Added basic tripal_stock with add/delete/edit/view capabilities for main stock table; also administration menu w/ syncing; views support for stock, stockprop, stock_relationships, stock_dbxrefs

tripal_core/views_handlers/views_handler_field_stock_dbxref_by_type.inc

@@ -39,10 +39,10 @@ class views_handler_field_stock_dbxref_by_type extends views_handler_field_prere
 				'db_name' => 'Database Name',
 				'link' => 'Link to External Record',
 			),
-			'#default_value' => $this->options['display_options'],
+			'#default_value' => array($this->options['display_options']['accession'], $this->options['display_options']['db_name'], $this->options['display_options']['link']),
 		);
 		
-    $db_options = _get_db_options();
+    $db_options = get_chado_db_options();
 	  $db_options[0] = 'Select a Database';
 	  ksort($db_options);
     $form['db_ids'] = array(
@@ -98,15 +98,19 @@ class views_handler_field_stock_dbxref_by_type extends views_handler_field_prere
 
   function render_item($count, $item) {
 		$text = array();
-		if ($this->options['display_options']['accession']) {
-			if ($this->options['display_options']['link']) {
-				if (!empty($item['urlprefix'])) {
-					$text[] = l($item['accession'],$item['urlprefix'].$item['accession']);
-				}
+		if ($this->options['display_options']['link']) {
+			if ($this->options['display_options']['accession']) {
+				$text[] = l($item['accession'],$item['urlprefix'].$item['accession']);
 			} else {
+				$text[] = l('External Record',$item['urlprefix'].$item['accession']);
+			}	
+		} else {
+			if ($this->options['display_options']['accession']) {
 				$text[] = $item['accession'];
 			}
 		}
+		
+		
 		if ($this->options['display_options']['db_name']) {
 			$text[] = $item['db_name'];
 		}

tripal_core/views_handlers/views_handler_field_stockprop_by_type.inc

@@ -6,18 +6,13 @@
  */
 class views_handler_field_stockprop_by_type extends views_handler_field_prerender_list {
   function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // Boolean to determine whether
-    //    TRUE =>  value (property type)      -more than one property type displayed
-    //    FALSE => or just value is rendered  -only 1 porperty type is displayed    
-    $this->display_type = TRUE;
-
+    parent::init($view, $options);    
   }
 
   function option_definition() {
     $options = parent::option_definition();
     $options['stockprop_type_ids'] = array('default' => array());
+    $options['stockprop_display_options'] = array('default' => array('type', 'value'));
     return $options;
   }
 
@@ -27,7 +22,23 @@ class views_handler_field_stockprop_by_type extends views_handler_field_prerende
   function options_form(&$form, &$form_state) {
     parent::options_form($form, $form_state);
 
-    $options = _get_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') );
+		$form['stockprop_display_options'] = array(
+		  '#prefix' => '<div><div id="edit-options-display_options">',
+      '#suffix' => '</div></div>',
+			'#type' => 'checkboxes',
+			'#title' => t('Display Relationship Parts'),
+			'#description' => t('Check each part of the property you want displayed where the parts '
+				.'of a property are: <type> and <value>. '
+				.'For example, with the property temperature 54 degrees Celcius the type=temperature and the value=54 degrees Celcius. '
+				.'Thus, if you checked only value then "54 degrees Celcius" would be displayed.'),
+			'#options' => array(
+				'type' => 'Type',
+				'value' => 'Value',
+			),
+			'#default_value' => array($this->options['stockprop_display_options']['type'], $this->options['stockprop_display_options']['value']),
+		);
+		
+    $options = get_chado_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') );
     $form['stockprop_type_ids'] = array(
       '#prefix' => '<div><div id="edit-options-stockprop_type_ids">',
       '#suffix' => '</div></div>',
@@ -49,11 +60,6 @@ class views_handler_field_stockprop_by_type extends views_handler_field_prerende
 		$this->aliases['properties'] = 'properties';
 		$this->aliases['stock_id'] = 'stock_id';
 		$this->field_alias = $this->aliases['stock_id'];
-
-		// $this->display_type is used to hide (type name) when only one type is displayed in the column
-		if (sizeof(array_filter($this->options['stockprop_type_ids'])) == 1) {
-			$this->display_type = FALSE;        
-		}
 		
 		//for each stock in this view page
 		foreach ($values as $result) {
@@ -83,17 +89,27 @@ class views_handler_field_stockprop_by_type extends views_handler_field_prerende
 	}
 
   function render_item($count, $item) {
-    if ($this->display_type) {
-      return $item['value'].' ('.$item['type_name'].')';
-    } else {
-      if ($item['value']) {
-        return $item['value'];
+  	$text = array();
+  	
+  dpm($this->options['stockprop_display_options']);
+  	if ($this->options['stockprop_display_options']['value']) {
+  		if ($item['value']) {
+        $text[] =  $item['value'];
       } else {
         //display checkmark image
-				$image_path = drupal_get_path('module','chado_views').'/images/checkmark.gif';
-        return '<img border="0" src="'.url($image_path).'" alt="checkmark" />';
+				$image_path = drupal_get_path('module','tripal_core').'/images/checkmark.gif';
+        $text[] = '<img border="0" src="'.url($image_path).'" alt="checkmark" />';
       }
-    }
+  	} 
+  	if ($this->options['stockprop_display_options']['type']) {
+  		$text[] = $item['type_name'];
+  	}
+  
+		if (sizeof($text) > 1) {
+			return $text[0].' ('.$text[1].')';
+		} else {
+			return $text[0];
+		}
   }
 
   function document_self_tokens(&$tokens) {

tripal_core/views_handlers/views_handler_field_stockrel_by_type.inc

@@ -17,8 +17,8 @@ class views_handler_field_stockrel_by_type extends views_handler_field_prerender
 
   function option_definition() {
     $options = parent::option_definition();
-    $options['stockprop_type_ids'] = array('default' => array());
-		$options['display_options'] = array('default' => array('subject','type','object'));
+    $options['stockrel_type_ids'] = array('default' => array());
+		$options['stockrel_display_options'] = array('default' => array('subject','type','object'));
     return $options;
   }
 
@@ -28,7 +28,9 @@ class views_handler_field_stockrel_by_type extends views_handler_field_prerender
   function options_form(&$form, &$form_state) {
     parent::options_form($form, $form_state);
 
-		$form['display_options'] = array(
+		$form['stockrel_display_options'] = array(
+		  '#prefix' => '<div><div id="edit-options-display_options">',
+      '#suffix' => '</div></div>',
 			'#type' => 'checkboxes',
 			'#title' => t('Display Relationship Parts'),
 			'#description' => t('Check each part of the relationship you want displayed where the part '
@@ -40,10 +42,10 @@ class views_handler_field_stockrel_by_type extends views_handler_field_prerender
 				'type' => 'Relationship Type',
 				'object' => 'Object',
 			),
-			'#default_value' => $this->options['display_options'],
+			'#default_value' => array($this->options['stockrel_display_options']['subject'], $this->options['stockrel_display_options']['type'], $this->options['stockrel_display_options']['object']),
 		);
 		
