Various bug fixes and theming adjustments

theme_tripal/css/tripal.css

@@ -7,7 +7,11 @@
 }
 .tripal-table th, 
 .tripal-table td {
-   padding: 5px;
+   vertical-align:text-top;
+   padding-left: 10px;
+   padding-right: 10px;
+   padding-top: 5px;
+   padding-bottom: 5px;
 }
 .tripal-table-horz {
    border-top: 2px solid #999999;

theme_tripal/node-chado_analysis.tpl.php

@@ -1,56 +1,156 @@
 <?php
+// Purpose: This template provides the layout of the organism node (page)
+//   using the same templates used for the various feature content blocks.
 //
-// Copyright 2009 Clemson University
+// To Customize the Featture 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 the
+//       print_r $node line below or install the Drupal Devel module which 
+//       provides an extra tab at the top of the node page labelled Devel
 ?>
 
-   <?php if ($picture) {
+<?php
-      print $picture;
+ //uncomment this line to see a full listing of the fields avail. to $node
-   }?>
+ //print '<pre>'.print_r($variables,TRUE).'</pre>';
-    
+
-   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+$node = $variables['node'];
-
+$organism = $variables['node']->organism;
-   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+?>
-	<?php global $base_url;
+
-	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
+<?php if ($teaser) { 
-	</h2><?php }; ?>
+  include('tripal_analysis/tripal_analysis_teaser.tpl.php'); 
-    
+} else { ?>
-	<?php if (!$teaser): ?>
+
-	<?php if ($submitted): ?>
+<script type="text/javascript">
-      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
+if (Drupal.jsEnabled) {
-      <div>
+   $(document).ready(function() {
-      <!-- tripal_analysis theme -->
+      // hide all tripal info boxes at the start
-         <table>
+      $(".tripal-info-box").hide();
-            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
+ 
-            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
+      // iterate through all of the info boxes and add their titles
-            <?php
+      // to the table of contents
-               $ver = $node->sourceversion;
+      $(".tripal-info-box-title").each(function(){
-               if ($node->sourceversion) {
+        var parent = $(this).parent();
-                  $ver = "($node->sourceversion)";
+        var id = $(parent).attr('id');
-               }
+        var title = $(this).text();
-               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
+        $('#tripal_analysis_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_toc_item">'+title+'</a></li>');
-            ?>
+      });
-            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
+
-            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
+      // when a title in the table of contents is clicked, then
-            <tr><th>Executed</th><td><?php print $date?></td></tr>
+      // show the corresponding item in the details box
-            <tr><th>Description</th><td><?php print $node->description?></td></tr>
+      $(".tripal_analysis_toc_item").click(function(){
-         </table>
+         $(".tripal-info-box").hide();
-      <!-- End of tripal_analysis theme-->
+         href = $(this).attr('href');
-	  </div> 
+         $(href).fadeIn('slow');
-    <?php endif; ?>
+         // we want to make sure our table of contents and the details
-    <?php endif; ?>
+         // box stay the same height
-    
+         $("#tripal_analysis_toc").height($(href).parent().height());
-    <div class="content"><?php print $content?></div>
+         return false;
-    
+      }); 
-    <?php if (!$teaser): ?>
+
-    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
+      // we want the base details to show up when the page is first shown 
-    <?php endif; ?>
+      // unless the user specified a specific block
-    
+      var block = window.location.href.match(/\?block=.*/);
-    <?php if ($teaser): ?>
+      if(block != null){
-    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
+         block_title = block.toString().replace(/\?block=/g,'');
-    <?php endif; ?>
+         $("#tripal_analysis-"+block_title+"-box").show();
-    
+      } else {
-    <?php if (!$teaser): ?>
+         $("#tripal_analysis-base-box").show();
-    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
+      }
-    <?php endif; ?>
+      
-  </div>
+      // make the height of the table of contents match the height of the details box
+      $("#tripal_analysis_toc").height($("#tripal_analysis-base-box").parent().height());
+      
+   });
+}
+</script>
+
+<style type="text/css">
+  /* these styles are specific for this template and is not included 
+     in the main CSS files for the theme as it is anticipated that the
+     elements on this page may not be used for other customizations */
+  #tripal_analysis_toc {
+     float: left;
+     width: 20%;
+     background-color: #EEEEEE;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_analysis_toc ul {
+    margin-left: 0px;
+    margin-top: 5px;
+    padding-left: 15px;
+  }
+  #tripal_analysis_toc_title {
+     font-size: 1.5em;
+     line-height: 110%;
+  }
+  #tripal_analysis_toc_desc {
+    /*font-style: italic; */
+  }
+  #tripal_analysis_details {
+     float: left;
+     width: 70%;
+     background-color: #FFFFFF;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     margin-right: 10px;
+     margin-bottom: 10px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_analysis-base-box img {
+    float: left;
+    margin-bottom: 10px;
+  }
+  #tripal_analysis-table-base {
+    float: left;
+    width: 100%;
+    margin-left: 0px;
+    margin-bottom: 10px;
+  }
+</style>
+
+
+<div id="tripal_analysis_details">
+
+   <!-- Basic Details Theme -->
+   <?php include('tripal_analysis/tripal_analysis_base.tpl.php'); ?>
+
+   <?php print $content ?>
+</div>
+
+<!-- Table of contents -->
+<div id="tripal_analysis_toc">
+   <div id="tripal_analysis_toc_title">Resources</i></div>
+   <span id="tripal_analysis_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_toc_list">
+
+   </ul>
+</div>
+
+<?php } ?>

theme_tripal/node-chado_analysis_blast.tpl.php

@@ -61,26 +61,16 @@ if (Drupal.jsEnabled) {
       }); 
 
