tripal/tripal_stock/tripal_stock.module

<?php
// $Id$

/**
 * @file
 * Implements Tripal Stock Module hooks
 */

/**
 * @defgroup tripal_stock Stock Module
 * @{
 * Provides functions for managing chado stocks including creating details pages for each stock
 *
 * The Tripal Stock Module provides functionality for adding, editing, deleting and accessing chado 
 * stocks. The stock module was designed to store information about stock collections in a 
 * laboratory. What is called a stock could also be called a strain or an accession. There is a lot 
 * in common between a Drosophila stock and a Saccharomyces strain and an Arabidopsis line. They all 
 * come from some taxon, have genotypes, physical locations in the lab, some conceivable 
 * relationship with a publication, some conceivable relationship with a sequence feature (such as a 
 * transgene), and could be described by some ontology term. For more information about the chado 
 * Stock Module see the GMOD Wiki Page (http://gmod.org/wiki/Chado_Stock_Module)
 * @}
 */
require("tripal_stock-administration.inc");

require("tripal_stock.api.inc");
require("other_module_api_functions.inc");

require("tripal_stock-secondary_tables.inc");
require("tripal_stock-properties.inc");
require("tripal_stock-relationships.inc");
require("tripal_stock-db_references.inc");

/**
 * Implements hook_menu(): Adds menu items for the tripal_stock
 *
 * @return
 *   Menu definitions for the tripal_stock
 *
 * @ingroup tripal_stock
 */
function tripal_stock_menu() {
  $items = array();

  //Administrative settings menu-----------------
  $items['admin/tripal/tripal_stock'] = array(
    'title' => t('Stocks'),
    'description' => t('Basic Description of Tripal Stock Module Functionality'),
    'page callback' => 'tripal_stock_module_description_page',
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_stock/configuration'] = array(
    'title' => t('Configuration'),
    '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,  
  );

  // Adding Secondary Properties-----------------
  $items['node/%cs_node/properties'] = array(       
    'title' => t('Add Properties & Synonyms'),                         
    'description' => t('Settings for Chado Stocks'),
    'page callback' => 'tripal_stock_add_ALL_property_page',           
    'page arguments' => array(1), 
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%cs_node/db_references'] = array(                        
    'title' => t('Add Database References'),                   
    'description' => t('Settings for Chado Stocks'),              
    'page callback' => 'tripal_stock_add_ALL_dbreferences_page',                         
    'page arguments' => array(1),
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%cs_node/relationships'] = array(                      
    'title' => t('Add Relationships'),                      
    'description' => t('Settings for Chado Stocks'),               
    'page callback' => 'tripal_stock_add_ALL_relationships_page',                          
    'page arguments' => array(1),
    'access arguments' => array('create chado_stock content'),
    'type' => MENU_CALLBACK
  );

  //Edit/Deleting Secondary Properties-------------
  $items['node/%cs_node/edit_properties'] = array(
    'title' => t('Edit Properties'),
    'description' => t('Settings for Chado Stocks'),
    'page callback' => 'tripal_stock_edit_ALL_properties_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 8,
  );

    $items['node/%cs_node/edit_relationships'] = array(
    'title' => t('Edit Relationships'),
    'description' => t('Settings for Chado Stocks'), 
    'page callback' => 'tripal_stock_edit_ALL_relationships_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 9,
  );

  $items['node/%cs_node/edit_db_references'] = array(
    'title' => t('Edit DB References'),
    'description' => t('Settings for Chado Stocks'),
    'page callback' => 'tripal_stock_edit_ALL_dbreferences_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_stock content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );
  return $items;
}

