Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_core/api/tripal_core_chado_nodes.api.inc

@@ -0,0 +1,367 @@
+<?php
+
+/**
+ * @file
+ * Functions for managing Drupal Nodes corresponding to chado content
+ *
+
+/**
+ * Sync'ing chado records with Drupal by creating nodes
+ *
+ * How to Use:
+ * @code
+
+  function modulename_menu() {
+
+    $module_name = 'tripal_stock';
+    $linking_table = 'chado_stock';
+    $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_core_chado_node_sync_form', $module_name, $linking_table),
+      'access arguments' => array('administer tripal stocks'),
+      'type' => MENU_LOCAL_TASK,
+      'weight' => 0
+    );
+
+    return $items;
+  }
+
+  modulename_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,
+        'chado_node_api' => array(
+          'base_table' => 'stock',
+          'hook_prefix' => 'chado_stock',
+          'title' => array(
+            'singular' => t('Stock'),
+            'plural' => t('Stocks')
+          ),
+          'select_by' => array(
+            'type_id' => TRUE,
+            'organism_id' => TRUE
+          ),
+        )
+      ),
+    );
+  }
+
+  // Create New Node
+  // @param $new_node: a basic new node object
+  // @param $record: the record object from chado specifying the biological data for this node
+  function chado_stock_chado_node_sync_create_new_node($new_node, $record) {
+
+    // Add relevant chado details to the new node object
+    // At a minimum you should add the primary key to the node
+    $new_node->stock_id = $record->stock_id;
+
+    return $new_node;
+  }
+
+  // Alter the sync form (optional)
+  function chado_stock_chado_node_sync_form($form, $form_state) {
+    // Change or add to the form array as needed
+    return $form;
+  }
+
+  // Bypass chado node api sync form submit (optional)
+  // Allows you to use this function as your own submit
+  function chado_stock_chado_node_sync_form ($form, $form_state) {}
+
+
+  // Alter the query for the chado database which gets the chado records to be sync'd (optional)
+  // @param $select: an array of select clauses
+  // @param $joins: an array of joins (ie: a single join could be 'LEFT JOIN {chadotable} alias ON base.id=alias.id')
+  // @param $where_clauses: an array of where clauses which will all be AND'ed together. Use :placeholders for values.
+  // @param $where_args: an associative array of arguments to be subbed in to the where clause
+  //           where the key = :placeholder and the value is the actual argument to be subbed in
+  function chado_stock_chado_node_sync_select_query (&$select, &$joins, &$where_clauses, &$where_args) {
+
+  }
+
+ * @endcode
+ */
+
+/**
+ * Generic Sync Form
+ */
+function tripal_core_chado_node_sync_form($form, &$form_state) {
+  $form = array();
+
+  if (isset($form_state['build_info']['args'][0])) {
+    $module = $form_state['build_info']['args'][0];
+    $linking_table = $form_state['build_info']['args'][1];
+    $node_info = call_user_func($module . '_node_info');
+    $args = $node_info[$linking_table]['chado_node_api'];
+    $form_state['chado_node_api'] = $args;
+  }
+
+  $form['description'] = array(
+  '#type' => 'item',
+  '#value' => t("%title_plural of the types listed ".
+     "below in the %title_singular Types box will be synced (leave blank to sync all types). You may limit the ".
+     "%title_plural to be synced by a specific organism. Depending on the ".
+     "number of %title_plural in the chado database this may take a long ".
+     "time to complete. ",
+     array(
+      '%title_singular' => $args['title']['singular'],
+      '%title_plural' => $args['title']['plural']
+    )),
+  );
+
+  if ($args['select_by']['type_id']) {
+    $form['type_ids'] = array(
+      '#title'       => t('%title_singular Types',
+         array(
+          '%title_singular' => $args['title']['singular'],
+          '%title_plural' => $args['title']['plural']
+      )),
+      '#type'        => 'textarea',
+      '#description' => t("Enter the names of the %title_singular types to sync. " .
+         "Leave blank to sync all %title_plural. Pages for these %title_singular ".
+         "types will be created automatically for %title_plural that exist in the ".
