Tripal views adheres to Drupal coding standards

tripal_views/tripal_views.coder_ignores.txt

@@ -7,4 +7,14 @@ tripal_views_integration_fields_form.tpl.php:48:style
 tripal_views_data_export_download_form.tpl.php:8:style
 
 ; All variables are set through the code and thus don't need to be filtered
-tripal_views_integration.inc:734:security
+tripal_views_integration.inc:734:security
+
+; SQL queries the chado database which does not use the drupal prefixing functionality
+; therefore, curly brackets ({}) are not appropriate.
+views/handlers/views_handler_filter_chado_select_cvterm_name.inc:53:sql
+views/handlers/views_handler_filter_chado_select_cvterm_name.inc:61:sql
+views/handlers/views_handler_field_dbxref_accession_link.inc:31:sql
+
+; SQL queries the pg_tables table to check if a table exists in chado; drupal
+; prefixing is not appropriate
+views/handlers/views_handler_field_chado_rel_by_type.inc:22:sql

tripal_views/tripal_views_data_export_download_form.tpl.php

@@ -9,3 +9,4 @@ print drupal_render($form);
 
 ?>
 
+<!-- END -->

tripal_views/tripal_views_integration_fields_form.tpl.php

@@ -51,3 +51,5 @@
 
 <?php print drupal_render($form); ?>
 
+<!-- END -->
+

tripal_views/views/handlers/chado_views_handler_field.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field extends views_handler_field {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field extends views_handler_field {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field extends views_handler_field {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_aggregate.inc

@@ -15,7 +15,7 @@ class chado_views_handler_field_aggregate extends chado_views_handler_field {
 
     if (!isset($this->chado_table_description)) {
       $this->chado_table_description = module_invoke_all('chado_' . $this->table . '_schema');
-      foreach($this->chado_table_description['foreign keys'] as $defn) {
+      foreach ($this->chado_table_description['foreign keys'] as $defn) {
         if ($defn['table'] != $this->view->base_table) {
           $join_table = module_invoke_all('chado_' . $defn['table'] . '_schema');
           foreach ($join_table['fields'] as $fname => $f) {
@@ -44,7 +44,7 @@ class chado_views_handler_field_aggregate extends chado_views_handler_field {
 
     $this->tokens = array();
     $value = array();
-    foreach( array_keys($this->chado_table_description['fields']) as $field ) {
+    foreach ( array_keys($this->chado_table_description['fields']) as $field ) {
       $t = '[' . $this->options['id'] . '-' . $field . ']';
       $this->tokens[$t] = t($field);
       $value[] = $t . ' == ' . $field;
@@ -60,7 +60,7 @@ class chado_views_handler_field_aggregate extends chado_views_handler_field {
     $form['format']['tokens'] = array(
       '#type' => 'item',
       '#title' => 'Format Tokens',
-      '#value' => implode("<br />",$value),
+      '#value' => implode("<br />", $value),
     );
 
   }
@@ -72,25 +72,25 @@ class chado_views_handler_field_aggregate extends chado_views_handler_field {
   }
 
 
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     if ($this->aggregated) {
-      foreach($values as $k => $v) {
+      foreach ($values as $k => $v) {
         $values[$k]->{$this->field_alias} = $this->split_array_agg_results($v->{$this->field_alias});
 
-        foreach($values[$k]->{$this->field_alias} as &$val) {
+        foreach ($values[$k]->{$this->field_alias} as &$val) {
 
           // First, get the token values
-          $subparts = explode(',',$val);
+          $subparts = explode(',', $val);
           $token_values = array();
-          foreach($subparts as $ssk => $ssv) {
-            if(preg_match('/(.*)::(.*)/',$ssv,$matches)) {
-              $token_values[ '[all-'.$matches[1].']' ] = $matches[2];
+          foreach ($subparts as $ssk => $ssv) {
+            if (preg_match('/(.*)::(.*)/', $ssv, $matches)) {
+              $token_values[ '[all-' . $matches[1] . ']' ] = $matches[2];
             }
           }
 
