fixed bug in vies file upload handler

base/tripal_db/views/handlers/views_handler_field_dbxref_accession_link.inc

@@ -1 +0,0 @@
-../../../tripal_core/views/handlers/views_handler_field_dbxref_accession_link.inc

base/tripal_db/views/handlers/views_handler_field_dbxref_accession_link.inc

@@ -0,0 +1 @@
+../../../tripal_core/views/handlers/views_handler_field_dbxref_accession_link.inc

base/tripal_feature/views/handlers/views_handler_field_readable_date.inc

@@ -1 +0,0 @@
-../../../tripal_core/views/handlers/views_handler_field_readable_date.inc

base/tripal_feature/views/handlers/views_handler_field_readable_date.inc

@@ -0,0 +1 @@
+../../../tripal_core/views/handlers/views_handler_field_readable_date.inc

base/tripal_library/views/handlers/views_handler_field_readable_date.inc

@@ -1 +0,0 @@
-../../../tripal_core/views/handlers/views_handler_field_readable_date.inc

base/tripal_library/views/handlers/views_handler_field_readable_date.inc

@@ -0,0 +1 @@
+../../../tripal_core/views/handlers/views_handler_field_readable_date.inc

base/tripal_views/views/handlers/views_handler_filter_file_upload.inc

@@ -1,6 +1,5 @@
 <?php
 
-require_once "/var/www/sites/all/modules/views/handlers/views_handler_filter_string.inc";
 /**
  * Purpose: This Handler provides a file upload field.
  *

extensions/tripal_analysis_blast/theme/tripal_feature/tripal_feature_blast_results.tpl.php

@@ -71,7 +71,7 @@ if(count($blast_results_list) > 0){
 		foreach($hits_array AS $hit) { 
          $class = 'tripal-table-odd-row tripal_analysis_blast-table-odd-row';
          if($i % 2 == 0 ){
-            $class = 'tripal-table-even-row tripal_analysis_blast-table-odd-row';
+            $class = 'tripal-table-even-row tripal_analysis_blast-table-even-row';
          }?>
          <tr class="<?php print $class ?> tripal_analysis_blast-result-first-row">
             <td><?php print $i+1 ?>.</td>

extensions/tripal_analysis_blast/tripal_analysis_blast.module

@@ -9,7 +9,7 @@ require_once "includes/parse_blast_XML.inc";
  ******************************************************************************/
 function tripal_analysis_blast_init(){
 	// Add javascript and style sheet
-	drupal_add_css(drupal_get_path('module', 'tripal_analysis_blast') .'/theme/css/tripal_analysis_blast.css');
+	drupal_add_css(drupal_get_path('module', 'tripal_analysis_blast') .'/theme/css/tripal_analysis_blast.css', 'theme');
 	drupal_add_js(drupal_get_path('module', 'tripal_analysis_blast') .'/theme/js/tripal_analysis_blast.js');
 }
 

extensions/tripal_analysis_go/tripal_analysis_go.module

@@ -4,7 +4,7 @@ require_once "includes/gaf_loader.inc";
 
 function tripal_analysis_go_init(){
    // Add style sheet
-   drupal_add_css(drupal_get_path('module', 'tripal_analysis_go').'/theme/css/tripal_analysis_go.css');
+   drupal_add_css(drupal_get_path('module', 'tripal_analysis_go').'/theme/css/tripal_analysis_go.css', 'theme');
 
    drupal_add_js(drupal_get_path('module', 'tripal_analysis_go').'/theme/js/tripal_analysis_go.js');
 }
@@ -390,7 +390,7 @@ function tripal_analysis_go_cv_chart($chart_id){
         )
      ",
      type             => 'p',
-     size             => '550x175',
+     size             => '650x260',
      title            => $title,
   );
   return $options;

extensions/tripal_analysis_interpro/node-chado_analysis_interpro.tpl.php

@@ -83,7 +83,7 @@ if (Drupal.jsEnabled) {
 <div id="tripal_analysis_interpro_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php'); ?>
+   <?php include('theme/tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php'); ?>
 
    <?php print $content ?>
 </div>

extensions/tripal_analysis_interpro/tripal_analysis_interpro.module

@@ -9,7 +9,7 @@ require_once "includes/parseInterpro.inc";
 function tripal_analysis_interpro_init(){
 
 	// Add javascript and style sheet
-   drupal_add_css(drupal_get_path('module', 'tripal_analysis_interpro').'/theme/css/tripal_analysis_interpro.css');
+   drupal_add_css(drupal_get_path('module', 'tripal_analysis_interpro').'/theme/css/tripal_analysis_interpro.css', 'theme');
    drupal_add_js( drupal_get_path('module', 'tripal_analysis_interpro').'/theme/js/tripal_analysis_interpro.js');
 }
 /*******************************************************************************
@@ -428,7 +428,7 @@ function tripal_analysis_interpro_preprocess_tripal_feature_interpro_results(&$v
 
    // we don't know how many analysis are the old style HTML version and how many are the newer
    // XML format.  So, to be backwards compatible we should get both.
-   $feature->tripal_analysis_interpro->results->html = tripal_get_interpro_HTML_results($feature->feature_id);
+  // $feature->tripal_analysis_interpro->results->html = tripal_get_interpro_HTML_results($feature->feature_id);
 	$feature->tripal_analysis_interpro->results->xml = tripal_get_interpro_XML_results($feature->feature_id);
 }
 

extensions/tripal_analysis_kegg/tripal_analysis_kegg.module

@@ -8,9 +8,9 @@
 function tripal_analysis_kegg_init(){
    // add the tripal_analysis_kegg JS and CSS
    drupal_add_js(drupal_get_path('module', 'tripal_analysis_kegg').'/theme/js/tripal_analysis_kegg.js');
-   drupal_add_css(drupal_get_path('module', 'tripal_analysis_kegg').'/theme/css/tripal_analysis_kegg.css');
+   drupal_add_css(drupal_get_path('module', 'tripal_analysis_kegg').'/theme/css/tripal_analysis_kegg.css', 'theme');
    // add the jsTree JS and CSS
-   drupal_add_css(drupal_get_path('theme', 'tripal').'/js/jsTree/source/tree_component.css');
+   drupal_add_css(drupal_get_path('theme', 'tripal').'/js/jsTree/source/tree_component.css', 'theme');
    drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jsTree/source/_lib.js');
    drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jsTree/source/tree_component.js');
 }

extensions/tripal_analysis_unigene/node-chado_analysis_unigene.tpl.php

@@ -86,7 +86,7 @@ if (Drupal.jsEnabled) {
 <div id="tripal_analysis_unigene_details" class="tripal_details">
 
    <!-- Basic Details Theme -->
-   <?php include('tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php'); ?>
+   <?php include('theme/tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php'); ?>
 
    <?php print $content ?>
 </div>

extensions/tripal_analysis_unigene/tripal_analysis_unigene.module

@@ -2,7 +2,7 @@
 
 function tripal_analysis_unigene_init(){
    // Add style sheet
-   drupal_add_css(drupal_get_path('module', 'tripal_analysis_unigene').'/theme/css/tripal_analysis_unigene.css');
+   drupal_add_css(drupal_get_path('module', 'tripal_analysis_unigene').'/theme/css/tripal_analysis_unigene.css', 'theme');
 }
 /**
 *