Updated Tripal stock to new Tripal API functions & created some needed API functions for cv, db, organism

tripal_core/views/handlers/views_handler_field_dbxref_accession_link.inc

@@ -19,9 +19,9 @@ class views_handler_field_dbxref_accession_link extends views_handler_field {
    $db_id = $values->{$this->aliases['db_id']};
 
    if (!empty($db_id)) {
-     $previous_db = db_set_active('chado');
+     $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
-     db_set_active($previous_db);   
+     tripal_db_set_active($previous_db);   
      $urlprefix = $result->urlprefix;
 
      if (!empty($urlprefix)) {

tripal_core/views/handlers/views_handler_field_stock_dbxref_by_type.inc

@@ -42,7 +42,7 @@ class views_handler_field_stock_dbxref_by_type extends views_handler_field_prere
 			'#default_value' => array($this->options['display_options']['accession'], $this->options['display_options']['db_name'], $this->options['display_options']['link']),
 		);
 		
-    $db_options = get_chado_db_options();
+    $db_options = tripal_db_get_db_options();
 	  $db_options[0] = 'Select a Database';
 	  ksort($db_options);
     $form['db_ids'] = array(

tripal_core/views/handlers/views_handler_field_stockprop_by_type.inc

@@ -38,7 +38,7 @@ class views_handler_field_stockprop_by_type extends views_handler_field_prerende
       '#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') );
+    $options = tripal_cv_get_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>',

tripal_core/views/handlers/views_handler_field_stockrel_by_type.inc

@@ -60,7 +60,7 @@ class views_handler_field_stockrel_by_type extends views_handler_field_prerender
       '#default_value' => $this->options['stockrel_display_rels'],
     );
     
-    $options = get_chado_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
+    $options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
     $form['stockrel_type_ids'] = array(
       '#type' => 'checkboxes',
       '#title' => t('Relationship Types'),

tripal_core/views/handlers/views_handler_filter_stockprop_id.inc

@@ -64,9 +64,9 @@ class views_handler_filter_stockprop_id extends views_handler_filter {
 	}
 	
   function types_form(&$form, &$form_state) {
-    $previous_db = db_set_active('chado');
+    $previous_db = tripal_db_set_active('chado');
     $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM cvterm cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM stockprop)");
-    db_set_active($previous_db);
+    tripal_db_set_active($previous_db);
 
     $types = array();
     while ($r = db_fetch_object($result)) { $types[$r->type_id] = $r->name; }
@@ -88,9 +88,9 @@ class views_handler_filter_stockprop_id extends views_handler_filter {
 		if ($this->options['expose']['display_type'] == 'select') {
 		
 			// Get options
-			$previous_db = db_set_active('chado');
+			$previous_db = tripal_db_set_active('chado');
 			$resource = db_query("SELECT value FROM stockprop WHERE type_id=".$this->type." ORDER BY value");
-			db_set_active($previous_db);
+		 tripal_db_set_active($previous_db);
 			while ($r = db_fetch_object($resource)) {
 				$options[$r->value] = $r->value;
 			}

tripal_cv/tripal_cv.api.inc

@@ -68,7 +68,7 @@ function tripal_cv_get_cv_options() {
   $result = db_query(
     "SELECT cv_id, name FROM cv"
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
   $options = array();
   while ( $r = db_fetch_object($result) ) {
@@ -116,6 +116,30 @@ function tripal_cv_get_cvterm ($where_options) {
   return $r;
 }
 
