theme_tripal/node-chado_analysis.tpl.php

@@ -90,7 +90,7 @@ if (Drupal.jsEnabled) {
 <!-- Table of contents -->
 <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>
+   <span id="tripal_analysis_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_analysis_toc_list"  class="tripal_toc_list">
 
    </ul>

theme_tripal/node-chado_analysis_blast.tpl.php

@@ -89,7 +89,7 @@ if (Drupal.jsEnabled) {
 <!-- Table of contents -->
 <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>
+   <span id="tripal_analysis_blast_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_analysis_blast_toc_list" class="tripal_toc_list">
 
    </ul>

theme_tripal/node-chado_analysis_interpro.tpl.php

@@ -89,7 +89,7 @@ if (Drupal.jsEnabled) {
 <!-- 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>
+   <span id="tripal_analysis_interpro_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_analysis_interpro_toc_list" class="tripal_toc_list">
 
    </ul>

theme_tripal/node-chado_analysis_kegg.tpl.php

@@ -90,7 +90,7 @@ if (Drupal.jsEnabled) {
 <!-- Table of contents -->
 <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>
+   <span id="tripal_analysis_kegg_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_analysis_kegg_toc_list" class="tripal_toc_list">
 
    </ul>

theme_tripal/node-chado_analysis_unigene.tpl.php

@@ -91,8 +91,8 @@ if (Drupal.jsEnabled) {
 
 <!-- Table of contents -->
 <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>
+   <div id="tripal_analysis_unigene_toc_title" class="tripal_toc_title">Resources</div>
+   <span id="tripal_analysis_unigene_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_analysis_unigene_toc_list" class="tripal_toc_list">
 
    </ul>

theme_tripal/node-chado_stock.tpl.php

@@ -154,8 +154,8 @@ drupal_add_css('./tripal-node-templates.css');
 
 <!-- Table of contents -->
 <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>
+   <div id="tripal_stock_toc_title" class="tripal_toc_title">Resources</div>
+   <span id="tripal_stock_toc_desc" class="tripal_toc_desc"></span>
    <ul id="tripal_stock_toc_list" class="tripal_toc_list">
 
    </ul>

theme_tripal/tripal_analysis/tripal_analysis_base.tpl.php

@@ -2,6 +2,10 @@
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
 
+// 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>

theme_tripal/tripal_analysis_blast/tripal_analysis_blast_base.tpl.php

@@ -1,8 +1,15 @@
 <?php
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
+
+// the description is a text field so we want to expand that
+$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
+
+// get the blast data 
 $blast = $node->analysis->tripal_analysis_blast;
 
+//dpm($analysis);
+
 ?>
 <div id="tripal_analysis_blast-base-box" class="tripal_analysis_blast-info-box tripal-info-box">
   <div class="tripal_analysis_blast-info-box-title tripal-info-box-title">Blast Analysis Details</div>

theme_tripal/tripal_analysis_interpro/tripal_analysis_interpro_base.tpl.php

@@ -1,6 +1,10 @@
 <?php
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
+
+// the description is a text field so we want to expand that
+$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
+
 $interpro = $node->analysis->tripal_analysis_interpro;
 
 ?>

theme_tripal/tripal_analysis_kegg/tripal_analysis_kegg_base.tpl.php

@@ -2,6 +2,10 @@
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
 
+// 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_kegg-base-box" class="tripal_analysis_kegg-info-box tripal-info-box">
   <div class="tripal_analysis_kegg-info-box-title tripal-info-box-title">KEGG Analysis Details</div>

theme_tripal/tripal_analysis_unigene/tripal_analysis_unigene_base.tpl.php

@@ -1,6 +1,10 @@
 <?php
 $node = $variables['node'];
 $analysis = $variables['node']->analysis;
+
+// the description is a text field so we want to expand that
+$analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description');
+
 $unigene = $node->analysis->tripal_analysis_unigene;
 //dpm($node);
 

tripal_analysis/tripal_analysis.module

@@ -303,6 +303,49 @@ function chado_analysis_update($node){
  */
 function chado_analysis_form ($node){
 