       // we want the base details to show up when the page is first shown 
-      // unless we're using the feature browser then we want that page to show
+      // unless the user specified a specific block
-      if(window.location.href.match(/\?page=\d+/)){
+      var block = window.location.href.match(/\?block=.*/);
-         $("#tripal_analysis_blast-feature_browser-box").show();
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_analysis_blast-"+block_title+"-box").show();
       } else {
          $("#tripal_analysis_blast-base-box").show();
       }
-      $("#tripal_analysis_blast_toc").height($("#tripal_analysis_blast-base-box").parent().height());
 
-      // we want to select the first GO/KEGG report by default
+      $("#tripal_analysis_blast_toc").height($("#tripal_analysis_blast-base-box").parent().height());
-		$('.form-select').each(function() {
-        var default_option = this.getElementsByTagName('option')[1];
-        if (default_option) {
-           this.selectedIndex =default_option.index ;
-           if (this.onchange.toString().match('tripal_analysis_go_org_charts')) {   
-              tripal_analysis_go_org_charts(default_option.value);
-           } else if (this.onchange.toString().match('tripal_analysis_kegg_org_report')) {            
-              tripal_analysis_kegg_org_report(default_option.value);
-           }
-        }
-		});
       
    });
 }

theme_tripal/node-chado_analysis_kegg.tpl.php

@@ -1,67 +1,157 @@
 <?php
+// Purpose: This template provides the layout of the organism node (page)
+//   using the same templates used for the various feature content blocks.
 //
-// Copyright 2009 Clemson University
+// To Customize the Featture 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 the
+//       print_r $node line below or install the Drupal Devel module which 
+//       provides an extra tab at the top of the node page labelled Devel
 ?>
 
-   <?php if ($picture) {
+<?php
-      print $picture;
+ //uncomment this line to see a full listing of the fields avail. to $node
-   }?>
+ //print '<pre>'.print_r($variables,TRUE).'</pre>';
-    
+
-   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+$node = $variables['node'];
+$organism = $variables['node']->organism;
+?>
+
+<?php if ($teaser) { 
+  include('tripal_analysis_kegg/tripal_analysis_kegg_teaser.tpl.php'); 
+} else { ?>
+
+<script type="text/javascript">
+if (Drupal.jsEnabled) {
+   $(document).ready(function() {
+      // hide all tripal info boxes at the start
+      $(".tripal-info-box").hide();
+ 
+      // iterate through all of the info boxes and add their titles
+      // to the table of contents
+      $(".tripal-info-box-title").each(function(){
+        var parent = $(this).parent();
+        var id = $(parent).attr('id');
+        var title = $(this).text();
+        $('#tripal_analysis_kegg_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_kegg_toc_item">'+title+'</a></li>');
+      });
+
+      // when a title in the table of contents is clicked, then
+      // show the corresponding item in the details box
+      $(".tripal_analysis_kegg_toc_item").click(function(){
+         $(".tripal-info-box").hide();
+         href = $(this).attr('href');
+         $(href).fadeIn('slow');
+         // we want to make sure our table of contents and the details
+         // box stay the same height
+         $("#tripal_analysis_kegg_toc").height($(href).parent().height());
+         return false;
+      }); 
+
+      // we want the base details to show up when the page is first shown 
+      // unless the user specified a specific block
+      var block = window.location.href.match(/\?block=.*/);
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_analysis_kegg-"+block_title+"-box").show();
+      } else {
+         $("#tripal_analysis_kegg-base-box").show();
+      }
+      
+      // make the height of the table of contents match the height of the details box
+      $("#tripal_analysis_kegg_toc").height($("#tripal_analysis_kegg-base-box").parent().height());
+      
+   });
+}
+</script>
+
+<style type="text/css">
+  /* these styles are specific for this template and is not included 
+     in the main CSS files for the theme as it is anticipated that the
+     elements on this page may not be used for other customizations */
+  #tripal_analysis_kegg_toc {
+     float: left;
+     width: 20%;
+     background-color: #EEEEEE;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_analysis_kegg_toc ul {
+    margin-left: 0px;
+    margin-top: 5px;
+    padding-left: 15px;
+  }
+  #tripal_analysis_kegg_toc_title {
+     font-size: 1.5em;
+     line-height: 110%;
+  }
+  #tripal_analysis_kegg_toc_desc {
+    /*font-style: italic; */
+  }
+  #tripal_analysis_kegg_details {
+     float: left;
+     width: 70%;
+     background-color: #FFFFFF;
+     -moz-border-radius: 15px;
+     border-radius: 15px;
+     -moz-box-shadow: 3px 3px 4px #000;
+	  -webkit-box-shadow: 3px 3px 4px #000;
+	  box-shadow: 3px 3px 4px #000;
+     padding: 20px;
+     min-height: 500px;
+     margin-right: 10px;
+     margin-bottom: 10px;
+     border-style:solid;
+     border-width:1px;
+  }
+  #tripal_analysis_kegg-base-box img {
+    float: left;
+    margin-bottom: 10px;
+  }
+  #tripal_analysis_kegg-table-base {
+    float: left;
+    width: 100%;
+    margin-left: 0px;
+    margin-bottom: 10px;
+  }
+</style>
+
+
+<div id="tripal_analysis_kegg_details">
+
+   <!-- Basic Details Theme -->
+   <?php include('tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php'); ?>
+   <?php include('tripal_analysis_kegg/tripal_analysis_kegg_report.tpl.php'); ?>
+
+   <?php print $content ?>
+</div>
+
+<!-- Table of contents -->
+<div id="tripal_analysis_kegg_toc">
+   <div id="tripal_analysis_kegg_toc_title">Resources</i></div>
+   <span id="tripal_analysis_kegg_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_kegg_toc_list">
+
+   </ul>
+</div>
 