+/*************************************************************************
+ * Purpose: Retrieve a chado cvterm object with a given name
+ *
+ * @params name: the cvterm.name
+ * @params cv_id: the cv_id of the term you are looking for
+ * @return cvterm object
+ */
+function tripal_cv_get_cvterm_by_name ($name, $cv_id=0) {
+
+  if (!empty($cv_id)) {
+    $sql = "SELECT * FROM cvterm WHERE name='%s' AND cv_id=%d";
+    $previous_db = tripal_db_set_active('chado');
+    $r = db_fetch_object(db_query($sql, $name, $cv_id));
+    tripal_db_set_active($previous_db);
+  } else {
+    $sql = "SELECT * FROM cvterm WHERE name='%s'";
+    $previous_db = tripal_db_set_active('chado');
+    $r = db_fetch_object(db_query($sql, $name));
+    tripal_db_set_active($previous_db);
+  }
+  
+  return $r;
+  
+}
 /*************************************************************************
  * Purpose: Create an options array to be used in a form element
  *   which provides a list of all chado cvterms
@@ -137,7 +161,7 @@ function tripal_cv_get_cvterm_options($cv_id = 0) {
     	"SELECT cvterm_id, name FROM cvterm"
   	);
   }
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
   $options = array();
   while ( $r = db_fetch_object($result) ) {

tripal_db/tripal_db.api.inc

@@ -1,5 +1,39 @@
 <?php
 
+/*************************************************************************
+ * Purpose: To retrieve a chado db object
+ *
+ * @params db.db_id
+ * @return chado db object with all fields from the chado db table
+ */
+function tripal_db_get_db_by_db_id ($db_id) {
+
+	$previous_db = tripal_db_set_active('chado');
+  $r = db_fetch_object(db_query(
+    "SELECT * FROM db WHERE db_id=%d", $db_id
+  ));
+  tripal_db_set_active($previous_db);
+
+  return $r;
+}
+
+/*************************************************************************
+ * Purpose: To retrieve a chado db object
+ *
+ * @params db.name
+ * @return chado db object with all fields from the chado db table
+ */
+function tripal_db_get_db_by_name ($name) {
+
+	$previous_db = tripal_db_set_active('chado');
+  $r = db_fetch_object(db_query(
+    "SELECT * FROM db WHERE name='%s'", $name
+  ));
+  tripal_db_set_active($previous_db);
+
+  return $r;
+}
+
 /*************************************************************************
  * Purpose: To retrieve a chado db object
  *
@@ -49,7 +83,7 @@ function tripal_db_get_db_options() {
   $result = db_query(
     "SELECT db_id, name FROM db"
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
   $options = array();
   while ( $r = db_fetch_object($result) ) {
@@ -96,3 +130,31 @@ function tripal_db_get_dbxref ($where_options) {
 
   return $r;
 }
+
+/*************************************************************************
+ * Purpose: To retrieve a chado dbxref object with a given accession
+ *
+ * @params dbxref.accession
+ * @params dbxref.db_id
+ * @return chado dbxref object with all fields from the chado dbxref table
+ */
+function tripal_db_get_dbxref_by_accession ($accession, $db_id=0) {
+
+  if (!empty($db_id)) {
+	  $previous_db = tripal_db_set_active('chado');
+    $r = db_fetch_object(db_query(
+      "SELECT * FROM dbxref WHERE accession='%s' AND db_id=%d",
+      $accession, $db_id
+    ));
+    tripal_db_set_active($previous_db);
+  } else {
+	  $previous_db = tripal_db_set_active('chado');
+    $r = db_fetch_object(db_query(
+      "SELECT * FROM dbxref WHERE accession='%s'",
+      $accession
+    ));
+    tripal_db_set_active($previous_db);  
+  }
+  
+  return $r;
+}

tripal_organism/tripal_organism.api.inc

@@ -25,28 +25,32 @@ function tripal_organism_get_organism_options() {
 }
 
 /*************************************************************************
- * Purpose: Return a given organism object using the nid or organism id
+ * Purpose: Return a given organism object using the nid
  *
  * @return organism object created by node load
  */
-function tripal_organism_get_organism($nid=0, $organism_id=0) {
+function tripal_organism_get_organism_by_nid ($nid) {
 