-    $options = _get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
+    $options = get_chado_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
     $form['stockrel_type_ids'] = array(
       '#prefix' => '<div><div id="edit-options-stockrel_type_ids">',
       '#suffix' => '</div></div>',
@@ -97,13 +99,13 @@ class views_handler_field_stockrel_by_type extends views_handler_field_prerender
 
   function render_item($count, $item) {
 	  $text = array();
-		if ($this->options['display_options']['subject']) {
+		if ($this->options['stockrel_display_options']['subject']) {
 			$text[] = $item['subject_name'];
 		}
-		if ($this->options['display_options']['type']) {
+		if ($this->options['stockrel_display_options']['type']) {
 			$text[] = $item['type_name'];
 		}
-		if ($this->options['display_options']['object']) {
+		if ($this->options['stockrel_display_options']['object']) {
 			$text[] = $item['object_name'];
 		}
 		return implode(' ', $text);

tripal_stock/LISENCE.txt

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
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+
+  Nothing in this License shall be construed as excluding or limiting
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+
+  12. No Surrender of Others' Freedom.
+
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+
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+    (at your option) any later version.
+
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+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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+
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+<http://www.gnu.org/licenses/>.
+
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+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

tripal_stock/other_module_api_functions.inc

@@ -0,0 +1,177 @@
+<?php
+
+///////////////////////////////////////////////////////////////////////////
+// Module: tripal_cv
+///////////////////////////////////////////////////////////////////////////
+
+/*************************************************************************
+ * Purpose: Create an options array to be used in a form element
+ *   which provides a list of all chado cvs
+ *
+ * @return an array(cv_id => name) for each cv in the chado cv table
+ */
+function get_chado_cv_options() {
+
+  $previous_db = tripal_db_set_active('chado');
+  $result = db_query(
+    "SELECT cv_id, name FROM cv"
+  );
+  db_set_active($previous_db);
+
+  $options = array();
+  while ( $r = db_fetch_object($result) ) {
+    $options[$r->cv_id] = $r->name;
+  }
+
+  return $options;
+
+}
+
+/*************************************************************************
+ * Purpose: Create an options array to be used in a form element
+ *   which provides a list of all chado cvterms
+ * 
+ * @params cv_id: the chado cv_id
+ *   only cvterms with the supplied cv_id will be returned
+ * @return an array(cvterm_id => name) 
+ *   for each cvterm in the chado cvterm table where cv_id=that supplied
+ */
+function get_chado_cvterm_options($cv_id = 0) {
+
+  $previous_db = tripal_db_set_active('chado');
+  if ($cv_id > 0) {
+  	$result = db_query(
+    	"SELECT cvterm_id, name FROM cvterm WHERE cv_id=%d", $cv_id
+  	);
+  } else {
+  	$result = db_query(
+    	"SELECT cvterm_id, name FROM cvterm"
+  	);
+  }
+  db_set_active($previous_db);
+
+  $options = array();
+  while ( $r = db_fetch_object($result) ) {
+    $options[$r->cvterm_id] = $r->name;
+  }
+
+  return $options;
+
+}
+
+///////////////////////////////////////////////////////////////////////////
+// Module: tripal_db
+///////////////////////////////////////////////////////////////////////////
+
+/*************************************************************************
+ * Purpose: Create an options array to be used in a form element
+ *   which provides a list of all chado dbs
+ *
+ * @return an array(db_id => name) for each db in the chado db table
+ */
+function get_chado_db_options() {
+
+  $previous_db = tripal_db_set_active('chado');
+  $result = db_query(
+    "SELECT db_id, name FROM db"
+  );
+  db_set_active($previous_db);
+
+  $options = array();
+  while ( $r = db_fetch_object($result) ) {
+    $options[$r->db_id] = $r->name;
+  }
+
+  return $options;
+
+}
+
+/*************************************************************************
+ *
+ * @params where_options: array(
+ *													<column_name> => array(
+ *														'type' => <type of column: INT/STRING>,
+ *														'value' => <the vlaue you want to filter on>,
+ *														'exact' => <if TRUE use =; if FALSE use ~>,
+ *													)
+ *				)
+ */
+function get_chado_dbxref($where_options) {
+	$previous_db = tripal_db_set_active('chado');
+
+	$where= array();
+	//generate the where clause from supplied options
+	// the key is the column name
+	foreach ($where_options as $key => $val_array) {
+		if (preg_match('/INT/', $val_array['type'])) {
+			$where[] = $key."=".$val_array['value'];
+		} else {
+			if ($val_array['exact']) { $operator='='; }
+			else { $operator='~'; }
+			$where[] = $key.$operator."'".$val_array['value']."'";
+		}
+	}
+	
+  $r = db_fetch_object(db_query(
+    "SELECT * FROM dbxref WHERE ".implode(' AND ',$where)
+  ));
+  
+  tripal_db_set_active($previous_db);
+
+  return $r;
+}
+
+///////////////////////////////////////////////////////////////////////////
+// Module: tripal_organism
+///////////////////////////////////////////////////////////////////////////
+
+/*************************************************************************
+ * Purpose: Create an options array to be used in a form element
+ *   which provides a list of all chado organisms
+ *
+ * @return an array(organism_id => common_name) 
+ *   for each organism in the chado organism table
+ */
+function get_chado_organism_options() {
+
+  $previous_db = tripal_db_set_active('chado');
+  $result = db_query(
+    "SELECT organism_id, common_name FROM organism"
+  );
+  tripal_db_set_active($previous_db);
+
+  $options = array();
+  while ( $r = db_fetch_object($result) ) {
+    $options[$r->organism_id] = $r->common_name;
+  }
+
+  return $options;
+
+}
+
+/*************************************************************************
+ * Purpose: Return a given organism object using the nid or organism id
+ *
+ * @return organism object created by node load
+ */
+function get_chado_organism($nid=0, $organism_id=0) {
+
+	if (!empty($nid)) {
+		return node_load($nid);
+	} else {
+		if (!empty($organism_id)) {
+			$sql = "SELECT nid FROM {chado_organism} WHERE organism_id=%d";
+			$r = db_fetch_object(db_query($sql, $organism_id));
+			if (!empty($r->nid)) {
+				return node_load($r->nid);
+			} else {
+				drupal_set_message("Function: get_chado_organism() -no organism with that organism id sync'd with drupal", 'error');
+			}
+		} else {
+			drupal_set_message("Function: get_chado_organism() -need to supply at least one of node ID or Organism ID",'error');
+		}
+	}
+
+	return 0;
+	
+}

