tripal/tripal_stock/tripal_stock.module

<?php

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

/**
 * @defgroup tripal_stock Stock Module
 * @ingroup tripal_modules
 * @{
 * 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_once("includes/tripal_stock.admin.inc");
require_once("includes/tripal_stock.sync_stocks.inc");
require_once("includes/other_module_api_functions.inc");
require_once("includes/tripal_stock-secondary_tables.inc");
require_once("includes/tripal_stock-properties.inc");
require_once("includes/tripal_stock-relationships.inc");
require_once("includes/tripal_stock-db_references.inc");
require_once("api/tripal_stock.api.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/chado/tripal_stock'] = array(
    'title' => 'Stocks',
    'description' => 'A stock is the physical entities of an organism, either living or preserved.',
    'page callback' => 'tripal_stock_admin_stock_view',
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_stock/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Settings for Chado Stocks',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_stock_help'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_stock/sync'] = array(
    'title' => ' Sync',
    'description' => 'Sync stocks from Chado with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_stock_sync_form'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );

  $items['admin/tripal/chado/tripal_stock/help'] = array(
    'title' => 'Help',
    'description' => 'Basic Description of Tripal Stock Module Functionality',
    'page callback' => 'theme',
    'page arguments' => array('tripal_stock_help'),
    'access arguments' => array('administer tripal stocks'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  // Adding Secondary Properties-----------------
  $items['node/%cs_node/properties'] = array(
    'title' => 'Add Properties & Synonyms',
    'description' => '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' => 'Add Database References',
    'description' => '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' => 'Add Relationships',
    'description' => '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' => 'Edit Properties',
    'description' => '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' => 'Edit Relationships',
    'description' => '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' => 'Edit DB References',
    'description' => '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,
  );

  // the menu link for addressing any stock (by name, uniquename, synonym)
  $items['stock/%'] = array(
    'page callback' => 'tripal_stock_match_stocks_page',
    'page arguments' => array(1),
    'access arguments' => array('access chado_stock content'),
    'type' => MENU_LOCAL_TASK,
  );
  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_permissions() {
  return array(
    'access chado_stock content' => array(
      'title' => t('View Stocks'),
      'description' => t('Allow users to view stock pages.'),
    ),
    'create chado_stock content' => array(
      'title' => t('Create Stocks'),
      'description' => t('Allow users to create new stock pages.'),
    ),
    'delete chado_stock content' => array(
      'title' => t('Delete Stocks'),
      'description' => t('Allow users to delete stock pages.'),
    ),
    'edit chado_stock content' => array(
      'title' => t('Edit Stocks'),
      'description' => t('Allow users to edit stock pages.'),
    ),
    'adminster tripal stock' => array(
      'title' => t('Administer Stocks'),
      'description' => t('Allow users to administer all stocks.'),
    ),
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_stock
 */
function chado_stock_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create chado_stock content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_stock content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_stock content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_stock content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}

/**
 * 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() {
  $theme_path = drupal_get_path('module', 'tripal_stock') . '/theme';
  $items = array(

    // property edit forms function templates
    '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',
    ),
    // tripal_stock templates
    'tripal_stock_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_base',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_properties',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_references',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_relationships',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_synonyms' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_synonyms',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_collections' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_collections',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_collections' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_collections',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_phenotypes' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_phenotypes',
      'path' => "$theme_path/tripal_stock",
    ),
    'tripal_stock_locations' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_locations',
      'path' => "$theme_path/tripal_stock",
    ),
    // tripal_organism templates
    'tripal_organism_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_organism_stocks',
      'path' => "$theme_path/tripal_organism",
    ),
    // help template
    'tripal_stock_help' => array(
      'template' => 'tripal_stock_help',
      'arguments' =>  array(NULL),
      'path' => $theme_path,
    ),
  );
  return $items;
}
/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_stock_help ($path, $arg) {
  if ($path == 'admin/help#tripal_stock') {
    return theme('tripal_stock_help', array());
  }
}
/**
 * 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'),
      'base' => '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) {

