Many bug fixes, and theme updates

theme_tripal/css/tripal.css

@@ -106,3 +106,58 @@ table.tripal-table-horz .tripal-table-odd-row {
    padding: 10px;
    background-color: #FFEEEE;
 }
+
+.tripal_toc {
+  float: left;
+  width: 20%;
+  background-color: #EEEEEE;
+
+  -moz-border-radius: 15px;
+  -webkit-border-radius: 15px;
+  -khtml-border-radius: 15px;
+  border-radius: 15px;
+
+  -moz-box-shadow: 3px 3px 4px #888888;
+  -webkit-box-shadow: 3px 3px 4px #888888;
+  box-shadow: 3px 3px 4px #888888;
+
+
+
+  padding: 20px;
+  min-height: 500px;
+  border-style:solid;
+  border-width:1px;
+}
+.tripal_toc ul {
+ margin-left: 0px;
+ margin-top: 5px;
+ padding-left: 15px;
+}
+.tripal_toc_title {
+  font-size: 1.5em;
+  line-height: 110%;
+  padding-bottom: 10px;
+}
+.tripal_toc_desc {
+ /*font-style: italic; */
+}
+.tripal_details {
+  float: left;
+  width: 69%;
+  background-color: #FFFFFF;
+
+  -moz-border-radius: 15px;
+  -webkit-border-radius: 15px;
+  -khtml-border-radius: 15px;
+  border-radius: 15px;
+
+  -moz-box-shadow: 3px 3px 4px #888888;
+  -webkit-box-shadow: 3px 3px 4px #888888;
+  box-shadow: 3px 3px 4px #888888;
+  padding: 20px;
+  min-height: 500px;
+  margin-right: 10px;
+  margin-bottom: 10px;
+  border-style:solid;
+  border-width:1px;
+}

theme_tripal/css/tripal_analysis_interpro.css

@@ -32,3 +32,13 @@
 .tripal_interpro_results_table tbody tr td table tr td{
    background: #FFFFFF;
 }
+/* feature node sepcific template */
+.tripal_feature_interpro-results-table {
+   padding-top: 10px;
+   padding-bottom: 10px;
+}
+.tripal_feature-interpro_results_subtitle{
+   padding-top: 10px;
+   padding-bottom: 10px;
+   font-weight: bold;
+}

theme_tripal/css/tripal_feature.css

@@ -67,3 +67,4 @@ table.tripal_feature-references-table th {
    float: none;
    display: block;
 }
+

theme_tripal/css/tripal_organism.css

@@ -17,3 +17,15 @@
    clear: left;
    width: auto;
 }
+
+#tripal_organism-base-box img {
+ float: left;
+ margin-bottom: 10px;
+}
+#tripal_organism-table-base {
+ float: left;
+ width: 330px;
+ margin-left: 10px;
+ margin-bottom: 10px;
+}
+

theme_tripal/js/tripal.js

@@ -1,6 +1,7 @@
 
 
 if (Drupal.jsEnabled) {
+
    //------------------------------------------------------------
    // On document load we want to make sure the analysis result is shown
    var path = '';
@@ -108,4 +109,6 @@ if (Drupal.jsEnabled) {
        }
        return baseurl;
    }
+
+   
 }

theme_tripal/node-chado_analysis.tpl.php

@@ -25,6 +25,8 @@
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
 
+drupal_add_css('./tripal-node-templates.css');
+
 $node = $variables['node'];
 $organism = $variables['node']->organism;
 ?>
@@ -77,66 +79,7 @@ if (Drupal.jsEnabled) {
 }
 </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 #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     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 #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     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">
+<div id="tripal_analysis_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_analysis/tripal_analysis_base.tpl.php'); ?>
@@ -145,10 +88,10 @@ if (Drupal.jsEnabled) {
 </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">
+<div id="tripal_analysis_toc" class="tripal_toc">
+   <div id="tripal_analysis_toc_title" class="tripal_toc_title">Resources</i></div>
+   <span id="tripal_analysis_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_toc_list"  class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_analysis_blast.tpl.php

@@ -24,6 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
+drupal_add_css('./tripal-node-templates.css');
 
 $node = $variables['node'];
 $organism = $variables['node']->organism;
@@ -76,66 +77,8 @@ if (Drupal.jsEnabled) {
 }
 </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_blast_toc {
-     float: left;
-     width: 20%;
-     background-color: #EEEEEE;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_analysis_blast_toc ul {
-    margin-left: 0px;
-    margin-top: 5px;
-    padding-left: 15px;
-  }
-  #tripal_analysis_blast_toc_title {
-     font-size: 1.5em;
-     line-height: 110%;
-  }
-  #tripal_analysis_blast_toc_desc {
-    /*font-style: italic; */
-  }
-  #tripal_analysis_blast_details {
-     float: left;
-     width: 70%;
-     background-color: #FFFFFF;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     margin-right: 10px;
-     margin-bottom: 10px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_analysis_blast-base-box img {
-    float: left;
-    margin-bottom: 10px;
-  }
-  #tripal_analysis_blast-table-base {
-    float: left;
-    width: 100%;
-    margin-left: 0px;
-    margin-bottom: 10px;
-  }
-</style>
 
-
-<div id="tripal_analysis_blast_details">
+<div id="tripal_analysis_blast_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_analysis_blast/tripal_analysis_blast_base.tpl.php'); ?>
@@ -144,10 +87,10 @@ if (Drupal.jsEnabled) {
 </div>
 
 <!-- Table of contents -->
-<div id="tripal_analysis_blast_toc">
-   <div id="tripal_analysis_blast_toc_title">Resources</i></div>
-   <span id="tripal_analysis_blast_toc_desc">Select a link below for more information</span>
-   <ul id="tripal_analysis_blast_toc_list">
+<div id="tripal_analysis_blast_toc" class="tripal_toc">
+   <div id="tripal_analysis_blast_toc_title" class="tripal_toc_title">Resources</i></div>
+   <span id="tripal_analysis_blast_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_blast_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_analysis_interpro.tpl.php

@@ -1,70 +1,98 @@
 <?php
+// Purpose: This template provides the layout of the organism node (page)
+//   using the same templates used for the various feature content blocks.
+//
+// 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
+ //uncomment this line to see a full listing of the fields avail. to $node
+ //print '<pre>'.print_r($variables,TRUE).'</pre>';
+drupal_add_css('./tripal-node-templates.css');
 
+$node = $variables['node'];
+$organism = $variables['node']->organism;
 ?>
 
-   <?php if ($picture) {
-      print $picture;
-   }?>
-    
-   <div class="node<?php if ($sticky) { print " sticky"; } ?><?php if (!$status) { print " node-unpublished"; } ?>">
+<?php if ($teaser) { 
+  include('tripal_analysis_interpro/tripal_analysis_interpro_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_interpro_toc_list').append('<li><a href="#'+id+'" class="tripal_analysis_interpro_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_interpro_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
+         $("#tripal_analysis_interpro_toc").height($(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_interpro-"+block_title+"-box").show();
+      } else {
+         $("#tripal_analysis_interpro-base-box").show();
+      }
+
+      $("#tripal_analysis_interpro_toc").height($("#tripal_analysis_interpro-base-box").parent().height());
+      
+   });
+}
+</script>
+
+
+<div id="tripal_analysis_interpro_details" class="tripal_details">
+
+   <!-- Basic Details Theme -->
+   <?php include('tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php'); ?>
+
+   <?php print $content ?>
+</div>
+
+<!-- Table of contents -->
+<div id="tripal_analysis_interpro_toc" class="tripal_toc">
+   <div id="tripal_analysis_interpro_toc_title" class="tripal_toc_title">Resources</i></div>
+   <span id="tripal_analysis_interpro_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_interpro_toc_list" class="tripal_toc_list">
+
+   </ul>
+</div>
 
-   <?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" />'; } ?>
-	</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_interpro 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>Interpro Settings</th>
-              <td>
-                <b>File:</b>
-                  <?php print preg_replace("/.*\/(.*)/", "$1", $node->interprofile); ?><br>
-                <b>Parameters:</b>
-                  <?php print $node->interproparameters?><br>
-                  <?php if ($node->interprojob) {
-                           print "A job for parsing interpro html output will be submitted.";
-                           if ($node->parsego) {
-                              print "<BR>GO terms will be parsed and stored.";
-                           }
-                        }
-                  ?>
-              </td>
-            </tr>
-         </table>
-      <!-- End of tripal_analysis_interpro 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>
+<?php } ?>

theme_tripal/node-chado_analysis_kegg.tpl.php

@@ -24,7 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
-
+drupal_add_css('./tripal-node-templates.css');
 $node = $variables['node'];
 $organism = $variables['node']->organism;
 ?>
@@ -77,66 +77,8 @@ if (Drupal.jsEnabled) {
 }
 </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 #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     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 #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     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">
+<div id="tripal_analysis_kegg_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php'); ?>
@@ -146,10 +88,10 @@ if (Drupal.jsEnabled) {
 </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">
+<div id="tripal_analysis_kegg_toc" class="tripal_toc">
+   <div id="tripal_analysis_kegg_toc_title" class="tripal_toc_title">Resources</i></div>
+   <span id="tripal_analysis_kegg_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_kegg_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_analysis_unigene.tpl.php

@@ -24,7 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
 // print '<pre>'.print_r($node,TRUE).'</pre>';
-
+drupal_add_css('./tripal-node-templates.css');
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
 $unigene_name = $analysis->tripal_analysis_unigene->unigene_name;
@@ -81,66 +81,7 @@ if (Drupal.jsEnabled) {
 }
 </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_unigene_toc {
-     float: left;
-     width: 20%;
-     background-color: #EEEEEE;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_analysis_unigene_toc ul {
-    margin-left: 0px;
-    margin-top: 5px;
-    padding-left: 15px;
-  }
-  #tripal_analysis_unigene_toc_title {
-     font-size: 1.5em;
-     line-height: 110%;
-  }
-  #tripal_analysis_unigene_toc_desc {
-    font-style: italic;
-  }
-  #tripal_analysis_unigene_details {
-     float: left;
-     width: 70%;
-     background-color: #FFFFFF;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     margin-right: 10px;
-     margin-bottom: 10px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_analysis_unigene-base-box img {
-    float: left;
-    margin-bottom: 10px;
-  }
-  #tripal_analysis_unigene-table-base {
-    float: left;
-    width: 100%;
-    margin-left: 0px;
-    margin-bottom: 10px;
-  }
-</style>
-
-
-<div id="tripal_analysis_unigene_details">
+<div id="tripal_analysis_unigene_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php'); ?>
@@ -149,10 +90,10 @@ if (Drupal.jsEnabled) {
 </div>
 
 <!-- Table of contents -->
-<div id="tripal_analysis_unigene_toc">
-   <div id="tripal_analysis_unigene_toc_title">Resources for Unigene <?php print $unigene_name ?></div>
-   <span id="tripal_analysis_unigene_toc_desc">Select a link below for more information</span>
-   <ul id="tripal_analysis_unigene_toc_list">
+<div id="tripal_analysis_unigene_toc" class="tripal_toc">
+   <div id="tripal_analysis_unigene_toc_title" class="tripal_toc_title">Resources for Unigene <?php print $unigene_name ?></div>
+   <span id="tripal_analysis_unigene_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_analysis_unigene_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_feature.tpl.php

@@ -24,6 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
+drupal_add_css('./tripal-node-templates.css');
 $feature  = $variables['node']->feature;
 ?>
 
@@ -73,56 +74,7 @@ if (Drupal.jsEnabled) {
 }
 </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_feature_toc {
-     float: left;
-     width: 20%;
-     background-color: #EEEEEE;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_feature_toc ul {
-    margin-left: 0px;
-    margin-top: 5px;
-    padding-left: 15px;
-  }
-  #tripal_feature_toc_title {
-     font-size: 1.5em;
-     line-height: 110%;
-  }
-  #tripal_feature_toc_desc {
-    font-style: italic;
-  }
-  #tripal_feature_details {
-     float: left;
-     width: 70%;
-     background-color: #FFFFFF;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     margin-right: 10px;
-     margin-bottom: 10px;
-     border-style:solid;
-     border-width:1px;
-  }
-</style>
-
-
-<div id="tripal_feature_details">
+<div id="tripal_feature_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_feature/tripal_feature_base.tpl.php'); ?>
@@ -158,10 +110,10 @@ if (Drupal.jsEnabled) {
 </div>
 
 <!-- Table of contents -->
-<div id="tripal_feature_toc">
-   <div id="tripal_feature_toc_title">Resources for <?php print $feature->cvname?><br><?php print $feature->featurename ?></div>
-   <span id="tripal_feature_toc_desc">Select a link below for more information</span>
-   <ul id="tripal_feature_toc_list">
+<div id="tripal_feature_toc" class="tripal_toc">
+   <div id="tripal_feature_toc_title" class="tripal_toc_title">Resources for <?php print $feature->cvname?><br><?php print $feature->featurename ?></div>
+   <span id="tripal_feature_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_feature_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_library.tpl.php