tripal_stock/tripal_stock-administration.inc

@@ -0,0 +1,235 @@
+<?php
+// $Id$
+
+/*************************************************************************
+ * Purpose: Provide administration options for chado_stocks
+ *
+ * @return form array (as described by the drupal form api)
+ */
+function tripal_stock_admin() {
+  $form = array();
+
+   // before proceeding check to see if we have any
+   // currently processing jobs. If so, we don't want
+   // to give the opportunity to sync Stocks
+   $active_jobs = FALSE;
+   if(tripal_get_module_active_jobs('tripal_stock')){
+      $active_jobs = TRUE;
+   }
+   if($active_jobs){
+   
+   $form['notice'] = array(
+         '#type' => 'fieldset',
+         '#title' => t('Stock Management Temporarily Unavailable')
+      );
+
+   $form['notice']['message'] = array(
+         '#value' => t("Currently, stock management jobs are waiting or ".
+            "are running. Managemment features have been hidden until these ".
+            "jobs complete.  Please check back later once these jobs have ".
+            "finished.  You can view the status of pending jobs in the Tripal ".
+            "jobs page."),
+      );
+
+   } else {
+
+   // SET Vocabularies -----------------------------------------------------------------------------------------
+   $form['set_cv'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Set Stock Controlled Vocabularies'),
+      '#weight' => -10
+   );   
+   
+   $form['set_cv']['message'] = array(
+         '#value' => t("This setting allows you to set which chado controlled vocabularies (cv)"
+	              ." are used. Cvs are used to control user input for the type of stock,"
+		      ." any properties they enter for a stock & the types of relationships"
+		      ." between stocks. Only cvs already loaded into chado can be selected here.")
+   );
+
+   $cv_options = get_chado_cv_options();
+   
+   $form['set_cv']['stock_types_cv'] = array(
+     '#type' => 'select',
+     '#title' => t('Controlled Vocabulary governing Stock Types'),
+     '#options' => $cv_options,
+     '#default_value' => variable_get('chado_stock_types_cv', 0)
+   );
+
+   $form['set_cv']['stock_prop_types_cv'] = array(
+     '#type' => 'select',
+     '#title' => t('Controlled Vocabulary governing Types of Stock Properties'),
+     '#description' => t("This cv must contain a cvterm entry where name='synonym'."),
+     '#options' => $cv_options,
+     '#default_value' => variable_get('chado_stock_prop_types_cv', 0)
+   );
+
+   $form['set_cv']['stock_relationship_cv'] = array(
+     '#type' => 'select',
+     '#title' => t('Controlled Vocabulary governing Types of Relationsips between Stocks'),
+     '#options' => $cv_options,
+     '#default_value' => variable_get('chado_stock_relationship_cv', 0)
+   );
+
+   $form['set_cv']['button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Set Controlled Vacabularies')
+   );
+
+   // SYNC STOCKS-----------------------------------------------------------------------------------------------
+   $form['sync'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Sync Stocks'),
+      '#weight' => -10
+   );
+
+   $form['sync']['description'] = array(
+      '#type' => 'item',
+      '#value' => t("Click the 'Sync all Germplasm' button to create Drupal ".
+         "content for stocks in chado. Depending on the ".
+         "number of stocks in the chado database this may take a long ".
+         "time to complete. ")
+   );
+
+   $form['sync']['organisms'] = array(
+      '#type' => 'checkboxes',
+      '#title' => t('Organisms for which Stocks should be sync\'d'),
+      '#description' => t('Only sync\'d Organisms are listed. Leaving an organism unchecked does not delete already sync\'d Stocks.'),
+      '#options' => get_chado_organism_options(),
+      '#required'    => FALSE,
+      '#prefix'      => '<div id="lib_boxes">',
+      '#suffix'      => '</div>'
+   );
+
+   $form['sync']['button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Sync Stocks')
+   );
+}
+
+  return system_settings_form($form);
+
+}
+
+/**
+ * Implements hook_form_submit()
+ *
+ * Handles Submit actions of all subforms
+ */
+function tripal_stock_admin_validate($form, &$form_state) {
+   global $user;  // we need access to the user info
+   $job_args = array();
+
+   // Sync Stocks
+   if ($form_state['values']['op'] == t('Sync Stocks')) {
+      // Array organism_id => organims common_name
+      //  which only includes those organisms which the user wants to select stocks for
+      $organisms_2b_syncd = $form_state['values']['organisms'];
+
+      //for each organism selected submit job (handled by tripal_stock_sync_stock_set)
+      //  which syncs all stocks with an organism_id equal to the selelcted organism
+      foreach ( $organisms_2b_syncd as $organism_id ) {
+        if($organism_id != 0) {
+          $job_args[0] = $organism_id;
+          tripal_add_job("Sync Stocks from Organism $organism_id",'tripal_stock',
+            'tripal_stock_sync_stock_set',$job_args,$user->uid);
+        }
+      }
+    }
+
+    if ($form_state['values']['op'] == t('Set Controlled Vacabularies')) {
+      variable_set('chado_stock_types_cv', $form_state['values']['stock_types_cv']);
+      variable_set('chado_stock_prop_types_cv', $form_state['values']['stock_prop_types_cv']);
+      variable_set('chado_stock_relationship_cv', $form_state['values']['stock_relationship_cv']);
+    }
+}
+
+/**************************************************************************************************************/
+/** 
+ * Syncs all Stocks associated with an organism
+ * Note: Handling of multiple organisms is done in tripal_stock_admin_validate()
+ *
+ * @params $organisms
+ */
+ function tripal_stock_sync_stock_set($organism_id, $job_id) {
+	global $user;
+
+	if(!$organism_id) {
+		print '0 Stocks to Sync -No Organisms Selected.\n';
+	} else {
+
+		// Get list of stocks to sync
+		$previous_db = tripal_db_set_active('chado');
+    $result = db_query(
+       "SELECT stock_id, uniquename, type_id, organism_id FROM stock WHERE organism_id=%d",
+       $organism_id
+    );
+    tripal_db_set_active($previous_db);
+
+    $stocks_created_count = 0; //keeps track of total number of stocks successfully created
+    $stocks_attempted = 0;
+    // foreach stock to be sync'd -> create node & add stock_id
+    while ( $r = db_fetch_object($result) ) {
+      // $r is the current stock to be sync'd
+      $stocks_attempted++;
+
+      print 'Processing '.$r->uniquename."\n";
+
+      // check not already in drupal
+      $in_drupal_query = db_query(
+      	"SELECT * FROM {chado_stock} WHERE stock_id=%d",
+	 			$r->stock_id
+      );
+      if ( !db_fetch_object($in_drupal_query) ) {
+
+        //create new chado_stock node
+        $new_node = new stdClass();
+	 			$new_node->type = 'chado_stock';
+        $new_node->uid = $user->uid;
+	 			$new_node->title = $r->uniquename;
+	 			$new_node->type_id = $r->type_id;
+	 			$new_node->organism_id = $r->organism_id;
+	 			$new_node->stock_id = $r->stock_id;
+	 			//print 'New Node:';
+	 			//print_r($new_node);
+	 			
+	 			node_validate($new_node);
+	 			
+        if(!form_get_errors()){
+	    		//print 'Try to Create Node ';
+        	$node = node_submit($new_node);
+          node_save($node);
+          if($node->nid){
+          	$stocks_created_count++;
+	 
+						//Add stock id to chado_stock table
+	 					db_query(
+	   	  			"UPDATE {chado_stock} SET stock_id=%d WHERE nid=%d AND vid=%d",
+	   	  			$r->stock_id,
+	   	  			$node->nid,
+	   	  			$node->vid
+	 					);
+          }
+        } else {
+        	print "\tCreate Stock Form Errors: ";
+	 				print_r(form_get_errors());
+        }
+	 			print "\n\tNid=".$node->nid."\n";
+			} else {
+				print "\tSkipped $r->uniquename because it's already in drupal.\n";
+      } //end of if not already in drupal
+    } //end of while still stocks to be sync'd
+  } //end of if organism_id not supplied
+   
+  if ($stocks_attempted == 0) {
+		print "No stocks retrieved for organism (".$organism_id.")\n";
+		return 1;
+	} else {
+		if ($stocks_created_count > 0) {
+			print "$stocks_created_count Stocks Successfully Created\n";
+			return 1;
+		} else {
+			return 0;
+		}
+	}
+}

tripal_stock/tripal_stock-api_functions.inc

@@ -0,0 +1,45 @@
+<?php
+
+/*************************************************************************
+ * Purpose: Returns all stocks currently sync'd with drupal
+ *
+ * @return array(
+ *			<stock_id> => <stock object created by node load>
+ *		)
+ */
+function get_chado_stocks() {
+	$sql = "SELECT stock_id, nid from {chado_stock}";
+	$resource = db_query($sql);
+	$stocks = array();
+	while ($r = db_fetch_object($resource)) {
+		$stocks[$r->stock_id] = node_load($r->nid);
+	}
+	return $stocks;
+}
+
+/*************************************************************************
+ * Purpose: Return a given stock object using the nid or stock id
+ *
+ * @return stock object created by node load
+ */
+function get_chado_stock($nid=0, $stock_id=0) {
+
+	if (!empty($nid)) {
+		return node_load($nid);
+	} else {
+		if (!empty($stock_id)) {
+			$sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
+			$r = db_fetch_object(db_query($sql, $stock_id));
+			if (!empty($r->nid)) {
+				return node_load($r->nid);
+			} else {
+				drupal_set_message("Function: get_chado_stock() -no stock with that stock id sync'd with drupal", 'error');
+			}
+		} else {
+			drupal_set_message("Function: get_chado_stock() -need to supply at least one of node ID or Stock ID",'error');
+		}
+	}
+
+	return 0;
+	
+}