-   <?php if ($page == 0) { ?><h2 class="nodeTitle"><a href="<?php print $node_url?>"><?php print $title?></a>
+<?php } ?>
-	<?php global $base_url;
-	if ($sticky) { print '<img src="'.base_path(). drupal_get_path('theme','sanqreal').'/img/sticky.gif" alt="sticky icon" class="sticky" />'; } ?>
-	</h2><?php }; ?>
-    
-	<?php if (!$teaser): ?>
-	   <?php if ($submitted): ?>
-      <div class="metanode"><p><?php print t('') .'<span class="author">'. theme('username', $node).'</span>' . t(' - Posted on ') . '<span class="date">'.format_date($node->created, 'custom', "d F Y").'</span>'; ?></p></div>
-      <?php endif; ?>
-      <div>
-      <!-- tripal_analysis_kegg theme -->
-         <table>
-            <tr><th>Name</th><td><?php print $node->analysisname;?></td></tr>
-            <tr><th>Program (version)</th><td><?php print $node->program.' ('.$node->programversion.')';?></td></tr>
-            <?php
-               $ver = $node->sourceversion;
-               if ($node->sourceversion) {
-                  $ver = "($node->sourceversion)";
-               }
-               $date = preg_replace("/^(\d+-\d+-\d+) .*/","$1",$node->timeexecuted);
-            ?>
-            <tr><th>Source (version)</th><td><?php print $node->sourcename.' '.$ver;?></td></tr>
-            <tr><th>Source URI</th><td><?php print $node->sourceuri;?></td></tr>
-            <tr><th>Executed</th><td><?php print $date?></td></tr>
-            <tr><th>Description</th><td><?php print $node->description?></td></tr>
-            <tr><th>KEGG Settings</th>
-              <td>
-                <b>File:</b>
-                  <?php print preg_replace("/.*\/(.*)/", "$1", $node->hierfile); ?><br>
-                  <?php if ($node->keggjob) {
-                           print "A job for parsing KAAS heir output will be submitted.";
-                        }
-                  ?>
-              </td>
-            </tr>
-         </table>
-      <!-- End of tripal_analysis_kegg theme-->
-	  </div> 
-    
-    <?php endif; ?>
-    
-    <div class="content"><?php print $content?></div>
-    
-    <?php if (!$teaser): ?>
-    <?php if ($links) { ?><div class="links"><?php print $links?></div><?php }; ?>
-    <?php endif; ?>
-    
-    <?php if ($teaser): ?>
-    <?php if ($links) { ?><div class="linksteaser"><div class="links"><?php print $links?></div></div><?php }; ?>
-    <?php endif; ?>
-    
-    <?php if (!$teaser): ?>
-    <?php if ($terms) { ?><div class="taxonomy"><span><?php print t('tags') ?></span> <?php print $terms?></div><?php } ?>
-    <?php endif; ?>
-  </div>

theme_tripal/node-chado_analysis_unigene.tpl.php

@@ -68,9 +68,11 @@ if (Drupal.jsEnabled) {
       }); 
 
       // we want the base details to show up when the page is first shown 
-      // unless we're using the feature browser then we want that page to show
+      // unless the user specified a specific block
-      if(window.location.href.match(/\?page=\d+/)){
+      var block = window.location.href.match(/\?block=.*/);
-         $("#tripal_analysis_unigene-feature_browser-box").show();
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_analysis_unigene-"+block_title+"-box").show();
       } else {
          $("#tripal_analysis_unigene-base-box").show();
       }

theme_tripal/node-chado_feature.tpl.php

@@ -58,8 +58,16 @@ if (Drupal.jsEnabled) {
          return false;
       }); 
 
-      // we want the base details to show up when the page is first shown
+      // we want the base details to show up when the page is first shown 
-      $("#tripal_feature-base-box").show();
+      // unless the user specified a specific block
+      var block = window.location.href.match(/\?block=.*/);
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_feature-"+block_title+"-box").show();
+      } else {
+         $("#tripal_feature-base-box").show();
+      }
+
       $("#tripal_organism_toc").height($("#tripal_feature-base-box").parent().height());
    });
 }

theme_tripal/node-chado_organism.tpl.php

@@ -62,25 +62,18 @@ if (Drupal.jsEnabled) {
 
       // we want the base details to show up when the page is first shown 
       // unless we're using the feature browser then we want that page to show
-      if(window.location.href.match(/\?page=\d+/)){
+      var block = window.location.href.match(/\?block=.*/);
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_orgnism-"+block_title+"-box").show();
+      } 
+      else if(window.location.href.match(/\?page=\d+/)){
          $("#tripal_organism-feature_browser-box").show();
-      } else {
+      } 
+      else {
          $("#tripal_organism-base-box").show();
       }
       $("#tripal_organism_toc").height($("#tripal_organism-base-box").parent().height());
-
-      // we want to select the first GO/KEGG report by default
-		$('.form-select').each(function() {
-        var default_option = this.getElementsByTagName('option')[1];
-        if (default_option) {
-           this.selectedIndex =default_option.index ;
-           if (this.onchange.toString().match('tripal_analysis_go_org_charts')) {   
-              tripal_analysis_go_org_charts(default_option.value);
-           } else if (this.onchange.toString().match('tripal_analysis_kegg_org_report')) {            
-              tripal_analysis_kegg_org_report(default_option.value);
-           }
-        }
-		});
       