  // get the stock details from chado
  $stock_id = chado_get_id_for_node('stock', $node->nid);

  // build the variable with all the stock details
  $values = array('stock_id' => $stock_id);
  $stock = tripal_core_generate_chado_var('stock', $values);


  // by default, the titles are saved using the unique constraint.  We will
  // keep it the same, but remove the duplicate name if the unique name and name
  // are identical
  $title_type = variable_get('chado_stock_title', 'unique_constraint');
  if($title_type == 'unique_constraint') {
    if (strcmp($stock->name, $stock->uniquename)==0) {
      $node->title = $stock->name . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
    }
    // in previous version of Tripal, the stock title was simply the unique name.
    // so, we recreate the title just to be sure all of our stock pages are consistent
    else {
      $node->title = $stock->name . ", " . $stock->uniquename . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
    }
  }
  // set the title to be the stock name or uniquename as configured
  if($title_type == 'stock_name') {
    $node->title = $stock->name;
  }
  if($title_type == 'stock_unique_name') {
    $node->title = $stock->uniquename;
  }

  // add this to the node
  $additions = new stdClass();
  $additions->stock = $stock;
  return $additions;
}


/**
 * 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) {

  // Expand all fields needed
  $fields_needed = array('stock.uniquename', 'stock.name', 'stock.stock_id', 'stock.type_id', 'stock.organism_id', 'stock.description', 'stock.dbxref_id', 'dbxref.accession', 'dbxref.description', 'dbxref.db_id', 'db.db_id');
  foreach ($fields_needed as $field_name) {
    // Check to see if it's excluded and expand it if so
    if ($node->expandable_fields) {
      if (in_array($field_name, $node->expandable_fields)) {
        $node = tripal_core_expand_chado_vars($node, 'field', $field_name);
      }
    }
  }

  // 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->stock->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']['sname'] = array(
    '#type' => 'textfield',
    '#title' => t('Name'),
    '#default_value' => $node->stock->name,
    '#required'       => TRUE
  );

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

  $form['names']['stock_id'] = array(
    '#type' => 'hidden',
    '#value' => $node->stock->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->cvterm_id;
  }
  $form['details']['type_id'] = array(
    '#type' => 'select',
    '#title' => t('Type of Stock'),
    '#options' => $type_options,
    '#default_value' => $type_default,
    '#required'    => TRUE,
  );


  // get the list of organisms
  $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
  $org_rset = chado_query($sql);
  $organisms = array();
  $organisms[''] = '';
  while ($organism = $org_rset->fetchObject()) {
    $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
  }
  $form['details']['organism_id'] = array(
    '#type' => 'select',
    '#title' => t('Source Organism for stock'),
    '#default_value' => $node->stock->organism_id->organism_id,
    '#options' => $organisms,
    '#required'    => TRUE
  );


  $form['details']['stock_description'] = array(
    '#type' => 'textarea',
    '#title' => t('Notes'),
    '#default_value' => $node->stock->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->stock->dbxref_id->accession
  );

  $form['database_reference']['db_description'] = array(
    '#type' => 'textarea',
    '#title' => t('Description of Database Reference'),
    '#default_value' => $node->stock->dbxref_id->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->stock->dbxref_id->db_id->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 {:table} WHERE :column = :value";
  $string_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";

  // if this is an update, we want to make sure that a different stock for
  // the organism doesn't already have this uniquename. We don't want to give
  // two sequences the same uniquename
  if ($node->stock_id) {
    $sql = "
      SELECT *
      FROM {stock} S
        INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
      WHERE
        uniquename = :uname AND organism_id = :organism_id AND
        CVT.name = :cvtname AND NOT stock_id = :stock_id
    ";
    $result = chado_query($sql, array(':uname' => $node->uniquename,
      ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type,
      ':stock_id' => $node->stock_id))->fetchObject();
    if ($result) {
      form_set_error('uniquename', t("Stock update cannot proceed. The stock name '$node->uniquename' is not unique for this organism. Please provide a unique name for this stock."));
    }
  }