/**
 * Implements Menu wildcard_load hook
 *
 * Purpose: Allows the node ID of a chado stock to be dynamically 
 *   pulled from the path. The node is loaded from this node ID
 *   and supplied to the page as an arguement. This is an example 
 *   of dynamic argument replacement using wildcards in the path.
 *
 * @param $nid
 *   The node ID passed in from the path
 *
 * @return
 *   The node object with the passed in nid
 *
 * @ingroup tripal_stock
 */
function cs_node_load($nid) {
  if (is_numeric($nid)) {
    $node = node_load($nid);
    if ($node->type == 'chado_stock') {
      return $node;
    }
  }

  return FALSE;
}

/**
 * Implementation of hook_perm()
 *
 * Purpose: Set the permission types that the chado stock module uses
 *
 * @return
 *   Listing of the possible permission catagories
 *
 * @ingroup tripal_stock
 */
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(): Maps permission catagories to actions
 *
 * @param $op
 *   The operation current operation: one of create, update, delete
 * @param $node
 *   The node object the current operation is being performed on
 * @param $account
 *   A user object representing the user for whom the operation is to be performed
 *
 * @return
 *   TRUE grants access; FALSE denies it
 *
 * @ingroup tripal_stock
 */
function chado_stock_access($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
 *
 * @return
 *   An array with fields important for views integration
 *
 * @ingroup tripal_stock
 */ 
function tripal_stock_views_api() {
   return array(
      'api' => 2.0,
   );
}

/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 * @return
 *   An array of themeing functions to register
 *
 * @ingroup tripal_stock
 */
function tripal_stock_theme() {
	return array(
		'tripal_stock_stock_table' => array (
			'arguments' => array('stocks'),
		),
		// Property edit forms--------------------------
    'tripal_stock_edit_ALL_properties_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_properties_form',
    ),
    'tripal_stock_edit_ALL_db_references_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_db_references_form',
    ),
    'tripal_stock_edit_ALL_relationships_form' => array(
      'arguments' => array('form'),
      'function' => 'theme_tripal_stock_edit_ALL_relationships_form',
    ),
    // Block Templates------------------------------
    'tripal_stock_base' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_base',
    ),
    'tripal_stock_properties' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_properties',
    ),
    'tripal_stock_references' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_references',
    ),
    'tripal_stock_relationships_as_object' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_relationships_as_object',
    ),    
    'tripal_stock_relationships_as_subject' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_relationships_as_subject',
    ),
    'tripal_stock_synonyms' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_stock_synonyms',
    ),
	);
}

/**
 * Purpose: show stocks stored in drupals chado_stock table
 *
 * This function provides the default html representation of the stock table. This
 * representation can be overridden using Drupal Views2 to create more flexible tables
 * listing stocks.
 *
 * @return
 *   HTML representation of a table of stocks
 *
 * @ingroup tripal_stock
 */
function tripal_stock_show_stocks () {
	$sql = "SELECT COUNT(stock_id) FROM {chado_stock}";
   $no_stocks = db_result(db_query($sql));
   if($no_stocks != 0) {
      $stocks = tripal_stock_get_all_stocks();
      if($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.");
   }
}

/**
 * A themeing funtion for the default tripal stock table
 *
 * @param $stocks
 *   An array of all stock nodes
 *
 * @return
 *   HTML representation of a table of stocks
 *
 * @ingroup tripal_stock
 */
function theme_tripal_stock_stock_table (&$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;
}

/**
 * Implements hook_node_info(): registers a stock node type
 *
 * @return
 *   An array describing various details of the node
 *
 * @ingroup tripal_stock
 */
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(): Prepares the chado_stock node
 *
 * @param $node
 *   The basic node containing all variables common to all nodes
 *
 * @return
 *   A stock node containing all the variables from the basic node and all stock specific variables
 *
 * @ingroup tripal_stock
 */
function chado_stock_load($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-----------------------------------
  $columns = array('name', 'uniquename', 'description', 'type_id', 'is_obsolete', 'organism_id', 'dbxref_id');
  $values = array('stock_id' => $node->stock_id);
  $results = tripal_core_chado_select('stock', $columns, $values);
  
  $node->stock_name = $results[0]->name;
  $node->uniquename = $results[0]->uniquename;
  $node->description = $results[0]->description;
  $node->stock_type_id = $results[0]->type_id;
  $node->organism->organism_id = $results[0]->organism_id;
  $node->main_db_reference->dbxref_id = $results[0]->dbxref_id;
  
  if (preg_match('/t/', $results[0]->is_obsolete)) {
    $node->is_obsolete = TRUE;
  } else {
    $node->is_obsolete = FALSE;
  }