    });
 }

theme_tripal/node-chado_stock.tpl.php

@@ -59,8 +59,16 @@
          return false;
       }); 
 
-      // we want the base details to show up when the page is first shown
+      // we want the base details to show up when the page is first shown 
-      $("#tripal_stock-base-box").show();
+      // unless the user specified a specific block
+      var block = window.location.href.match(/\?block=.*/);
+      if(block != null){
+         block_title = block.toString().replace(/\?block=/g,'');
+         $("#tripal_stock-"+block_title+"-box").show();
+      } else {
+         $("#tripal_stock-base-box").show();
+      }
+
       $("#tripal_stock_toc").height($("#tripal_stock-base-box").parent().height());
    });
 }
@@ -151,4 +159,4 @@
 
    </ul>
 </div>
-<?php } ?>
+<?php } ?>

theme_tripal/tripal_analysis/tripal_analysis_base.tpl.php

@@ -0,0 +1,49 @@
+<?php
+$node = $variables['node'];
+$analysis = $variables['node']->analysis;
+
+?>
+<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
+  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
+   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
+      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
+        <th>Analysis Name</th>
+        <td><?php print $analysis->name; ?></td>
+      </tr>
+      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
+        <th nowrap>Software</th>
+        <td><?php 
+          print $analysis->program; 
+          if($analysis->programversion){
+             print " (" . $analysis->programversion . ")"; 
+          }
+          if($analysis->algorithm){
+             print ". " . $analysis->algorithm; 
+          }
+          ?>
+        </td>
+      </tr>
+      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
+        <th nowrap>Source</th>
+        <td><?php 
+          if($analysis->sourceuri){
+             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
+          } else {
+             print $analysis->sourcename; 
+          }
+          if($analysis->sourceversion){
+             print " (" . $analysis->sourceversion . ")"; 
+          }
+          ?>
+          </td>
+      </tr>
+      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
+        <th nowrap>Date performed</th>
+        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
+      </tr>
+      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
+        <th nowrap>Description</th>
+        <td><?php print $analysis->description; ?></td>
+      </tr>             	                                
+   </table>   
+</div>

theme_tripal/tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php

@@ -0,0 +1,49 @@
+<?php
+$node = $variables['node'];
+$analysis = $variables['node']->analysis;
+
+?>
+<div id="tripal_analysis_kegg-base-box" class="tripal_analysis_kegg-info-box tripal-info-box">
+  <div class="tripal_analysis_kegg-info-box-title tripal-info-box-title">KEGG Analysis Details</div>
+   <table id="tripal_analysis_kegg-table-base" class="tripal_analysis_kegg-table tripal-table tripal-table-vert">
+      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
+        <th>Analysis Name</th>
+        <td><?php print $analysis->name; ?></td>
+      </tr>
+      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-odd-row">
+        <th nowrap>Software</th>
+        <td><?php 
+          print $analysis->program; 
+          if($analysis->programversion){
+             print " (" . $analysis->programversion . ")"; 
+          }
+          if($analysis->algorithm){
+             print ". " . $analysis->algorithm; 
+          }
+          ?>
+        </td>
+      </tr>
+      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
+        <th nowrap>Source</th>
+        <td><?php 
+          if($analysis->sourceuri){
+             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
+          } else {
+             print $analysis->sourcename; 
+          }
+          if($analysis->sourceversion){
+             print " (" . $analysis->sourceversion . ")"; 
+          }
+          ?>
+          </td>
+      </tr>
+      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-odd-row">
+        <th nowrap>Date performed</th>
+        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
+      </tr>
+      <tr class="tripal_analysis_kegg-table-odd-row tripal-table-even-row">
+        <th nowrap>Description</th>
+        <td><?php print $analysis->description; ?></td>
+      </tr>             	                                
+   </table>   
+</div>

theme_tripal/tripal_analysis_kegg/tripal_analysis_kegg_report.tpl.php

@@ -0,0 +1,11 @@
+<?php
+$analysis = $node->analysis;
+$report = $analysis->tripal_analysis_kegg->kegg_report;
+//dpm($analysis);
+?>
+
+<div id="tripal_analysis_kegg-report-box" class="tripal_analysis_kegg-box tripal-info-box">
+  <div class="tripal_analysis_kegg-info-box-title tripal-info-box-title">KEGG Report</div>
+  <div class="tripal_analysis_kegg-info-box-desc tripal-info-box-desc"><?php print $analysis->name ?></div>
+  <?php print $report ?>
+</div>