-	if (!empty($nid)) {
-		return node_load($nid);
+	return node_load($nid);
+	
+}
+
+/*************************************************************************
+ * Purpose: Return a given organism object using the organism id
+ *
+ * @return organism object created by node load
+ */
+function tripal_organism_get_organism_by_organism_id ($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($r->nid);
 	} else {
-		if (!empty($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: tripal_organism_get_organism() -no organism with that organism id sync'd with drupal", 'error');
-			}
-		} else {
-			drupal_set_message("Function: tripal_organism_get_organism() -need to supply at least one of node ID or Organism ID",'error');
-		}
+		drupal_set_message("Function: tripal_organism_get_organism_by_organism_id() -no organism with that organism id sync'd with drupal", 'error');
 	}
-
+	
 	return 0;
 	
 }
+

tripal_stock/tripal_stock-administration.inc

@@ -47,7 +47,7 @@ function tripal_stock_admin() {
 		      ." between stocks. Only cvs already loaded into chado can be selected here.")
    );
 
-   $cv_options = get_chado_cv_options();
+   $cv_options = tripal_cv_get_cv_options();
    
    $form['set_cv']['stock_types_cv'] = array(
      '#type' => 'select',
@@ -95,7 +95,7 @@ function tripal_stock_admin() {
       '#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(),
+      '#options' => tripal_organism_get_organism_options(),
       '#required'    => FALSE,
       '#prefix'      => '<div id="lib_boxes">',
       '#suffix'      => '</div>'

tripal_stock/tripal_stock-db_references.inc

@@ -8,14 +8,14 @@
 function tripal_stock_add_ALL_dbreferences_page($node) {
   $output = '';
 
-  $output .= implement_add_chado_properties_progress('db_references').'<br>';
+  $output .= tripal_stock_add_chado_properties_progress('db_references').'<br>';
   $output .= '<b>All Database References should strictly pertain to THE CURRENT Individual</b><br>';
   $output .= '<br><b>Current Database References</b><br>';
-  $output .= list_dbreferences_for_node($node->db_references);
+  $output .= tripal_stock_list_dbreferences_for_node($node->db_references);
   $output .= '<br><br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_add_chado_properties_navigate', 'db_references', $node->nid);
+  $output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'db_references', $node->nid);
   return $output;
 }
 
@@ -56,7 +56,7 @@ function tripal_stock_add_ONE_dbreference_form($form_state, $node) {
     '#description' => t('Optionally enter a description about the database accession.')
   );
 
-  $db_options = get_chado_db_options();
+  $db_options = tripal_db_get_db_options();
   $db_options[0] = 'Select a Database';
   ksort($db_options);
   $form['add_dbreference']['database'] = array(
@@ -129,8 +129,7 @@ function tripal_stock_add_ONE_dbreference_form_submit($form, &$form_state) {
     tripal_db_set_active($previous_db);
 
     //create stock_dbxref
-    $dbxref = get_chado_dbxref( array('db_id'=>array('type'=>'INT','value'=>$form_state['values']['database']), 
-    																	'accession'=>array('type'=>'STRING','exact'=>TRUE,'value'=>$form_state['values']['accession']) ) );
+    $dbxref = tripal_db_get_dbxref_by_accession(form_state['values']['accession'], $form_state['values']['database']);
 		if (!empty($dbxref->dbxref_id)) {
 			$previous_db = tripal_db_set_active('chado');
     	db_query(
@@ -160,7 +159,7 @@ function tripal_stock_edit_ALL_dbreferences_page($node) {
   $output .= '<br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_dbreference_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_back_to_stock_button', $node->nid);
+  $output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid);
 
   return $output;
 }
@@ -194,7 +193,7 @@ function tripal_stock_edit_ALL_db_references_form($form_state, $node) {
       '#default_value' => $ref->accession
     );
 
-    $db_options = get_chado_db_options();
+    $db_options = tripal_db_get_db_options();
     $db_options[0] = 'Select a Database';
     ksort($db_options);
     $form["database-$i"] = array( 
@@ -259,20 +258,20 @@ function tripal_stock_edit_ALL_db_references_form_submit($form, &$form_state) {
 
 function tripal_stock_update_db_reference($dbxref_id, $database_id, $accession) {
 