+         "chado database.  The names listed here should be spearated by ".
+         "spaces or entered separately on new lines. The names must match ".
+         "exactly (spelling and case) with terms in the ontologies",
+         array(
+          '%title_singular' => $args['title']['singular'],
+          '%title_plural' => $args['title']['plural']
+        )),
+      '#default_value' => (isset($form_state['values']['type_id'])) ? $form_state['values']['type_id'] : '',
+    );
+  }
+
+  // get the list of organisms
+  if ($args['select_by']['organism_id']) {
+    $sql = "SELECT * FROM {organism} ORDER BY genus, species";
+    $orgs = tripal_organism_get_synced();
+    $organisms[] = '';
+    foreach ($orgs as $organism) {
+      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+    }
+    $form['organism_id'] = array(
+      '#title'       => t('Organism'),
+      '#type'        => t('select'),
+      '#description' => t("Choose the organism for which %title_plural types set above will
+        be synced. Only organisms which also have been synced will appear in this list.",
+         array(
+          '%title_singular' => $args['title']['singular'],
+          '%title_plural' => $args['title']['plural']
+        )),
+      '#options'     => $organisms,
+      '#default_value' => (isset($form_state['values']['organism_id'])) ? $form_state['values']['organism_id'] : 0,
+    );
+  }
+
+  $form['max_sync'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Maximum number of records to Sync'),
+    '#description' => t('Leave this field empty to sync all records, regardless of number'),
+    '#default_value' => (isset($form_state['values']['max_sync'])) ? $form_state['values']['max_sync'] : '',
+  );
+
+  $form['button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Sync all ' . $args['title']['plural']),
+    '#weight' => 3,
+  );
+
+  // Allow each module to alter this form as needed
+  $hook_form_alter = $args['hook_prefix'] . '_chado_node_sync_form';
+  if (function_exists($hook_form_alter)) {
+    $form = call_user_func($hook_form_alter, $form, $form_state);
+  }
+
+  return $form;
+}
+
+/**
+ * Generic Sync Form Submit
+ */
+function tripal_core_chado_node_sync_form_submit($form, $form_state) {
+
+  global $user;
+
+  // get arguments
+  $args = $form_state['chado_node_api'];
+  $module = $form_state['chado_node_api']['hook_prefix'];
+  $base_table = $form_state['chado_node_api']['base_table'];
+
+  // Allow each module to hijack the submit if needed
+  $hook_form_hijack_submit = $args['hook_prefix'] . '_chado_node_sync_form_submit';
+  if (function_exists($hook_form_hijack_submit)) {
+    return call_user_func($hook_form_hijack_submit, $form, $form_state);
+  }
+
+  // Get the types separated into a consistent string
+  if (isset($form_state['values']['type_ids'])) {
+    $types = preg_replace("/[\s\n\r]+/", '|||', $form_state['values']['type_ids']);
+  }
+  else {
+    $types = '';
+  }
+
+  // Job Arguments
+  $job_args = array(
+    'base_table' => $base_table,
+    'max_sync' => (!empty($form_state['values']['max_sync'])) ? $form_state['values']['max_sync'] : FALSE,
+    'organism_id' => FALSE,
+    'types' => $types,
+  );
+
+  // Create Job based on presence of organism
+  if (isset($form_state['values']['organism_id'])) {
+    $organism_id = $form_state['values']['organism_id'];
+    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $organism_id));
+    $title = "Sync all " . $args['title']['plural'] . " for " . $organism[0]->genus . " " . $organism[0]->species;
+
+    $job_args['organism_id'] = $organism_id;
+    tripal_add_job($title, $module, 'tripal_core_chado_node_sync_records', $job_args, $user->uid);
+  }
+  else {
+    $title = t('Sync all ' . $args['title']['plural'] . ' for all synced organisms');
+    tripal_add_job($title, $module, 'tripal_core_chado_node_sync_records', $job_args, $user->uid);
+  }
+}
+
+/**
+ * Actual Sync Function. Works on a group of records