tripal_analysis_blast/tripal_analysis_blast.module

@@ -728,44 +728,9 @@ function chado_analysis_blast_submit_jobs($node){
  * Delete blast anlysis
  */
 function chado_analysis_blast_delete($node){
-	// Before removing, get analysis_id so we can remove it from chado database
+	chado_analysis_delete($node);
-	// later
-	$sql_drupal = "SELECT analysis_id ".
-                 "FROM {chado_analysis} ".
-                 "WHERE nid = %d ".
-                 "AND vid = %d";
-	$analysis_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));
-
-	// Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
-	$sql_del = "DELETE FROM {chado_analysis} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-	db_query($sql_del, $node->nid, $node->vid);
-	$sql_del = "DELETE FROM {node} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-	db_query($sql_del, $node->nid, $node->vid);
-	$sql_del = "DELETE FROM {node_revisions} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-	db_query($sql_del, $node->nid, $node->vid);
-
-	//Remove from analysisfeatureprop, analysisfeature, analysis, and analysisprop tables
-	$previous_db = tripal_db_set_active('chado');
-	$sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE analysis_id=%d";
-	$results = db_query($sql, $analysis_id);
-	while ($af = db_fetch_object($results)) {
-		db_query("DELETE FROM {analysisfeatureprop} WHERE analysisfeature_id = %d", $af->analysisfeature_id);
-	}
-	db_query("DELETE FROM {analysisfeature} WHERE analysis_id = %d", $analysis_id);
-	db_query("DELETE FROM {analysisprop} WHERE analysis_id = %d", $analysis_id);
-	db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
-	tripal_db_set_active($previous_db);
 }
 
-
-
-
 /*******************************************************************************
  *  This function customizes the view of the chado_analysis node.  It allows
  *  us to generate the markup.

tripal_analysis_kegg/tripal_analysis_kegg.module

@@ -49,7 +49,7 @@ function tripal_analysis_kegg_menu() {
    $items['tripal_analysis_kegg_org_report'] = array(
       'path' => 'tripal_analysis_kegg_org_report',
       'title' => t('Analysis KEGG report'),
-      'page callback' => 'tripal_analysis_kegg_org_report',
+      'page callback' => 'f',
       'page arguments' => array(1),
       'access arguments' => array('access chado_analysis_kegg content'),
       'type' => MENU_CALLBACK
@@ -176,95 +176,13 @@ function tripal_analysis_kegg_brite($analysis_id, $type_id, $ajax){
  *  Provide a KEGG Analysis form
  */
 function chado_analysis_kegg_form ($node){
+   // add in the default fields
+   $form = chado_analysis_form($node);
 
-   $type = node_get_types('type', $node);
+   // set the defaults
-   $form = array();
+   $kegg = $node->analysis->tripal_analysis_kegg;
-   $form['title']= array(
+   $hierfile = $kegg->hierfile;
-      '#type' => 'hidden',
-      '#default_value' => $node->title,
-   );
-   $form['analysisname']= array(
-      '#type' => 'textfield',
-      '#title' => t('Analysis Name'),
-      '#required' => FALSE,
-      '#default_value' => $node->analysisname,
-      '#weight' => 1
-   );
-   $form['program']= array(
-      '#type' => 'textfield',
-      '#title' => t('Program'),
-      '#required' => TRUE,
-      '#default_value' => $node->program,
-      '#weight' => 2
-   );
-   $form['programversion']= array(
-      '#type' => 'textfield',
-      '#title' => t('Program Version'),
-      '#required' => TRUE,
-      '#default_value' => $node->programversion,
-      '#weight' => 3
-   );
-   $form['algorithm']= array(
-      '#type' => 'textfield',
-      '#title' => t('Algorithm'),
-      '#required' => FALSE,
-      '#default_value' => $node->algorithm,
-      '#weight' => 4
-   );
-   $form['sourcename']= array(
-      '#type' => 'textfield',
-      '#title' => t('Source Name'),
-      '#required' => FALSE,
-      '#default_value' => $node->sourcename,
-      '#weight' => 5
-   );
-   $form['sourceversion']= array(
-      '#type' => 'textfield',
-      '#title' => t('Source Version'),
-      '#required' => FALSE,
-      '#default_value' => $node->sourceversion,
-      '#weight' => 6
-   );
-   $form['sourceuri']= array(
-      '#type' => 'textfield',
-      '#title' => t('Source URI'),
-      '#required' => FALSE,
-      '#default_value' => $node->sourceuri,
-      '#weight' => 7
-   );
-   // Get time saved in chado
-   $default_time = $node->timeexecuted;
-   $year = preg_replace("/^(\d+)-\d+-\d+ .*/", "$1", $default_time);
-   $month = preg_replace("/^\d+-0?(\d+)-\d+ .*/", "$1", $default_time);
-   $day = preg_replace("/^\d+-\d+-0?(\d+) .*/", "$1", $default_time);
-   // If the time is not set, use current time
-   if (!$default_time) {
-      $default_time = time();
-      $year = format_date($default_time, 'custom', 'Y');
-      $month = format_date($default_time, 'custom', 'n');
-      $day = format_date($default_time, 'custom', 'j');
-   }
-   $form['timeexecuted']= array(
-      '#type' => 'date',
-      '#title' => t('Time Executed'),
-      '#required' => TRUE,
-      '#default_value' => array(
-         'year' => $year,
-         'month' => $month,
-         'day' => $day,
-   ),
-      '#weight' => 8
-   );
-   $form['description']= array(
-      '#type' => 'textarea',
-      '#rows' => 15,
-      '#title' => t('Description and/or Program Settings'),
-      '#required' => FALSE,
-      '#default_value' => $node->description,
-      '#weight' => 9
-   );
 