-  $previous_db = db_set_active('chado');
+  $previous_db = tripal_db_set_active('chado');
   db_query(
     "UPDATE dbxref SET db_id=%d, accession='%s' WHERE dbxref_id=%d",
     $database_id, 
     $accession,
     $dbxref_id
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
 }
 
 function tripal_stock_delete_db_reference($dbxref_id) {
 
-  $previous_db = db_set_active('chado');
+  $previous_db = tripal_db_set_active('chado');
   db_query(
     "DELETE FROM dbxref WHERE dbxref_id=%d",
     $dbxref_id
@@ -282,7 +281,7 @@ function tripal_stock_delete_db_reference($dbxref_id) {
     "DELETE FROM stock_dbxref WHERE dbxref_id=%d",
     $dbxref_id
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
 }
 
@@ -318,7 +317,7 @@ function theme_tripal_stock_edit_ALL_db_references_form ($form) {
 /**
  * 
  */
-function list_dbreferences_for_node($db_references) {
+function tripal_stock_list_dbreferences_for_node($db_references) {
 
   if (!empty($db_references) ) {
     $output = '<table>';

tripal_stock/tripal_stock-properties.inc

@@ -12,14 +12,14 @@
 function tripal_stock_add_ALL_property_page($node) {
   $output = '';
 
-  $output .= implement_add_chado_properties_progress('properties').'<br>';
+  $output .= tripal_stock_add_chado_properties_progress('properties').'<br>';
   $output .= '<b>All Properties should strictly pertain to THE CURRENT Individual</b><br>';
   $output .= '<br><b>Current Properties</b><br>';
-  $output .= list_properties_for_node($node->properties, $node->synonyms);
+  $output .= tripal_stock_list_properties_for_node($node->properties, $node->synonyms);
   $output .= '<br><br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_property_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_add_chado_properties_navigate', 'properties', $node->nid);
+  $output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'properties', $node->nid);
   return $output;
 }
 
@@ -37,11 +37,10 @@ function tripal_stock_add_ONE_property_form($form_state, $node) {
     '#value' => $node->nid
   );
 
-  $tmp_obj = get_chado_cvterm(array('name' => array('type'=>'STRING','exact'=>TRUE, 'value'=>'synonym'),
-  																	'cv_id' => array('type'=>'INT','value'=>variable_get('chado_stock_prop_types_cv', 'null') )));
+	$tmp_obj = tripal_cv_get_cvterm_by_name('synonym', variable_get('chado_stock_prop_types_cv', 'null'));
 	$synonym_id = $tmp_obj->cvterm_id;
 	
-  $prop_type_options = get_chado_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') ); 
+  $prop_type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') ); 
   $prop_type_options[0] = 'Select a Type';
   ksort($prop_type_options);
   $form['add_properties']['prop_type_id'] = array(
@@ -99,8 +98,7 @@ function tripal_stock_add_ONE_property_form_validate($form, &$form_state) {
 
     // only check preferred synonym if type is synonym
     if ($form_state['values']['preferred_synonym'] == 1) {
-    $tmp_obj = get_chado_cvterm(array('name' => array('type'=>'STRING','exact'=>TRUE, 'value'=>'synonym'),
-  																	'cv_id' => array('type'=>'INT','value'=>variable_get('chado_stock_prop_types_cv', 'null') )));
+      $tmp_obj = tripal_cv_get_cvterm_by_name('synonym', variable_get('chado_stock_prop_types_cv', 'null'));
       if ($form_state['values']['prop_type_id'] != $tmp_obj->cvterm_id) {
         form_set_error('preferred_synonym', 'Preferred Synonym Checkbox Only Applicable if Type of Property is Synonym');
       }
@@ -165,7 +163,7 @@ function tripal_stock_edit_ALL_properties_page($node) {
   $output .= '<br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_property_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_back_to_stock_button', $node->nid);
+  $output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid);
 
   return $output;
 }
@@ -204,7 +202,7 @@ function tripal_stock_edit_ALL_properties_form($form_state, $node) {
       '#value' => $property->stockprop_id
     );
 
-    $prop_type_options = get_chado_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') );
+    $prop_type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') );
     ksort($prop_type_options);
  