tripal_stock/tripal_stock.info

@@ -0,0 +1,9 @@
+; $Id$
+package = Tripal
+name = Tripal Chado Stock
+version = 0.1a
+description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of stocks (including stock relationships and properties).
+core = 6.x
+
+dependencies[] = tripal_core
+dependencies[] = tripal_organism

tripal_stock/tripal_stock.install

@@ -0,0 +1,62 @@
+<?php
+// $Id$
+
+/**
+ * Install the tripal stock module including it's content type
+ * @file
+ */
+
+/** Implementation of hook_install() */
+function tripal_stock_install() {
+	drupal_install_schema('tripal_stock');
+}
+
+/** Implementation of hook_uninstall() */
+function tripal_stock_uninstall() {
+	drupal_uninstall_schema('tripal_stock');
+
+	// Get the list of nodes to remove
+	$sql_lib_id = "SELECT nid, vid ".
+                 "FROM {node} ".
+                 "WHERE type='chado_stock'";
+	$result = db_query($sql_lib_id);
+
+	//delete all nodes
+	while ($node = db_fetch_object($result)) {
+	node_delete($node->nid);
+	}
+
+}
+
+/** Implementation of hook_schema() */
+function tripal_stock_schema() {
+	$schema['chado_stock'] = array(
+		'fields' => array(
+      'vid' => array(
+				'type' => 'int',
+				'unsigned' => TRUE,
+				'not null' => TRUE,
+ 	 	  ),
+  	  'nid' => array(
+   	   	'type' => 'int',
+   	   	'unsigned' => TRUE,
+   	   	'not null' => TRUE,
+  	  ),
+   	 	'stock_id' => array(
+   	   	'type' => 'int',
+   	   	'unsigned' => TRUE,
+   	   	'not null' => TRUE,
+    	),
+  	),
+  	'indexes' => array(
+    	'stock_id' => array('stock_id'),
+     	'nid' => array('nid'),
+  	),
+  	'unique' => array(
+    	'stock_id' => array('stock_id'),
+  	),
+  	'primary key' => array('vid'),
+	);
+
+  return $schema;
+}