           // Now manually sub them in
-          $val = str_replace(array_keys($token_values),$token_values,$this->options['format']['format_string']);
+          $val = str_replace(array_keys($token_values), $token_values, $this->options['format']['format_string']);
 
         }
       }

tripal_views/views/handlers/chado_views_handler_field_boolean.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_boolean extends views_handler_field_boolean {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_boolean extends views_handler_field_boolean {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_boolean extends views_handler_field_boolean {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_counter.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_counter extends views_handler_field_counter {
 
-  function init (&$view, $options) {
+  function init =(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_counter extends views_handler_field_counter {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_counter extends views_handler_field_counter {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_custom.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_custom extends views_handler_field_custom {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_custom extends views_handler_field_custom {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_custom extends views_handler_field_custom {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_markup.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_markup extends views_handler_field_markup {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_markup extends views_handler_field_markup {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_markup extends views_handler_field_markup {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_math.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_math extends views_handler_field_math {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_math extends views_handler_field_math {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_math extends views_handler_field_math {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_field_numeric.inc

@@ -10,9 +10,9 @@
  */
 class chado_views_handler_field_numeric extends views_handler_field_numeric {
 
-  function init (&$view, $options) {
+  function init(&$view, $options) {
     include_once('chado_wrapper_functions.inc');
-    parent::init($view,$options);
+    parent::init($view, $options);
   }
 
   /**
@@ -57,7 +57,7 @@ class chado_views_handler_field_numeric extends views_handler_field_numeric {
    * Determines whether the current field is aggregated or not
    * Note: The parent::query() takes care of adding the field to the query, etc.
    */
-  function query () {
+  function query() {
     parent::query();
     $this->aggregated = chado_wrapper_is_aggregated_by_join($this);
   }
@@ -65,7 +65,7 @@ class chado_views_handler_field_numeric extends views_handler_field_numeric {
   /**
    * Splits the aggregated values up for use in rendering
    */
-  function pre_render (&$values) {
+  function pre_render(&$values) {
 
     // further check the results to see if this field is a postgresql array
     $this->aggregated = chado_wrapper_is_aggregated_by_result($this, $values);

tripal_views/views/handlers/chado_views_handler_filter_boolean_operator_string.inc

@@ -29,14 +29,14 @@ class chado_views_handler_filter_boolean_operator_string extends views_handler_f
     $form['agg']['records_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
-      '#description' => t('Filters '.$this->view->base_table.' to only those with the value in the aggregate array.'),
+      '#description' => t('Filters %table to only those with the value in the aggregate array.', array('%table' => $this->view->base_table)),
       '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
-      '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of '.$this->view->base_table.' records.'),
+      '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %table records.', array('%table' => $this->view->base_table)),
       '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
     );
 
@@ -46,20 +46,21 @@ class chado_views_handler_filter_boolean_operator_string extends views_handler_f
    * If the table to be filtered is not aggregated uses the parent::query()
    * However, if it is uses postgresql any() function to compare
    */
-  function query () {
+  function query() {
     $this->ensure_my_table();
 
-
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 
     if (!$this->aggregated) {
       parent::query();
-    } else {
+    }
+    else {
 
       // Only base records with value in the aggregated field
       // This doesn't restrict the items in the aggregate field
@@ -74,7 +75,7 @@ class chado_views_handler_filter_boolean_operator_string extends views_handler_f
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field ." = '". $this->value."'";
+        $table['join']->filter[] = $field . " = '" . $this->value . "'";
       }
     }
 

tripal_views/views/handlers/chado_views_handler_filter_date.inc

@@ -46,20 +46,22 @@ class chado_views_handler_filter_date extends views_handler_filter_date {
    * If the table to be filtered is not aggregated uses the parent::query()
    * However, if it is uses postgresql any() function to compare
    */
-  function query () {
+  function query() {
     $this->ensure_my_table();
 
 
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 
     if (!$this->aggregated) {
       parent::query();
-    } else {
+    }
+    else {
 