     $default = array_search($property->type, $prop_type_options);
@@ -362,7 +360,7 @@ function theme_tripal_stock_edit_ALL_properties_form ($form) {
 /**
  * 
  */
-function list_properties_for_node($properties, $synonyms) {
+function tripal_stock_list_properties_for_node($properties, $synonyms) {
 
   if (!empty($properties) OR !empty($synonyms) ) {
     $output = '<table>';

tripal_stock/tripal_stock-relationships.inc

@@ -8,14 +8,14 @@
 function tripal_stock_add_ALL_relationships_page($node) {
   $output = '';
 
-  $output .= implement_add_chado_properties_progress('relationships').'<br>';
+  $output .= tripal_stock_add_chado_properties_progress('relationships').'<br>';
   $output .= '<b>All Relationships should include the CURRENT Individual ('.$node->uniquename.')</b><br>';
   $output .= '<br><b>Current Relationships</b><br>';
-  $output .= list_relationships_for_node($node->uniquename, $node->subject_relationships, $node->object_relationships);
+  $output .= tripal_stock_list_relationships_for_node($node->uniquename, $node->subject_relationships, $node->object_relationships);
   $output .= '<br><br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_relationship_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_add_chado_properties_navigate', 'relationships', $node->nid);
+  $output .= drupal_get_form('tripal_stock_add_chado_properties_navigate', 'relationships', $node->nid);
   return $output;
 }
 
@@ -50,7 +50,7 @@ function tripal_stock_add_ONE_relationship_form($form_state, $node) {
     '#description' => 'The Uniquename, Name, Database Reference or Synonym of a Stock can be used here',
   );
 
-  $type_options = get_chado_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
+  $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
   $type_options[0] = 'Select a Type';
   ksort($type_options);
   $form['add_relationships']['type_id'] = array(
@@ -101,7 +101,7 @@ function tripal_stock_add_ONE_relationship_form_validate($form, &$form_state) {
     // check valid stock selected for subject
     $criteria = array('unknown' => array('value'=> $form_state['values']['subject_id'], 
       																		'columns'=>array('name','uniquename','accession','synonym') ));
-    $subject_results = get_chado_stocks($criteria,'ANY',$_SESSION['organism']);
+    $subject_results = tripal_stock_get_stocks($criteria,'ANY',$_SESSION['organism']);
     if (sizeof($subject_results) > 1) {
       $links= array();
       for ($i=0; $i<sizeof($subject_results); $i++) { $links[] = l($i+1, "node/".$subject_results[$i]->nid); }
@@ -119,7 +119,7 @@ function tripal_stock_add_ONE_relationship_form_validate($form, &$form_state) {
     // check valid stock selected for object
     $criteria = array('unknown' => array('value'=> $form_state['values']['object_id'], 
       																		'columns'=>array('name','uniquename','accession','synonym') ));
-    $object_results = get_chado_stocks($criteria,'ANY',$_SESSION['organism']);
+    $object_results = tripal_stock_get_stocks($criteria,'ANY',$_SESSION['organism']);
     if (sizeof($object_results) > 1) {
       $links= array();
       for ($i=0; $i<sizeof($object_results); $i++) { $links[] = l($i+1, "node/".$object_results[$i]->nid); } 
@@ -159,7 +159,7 @@ function tripal_stock_add_ONE_relationship_form_validate($form, &$form_state) {
 function tripal_stock_add_ONE_relationship_form_submit($form, &$form_state) {
 
   if ($form_state['values']['subject_id'] > 0) {
-    $previous_db = db_set_active('chado');
+    $previous_db = tripal_db_set_active('chado');
     db_query(
       "INSERT INTO stock_relationship (subject_id, type_id, object_id, value) VALUES (%d, %d, %d, '%s')",
       $form_state['values']['subject_id'],
@@ -167,7 +167,7 @@ function tripal_stock_add_ONE_relationship_form_submit($form, &$form_state) {
       $form_state['values']['object_id'],
       $form_state['values']['r_description']
     );
-    db_set_active($previous_db);
+    tripal_db_set_active($previous_db);
 