-   //----KEGG/KAAS Settings (Shown only when Tripal KASS is enabled) ----
    $moreSettings ['kegg'] = 'KEGG Analysis Settings';
    $form['kegg'] = array(
       '#title' => t('KEGG Settings'),
@@ -280,7 +198,7 @@ function chado_analysis_kegg_form ($node){
       '#description' => t('The full path to the hier.tar.gz file generated by KAAS. 
                            Alternatively, you can input the full path to the directory
                            that contains decompressed kegg files.'),
-      '#default_value' => $node->hierfile,
+      '#default_value' => $hierfile,
    );
    $form['kegg']['keggjob'] = array(
       '#type' => 'checkbox',
@@ -289,7 +207,6 @@ function chado_analysis_kegg_form ($node){
                           'exist in chado before parsing the file. Otherwise, KEGG '.
                           'results that cannot be linked to a feature will be '.
                           'discarded.'),
-      '#default_value' => $node->keggjob,
    );
    return $form;
 }
@@ -297,268 +214,77 @@ function chado_analysis_kegg_form ($node){
  *
  */
 function chado_analysis_kegg_insert($node){
-   global $user;
+   // insert the analysis
-   // Create a timestamp so we can insert it into the chado database
+   chado_analysis_insert($node);
-   $time = $node->timeexecuted;
-   $month = $time['month'];
-   $day = $time['day'];
-   $year = $time['year'];
-   $timestamp = $month.'/'.$day.'/'.$year;
 
-   // If this analysis already exists then don't recreate it in chado
+   // set the type for this analysis
-   $analysis_id = $node->analysis_id;
+   tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_type','tripal_analysis_kegg');
-   if ($analysis_id) {
-      $sql = "SELECT analysis_id ".
-             "FROM {Analysis} ".
-             "WHERE analysis_id = %d ";
-      $previous_db = tripal_db_set_active('chado');
-      $analysis = db_fetch_object(db_query($sql, $node->analysis_id));
-      tripal_db_set_active($previous_db);
-   }
-
-   // If the analysis doesn't exist then let's create it in chado.
-   if(!$analysis){
-      // First add the item to the chado analysis table
-      $sql = "INSERT INTO {analysis} ".
-             "  (name, description, program, programversion, algorithm, ".
-             "   sourcename, sourceversion, sourceuri, timeexecuted) ".
-             "VALUES ('%s','%s','%s','%s','%s','%s','%s','%s','%s')";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      db_query($sql,$node->analysisname, $node->description,
-      $node->program,$node->programversion,$node->algorithm,
-      $node->sourcename, $node->sourceversion, $node->sourceuri,
-      $timestamp);
 
-      // find the newly entered analysis_id
+   // now add in the remaining settings as a single property but separated by bars
-      $sql = "SELECT analysis_id ".
+   tripal_analysis_insert_property($node->analysis_id,'analysis_kegg_settings',$node->hierfile);
-             "FROM {Analysis} ".
+     
-             "WHERE program='%s'".
+   // Add a job if the user wants to parse the html output
-             "AND programversion='%s'".
+   chado_analysis_kegg_submit_job($node);
-             "AND sourcename='%s'";
+}
-      $analysis_id = db_result(db_query($sql, $node->program,
+/**
-      $node->programversion, $node->sourcename));
+*
-
+*/
-      // Get cvterm_id for 'analysis_kegg_settings'
+function chado_analysis_kegg_submit_job($node){
-      $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
+   global $user;
-             "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
-             "WHERE CVT.name = 'analysis_kegg_settings' ".
-             "AND CV.name = 'tripal'";
-      $type_id = db_result(db_query($sql));
-      
-      // Insert the analysis type into the analysisprop table
-      $sql = "
-         INSERT INTO {analysisprop} (analysis_id, type_id, value) 
-         VALUES (%d, %d, '%s')
-      ";
-      $keggsettings = $node->hierfile;
-      db_query($sql, $analysis_id, $type_id, $keggsettings);
-
-      tripal_db_set_active($previous_db);  // switch back to drupal database
-      // Add a job if the user wants to parse the html output
-      if($node->keggjob) {
-         $job_args[0] = $analysis_id;
-         $job_args[1] = $node->hierfile;
-         $job_args[2] = base_path();
-         if (is_readable($node->hierfile)) {
-         	$fname = preg_replace("/.*\/(.*)/", "$1", $node->hierfile);
-            tripal_add_job("Parse KAAS output: $fname",'tripal_analysis_kegg',
-                           'tripal_analysis_kegg_parseHierFile', $job_args, $user->uid);
-         } else {
-            drupal_set_message("Can not open KAAS hier.tar.gz output file. Job not scheduled.");
-         }
-      }
-   }
 