tripal_stock/tripal_stock.module

@@ -0,0 +1,645 @@
+<?php
+// $Id$
+
+require("tripal_stock-administration.inc");
+require("tripal_stock-api_functions.inc");
+require("other_module_api_functions.inc");
+
+/*************************************************************************
+ * Implementation of hook_menu()
+ * Purpose: Add menu items for this module
+ * Note: A Menu item for the Create chado_stock form is automatically
+ *   added to the 'Create Content' Navigation menu
+ *
+ * @return and array for menu descriptions
+ */
+function tripal_stock_menu() {
+  $items = array();
+
+  //Administrative settings menu
+  $items['admin/tripal/tripal_stock'] = array(
+    'title' => t('Stocks'),
+    'description' => t('Settings for Chado Stocks'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_stock_admin'),
+    'access arguments' => array('administer site configuration'),
+    'type' => MENU_NORMAL_ITEM
+  );
+  
+  //Displaying stocks
+  $items['stocks'] = array(
+  	'menu_name' => ('primary-links'),
+    'title' => t('Stocks'),
+    'page callback' => 'tripal_stock_show_stocks',
+    'access arguments' => array('access chado_stock content'),
+    'type' => MENU_NORMAL_ITEM,  
+  );
+
+  return $items;
+}
+
+
+/*************************************************************************
+ * Implementation of hook_perm()
+ * Purpose: Set the permission types that the chado stock module uses
+ *
+ * @return an array listing the possible permission catagories
+ */
+function tripal_stock_perm() {
+  return array(
+    'access chado_stock content',
+    'create chado_stock content',
+    'edit chado_stock content',
+    'delete chado_stock content'
+  );
+}
+
+/*************************************************************************
+ * Implements hook_access()
+ * Purpose: Maps permission catagories to actions; 
+ *   TRUE grants access; FALSE denies it
+ */
+function tripal_stock_access($op, $node, $account) {
+   if ($op == 'create') {
+      return user_access('create chado_stock content', $account);
+   }
+
+   if ($op == 'update') {
+      if (user_access('edit chado_stock content', $account)) {
+         return TRUE;
+      }
+   }
+   if ($op == 'delete') {
+      if (user_access('delete chado_stock content', $account)) {
+         return TRUE;
+      }
+   }
+   if ($op == 'view') {
+      if (user_access('access chado_stock content', $account)) {
+         return TRUE;
+      }
+   }
+   return FALSE;
+}
+
+/*************************************************************************
+ * Implements hook_views_api()
+ * Purpose: Essentially this hook tells drupal that there is views support for
+ *  for this module which then includes tripal_stock.views.inc where all the
+ *  views integration code is
+ */ 
+function tripal_stock_views_api() {
+   return array(
+      'api' => 2.0,
+   );
+}
+
+/*************************************************************************
+ * Implements hook_theme()
+ * Purpose: Register themeing functions for this module
+ *
+ * @return an array of themeing functions to register
+ */
+function tripal_stock_theme() {
+	return array(
+		'tripal_stock_stock_table' => array (
+			'arguments' => array('stocks'),
+		),
+	);
+}
+
+/*************************************************************************
+ * Purpose: show stocks stored in drupals chado_stock table
+ */
+function tripal_stock_show_stocks () {
+	$sql = "SELECT COUNT(stock_id) FROM {chado_stock}";
+   $no_stocks = db_result(db_query($sql));
+   if($no_stocks != 0) {
+      $stocks = get_chado_stocks();
+      if($no_stocks != count($stocks)) {
+         drupal_set_message("Synchronization needed.");
+      }
+      return theme('tripal_stock_stock_table',&$stocks);
+   } else {
+      return t("No Stocks exists. Please contact administrators to ".
+               "synchronize stocks.");
+   }
+}
+
+function theme_tripal_stock_stock_table (&$stocks) {
+
+	// cycle through the stocks and build the stocks page
+	$output = "<div id=\"stocks\">";
+	$output .= '<table>';
+  $output .= "<tr>";
+  $output .= "<th>Name</th>";
+  $output .= "<th>Type</th>";
+  $output .= "<th>Organism</th>";
+  $output .= "<th>Description</th>";
+  $output .= "</tr>";
+
+  foreach($stocks as $stock){
+		$output .= "<tr>";
+		$output .= "<td>".l($stock->stock_name, "node/".$stock->nid)."</td>";
+		$output .= "<td>".$stock->stock_type."</td>";
+		$output .= "<td nowrap>".$stock->organism->common_name."</td>";
+		$output .= "<td>".$stock->description."</td>";
+		$output .= "</tr>";
+	}
+	$output .= "</table>";
+	$output .= "</div>";
+
+   return $output;
+}
+
+/*************************************************************************
+ * @section Implementation of stock Node
+ * including node_load, form, insert, update, delete(by nid and vid)
+ *************************************************************************/
+
+/*************************************************************************
+ * Implements hook_node_info() 
+ */
+function tripal_stock_node_info() {
+  return array(
+    'chado_stock' => array(
+      'name' => t('Stock'),
+      'module' => 'chado_stock',
+      'description' => t('A Chado Stock is a collection of material that can be sampled and have experiments performed on it.'),
+      'has_title' => TRUE,
+      'has_body' => FALSE,
+    ),
+  );
+}
+
+/*************************************************************************
+ * Implements hook_load()
+ * Everytime a chado_stock node is viewed or manipulated this hook is called first to prepare the data
+ */
+function chado_stock_load($node) {
+
+  // Gets the stock_id from the drupal chado_stock table---------------------------------------
+  $map = db_fetch_object(db_query(
+    "SELECT stock_id as stock_id FROM {chado_stock} WHERE vid=%d",
+    $node->vid
+  ));
+  $node->stock_id = $map->stock_id;  
+  
+  //Get the main stock information from the chado stock table-----------------------------------
+  $previous_db = tripal_db_set_active('chado');
+  $chado_stock = db_fetch_object(db_query(
+    "SELECT s.name, s.uniquename, s.description, c.name as type, c.cvterm_id as type_id, s.is_obsolete, s.organism_id "
+    ."FROM stock s, cvterm c WHERE s.type_id=c.cvterm_id AND stock_id=%d",
+    $map->stock_id
+  ));
+  tripal_db_set_active($previous_db);
+  //add to node
+  $node->stock_name = $chado_stock->name;
+  $node->uniquename = $chado_stock->uniquename;
+  $node->description = $chado_stock->description;
+  $node->stock_type = $chado_stock->type;
+  $node->stock_type_id = $chado_stock->type_id;
+  $node->is_obsolete = $chado_stock->is_obsolete;
+
+  // Get organism details from chado & add to node-----------------------------------------------
+  // get organism if for current stock
+  // pull all data from chado for the organism and assign it to the current node
+  $node->organism = get_chado_organism(NULL,$chado_stock->organism_id);
+
+  // Add Synonyms for stock----------------------------------------------------------------------
+  // These are a special case of property (stockprop table) where cvterm='synonym'
+  $previous_db = tripal_db_set_active('chado');
+  $results = db_query(
+    "SELECT sp.stockprop_id, sp.value as value, sp.type_id, 'synonym' as type FROM stockprop sp, cvterm c "
+    ."WHERE sp.stock_id=%d AND sp.type_id=c.cvterm_id AND c.name='synonym'",
+    $map->stock_id
+  );
+  tripal_db_set_active($previous_db);
+  $i=0;
+  // Node->synonyms is an array of synonyms(strings)
+  while ($r = db_fetch_object($results) ) {
+    $synonyms[$i++] = $r;
+  }
+  $node->synonyms = $synonyms;
+
+  // Add properties for stock (not including synonyms)-------------------------------------------
+  // $node->properties is an array of objects where each object describes a single property and has a type and value
+  $previous_db = tripal_db_set_active('chado');
+  $results = db_query(
+    "SELECT sp.stockprop_id, c.name as type, sp.value as value FROM stockprop sp, cvterm c "
+    ."WHERE sp.stock_id=%d AND sp.type_id=c.cvterm_id AND c.name != 'synonym'",
+    $map->stock_id
+  );
+  tripal_db_set_active($previous_db);
+  $i=0;
+  while ($r = db_fetch_object($results) ) {
+    $properties[$i++] = $r;
+  }
+  $node->properties = $properties;
+
+  // Add in main db reference-----------------------------------------------------------------------
+  // this is the dbxref_id in the stock table
+  //$node->main_db_reference is an object describing the dbxref and has an accession, version, description, db_name, db_description, & urlprefix
+  $previous_db = tripal_db_set_active('chado');
+  $db_reference = db_fetch_object(db_query(
+    "SELECT dbx.dbxref_id, dbx.accession, dbx.version, dbx.description, db.db_id, db.name as db_name, db.description as db_description, db.urlprefix as db_urlprefix "
+    ."FROM dbxref dbx, db db, stock s WHERE stock_id=%d AND s.dbxref_id=dbx.dbxref_id AND dbx.db_id=db.db_id",
+    $map->stock_id
+  ));
+  tripal_db_set_active($previous_db);
+  $node->main_db_reference = $db_reference;
+
+  // Add in extra references to external databases---------------------------------------------------
+  // this includes all the dbxref entries in stock_dbxref
+  // $node->db_referencesi s an array of objects where each object describes a given dbxref and has the same fields as the main db references
+  $previous_db = tripal_db_set_active('chado');
+  $results = db_query(
+    "SELECT dbx.dbxref_id, dbx.accession, dbx.version,	dbx.description, db.db_id, db.name as db_name, db.description as db_description, db.urlprefix as db_urlprefix "
+    ."FROM dbxref dbx, db db, stock_dbxref s WHERE stock_id=%d AND s.dbxref_id=dbx.dbxref_id AND dbx.db_id=db.db_id",
+    $map->stock_id
+  );
+  tripal_db_set_active($previous_db);
+    $i=0;
+  while ($r = db_fetch_object($results) ) {
+    $db_references[$i++] = $r;
+  }
+  $node->db_references = $db_references;
+
+  // Add relationships for stock---------------------------------------------------------------------
+  // Relationships are broken down into those where the current stock is the subject (other details stored in $node->object_relationships)
+  // and those where the current stock is the object (other details stored in $node->subject_relationships)
+  // fields available to each include object/subject_name, object/subject_id (stock_id in chado) and object/subject_nid (node id in drupal)
+     // where current is subject.............................
+     $previous_db = tripal_db_set_active('chado');
+     $result = db_query(
+       "SELECT sr.stock_relationship_id, c.name as relationship_type, sr.type_id as relationship_type_id, s.uniquename as object_uniquename, s.name as object_name, s.stock_id as object_id "
+       . "FROM stock_relationship sr, stock s, cvterm c "
+       . "WHERE sr.subject_id=%d AND sr.object_id=s.stock_id AND sr.type_id=c.cvterm_id",
+       $map->stock_id
+     );
+     tripal_db_set_active($previous_db);
+     $i=0;
+     $relationships= array();
+     while ($r = db_fetch_object($result) ) {
+
+       //get nid
+       $object = db_fetch_object(db_query("SELECT * FROM {node} n, {chado_stock} c WHERE c.nid=n.nid AND c.vid=n.vid AND c.stock_id=%d", $r->object_id ));
+       $r->object_nid = $object->nid;
+
+       $relationships[$i++] = $r;
+     }
+     $node->object_relationships = $relationships;
+
+     // where current is object.............................
+     $previous_db = tripal_db_set_active('chado');
+     $result = db_query(
+       "SELECT sr.stock_relationship_id, c.name as relationship_type, sr.type_id as relationship_type_id, s.uniquename as subject_uniquename, s.name as subject_name, s.stock_id as subject_id "
+       . "FROM stock_relationship sr, stock s, cvterm c "
+       . "WHERE	sr.object_id=%d AND sr.subject_id=s.stock_id AND sr.type_id=c.cvterm_id",
+       $map->stock_id
+     );