     drupal_set_message('Successfully Added Relationship.');
   } //end of insert relationship
@@ -186,7 +186,7 @@ function tripal_stock_edit_ALL_relationships_page($node) {
   $output .= '<br>';
   $output .= drupal_get_form('tripal_stock_add_ONE_relationship_form', $node);
   $output .= '<br>';
-  $output .= drupal_get_form('implement_back_to_stock_button', $node->nid);
+  $output .= drupal_get_form('tripal_stock_back_to_stock_button', $node->nid);
 
   return $output;
 }
@@ -238,7 +238,7 @@ function tripal_stock_edit_ALL_relationships_form($form_state, $node) {
       '#description' => $description,
     ); 
 
-    $type_options = get_chado_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
+    $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
     ksort($type_options);          
     $form["type_id-$i"] = array(  
       '#type' => 'select',    
@@ -291,7 +291,7 @@ function tripal_stock_edit_ALL_relationships_form_validate($form, &$form_state)
       // check valid stock selected for subject
       $criteria = array('unknown' => array('value'=>$form_state['values']["subject_id-$i"], 
       																		'columns'=>array('name','uniquename','accession','synonym') ));
-      $subject_results = get_chado_stocks($criteria,'ANY',$_SESSION['organism']);
+      $subject_results = tripal_stock_get_stocks($criteria,'ANY',$_SESSION['organism']);
       if (sizeof($subject_results) > 1) {
         $links= array();
         for ($j=0; $j<sizeof($subject_results); $j++) { $links[] = l($j+1, "node/".$subject_results[$j]->nid); }
@@ -309,7 +309,7 @@ function tripal_stock_edit_ALL_relationships_form_validate($form, &$form_state)
       // check valid stock selected for object
       $criteria = array('unknown' => array('value'=> $form_state['values']["object_id-$i"], 
       																		'columns'=>array('name','uniquename','accession','synonym') ));
-      $object_results = get_chado_stocks($criteria,'ANY',$_SESSION['organism']);
+      $object_results = tripal_stock_get_stocks($criteria,'ANY',$_SESSION['organism']);
       if (sizeof($object_results) > 1) {
         $links= array();
         for ($j=0; $j<sizeof($object_results); $j++) { $links[] = l($j+1, "node/".$object_results[$j]->nid); }
@@ -382,7 +382,7 @@ function tripal_stock_edit_ALL_relationships_form_submit($form, &$form_state) {
 
 function tripal_stock_update_relationship ($stock_relationship_id, $subject_id, $cvterm_id, $object_id) {
 
-  $previous_db = db_set_active('chado');
+  $previous_db = tripal_db_set_active('chado');
   db_query(
     "UPDATE stock_relationship SET subject_id=%d, type_id=%d, object_id=%d WHERE stock_relationship_id=%d",
     $subject_id,
@@ -390,18 +390,18 @@ function tripal_stock_update_relationship ($stock_relationship_id, $subject_id,
     $object_id,
     $stock_relationship_id
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
 }
 
 function tripal_stock_delete_relationship ($stock_relationship_id) {
 
-  $previous_db = db_set_active('chado');
+  $previous_db = tripal_db_set_active('chado');
   db_query(
     "DELETE FROM stock_relationship WHERE stock_relationship_id=%d",
     $stock_relationship_id
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
 }
 
@@ -439,7 +439,7 @@ function theme_tripal_stock_edit_ALL_relationships_form ($form) {
 /**
  *
  */
-function list_relationships_for_node($stock_name, $subject_relationships, $object_relationships) {
+function tripal_stock_list_relationships_for_node($stock_name, $subject_relationships, $object_relationships) {
 
   if (!empty($subject_relationships) OR !empty($object_relationships) ) {
     $output = '<table>';

tripal_stock/tripal_stock-secondary_tables.inc

@@ -1,7 +1,7 @@
 <?php
 // $Id$
 
-function implement_back_to_stock_button($form_state, $nid) {
+function tripal_stock_back_to_stock_button($form_state, $nid) {
   $form = array();
 
