description of Database Reference'),
    '#default_value' => $node->main_db_reference->db_description,
    '#description' => t('Optionally enter a description about the database accession.')
  );

  $db_options = get_chado_db_options();
  $db_options[0] = 'Select a Database';
  if ($node->nid == '') { $db_default = 0; } else { $db_default = $node->main_db_reference->db_id; }
  $form['database_reference']['database'] = array(
    '#type' => 'select',
    '#title' => t('Database'),
    '#options' => $db_options,
    '#default_value' => $db_default
  );

  return $form;
}

/*************************************************************************
 * Implements hook_validate()
 */
function chado_stock_validate($node, &$form) {

	$int_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s=%d";
	$string_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s='%s'";
	
  // Validate Uniquename only if add
  if (empty($node->stock_id)) {
  	$previous_db = tripal_db_set_active('chado');
  	$chado_row = db_fetch_object(db_query("SELECT * FROM stock WHERE uniquename='".$node->uniquename."'"));
  	tripal_db_set_active($previous_db);
  	if(!empty($chado_row->stock_id)) {
  		$drupal_row = db_fetch_object(db_query("SELECT * FROM {chado_stock} WHERE stock_id=".$chado_row->stock_id));
  		if (!empty($drupal_row->nid)) {
  			$link = l('node/'.$drupal_row->nid, $node->uniquename);
  			form_set_error('uniquename', "There is already a stock with that uniquename $link. Please enter another uniquename.");
			} else {
				form_set_error('uniquename', "There is already a stock with that uniquename (although it's not sync'd with drupal). Please enter another uniquename.");
			}
  	}
  }


  // Check Type of Stock is valid cvterm_id in chado ( $form['values']['details']['type_id'] )
  if ( $node->type_id == 0) {
    form_set_error('type_id', 'Please select a type of stock.');
  } else {
  	$previous_db = tripal_db_set_active('chado');
    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
    tripal_db_set_active($previous_db);
    if ( $num_rows->count != 1) {
      form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
  }

  // Check Source Organism is valid organism_id in chado ( $form['values']['details']['organism_id'] )
  if ( $node->organism_id == 0) {
    form_set_error('organism_id', 'Please select a source organism for this stock');
  } else {
  	$previous_db = tripal_db_set_active('chado');
    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
    tripal_db_set_active($previous_db);
    if ( $num_rows->count != 1 ) {
      form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
  }

  // Check if Accession also database
  if ($node->accession != '') { 
    if ($node->database == 0) {
      // there is an accession but no database selected
      form_set_error('database', 'You need to enter both a database and an accession for that database in order to add a database reference.');
    }
  } else {
    if ($node->database > 0) {
      // there is a database selected but no accession
      form_set_error('accession', 'You need to enter both a database and an accession for that database in order to add a database reference.');
    }
  }

  // Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
  if ( $node->database > 0) {
  	$previous_db = tripal_db_set_active('chado');
    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'db', 'db_id', $node->database));
    tripal_db_set_active($previous_db);
    if ($num_rows->count != 1) {
      form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
  }

  // Check Accession is unique for database ( $form['values']['database_reference']['accession'] )
  if ( $node->accession != '') {
  	$previous_db = tripal_db_set_active('chado');
    $num_rows = db_fetch_object(db_query($string_in_chado_sql, 'dbxref', 'accession', $node->accession));
    tripal_db_set_active($previous_db);
    if ($num_rows->count > 0) {
      form_set_error('accession', 'This accession ('.$node->accession.') has already been assigned to another stock.'); }
  }

}

/*************************************************************************
 * Implements hook_insert()
 * Inserts data from chado_stock_form() into drupal and chado
 */
function chado_stock_insert($node) {

  $previous_db = tripal_db_set_active('chado');
	// create dbxref
  if ( !empty($node->accession) ) {
    if ( !empty($node->database) ) { 
      db_query(
        "INSERT INTO dbxref (db_id, accession, description) VALUES (%d, '%s', '%s')",
        $node->database,
        $node->accession,
				$node->db_description	
      );
    }
  }

  // create stock
  $dbxref_options['db_id'] = array(
  	'value' =>$node->database,
  	'type' => 'INT',
  );
  $dbxref_options['accession'] = array(
  	'value' =>$node->accession,
  	'type' => 'STRING',
  );
  $dbxref = get_chado_dbxref($dbxref_options);
  if($dbxref->dbxref_id != 0) {
    db_query(
      "INSERT INTO stock (dbxref_id, organism_id, name, uniquename, description, type_id, is_obsolete) VALUES (%d, %d, '%s', '%s', '%s', %d, 'f')",
      $dbxref->dbxref_id,
      $node->organism_id,
      $node->title,
      $node->uniquename,
      $node->description,
      $node->type_id
    );
  } else {
    db_query(
      "INSERT INTO stock (organism_id, name, uniquename, description, type_id, is_obsolete) VALUES (%d, '%s', '%s', '%s', %d, 'f')",
      $node->organism_id,
      $node->title,
      $node->uniquename,
      $node->description,
      $node->type_id
    );
  }
  tripal_db_set_active($previous_db);

  // create drupal chado_stock entry
  $previous_db = tripal_db_set_active('chado');
  $chado_stock = db_fetch_object(db_query("SELECT stock_id FROM stock WHERE uniquename='".$node->uniquename."' AND type_id=".$node->type_id.' AND organism_id='.$node->organism_id));
	tripal_db_set_active($previous_db);
  if (!empty($chado_stock->stock_id)) {
  	db_query(
    	"INSERT INTO {chado_stock} (nid, vid, stock_id) "
    	."VALUES (%d, %d, %d)",
    	$node->nid,
    	$node->vid,
    	$chado_stock->stock_id
  	);

  	//Move on to next stage of Stock Creation based on next_stage_path field
  	if ($node->simulate_multipart) {
    	$next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);  
    	$_REQUEST['destination'] = $next_stage_path;
  	}
  } else {
		drupal_set_message('Error during stock creation.', 'error');
  }

}

/*************************************************************************
 * Implements hook_update()
 * Handles Editing/Updating of main stock info (that in the chado stock table)
 * Currently just writes over all old data
 */
function chado_stock_update($node) {

  if ($node->revision) {
    chado_stock_insert($node);
  } else {

    //can't change stock id which is all thats stored in drupal thus only update chado
    $previous_db = tripal_db_set_active('chado');
    db_query(
      "UPDATE stock SET organism_id=%d, name='%s', uniquename='%s', description='%s', type_id=%d WHERE stock_id=%d",
      $node->organism_id,
      $node->title,
      $node->uniquename,
      $node->description,
      $node->type_id,
      $node->stock_id
    );
    tripal_db_set_active($previous_db);
  }

}

/*************************************************************************
 * Implements hook_delete()
 * Handles deleting of chado_stocks
 */
function chado_stock_delete($node) {

  //remove drupal node and all revisions
  db_query(
    "DELETE FROM {chado_stock} WHERE nid=%d",
    $node->nid
  );
  
  // Set stock in chado: is_obsolete = TRUE
  $previous_db = tripal_db_set_active('chado');
  db_query(
    "DELETE FROM stock WHERE stock_id=%d",
    $node->stock_id
  );
  tripal_db_set_active($previous_db);
}