+     tripal_db_set_active($previous_db);
+     $i=0;
+     $relationships= array();
+     while ($r = db_fetch_object($result) ) {
+
+       //get nid
+       $subject = db_fetch_object(db_query("SELECT * FROM {node} n, {chado_stock} c WHERE c.nid=n.nid AND c.vid=n.vid AND c.stock_id=%d", $r->subject_id ));
+       $r->subject_nid = $subject->nid;
+
+       $relationships[$i++] = $r;
+     }
+     $node->subject_relationships = $relationships;
+
+     return $node;
+}
+
+
+/*************************************************************************
+ * Implements hook_form()	
+ * Creates the main Add/Edit/Delete Form for chado stocks
+ *
+ * Parts to be added by this form
+ *     name, 
+ *     uniquename, 
+ *     description, 
+ *     type => select from cvterm with key cvterm_id,
+ *     organism => select from available with key organism_id
+ *     main_db_reference => accession, version, description, db_name(select from dropdown) 
+ */
+function chado_stock_form($node, $form_state) {
+  $type = node_get_types('type', $node);
+
+  // This defines the path for the next step in a simulated multipart form
+  // NOTE: The %node gets replaced with the nid in insert
+  $form['next_step_path'] = array(
+    '#type' => 'hidden',
+    '#value' => 'node/%node/properties'
+  );
+
+  // If you don't want a multipart form set this to false
+  // Will then do default redirect (to new node) on submit
+  $form['simulate_multipart'] = array(
+    '#type' => 'textfield',
+    '#attributes'=>array('style'=>"display:none"),
+    '#default_value' => TRUE
+  );
+
+  if (!isset($node->uniquename)) {
+    $form['progress'] = array( 
+      '#type' => 'item', 
+      '#value' => 'blank', //implement_add_chado_properties_progress('main')
+    );
+  }
+
+  $form['names'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Stock Name')
+  );
+
+  $form['names']['title'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Name'),
+    '#default_value' => $node->title,
+    '#required'	     => TRUE
+  );
+
+  $form['names']['uniquename'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Unique Name'),
+    '#default_value' => $node->uniquename,
+    '#required'	     => TRUE
+  );
+
+  $form['names']['stock_id'] = array(
+    '#type' => 'hidden',
+    '#value' => $node->stock_id
+  );
+
+  $form['details'] = array(
+    '#type' => 'fieldset',
+    '#title' =>	t('Stock Details')
+  );
+
+  $type_options = get_chado_cvterm_options( variable_get('chado_stock_types_cv', 'null') );
+  $type_options[0] = 'Select a Type';
+  if ($node->nid == '') { $type_default = 0; } else { $type_default = $node->stock_type_id; }
+  $form['details']['type_id'] = array(
+    '#type' => 'select',
+    '#title' => t('Type of Stock'),
+    '#options' => $type_options,
+    '#default_value' => $type_default,
+    '#required'	  => TRUE,
+  );
+
+  $stock_oganism_options = get_chado_organism_options();
+  $stock_oganism_options[0] = 'Select An Organism';
+  if ($node->nid == '') { $organism_default = 0; } else {  $organism_default = $node->organism->organism_id; }
+  $form['details']['organism_id'] = array(
+    '#type' => 'select',
+    '#title' => t('Source Organism for stock'),
+    '#default_value' => $organism_default,
+    '#options' => $stock_oganism_options,
+    '#required'	  => TRUE
+  );
+
+  $form['details']['stock_description'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Notes'),
+    '#default_value' => $node->description,
+    '#description' => t('Briefly enter any notes on the above stock. This should not include phenotypes or genotypes.'),
+  );
+
+  $form['database_reference'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Stock Database Reference')
+  );
+
+  $form['database_reference']['accession'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Accession'),
+    '#default_value' => $node->main_db_reference->accession
+  );
+
+  $form['database_reference']['db_description'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Description of Database Reference'),
+    '#default_value' => $node->main_db_reference->db_description,
+    '#description' => t('Optionally enter a description about the database accession.')
+  );
+
+  $db_options = get_chado_db_options();
+  $db_options[0] = 'Select a Database';
+  if ($node->nid == '') { $db_default = 0; } else { $db_default = $node->main_db_reference->db_id; }
+  $form['database_reference']['database'] = array(
+    '#type' => 'select',
+    '#title' => t('Database'),
+    '#options' => $db_options,
+    '#default_value' => $db_default
+  );
+
+  return $form;
+}
+
+/*************************************************************************
+ * Implements hook_validate()
+ */
+function chado_stock_validate($node, &$form) {
+
+	$int_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s=%d";
+	$string_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s='%s'";
+	
+  // Validate Uniquename only if add
+  if (empty($node->stock_id)) {
+  	$previous_db = tripal_db_set_active('chado');
+  	$chado_row = db_fetch_object(db_query("SELECT * FROM stock WHERE uniquename='".$node->uniquename."'"));
+  	tripal_db_set_active($previous_db);
+  	if(!empty($chado_row->stock_id)) {
+  		$drupal_row = db_fetch_object(db_query("SELECT * FROM {chado_stock} WHERE stock_id=".$chado_row->stock_id));
+  		if (!empty($drupal_row->nid)) {
+  			$link = l('node/'.$drupal_row->nid, $node->uniquename);
+  			form_set_error('uniquename', "There is already a stock with that uniquename $link. Please enter another uniquename.");
+			} else {
+				form_set_error('uniquename', "There is already a stock with that uniquename (although it's not sync'd with drupal). Please enter another uniquename.");
+			}
+  	}
+  }
+
+
+  // Check Type of Stock is valid cvterm_id in chado ( $form['values']['details']['type_id'] )
+  if ( $node->type_id == 0) {
+    form_set_error('type_id', 'Please select a type of stock.');
+  } else {
+  	$previous_db = tripal_db_set_active('chado');
+    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
+    tripal_db_set_active($previous_db);
+    if ( $num_rows->count != 1) {
+      form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
+  }
+
+  // Check Source Organism is valid organism_id in chado ( $form['values']['details']['organism_id'] )
+  if ( $node->organism_id == 0) {
+    form_set_error('organism_id', 'Please select a source organism for this stock');
+  } else {
+  	$previous_db = tripal_db_set_active('chado');
+    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
+    tripal_db_set_active($previous_db);
+    if ( $num_rows->count != 1 ) {
+      form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
+  }
+
+  // Check if Accession also database
+  if ($node->accession != '') { 
+    if ($node->database == 0) {
+      // there is an accession but no database selected
+      form_set_error('database', 'You need to enter both a database and an accession for that database in order to add a database reference.');
+    }
+  } else {
+    if ($node->database > 0) {
+      // there is a database selected but no accession
+      form_set_error('accession', 'You need to enter both a database and an accession for that database in order to add a database reference.');
+    }
+  }
+
+  // Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
+  if ( $node->database > 0) {
+  	$previous_db = tripal_db_set_active('chado');
+    $num_rows = db_fetch_object(db_query($int_in_chado_sql, 'db', 'db_id', $node->database));
+    tripal_db_set_active($previous_db);
+    if ($num_rows->count != 1) {
+      form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
+  }
+
+  // Check Accession is unique for database ( $form['values']['database_reference']['accession'] )
+  if ( $node->accession != '') {
+  	$previous_db = tripal_db_set_active('chado');
+    $num_rows = db_fetch_object(db_query($string_in_chado_sql, 'dbxref', 'accession', $node->accession));
+    tripal_db_set_active($previous_db);
+    if ($num_rows->count > 0) {
+      form_set_error('accession', 'This accession ('.$node->accession.') has already been assigned to another stock.'); }
+  }
+
+}
+
+/*************************************************************************
+ * Implements hook_insert()
+ * Inserts data from chado_stock_form() into drupal and chado
+ */
+function chado_stock_insert($node) {
+
+  $previous_db = tripal_db_set_active('chado');
+	// create dbxref
+  if ( !empty($node->accession) ) {
+    if ( !empty($node->database) ) { 
+      db_query(
+        "INSERT INTO dbxref (db_id, accession, description) VALUES (%d, '%s', '%s')",
+        $node->database,
+        $node->accession,
+				$node->db_description	
+      );
+    }
+  }
+
+  // create stock
+  $dbxref_options['db_id'] = array(
+  	'value' =>$node->database,
+  	'type' => 'INT',
+  );
+  $dbxref_options['accession'] = array(
+  	'value' =>$node->accession,
+  	'type' => 'STRING',
+  );
+  $dbxref = get_chado_dbxref($dbxref_options);
+  if($dbxref->dbxref_id != 0) {
+    db_query(
+      "INSERT INTO stock (dbxref_id, organism_id, name, uniquename, description, type_id, is_obsolete) VALUES (%d, %d, '%s', '%s', '%s', %d, 'f')",
+      $dbxref->dbxref_id,
+      $node->organism_id,
+      $node->title,
+      $node->uniquename,
+      $node->description,
+      $node->type_id
+    );
+  } else {
+    db_query(
+      "INSERT INTO stock (organism_id, name, uniquename, description, type_id, is_obsolete) VALUES (%d, '%s', '%s', '%s', %d, 'f')",
+      $node->organism_id,
+      $node->title,
+      $node->uniquename,
+      $node->description,
+      $node->type_id
+    );
+  }
+  tripal_db_set_active($previous_db);
+
+  // create drupal chado_stock entry
+  $previous_db = tripal_db_set_active('chado');
+  $chado_stock = db_fetch_object(db_query("SELECT stock_id FROM stock WHERE uniquename='".$node->uniquename."' AND type_id=".$node->type_id.' AND organism_id='.$node->organism_id));
+	tripal_db_set_active($previous_db);
+  if (!empty($chado_stock->stock_id)) {
+  	db_query(
+    	"INSERT INTO {chado_stock} (nid, vid, stock_id) "
+    	."VALUES (%d, %d, %d)",
+    	$node->nid,
+    	$node->vid,
+    	$chado_stock->stock_id
+  	);
+
+  	//Move on to next stage of Stock Creation based on next_stage_path field
+  	if ($node->simulate_multipart) {
+    	$next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);  
+    	$_REQUEST['destination'] = $next_stage_path;
+  	}
+  } else {
+		drupal_set_message('Error during stock creation.', 'error');
+  }
+
+}
+
+/*************************************************************************
+ * Implements hook_update()
+ * Handles Editing/Updating of main stock info (that in the chado stock table)
+ * Currently just writes over all old data
+ */
+function chado_stock_update($node) {
+
+  if ($node->revision) {
+    chado_stock_insert($node);
+  } else {
+
+    //can't change stock id which is all thats stored in drupal thus only update chado
+    $previous_db = tripal_db_set_active('chado');
+    db_query(
+      "UPDATE stock SET organism_id=%d, name='%s', uniquename='%s', description='%s', type_id=%d WHERE stock_id=%d",
+      $node->organism_id,
+      $node->title,
+      $node->uniquename,
+      $node->description,
+      $node->type_id,
+      $node->stock_id
+    );
+    tripal_db_set_active($previous_db);
+  }
+
+}
+
+/*************************************************************************
+ * Implements hook_delete()
+ * Handles deleting of chado_stocks
+ */
+function chado_stock_delete($node) {
+
+  //remove drupal node and all revisions
+  db_query(
+    "DELETE FROM {chado_stock} WHERE nid=%d",
+    $node->nid
+  );
+  
+  // Set stock in chado: is_obsolete = TRUE
+  $previous_db = tripal_db_set_active('chado');
+  db_query(
+    "DELETE FROM stock WHERE stock_id=%d",
+    $node->stock_id
+  );
+  tripal_db_set_active($previous_db);
+}

