Added subtemplates needed for block content and used them for the default node template. Blocks not working

theme_tripal/node-chado_stock.tpl.php

@@ -1,159 +1,43 @@
 <?php
-// $Id: node.tpl.php,v 1.3 2010/04/12 10:04:07 antsin Exp $
-
-/*
-+----------------------------------------------------------------+
-|   BlogBuzz for Dupal 6.x - Version 1.0                         |
-|   Copyright (C) 2009 Antsin.com All Rights Reserved.           |
-|   @license - GNU GENERAL PUBLIC LICENSE                        |
-|----------------------------------------------------------------|
-|   Theme Name: BlogBuzz                                         |
-|   Description: BlogBuzz by Antsin                              |
-|   Author: Antsin.com                                           |
-|   Website: http://www.antsin.com/                              |
-|----------------------------------------------------------------+
-*/  
+// Copyright 2010 University of Saskatchewan (Lacey-Anne Sanderson)
+//
+// Purpose: This template provides the layout of the stock node (page)
+//   using the same templates used for the various stock content blocks.
+//
+// To Customize the Stock Node Page:
+//   - This Template: customize basic layout and which elements are included
+//   - Using Panels: Override the node page using Panels3 and place the blocks
+//       of content as you please. This method requires no programming. See
+//       the Tripal User Guide for more details
+//   - Block Templates: customize the content/layout of each block of stock 
+//       content. These templates are found in the tripal_stock subdirectory
+//
+// Variables Available:
+//   - $node: a standard object which contains all the fields associated with
+//       nodes including nid, type, title, taxonomy. It also includes stock
+//       specific fields such as stock_name, uniquename, stock_type, synonyms,
+//       properties, db_references, object_relationships, subject_relationships,
+//       organism, etc.
+//   NOTE: For a full listing of fields available in the node object add
+//       <pre><?php print_r($node); ?></pre> to this template or install
+//       the Drupal Devel module which provides an extra tab at the top of
+//       the node page labelled Devel
 ?>
 
