Fixed bugs in organism module, and fixed teaser templates for organism and analysis

tripal_analysis/theme/tripal_analysis/tripal_analysis_base.tpl.php

@@ -37,7 +37,7 @@ $analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.descriptio
   }
   $rows[] = array(
     array(
-      'data' => 'Implementation',
+      'data' => 'Method',
       'header' => TRUE
     ),
     $software

tripal_analysis/theme/tripal_analysis/tripal_analysis_properties.tpl.php

@@ -16,7 +16,6 @@ if (count($properties) > 0) { ?>
   <div id="tripal_analysis-properties-box" class="tripal_analysis-info-box tripal-info-box">
     <div class="tripal_analysis-info-box-title tripal-info-box-title">More Details</div>
     <div class="tripal_analysis-info-box-desc tripal-info-box-desc">Additional information about this analysis:</div><?php
-    
     // the $headers array is an array of fields to use as the colum headers.
     // additional documentation can be found here
     // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7

tripal_analysis/theme/tripal_analysis/tripal_analysis_teaser.tpl.php

@@ -1,53 +1,16 @@
 <?php
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
+$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description'); ?>
 
-// the description is a text field so we want to expand that
-$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
-
-
-?>
-<div id="tripal_analysis-base-box" class="tripal_analysis-info-box tripal-info-box">
-  <div class="tripal_analysis-info-box-title tripal-info-box-title">Details</div>
-   <table id="tripal_analysis-table-base" class="tripal_analysis-table tripal-table tripal-table-vert">
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th>Analysis Name</th>
-        <td><?php print $analysis->name; ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Software</th>
-        <td><?php 
-          print $analysis->program; 
-          if($analysis->programversion){
-             print " (" . $analysis->programversion . ")"; 
-          }
-          if($analysis->algorithm){
-             print ". " . $analysis->algorithm; 
-          }
-          ?>
-        </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Source</th>
-        <td><?php 
-          if($analysis->sourceuri){
-             print "<a href=\"$analysis->sourceuri\">$analysis->sourcename</a>"; 
-          } else {
-             print $analysis->sourcename; 
-          }
-          if($analysis->sourceversion){
-             print " (" . $analysis->sourceversion . ")"; 
-          }
-          ?>
-          </td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-odd-row">
-        <th nowrap>Date performed</th>
-        <td><?php print preg_replace("/^(\d+-\d+-\d+) .*/","$1",$analysis->timeexecuted); ?></td>
-      </tr>
-      <tr class="tripal_analysis-table-odd-row tripal-table-even-row">
-        <th nowrap>Description</th>
-        <td><?php print $analysis->description; ?></td>
-      </tr>             	                                
-   </table>   
-</div>
+<div class="tripal_analysis-teaser tripal-teaser"> 
+  <div class="tripal-analysis-teaser-title tripal-teaser-title"><?php 
+    print l($node->title, "node/$node->nid", array('html' => TRUE));?>
+  </div>
+  <div class="tripal-analysis-teaser-text tripal-teaser-text"><?php 
+    print substr($analysis->description, 0, 650);
+    if (strlen($analysis->description) > 650) {
+      print "... " . l("[more]", "node/$node->nid");
+    } ?>
+  </div>
+</div>

tripal_analysis/tripal_analysis.module

@@ -169,6 +169,11 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
       'template' => 'tripal_analysis_properties',
       'path' => "$path/theme/tripal_analysis",
     ),
+    'tripal_analysis_teaser' => array(
+      'variables' => array('node' => NULL),
+      'template' => 'tripal_analysis_teaser',
+      'path' => "$path/theme/tripal_analysis",
+    ),
     'tripal_analysis_help' => array(
       'template' => 'tripal_analysis_help',
       'variables' =>  array(NULL),
@@ -249,6 +254,11 @@ function tripal_analysis_node_view($node, $view_mode, $langcode) {
           '#value' => theme('tripal_analysis_properties', array('node' => $node)),
         );
       }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_analysis_teaser'] = array(
+          '#value' => theme('tripal_analysis_teaser', array('node' => $node)),
+        );
+      }
       break;
   }
 }

tripal_core/api/tripal_core_chado.api.inc

@@ -2971,7 +2971,7 @@ function tripal_core_clean_orphaned_nodes($table, $job_id) {
 