@@ -1,7 +1,5 @@
 <?php
-/*
- Copyright 2009 Clemson University
-*/
+
 ?>
 
    <?php if ($picture) { print $picture; }?>

theme_tripal/node-chado_organism.tpl.php

@@ -24,7 +24,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($variables,TRUE).'</pre>';
-
+drupal_add_css('./tripal-node-templates.css');
 $node = $variables['node'];
 $organism = $variables['node']->organism;
 ?>
@@ -79,66 +79,9 @@ if (Drupal.jsEnabled) {
 }
 </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_organism_toc {
-     float: left;
-     width: 20%;
-     background-color: #EEEEEE;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_organism_toc ul {
-    margin-left: 0px;
-    margin-top: 5px;
-    padding-left: 15px;
-  }
-  #tripal_organism_toc_title {
-     font-size: 1.5em;
-     line-height: 110%;
-  }
-  #tripal_organism_toc_desc {
-    /*font-style: italic; */
-  }
-  #tripal_organism_details {
-     float: left;
-     width: 70%;
-     background-color: #FFFFFF;
-     -moz-border-radius: 15px;
-     border-radius: 15px;
-     -moz-box-shadow: 3px 3px 4px #888888;
-	  -webkit-box-shadow: 3px 3px 4px #888888;
-	  box-shadow: 3px 3px 4px #888888;
-     padding: 20px;
-     min-height: 500px;
-     margin-right: 10px;
-     margin-bottom: 10px;
-     border-style:solid;
-     border-width:1px;
-  }
-  #tripal_organism-base-box img {
-    float: left;
-    margin-bottom: 10px;
-  }
-  #tripal_organism-table-base {
-    float: left;
-    width: 330px;
-    margin-left: 10px;
-    margin-bottom: 10px;
-  }
-</style>
 
 
-<div id="tripal_organism_details">
+<div id="tripal_organism_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
    <?php include('tripal_organism/tripal_organism_base.tpl.php'); ?>
@@ -147,10 +90,10 @@ if (Drupal.jsEnabled) {
 </div>
 
 <!-- Table of contents -->
-<div id="tripal_organism_toc">
-   <div id="tripal_organism_toc_title">Resources for <br><i><?php print $organism->genus ?> <?php print $organism->species ?></i></div>
-   <span id="tripal_organism_toc_desc">Select a link below for more information</span>
-   <ul id="tripal_organism_toc_list">
+<div id="tripal_organism_toc" class="tripal_toc">
+   <div id="tripal_organism_toc_title" class="tripal_toc_title">Resources for <br><i><?php print $organism->genus ?> <?php print $organism->species ?></i></div>
+   <span id="tripal_organism_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_organism_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/node-chado_stock.tpl.php

@@ -26,6 +26,7 @@
 <?php
  //uncomment this line to see a full listing of the fields avail. to $node
  //print '<pre>'.print_r($node,TRUE).'</pre>';
+drupal_add_css('./tripal-node-templates.css');
 ?>
 
 <?php if ($teaser) { 
@@ -130,7 +131,7 @@
   }
 </style>
 
-<div id="tripal_stock_details">
+<div id="tripal_stock_details" class="tripal_details">
 
   <!-- Base Theme -->
   <?php include('tripal_stock/tripal_stock_base.tpl.php'); ?>
@@ -152,10 +153,10 @@
 </div>
 
 <!-- Table of contents -->
-<div id="tripal_stock_toc">
-   <div id="tripal_stock_toc_title"><?php print $node->stock_name ?></div>
-   <span id="tripal_stock_toc_desc">Select a link below for more information</span>
-   <ul id="tripal_stock_toc_list">
+<div id="tripal_stock_toc" class="tripal_toc">
+   <div id="tripal_stock_toc_title" class="tripal_toc_title"><?php print $node->stock_name ?></div>
+   <span id="tripal_stock_toc_desc" class="tripal_toc_desc">Select a link below for more information</span>
+   <ul id="tripal_stock_toc_list" class="tripal_toc_list">
 
    </ul>
 </div>

theme_tripal/tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php

@@ -0,0 +1,54 @@
+<?php
+$node = $variables['node'];
+$analysis = $variables['node']->analysis;
+$interpro = $node->analysis->tripal_analysis_interpro;
+
+?>
+<div id="tripal_analysis_interpro-base-box" class="tripal_analysis_interpro-info-box tripal-info-box">
+  <div class="tripal_analysis_interpro-info-box-title tripal-info-box-title">Details</div>
+   <table id="tripal_analysis_interpro-table-base" class="tripal_analysis_interpro-table tripal-table tripal-table-vert">
+      <tr class="tripal_analysis_interpro-table-even-row tripal-table-even-row">
+        <th>Analysis Name</th>
+        <td><?php print $analysis->name; ?></td>
+      </tr>
+      <tr class="tripal_analysis_interpro-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 ". " . $analysis->algorithm; 
+          }
+          ?>
+        </td>
+      </tr>
+      <tr class="tripal_analysis_interpro-table-even-row tripal-table-even-row">
+        <th nowrap>Source</th>
+        <td><?php 
+          if($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_interpro-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_interpro-table-even-row tripal-table-even-row">
+        <th nowrap>Description</th>
+        <td><?php print $analysis->description; ?></td>
+      </tr>      
+      <tr class="tripal_analysis_interpro-table-odd-row tripal-table-odd-row">
+        <th nowrap>InterProScan Arguments</th>
+        <td><?php print $interpro->interproparameters ?></td>
+      </tr>        	                                
+   </table>   
+</div>

theme_tripal/tripal_feature/tripal_feature_interpro_results.tpl.php

@@ -1,13 +1,104 @@
 <?php
 $results = $variables['tripal_analysis_interpro']['results'];
+$feature  = $variables['node']->feature;
+//dpm($results);
+if($feature->cvname != 'gene' and count($results) > 0){ 
+   $i = 0;
+   foreach($results as $analysis_id => $analysisprops){ 
+     $analysis = $analysisprops['analysis'];
+     $protein_ORFs = $analysisprops['protein_ORFs']; 
+     $terms = $analysisprops['allterms']; 
+     ?>
+     <div id="tripal_feature-interpro_results_<?php print $i?>-box" class="tripal_analysis_interpro-box tripal-info-box">
+        <div class="tripal_feature-info-box-title tripal-info-box-title">InterPro Report <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></div>
+        <div class="tripal_feature-info-box-desc tripal-info-box-desc"><?php 
+            if($analysis->nid){ ?>
+               Analysis name: <a href="<?php print url('node/'.$analysis->nid) ?>"><?php print $analysis->name?></a><?php
+            } else { ?>
+               Analysis name: <?php print $analysis->name;
+            } ?><br>
+            Date Performed: <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?>
+        </div>
+
+     <div class="tripal_feature-interpro_results_subtitle">Summary of Annotated IPR terms</div>
+     <table id="tripal_feature-interpro_summary-<?php $i ?>-table" class="tripal_analysis_interpro-summary-table tripal-table tripal-table-horz">
+      <tr>
+        <th>Term</td>
+        <th>Name</td>
+      </tr>
+     <?php 
+     $j=0;
+     foreach($terms as $term){ 
+       $ipr_id = $term[0];
+       $ipr_name = $term[1];
+       $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+       if($j % 2 == 0 ){
+         $class = 'tripal_feature-table-even-row tripal-table-even-row';
+       }?>
+       <tr class="<?php print $class ?>">
+         <td><?php print $ipr_id ?></td>
+         <td><?php print $ipr_name ?></td>         
+       </tr>
+       <?php
+       $j++;
+     } ?>
+     </table>
+     <br><br>
+     <div class="tripal_feature-interpro_results_subtitle">Analysis Details</div>
+     <table id="tripal_feature-interpro_results-<?php $i ?>-table" class="tripal-table tripal_feature_interpro-results-table tripal-table-horz" style="border-top: 0px; border-bottom: 0px">
+     <?php
+     foreach($protein_ORFs as $orf){  
+        $terms = $orf['terms'];
+        $orf = $orf['orf'];  
+        ?>
+        <?php foreach($terms as $term){ 
+          $matches = $term['matches'];
+          $ipr_id = $term['ipr_id'];
+          $ipr_name = $term['ipr_name'];
+          $ipr_type = $term['ipr_type']; ?>          
+            <tr>
+              <td colspan="4" style="padding-left: 0px">ORF: <?php print $orf['orf_id'] ?>, Length: <?php print $orf['orf_length'] ?> <br>
+                              IPR Term: <?php print "$ipr_id $ipr_name ($ipr_type)"; ?></th>
+            </tr>
+            <tr style="border-top: solid 1px;">
+              <th>Method</th>
+              <th>Identifier</th>
+              <th>Description</th>
+              <th>Matches</th>
+            </tr>
+            <?php $j = 0; 
+            foreach ($matches as $match){
+               $match_id = $match['match_id'];
+               $match_name = $match['match_name'];
+               $match_dbname = $match['match_dbname'];
+               $match_start = $match['match_start'];
+               $match_end = $match['match_end'];
+               $match_score = $match['match_score'];
+               $match_status = $match['match_status'];
+               $match_evidence =  $match['match_evidence'];
+
+               $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+               if($j % 2 == 0 ){
+                  $class = 'tripal_feature-table-even-row tripal-table-even-row';
+               }?>
+               <tr class="<?php print $class ?>">
+                <td><?php print $match_dbname ?></td>
+                <td><?php print $match_id ?></td>
+                <td><?php print $match_name ?></td>
+                <td nowrap>Score: <?php print $match_score ?> <br>
+                    Position: <?php print $match_start ?>..<?php print $match_end ?><br>
+                    Status: <?php print $match_status ?></td>
+               </tr>
+               <?php
+               $j++;  
+            } // end foreach matches ?>
+            <tr><td colspan="4">&nbsp;</td></tr> <?php
+        } // end foreach terms
+        $i++;
+     } // end foreach orfs ?>
+     </table>
+     </div> <?php
+   } // end for each analysis 
+} // end if
 ?>
 
-<div id="tripal_feature-interpro_results-box" class="tripal_analysis_interpro-box tripal-info-box">
-  <div class="tripal_feature-info-box-title tripal-info-box-title">InterPro Report</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc"></div>
-  <?php if($results){?>
-     <?php print $results ?>
-  <?php } else { ?>
-    <div class="tripal-no-results">There is no InterPro report for this feature</div> 
-  <?php }?>
-</div>

theme_tripal/tripal_feature/tripal_feature_kegg_terms.tpl.php

@@ -0,0 +1,44 @@
+<?php
+$results = $variables['tripal_analysis_kegg']['results'];
+$feature  = $variables['node']->feature;
+if($feature->cvname != 'gene' and count($results) > 0){ 
+   $i = 0;
+   foreach($results as $analysis_id => $analysisprops){ 
+     $analysis = $analysisprops['analysis'];
+     $terms = $analysisprops['terms']; 
+     ?>
+     <div id="tripal_feature-kegg_results_<?php print $i?>-box" class="tripal_analysis_kegg-box tripal-info-box">
+        <div class="tripal_feature-info-box-title tripal-info-box-title">KEGG Report <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></div>
+        <div class="tripal_feature-info-box-desc tripal-info-box-desc"><?php 
+            if($analysis->nid){ ?>
+               Analysis name: <a href="<?php print url('node/'.$analysis->nid) ?>"><?php print $analysis->name?></a><?php
+            } else { ?>
+               Analysis name: <?php print $analysis->name;
+            } ?><br>
+            Date Performed: <?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?>
+        </div>
+
+     <div class="tripal_feature-kegg_results_subtitle">Annotated Terms</div>
+     <table id="tripal_feature-kegg_summary-<?php $i ?>-table" class="tripal_analysis_kegg-summary-table tripal-table tripal-table-horz">
+     <?php 
+     $j=0;
+     foreach($terms as $term){ 
+       $ipr_id = $term[0];
+       $ipr_name = $term[1];
+       $class = 'tripal_feature-table-odd-row tripal-table-odd-row';
+       if($j % 2 == 0 ){
+         $class = 'tripal_feature-table-even-row tripal-table-even-row';
+       }?>
+       <tr class="<?php print $class ?>">
+         <td><?php print $term ?></td>
+       </tr>
+       <?php
+       $j++;
+     } ?>
+     </table>     
+     </div> <?php
+     $i++;
+   } // end for each analysis 
+} // end if
+?>
+