   $form['nid'] = array(
@@ -17,11 +17,11 @@ function implement_back_to_stock_button($form_state, $nid) {
   return $form;
 }
 
-function implement_back_to_stock_button_submit($form, $form_state) {
+function tripal_stock_back_to_stock_button_submit($form, $form_state) {
   drupal_goto('node/'.$form_state['values']['nid']);
 }
 
-function implement_add_chado_properties_progress($current) {
+function tripal_stock_add_chado_properties_progress($current) {
 
     $value = '<div class="form_progress"><div class="form_progress-text">'; 
 
@@ -49,7 +49,7 @@ function implement_add_chado_properties_progress($current) {
 
 }
 
-function implement_add_chado_properties_navigate($form_state, $step, $nid) {
+function tripal_stock_add_chado_properties_navigate($form_state, $step, $nid) {
   $form = array();
 
   $form['current_step'] = array(
@@ -110,7 +110,7 @@ function implement_add_chado_properties_navigate($form_state, $step, $nid) {
   return $form;
 }
 
-function implement_add_chado_properties_navigate_submit($form, $form_state) {
+function tripal_stock_add_chado_properties_navigate_submit($form, $form_state) {
 
   $raw_steps = preg_split('/::/', $form_state['values']['steps']); 
 
@@ -179,12 +179,12 @@ function tripal_stock_is_obsolete_form($node, $stock_id) {
 
 function tripal_stock_is_obsolete_form_submit($form, &$form_state) {
 
-  $previous_db = db_set_active('chado');
+  $previous_db = tripal_db_set_active('chado');
   db_query(
     "UPDATE stock SET is_obsolete='t' WHERE stock_id=%d",
     $form_state['values']['make_obsolete_stock_id']
   );
-  db_set_active($previous_db);
+  tripal_db_set_active($previous_db);
 
 }
 

tripal_stock/tripal_stock.module

@@ -3,7 +3,7 @@
 
 require("tripal_stock-administration.inc");
 
-require("tripal_stock-api_functions.inc");
+require("tripal_stock.api.inc");
 require("other_module_api_functions.inc");
 
 require("tripal_stock-secondary_tables.inc");
@@ -208,7 +208,7 @@ 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_all_chado_stocks();
+      $stocks = tripal_stock_get_all_stocks();
       if($no_stocks != count($stocks)) {
          drupal_set_message("Synchronization needed.");
       }
@@ -297,7 +297,7 @@ function chado_stock_load($node) {
   // 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);
+  $node->organism = tripal_organism_get_organism_by_organism_id($chado_stock->organism_id);
 
   // Add Synonyms for stock----------------------------------------------------------------------
   // These are a special case of property (stockprop table) where cvterm='synonym'
@@ -441,7 +441,7 @@ function chado_stock_form($node, $form_state) {
   if (!isset($node->uniquename)) {
     $form['progress'] = array( 
       '#type' => 'item', 
-      '#value' => implement_add_chado_properties_progress('main')
+      '#value' => tripal_stock_add_chado_properties_progress('main')
     );
   }
 
@@ -474,7 +474,7 @@ function chado_stock_form($node, $form_state) {
     '#title' =>	t('Stock Details')
   );
 
-  $type_options = get_chado_cvterm_options( variable_get('chado_stock_types_cv', 'null') );
+  $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_types_cv', 'null') );
   $type_options[0] = 'Select a Type';
   if ($node->nid == '') { $type_default = 0; } else { $type_default = $node->stock_type_id; }
   $form['details']['type_id'] = array(
@@ -485,7 +485,7 @@ function chado_stock_form($node, $form_state) {
     '#required'	  => TRUE,
   );
 
-  $stock_oganism_options = get_chado_organism_options();
+  $stock_oganism_options = tripal_organism_get_organism_options();
   $stock_oganism_options[0] = 'Select An Organism';
   if ($node->nid == '') { $organism_default = 0; } else {  $organism_default = $node->organism->organism_id; }
   $form['details']['organism_id'] = array(
@@ -521,7 +521,7 @@ function chado_stock_form($node, $form_state) {
     '#description' => t('Optionally enter a description about the database accession.')
   );
 