+ */
+function tripal_core_chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id = FALSE, $types = '') {
+
+  global $user;
+  $base_table_id = $base_table . '_id';
+
+  print "\nSync'ing records from $base_table restricted to\n";
+
+  // START BUILDING QUERY TO GET ALL RECORD FROM BASE TABLE THAT MATCH
+  $select = array("$base_table.*");
+  $joins = array();
+  $where_clauses = array();
+  $where_args = array();
+
+  // If types are supplied then handle them
+  if (!empty($types)) {
+    $types = explode('|||',$types);
+    print "  Types: " . implode(', ',$types) . "\n";
+
+    $select[] = 'cvterm.name as cvtname';
+    $joins[] = "LEFT JOIN {cvterm} cvterm ON $base_table.type_id = cvterm.cvterm_id";
+    if (sizeof($types) == 1) {
+      $where_clauses[] = 'cvterm.name = :type_name';
+      $where_args[':type_name'] = $types[0];
+    } elseif (sizeof($types) > 1) {
+      $where_clauses[] = "cvterm.name IN ('" . implode("', '", $types) . "')";
+    }
+  }
+
+  // If Organism is supplied
+  if ($organism_id) {
+    print "  Organism ID: $organism_id\n";
+
+    $select[] = 'organism.*';
+    $joins[] = "LEFT JOIN {organism} organism ON organism.organism_id = $base_table.organism_id";
+    $where_clauses[] = 'organism.organism_id = :organism_id';
+    $where_args[':organism_id'] = $organism_id;
+  }
+
+  // Allow module to add to query
+  $hook_query_alter = 'chado_' . $base_table . '_chado_node_sync_select_query';
+  if (function_exists($hook_query_alter)) {
+    call_user_func($hook_query_alter, $select, $joins, $where_clauses, $where_args);
+  }
+
+  // Build Query
+  $query = "SELECT " . implode(', ',$select)
+    . ' FROM {' . $base_table . '} ' . $base_table . ' '
+    . implode(' ', $joins)
+    . " WHERE " . implode(' AND ', $where_clauses)
+    . " ORDER BY " . $base_table_id;
+
+  // If Maximum number to Sync is supplied
+  if ($max_sync) {
+    $query .= " LIMIT $max_sync";
+  }
+
+  print "\nQuery: " . preg_replace(array("/FROM/","/LEFT/","/WHERE/"), array("\nFROM","\nLEFT","\nWHERE"), $query) . "\n";
+
+  print "Executing Query...\n";
+  $results = chado_query($query, $where_args);
+
+  // Iterate through features that need to be synced
+  $count = $results->rowCount();
+  $interval = intval($count * 0.01);
+  if ($interval < 1) {
+    $interval = 1;
+  }
+
+  print "\n$count $base_table records found.\nLoading...\n";
+
+  $i = 0;
+  $transaction = db_transaction();
+  try {
+    foreach ($results as $record) {
+
+      print "\nLoading $base_table $i of $count ($base_table_id=".$record->{$base_table_id}.")...";
+
+      // update the job status every 1% features
+      if ($job_id and $i % $interval == 0) {
+        $percent = sprintf("%.2f", ($i / $count) * 100);
+        print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\n";
+        tripal_job_set_progress($job_id, intval(($i/$count)*100));
+      }
+
+      // Check if it is in the chado linking table (ie: check to see if it is already linked to a node)
+      $result = db_select('chado_'.$base_table, 'lnk')
+        ->fields('lnk',array('nid'))
+        ->condition($base_table_id, $record->{$base_table_id}, '=')
+        ->execute()
+        ->fetchObject();
+
+      if (!empty($result)) {
+        print " Previously Sync'd";
+      }
+      else {
+
+        // Create generic new node
+        $new_node = new stdClass();
+        $new_node->type = 'chado_' . $base_table;
+        $new_node->uid = $user->uid;
+        $new_node->{$base_table_id} = $record->{$base_table_id};
+
+        // allow base module to set additional fields as needed
+        $hook_create_new_node = 'chado_' . $base_table . '_chado_node_sync_create_new_node';
+        $new_node = call_user_func($hook_create_new_node, $new_node, $record);
+
+        // Validate and Save New Node
+        $form = array();
+        $form_state = array();
+        node_validate($new_node, $form, $form_state);
+        if (!form_get_errors()) {