tripal_analysis_interpro/parseInterpro.inc

@@ -0,0 +1,516 @@
+<?php
+
+/*******************************************************************************
+ * Parse Interpro HTML Output file into analysisfeatureprop table
+ */
+function tripal_analysis_interpro_parseHTMLFile ($analysis_id, $interprofile, $parsego, $job_id) {
+
+	// Prepare log
+	$filename = preg_replace("/.*\/(.*)/", "$1", $interprofile);
+	$logfile = file_directory_path() . "/tripal/tripal_analysis_interpro/load_$filename.log";
+	$log = fopen($logfile, 'a'); // append parsing results to log file
+
+	// Parsing started
+	print "Parsing File:".$interprofile." ...\n";
+	fwrite($log, date("D M j G:i:s Y").". Loading $interprofile\n");
+
+	// Get cvterm_id for 'analysis_interpro_output_iteration_hits' which is required
+	// for inserting into the analysisfeatureprop table
+	$previous_db = tripal_db_set_active('chado'); // use chado database
+	$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
+          "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
+          "WHERE CVT.name = 'analysis_interpro_output_hit' ".
+          "AND CV.name = 'tripal'";
+	$type_id = db_result(db_query($sql));
+	print "cvterm_id for analysis_interpro_output_iteration_hits is $type_id\n";
+
+	// Load the HTML file and convert it into XML for loading
+	$dom = new domDocument;
+	$dom->loadHTMLFile($interprofile);
+	$xml = $dom->saveXML();
+	$interproput = simplexml_load_string($xml);
+
+	// Get html tables for parsing
+	$tables = $interproput->children()->children();
+
+	// Count the number of tables to be processed
+	$no_iterations = 0;
+	foreach($tables as $tmp) {
+		if ($tmp->getName() == 'table') {
+			$no_iterations ++;
+		}
+	}
+	print "$no_iterations html tables to be processed.\n";
+	$interval = intval($no_iterations * 0.01);
+	$idx_iterations = 0;
+
+	// Processed the tables
+	foreach ($tables as $table) {
+        //if (preg_match('/No hits reported/', $table->asXML()) ) {
+            //print "skipping this table b/c no hits are reported\n";
+        //}
+        // make sure we are looking at a table and its not an empty table
+        if ($table->getName() == 'table' && !preg_match('/No hits reported/', $table->asXML()) ) {
+            $idx_iterations ++;
+            if ($idx_iterations % $interval == 0) {
+                    $percentage = (int) ($idx_iterations / $no_iterations * 100);
+                    tripal_db_set_active($previous_db);
+                    tripal_job_set_progress($job_id, $percentage);
+                    $previous_db = tripal_db_set_active('chado');
+                    print $percentage."% ";
+            }
+
+            // Set job status
+            // Get the first row and match its name with the feature name
+            $firsttd = $table->children()->children()->children();
+            $feature_id = 0;
+            foreach($firsttd as $b) {
+                foreach($b->children() as $a) {
+                    if ($a->getName() == 'a') {
+                        // Remove _ORF from the sequence name
+                        $seqname = preg_replace('/^(.+?)_\d_.+/', "$1", $a);
+                        print "seqname is $seqname\n";
+    
+                        // Find out how many features match this uniquename
+                        $sql = "SELECT count(feature_id) FROM {feature} ".
+                        "WHERE uniquename = '%s' ";
+                        $no_features = db_result(db_query($sql, $seqname));
+						    
+                        // If there is only one match, get the feature_id
+                        if ($no_features == 1) {
+                            $sql = "SELECT feature_id FROM {feature} ".
+                                    "WHERE uniquename = '%s' ";
+                            $feature_id = db_result(db_query($sql, $seqname));
+                            print "\tfeature id is $feature_id\n";
+    
+                            // If the uniquename matches more than one features then skip and print 'Ambiguous'
+                        } else if ($no_features > 1) {
+                            fwrite($log, "Ambiguous: ".$seqname." matches more than one feature and is not processed.\n");
+                            continue;
+    
+                        // If the uniquename did not match, skip and print 'Failed'
+                        } else {
+                            fwrite($log, "Failed: ".$seqname."\n");
+                        }
+    
+                    }
+                }
+            }
+
+            // Successfully matched. print 'Succeeded'. Add analysis_id and
+            // feature_id to analysisfeature. Add the table as XML to analysisfeatureprop
+            if ($feature_id) {
+
+                //------------------------------------
+                // Clease unwanted rows from the table
+                //------------------------------------
+
+                $parent_row =   "/<tr><td valign=\"top\"><b>Parent<\/b><\/td>\s*<td valign=\"top\">\s*no.*?parent<\/td>\s*<\/tr>/";
+                $children_row = "/<tr><td valign=\"top\"><b>Children<\/b><\/td>\s*<td valign=\"top\">\s*no.*?children<\/td>\s*<\/tr>/";
+                $found_row    = "/<tr><td valign=\"top\"><b>Found.*?in<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
+                $contains_row = "/<tr><td valign=\"top\"><b>Contains<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
+                $go_row       = "/<tr><td valign=\"top\"><b>GO.*?terms<\/b><\/td>\s*<td valign=\"top\">\s*none<\/td>\s*<\/tr>/";
+    
+                $table_txt = $table->asXML();
+                $table_txt = preg_replace($parent_row, "", $table_txt);
+                $table_txt = preg_replace($children_row, "", $table_txt);
+                $table_txt = preg_replace($found_row, "", $table_txt);
+                $table_txt = preg_replace($contains_row, "", $table_txt);
+                $table_txt = preg_replace($go_row, "", $table_txt);
+
+                //------------------------------------
+                // Clease unwanted ORF link from table 
+                //------------------------------------
+                $orf_link = "/<b><a href=\"\/iprscan\/wget.*?\">(.*?)<\/a><\/b>/";
+                $table_txt = preg_replace($orf_link, "$1", $table_txt);
+
+                //print "----------------------------\n";
+                //print "old: ".$table->asXML()."\n\n\n";
+                //print "----------------------------\n";
+                //print "Fixed: $table_txt\n";
+                //print "----------------------------\n";
+
+                //------------------------------------
+                // If this feature has already been associated with this analysis, do not reinsert
+                // Otherwise, Insert into analysisfeature table
+                //------------------------------------
+                $sql = "Select analysisfeature_id as id from {analysisfeature} where feature_id = %d and analysis_id = %d";
+                $analysisfeature =  db_fetch_object(db_query($sql, $feature_id, $analysis_id));
+                if($analysisfeature){ $analysisfeature_id = $analysisfeature->id; }
+                if(!$analysisfeature_id){
+                    print "inserting analysisfeature\n";
+                   $sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
+                        "VALUES (%d, %d)";
+                   db_query ($sql, $feature_id, $analysis_id);
+                   $sql = "Select analysisfeature_id from {analysisfeature} where feature_id = %d and analysis_id = %d";
+                   $analysisfeature =  db_fetch_object(db_query($sql, $feature_id, $analysis_id));
+                   $analysisfeature_id = $analysisfeature->id;
+                }
+
+                print "analysisfeature_id is $analysisfeature_id (analysis_id = $analysis_id; feature_id = $feature_id)\n";
+
+
+                // Get the higest rank for this feature_id in analysisfeatureprop table.
+                // If the value of the inserting content is not duplicate, add it to  
+                // analysisfeaturepro with 'higest_rank + 1'
+                $sql = "SELECT MAX(rank) FROM {analysisfeatureprop} AFP ".
+                        "INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id ".       
+                        "WHERE feature_id=%d ".
+                        "AND analysis_id=%d ".
+                        "AND type_id=%d ";
+
+                $afp =  db_fetch_object(db_query($sql, $feature_id, $analysis_id, $type_id));
+                $hi_rank = 0;
+                if ($afp) {
+                    $hi_rank = $afp->max + 1;
+                }
+            
+				//------------------------------------------------------------
+				// Insert interpro html tags into analysisfeatureprop table
+				//------------------------------------------------------------
+				// Before inserting, make sure it's not a duplicate
+				$sql = "SELECT value FROM {analysisfeatureprop} WHERE analysisfeature_id = %d AND type_id = %d";
+				$result = db_query($sql, $analysisfeature_id, $type_id);
+				$duplicate = 0;
+				while ($afp_value = db_fetch_object($result)) {
+				    if ($table_txt == $afp_value->value) {
+                        $duplicate = 1;
+				    }
+				}
+				if (!$duplicate) {
+				    $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
+                            "VALUES (%d, %d, '%s', %d)";
+				    db_query($sql, $analysisfeature_id, $type_id, $table_txt, $hi_rank);
+				    fwrite($log, " (Insert)\n"); // write to log
+                    print "\twriting table\n";
+				} else {
+				   fwrite($log, " (Skipped)\n");
+                    print "\tskipping table - dup\n";
+				}
+				
+                // Parse GO terms. Make sure GO database schema is installed in chado
+                $go_db_id = db_result(db_query("SELECT db_id FROM {db} WHERE name='GO'"));
+                if (!$go_db_id) {
+                    print 'GO schema not installed in chado. GO terms are not processed.';
+                }
+                if ($go_db_id && $parsego) {
+                    $trs = $table->children();
+                    foreach ($trs as $tr) {
+                        $tds = $tr->children();
+                        foreach($tds as $td) {
+                            $gotags = $td->children();
+                            foreach ($gotags as $gotag) {
+                                // Look for 'GO:accession#'
+                                if (preg_match("/^.*?GO:(\d+).*$/", $gotag, $matches)) {
+                        	
+                                    // Find cvterm_id for the matched GO term
+                                    $sql = "SELECT cvterm_id FROM {cvterm} CVT 
+                                            INNER JOIN dbxref DBX ON CVT.dbxref_id = DBX.dbxref_id
+                                            WHERE DBX.accession = '%s' AND DBX.db_id = %d";
+                                    $goterm_id = db_result(db_query($sql, $matches[1], $go_db_id));
+                           
+                                    //-------------------------------------------
+                                    // Insert GO terms into feature_cvterm table
+                                    //-------------------------------------------
+                                    // Default pub_id = 1 (NULL) was used
+                                    $sql = "INSERT INTO {feature_cvterm} (feature_id, cvterm_id, pub_id)
+                                            VALUES (%d, %d, 1)";
+                                    db_query($sql, $feature_id, $goterm_id);
+
+                                    //------------------------------------------------
+                                    // Insert GO terms into analysisfeatureprop table
+                                    //------------------------------------------------
+                                    $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank) ".
+                                            "VALUES (%d, %d, '%s', 0)";
+                                    db_query($sql, $analysisfeature_id, $goterm_id, $matches[1]);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    tripal_db_set_active ($previous_db); // Use drupal database
+    print "Done.\nSuccessful and failed entries have been saved in the log file:\n $logfile\n";
+	
+    fwrite($log, "\n");
+    fclose($log);
+    return;
+}
+/**
+*
+*/
+function tripal_analysis_interpro_parseXMLFile ($analysis_id, $interproxmlfile, 
+   $parsego, $query_re, $query_type, $query_uniquename, $job_id) 
+{
+
+   // clear out the anslysisfeature table for this analysis before getting started
+   tripal_core_chado_delete('analysisfeature',array('analysis_id' => $analysis_id));
+
+   // Prepare log
+   $filename = preg_replace("/.*\/(.*)/", "$1", $interproxmlfile);
+   $logfile = file_directory_path() . "/tripal/tripal_analysis_interpro/load_$filename.log";
+   $log = fopen($logfile, 'a'); // append parsing results to log file
+
+   // Parsing started
+   print "Parsing File:".$interproxmlfile." ...\n";
+   fwrite($log, date("D M j G:i:s Y").". Loading $interproxmlfile\n");
+
+   // Get cvterm_id for 'analysis_interpro_xmloutput_hits' which is required
+   // for inserting into the analysisfeatureprop table
+   $previous_db = db_set_active('chado'); // use chado database
+   $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
+   "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
+   "WHERE CVT.name = 'analysis_interpro_xmloutput_hit' ".
+   "AND CV.name = 'tripal'";
+   $type_id = db_result(db_query($sql));
+
+   // Load the XML file
+   $interproput =  simplexml_load_file($interproxmlfile);
+
+   // Get entries parsing
+   $proteins = $interproput->children();
+
+   // Count the number of entires to be processed
+   $no_iterations = 0;
+   foreach($proteins as $tmp) {
+      $no_iterations ++;
+   }
+   print "$no_iterations proteins to be processed.\n";
+   $interval = intval($no_iterations * 0.01);
+   $idx_iterations = 0;
+
+   // get the DB id for the GO database
+   $parsego = tripal_analysis_get_property($analysis_id,'analysis_interpro_parsego');
+   $go_db_id = db_result(db_query("SELECT db_id FROM {db} WHERE name='GO'"));
+   if ($parsego and !$go_db_id) {
+     print 'GO schema not installed in chado. GO terms are not processed.';;
+   }
+
+   // Processed each protein
+   foreach ($proteins as $protein) {
+      // Set job status
+      $idx_iterations ++;
+      if ($idx_iterations % $interval == 0) {
+         $percentage = (int) ($idx_iterations / $no_iterations * 100);
+         db_set_active($previous_db);
+         tripal_job_set_progress($job_id, $percentage);
+         $previous_db = db_set_active('chado');
+         print $percentage."% ";
+      }
+
+      // match the protein id with the feature name
+      $feature_id = 0;
+      $attr = $protein->attributes();
+      $seqname =$attr ['id'];
+
+      // Remove _ORF from the sequence name
+      $seqname = preg_replace('/^(.+)_\d+_ORF\d+.*/', '$1', $seqname);
+     
+      // if a regular expression is provided then pick out the portion requested
+		if ($query_re and preg_match("/$query_re/", $seqname, $matches)) {
+			$feature = $matches[1];
+		} 
+      // If no match by the regular expression then get everything up to the first space
+      else {
+			if (preg_match('/^(.*?)\s.*$/',  $seqname, $matches)) {
+				$feature = $matches[1];
+         } 
+         // if no match up to the first space then just use the entire string
+         else {
+            $feature =  $seqname;
+         }
+      }   
+
+      if(!$feature and $query_re){
+         print fwrite($log, "Failed: Cannot find feature for '$seqname' using the regular expression: $query_re\n");
+         continue;
+      }
+
+      // now find the feature in chado
+      $select = array();
+      if($query_uniquename){
+         $select['uniquename'] = $feature;
+      } else {
+         $select['name'] = $feature;
+      }
+      if($query_type){
+         $select['type_id'] = array(
+           'cv_id' => array(
+              'name' => 'sequence'
+           ),
+           'name' => $query_type,
+         );
+      }
+
+      $feature_arr = tripal_core_chado_select('feature',array('feature_id'),$select);
+      if(count($feature_arr) > 1){
+		   fwrite($log, "Ambiguous: '$feature' matches more than one feature and is being skipped.\n");
+			continue;
+      }
+      if(count($feature_arr) == 0){
+			fwrite($log, "Failed: '$feature' cannot find a matching feature in the database.\n");
+         continue;
+      }
+      $feature_id = $feature_arr[0]->feature_id;
+
+     
+      // Successfully matched. print 'Succeeded'. Add analysis_id and
+      // feature_id to analysisfeature. Add the table as XML to analysisfeatureprop
+      if ($feature_id) {
+
+         print "$idx_iterations Adding InterPro results for feature '$seqname' ($feature_id)\n";
+
+         // If a matched feature is found, write to log.
+         fwrite($log, "Succeeded: ".$seqname." => feature id:".$feature_id);
+
+         //------------------------------------
+         // Insert into analysisfeature table
+         //------------------------------------
+         $sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
+                "VALUES (%d, %d)";
+         db_query ($sql, $feature_id, $analysis_id);                     
+
+         // Get the analysisfeature_id
+         $sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE feature_id = %d AND analysis_id = %d";
+         $analysisfeature_id = db_result(db_query($sql, $feature_id, $analysis_id));
+
+         //------------------------------------------------------------
+         // Insert interpro xml results into analysisfeatureprop table
+         //------------------------------------------------------------
+         // Check to see if we have an existing entry
+         $sql = "SELECT analysisfeatureprop_id,rank 
+                 FROM {analysisfeatureprop} 
+                 WHERE analysisfeature_id = %d AND type_id = %d 
+                 ORDER BY rank DESC";
+         $result = db_fetch_object(db_query($sql, $analysisfeature_id, $type_id));
+         $rank = 0;
+         if($result){
+            $afp_id = $result->analysisfeatureprop_id; 
+            $rank = $result->rank + 1; 
+         }
+         $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
+                "VALUES (%d, %d, '%s', %d)";
+         db_query($sql, $analysisfeature_id, $type_id, $protein->asXML(), $rank);
+         fwrite($log, " (Insert)\n"); // write to log
+
+         // parse the XML for each protein if GO terms are requested
+
+         if($parsego and $go_db_id){		
+
+            $protein = tripal_analysis_interpro_get_result_object($protein->asXML(),$feature_id); 
+            $goterms = $protein['goterms'];                 
+
+            // cycle through the GO terms and add them to the database
+            foreach($goterms as $goterm){ 
+                   
+               // seperate the 'GO:' from the term
+               if (preg_match("/^.*?GO:(\d+).*$/", $goterm, $matches)) {
+
+                  // Find cvterm_id for the matched GO term
+                  $sql = "SELECT cvterm_id FROM {cvterm} CVT 
+                          INNER JOIN dbxref DBX ON CVT.dbxref_id = DBX.dbxref_id
+                          WHERE DBX.accession = '%s' AND DBX.db_id = %d";
+                  $goterm_id = db_result(db_query($sql, $matches[1], $go_db_id));
+
+                  // Insert GO terms into feature_cvterm table
+                  // Default pub_id = 1 (NULL) was used
+                  $sql = "INSERT INTO {feature_cvterm} (feature_id, cvterm_id, pub_id)
+                          VALUES (%d, %d, 1)";
+                  db_query($sql, $feature_id, $goterm_id);
+
+
+                  // Insert GO terms into analysisfeatureprop table
+                  $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank) ".
+                          "VALUES (%d, %d, '%s', 0)";
+                  db_query($sql, $analysisfeature_id, $goterm_id, $matches[1]);
+               } // end if preg_match
+            } // end for each goterm
+         } // end if($parsego and $go_db_id)
+      } // end if($feature_id)            
+   } // end foreach ($proteins as $protein)
+   db_set_active ($previous_db); // Use drupal database
+   print "Done.\nSuccessful and failed entries have been saved in the log file:\n $logfile\n";
+
+   fwrite($log, "\n");
+   fclose($log);
+   return;
+}
+/********************************************************************************
+ * 
+ */
+function tripal_analysis_interpro_get_result_object($interpro_xml,$feature_id){
+
+	// Load the XML into an object
+	$xmlObj = simplexml_load_string($interpro_xml);
+
+   // iterate through each interpro results for this protein
+   $results = array();
+   $terms = array();
+   $protein = array();
+   $iprterms = array();
+   $goterms = array();
+
+   $term_count = 0;
+   $match_count = 0;
+   
+   // get the properties of this result
+   $attr = $xmlObj->attributes();
+   $protein['orf_id'] = (string) $attr["id"];
+   $protein['orf_length'] = (string) $attr["length"];
+   $protein['orf_crc64'] = (string) $attr["crc64"];
+   
+	foreach($xmlObj->children() as $intepro){
+      // get the interpro term for this match
+      $attr = $intepro->attributes();
+	   $terms[$term_count]['ipr_id'] = (string) $attr["id"];
+	   $terms[$term_count]['ipr_name'] = (string) $attr["name"];
+	   $terms[$term_count]['ipr_type'] = (string) $attr["type"];
+      $iprterms[] = array($terms[$term_count]['ipr_id'],$terms[$term_count]['ipr_name']);
+ 
+      // iterate through the elements of the interpro result
+      $matches[$term_count]['matches'] = array();
+      $match_count = 0;
+  	   foreach($intepro->children() as $level1){
+			$element_name = $level1->getName();
+			if($element_name == 'match'){
+            // get the match name for this match
+            $attr = $level1->attributes();
+	         $terms[$term_count]['matches'][$match_count]['match_id'] = (string) $attr["id"];
+	         $terms[$term_count]['matches'][$match_count]['match_name'] = (string) $attr["name"];
+	         $terms[$term_count]['matches'][$match_count]['match_dbname'] = (string) $attr["dbname"];
+            
+            // get the location information for this match     
+            $loc_count = 0;
+            foreach($level1->children() as $level2){
+			      $element_name = $level2->getName();
+			      if($element_name == 'location'){
+                  $attr = $level2->attributes();
+	               $terms[$term_count]['matches'][$match_count]['locations'][$loc_count]['match_start'] = (string) $attr["start"];
+	               $terms[$term_count]['matches'][$match_count]['locations'][$loc_count]['match_end'] = (string) $attr["end"];
+	               $terms[$term_count]['matches'][$match_count]['locations'][$loc_count]['match_score'] = (string) $attr["score"];
+	               $terms[$term_count]['matches'][$match_count]['locations'][$loc_count]['match_status'] = (string) $attr["status"];
+	               $terms[$term_count]['matches'][$match_count]['locations'][$loc_count]['match_evidence'] = (string) $attr["evidence"];
+                  $loc_count++;
+               }
+            }
+            $match_count++;
+         }
+
+			if($element_name == 'classification'){
+            $attr = $level1->attributes();
+            if($attr['class_type'] == 'GO'){
+               $terms[$term_count]['matches'][$match_count]['go_terms'][] = (string) $attr['id'];
+               $goterms[] = (string) $attr['id'];
+            }
+         }
+      }
+      $term_count++;
+	}
+   $results['terms'] = $terms;
+   $results['orf'] = $protein;
+   $results['iprterms'] = $iprterms;
+   $results['goterms'] = $goterms;
+	return $results;
+}