  // if this is an insert then we just need to make sure this name doesn't
  // already exist for this organism if it does then we need to throw an error
  else {
    $sql = "
      SELECT *
      FROM {Stock} S
        INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
      WHERE uniquename = :uname'AND organism_id = :organism_id AND CVT.name = :cvtname";
    $result = chado_query($sql, array(':uname' => $node->uniquename,
      ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type))->fetchObject();
    if ($result) {
      form_set_error('uniquename', t("Stock insert cannot proceed. The stock name '$node->uniquename' already exists for this organism. Please provide a unique name for this stock."));
    }
  }


  // 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 {
    $num_rows = chado_query($int_in_chado_sql, array(':table' => 'cvterm', ':column' => 'cvterm_id', ':value' => $node->type_id))->fetchObject();
    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 {
    $num_rows = chado_query($int_in_chado_sql, array(':table' => 'organism', ':column' => 'organism_id', ':value' => $node->organism_id))->fetchObject();
    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) {
    $num_rows = chado_query($int_in_chado_sql, array(':table' => 'db', ':column' => 'db_id', ':value' => $node->database))->fetchObject();
    if ($num_rows->count != 1) {
      form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
  }
}


/**
 * 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) {

  // If the chado stock exists (e.g. this is only a syncing operation)
  // then don't create but simply link to node
  if ($node->chado_stock_exists) {
    if (!empty($node->stock_id)) {
      $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES (:nid, :vid, :stock_id)";
      db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':stock_id' => $node->stock_id));
    }

    return $node;
  }

  // before we can add the stock, we must add the dbxref if one has been
  // provided by the user.
  $dbxref_status = 0;
  if (!empty($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(t('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 including the dbxref
  $stock = '';
  if ($dbxref_status) {
    $values = array(
      'dbxref_id' => array(
        'db_id' => $node->database,
        'accession' => $node->accession
      ),
      'organism_id' => $node->organism_id,
      'name' => $node->sname,
      'uniquename' => $node->uniquename,
      'description' => $node->stock_description,
      'type_id' => $node->type_id
    );
    $stock = tripal_core_chado_insert('stock', $values);
  }
  // create a stock without a dbxref
  else {
    $values = array(
      'organism_id' => $node->organism_id,
      'name'        => $node->sname,
      'uniquename'  => $node->uniquename,
      'description' => $node->stock_description,
      'type_id'     => $node->type_id
    );
    $stock = tripal_core_chado_insert('stock', $values);
  }

  // if the stock creation was succesful then add the URL and the entry in the
  // chado_stock table
  if (is_array($stock)) {

    // convert the stock into an object
    $stock = (object) $stock;

    // add the entry to the chado_stock table
    $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES :nid, :vid, :stock_id)";
    db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':stock_id' => $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'] = $next_stage_path;
    }
  }
  else {
    drupal_set_message(t('Error during stock creation.'), 'error');
    watchdog('tripal_stock',
      'Insert Stock: Unable to create stock where values:%values',
      array('%values' => print_r($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) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }

  //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
          );
          $dbxref_mode = 'Create';
        }
        else {
          drupal_set_message(t('Unable to find stock to Update'), 'error');
          watchdog(
            'tripal_stock',
            'Stock Update: Unable to find stock to update using values: %values',
            array('%values', print_r($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->sname,
    'uniquename' => $node->uniquename,
    'description' => $node->stock_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(t('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
    );
  }
  else {
    // set the URL for this stock page
    $values = array('stock_id' => $node->stock_id);
    $stock = tripal_core_chado_select('stock', array('*'), $values);
  }
}

/**
 * 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) {

  // Set stock in chado: is_obsolete = TRUE
  chado_query("DELETE FROM {stock} WHERE stock_id = :stock_id", array(':stock_id' => $node->stock->stock_id));

  //remove drupal node and all revisions
  db_query("DELETE FROM {chado_stock} WHERE nid = :nid", array(':nid' => $node->nid));
}