+          $node = node_submit($new_node);
+          node_save($node);
+          print " Node Created (nid=".$node->nid.")";
+        }
+        else {
+          watchdog('trp-fsync', "Failed to insert $base_table: %title", array('%title' => $new_node->title), WATCHDOG_ERROR);
+        }
+      }
+      $i++;
+    }
+
+    print "\n\nComplete!\n";
+  }
+  catch (Exception $e) {
+    print "\n"; // make sure we start errors on new line
+    watchdog_exception('trp-fsync', $e);
+    $transaction->rollback();
+    print "FAILED: Rolling back database changes...\n";
+  }
+
+}

tripal_core/tripal_core.module

@@ -38,6 +38,7 @@
 
 require_once "api/tripal_core_chado.api.inc";
 require_once "api/tripal_core_files.api.inc";
+require_once "api/tripal_core_chado_nodes.api.inc";
 require_once "api/tripal_core_custom_tables.api.inc";
 require_once "api/tripal_core_jobs.api.inc";
 require_once "api/tripal_core_mviews.api.inc";
@@ -49,7 +50,7 @@ require_once "includes/chado_install.inc";
 require_once "includes/form_elements.inc";
 
 
-tripal_core_set_globals();  
+tripal_core_set_globals();
 
 /**
  * Implements hook_init().
@@ -64,7 +65,7 @@ function tripal_core_init() {
   drupal_add_js(drupal_get_path('module', 'tripal_core') . '/theme/js/tripal.js');
   drupal_add_css(drupal_get_path('module', 'tripal_core') . '/theme/css/tripal.css');
 
-  
+
   // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
   // only if the chado database is present.
   if ($GLOBALS["chado_is_installed"]) {
@@ -410,7 +411,7 @@ function tripal_core_theme($existing, $type, $theme, $path) {
       'variables' =>  array(NULL),
       'path' => "$path/theme"
     ),
-    
+
     // form theme
     'tripal_core_properties_form' => array(
       'render element' => 'form',

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -0,0 +1,800 @@
+<?php
+
+/**
+ * @file Stock Node Functionality
+ */
+
+/**
+ * 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,
+      'chado_node_api' => array(
+        'base_table' => 'stock',
+        'hook_prefix' => 'chado_stock',
+        'title' => array(
+          'singular' => t('Stock'),
+          'plural' => t('Stocks')
+        ),
+        'select_by' => array(
+          'type_id' => TRUE,
+          'organism_id' => TRUE
+        ),
+      )
+    ),
+  );
+}
+
+/**
+ * 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
+ *
+ * D7 @todo: Make optimizations to take advantage of $nodes
+ *
+ * @ingroup tripal_stock
+ */
+function chado_stock_load($nodes) {
+
+  $new_nodes = array();
+  foreach ($nodes as $nid => $node) {
+    // get the stock details from chado
+    $stock_id = chado_get_id_for_node('stock', $node->nid);
+    if (empty($stock_id)) {
+      tripal_core_report_error(
+        'tripal_stock',
+        TRIPAL_ERROR,
+        'Unable to retrieve stock_id for %title (NID = %nid).',
+        array('%title' => $node->title, '%nid' => $node->nid)
+      );
+    }
+    else {
+
+      // 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
+      $node->stock = $stock;
+    }
+
+    $new_nodes[$nid] = $node;
+
+  }
+
+  return $new_nodes;
+}
+
+
+/**
+ * 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, $form_state) {
+
+  // If existing stock then expand all fields needed using the chado API
+  if (isset($node->nid)) {
+    $fields_needed = array('stock.uniquename', 'stock.name', 'stock.stock_id', 'stock.type_id', 'stock.organism_id', 'stock.description', 'stock.dbxref_id', 'dbxref.accession', 'dbxref.description', 'dbxref.db_id', 'db.db_id');
+    foreach ($fields_needed as $field_name) {
+      // Check to see if it's excluded and expand it if so
+      if (isset($node->expandable_fields)) {
+        if (in_array($field_name, $node->expandable_fields)) {
+          $node = tripal_core_expand_chado_vars($node, 'field', $field_name);
+        }
+      }
+    }
+  }
+
+  // Default values can come in the following ways:
+  //