-  $db_options = get_chado_db_options();
+  $db_options = tripal_db_get_db_options();
   $db_options[0] = 'Select a Database';
   if ($node->nid == '') { $db_default = 0; } else { $db_default = $node->main_db_reference->db_id; }
   $form['database_reference']['database'] = array(
@@ -631,15 +631,7 @@ function chado_stock_insert($node) {
 				$node->db_description	
       );
 
-  		$dbxref_options['db_id'] = array(
-  			'value' =>$node->database,
-  			'type' => 'INT',
-  		);
-  		$dbxref_options['accession'] = array(
-  			'value' =>$node->accession,
-  			'type' => 'STRING',
-  		);
-  		$dbxref = get_chado_dbxref($dbxref_options);
+  		$dbxref = tripal_db_get_dbxref_by_accession($node->accession, $node->database);
   	}
   }
   

tripal_stock/tripal_stock.views.inc

@@ -110,9 +110,9 @@ function tripal_stock_views_pre_render	(&$view) {
 				$sql = "SELECT stockprop.*, cvterm.name as type_name FROM stockprop "
 					."INNER JOIN cvterm cvterm ON stockprop.type_id=cvterm.cvterm_id "
 					."WHERE stockprop.stock_id IN (".implode(',',$stock_ids).")";
-				$previous_db = db_set_active('chado');
+				$previous_db = tripal_db_set_active('chado');
 				$resource = db_query($sql);
-				db_set_active($previous_db);
+			 tripal_db_set_active($previous_db);
 		
 				$view->result[$key]->properties = array();
 				while ($r = db_fetch_object($resource)) {
@@ -133,9 +133,9 @@ function tripal_stock_views_pre_render	(&$view) {
 					."LEFT JOIN cvterm cvterm ON stock_relationship.type_id = cvterm.cvterm_id "
 					."WHERE stock_relationship.subject_id IN (".implode(',',$stock_ids).") "
 					."OR stock_relationship.object_id IN (".implode(',',$stock_ids).") ";
-				$previous_db = db_set_active('chado');
+				$previous_db = tripal_db_set_active('chado');
 				$resource = db_query($sql);
-				db_set_active($previous_db);
+			 tripal_db_set_active($previous_db);
 			
 				while ($r = db_fetch_object($resource)) {
 					if (in_array($r->subject_id, $stock_ids)) {
@@ -161,9 +161,9 @@ function tripal_stock_views_pre_render	(&$view) {
 					."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');
+				$previous_db = tripal_db_set_active('chado');
 				$resource = db_query($sql);
-				db_set_active($previous_db);
+			 tripal_db_set_active($previous_db);
 		
 				$view->result[$key]->dbxref = array();
 				while ($r = db_fetch_object($resource)) {

tripal_stock/views/handlers/views_handler_argument_stockprop_id.inc

@@ -10,9 +10,9 @@ class views_handler_argument_stockprop_id extends views_handler_argument_string
     unset($form['require_value']);
     
     //get options & display as options
-	  $previous_db = db_set_active('chado');
+	  $previous_db = tripal_db_set_active('chado');
     $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM cvterm cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM stockprop)");
-    db_set_active($previous_db);
+    tripal_db_set_active($previous_db);
     $types = array();
     while ($r = db_fetch_object($result)) { $types[$r->type_id] = $r->name; }
 		$form['stockprop_type_id'] = array(

tripal_stock/views/handlers/views_handler_filter_stock_dbxref_id.inc

@@ -53,8 +53,7 @@ class views_handler_filter_stock_dbxref_id extends views_handler_filter {
   /////////// Form Parts/////////////////////////
   function types_form(&$form, &$form_state) {
   
-    $db_options = get_chado_db_options();
-	  $db_options[0] = 'Select a Database';
+    $db_options = tripal_db_get_db_options();
 	  ksort($db_options);
     $form['db'] = array(
       '#type' => 'checkboxes',