tripal_analysis_interpro/tripal_analysis_interpro.install

@@ -17,12 +17,8 @@ function tripal_analysis_interpro_install() {
    // Inert into drupal's {tripal_analysis}
    tripal_analysis_register_child('tripal_analysis_interpro');
    
-   // Add cvterm 'analysis_interpro_output_iteration_hits' for inserting into featureprop table
-   tripal_add_cvterms('analysis_interpro_output_hit', 'Hit in the interpro html '.
-      'output. Each hit belongs to a chado feature. This cvterm represents a hit in the output');
-   // Add cvterm 'analysis_interpro_settings' for inserting into analysisprop table
-   tripal_add_cvterms('analysis_interpro_settings', 'Settings of an interpro analysis, '.
-      'including output file and run parameters separated by a bar |');
+   // add the CVterms needed for this module
+   tripal_analysis_interpro_add_cvterms();
 }
 
 /*******************************************************************************
@@ -44,7 +40,34 @@ function tripal_analysis_interpro_uninstall() {
             'tripal_analysis_interpro_setting');
 
 }
+/**
+*
+*/
+function tripal_analysis_interpro_add_cvterms(){
+   // Add cvterm 'analysis_interpro_output_iteration_hits' for inserting into featureprop table
+   tripal_add_cvterms('analysis_interpro_output_hit', 'Hit in the interpro html output. Each hit belongs to a chado feature. This cvterm represents a hit in the output');
+   tripal_add_cvterms('analysis_interpro_settings', 'Settings of an interpro analysis, including output file and run parameters separated by a bar |');
+   tripal_add_cvterms('analysis_interpro_interproparameters','The parameters used when executing an InterProScan job');
+   tripal_add_cvterms('analysis_interpro_interprofile','Used to hold the name of the XML file containing the InterProScan results');
+   tripal_add_cvterms('analysis_interpro_parsego','Indicates whether or not the GO terms should be extracted when parsing the InterProScan XML file');
+   tripal_add_cvterms('analysis_interpro_query_re','The regular expression for finding the feature name in the query definition line of the InterPro results');
+   tripal_add_cvterms('analysis_interpro_query_type','The feature type (e.g. mRNA, polypeptide) of the query input file. This type is used to identify the query feature when multiple features have the same name');
+   tripal_add_cvterms('analysis_interpro_query_uniquename','Indicates if the matched name in the query definition line of the blast results is feature uniquename');
+}
+/**
+ * 
+ */
+function tripal_analysis_interpro_update_6000(){
 
+   // we have some new cvterms to add
+   tripal_analysis_interpro_add_cvterms();
+
+   $ret = array(
+      '#finished' => 1,
+   );
+   
+   return $ret;
+}
 /*******************************************************************************
  * Implementation of hook_requirements(). Make sure 'Tripal Core' and 'Tripal
  * Analysis' are enabled before installation
@@ -61,4 +84,4 @@ function tripal_analysis_interpro_requirements($phase) {
       }
    }
    return $requirements;
-}
+}

tripal_analysis_interpro/tripal_analysis_interpro.module

@@ -1,15 +1,16 @@
 <?php
+
+require_once "parseInterpro.inc";
+
 /*******************************************************************************
  * Tripal Interpro lets users show/hide iprscan results associated with a tripal
  * feature
  ******************************************************************************/
 function tripal_analysis_interpro_init(){
 	// Add javascript and style sheet
-	drupal_add_css(drupal_get_path('theme', 'tripal').
-                                  '/css/tripal_analysis_interpro.css');
+	drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_interpro.css');
 	// Add javascript and style sheet
-   drupal_add_js(drupal_get_path('theme', 'tripal').
-                                  '/js/tripal_analysis_interpro.js');
+   drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_analysis_interpro.js');
 }
 /*******************************************************************************
  *  Provide information to drupal about the node types that we're creating
@@ -60,99 +61,19 @@ function tripal_analysis_interpro_block($op = 'list', $delta = 0, $edit=array())
  */
 function chado_analysis_interpro_form ($node){
 
-	$type = node_get_types('type', $node);
-	$form = array();
-	$form['title']= array(
-      '#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
-	);
+   // add in the default fields for the analysis
+   $form = chado_analysis_form($node);
+
+   $analysis = $node->analysis;
+
+   $interprofile = $analysis->tripal_analysis_interpro->interprofile;
+   $interproparameters = $analysis->tripal_analysis_interpro->interproparameters;
+   $parsego = $analysis->tripal_analysis_interpro->parsego;
+   $query_re = $analysis->tripal_analysis_interpro->query_re;
+   $query_type = $analysis->tripal_analysis_interpro->query_type;
+   $query_uniquename = $analysis->tripal_analysis_interpro->query_uniquename;
+
 