  // Get type for current stock------------------------------------------------------------------
  $columns = array('name');
  $values = array('cvterm_id' => $node->stock_type_id);
  $results = tripal_core_chado_select('cvterm', $columns, $values);
  
  $node->stock_type = $results[0]->name;
  
  // 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
  $node->organism = tripal_organism_get_organism_by_organism_id($node->organism->organism_id);

  // Add Synonyms for stock----------------------------------------------------------------------
  // These are a special case of property (stockprop table) where cvterm='synonym'
  $columns = array('stockprop_id', 'type_id', 'value', 'rank');
  $values = array(
    'stock_id' => $node->stock_id, 
    'type_id' => array(
      'cv_id' => variable_get('chado_stock_prop_types_cv', 'null'), 
      'name' => 'synonym'
    ) 
  );
  $results = tripal_core_chado_select('stockprop', $columns, $values);
  if (!empty($results)) {
  	foreach ($results as $r) {
    	$r->type = 'synonym';
    	$node->synonyms[] = $r;
  	}
	}
	
  // 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
  $columns = array('stockprop_id', 'type_id', 'value', 'rank');
  $values = array(
    'stock_id' => $node->stock_id, 
  );
  $results = tripal_core_chado_select('stockprop', $columns, $values);
  foreach ($results as $r) {
    $columns = array('name');
    $values = array('cvterm_id' => $r->type_id);
    $type_results = tripal_core_chado_select('cvterm', $columns, $values);
    $r->type = $type_results[0]->name;
    
    $node->properties[] = $r;
  }
  
  // Add in main db reference-----------------------------------------------------------------------
  // this is the dbxref_id in the stock table
  if (!empty($node->main_db_reference->dbxref_id)) {
    $columns = array('dbxref_id', 'accession', 'version', 'description', 'db_id');
    $values = array('dbxref_id' => $node->main_db_reference->dbxref_id);
    $results = tripal_core_chado_select('dbxref', $columns, $values);
    $node->main_db_reference = $results[0];
    
    //get db info
    $columns = array('name', 'description', 'url', 'urlprefix');
    $values = array('db_id' => $node->main_db_reference->db_id);
    $results = tripal_core_chado_select('db', $columns, $values);
    $node->main_db_reference->db_name = $results[0]->name;
    $node->main_db_reference->db_description = $results[0]->description;
    $node->main_db_reference->db_url = $results[0]->url;
    $node->main_db_reference->db_urlprefix = $results[0]->urlprefix;
  }

  // Add in extra references to external databases--------------------------------------------------
  // this includes all the dbxref entries in stock_dbxref
  $columns = array('dbxref_id');
  $values = array('stock_id' => $node->stock_id);
  $results = tripal_core_chado_select('stock_dbxref',$columns,$values);
  $node->db_references = array();
  foreach ($results as $r) {
    $columns = array('dbxref_id', 'accession', 'version', 'description', 'db_id');
    $values = array('dbxref_id' => $r->dbxref_id);
    $sub_results = tripal_core_chado_select('dbxref', $columns, $values);   
    $dbxref = $sub_results[0];
    
    //get db info
    $columns = array('name', 'description', 'url', 'urlprefix');
    $values = array('db_id' => $dbxref->db_id);
    $results = tripal_core_chado_select('db', $columns, $values);
    $dbxref->db_name = $results[0]->name;
    $dbxref->db_description = $results[0]->description;
    $dbxref->db_url = $results[0]->url;
    $dbxref->db_urlprefix = $results[0]->urlprefix;    
    
    $node->db_references[] = $dbxref;
  }
  
  // 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.............................
    $columns = array('stock_relationship_id', 'subject_id', 'type_id', 'object_id', 'value', 'rank');
    $values = array('subject_id' => $node->stock_id);
    $results = tripal_core_chado_select('stock_relationship', $columns, $values);
    