+  // 1) as elements of the $node object.  This occurs when editing an existing stock
+  // 2) in the $form_state['values'] array which occurs on a failed validation or
+  //    ajax callbacks from non submit form elements
+  // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
+  //    form elements and the form is being rebuilt
+  //
+  // set form field defaults
+  $sname = '';
+  $uniquename = '';
+  $stock_id = 0;
+  $type_id = 0;
+  $organism_id = 0;
+  $sdescription = '';
+  $dbxref_accession = '';
+  $dbxref_description = '';
+  $dbxref_database = 0;
+
+  // 1) if we are editing an existing node then the stock is already part of the node
+  if (property_exists($node, 'stock')) {
+    $sname = $node->stock->name;
+    $uniquename = $node->stock->uniquename;
+    $stock_id = $node->stock->stock_id;
+    $type_id = $node->stock->type_id->cvterm_id;
+    $organism_id = $node->stock->organism_id->organism_id;
+    $sdescription = $node->stock->description;
+    $dbxref_accession = $node->stock->dbxref_id->accession;
+    $dbxref_description = $node->stock->dbxref_id->description;
+    $dbxref_database = $node->stock->dbxref_id->db_id->db_id;
+  }
+
+  // 2) if we are re constructing the form from a failed validation or ajax callback
+  // then use the $form_state['values'] values
+  if (array_key_exists('values', $form_state)) {
+    $sname = $form_state['values']['sname'];
+    $uniquename = $form_state['values']['uniquename'];
+    $stock_id = $form_state['values']['stock_id'];
+    $type_id = $form_state['values']['type_id'];
+    $organism_id = $form_state['values']['organism_id'];
+    $sdescription = $form_state['values']['description'];
+    $dbxref_accession = $form_state['values']['accession'];
+    $dbxref_description = $form_state['values']['db_description'];
+    $dbxref_database = $form_state['values']['database'];
+  }
+
+  // 3) if we are re building the form from after submission (from ajax call) then
+  // the values are in the $form_state['input'] array
+  if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
+    $sname = $form_state['input']['sname'];
+    $uniquename = $form_state['input']['uniquename'];
+    $stock_id = $form_state['input']['stock_id'];
+    $type_id = $form_state['input']['type_id'];
+    $organism_id = $form_state['input']['organism_id'];
+    $sdescription = $form_state['input']['description'];
+    $dbxref_accession = $form_state['input']['accession'];
+    $dbxref_description = $form_state['input']['db_description'];
+    $dbxref_database = $form_state['input']['database'];
+  }
+
+  $form['names'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Stock Name')
+  );
+
+  $form['names']['sname'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Name'),
+    '#default_value' => $sname,
+    '#required'       => TRUE
+  );
+
+  $form['names']['uniquename'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Unique Name'),
+    '#default_value' => $uniquename,
+    '#required'       => TRUE
+  );
+
+  $form['names']['stock_id'] = array(
+    '#type' => 'hidden',
+    '#value' => $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';
+  $form['details']['type_id'] = array(
+    '#type' => 'select',
+    '#title' => t('Type of Stock'),
+    '#options' => $type_options,
+    '#default_value' => $type_id,
+    '#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' => $organism_id,
+    '#options' => $organisms,
+    '#required'    => TRUE
+  );
+
+
+  $form['details']['stock_description'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Notes'),
+    '#default_value' => $sdescription,
+    '#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' => $dbxref_accession,
+  );
+
+  $form['database_reference']['db_description'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Description of Database Reference'),
+    '#default_value' => $dbxref_description,
+    '#description' => t('Optionally enter a description about the database accession.')