-	//----InterProScan Settings (Shown only when Tripal Interpro is enabled) ----
-	if (preg_match("/.*\|.*/",$node->interprofile)) {
-		$prop_values = explode("|", $node->interprofile);
-		$node->interprofile = $prop_values[0];
-		$node->interproparameters = $prop_values[1];
-	}
 	$moreSettings ['interpro'] = 'Interpro Settings';
 	$form['interpro'] = array(
       '#title' => t('Interpro Settings'),
@@ -163,19 +84,19 @@ function chado_analysis_interpro_form ($node){
       '#weight' => 11
 	);
 	$form['interpro']['interprofile'] = array(
-      '#title' => t('Interproscan Output File (in html format)'),
+      '#title' => t('Interproscan Output File (in XML format)'),
       '#type' => 'textfield',
-      '#description' => t('The html output file generated by Interproscan in full path.'),
-      '#default_value' => $node->interprofile,
+      '#description' => t('Please provide the full path to the XML output file generated by InterProScan.'),
+      '#default_value' => $interprofile,
 	);
 	$form['interpro']['interprojob'] = array(
       '#type' => 'checkbox',
-      '#title' => t('Submit a job to parse the Interpro html output'),
+      '#title' => t('Submit a job to parse the InterProScan XML file'),
       '#description' => t('Note: features associated with the interpro results must '.
                              'exist in chado before parsing the file. Otherwise, interpro '.
                              'results that cannot be linked to a feature will be '.
-                             'discarded. Also, Triapl Interpro module needs to be enabled.'),
-      '#default_value' => $node->interprojob,
+                             'discarded.'),
+      '#default_value' => $interprojob,
 	   '#attributes' => array(
         'onclick' => 'return isSubmittingJob(this)'
       )
@@ -184,290 +105,167 @@ function chado_analysis_interpro_form ($node){
       '#type' => 'checkbox',
       '#title' => t('Load GO terms to the database'),
       '#description' => t('Check the box to load GO terms to chado database'),
-      '#default_value' => $node->parsego
+      '#default_value' => $parsego
    );
 	$form['interpro']['interproparameters'] = array(
       '#title' => t('Parameters'),
       '#type' => 'textfield',
-      '#description' => t('The parameters for running the interpro analysis.'),
-      '#default_value' => $node->interproparameters,
+      '#description' => t('The parameters used when running the InterProScan analysis.'),
+      '#default_value' => $interproparameters,
+	);
+
+	$form['interpro']['query_re'] = array(
+      '#title' => t('Query Name RE'),
+      '#type' => 'textfield',
+      '#description' => t('Enter the regular expression that will extract the '.
+         'feature name from the query line in the interpro results. This should be '.
+         'the same as the definition line in the query FASTA file.  This option is '.
+         'is only required when the query does not identically match a feature '.
+         'in the database.'),
+      '#default_value' => $query_re,
+	);
+
+	$form['interpro']['query_type'] = array(
+      '#title' => t('Query Type'),
+      '#type' => 'textfield',
+      '#description' => t('Please enter the Sequence Ontology term that describes '.
+         'the query sequences used for InterProScan.  This is only necessary if two '.
+         'or more sequences have the same name.'),
+      '#default_value' => $query_type,
+	);
+
+	$form['interpro']['query_uniquename'] = array(
+      '#title' => t('Use Unique Name'),
+      '#type' => 'checkbox',
+      '#description' => t('Select this checboxk if the query name in the results file '.
+        'matches the uniquename of the feature.  By default, the blast results will '.
+        'mapped to the "name" of the feature.'),
+      '#default_value' => $query_uniquename,
 	);
 	return $form;
 }
-/*******************************************************************************
+/**
+ * 
+ * 
+ */
+function chado_analysis_interpro_load($node){
+
+   // load the default set of analysis fields
+	$additions = chado_analysis_load($node);
+
+   // create some variables for easier lookup
+   $analysis = $additions->analysis;
+   $analysis_id = $analysis->analysis_id;
+
+   $intepro_settings  = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_settings');	
+   $interprofile      = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_interprofile');
+   $interproparameters= tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_interproparameters');
+   $parsego           = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_parsego');		
+   $query_re          = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_re');	
+   $query_type        = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_type');	
+   $query_uniquename  = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_uniquename');	
+
+   $analysis->tripal_analysis_interpro->interprofile      = $interprofile->value;
+   $analysis->tripal_analysis_interpro->interproparameters= $interproparameters->value;
+   $analysis->tripal_analysis_interpro->parsego           = $parsego->value;
+   $analysis->tripal_analysis_interpro->query_re          = $query_re->value;
+   $analysis->tripal_analysis_interpro->query_type        = $query_type->value;
+   $analysis->tripal_analysis_interpro->query_uniquename  = $query_uniquename->value;
+
+   // if there is an old style 'interpro_settings' array, then break these out for
+   // use in the new format
+   if(count($interpro_settings)>0){
+	   $prop_values = explode ("|", $interpro_settings->value);
+      $analysis->tripal_analysis_interpro->interprofile       = $prop_values[0];
+      $analysis->tripal_analysis_interpro->interproparameters = $prop_values[1];
+   }
+	return $additions;
+}
+/**
  *  
  */
 function chado_analysis_interpro_insert($node){
-	global $user;
-	// 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;
-
-	// If this analysis already exists then don't recreate it in chado
-	$analysis_id = $node->analysis_id;
-	if ($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);
-	}
+  // insert the analysistripal_core_generate_chado_var
+   chado_analysis_insert($node);
+
+   // set the type for this analysis
+   tripal_analysis_insert_property($node->analysis_id,'analysis_type','tripal_analysis_interpro');
+
+   // now add in the remaining settings as a single property but separated by bars
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_interprofile',$node->interprofile);
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_interproparameters',$node->interproparameters);
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_parsego',$node->parsego);		
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_re',$node->query_re);	
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_type',$node->query_type);	
+   tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_uniquename',$node->query_uniquename);	
+  
+   // submit the parsing jobs
+   chado_analysis_interpro_submit_job($node);
 
-	// 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
-		$sql = "SELECT analysis_id ".
-             "FROM {Analysis} ".
-             "WHERE program='%s'".
-             "AND programversion='%s'".
-             "AND sourcename='%s'";
-		$analysis_id = db_result(db_query($sql, $node->program,
-		$node->programversion, $node->sourcename));
-
-		// Get cvterm_id for 'analysis_interpro_settings'
-		$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-             "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
-             "WHERE CVT.name = 'analysis_interpro_settings' ".
-             "AND CV.name = 'tripal'";
-		$type_id = db_result(db_query($sql));
-
-		// Insert into chado {analysisprop} table
-		$sql = "INSERT INTO {analysisprop} (analysis_id, type_id, value) ".
-             "VALUES (%d, %d, '%s')";
-		$interprosettings = $node->interprofile."|".$node->interproparameters;
-		db_query($sql, $analysis_id, $type_id, $interprosettings);
-
-		tripal_db_set_active($previous_db);  // switch back to drupal database
-		// Add a job if the user wants to parse the html output
-		if($node->interprojob) {
-			$job_args[0] = $analysis_id;
-			$job_args[1] = $node->interprofile;
-			if ($node->parsego) {
-			   $job_args[2] = 1;
-			} else {
-            $job_args[2] = 0;
-         }
-			if (is_readable($node->interprofile)) {
-				$fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
-				tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
-                           'tripal_analysis_interpro_parseHTMLFile', $job_args, $user->uid);
-			} else {
-				drupal_set_message("Can not open interpro output file. Job not scheduled.");
-			}
-		}
-	}
-
-	// Make sure the entry for this analysis doesn't already exist in the
-	// chado_analysis table if it doesn't exist then we want to add it.
-	$node_check_sql = "SELECT * FROM {chado_analysis} ".
-                     "WHERE analysis_id = %d";
-	$node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
-	if(!$node_check){
-		// next add the item to the drupal table
-		$sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) ".
-             "VALUES (%d, %d, %d)";
-		db_query($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)
-			$record->title = "$node->program ($node->programversion)";
-		}
-		$record->nid = $node->nid;
-		drupal_write_record('node',$record,'nid');
-		drupal_write_record('node_revisions',$record,'nid');
-	}
 }
-/*******************************************************************************
- * Delete interpro anlysis
+/**
+ * 
  */
-function chado_analysis_interpro_delete($node){
-	// Before removing, get analysis_id so we can remove it from chado database
-	// 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", $af->analysisfeature_id);
+function chado_analysis_interpro_update($node){
+  // insert the analysistripal_core_generate_chado_var
+   chado_analysis_update($node);
+
+   // set the type for this analysis
+   tripal_analysis_update_property($node->analysis_id,'analysis_type','tripal_analysis_interpro',1);
+
+   // now add in the remaining settings as a single property but separated by bars
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_interprofile',$node->interprofile,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_interproparameters',$node->interproparameters,1);
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_parsego',$node->parsego,1);		
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_re',$node->query_re,1);	
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_type',$node->query_type,1);	
+   tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_uniquename',$node->query_uniquename,1);	
+
+   // if this analysis uses the old style settings cvterm then remove that term
+   $old = tripal_analysis_get_property($node->analysis_id,'analysis_interpro_settings');
+   if(count($old) > 0){
+      tripal_analysis_delete_property($node->analysis_id,'analysis_interpro_settings');
    }
-   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);
+  
+   // submit the parsing jobs
+   chado_analysis_interpro_submit_job($node);
 }
-
 /*******************************************************************************
- * Update interpro analysis
+ * Delete interpro anlysis
  */
-function chado_analysis_interpro_update($node){
-	global $user;
-	if($node->revision){
-		// 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:
-		$sql = "SELECT analysis_id ".
-             "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_interpro_settings'
-		$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-             "INNER JOIN cv CV ON CV.cv_id = CVT.cv_id ".
-             "WHERE CVT.name = 'analysis_interpro_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";
-		$interprosettings = $node->interprofile."|".$node->interproparameters;
-		db_query($sql, $interprosettings, $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->interprojob) {
-			$job_args[0] = $analysis_id;
-			$job_args[1] = $node->interprofile;
-		   if ($node->parsego) {
-            $job_args[2] = 1;
-         } else {
-            $job_args[2] = 0;
-         }
-			if (is_readable($node->interprofile)) {
-				$fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
-				tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
-                           'tripal_analysis_interpro_parseHTMLFile', $job_args, $user->uid);
-			} else {
-				drupal_set_message("Can not open interpro output file. Job not scheduled.");
-			}
-		}
+function chado_analysis_interpro_delete($node){
+	chado_analysis_delete($node);
+}
 
-		// 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 = $node->analysisname;
+/**
+*
+*/
+function chado_analysis_interpro_submit_job($node){
+   global $user;
+
+	// Add a job if the user wants to parse the html output
+	if($node->interprojob) {
+		$job_args[0] = $node->analysis_id;
+		$job_args[1] = $node->interprofile;
+		if ($node->parsego) {
+		   $job_args[2] = 1;
+		} else {
+         $job_args[2] = 0;
+      }
+		$job_args[3] = $node->query_re;
+		$job_args[4] = $node->query_type;
+		$job_args[5] = $node->query_uniquename;
+
+		if (is_readable($node->interprofile)) {
+			$fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
+			tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
+                        'tripal_analysis_interpro_parseXMLFile', $job_args, $user->uid);
 		} else {
-			//Construct node title as "program (version)
-			$record->title = "$node->program ($node->programversion)";
+			drupal_set_message("Can not open interpro output file. Job not scheduled.");
 		}
-		$record->nid = $node->nid;
-		drupal_write_record('node',$record,'nid');
-		drupal_write_record('node_revisions',$record,'nid');
 	}
 }
-/*******************************************************************************
- *  When a node is requested by the user this function is called to allow us
- *  to add auxiliary data to the node object.
- */
-function chado_analysis_interpro_load($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_interpro_settings'
-		$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-             "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
-             "WHERE CVT.name = 'analysis_interpro_settings' ".
-             "AND CV.name = 'tripal'";
-		$type_id = db_result(db_query($sql));
-		// get analysisprop information
-		$sql = "SELECT value FROM {analysisprop} ".
-             "WHERE analysis_id = %d ".
-             "AND type_id = %d";
-		$analysisprop = db_result(db_query($sql, $ana_node->analysis_id, $type_id));
-		$prop_values = explode ("|", $analysisprop, 1);
-		$additions->interprofile = $prop_values[0];
-		$additions->interproparameters = $prop_values[1];
-
-		tripal_db_set_active($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;
-}
+
 
 /*******************************************************************************
  *  This function customizes the view of the chado_analysis node.  It allows
@@ -498,244 +296,6 @@ function chado_analysis_interpro_view ($node, $teaser = FALSE, $page = FALSE) {
 	return $node;
 }
 