-<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?>"><div class="node-inner">
-  <div class="content">
-    <?php print $picture; ?>
-    <?php if ($submitted): ?>
-      <div class="submitted">
-        <?php print $date ?>
-      </div>
-    <?php endif; ?>
-    <h1 class="title">
-      <a href="<?php print $node_url; ?>" title="<?php print $title ?>"><?php print $title; ?></a>
-    </h1>
-
-    <?php if ($unpublished): ?>
-      <div class="unpublished"><?php print t('Unpublished'); ?></div>
-    <?php endif; ?>
-
-    <div class="detail clear-block">
-
-<!-- Tripal Stock Starts --!>
-
-<?php if ($node->is_obsolete == 't') { print "<h4><i>This Stock is obsolete.</i></h4>"; } ?>
-<table>
-  <?php if(!empty($node->stock_name)) { ?>
-    <tr><th>Name</th><td><?php print $node->stock_name; ?></td></tr>
-  <?php } ?>
-  <tr><th>Uniquename</th><td><?php print $node->uniquename; ?></td></tr>
-  <tr><th>Organism</th><td><?php print l($node->organism->common_name, "node/".$node->organism->nid); print " (<i>". $node->organism->genus ." ". $node->organism->species ."</i>)"; ?></td></tr>
-  <tr><th>Type</th><td><?php print $node->stock_type; ?></td></tr>
-  <?php if (!empty($node->main_db_reference->db_name)) { ?>
-    <tr><th>Database (<?php print $node->main_db_reference->db_name; ?>)</th>
-      <?php if( !empty($node->main_db_reference->urlprefix) ) { ?>
-        <td><?php print l($node->main_db_reference->accession, $node->main_db_reference->urlprefix.$node->main_db_reference->accession); ?></td></tr>
-      <?php } else { ?>
-	<td><?php print $node->main_db_reference->accession; ?></td></tr>
-      <?php } 
-  } ?>
-  <?php if(!empty($node->description)) { ?>
-    <tr><th>Description</th><td><?php print $node->description; ?></td></tr>
-  <?php } ?>
-  <?php if(!empty($node->crossingblock->season) && ($node->crossingblock->season != '---')) { ?>
-    <tr><th>Crossing Block</th><td><?php print $node->crossingblock->year.' '.$node->crossingblock->season; ?></td></tr>
-  <?php } ?>
-</table>
-
-<!-- Start of Expandable Boxes -->
-   <?php if (!$teaser) { ?>
-     <!-- Control link for the expandableBoxes -->
-       <br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
-     <!-- End of Control link for the expandableBoxes -->
-
-     <!-- Display of Chado Stock Properties from table stockprop in Chado --!>
-     <?php $properties = $node->properties; 
-     if ( (sizeof($node->synonyms) + sizeof($properties)) > 0 ) { ?>
-     <div id="feature-references" class="tripal_feature-info-box">
-     <div class="tripal_expandableBox"><h3>Properties</h3></div>
-     <div class="tripal_expandableBoxContent">
-     <table>
-       <?php if(!empty($node->synonyms)) { ?>
-         <tr><th>Synonyms</th><td>
-           <?php print $node->synonyms[0]->value;
-           array_shift($node->synonyms);
-           if (sizeof($node->synonyms) >= 1) {
-             foreach($node->synonyms as $synonym) {print ", ".$synonym->value;}
-           } ?>
-	    </td></tr>
-       <?php } ?>
-      </table>
-      <table>
-       <?php if (sizeof($properties) > 0) { ?>
-         <tr><th>Type of Property</th><th>Value</th></tr>
-         <?php foreach ($properties as $result) { ?>
-           <tr><td><?php print $result->type; ?></td>
-	      <td><?php  if( $result->value == 't') { print 'TRUE';
-	           } elseif ($result->value == 'f') { print "FALSE";
-		        } else { print $result->value; } ?>
-			   </td></tr>
-         <?php } 
-	   } ?>
-     </table>
-     </div></div>
-     <br>
-     <?php } ?>
-     <br>
-
-    <!-- Display of External Database entries for the current stock --!>
-    <?php $references = $node->db_references; 
-    if ( count($references) > 0 ) { ?>
-      <div id="feature-references" class="tripal_feature-info-box">
-      <div class="tripal_expandableBox"><h3>External References</h3></div>
-      <div class="tripal_expandableBoxContent">
-      <table>
-        <tr><th>Database</th><th>Accession</th></tr>
-        <?php foreach($references as $result) { ?>
-	  <tr><td><?php print $result->db_name; ?></td><td>
-	      <?php if ( !empty($result->db_urlprefix) ) {
-	            print l($result->accession, $result->db_urlprefix.$result->accession); 
-		        } else {
-			      print $result->accession;
-			          }?>
-				    </td></tr>
-				    <?php } ?>
-      </table></div></div>
-      <br>
-    <?php } ?>
-    <br>
+<!-- Base Theme -->
+<?php include('tripal_stock/tripal_stock_base.tpl.php'); ?>
 
-    <!-- Display of Relationships between this stock and other stocks --!>
-    <?php $o_relationships = $node->object_relationships; ?>
-    <?php $s_relationships = $node->subject_relationships; ?>
-    <?php if ( (count($o_relationships) + count($s_relationships)) > 0 ) { ?>
-      <div id="feature-references" class="tripal_feature-info-box">
-      <div class="tripal_expandableBox"><h3>Relationships</h3></div>
-      <div class="tripal_expandableBoxContent">
-      <table>
-        <?php if ( count($o_relationships) > 0 ) {
-          foreach ($o_relationships as $result) { ?>
-            <tr><td><?php print $node->uniquename; ?></td><td><?php print $result->relationship_type ?></td><td><?php print l($result->object_name, "node/".$result->object_nid); ?></td></tr>
-          <?php } //end of foreach?>
-        <? } if ( count($s_relationships) > 0 ) {
-          foreach ($s_relationships as $result) { ?>
-            <tr><td><?php print l($result->subject_name, "node/".$result->subject_nid); ?></td><td><?php print $result->relationship_type ?></td><td><?php print $node->uniquename; ?></td></tr>
-          <?php } //end	    of foreach
-       } ?>
-      </table></div></div>
-      <br>
-    <?php } ?>
-    <br>
+<!-- Database References -->
+<?php include('tripal_stock/tripal_stock_references.tpl.php'); ?>
 