       // Only base records with value in the aggregated field
       // This doesn't restrict the items in the aggregate field
@@ -74,7 +76,7 @@ class chado_views_handler_filter_date extends views_handler_filter_date {
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field ." = '". $this->value."'";
+        $table['join']->filter[] = $field . " = '" . $this->value . "'";
       }
     }
 

tripal_views/views/handlers/chado_views_handler_filter_equality.inc

@@ -46,20 +46,22 @@ class chado_views_handler_filter_equality extends views_handler_filter_equality
    * If the table to be filtered is not aggregated uses the parent::query()
    * However, if it is uses postgresql any() function to compare
    */
-  function query () {
+  function query() {
     $this->ensure_my_table();
 
 
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 
     if (!$this->aggregated) {
       parent::query();
-    } else {
+    }
+    else {
 
       // Only base records with value in the aggregated field
       // This doesn't restrict the items in the aggregate field
@@ -74,7 +76,7 @@ class chado_views_handler_filter_equality extends views_handler_filter_equality
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field ." = '". $this->value."'";
+        $table['join']->filter[] = $field . " = '" . $this->value . "'";
       }
     }
 

tripal_views/views/handlers/chado_views_handler_filter_float.inc

@@ -46,20 +46,22 @@ class chado_views_handler_filter_float extends views_handler_filter_float {
    * If the table to be filtered is not aggregated uses the parent::query()
    * However, if it is uses postgresql any() function to compare
    */
-  function query () {
+  function query() {
     $this->ensure_my_table();
 
 
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 
     if (!$this->aggregated) {
       parent::query();
-    } else {
+    }
+    else {
 
       // Only base records with value in the aggregated field
       // This doesn't restrict the items in the aggregate field
@@ -74,7 +76,7 @@ class chado_views_handler_filter_float extends views_handler_filter_float {
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field ." = '". $this->value."'";
+        $table['join']->filter[] = $field . " = '" . $this->value . "'";
       }
     }
 

tripal_views/views/handlers/chado_views_handler_filter_string.inc

@@ -46,20 +46,22 @@ class chado_views_handler_filter_string extends views_handler_filter_string {
    * If the table to be filtered is not aggregated uses the parent::query()
    * However, if it is uses postgresql any() function to compare
    */
-  function query () {
+  function query() {
     $this->ensure_my_table();
 
 
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 
     if (!$this->aggregated) {
       parent::query();
-    } else {
+    }
+    else {
 
       // Only base records with value in the aggregated field
       // This doesn't restrict the items in the aggregate field
@@ -74,7 +76,7 @@ class chado_views_handler_filter_string extends views_handler_filter_string {
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field ." = '". $this->value."'";
+        $table['join']->filter[] = $field . " = '" . $this->value . "'";
       }
     }
 

tripal_views/views/handlers/chado_views_handler_sort.inc

@@ -27,13 +27,14 @@ class chado_views_handler_sort extends views_handler_sort {
    * Adds the sort to the query only if the field isn't aggregated
    * If the field is aggregated then the sort has to be applied at the join handler level
    */
-  function query () {
+  function query() {
 
     // Determine if the current field is part of an aggregated table
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 

tripal_views/views/handlers/chado_views_handler_sort_date.inc

@@ -27,13 +27,14 @@ class chado_views_handler_sort extends views_handler_sort_date {
    * Adds the sort to the query only if the field isn't aggregated
    * If the field is aggregated then the sort has to be applied at the join handler level
    */
-  function query () {
+  function query() {
 
     // Determine if the current field is part of an aggregated table
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 

tripal_views/views/handlers/chado_views_handler_sort_formula.inc

@@ -27,13 +27,14 @@ class chado_views_handler_sort extends views_handler_sort_formula {
    * Adds the sort to the query only if the field isn't aggregated
    * If the field is aggregated then the sort has to be applied at the join handler level
    */
-  function query () {
+  function query() {
 