/**
 * @ingroup tripal_stock
 */
function tripal_stock_block_info() {
  $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');
  $blocks['relationships_as_object']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
  $blocks['synonyms']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['collections']['info'] = t('Tripal Stock Collections');
  $blocks['collections']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
  $blocks['phenotypes']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
  $blocks['genotypes']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['locations']['info'] = t('Tripal Stock Locations');
  $blocks['locations']['cache'] = 'BLOCK_NO_CACHE';

  $blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
  $blocks['orgstocks']['cache'] = 'BLOCK_NO_CACHE';

  return $blocks;
}
/**
 *
 * @ingroup tripal_stock
 */
function tripal_stock_block_view($delta = '') {

  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':
        $block['subject'] = t('Relationships');
        $block['content'] = theme('tripal_stock_relationships', $node);
        break;

      case 'synonyms':
        $block['subject'] = t('Synonyms');
        $block['content'] = theme('tripal_stock_synonyms', $node);
        break;

      case 'collections':
        $block['subject'] = t('Stock Collections');
        $block['content'] = theme('tripal_stock_collections', $node);
        break;

      case 'phenotypes':
        $block['subject'] = t('Stock Phenotypes');
        $block['content'] = theme('tripal_stock_phenotypes', $node);
        break;

      case 'genotypes':
        $block['subject'] = t('Stock Genotypes');
        $block['content'] = theme('tripal_stock_genotypes', $node);
        break;

      case 'locations':
        $block['subject'] = t('Stock Locations');
        $block['content'] = theme('tripal_stock_locations', $node);
        break;

      case 'orgstocks':
        $block['subject'] = t('Organism Stocks');
        $block['content'] = theme('tripal_organism_stocks', $node);
        break;

    }
    return $block;
  }
}

/**
 *
 *
 * @ingroup tripal_stock
 */
function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
  // we want to provide a new variable that contains the matched stocks.
  $stock = $variables['node']->stock;

  // normally we would use tripal_core_expand_chado_vars to expand our
  // organism object and add in the relationships, however whan a large
  // number of relationships are present this significantly slows the
  // query, therefore we will manually perform the query
  $sql = "
    SELECT
      S.name, S.uniquename, S.stock_id, CS.nid,
      CVT.name as rel_type, CVTs.name as obj_type,
      SR.value
    FROM {stock_relationship} SR
      INNER JOIN {stock} S on SR.object_id = S.stock_id
      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
    WHERE SR.subject_id = :stock_id
  ";
  $as_subject = chado_query($sql, array(':stock_id' => $stock->stock_id));
  $sql = "
    SELECT
      S.name, S.uniquename,  S.stock_id, CS.nid,
      CVT.name as rel_type, CVTs.name as sub_type,
      SR.value
    FROM {stock_relationship} SR
      INNER JOIN {stock} S on SR.subject_id = S.stock_id
      INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
      INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
      LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
    WHERE SR.object_id = :stock_id
  ";
  $as_object = chado_query($sql, array(':stock_id' => $stock->stock_id));

  // combine both object and subject relationshisp into a single array
  $relationships = array();
  $relationships['object'] = array();
  $relationships['subject'] = array();

  // iterate through the object relationships
  while ($relationship = $as_object->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));

     if (!array_key_exists($rel_type, $relationships['object'])) {
       $relationships['object'][$rel_type] = array();
     }
     if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
       $relationships['object'][$rel_type][$sub_type] = array();
     }
     $relationships['object'][$rel_type][$sub_type][] = $relationship;
  }

  // now add in the subject relationships
  while ($relationship = $as_subject->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));

     if (!array_key_exists($rel_type, $relationships['subject'])) {
       $relationships['subject'][$rel_type] = array();
     }
     if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
       $relationships['subject'][$rel_type][$obj_type] = array();
     }
     $relationships['subject'][$rel_type][$obj_type][] = $relationship;
  }


  $stock->all_relationships = $relationships;