    $node->object_relationships = array();
    foreach ($results as $r) {
      $columns = array('name', 'uniquename', 'description', 'type_id', 'is_obsolete', 'organism_id', 'dbxref_id');

      $values = array('stock_id' => $r->object_id);
      $results = tripal_core_chado_select('stock', $columns, $values);

			// Type
			$type_results = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id' => $r->type_id));
			$r->type = $type_results[0]->name;
			
			// Object
      $r->object->stock_id = $r->object_id;
      unset($r->object_id);
      
      $r->object->stock_name = $results[0]->name;
      $r->object->uniquename = $results[0]->uniquename;
      $r->object->description = $results[0]->description;
      $r->object->stock_type_id = $results[0]->type_id;
      $r->object->organism->organism_id = $results[0]->organism_id;
      $r->object->main_db_reference->dbxref_id = $results[0]->dbxref_id;        

      $sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
      $object_node = db_fetch_object(db_query($sql, $r->object->stock_id));
      $r->object->nid = $object_node->nid;
      
      $node->object_relationships[] = $r;
    }

     // where current is object.............................
    $columns = array('stock_relationship_id', 'subject_id', 'type_id', 'object_id', 'value', 'rank');
    $values = array('object_id' => $node->stock_id);
    $results = tripal_core_chado_select('stock_relationship', $columns, $values);

    $node->subject_relationships = array();    
    foreach ($results as $r) {
      $columns = array('name', 'uniquename', 'description', 'type_id', 'is_obsolete', 'organism_id', 'dbxref_id');
      $values = array('stock_id' => $r->subject_id);
      $results = tripal_core_chado_select('stock', $columns, $values);

			// Type
			$type_results = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id' => $r->type_id));
			$r->type = $type_results[0]->name;
			
			// Subject
      $r->subject->stock_id = $r->subject_id;
      unset($r->subject_id);  
      
      $r->subject->stock_name = $results[0]->name;
      $r->subject->uniquename = $results[0]->uniquename;
      $r->subject->description = $results[0]->description;
      $r->subject->stock_type_id = $results[0]->type_id;
      $r->subject->organism->organism_id = $results[0]->organism_id;        
      $r->subject->main_db_reference->dbxref_id = $results[0]->dbxref_id;        

      $sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
      $subject_node = db_fetch_object(db_query($sql, $r->subject->stock_id));
      $r->subject->nid = $subject_node->nid;
      
      $node->subject_relationships[] = $r;
    }

     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) 
 *
 * @param $node
 *   An empty node object on insert OR the current stock node object on update
 * @param $form_state
 *   The current state of the form
 *
 * @return
 *   A description of the form to be rendered by drupal_get_form()
 *
 * @ingroup tripal_stock
 */
function chado_stock_form($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' => tripal_stock_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 = tripal_cv_get_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 = tripal_organism_get_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 = tripal_db_get_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(): Validate the input from the chado_stock node form
 *
 * @param $node
 *   The current node including fields with the form element names and submitted values
 * @param $form
 *   A description of the form to be rendered by drupal_get_form()
 *
 * @ingroup tripal_stock
 */
function chado_stock_validate($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
 *
 * @param $node
 *   The current node including fields with the form element names and submitted values
 *
 * @return
 *   TRUE if the node was successfully inserted into drupal/chado; FALSE otherwise
 *
 * @ingroup tripal_stock
 */
function chado_stock_insert($node) {

	// create dbxref
  if ( !empty($node->accession) ) {
    if ( !empty($node->database) ) { 
      $values = array(
      	'db_id' => $node->database,
      	'accession' => $node->accession,
      );
      if (!tripal_core_chado_select('dbxref',array(dbxref_id), $values)) {
      	$values['description'] = $node->db_description;
      	$values['version'] = '1';
      	$dbxref_status = tripal_core_chado_insert('dbxref', $values);
      	if (!$dbxref_status) {
      		drupal_set_message('Unable to add database reference to this stock.', 'warning');
      		watchdog('tripal_stock', 
      			'Insert Stock: Unable to create dbxref where values:%values', 
      			array('%values' => print_r($values, TRUE)),
      			WATCHDOG_WARNING
      		);
      	}
      } else { $dbxref_status = 1; }
  	}
  }
  