-/*******************************************************************************
- * Parse Interpro HTML Output file into analysisfeatureprop table
- */
-function tripal_analysis_interpro_parseHTMLFile ($analysis_id, $interprofile, $parsego, $job_id) {
-
-	// Prepare log
-	$filename = preg_replace("/.*\/(.*)/", "$1", $interprofile);
-	$logfile = file_directory_path() . "/tripal/tripal_analysis_interpro/load_$filename.log";
-	$log = fopen($logfile, 'a'); // append parsing results to log file
-
-	// Parsing started
-	print "Parsing File:".$interprofile." ...\n";
-	fwrite($log, date("D M j G:i:s Y").". Loading $interprofile\n");
-
-	// Get cvterm_id for 'analysis_interpro_output_iteration_hits' which is required
-	// for inserting into the analysisfeatureprop table
-	$previous_db = tripal_db_set_active('chado'); // use chado database
-	$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-          "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
-          "WHERE CVT.name = 'analysis_interpro_output_hit' ".
-          "AND CV.name = 'tripal'";
-	$type_id = db_result(db_query($sql));
-	print "cvterm_id for analysis_interpro_output_iteration_hits is $type_id\n";
-
-	// Load the HTML file and convert it into XML for loading
-	$dom = new domDocument;
-	$dom->loadHTMLFile($interprofile);
-	$xml = $dom->saveXML();
-	$interproput = simplexml_load_string($xml);
-
-	// Get html tables for parsing
-	$tables = $interproput->children()->children();
-
-	// Count the number of tables to be processed
-	$no_iterations = 0;
-	foreach($tables as $tmp) {
-		if ($tmp->getName() == 'table') {
-			$no_iterations ++;
-		}
-	}
-	print "$no_iterations html tables to be processed.\n";
-	$interval = intval($no_iterations * 0.01);
-	$idx_iterations = 0;
-
-	// Processed the tables
-	foreach ($tables as $table) {
-        //if (preg_match('/No hits reported/', $table->asXML()) ) {
-            //print "skipping this table b/c no hits are reported\n";
-        //}
-        // make sure we are looking at a table and its not an empty table
-        if ($table->getName() == 'table' && !preg_match('/No hits reported/', $table->asXML()) ) {
-            $idx_iterations ++;
-            if ($idx_iterations % $interval == 0) {
-                    $percentage = (int) ($idx_iterations / $no_iterations * 100);
-                    tripal_db_set_active($previous_db);
-                    tripal_job_set_progress($job_id, $percentage);
-                    $previous_db = tripal_db_set_active('chado');
-                    print $percentage."% ";
-            }
-
-            // Set job status
-            // Get the first row and match its name with the feature name
-            $firsttd = $table->children()->children()->children();
-            $feature_id = 0;
-            foreach($firsttd as $b) {
-                foreach($b->children() as $a) {
-                    if ($a->getName() == 'a') {
-                        // Remove _ORF from the sequence name
-                        $seqname = preg_replace('/^(.+?)_\d_.+/', "$1", $a);
-                        print "seqname is $seqname\n";
-    
-                        // Find out how many features match this uniquename
-                        $sql = "SELECT count(feature_id) FROM {feature} ".
-                        "WHERE uniquename = '%s' ";
-                        $no_features = db_result(db_query($sql, $seqname));
-						    
-                        // If there is only one match, get the feature_id
-                        if ($no_features == 1) {
-                            $sql = "SELECT feature_id FROM {feature} ".
-                                    "WHERE uniquename = '%s' ";
-                            $feature_id = db_result(db_query($sql, $seqname));
-                            print "\tfeature id is $feature_id\n";
-    
-                            // If the uniquename matches more than one features then skip and print 'Ambiguous'
-                        } else if ($no_features > 1) {
-                            fwrite($log, "Ambiguous: ".$seqname." matches more than one feature and is not processed.\n");
-                            continue;
-    
-                        // If the uniquename did not match, skip and print 'Failed'
-                        } else {
-                            fwrite($log, "Failed: ".$seqname."\n");
-                        }
-    
-                    }
-                }
-            }
-
-            // Successfully matched. print 'Succeeded'. Add analysis_id and
-            // feature_id to analysisfeature. Add the table as XML to analysisfeatureprop
-            if ($feature_id) {
-
-                //------------------------------------
-                // Clease unwanted rows from the table
-                //------------------------------------
-
-                $parent_row =   "/<tr><td valign=\"top\"><b>Parent<\/b><\/td>\s*<td valign=\"top\">\s*no.*?parent<\/td>\s*<\/tr>/";
-                $children_row = "/<tr><td valign=\"top\"><b>Children<\/b><\/td>\s*<td valign=\"top\">\s*no.*?children<\/td>\s*<\/tr>/";
-                $found_row    = "/<tr><td valign=\"top\"><b>Found.*?in<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
-                $contains_row = "/<tr><td valign=\"top\"><b>Contains<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
-                $go_row       = "/<tr><td valign=\"top\"><b>GO.*?terms<\/b><\/td>\s*<td valign=\"top\">\s*none<\/td>\s*<\/tr>/";
-    
-                $table_txt = $table->asXML();
-                $table_txt = preg_replace($parent_row, "", $table_txt);
-                $table_txt = preg_replace($children_row, "", $table_txt);
-                $table_txt = preg_replace($found_row, "", $table_txt);
-                $table_txt = preg_replace($contains_row, "", $table_txt);
-                $table_txt = preg_replace($go_row, "", $table_txt);
-
-                //------------------------------------
-                // Clease unwanted ORF link from table 
-                //------------------------------------
-                $orf_link = "/<b><a href=\"\/iprscan\/wget.*?\">(.*?)<\/a><\/b>/";
-                $table_txt = preg_replace($orf_link, "$1", $table_txt);
-
-                //print "----------------------------\n";
-                //print "old: ".$table->asXML()."\n\n\n";
-                //print "----------------------------\n";
-                //print "Fixed: $table_txt\n";
-                //print "----------------------------\n";
-
-                //------------------------------------
-                // If this feature has already been associated with this analysis, do not reinsert
-                // Otherwise, Insert into analysisfeature table
-                //------------------------------------
-                $sql = "Select analysisfeature_id as id from {analysisfeature} where feature_id = %d and analysis_id = %d";
-                $analysisfeature =  db_fetch_object(db_query($sql, $feature_id, $analysis_id));
-                if($analysisfeature){ $analysisfeature_id = $analysisfeature->id; }
-                if(!$analysisfeature_id){
-                    print "inserting analysisfeature\n";
-                   $sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
-                        "VALUES (%d, %d)";
-                   db_query ($sql, $feature_id, $analysis_id);
-                   $sql = "Select analysisfeature_id from {analysisfeature} where feature_id = %d and analysis_id = %d";
-                   $analysisfeature =  db_fetch_object(db_query($sql, $feature_id, $analysis_id));
-                   $analysisfeature_id = $analysisfeature->id;
-                }
-
-                print "analysisfeature_id is $analysisfeature_id (analysis_id = $analysis_id; feature_id = $feature_id)\n";
-
-
-                // Get the higest rank for this feature_id in analysisfeatureprop table.
-                // If the value of the inserting content is not duplicate, add it to  
-                // analysisfeaturepro with 'higest_rank + 1'
-                $sql = "SELECT MAX(rank) FROM {analysisfeatureprop} AFP ".
-                        "INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id ".       
-                        "WHERE feature_id=%d ".
-                        "AND analysis_id=%d ".
-                        "AND type_id=%d ";
-
-                $afp =  db_fetch_object(db_query($sql, $feature_id, $analysis_id, $type_id));
-                $hi_rank = 0;
-                if ($afp) {
-                    $hi_rank = $afp->max + 1;
-                }
-            
-				//------------------------------------------------------------
-				// Insert interpro html tags into analysisfeatureprop table
-				//------------------------------------------------------------
-				// Before inserting, make sure it's not a duplicate
-				$sql = "SELECT value FROM {analysisfeatureprop} WHERE analysisfeature_id = %d AND type_id = %d";
-				$result = db_query($sql, $analysisfeature_id, $type_id);
-				$duplicate = 0;
-				while ($afp_value = db_fetch_object($result)) {
-				    if ($table_txt == $afp_value->value) {
-                        $duplicate = 1;
-				    }
-				}
-				if (!$duplicate) {
-				    $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
-                            "VALUES (%d, %d, '%s', %d)";
-				    db_query($sql, $analysisfeature_id, $type_id, $table_txt, $hi_rank);
-				    fwrite($log, " (Insert)\n"); // write to log
-                    print "\twriting table\n";
-				} else {
-				   fwrite($log, " (Skipped)\n");
-                    print "\tskipping table - dup\n";
-				}
-				
-                // Parse GO terms. Make sure GO database schema is installed in chado
-                $go_db_id = db_result(db_query("SELECT db_id FROM {db} WHERE name='GO'"));
-                if (!$go_db_id) {
-                    print 'GO schema not installed in chado. GO terms are not processed.';
-                }
-                if ($go_db_id && $parsego) {
-                    $trs = $table->children();
-                    foreach ($trs as $tr) {
-                        $tds = $tr->children();
-                        foreach($tds as $td) {
-                            $gotags = $td->children();
-                            foreach ($gotags as $gotag) {
-                                // Look for 'GO:accession#'
-                                if (preg_match("/^.*?GO:(\d+).*$/", $gotag, $matches)) {
-                        	
-                                    // Find cvterm_id for the matched GO term
-                                    $sql = "SELECT cvterm_id FROM {cvterm} CVT 
-                                            INNER JOIN dbxref DBX ON CVT.dbxref_id = DBX.dbxref_id
-                                            WHERE DBX.accession = '%s' AND DBX.db_id = %d";
-                                    $goterm_id = db_result(db_query($sql, $matches[1], $go_db_id));
-                           
-                                    //-------------------------------------------
-                                    // Insert GO terms into feature_cvterm table
-                                    //-------------------------------------------
-                                    // Default pub_id = 1 (NULL) was used
-                                    $sql = "INSERT INTO {feature_cvterm} (feature_id, cvterm_id, pub_id)
-                                            VALUES (%d, %d, 1)";
-                                    db_query($sql, $feature_id, $goterm_id);
-
-                                    //------------------------------------------------
-                                    // Insert GO terms into analysisfeatureprop table
-                                    //------------------------------------------------
-                                    $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank) ".
-                                            "VALUES (%d, %d, '%s', 0)";
-                                    db_query($sql, $analysisfeature_id, $goterm_id, $matches[1]);
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        }
-    }
-    tripal_db_set_active ($previous_db); // Use drupal database
-    print "Done.\nSuccessful and failed entries have been saved in the log file:\n $logfile\n";
-	
-    fwrite($log, "\n");
-    fclose($log);
-    return;
-}
 
 /*******************************************************************************
  * tripal_analysis_interpro_nodeapi()
@@ -798,7 +358,7 @@ function tripal_analysis_interpro_theme () {
 
 function tripal_analysis_interpro_preprocess_tripal_feature_interpro_results(&$variables){
    $feature = $variables['node']->feature;
-	$variables['tripal_analysis_interpro']['results'] = tripal_get_interpro_results($feature->feature_id);
+	$variables['tripal_analysis_interpro']['results'] = tripal_get_interpro_XML_results($feature->feature_id);
 }
 
 /*******************************************************************************
@@ -809,12 +369,67 @@ function theme_parse_EBI_Interpro_XML_index_version ($node) {
 	$content = tripal_get_interpro_results_index_version($feature->feature_id);
 	return $content;
 }
+/**
+ * 
+ */
+function tripal_get_interpro_XML_results($feature_id){
+
+	// Get the blast results stored as XML from the analysisfeatureprop table
+   // the type for the property is named 'analysis_blast_output_iteration_hits'
+   // and is found in the 'tripal' controlled vocabulary.  This CV term was
+   // added by this module.
+   $select = array(
+      'analysisfeature_id' => array(
+         'feature_id' => $feature_id,
+      ), 
+      'type_id' => array(
+         'name' => 'analysis_interpro_xmloutput_hit',
+         'cv_id' => array(
+            'name' => 'tripal'
+         ),
+      ),         
+   );
+   $afeatureprops = tripal_core_chado_select('analysisfeatureprop',array('*'),$select);
+
+   // iterate through all of the interpro XML properties for this feature
+	$results = array ();
+	foreach ($afeatureprops as $index => $afeatureprop) {
+
+      // get the analysis feature record
+      $analysisfeature_arr = tripal_core_chado_select('analysisfeature',array('analysis_id'),
+         array('analysisfeature_id' => $afeatureprop->analysisfeature_id));
+      $analysisfeature = $analysisfeature_arr[0];
+
+      // get the analysis record and the analysis_id
+      $analysis = tripal_core_generate_chado_var('analysis',
+         array('analysis_id' => $analysisfeature->analysis_id));
+      $analysis_id = $analysis->analysis_id;
 
+
+      // parse the XML and add it to the array of blast results to be returned
+      $interpro_xml = $afeatureprop->value;
+      $orf = tripal_analysis_interpro_get_result_object($interpro_xml,$feature_id);
+		$results[$analysis->analysis_id]['protein_ORFs'][] = $orf;
+      $results[$analysis->analysis_id]['analysis'] = $analysis;
+
+      // iterate through all of the protein ORFs and combine the terms into one large list
+      if(!is_array($results[$analysis->analysis_id]['allterms'])){
+        $results[$analysis->analysis_id]['allterms'] = array();
+      }
+      if(!is_array($results[$analysis->analysis_id]['goterms'])){
+        $results[$analysis->analysis_id]['goterms'] = array();
+      }
+      $results[$analysis->analysis_id]['allterms'] = array_merge($results[$analysis->analysis_id]['allterms'],$orf['iprterms']);
+      $results[$analysis->analysis_id]['goterms'] = array_merge($results[$analysis->analysis_id]['goterms'],$orf['goterms']);
+      $i++;
+	}
+   return $results;
+}
 /*******************************************************************************
  * tripal_get_interpro_results()
  * Get interpro result from featureprop table for the feature
  */
-function tripal_get_interpro_results($feature_id){
+function tripal_get_interpro_HTML_results($feature_id){
 	// Get cvterm_id for 'analysis_interpro_output_hit' which is required
 	// for inserting into the analysisfeatureprop table
 	$previous_db = tripal_db_set_active('chado');

tripal_analysis_kegg/tripal_analysis_kegg.module

@@ -379,10 +379,11 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
    $interval = intval($total_files * 0.01);
    $no_file = 0;
 
-   // Remove the analysis features for this analysis
+   // Remove the analysis feature this analysis
    // we will rebuild them from just this parsing
-   if(!tripal_core_chado_delete('analysisfeature',array('analysis_id' => $analysis_id))){
-      print "ERROR: Cannot prepare the analysis for addint features\n";
+   $select =  array('analysis_id' => $analysis_id);
+   if(!tripal_core_chado_delete('analysisfeature',$select)){
+      print "ERROR: Cannot prepare the analysis for adding features\n";
       exit;
    }
 
@@ -397,17 +398,17 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
          }
          $no_file ++;
          
-         # $type variable will be set in tripal_analysis_kegg_parse_kegg_file()
-         $content = tripal_analysis_kegg_parse_kegg_file("$hierdir/$file",$type,
+         # $heirarchy variable will be set in tripal_analysis_kegg_parse_kegg_file()
+         $results = tripal_analysis_kegg_parse_kegg_file("$hierdir/$file",$heirarchy,
             $analysis_id, $base_path, $query_re,$query_type,$query_uniquename);
 
          # add the item to the database
-         if($content){
+         if(count($results) > 0){
             //------------------------------------------------------
             // Insert into analysisprop table
             //------------------------------------------------------
-            // Make sure the same value doesn't exist before inserting into chado
-            $sql = "SELECT value
+            // Remove the property if it already exists we'll replace it
+            $sql = "DELETE
                     FROM {analysisprop}
                     WHERE analysis_id = %d
                     AND type_id = (SELECT cvterm_id 
@@ -416,31 +417,35 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
                                    WHERE CV.name = 'tripal' AND CVT.name = '%s'
                                    )
                    ";
+
             $previous_db = tripal_db_set_active('chado');
-            $oldvalue = db_result(db_query($sql, $analysis_id, $type));
+            db_result(db_query($sql, $analysis_id, $heirarchy));
             tripal_db_set_active($previous_db);
             
-            // Insert the content
-            if ($oldvalue != $content) {
-            	
-            	$previous_db = tripal_db_set_active('chado'); // Use chado database
-            	// Get type_id for the BRITE term
-            	$sql = "SELECT cvterm_id 
-                       FROM {cvterm} CVT 
-                       INNER JOIN CV ON CVT.cv_id = CV.cv_id
-                       WHERE CV.name = 'tripal' AND CVT.name = '%s'";
-            	$brite_cvterm_id = db_result(db_query($sql, $type)); 
-
-            	// Replace all single quote as HTML code before insert
-            	$content = preg_replace("/\'/", "'", $content);
             	