+  );
+
+  $db_options = tripal_db_get_db_options();
+  $db_options[0] = 'Select a Database';
+  $form['database_reference']['database'] = array(
+    '#type' => 'select',
+    '#title' => t('Database'),
+    '#options' => $db_options,
+    '#default_value' => $dbxref_database
+  );
+
+  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, $form, &$form_state) {
+
+  // remove surrounding whitespace
+  $node->uniquename = trim($node->uniquename);
+  $node->sname = trim($node->sname);
+  $node->stock_description = trim($node->stock_description);
+  $node->accession = trim($node->accession);
+  $node->db_description = trim($node->db_description);
+
+  // if this is a delete then don't validate
+  if($node->op == 'Delete') {
+    return;
+  }
+
+  // we are syncing if we do not have a node ID but we do have a stock_id. We don't
+  // need to validate during syncing so just skip it.
+  if (is_null($node->nid) and property_exists($node, 'stock_id') and $node->stock_id != 0) {
+    return;
+  }
+
+  $int_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
+  $string_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
+
+  // if this is an update, we want to make sure that a different stock for
+  // the organism doesn't already have this uniquename. We don't want to give
+  // two sequences the same uniquename
+  if (property_exists($node, 'nid')) {
+    $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->type_id,
+      ':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' => $node->type_id))->fetchObject();
+    if ($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 {
+    $replace = array(':table' => 'cvterm', ':column' => 'cvterm_id');
+    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
+    $num_rows = chado_query($new_sql, array(':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 {
+    $replace = array(':table' => 'organism', ':column' => 'organism_id');
+    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
+    $num_rows = chado_query($new_sql, array(':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) {
+    $replace = array(':table' => 'db', ':column' => 'db_id');
+    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
+    $num_rows = chado_query($new_sql, array(':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 (isset($node->chado_stock_exists)) {
+    if ($node->chado_stock_exists) {
+      if (!empty($node->stock_id)) {
+        db_insert('chado_stock')->fields(array(
+          'nid' => $node->nid,
+          'vid' => $node->vid,
+          'stock_id' => $node->stock_id
+        ));
+      }
+
+      return $node;
+    }
+  }
+
+  // if there is an stock_id in the $node object then this must be a sync so
+  // we can skip adding the stock to chado as it is already there, although
+  // we do need to proceed with the rest of the insert
+  if (!property_exists($node, 'stock_id')) {
+
+    // 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', $values);
+    }
+
+    if (is_array($stock)) {
+      $stock_added = TRUE;
+    }
+    else {
+      $stock_added = FALSE;
+    }
+  } //end of adding stock to chado
+  else {
+    // stock already exists since this is a sync
+    $stock_added = TRUE;
+    $stock['stock_id'] = $node->stock_id;
+  }
+
+  // if the stock creation was succesful then add the URL and the entry in the
+  // chado_stock table
+  if ($stock_added) {
+
+    // add the entry to the chado_stock table
+    db_insert('chado_stock')->fields(array(
+      'nid' => (int) $node->nid,
+      'vid' => (int) $node->vid,
+      'stock_id' => (int) $stock['stock_id']
+    ))->execute();
+
+  }
+  else {
+    drupal_set_message(t('Error during stock creation.'), 'error');
+    watchdog('tripal_stock',
+      'Insert Stock: Unable to create stock where values:%values',
+      array('%values' => print_r($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' => $node->nid));
+}
+
+/**
+ * Used by Tripal Chado Node API during sync'ing of nodes
+ */
+function chado_stock_chado_node_sync_create_new_node($new_node, $record) {
+
+  $new_node->organism_id = $record->organism_id;
+  $new_node->sname = $record->name;
+  $new_node->uniquename = $record->uniquename;
+  $new_node->type_id = $record->type_id;
+
+  return $new_node;
+}
+
+/**
+ * @ingroup tripal_stock
+ */
+function tripal_stock_node_presave($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 = $chado_stock->stock_id;
+      }
+
+      // remove any previous alias
+      db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$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 source = :source", array(':source' => "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', $node),
+        );
+      }
+      break;
+    case 'chado_stock':
+      if ($view_mode == 'full') {
+        $node->content['tripal_stock_base'] = array(
+          '#value' => theme('tripal_stock_base', array('node' => $node)),
+        );
+        // Cross References
+        $node->content['tripal_stock_references'] = array(
+          '#value' => theme('tripal_stock_references', array('node' => $node)),
+        );