  // create stock
  if($dbxref_status) {
		$values = array(
      'dbxref_id' => array(
      	'db_id' => $node->database, 
      	'accession' => $node->accession
      ),
      'organism_id' => $node->organism_id,
      'name' => $node->title,
      'uniquename' => $node->uniquename,
      'description' => $node->description,
      'type_id' => $node->type_id
    );
    $stock_status = tripal_core_chado_insert('stock', $values);
  } else {
		$values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->title,
      'uniquename' => $node->uniquename,
      'description' => $node->description,
      'type_id' => $node->type_id
    );
    $stock_status = tripal_core_chado_insert('stock', $values);
  }

  // create drupal chado_stock entry
  if ($stock_status) {
	  $values = array(
    	'organism_id' => $node->organism_id,
    	'uniquename' => $node->uniquename,
    	'type_id' => $node->type_id
  	);
  	$chado_stock = tripal_core_chado_select('stock', array('stock_id'), $values);
  	if (!empty($chado_stock[0]->stock_id)) {
  		db_query(
    		"INSERT INTO {chado_stock} (nid, vid, stock_id) "
    		."VALUES (%d, %d, %d)",
    		$node->nid,
    		$node->vid,
    		$chado_stock[0]->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'] = $next_stage_path;
  		}
  	} else {
			drupal_set_message('Error during stock creation.', 'error');
			watchdog('tripal_stock', 
      	'Insert Stock: Unable to find newly created stock where values:%values', 
      	array('%values' => print_r($values, TRUE)),
      	WATCHDOG_ERROR
      );
      return FALSE;
  	}
  } else {
  	drupal_set_message('Error during stock creation.', 'error');
    watchdog('tripal_stock', 
    	'Insert Stock: Unable to create stock where values:%values', 
      array('%values' => print_r($values, TRUE)),
      WATCHDOG_WARNING
    );
    return FALSE;
  }

}

/**
 * Implements hook_update(): Handles Editing/Updating of main stock info
 *
 * NOTE: Currently just writes over all old data
 *
 * @param $node
 *   The current node including fields with the form element names and submitted values
 *
 * @return
 *   TRUE if the node was successfully updated in drupal/chado; FALSE otherwise
 *
 * @ingroup tripal_stock
 */
function chado_stock_update($node) {

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

		//update dbxref
		if ($node->database) {
			if($node->accession) {
				$dbxref_mode = '';
				$stock = tripal_core_chado_select(
					'stock', 
					array('dbxref_id', 'type_id'), 
					array('stock_id' => $node->stock_id)
				);
			
				if ($stock[0]->dbxref_id) {
					$values = array(
						'db_id' => $node->database,
						'accession' => $node->accession,
						'description' => $node->db_description
					);
					$dbxref_status = tripal_core_chado_update(
						'dbxref', 
						array('dbxref_id' => $stock[0]->dbxref_id), 
						$values
					);
					$dbxref_mode = 'Update';
				} else {
					if ($stock[0]->type_id) {
						//create the dbxref
						//used the type_id as a control to check we have a stock but not a dbxref
						$values = array(
							'db_id' => $node->database,
							'accession' => $node->accession,
							'description' => $node->db_description,
							'version' => '1',
						);						
						$dbxref_status = tripal_core_chado_insert(
							'dbxref',
							$values
						);
						$dbxref_mode = 'Create';
					} else {
						drupal_set_message('Unable to find stock to Update', 'error');
						watchdog(
							'tripal_stock',
							'Stock Update: Unable to find stock to update using values: %values',
							array('%values', print_r($values, TRUE)),
							WATCHDOG_ERROR
						);
						return FALSE;
					}
				}
			}
		}
		
		if (!$dbxref_status) {
			watchdog(
				'tripal_stock',
				'Stock Update: Unable to %mode main stock dbxref with values: %values',
				array('%values' => print_r($values,TRUE), '%mode' => $dbxref_mode),
				WATCHDOG_WARNING
			);
		}