-            	// Insert the value
-               $sql = "INSERT INTO {analysisprop} (analysis_id, type_id, value) 
-                       VALUES (%d, %d,'$content')";   
-               
-               db_query($sql, $analysis_id, $brite_cvterm_id);
-               tripal_db_set_active($previous_db); // Use drupal database
-            }
+         	$previous_db = tripal_db_set_active('chado'); // Use chado database
+         	// Get type_id for the BRITE term
+         	$sql = "SELECT cvterm_id 
+                    FROM {cvterm} CVT 
+                    INNER JOIN CV ON CVT.cv_id = CV.cv_id
+                    WHERE CV.name = 'tripal' AND CVT.name = '%s'";
+         	$brite_cvterm_id = db_result(db_query($sql, $heirarchy)); 
+
+            // convert the array to text for saving in the database
+         	// Replace all single quote as HTML code before insert
+            $i = 0;
+            $content = '<ul>';
+            tripal_analysis_kegg_array2list($results,$content,$i);
+            $content .= '</ul>';
+         	$content = preg_replace("/\'/", "&#39;", $content);
+         	
+         	// Insert the value
+            $sql = "INSERT INTO {analysisprop} (analysis_id, type_id, value) 
+                    VALUES (%d, %d,'$content')";   
+            
+            db_query($sql, $analysis_id, $brite_cvterm_id);
+            tripal_db_set_active($previous_db); // Use drupal database
+
             
          }
       }
@@ -455,200 +460,294 @@ function tripal_analysis_kegg_parseHierFile ($analysis_id, $hierfile, $base_path
    }
    return;
 }
+/**
+*
+*/
+function tripal_analysis_kegg_array2list($array,&$content,&$i){
+   foreach($array as $index => $item){
+      if(is_array($item)){
+         if(is_numeric($index)){
+            tripal_analysis_kegg_array2list($item,$content,$i);
+         } else {
+            $content .= "<li id=\"term_$i\"><a></a>$index\n<ul>";
+            $i++;
+            tripal_analysis_kegg_array2list($item,$content,$i);
+            $content .= "</ul>\n</li>\n";
+         }
+      } else {
+         $content .= "<li id=\"term_$i\"><a></a>$item</li>\n";
+         $i++;
+      }
+   }   
+}
 /*******************************************************************************
  * Parse *.keg files. 
  * Each file has a definition line. BRITE term is extracted * from this line 
  * and added to chado as a cvterm. Tree structure for this cvterm is then 
  * generated and saved to analysisfeature and analysisfeatureprop tables.
  */
-function tripal_analysis_kegg_parse_kegg_file ($file,&$type,$analysis_id, $base_path, $query_re,$query_type,$query_uniquename){
-   $handle = fopen($file,'r');
-   $depth = array();
-   $current = '@';  # this is one character below 'A' in the ASCII table
-   $prev = '@';
-   $id = 0;
-   $type_id = 0;
-   $no_line = 0;
-   $ul_content = array();
-   $has_feature = 0;
-   $level = -1;
+function tripal_analysis_kegg_parse_kegg_file ($file, &$heirarchy, $analysis_id, 
+   $base_path, $query_re, $query_type, $query_uniquename)
+{
+
+   print "Parsing $file\n";
 
+   // get the 'kegg_brite_data' cvterm
+   $select = array('name' => 'kegg_brite_data', 
+                   'cv_id' => array('name' => 'tripal'));
+   $bdt_arr = tripal_core_chado_select('cvterm',array('cvterm_id'),$select);
+   $brite_id = $bdt_arr[0]->cvterm_id;
+
+   $filepos = 0;
+
+   // iterate through the lines of the file and recurse through the various levels
+   $handle = fopen($file,'r');
    while($line = fgets($handle)){
-      $no_line ++;
-      // Find out what kind of file we're looking at.
+      $filepos += strlen($line);
+      $line = trim($line);
+
+      // the first line of the file provides the BRITE heirarchy name
       if(preg_match("/#.*nbsp;\s(.*)<\/h2>$/",$line,$matches)){
-         // Set type as the matched term in the DEFINITION line and add it as a new cvterm
-         $type = $matches[1];
-         // Before inserting, make sure this cvterm doesn't exist
-         $previous_db = tripal_db_set_active('chado');
-         $sql = "SELECT cvterm_id 
-                 FROM {cvterm} CVT
-                 INNER JOIN cv ON cv.cv_id = CVT.cv_id
-                 WHERE cv.name = 'tripal'
-                 AND CVT.name = '%s'";
-         $type_id = db_result(db_query($sql, $type));
-         tripal_db_set_active($previous_db);
-         if (!$type_id) {
+         // For each BRITE heirarchy file we'll add an analysisprop where we'll
+         // store the report.  If the CVTerm doesn't exist then add it.
+         $heirarchy = $matches[1];
+         $select = array('name' => $heirarchy,'cv_id' => array('name' => 'tripal'));
+         $cvt_arr = tripal_core_chado_select('cvterm',array('cvterm_id'),$select);
+         if (count($cvt_arr) == 0) {
             tripal_add_cvterms($type, "KEGG BRITE term: $type");
-            // Get newly added type_id
-            $sql = "SELECT cvterm_id 
-                    FROM {cvterm} CVT
-                    INNER JOIN cv ON cv.cv_id = CVT.cv_id
-                    WHERE cv.name = 'tripal'
-                    AND CVT.name = '%s'";
-            $previous_db = tripal_db_set_active('chado');
-            $type_id = db_result(db_query($sql, $type));
-            tripal_db_set_active($previous_db);
+            $cvt_arr = tripal_core_chado_select('cvterm',array('cvterm_id'),$select);
+         }
+         $heirarchy_id = $cvt_arr[0]->cvterm_id;
+
+         // now that we have the file type we can recurse
+         $next = tripal_analysis_kegg_get_next_line($handle,$filepos);
+         $results = tripal_analysis_kegg_recurse_heir($handle,$next,$query_re,
+            $query_type,$query_uniquename,$base_path,$analysis_id,
+            $brite_id,$heirarchy,$filepos);
+      }
+   }
+   fclose($handle);
+   return $results;
+}
+
+/**
+*
+*/
+function tripal_analysis_kegg_recurse_heir($handle, $line,$query_re,
+   $query_type, $query_uniquename, $base_path, $analysis_id, $brite_id, 
+   $heirarchy,&$filepos)
+{
+   $results = array(); 
+
+   // get the current level and the value
+   $level = $line[0];
+   $value = $line[1];
+
+   // now get the next line to see what is coming next.  If the 
+   // next level is greater then recurse immediately. 
+   $prevpos = $filepos;
+   while($next = tripal_analysis_kegg_get_next_line($handle,$filepos)){
+      $next_level = $next[0];
+      $next_value = $next[1];
+
+      // check this line to see if it has a feature we need to keep
+      $ret = tripal_analysis_kegg_check_line_handle_feature($query_re,
+         $query_type, $query_uniquename, $base_path, $analysis_id, $brite_id, 
+         $heirarchy,$value);
+      if($ret){
+         $results[] = $ret;
+      }
+
+      // if we're going up a level then recurse immediately and add results to our array
+      if(ord($next_level) > ord($level)){
+         // now recurse
+         $ret = tripal_analysis_kegg_recurse_heir($handle,$next, 
+            $query_re,$query_type, $query_uniquename, $base_path, $analysis_id,
+            $brite_id,$heirarchy,$filepos);
+         if(count($ret) > 0){
+            $results[][$value] = $ret; 
          }
       }
-      // get the depth of the hierarch (e.g. A,B,C or D);
+
+      // if we go down a level on the next line then reset the 
+      // filepointer and return
+      elseif(ord($next_level) < ord($level)){
+          fseek($handle,$prevpos);
+          $filepos = $prevpos;
+          return $results;
+      }
+      else {
+         $line = $next;
+         $level = $next[0];
+         $value = $next[1];
+      }
+      $prevpos = $filepos; 
+   }
+
+   return $results;
+}
+/**
+*
+*/
+
+function tripal_analysis_kegg_get_next_line($handle,&$filepos){
+   $good = 0;
+
+   // get the next line in the file
+   $line = fgets($handle);
+   $filepos += strlen($line);
+
+   // we hit the end of the file, so exit with a null
+   if(!$line){
+      return null;
+   }  
+   while(!$good){
+      $line = trim($line);
       preg_match("/^([ABCDEFGHIJKLMNOP])\s*(.*)/",$line,$matches);
+      $level = $matches[1];
+      $value = $matches[2];
 
       // skip lines that aren't data or are empty
-      if(!$matches[1] or !$matches[2]){continue;}
- 
-      // set the current level and keep track of the previous level (e.g. A,B,C...)
-      $prev = $current;
-      $current = $matches[1];
-
-      // if we have matches and we are going down to a lower level then we 
-      // want to close off each <ul> until we hit the level we are currently at
-      // and at the same time we want to keep the text. If we don't have a 
-      // match then we'll throw out the text.
-      if($has_feature){
-         for($i = (ord($current) - ord($prev)); $i < 0; $i++){
-            $ul_content[$level] .= "</ul>\n";
-            $content .= $ul_content[$level];
-            $ul_content[$level--] = '';
-         }
-         $has_feature = 0;
+      if($level and $value) {
+
+         // change all relative paths to absolute paths pointing to KEGG (www.genome.jp)
+         // add id to <a> tags so we can link kegg.gif to it in tripal_analysis_kegg.css
+         $value = preg_replace("/<a href=\"\//i","<a href=\"http://www.genome.jp/",$value);     
+         $value = preg_replace("/<a href=\"/i","<a id=\"tripal_kegg_brite_links\" target=\"_blank\" href=\"",$value);
+
+         // this line is good so let's exit out
+         $good = 1;
       } else {
-         for($i = (ord($current) - ord($prev)); $i < 0; $i++){
-            $ul_content[$level--] = '';
+         $line = fgets($handle);
+         $filepos += strlen($line);
+         // we hit the end of the file, so exit with a null
+         if(!$line){
+            return null;
+         }         
+      }
+   }
+   return array($level,$value);
+}
+/**
+*
+*/
+function tripal_analysis_kegg_check_line_handle_feature($query_re,
+   $query_type, $query_uniquename, $base_path, $analysis_id, $brite_id, 
+   $heirarchy,$value)
+{
+
+   // extract the features that have been mapped to the KEGG IDs
+   if(preg_match("/^(.*?);\s*(\<a.+)/",$value,$matches)){
+      $has_feature = 1;
+      $fname = $matches[1];
+      $keggterm = $matches[2];
+
+		// get the feature name using the user's regular expression
+		if ($query_re and preg_match("/$query_re/", $fname, $matches)) {
+			$feature = $matches[1];
+		} 
+      // If not in above format then pull up to the first space
+      else {
+			if (preg_match('/^(.*?)\s.*$/', $fname, $matches)) {
+				$feature = $matches[1];
+         } 
+         // if no match up to the first space then just use the entire string
+         else {
+            $feature = $fname;
          }
+      } 
+
+      // now find the feature in chado
+      $select = array();
+      if($query_uniquename){
+         $select['uniquename'] = $feature;
+      } else {
+         $select['name'] = $feature;
       }
-      // if we've gone up a level then add a new <ul> block
-      for($i = 0; $i < (ord($current) - ord($prev)); $i++){
-         $ul_content[++$level] .= "<ul>\n";
+      if($query_type){
+         $select['type_id'] = array(
+           'cv_id' => array(
+              'name' => 'sequence'
+           ),
+           'name' => $query_type,
+         );
       }
-      
-      // change all relative paths to absolute paths pointing to KEGG (www.genome.jp)
-      $matches[2] = preg_replace("/<a href=\"\//i","<a href=\"http://www.genome.jp/",$matches[2]);
-      
-      // add id to <a> tags so we can link kegg.gif to it in tripal_analysis_kegg.css
-      $matches[2] = preg_replace("/<a href=\"/i","<a id=\"tripal_kegg_brite_links\" target=\"_blank\" href=\"",$matches[2]);
-
-      // extract the features that have been mapped to the KEGG IDs
-      if(preg_match("/^(.*?);\s*(\<a.+)/",$matches[2],$keggline)){
-         $has_feature = 1;
-
-         // Find cvterm_id for 'kegg_brite_data'
-         $sql = "SELECT cvterm_id 
-                 FROM {cvterm} CVT
-                 INNER JOIN cv ON cv.cv_id = CVT.cv_id
-                 WHERE cv.name = 'tripal'
-                 AND CVT.name = '%s'";
-         $previous_db = tripal_db_set_active('chado');
-         $brite_data_type_id = db_result(db_query($sql, 'kegg_brite_data'));
-         tripal_db_set_active($previous_db);
-
-			// get the feature name using the user's regular expression
-			if ($query_re and preg_match("/$query_re/", $keggline[1], $parts)) {
-				$feature = $parts[1];
-			} 
-         // If not in above format then pull up to the first space
-         else {
-				if (preg_match('/^(.*?)\s.*$/', $keggline[1], $parts)) {
-					$feature = $parts[1];
-            } 
-            // if no match up to the first space then just use the entire string
-            else {
-               $feature = $keggline[1];
-            }
-         } 
+      $feature_arr = tripal_core_chado_select('feature',array('feature_id'),$select);
 
-         // now find the feature in chado
-         $select = array();
-         if($query_uniquename){
-            $select['uniquename'] = $feature;
-         } else {
-            $select['name'] = $feature;
-         }
-         if($query_type){
-            $select['type_id'] = array(
-              'cv_id' => array(
-                 'name' => 'sequence'
-              ),
-              'name' => $query_type,
-            );
-         }
-         $feature_arr = tripal_core_chado_select('feature',array('feature_id'),$select);
+      if(count($feature_arr) > 1){
+		   print "Ambiguous: '$feature' matches more than one feature and is being skipped.\n";
+			continue;
+      }
+      if(count($feature_arr) == 0){
+			print "Failed: '$feature' cannot find a matching feature in the database.\n";
+         continue;
+      }
+      $feature_id = $feature_arr[0]->feature_id;
 
-         if(count($feature_arr) > 1){
-			   print "Ambiguous: '$feature' matches more than one feature and is being skipped.\n";
-				continue;
-         }
-         if(count($feature_arr) == 0){
-				print "Failed: '$feature' cannot find a matching feature in the database.\n";
-            continue;
-         }
-         print "Adding KEGG results for $feature ($feature_id,$analysis_id): $type\n";
-         $feature_id = $feature_arr[0]->feature_id;
+      if($feature_id){
+         print "Adding KEGG term for $feature ($feature_id,$analysis_id). $heirarchy\n";
 