tripal_stock/tripal_stock.views.inc

@@ -0,0 +1,170 @@
+<?php
+
+/**
+ *  @file
+ *  This file contains the basic functions for views integration of
+ *  chado/tripal stock tables. Supplementary functions can be found in
+ *  ./views/
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/*************************************************************************
+ * Implements hook_views_data()
+ * Purpose: Describe chado/tripal tables & fields to views
+ *
+ * @return: a data array which follows the structure outlined in the
+ *   views2 documentation for this hook. Essentially, it's an array of table
+ *   definitions keyed by chado/tripal table name. Each table definition 
+ *   includes basic details about the table, fields in that table and
+ *   relationships between that table and others (joins)
+ */
+require_once('views/stock.views.inc');
+function tripal_stock_views_data()  {
+  $data = array();
+
+  $data = array_merge($data, retrieve_stock_views_data());
+  
+  return $data;
+}
+
+/*************************************************************************
+ * Implements hook_views_handlers()
+ * Purpose: Register all custom handlers with views
+ *   where a handler describes either "the type of field", 
+ *   "how a field should be filtered", "how a field should be sorted"
+ *
+ * @return: An array of handler definitions
+ */
+function tripal_stock_views_handlers() {
+ return array(
+   'info' => array(
+     'path' => drupal_get_path('module', 'tripal_stock') . '/views/handlers',
+   ),
+   'handlers' => array(
+     'views_handler_field_computed_nid' => array(
+       'parent' => 'views_handler_field_numeric',
+     ),
+     'views_handler_field_stockprop_by_type' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+		'views_handler_field_stockprop_all' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+		'views_handler_field_stockrel_by_type' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+		'views_handler_field_stockrel_all' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+		'views_handler_field_stock_dbxref_by_type' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+		'views_handler_field_stock_dbxref_all' => array(
+       'parent' => 'views_handler_field_prerender_list',
+     ),
+   ),
+ );
+}
+
+/**
+ * Implements hook_views_pre_render
+ * Purpose: Intercepts the view after the query has been executed
+ *   All the results are stored in $view->result
+ *   Looking up the NID here ensures the query is only executed once
+ *   for all stocks in the table.
+ *
+ * @todo add if !<chado/drupal same db> around NID portion
+ */
+function tripal_stock_views_pre_render	(&$view) {
+	if (preg_match('/stock/', $view->base_table)) {
+		
+		// retrieve the stock_id for each record in the views current page
+		$stock_ids = array();
+		foreach ($view->result as $row_num => $row) {
+			$stock_ids[$row_num] = $row->stock_id;
+		}
+
+		// Using the list of stock_ids from the view
+		// lookup the NIDs from drupal
+		// and add that to the results of the view
+		$sql = "SELECT nid, stock_id FROM chado_stock WHERE stock_id IN (".implode(',',$stock_ids).")";
+		$resource = db_query($sql);
+		while ($r = db_fetch_object($resource)) {
+			$key = array_search($r->stock_id, $stock_ids);
+			$view->result[$key]->nid = $r->nid;
+		}
+		
+		//-----Properties------------------------------------------
+		$field_names = array_keys($view->field);
+		//if any property fields are in the current view
+		$property_field_names = preg_grep('/properties/',$field_names);
+		if (!empty($property_field_names)) {
+			$sql = "SELECT stockprop.*, cvterm.name as type_name FROM stockprop "
+				."INNER JOIN cvterm cvterm ON stockprop.type_id=cvterm.cvterm_id "
+				."WHERE stockprop.stock_id IN (".implode(',',$stock_ids).")";
+			$previous_db = db_set_active('chado');
+			$resource = db_query($sql);
+			db_set_active($previous_db);
+		
+			$view->result[$key]->properties = array();
+			while ($r = db_fetch_object($resource)) {
+				$key = array_search($r->stock_id, $stock_ids);
+				$view->result[$key]->properties[] = $r;
+			}
+		}
+		
+		//-----Relationships----------------------------------------
+		//if any relationship fields are in the current view
+		$relationship_field_names = preg_grep('/relationships/', $field_names);
+		if (!empty($relationship_field_names)) {
+			$sql = "SELECT stock_relationship.*, cvterm.name as type_name, "
+				."subject_stock.name as subject_name, object_stock.name as object_name "
+				."FROM stock_relationship "
+				."LEFT JOIN stock subject_stock ON stock_relationship.subject_id=subject_stock.stock_id "
+				."LEFT JOIN stock object_stock ON stock_relationship.object_id=object_stock.stock_id "
+				."LEFT JOIN cvterm cvterm ON stock_relationship.type_id = cvterm.cvterm_id "
+				."WHERE stock_relationship.subject_id IN (".implode(',',$stock_ids).") "
+				."OR stock_relationship.object_id IN (".implode(',',$stock_ids).") ";
+			$previous_db = db_set_active('chado');
+			$resource = db_query($sql);
+			db_set_active($previous_db);
+			
+			while ($r = db_fetch_object($resource)) {
+				if (in_array($r->subject_id, $stock_ids)) {
+					$key = array_search($r->subject_id, $stock_ids);
+					$r->stock_id = $r->subject_id;
+					$view->result[$key]->relationships[] = clone $r;
+				}
+				if (in_array($r->object_id, $stock_ids)) {
+					$key = array_search($r->object_id, $stock_ids);
+					$r->stock_id = $r->object_id;
+					$view->result[$key]->relationships[] = clone $r;
+				}
+			}
+		}
+		
+		//-----DB References--------------------------------------------
+		//if any dbxref fields are in the current view
+		$dbxref_field_names = preg_grep('/dbxref/',$field_names);
+		if (!empty($dbxref_field_names)) {
+			$sql = "SELECT stock_dbxref.*, dbxref.db_id, db.name as db_name, db.urlprefix, "
+				."dbxref.accession, dbxref.version, dbxref.description "
+				."FROM stock_dbxref "
+				."LEFT JOIN dbxref dbxref ON stock_dbxref.dbxref_id=dbxref.dbxref_id "
+				."LEFT JOIN db db ON dbxref.db_id=db.db_id "
+				."WHERE stock_dbxref.stock_id IN (".implode(',',$stock_ids).")";
+			$previous_db = db_set_active('chado');
+			$resource = db_query($sql);
+			db_set_active($previous_db);
+		
+			$view->result[$key]->dbxref = array();
+			while ($r = db_fetch_object($resource)) {
+				$key = array_search($r->stock_id, $stock_ids);
+				$view->result[$key]->dbxref[] = $r;
+			}
+		}
+		
+	} //if we're dealing with a stock view
+}