+        // Properties
+        $node->content['tripal_stock_properties'] = array(
+          '#value' => theme('tripal_stock_properties', array('node' => $node)),
+        );
+        // Synonyms
+        $node->content['tripal_stock_synonyms'] = array(
+          '#value' => theme('tripal_stock_synonyms', array('node' => $node)),
+        );
+        // Relationships
+        $node->content['tripal_stock_relationships'] = array(
+          '#value' => theme('tripal_stock_relationships', array('node' => $node)),
+        );
+        // Stock Collections
+        $node->content['tripal_stock_collections'] = array(
+          '#value' => theme('tripal_stock_collections', array('node' => $node)),
+        );
+        // Stock Genotypes
+        $node->content['tripal_stock_genotypes'] = array(
+          '#value' => theme('tripal_stock_genotypes', array('node' => $node)),
+        );
+      }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_stock_teaser'] = array(
+          '#value' => theme('tripal_stock_teaser', array('node' => $node)),
+        );
+      }
+      break;
+  }
+
+}

tripal_stock/tripal_stock.module

@@ -28,7 +28,9 @@ 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("includes/tripal_stock.chado_node.inc");
 require_once("api/tripal_stock.api.inc");
+
 /**
  * Implements hook_menu(): Adds menu items for the tripal_stock
  *
@@ -63,7 +65,8 @@ function tripal_stock_menu() {
     'title' => ' Sync',
     'description' => 'Sync stocks from Chado with Drupal',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_stock_sync_form'),
+    //'page arguments' => array('tripal_stock_sync_form'),
+    'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_stock', 'chado_stock'),
     'access arguments' => array('administer tripal stocks'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
@@ -377,612 +380,6 @@ function tripal_stock_help ($path, $arg) {
     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
- *
- * D7 @todo: Make optimizations to take advantage of $nodes
- *
- * @ingroup tripal_stock
- */
-function chado_stock_load($nodes) {
-
-  $new_nodes = array();
-  foreach ($nodes as $nid => $node) {
-    // get the stock details from chado
-    $stock_id = chado_get_id_for_node('stock', $node->nid);
-    if (empty($stock_id)) {
-      tripal_core_report_error(
-        'tripal_stock',
-        TRIPAL_ERROR,
-        'Unable to retrieve stock_id for %title (NID = %nid).',
-        array('%title' => $node->title, '%nid' => $node->nid)
-      );
-    }
-    else {
-
-      // 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
-      $node->stock = $stock;
-    }
-
-    $new_nodes[$nid] = $node;
-
-  }
-
-  ddl($new_nodes, 'nodes at end of load');
-
-  return $new_nodes;
-}
-
-
-/**
- * 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, $form_state) {
-
-  ddl($node, 'node');
-  if (isset($node->nid)) {
-    // 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 $field_name) {
-      // Check to see if it's excluded and expand it if so
-      if (isset($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')
-  );
-
-  $form['names']['sname'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Name'),
-    '#default_value' => (isset($node->stock->name)) ? $node->stock->name : '',
-    '#required'       => TRUE
-  );
-
-  $form['names']['uniquename'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Unique Name'),
-    '#default_value' => (isset($node->stock->uniquename)) ? $node->stock->uniquename : '',
-    '#required'       => TRUE
-  );
-
-  $form['names']['stock_id'] = array(
-    '#type' => 'hidden',
-    '#value' => (isset($node->stock->stock_id)) ? $node->stock->stock_id : NULL
-  );
-
-  $form['details'] = array(
-    '#type' => 'fieldset',
-    '#title' =>  t('Stock Details')
-  );
-
-  $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_types_cv', 'NULL') );
-  $type_options[0] = 'Select a Type';
-  if (!isset($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)";
-  }
-  $form['details']['organism_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Source Organism for stock'),
-    '#default_value' => (isset($node->stock->organism_id->organism_id)) ? $node->stock->organism_id->organism_id : '',
-    '#options' => $organisms,
-    '#required'    => TRUE
-  );
-
-
-  $form['details']['stock_description'] = array(
-    '#type' => 'textarea',
-    '#title' => t('Notes'),
-    '#default_value' => (isset($node->stock->description)) ? $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')
-  );
-
-  $form['database_reference']['accession'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Accession'),
-    '#default_value' => (isset($node->stock->dbxref_id->accession)) ? $node->stock->dbxref_id->accession : ''
-  );
-
-  $form['database_reference']['db_description'] = array(
-    '#type' => 'textarea',
-    '#title' => t('Description of Database Reference'),
-    '#default_value' => (isset($node->stock->dbxref_id->description)) ? $node->stock->dbxref_id->description : '',
-    '#description' => t('Optionally enter a description about the database accession.')
