Merge branch 'master' of github.com:tripal/tripal_analysis_expression

README.md

@@ -174,10 +174,8 @@ The following panes are added to the following content types:
 
 ### Biomaterial
 * **Overview (base)** - The generic tripal overview pane.
-* **Feature Browser** - A list of features associated with the biomaterial.
 * **Properties** - Properties associated with the biomaterial.
 * **Cross References** - Accession terms associated with the biomaterial.
-* **Relationships** - Relationships associated with the biomaterial.
 
 ### Array Design
 * **Overview (base)** - The generic tripal overview pane.
@@ -200,7 +198,15 @@ Each Analysis: Expression content type has administrative pages. As an administr
 ![Administrator Pages for Content Types](https://cloud.githubusercontent.com/assets/14822959/13010514/2d2dc7be-d170-11e5-8670-92bdded6659d.png)
 
 ### Expression Display Administrative Page
-The display of expression data on feature pages can be configured.
+The display of expression data on feature pages can be configured. To configure the expression figure, navigate to **Tripal->Extensions->Expression Analysis->Tripal Expression Analysis Settings**. Available options are:
+
+* **Hide Expression Figure** - Hide expression figures on all feature pages. With this option you can load expression data without displaying the expression figure.
+* **Hide Biomaterial Labels** - Hide the name of the biomaterial under the expression figure tile or column. Biomaterial names will still appear in tooltips.
+* **Maximum Label Length** - Set the maximum acceptable biomaterial name length. Biomaterial names that are longer than this length will be truncated.
+* **Expession Column Width** - Change the size of the width of the tile or column in the figure. Value must be 15 or greater. 
+* **Default Heatmap Display** - The default display can be either a one dimensional heatmap or a bar chart. 
+
+
 
 
 

includes/tripal_analysis_expression.chado_node.inc

@@ -711,12 +711,18 @@ function chado_analysis_expression_biomaterial_validator_submit($form, &$form_st
     $re_ext = '/^.+\.(' . $fileext . ')/';
 
     // A matrix file.
-    if ($filetype == 'mat' and is_file($filepath) and preg_match($re_ext,$filepath)) {
+    if ($filetype == 'mat' and is_file($filepath)) {
       $data_ln = 0;
       $mat_fp = fopen($filepath, 'r');
       //Check a single matrix file.
       while($line = fgets($mat_fp)) {
         if ($data_ln == 1 or !$re_start) {
+          // Make sure this is actually a tab separated file.
+          if (!preg_match('/\t/', $line, $matches)) {
+            drupal_set_message(t('Warning: the expression loader expects a tab separated file. Please ensure the expression file is a tab separated file. Warning thrown on line:') . "\n", 'warning');
+            drupal_set_message($line, 'warning');
+            return;
+          }
           $linepart = preg_split('/\t/',$line,-1,PREG_SPLIT_NO_EMPTY);
           // Trim whitespace from biomaterial names.
           foreach ($linepart as $biomaterial) {

includes/tripal_analysis_expression_config.admin.inc

@@ -67,10 +67,10 @@ function tripal_analysis_expression_config_admin() {
 
   $form['feature_expression']['expression_display'] = array(
     '#type' => 'radios',
-    '#title' => t('Heatmap Display'),
+    '#title' => t('Default Heatmap Display'),
     '#options' => array(
       'tile' => t('One Dimensional Heatmap'),
-      'column' => t('Column Display'),
+      'column' => t('Chart Display'),
     ),
     '#default_value' => variable_get('chado_feature_expression_expression_display','column'),
   );

includes/tripal_biomaterial_loader.inc

@@ -383,7 +383,8 @@ function flat_biomaterial_parser($flat_path, $organism_id, $flat_file_type) {
         $db_id - create_ncbi_db('bioproject', 'NCBI BioProject', '');     
       }
       // First check to see if there is a dbxref record in the database corresponding to the accession number from the file.
-      if (empty(chado_select_record('dbxref', array('dbxref_id'), array('accession' => $line[$index], 'db_id' => $db_id)))) {
+      $record = chado_select_record('dbxref', array('dbxref_id'), array('accession' => $line[$index], 'db_id' => $db_id));
+      if (empty($record)) {
         // Insert value into dbxref table.
         $values = array(
           'accession' => $line[$index],

tripal_analysis_expression.install

@@ -464,11 +464,11 @@ function tripal_analysis_expression_add_cvterms() {
  * @ingroup tripal_analysis_expression
  */
 function tripal_analysis_expression_uninstall() {
-
+/*
   // Get localization function for installation.
   $t = get_t();
 
   // Unregister the analysis.
   tripal_unregister_analysis_child('tripal_analysis_expression');
-
+*/
 }