     // see if the record in chado exist, if not remove the entry from the chado_$table
     $table_id = $table . "_id";
-    $results = chado_query($lsql, array(":" . $table . "_id " => $nid->$table_id));
+    $results = chado_query($lsql, array(":" . $table . "_id" => $nid->$table_id));
     $record = $results->fetchObject();
     if (!$record) {
       $deleted++;

tripal_core/theme/css/tripal.css

@@ -219,3 +219,22 @@ table.tripal-table-horz .tripal-table-odd-row {
 .tripal-notice {
   color: red;
 }
+
+/**
+ * Teaser
+ */
+.tripal-teaser {
+	 clear_both;
+	 margin-bottom: 10px;
+}
+.tripal-teaser-title {
+}
+.tripal-teaser-text {
+}
+.tripal-teaser-img {
+  width: 100px; 
+  height: 100px;
+  float: left; 
+  padding-right: 10px; 
+  padding-bottom: 5px;
+}

tripal_organism/theme/tripal_organism/tripal_organism_teaser.tpl.php

@@ -1,9 +1,16 @@
 <?php
-
+$organism  = $variables['node']->organism;
 $image_url = tripal_organism_get_image_url($organism, $node->nid); ?>
 
-<div style="clear:both">
-  <a href="<?php print url("node/" . $node->nid) ?>"><?php print $organism->genus. " " . $organism->species . ", " . $organism->common_name; ?></a>
-  <img src="<?php print $image_url ?>" width="100px" height="100px" style="float: left; padding-right: 10px; padding-bottom: 5px;">   
-  <?php print $organism->comment; ?>
+<div class="tripal_organism-teaser tripal-teaser"> 
+  <div class="tripal-organism-teaser-title tripal-teaser-title"><?php 
+    print l("<i>$organism->genus $organism->species</i> ($organism->common_name)", "node/$node->nid", array('html' => TRUE));?>
+  </div>
+  <div class="tripal-organism-teaser-text tripal-teaser-text">
+    <img class="tripal-teaser-img" src="<?php print $image_url ?>" ><?php
+    print substr($organism->comment, 0, 650);
+    if (strlen($organism->comment) > 650) {
+      print "... " . l("[more]", "node/$node->nid");
+    } ?>
+  </div>
 </div>

tripal_organism/tripal_organism.module

@@ -224,6 +224,11 @@ function tripal_organism_node_view($node, $view_mode, $langcode) {
           '#value' => theme('tripal_organism_base', array('node' => $node)),
         );
       }
+      if ($view_mode == 'teaster') {
+        $node->content['tripal_organism_teaser'] = array(
+          '#value' => theme('tripal_organism_teaser', array('node' => $node)),
+        );
+      }
       break;
   }
 }
@@ -588,12 +593,6 @@ function chado_organism_form($node, $form_state) {
     $organism_image = property_exists($node, 'organism_image') ? property_exists($node, 'organism_image') : '';
   }
 
-  $form['abbreviation']= array(
-    '#type' => 'textfield',
-    '#title' => t('Abbreviation'),
-    '#required' => TRUE,
-    '#default_value' => $abbreviation,
-  );
   $form['genus']= array(
     '#type' => 'textfield',
     '#title' => t('Genus'),
@@ -606,6 +605,12 @@ function chado_organism_form($node, $form_state) {
     '#required' => TRUE,
     '#default_value' => $species,
   );
+  $form['abbreviation']= array(
+    '#type' => 'textfield',
+    '#title' => t('Abbreviation'),
+    '#required' => TRUE,
+    '#default_value' => $abbreviation,
+  );
   $form['common_name']= array(
     '#type' => 'textfield',
     '#title' => t('Common Name'),