-  );
-
-  $db_options = tripal_db_get_db_options();
-  $db_options[0] = 'Select a Database';
-  if (!isset($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, $node, $form, &$form_state) {
-
-  $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->type_id,
-      ':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' => $node->type_id))->fetchObject();
-    if ($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 {
-    $replace = array(':table' => 'cvterm', ':column' => 'cvterm_id');
-    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
-    $num_rows = chado_query($new_sql, array(':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 {
-    $replace = array(':table' => 'organism', ':column' => 'organism_id');
-    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
-    $num_rows = chado_query($new_sql, array(':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) {
-    $replace = array(':table' => 'db', ':column' => 'db_id');
-    $new_sql = str_replace(array_keys($replace),$replace,$int_in_chado_sql);
-    $num_rows = chado_query($new_sql, array(':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 (isset($node->chado_stock_exists)) {
-    if ($node->chado_stock_exists) {
-      if (!empty($node->stock_id)) {
-        db_insert('chado_stock')->fields(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', $values);
-  }
-
-  ddl($stock, 'stock in insert');
-  ddl($node, 'node in insert');
-
-  // if the stock creation was succesful then add the URL and the entry in the
-  // chado_stock table
-  if (is_array($stock)) {
-
-    // add the entry to the chado_stock table
-    db_insert('chado_stock')->fields(array(
-      'nid' => (int) $node->nid,
-      'vid' => (int) $node->vid,
-      'stock_id' => (int) $stock['stock_id']
-    ))->execute();
-
-    // Move on to next stage of Stock Creation based on next_stage_path field
-    if ($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
@@ -1167,114 +564,6 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
 
   $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 = $chado_stock->stock_id;
-      }
-
-      // remove any previous alias
-      db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$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 source = :source", array(':source' => "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', $node),
-        );
-      }
-      break;
-    case 'chado_stock':
-      if ($view_mode == 'full') {
-        $node->content['tripal_stock_base'] = array(
-          '#value' => theme('tripal_stock_base', array('node' => $node)),
-        );
-        // Cross References
-        $node->content['tripal_stock_references'] = array(
-          '#value' => theme('tripal_stock_references', array('node' => $node)),
-        );
-        // Properties
-        $node->content['tripal_stock_properties'] = array(
-          '#value' => theme('tripal_stock_properties', array('node' => $node)),
-        );
-        // Synonyms
-        $node->content['tripal_stock_synonyms'] = array(
-          '#value' => theme('tripal_stock_synonyms', array('node' => $node)),
-        );
-        // Relationships
-        $node->content['tripal_stock_relationships'] = array(
-          '#value' => theme('tripal_stock_relationships', array('node' => $node)),
-        );
-        // Stock Collections
-        $node->content['tripal_stock_collections'] = array(
-          '#value' => theme('tripal_stock_collections', array('node' => $node)),
-        );
-        // Stock Genotypes
-        $node->content['tripal_stock_genotypes'] = array(
-          '#value' => theme('tripal_stock_genotypes', array('node' => $node)),
-        );
-      }
-      if ($view_mode == 'teaser') {
-        $node->content['tripal_stock_teaser'] = array(
-          '#value' => theme('tripal_stock_teaser', array('node' => $node)),
-        );
-      }
-      break;
-  }
-
 }
 
 /*