-  <?php } ?> <!-- End of if not Teaser --!>
+<!-- Properties -->
+<?php include('tripal_stock/tripal_stock_properties.tpl.php'); ?>
 
-<!-- Tripal Stock Ends --!>
+<!-- Synonyms -->
+<?php include('tripal_stock/tripal_stock_synonyms.tpl.php'); ?>
 
-      <?php print $content; ?>
-    </div>
-  </div>
-  
-  <div class="extra-links">
-    <div class="terms terms-inline"><?php print theme('links', $taxonomy, array('class' => 'links term-links')) ?></div>
-    <?php print $links; ?>
-  </div>
+<!-- Object Relationships -->
+<?php include('tripal_stock/tripal_stock_relationships_as_object.tpl.php'); ?>
 
-</div></div> <!-- /node-inner, /node -->
+<!-- Subject Relationships -->
+<?php include('tripal_stock/tripal_stock_relationships_as_subject.tpl.php'); ?>

tripal_stock/tripal_stock.module

@@ -206,9 +206,56 @@ function tripal_stock_theme() {
       'arguments' => array('form'),
       'function' => 'theme_tripal_stock_edit_ALL_relationships_form',
     ),
+//    'tripal_stock_base' => array (
+//      'arguments' => array('node'=> null),
+//      'template' => 'tripal_stock_base',
+//    ),
 	);
 }
 
+/*************************************************************************
+ * Purpose: Implement Blocks relating to stock content
+ */
+function tripal_stock_block ($op = 'list', $delta = 0, $edit=array()) {
+  switch($op) {
+    case 'list':
+      $blocks['base']['info'] = t('Tripal Stock Details');
+      $blocks['base']['cache'] = BLOCK_NO_CACHE;
+         
+      return $blocks;
+
+ 		case 'view':
+ 			if(user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
+      	$nid = arg(1);
+      	$node = node_load($nid);
+ 
+        $block = array();
+        switch($delta){
+					case 'base':
+						$block['subject'] = t('Stock Details');
+//						$block['content'] = theme('tripal_stock_base',$node);
+						break;
+        }
+				return $blocks;
+			}
+	}
+}
+
+/*************************************************************************
+ * Purpose:
+ */
+function tripal_stock_nodeapi (&$node, $op, $teaser, $page) {
+	if ($node->type == 'chado_stock') {
+		switch ($op) {
+			case 'view':
+				$node->content['tripal_stock_base'] = array(
+//					'#value' => theme('tripal_stock_base', $node),
+					'#weight' => 0
+				);				
+		}	
+	}
+}
+
 /*************************************************************************
  * Purpose: show stocks stored in drupals chado_stock table
  */
@@ -327,11 +374,13 @@ function chado_stock_load($node) {
     ) 
   );
   $results = tripal_core_chado_select('stockprop', $columns, $values);
-  foreach ($results as $r) {
-    $r->type = 'synonym';
-    $node->synonyms[] = $r;
-  }
-
+  if (!empty($results)) {
+  	foreach ($results as $r) {
+    	$r->type = 'synonym';
+    	$node->synonyms[] = $r;
+  	}
+	}
+	
   // Add properties for stock (not including synonyms)-------------------------------------------
   // $node->properties is an array of objects where each object describes a single property and has a type and value
   $columns = array('stockprop_id', 'type_id', 'value', 'rank');
@@ -403,9 +452,15 @@ function chado_stock_load($node) {
     $node->object_relationships = array();
     foreach ($results as $r) {
       $columns = array('name', 'uniquename', 'description', 'type_id', 'is_obsolete', 'organism_id', 'dbxref_id');
+
       $values = array('stock_id' => $r->object_id);
       $results = tripal_core_chado_select('stock', $columns, $values);
 