+   $analysis = $node->analysis;
+
+   // get form defaults
+   $analysis_id = $node->analysis_id;
+   if(!$analysis_id){
+      $analysis_id = $analysis->analysis_id;
+   }
+   $analysisname = $node->analysisname;
+   if(!$analysisname){
+      $analysisname = $analysis->name;
+   }
+   $program = $node->program;
+   if(!$program){
+      $program = $analysis->program;
+   }
+   $programversion = $node->programversion;
+   if(!$programversion){
+      $programversion = $analysis->programversion;
+   }
+   $algorithm = $node->algorithm;
+   if(!$algorithm){
+      $algorithm = $analysis->algorithm;
+   }
+   $sourcename = $node->sourcename;
+   if(!$sourcename){
+      $sourcename = $analysis->sourcename;
+   }
+   $sourceversion = $node->sourceversion;
+   if(!$sourceversion){
+      $sourceversion = $analysis->sourceversion;
+   }
+   $sourceuri = $node->sourceuri;
+   if(!$sourceuri){
+      $sourceuri = $analysis->sourceuri;
+   }
+   $timeexecuted = $node->timeexecuted;
+   if(!$timeexecuted){
+      $timeexecuted = $analysis->timeexecuted;
+   }
+   $description = $node->description;
+   if(!$description){
+      $description = $analysis->description;
+   }
 	$form = array();
 	$form['title']= array(
       '#type' => 'hidden',
@@ -310,13 +353,13 @@ function chado_analysis_form ($node){
 	);
 	$form['analysis_id']= array(
       '#type' => 'hidden',
-      '#default_value' => $node->analysis->analysis_id,
+      '#default_value' => $analysis_id,
 	);
 	$form['analysisname']= array(
       '#type' => 'textfield',
       '#title' => t('Analysis Name'),
       '#required' => FALSE,
-      '#default_value' => $node->analysis->name,
+      '#default_value' => $analysisname,
       '#description' => t("This should be a handy short identifier that 
          describes the analysis succintly as possible which helps the user find analyses."),
 	);
@@ -324,28 +367,28 @@ function chado_analysis_form ($node){
       '#type' => 'textfield',
       '#title' => t('Program'),
       '#required' => TRUE,
-      '#default_value' => $node->analysis->program,
+      '#default_value' => $program,
       '#description' => t("Program name, e.g. blastx, blastp, sim4, genscan."),
 	);
 	$form['programversion']= array(
       '#type' => 'textfield',
       '#title' => t('Program Version'),
       '#required' => TRUE,
-      '#default_value' => $node->analysis->programversion,
+      '#default_value' => $programversion,
       '#description' => t("Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]"),
 	);
 	$form['algorithm']= array(
       '#type' => 'textfield',
       '#title' => t('Algorithm'),
       '#required' => FALSE,
-      '#default_value' => $node->analysis->algorithm,
+      '#default_value' => $algorithm,
       '#description' => t("Algorithm name, e.g. blast."),
 	);
 	$form['sourcename']= array(
       '#type' => 'textfield',
       '#title' => t('Source Name'),
       '#required' => TRUE,
-      '#default_value' => $node->analysis->sourcename,
+      '#default_value' => $sourcename,
       '#description' => t('The name of the source data.  This could be a file name, data set name or a 
            small description for how the data was collected.  For long descriptions use the description field below'),
 
@@ -354,20 +397,20 @@ function chado_analysis_form ($node){
       '#type' => 'textfield',
       '#title' => t('Source Version'),
       '#required' => FALSE,
-      '#default_value' => $node->analysis->sourceversion,
+      '#default_value' => $sourceversion,
       '#description' => t('If the source dataset has a version, include it here'),
 	);
 	$form['sourceuri']= array(
       '#type' => 'textfield',
       '#title' => t('Source URI'),
       '#required' => FALSE,
-      '#default_value' => $node->analysis->sourceuri,
+      '#default_value' => $sourceuri,
       '#description' => t("This is a permanent URL or URI for the source of the analysis. 
          Someone could recreate the analysis directly by going to this URI and 
          fetching the source data (e.g. the blast database, or the training model)."),
 	);
 	// Get time saved in chado
-	$default_time = $node->analysis->timeexecuted;
+	$default_time = $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", $default_time);
@@ -393,7 +436,7 @@ function chado_analysis_form ($node){
       '#rows' => 15,
       '#title' => t('Description and/or Program Settings'),
       '#required' => FALSE,
-      '#default_value' => $node->analysis->description,
+      '#default_value' => $description,
       '#description' => t('Please provide all necessary information to allow
          someone to recreate the analysis, including materials and methods
          for collection of the source data and performing the analysis'),
@@ -409,38 +452,15 @@ function chado_analysis_form ($node){
  * @ingroup tripal_analysis
  */
 function chado_analysis_load($node){
-	$additions = new stdClass();
 
-	// get the analysis_id for this node:
-	$sql = "SELECT analysis_id FROM {chado_analysis} WHERE nid = %d";
-	$ana_node = db_fetch_object(db_query($sql, $node->nid));
-	if ($ana_node) {
-		// get analysis information
-		$sql = "SELECT Analysis_id, name, 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
-		$additions->analysis = db_fetch_object(db_query($sql));
+   // get the feature details from chado
+   $analysis_id = chado_get_id_for_node('analysis',$node);
 
-      // get number of features assc with this analysis
-//     $sql = "SELECT count(feature_id) as featurecount ".
-//            "FROM {Analysisfeature} ".
-//            "WHERE Analysis_id = %d";
-//      $additions->featurecount = db_result(db_query($sql, $ana_node->analysis_id));
+   $values = array('analysis_id' => $analysis_id);
+   $analysis = tripal_core_generate_chado_var('analysis',$values);
 
-		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->analysis->name) {
-		$additions->title = $additions->analysis->name;
-	} else {
-		// Construct node title as "program version (source)
-		$additions->title = "$additions->analysis->program ($additions->analysis->programversion)";
-	}
-	return $additions;
+   $additions->analysis = $analysis;
+   return $additions;
 }
 
 /*******************************************************************************