    //can't change stock id which is all thats stored in drupal thus only update chado
		$update_values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->title,
      'uniquename' => $node->uniquename,
      'description' => $node->description,
      'type_id' => $node->type_id,
    );
    if ($dbxref_status) {
    	$update_values['dbxref_id'] = array(
    		'db_id' => $node->database, 
    		'accession' => $node->accession
    	);
    }
    $status = tripal_core_chado_update(
    	'stock',
    	array('stock_id' => $node->stock_id), 
    	$update_values
    );
    
    if (!$status) {
    	drupal_set_message('Unable to update stock', 'error');
    	watchdog(
    		'tripal_stock',
    		'Stock Update: Unable to update stock using match values: %mvalues and update values: %uvalues',
				array('%mvalues' => print_r(array('stock_id' => $node->stock_id),TRUE), '%uvalues' => print_r($update_values,TRUE)),
				WATCHDOG_ERROR
    	);
    }
  }

}

/**
 * Implements hook_delete(): Handles deleting of chado_stocks
 *
 * NOTE: Currently deletes data -no undo or record-keeping functionality
 *
 * @param $node
 *   The current node including fields with the form element names and submitted values
 *
 * @return
 *   TRUE if the node was successfully deleted from drupal/chado; FALSE otherwise
 *
 * @ingroup tripal_stock
 */
function chado_stock_delete($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);
}

/**
 * Purpose: Implement Blocks relating to stock content
 *
 * @param $op
 *   What kind of information to retrieve about the block or blocks. 
 *   Possible values include list, configure, save, view.
 * @param $delta
 *   Which block to return (not applicable if $op is 'list').
 * @param $edit
 *   If $op is 'save', the submitted form data from the configuration form.
 *
 * @return
 *   One of the following depending on $op: An array of block descriptions (list), the configuration 
 *   form (configure), nothing (save), an array defining subject and content for the block indexed 
 *   by $delta (view)
 *
 * @ingroup tripal_stock
 */
function tripal_stock_block ($op = 'list', $delta = 0, $edit=array()) {
  switch($op) {
    case 'list':
      $blocks['base']['info'] = t('Tripal Stock Details');
      $blocks['base']['cache'] = BLOCK_NO_CACHE;

      $blocks['properties']['info'] = t('Tripal Stock Properties');
      $blocks['properties']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['references']['info'] = t('Tripal Stock References');
      $blocks['references']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['relationships_as_object']['info'] = t('Tripal Stock Relationships as Object');
      $blocks['relationships_as_object']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['relationships_as_subject']['info'] = t('Tripal Stock Relationships as Subject');
      $blocks['relationships_as_subject']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
      $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
                  
      return $blocks;

 		case 'view':
 			if(user_access('access chado_stock content') and arg(0) == 'node' and is_numeric(arg(1))) {
      	$nid = arg(1);
      	$node = node_load($nid);
 
        $block = array();
        switch($delta){
					case 'base':
						$block['subject'] = t('Stock Details');
						$block['content'] = theme('tripal_stock_base',$node);
						break;
						
					case 'properties':
						$block['subject'] = t('Properties');
						$block['content'] = theme('tripal_stock_properties',$node);
						break;
						
					case 'references':
						$block['subject'] = t('References');
						$block['content'] = theme('tripal_stock_references',$node);
						break;
						
					case 'relationships_as_object':
						$block['subject'] = t('Object Relationships');
						$block['content'] = theme('tripal_stock_relationships_as_object',$node);
						break;
						
					case 'relationships_as_subject':
						$block['subject'] = t('Subject Relationships');
						$block['content'] = theme('tripal_stock_relationships_as_subject',$node);
						break;
						
					case 'synonyms':
						$block['subject'] = t('Synonyms');
						$block['content'] = theme('tripal_stock_synonyms',$node);
						break;
						
        }
				return $block;
			}
	}
}