+			// Type
+			$type_results = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id' => $r->type_id));
+			$r->type = $type_results[0]->name;
+			
+			// Object
       $r->object->stock_id = $r->object_id;
       unset($r->object_id);
       
@@ -434,6 +489,11 @@ function chado_stock_load($node) {
       $values = array('stock_id' => $r->subject_id);
       $results = tripal_core_chado_select('stock', $columns, $values);
 
+			// Type
+			$type_results = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id' => $r->type_id));
+			$r->type = $type_results[0]->name;
+			
+			// Subject
       $r->subject->stock_id = $r->subject_id;
       unset($r->subject_id);  
       
@@ -441,7 +501,8 @@ function chado_stock_load($node) {
       $r->subject->uniquename = $results[0]->uniquename;
       $r->subject->description = $results[0]->description;
       $r->subject->stock_type_id = $results[0]->type_id;
-      $r->subject->organism->organism_id = $results[0]->organism_id;        $r->subject->main_db_reference->dbxref_id = $results[0]->dbxref_id;        
+      $r->subject->organism->organism_id = $results[0]->organism_id;        
+      $r->subject->main_db_reference->dbxref_id = $results[0]->dbxref_id;        
 
       $sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
       $subject_node = db_fetch_object(db_query($sql, $r->subject->stock_id));
@@ -666,64 +727,93 @@ function chado_stock_validate($node, &$form) {
  */
 function chado_stock_insert($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	
+      $values = array(
+      	'db_id' => $node->database,
+      	'accession' => $node->accession,
       );
-
-  		$dbxref = tripal_db_get_dbxref_by_accession($node->accession, $node->database);
+      if (!tripal_core_chado_select('dbxref',array(dbxref_id), $values)) {
+      	$values['description'] = $node->db_description;
+      	$values['version'] = '1';
+      	$dbxref_status = tripal_core_chado_insert('dbxref', $values);
+      	if (!$dbxref_status) {
+      		drupal_set_message('Unable to add database reference to this stock.', 'warning');
+      		watchdog('tripal_stock', 
+      			'Insert Stock: Unable to create dbxref where values:%values', 
+      			array('%values' => print_r($values, TRUE)),
+      			WATCHDOG_WARNING
+      		);
+      	}
+      } else { $dbxref_status = 1; }
   	}
   }
   
   // create stock
-  if($dbxref->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,
-      $node->type_id
+  if($dbxref_status) {
+		$values = array(
+      'dbxref_id' => array(
+      	'db_id' => $node->database, 
+      	'accession' => $node->accession
+      ),
+      'organism_id' => $node->organism_id,
+      'name' => $node->title,
+      'uniquename' => $node->uniquename,
+      'description' => $node->description,
+      'type_id' => $node->type_id
     );
+    $stock_status = tripal_core_chado_insert('stock', $values);
   } else {
-    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
+		$values = array(
+      'organism_id' => $node->organism_id,
+      'name' => $node->title,
+      'uniquename' => $node->uniquename,
+      'description' => $node->description,
+      'type_id' => $node->type_id
     );
+    $stock_status = tripal_core_chado_insert('stock', $values);
   }
-  tripal_db_set_active($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,
-    	$chado_stock->stock_id
+  if ($stock_status) {
+	  $values = array(
+    	'organism_id' => $node->organism_id,
+    	'uniquename' => $node->uniquename,
+    	'type_id' => $node->type_id
   	);
-
-  	//Move on to next stage of Stock Creation based on next_stage_path field
-  	if ($node->simulate_multipart) {
-    	$next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);  
-    	$_REQUEST['destination'] = $next_stage_path;
+  	$chado_stock = tripal_core_chado_select('stock', array('stock_id'), $values);
+  	if (!empty($chado_stock[0]->stock_id)) {
+  		db_query(
+    		"INSERT INTO {chado_stock} (nid, vid, stock_id) "
+    		."VALUES (%d, %d, %d)",
+    		$node->nid,
+    		$node->vid,
+    		$chado_stock[0]->stock_id
+  		);
+
+ 	 		//Move on to next stage of Stock Creation based on next_stage_path field
+  		if ($node->simulate_multipart) {
+    		$next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);  
+    		$_REQUEST['destination'] = $next_stage_path;
+  		}
+  	} else {
+			drupal_set_message('Error during stock creation.', 'error');
+			watchdog('tripal_stock', 
+      	'Insert Stock: Unable to find newly created stock where values:%values', 
+      	array('%values' => print_r($values, TRUE)),
+      	WATCHDOG_ERROR
+      );
+      return FALSE;
   	}
   } else {
-		drupal_set_message('Error during stock creation.', 'error');
+  	drupal_set_message('Error during stock creation.', 'error');
+    watchdog('tripal_stock', 
+    	'Insert Stock: Unable to create stock where values:%values', 
+      array('%values' => print_r($values, TRUE)),
+      WATCHDOG_WARNING
+    );
+    return FALSE;
   }
 