tripal_stock/views/handlers/views_handler_field_computed_nid.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_computed_nid.inc

tripal_stock/views/handlers/views_handler_field_stock_dbxref_all.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stock_dbxref_all.inc

tripal_stock/views/handlers/views_handler_field_stock_dbxref_by_type.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stock_dbxref_by_type.inc

tripal_stock/views/handlers/views_handler_field_stockprop_all.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stockprop_all.inc

tripal_stock/views/handlers/views_handler_field_stockprop_by_type.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stockprop_by_type.inc

tripal_stock/views/handlers/views_handler_field_stockrel_all.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stockrel_all.inc

tripal_stock/views/handlers/views_handler_field_stockrel_by_type.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_stockrel_by_type.inc

tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_filter_stockprop_id.inc

tripal_stock/views/stock.views.inc

@@ -0,0 +1,231 @@
+<?php
+
+/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the stock table, it's fields and any joins between it and other tables
+ * @see tripal_stock_views_data() --in tripal_stock.views.inc
+ *
+ * @todo add better support for is_obsolete -through a field handler
+ * @todo Add support for the following tables: stock_cvterm, stock_pub, stock_genotype
+ * @todo Add join to node table within if <chado/drupal same db>; also addd if not around nid field
+ *
+ * BASE TABLE: stock
+ * @code
+ *     create table stock (
+ *             stock_id serial not null,
+ *             primary key (stock_id),
+ *     R       dbxref_id int,
+ *             foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null INITIALLY DEFERRED,
+ *     R       organism_id int,
+ *             foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED,
+ *     F       name varchar(255),
+ *     F       uniquename text not null,
+ *     F       description text,
+ *     R       type_id int not null,
+ *             foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ *     F       is_obsolete boolean not null default 'false',
+ *             constraint stock_c1 unique (organism_id,uniquename,type_id)
+ *     );
+ * @endcode
+ */
+function retrieve_stock_views_data() {
+  $data = array();
+
+	// Basic table definition
+  $data['stock']['table']['group'] = t('Chado Stock');
+  $data['stock']['table']['base'] = array(
+    'field' => 'stock_id',
+    'title' => t('Chado Stock'),
+    'help' => t('Chado Stocks are a record of any material upon which an experiment can be done. For example, a DNA sample, an individual or a population.'),
+    'database' => 'chado'
+  );
+
+	// Define relationships between this table and others
+  $data['stock']['table']['join'] = array(
+    'organism' => array(
+      'left_field' => 'organism_id',
+      'field' => 'organism_id',
+    ),
+    'dbxref' => array(
+     'left_field' => 'dbxref_id',                                                                                                                                                                                                   
+      'field' => 'dbxref_id',
+    ),
+  );  
+
+	// Table Field Definitions----------------------
+  // Field: feature_id (primary key)
+  $data['stock']['stock_id'] = array(
+    'title' => 'Stock ID',
+    'help' => 'The primary key of a stock',
+    'field' => array(
+     	'handler' => 'views_handler_field_numeric',
+ 		  'click sortable' => TRUE,
+    ),
+    'filter' => array(
+     	'handler' => 'views_handler_filter_numeric',
+    ),
+    'sort' => array(
+     	'handler' => 'views_handler_sort',
+    ),
+  );
+  
+  // Calculated Field: Node ID
+  //  use custom field handler to query drupal for the node ID
+  //  this is only needed if chado is in a separate database from drupal
+  $data['stock']['nid'] = array(
+    'title' => 'Node ID',
+    'help' => 'This is the node ID of this feature. It can be used as a link to the node.',
+    'field' => array(
+       'handler' => 'views_handler_field_computed_nid',
+      ),
+  );
+
+  //Field: unique name (text)
+  $data['stock']['uniquename'] = array(
+    'title' => t('Unique Name'),
+    'help' => t('A unique name for this stock.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: name (varchar 255)
+  $data['stock']['name'] = array(
+    'title' => t('Name'),
+    'help' => t('The human-readable name of this stock.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: description (varchar 255)
+  $data['stock']['description'] = array(
+    'title' => t('Description'),
+    'help' => t('Provides a short description for a given stock.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  //Field: is_obsolete (boolean t/f)
+  $data['stock']['is_obsolete'] = array(
+    'title' => t('Is Obsolete'),
+    'help' => t('A yes/no field indicating whether a given stock is obsolete or not.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+  );
+
+	//Calculated Field: stock properties
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['properties'] = array(
+    'title' => t('Stock Properties'),
+    'help' => t('Properties of the current stock.'),
+    'field' => array(
+      'title' => t('Properties'),
+      'help' => t('Display a given type of properties associated with a stock.'),
+      'handler' => 'views_handler_field_stockprop_by_type',
+    ),
+  );
+
+	//Calculated Field: stock properties (ALL)
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['all_properties'] = array(
+  	'title' => t('All Stock Properties'),
+  	'help' => t('Properties of the current stock.'),
+  	'field' => array(
+    	'title' => t('All Properties'),
+    	'help' => t('Display all properties associated with a stock.'),
+    	'handler' => 'views_handler_field_stockprop_all',
+  	),
+	);
+	
+	//Calculated Field: stock relationships
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['relationships'] = array(
+    'title' => t('Stock Relationships'),
+    'help' => t('Relationships including the current stock.'),
+    'field' => array(
+      'title' => t('Relationships'),
+      'help' => t('Display a given type of relationships including the current stock.'),
+      'handler' => 'views_handler_field_stockrel_by_type',
+    ),
+  );
+
+	//Calculated Field: stock relationships (ALL)
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['all_relationships'] = array(
+  	'title' => t('All Stock Relationships'),
+  	'help' => t('Relationships including the current stock.'),
+  	'field' => array(
+    	'title' => t('All Relationships'),
+    	'help' => t('Display all relationships including the stock.'),
+    	'handler' => 'views_handler_field_stockrel_all',
+  	),
+	);
+	
+	//Calculated Field: stock dbxrefs 
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['dbxref'] = array(
+    'title' => t('Stock Database References'),
+    'help' => t('Database References associated with the current stock.'),
+    'field' => array(
+      'title' => t('Database References'),
+      'help' => t('Display database references from a given database for the current stock.'),
+      'handler' => 'views_handler_field_stock_dbxref_by_type',
+    ),
+  );
+
+	//Calculated Field: stock dbxrefs (ALL)
+	// uses a custom field handler which pulls results from the view
+	// actual query performed in chado_stock_views_views_pre_render	(&$view) -file:tripal_stock.views.inc
+	$data['stock']['all_dbxref'] = array(
+  	'title' => t('All Stock Database References'),
+  	'help' => t('Database References associated with the current stock.'),
+  	'field' => array(
+    	'title' => t('All Database References'),
+    	'help' => t('Display all database references for the current stock.'),
+    	'handler' => 'views_handler_field_stock_dbxref_all',
+  	),
+	);
+  return $data;
+}