}
/**
 * @ingroup tripal_stock
 */
function tripal_stock_node_presave($node) {

  switch ($node->type) {
    case 'chado_stock':
      $values = array('organism_id' => $node->organism_id);
      $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
      $values = array('cvterm_id' => $node->type_id);
      $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
      $node->title = $node->sname . ', ' . $node->uniquename . ' (' . $cvterm[0]->name . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
      break;
  }
}
/**
 * @ingroup tripal_stock
 */
function tripal_stock_node_insert($node) {
  switch ($node->type) {
    case 'chado_stock':
      if (!$node->stock_id) {
        $sql = "SELECT * FROM {chado_stock} WHERE nid = :nid";
        $chado_stock = db_query($sql, array(':nid' => $node->nid))->fetchObject();
        $node->stock_id = $chado_stock->stock_id;
      }

      // remove any previous alias
      db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));

      // set the URL for this stock page
      $url_alias = tripal_stock_get_stock_url($node);
      $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
      path_save($path_alias);
      break;
  }
}
/**
 * @ingroup tripal_stock
 */
function tripal_stock_node_update($node) {

  switch ($node->type) {
    case 'chado_stock':

      // remove any previous alias
      db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));

      // set the URL for this stock page
      $url_alias = tripal_stock_get_stock_url($node);
      $path_alias = array("source" => "node/$node->nid", "alias" => $url_alias);
      path_save($path_alias);
      break;
  }
}
/**
 * @ingroup tripal_stock
 */
function tripal_stock_node_view($node, $view_mode, $langcode) {

  switch ($node->type) {
    case 'chado_organism':
      if ($view_mode == 'full') {
        // Show stock if the organism/feature is not at teaser view
        $node->content['tripal_organism_stocks'] = array(
          '#value' => theme('tripal_organism_stocks', $node),
        );
      }
      break;
  }

}

/*
 * Uses the value provided in the $id argument to find all stocks that match
 * that ID by name, stockname or synonym.  If it matches uniquenly to a single
 * stock it will redirect to that stock page, otherwise, a list of matching
 * stocks is shown.
 */
function tripal_stock_match_stocks_page($id) {

  // if the URL alias configuration is set such that the URL
  // always begins with 'stock' then we want to use the ID as it is and
  // forward it on. Otherwise, try to find the matching stock.
  $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]');
  if (!$url_alias) {
    $url_alias = '/stock/[genus]/[species]/[type]/[uniquename]';
  }
  $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
  if (preg_match('/^stock\//', $url_alias)) {
    drupal_goto($id);
  }


  $sql = "
    SELECT
      S.name, S.uniquename, S.stock_id,
      O.genus, O.species, O.organism_id,
      CVT.cvterm_id, CVT.name as type_name,
      CS.nid
    FROM {stock} S
      INNER JOIN {organism} O on S.organism_id = O.organism_id
      INNER JOIN {cvterm} CVT on CVT.cvterm_id = S.type_id
      INNER JOIN public.chado_stock CS on CS.stock_id = S.stock_id
    WHERE
      S.uniquename = :uname or S.name = :name
  ";
  $results = chado_query($sql, array(':uname' => $id, ':name' => $id));

  $num_matches = 0;

  // iterate through the matches and build the table for showing matches
  $header = array('Uniquename', 'Name', 'Type', 'Species');
  $rows = array();
  $curr_match;
  while ($match = $results->fetchObject()) {
    $curr_match = $match;
    $rows[] = array(
       $match->uniquename,
       "<a href=\"" . url("node/". $match->nid) ."\">" . $match->name . "</a>",
       $match->type_name,
       '<i>' . $match->genus . ' ' . $match->species . '</i>',
    );
    $num_matches++;
  }

  // if we have more than one match then generate the table, otherwise, redirect
  // to the matched stock
  if ($num_matches == 1) {
    drupal_goto("node/" . $curr_match->nid);
  }
  if ($num_matches == 0) {
    return "<p>No stocks matched the given name '$id'</p>";
  }

  $table_attrs = array(
    'class' => 'tripal-table tripal-table-horz'
  );
  $output = "<p>The following stocks match the name '$id'.</p>";
  $output .= theme_table($header, $rows, $table_attrs, $caption);
  return $output;
}

/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_stock_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_stock_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
}