-         if($feature_id){
-            // get the node ID of the feature if one exists
-            $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
-            $nid = db_result(db_query($sql, $feature_id)); 
-    
-            //------------------------------------------------------
-            // Insert into analysisfeature table
-            //------------------------------------------------------
-            // Get the higest rank for this feature_id in analysisfeatureprop table
-            $sql = "SELECT MAX(rank) FROM {analysisfeatureprop} AFP ".
-                   "INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id ".       
-                   "WHERE feature_id=%d ".
-                   "AND analysis_id=%d ".
-                   "AND type_id=%d ";
-            $previous_db = tripal_db_set_active('chado');
-            $afp =  db_fetch_object(db_query($sql, $feature_id, $analysis_id, $brite_data_type_id));
-            tripal_db_set_active($prevous_db);
-            $hi_rank = 0;
-            if ($afp) {
-               $hi_rank = $afp->max + 1;
-            }
+         // add this term to the analysis feature properties
+         tripal_analysis_kegg_insert_featureprop($feature_id,$analysis_id,
+            $brite_id,$keggterm);
 
-            $sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
-                   "VALUES (%d, %d)";
-            $previous_db = tripal_db_set_active('chado');
-            db_query ($sql, $feature_id, $analysis_id);
-            tripal_db_set_active($previous_db);
+         // get the node ID of the feature if one exists
+         $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
+         $nid = db_result(db_query($sql, $feature_id)); 
 
-            // Get the newly inserted analysisfeature_id
-            $sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE feature_id = %d AND analysis_id = %d";
-            $previous_db = tripal_db_set_active('chado');
-            $analysisfeature_id = db_result(db_query($sql, $feature_id, $analysis_id));
-            tripal_db_set_active($previous_db);
-            
-            // Insert into analysisfeatureprop table
-            $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
-                   "VALUES (%d, %d, '%s', %d)";
-            $previous_db = tripal_db_set_active('chado');
-            db_query($sql, $analysisfeature_id, $brite_data_type_id, $keggline[2], $hi_rank);
-            tripal_db_set_active($previous_db);
+         // Add link to each matched feature
+         if($nid){
+            $value = preg_replace("/^(.*?)(;\s*\<a)/","<a id=\"tripal_kegg_feature_links\" target=\"_blank\" href=\"".url("node/$nid")."\">"."$1"."</a>"."$2",$value);
 
-            // Add link to each matched feature
-            if($nid){
-               $matches[2] = preg_replace("/^(.*?)(;\s*\<a)/","<a id=\"tripal_kegg_feature_links\" target=\"_blank\" href=\"".url("/node/$nid")."\">"."$1"."</a>"."$2",$matches[2]);
-            }
          }
-         // we only want to store results with features
-         $ul_content[$level] .= "<li id=\"term_$id\">$matches[2]</li>\n";
-      }     
-      $id++;
+         // if we have a feature match then add this to our results array
+         return $value;  
+      }       
+   }
+   return null;
+}
+/**
+*
+*/
+function tripal_analysis_kegg_insert_featureprop ($feature_id, $analysis_id,
+   $brite_id,$keggterm)
+{
+
+   // add the analysisfeature record if it doesn't already exist.
+   $values = array('feature_id' => $feature_id,'analysis_id' => $analysis_id);
+   $analysisfeature_arr = tripal_core_chado_select('analysisfeature',
+      array('analysisfeature_id'),$values);
+   if(count($analysisfeature_arr) == 0){
+      tripal_core_chado_insert('analysisfeature',$values);
+      $analysisfeature_arr = tripal_core_chado_select('analysisfeature',
+         array('analysisfeature_id'),$values);
+   }
+   $analysisfeature_id = $analysisfeature_arr[0]->analysisfeature_id;            
+   // Insert into analysisfeatureprop if the value doesn't already exist
+   // KEGG heir results sometimes have the same record more than once.
+   if($analysisfeature_id){
+      // Get the highest rank for this feature_id in analysisfeatureprop table
+      $sql = "SELECT rank FROM analysisfeatureprop WHERE analysisfeature_id = %d and type_id = %d ORDER BY rank DESC";
+      $previous_db = tripal_db_set_active('chado');
+      $result = db_fetch_object(db_query($sql,$analysisfeature_id,$brite_id));
+      tripal_db_set_active($previous);
+      $rank = 0;
+      if ($result and $result->rank > 0) {
+         $rank = $result->rank + 1;
+      }
+
+      $values = array(
+         'analysisfeature_id' => $analysisfeature_id, 
+         'type_id' => $brite_id,
+         'value' => $keggterm,
+         'rank' => $rank,
+      );
+
+      return tripal_core_chado_insert('analysisfeatureprop',$values);
+   }
+   else {
+      return 0;
    }
-   $content .= "</ul>";
-   fclose($handle);
-   return $content;
 }
 /*******************************************************************************
  * HOOK: Implementation of hook_nodeapi()
@@ -673,12 +772,16 @@ function tripal_analysis_kegg_nodeapi(&$node, $op, $teaser, $page) {
          } else {
             switch($node->type){
                case 'chado_organism':
-                  // Show KEGG BRITE on an analysis page OR KEGG info box on a feature page
+                  // Show KEGG report on the analysis page
                   $node->content['tripal_organism_kegg_summary'] = array(
                      '#value' => theme('tripal_organism_kegg_summary', $node),
-                     '#weight' => 6
                   );
                   break;
+               case 'chado_feature':
+                  // Show KEGG terms on a feature page
+                  $node->content['tripal_feature_kegg_terms'] = array(
+                     '#value' => theme('tripal_feature_kegg_terms', $node),
+                  );
             }
 
          }
@@ -703,6 +806,10 @@ function tripal_analysis_kegg_theme () {
          'arguments' => array('node'=> null),
          'template' => 'tripal_organism_kegg_summary',
       ),
+      'tripal_feature_kegg_terms' => array (
+         'arguments' => array('node'=> null),
+         'template' => 'tripal_feature_kegg_terms',
+      ),
       'tripal_analysis_kegg_report' => array (
          'arguments' => array('node'=> null),
          'template' => 'tripal_analysis_kegg_report',
@@ -731,6 +838,14 @@ function tripal_analysis_kegg_preprocess_tripal_organism_kegg_summary(&$variable
    $node = $variables['node'];
    $variables['tripal_analysis_kegg']['select_form'] = tripal_analysis_kegg_load_organism_kegg_summary($node);
 }
+/**
+*
+*/
+function tripal_analysis_kegg_preprocess_tripal_feature_kegg_terms(&$variables){
+   $node = $variables['node'];
+   $feature = $node->feature;
+   $variables['tripal_analysis_kegg']['results'] = tripal_analysis_kegg_load_feature_terms($feature);
+}
 /************************************************************************
  */
 function theme_tripal_analysis_kegg_search_index($node){
@@ -742,7 +857,7 @@ function theme_tripal_analysis_kegg_search_index($node){
               WHERE cv.name = 'tripal'
               AND CVT.name = '%s'";
       $previous_db = tripal_db_set_active('chado');
-      $brite_data_type_id = db_result(db_query($sql, 'kegg_brite_data'));
+      $brite_id = db_result(db_query($sql, 'kegg_brite_data'));
       
       // Get analysis id
       $sql = "SELECT analysis_id AS aid 
@@ -753,8 +868,8 @@ function theme_tripal_analysis_kegg_search_index($node){
               GROUP BY analysis_id";
       $feature = $node->feature;
       $feature_id = $feature->feature_id;
-      $hasResult = db_result(db_query($sql, $feature_id, $brite_data_type_id));
-      $result = db_query($sql, $feature->feature_id, $brite_data_type_id);
+      $hasResult = db_result(db_query($sql, $feature_id, $brite_id));
+      $result = db_query($sql, $feature->feature_id, $brite_id);
 
       // Show kegg result ORDER BY time
       if ($hasResult) { // If there is any result, show expandable box
@@ -800,6 +915,7 @@ function theme_tripal_analysis_kegg_search_result($node){
    return $content;
 }
 
+
 /************************************************************************
  */
 function tripal_analysis_kegg_load_organism_kegg_summary($node) {
@@ -905,67 +1021,62 @@ function tripal_analysis_kegg_organism_results($node) {
 }
 /************************************************************************
 */
-function tripal_analysis_kegg_feature_add($node) {
-      // Find cvterm_id for 'kegg_brite_data'
-      $sql = "SELECT cvterm_id 
-              FROM {cvterm} CVT
-              INNER JOIN cv ON cv.cv_id = CVT.cv_id
-              WHERE cv.name = 'tripal'
-              AND CVT.name = '%s'";
-      $previous_db = tripal_db_set_active('chado');
-      $brite_data_type_id = db_result(db_query($sql, 'kegg_brite_data'));
-      
-      // Get analysis id
-      $sql = "SELECT analysis_id AS aid 
-              FROM {analysisfeature} AF 
-              INNER JOIN analysisfeatureprop AFP ON AF.analysisfeature_id = AFP.analysisfeature_id
-              WHERE feature_id = %d
-              AND AFP.type_id = %d
-              GROUP BY analysis_id";
-      $feature = $node->feature;
-      $feature_id = $feature->feature_id;
-      $hasResult = db_result(db_query($sql, $feature_id, $brite_data_type_id));
-      $result = db_query($sql, $feature->feature_id, $brite_data_type_id);
+function tripal_analysis_kegg_load_feature_terms($feature) {
+  
+   $feature_id = $feature->feature_id;
+
+	// Get the KEGG results stored using the term 'kegg_brite_data'
+   $select = array(
+      'analysisfeature_id' => array(
+         'feature_id' => $feature_id,
+      ), 
+      'type_id' => array(
+         'name' => 'kegg_brite_data',
+         'cv_id' => array(
+            'name' => 'tripal'
+         ),
+      ),         
+   );
+   $afeatureprops = tripal_core_chado_select('analysisfeatureprop',array('*'),$select);
 
-      // Show kegg result ORDER BY time
-      if ($hasResult) { // If there is any result, show expandable box
-         $content .= "<div id=\"tripal_kegg-hits\" class=\"tripal_kegg-info-box\">
-                        <table class=\"tripal_kegg_results_table\">
-                          <tr><td>";
+   // iterate through all of the KEGG properties for this feature
+   $results = array();
+	foreach ($afeatureprops as $index => $afeatureprop) {
 
-         while ($ana = db_fetch_object($result)) {
-            // Show analysis date
-            $sql = "SELECT name, to_char(timeexecuted, 'MM-DD-YYYY') AS time 
-                    FROM {analysis} 
-                    WHERE analysis_id = %d";
-            $ana_details = db_fetch_object(db_query($sql, $ana->aid));
-            // Find node id for the analysis
-            tripal_db_set_active($previous_db);
-            $ana_nid = db_result(db_query("SELECT nid FROM {chado_analysis} WHERE analysis_id = %d", $ana->aid));
-            $ana_url = url("node/".$ana_nid);
-            $previous_db = tripal_db_set_active('chado');
-       
-            // Show content
-            $content .= "<strong>Analysis Date:</strong> $ana_details->time
-                           (<a href=$ana_url>$ana_details->name</a>)<br>";
-         
-            // Show Kegg results
-            $sql = "SELECT AFP.value AS afpvalue
-                    FROM {analysisfeatureprop} AFP
-                    INNER JOIN analysisfeature AF on AF.analysisfeature_id = AFP.analysisfeature_id
-                    WHERE AF.analysis_id = %d
-                    AND AF.feature_id = %d
-                   ";
-            $kegg_results = db_query($sql, $ana->aid, $feature_id);
-            while ($afp = db_fetch_object($kegg_results)) {
-               $content .= "$afp->afpvalue<br>";
-            }
-            $content .= "<br>";
-         }
-         $content .= '</td></tr></table></div>';
+      // get the analysis feature record
+      $analysisfeature_arr = tripal_core_chado_select('analysisfeature',array('analysis_id'),
+         array('analysisfeature_id' => $afeatureprop->analysisfeature_id));
+      $analysisfeature = $analysisfeature_arr[0];
+
+      // get the analysis record and the analysis_id
+      $analysis = tripal_core_generate_chado_var('analysis',
+         array('analysis_id' => $analysisfeature->analysis_id));
+      $analysis_id = $analysis->analysis_id;
+    
+      $results[$analysis_id]['analysis'] = $analysis;
+   }
+
+   // now get all the terms for each analysis
+   foreach($results as $analysis_id => $arr){
+      $select = array(
+         'analysisfeature_id' => array(
+            'analysis_id' => $analysis_id,
+            'feature_id' => $feature_id,
+         ),
+         'type_id' => array(
+            'name' => 'kegg_brite_data',
+            'cv_id' => array(
+               'name' => 'tripal',
+            ),
+         ),
+      );
+      $terms = tripal_core_chado_select('analysisfeatureprop',array('*'),$select);
+      foreach ($terms as $term){
+         $results[$analysis_id]['terms'][] = $term->value;
       }
-      tripal_db_set_active($previous_db);
-   return $content;
+   }
+
+   return $results;
 }
 /************************************************************************
 */

tripal_core/tripal_core.module

@@ -44,6 +44,10 @@ function tripal_core_init(){
       }  
       tripal_db_set_active($previous_db);  // now use drupal database
    }
+
+   // the tripal themeing uses rounded corners. We could use CSS but IE8 doesn't supprt
+   // rouneded corners so we will use the JQuery method.
+   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jquery-corners-0.3/jquery.corners.min.js');
 }
 
 /**