 }
@@ -739,18 +829,95 @@ function chado_stock_update($node) {
     chado_stock_insert($node);
   } else {
 
+		//update dbxref
+		if ($node->database) {
+			if($node->accession) {
+				$dbxref_mode = '';
+				$stock = tripal_core_chado_select(
+					'stock', 
+					array('dbxref_id', 'type_id'), 
+					array('stock_id' => $node->stock_id)
+				);
+			
+				if ($stock[0]->dbxref_id) {
+					$values = array(
+						'db_id' => $node->database,
+						'accession' => $node->accession,
+						'description' => $node->db_description
+					);
+					$dbxref_status = tripal_core_chado_update(
+						'dbxref', 
+						array('dbxref_id' => $stock[0]->dbxref_id), 
+						$values
+					);
+					$dbxref_mode = 'Update';
+				} else {
+					if ($stock[0]->type_id) {
+						//create the dbxref
+						//used the type_id as a control to check we have a stock but not a dbxref
+						$values = array(
+							'db_id' => $node->database,
+							'accession' => $node->accession,
+							'description' => $node->db_description,
+							'version' => '1',
+						);						
+						$dbxref_status = tripal_core_chado_insert(
+							'dbxref',
+							$values
+						);
+						$dbxref_mode = 'Create';
+					} else {
+						drupal_set_message('Unable to find stock to Update', 'error');
+						watchdog(
+							'tripal_stock',
+							'Stock Update: Unable to find stock to update using values: %values',
+							array('%values', print_r($values, TRUE)),
+							WATCHDOG_ERROR
+						);
+						return FALSE;
+					}
+				}
+			}
+		}
+		
+		if (!$dbxref_status) {
+			watchdog(
+				'tripal_stock',
+				'Stock Update: Unable to %mode main stock dbxref with values: %values',
+				array('%values' => print_r($values,TRUE), '%mode' => $dbxref_mode),
+				WATCHDOG_WARNING
+			);
+		}
+
     //can't change stock id which is all thats stored in drupal thus only update chado
-    $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
+		$update_values = array(
+      'organism_id' => $node->organism_id,
+      'name' => $node->title,
+      'uniquename' => $node->uniquename,
+      'description' => $node->description,
+      'type_id' => $node->type_id,
     );
-    tripal_db_set_active($previous_db);
+    if ($dbxref_status) {
+    	$update_values['dbxref_id'] = array(
+    		'db_id' => $node->database, 
+    		'accession' => $node->accession
+    	);
+    }
+    $status = tripal_core_chado_update(
+    	'stock',
+    	array('stock_id' => $node->stock_id), 
+    	$update_values
+    );
+    
+    if (!$status) {
+    	drupal_set_message('Unable to update stock', 'error');
+    	watchdog(
+    		'tripal_stock',
+    		'Stock Update: Unable to update stock using match values: %mvalues and update values: %uvalues',
+				array('%mvalues' => print_r(array('stock_id' => $node->stock_id),TRUE), '%uvalues' => print_r($update_values,TRUE)),
+				WATCHDOG_ERROR
+    	);
+    }
   }
 
 }