-   // Make sure the entry for this analysis doesn't already exist in the
+   if($node->keggjob) {
-   // chado_analysis table if it doesn't exist then we want to add it.
+      $job_args[0] = $analysis_id;
-   $node_check_sql = "SELECT * FROM {chado_analysis} ".
+      $job_args[1] = $node->hierfile;
-                     "WHERE analysis_id = %d";
+      $job_args[2] = base_path();
-   $node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
+      if (is_readable($node->hierfile)) {
-   if(!$node_check){
+      	$fname = preg_replace("/.*\/(.*)/", "$1", $node->hierfile);
-      // next add the item to the drupal table
+         tripal_add_job("Parse KAAS output: $fname",'tripal_analysis_kegg',
-      $sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) ".
+                        'tripal_analysis_kegg_parseHierFile', $job_args, $user->uid);
-             "VALUES (%d, %d, %d)";
-      db_query($sql,$node->nid,$node->vid,$analysis_id);
-      // Create a title for the analysis node using the unique keys so when the
-      // node is saved, it will have a title
-      $record = new stdClass();
-      // If the analysis has a name, use it as the node title. If not, construct
-      // the title using program, programversion, and sourcename
-      if ($node->analysisname) {
-         $record->title = $node->analysisname;
       } else {
-         //Construct node title as "program (version)
+         drupal_set_message("Can not open KAAS hier.tar.gz output file. Job not scheduled.");
-         $record->title = "$node->program ($node->programversion)";
       }
-      $record->nid = $node->nid;
-      drupal_write_record('node',$record,'nid');
-      drupal_write_record('node_revisions',$record,'nid');
    }
 }
 /*******************************************************************************
  * Delete KEGG anlysis
  */
 function chado_analysis_kegg_delete($node){
-   // Before removing, get analysis_id so we can remove it from chado database
+   chado_analysis_delete($node);
-   // later
-   $sql_drupal = "SELECT analysis_id ".
-                 "FROM {chado_analysis} ".
-                 "WHERE nid = %d ".
-                 "AND vid = %d";
-   $analysis_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));
-
-   // Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
-   $sql_del = "DELETE FROM {chado_analysis} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-   db_query($sql_del, $node->nid, $node->vid);
-   $sql_del = "DELETE FROM {node} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-   db_query($sql_del, $node->nid, $node->vid);
-   $sql_del = "DELETE FROM {node_revisions} ".
-              "WHERE nid = %d ".
-              "AND vid = %d";
-   db_query($sql_del, $node->nid, $node->vid);
-
-   //Remove from analysisfeatureprop, analysisfeature, analysis, and analysisprop tables
-   $previous_db = tripal_db_set_active('chado');
-   $sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE analysis_id=%d";
-   $results = db_query($sql, $analysis_id);
-   while ($af = db_fetch_object($results)) {
-      db_query("DELETE FROM {analysisfeatureprop} WHERE analysisfeature_id = %d", $af->analysisfeature_id);
-   }
-   db_query("DELETE FROM {analysisfeature} WHERE analysis_id = %d", $analysis_id);
-   db_query("DELETE FROM {analysisprop} WHERE analysis_id = %d", $analysis_id);
-   db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
-   tripal_db_set_active($previous_db);
 }
 
 /*******************************************************************************
  * Update KEGG analysis
  */
 function chado_analysis_kegg_update($node){
-   global $user;
+   // insert the analysis
-   if($node->revision){
+   chado_analysis_update($node);
-      // TODO -- decide what to do about revisions
-   } else {
-      // Create a timestamp so we can insert it into the chado database
-      $time = $node->timeexecuted;
-      $month = $time['month'];
-      $day = $time['day'];
-      $year = $time['year'];
-      $timestamp = $month.'/'.$day.'/'.$year;
 
-      // get the analysis_id for this node:
+   // set the type for this analysis
-      $sql = "SELECT analysis_id ".
+   tripal_analysis_update_property($node->analysis->analysis_id,'analysis_type','tripal_analysis_kegg',1);
-             "FROM {chado_analysis} ".
-             "WHERE vid = %d";
-      $analysis_id = db_fetch_object(db_query($sql, $node->vid))->analysis_id;
-
-      $sql = "UPDATE {analysis} ".
-             "SET name = '%s', ".
-             "    description = '%s', ".
-             "    program = '%s', ".
-             "    programversion = '%s', ".
-             "    algorithm = '%s', ".
-             "    sourcename = '%s', ".
-             "    sourceversion = '%s', ".
-             "    sourceuri = '%s', ".
-             "    timeexecuted = '%s' ".
-             "WHERE analysis_id = %d ";
-
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      db_query($sql, $node->analysisname, $node->description, $node->program,
-      $node->programversion,$node->algorithm,$node->sourcename,
-      $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
-
-      // Get cvterm_id for 'analysis_kegg_settings'
-      $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-             "INNER JOIN cv CV ON CV.cv_id = CVT.cv_id ".
-             "WHERE CVT.name = 'analysis_kegg_settings' ".
-             "AND CV.name = 'tripal'";
-      $type_id = db_result(db_query($sql));
-       
-      $sql = "UPDATE {analysisprop} ".
-             "SET value = '%s' ".
-             "WHERE analysis_id = %d AND type_id = %d";
-      $keggsettings = $node->hierfile;
-      db_query($sql, $keggsettings, $analysis_id, $type_id);
-
-      tripal_db_set_active($previous_db);  // switch back to drupal database
-      // Add a job if the user wants to parse the html output
-      if($node->keggjob) {
-         $job_args[0] = $analysis_id;
-         $job_args[1] = $node->hierfile;
-         $job_args[2] = base_path();
-         if (is_readable($node->hierfile)) {
-         	$fname = preg_replace("/.*\/(.*)/", "$1", $node->hierfile);
-            tripal_add_job("Parse KAAS output: $fname",'tripal_analysis_kegg',
-                           'tripal_analysis_kegg_parseHierFile', $job_args, $user->uid);
-         } else {
-            drupal_set_message("Can not open KAAS hier.tar.gz output file. Job not scheduled.");
-         }
-      }
 
-      // Create a title for the analysis node using the unique keys so when the
+   // now add in the remaining settings as a single property but separated by bars
-      // node is saved, it will have a title
+   tripal_analysis_update_property($node->analysis_id,'analysis_kegg_settings',$node->hierfile,1);
-      $record = new stdClass();
+     
-      // If the analysis has a name, use it as the node title. If not, construct
+   // Add a job if the user wants to parse the html output
-      // the title using program, programversion, and sourcename
+   chado_analysis_kegg_submit_job($node);
-      if ($node->analysisname) {
-         $record->title = $node->analysisname;
-      } else {
-         //Construct node title as "program (version)
-         $record->title = "$node->program ($node->programversion)";
-      }
-      $record->nid = $node->nid;
-      drupal_write_record('node',$record,'nid');
-      drupal_write_record('node_revisions',$record,'nid');
-   }
 }
 /*******************************************************************************
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  */
 function chado_analysis_kegg_load($node){
-   // get the analysis_id for this node:
-   $sql = "SELECT analysis_id FROM {chado_analysis} WHERE vid = %d";
-   $ana_node = db_fetch_object(db_query($sql, $node->vid));
-   $additions = new stdClass();
-   if ($ana_node) {
-      // get analysis information
-      $sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
-             "  programversion, algorithm, sourcename, sourceversion, ".
-             "  sourceuri, timeexecuted ".
-             "FROM {Analysis} ".
-             "WHERE Analysis_id = $ana_node->analysis_id";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $additions = db_fetch_object(db_query($sql));
 
-      // get cvterm_id for 'analysis_kegg_settings'
+   // load the default set of analysis fields
-      $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
+	$additions = chado_analysis_load($node);
-             "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
+
-             "WHERE CVT.name = 'analysis_kegg_settings' ".
+   // create some variables for easier lookup
-             "AND CV.name = 'tripal'";
+   $analysis = $additions->analysis;
-      $type_id = db_result(db_query($sql));
+   $analysis_id = $analysis->analysis_id;
-      // get analysisprop information
+
-      $sql = "SELECT value FROM {analysisprop} ".
+   // get the heirfile name
-             "WHERE analysis_id = %d ".
+   $hierfile  = tripal_analysis_get_property($analysis_id,'analysis_kegg_settings');	
-             "AND type_id = %d";
+   $analysis->tripal_analysis_kegg->hierfile = $hierfile->value;
-      $analysisprop = db_result(db_query($sql, $ana_node->analysis_id, $type_id));
-      
-      $additions->hierfile = $analysisprop;
 
-      tripal_db_set_active($previous_db);  // now use drupal database
-   }
-   // If the analysis has a name, use it as the node title. If not, construct
-   // the title using program programversion, and sourcename
-   if ($additions->analysisname) {
-      $additions->title = $additions->analysisname;
-   } else {
-      // Construct node title as "program version (source)
-      $additions->title = "$additions->program ($additions->programversion)";
-   }
    return $additions;
 }
 
@@ -864,8 +590,27 @@ function tripal_analysis_kegg_theme () {
          'arguments' => array('node'=> null),
          'template' => 'tripal_organism_kegg_summary',
       ),
+      'tripal_analysis_kegg_report' => array (
+         'arguments' => array('node'=> null),
+         'template' => 'tripal_analysis_kegg_report',
+      ),
    );
 }
+/**
+ *  
+ *
+ * @ingroup tripal_analysis_kegg
+ */
+function tripal_analysis_kegg_preprocess(&$variables){
+
+   // if the template file is the default node template file then we want
+   // to add all of our variables.
+   if($variables['template_files'][0] == 'node-chado_analysis_kegg'){
+      $analysis = $variables['node']->analysis;
+      $report = tripal_analysis_kegg_full_report($analysis->analysis_id);
+      $analysis->tripal_analysis_kegg->kegg_report = $report;
+   }
+}
 /*******************************************************************************
  *  
  */

tripal_analysis_unigene/tripal_analysis_unigene.module

@@ -66,7 +66,8 @@ function chado_analysis_unigene_access($op, $node, $account){
 */
 function chado_analysis_unigene_form ($node){
 
-	$form = array();
+   // add in the default fields
+   $form = chado_analysis_form($node);
 
    $unigene = $node->analysis->tripal_analysis_unigene;
    $unigene_name = $unigene->unigene_name;
@@ -114,15 +115,6 @@ function chado_analysis_unigene_form ($node){
       '#description' => t('Provide the number of singlets remaining in the assembly'),
       '#default_value' => $num_singlets,
 	);
-
-
-
-   // add in the analysis fields
-   $analysis_form_elements = chado_analysis_form($node);
-   foreach ($analysis_form_elements as $key => $element){
-      $form[$key] = $element;
-   }
-   return $form;
 }
 /**
 *
@@ -155,9 +147,6 @@ function chado_analysis_unigene_update($node){
 *
 */
 function chado_analysis_unigene_delete($node){
-  // delete the unigene name as a property of the anslysis
-//  tripal_analysis_delete_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);	
-
   chado_analysis_delete($node);
 }
 /**

tripal_organism/tripal_organism.module

@@ -117,26 +117,16 @@ function tripal_organism_menu() {
  *  perform actions on data managed by this module
  */
 function chado_organism_access($op, $node, $account){
-  if ($op == 'create') {
+   switch ($op){
-      return user_access('create chado_organism content', $account);
+      case 'create': 
+        return user_access('create chado_organism content', $account);
+      case 'update':
+        return user_access('edit chado_organism content', $account);
+      case 'delete':
+        return user_access('delete chado_organism content', $account);
+      case 'view' :
+        return user_access('access chado_organism content', $account);
    }
-
-   if ($op == 'update') {
-      if (user_access('edit chado_organism content', $account)) {
-         return TRUE;
-      }
-   }
-   if ($op == 'delete') {
-      if (user_access('delete chado_organism content', $account)) {
-         return TRUE;
-      }
-   }
-   if ($op == 'view') {
-      if (user_access('access chado_organism content', $account)) {
-         return TRUE;
-      }
-   }
-   return FALSE;
 }
 /*******************************************************************************
 *  Set the permission types that the chado module uses.  Essentially we