     // Determine if the current field is part of an aggregated table
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 

tripal_views/views/handlers/chado_views_handler_sort_menu_hierarchy.inc

@@ -27,13 +27,14 @@ class chado_views_handler_sort extends views_handler_sort_menu_hierarchy {
    * Adds the sort to the query only if the field isn't aggregated
    * If the field is aggregated then the sort has to be applied at the join handler level
    */
-  function query () {
+  function query() {
 
     // Determine if the current field is part of an aggregated table
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 

tripal_views/views/handlers/chado_views_handler_sort_random.inc

@@ -27,13 +27,14 @@ class chado_views_handler_sort extends views_handler_sort_random {
    * Adds the sort to the query only if the field isn't aggregated
    * If the field is aggregated then the sort has to be applied at the join handler level
    */
-  function query () {
+  function query() {
 
     // Determine if the current field is part of an aggregated table
     $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
-    } else {
+    }
+    else {
       $this->aggregated = FALSE;
     }
 

tripal_views/views/handlers/chado_wrapper_functions.inc

@@ -17,11 +17,12 @@
 function chado_wrapper_split_array_agg_results($handler, &$values) {
 
   if ($handler->aggregated) {
-    foreach($values as $k => $v) {
+    foreach ($values as $k => $v) {
 
-      if(preg_match('/^{(.*)}$/',$v->{$handler->field_alias}, $matches)) {
+      if (preg_match('/^{(.*)}$/', $v->{$handler->field_alias}, $matches)) {
         $values[$k]->{$handler->field_alias} = str_getcsv($matches[1]);
-      } else {
+      }
+      else {
         $values[$k]->{$handler->field_alias} = array();
       }
     }
@@ -39,11 +40,11 @@ function chado_wrapper_split_array_agg_results($handler, &$values) {
  * @return
  *   TRUE/FALSE if or if not the field has the aggregated join handler
  */
-function chado_wrapper_is_aggregated_by_join ($handler) {
+function chado_wrapper_is_aggregated_by_join($handler) {
   $aggregated = FALSE;
 
   $table = $handler->query->get_table_info($handler->table);
-  if (preg_match('/aggregator/',$table['join']->definition['handler'])) {
+  if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
     $aggregated = TRUE;
   }
 
@@ -61,10 +62,10 @@ function chado_wrapper_is_aggregated_by_join ($handler) {
  * @return
  *   TRUE/FALSE if or if not the field is aggregated
  */
-function chado_wrapper_is_aggregated_by_result ($handler, $values) {
+function chado_wrapper_is_aggregated_by_result($handler, $values) {
   $aggregated = FALSE;
 
-  if (preg_match('/^{.*}$/',$values[0]->{$handler->field_alias})) {
+  if (preg_match('/^{.*}$/', $values[0]->{$handler->field_alias})) {
     $aggregated = TRUE;
   }
 
@@ -96,7 +97,8 @@ function chado_wrapper_render_items($handler, $values) {
 
   // Otherwise it is not aggragated
   // Just render like the default handler would
-  } else {
+  }
+  else {
     return $handler->parent_render($values);
   }
 }

tripal_views/views/handlers/views_handler_field_chado_count.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Purpose: Provide a field that counts the number of records in the current table
  *   are connected to the base table. For example, this field could be used to count
  *   the number of features connected to a given organism -base table=organism,
@@ -19,7 +20,8 @@ class views_handler_field_chado_count extends views_handler_field {
     // check that it was provided in the field definition and if not warn
     if ($this->definition['table_to_query']) {
       $this->aliases['current_table'] = $this->definition['table_to_query'];
-    } else {
+    }
+    else {
       drupal_set_message(t("The field definition ( in hook_views_data() ) needs to specify the 'table_to_query' in order for this fields to work. Field:%field in the %table table definition"), array('%field' => $this->field, '%table' => $this->table), 'error');
     }
 
@@ -35,7 +37,7 @@ class views_handler_field_chado_count extends views_handler_field {
 
   function pre_render(&$values) {
     // Render nothing if the current table wasn't set in the field definition
-    if(!$this->aliases['current_table']) {
+    if (!$this->aliases['current_table']) {
       return '';
     }
 

tripal_views/views/handlers/views_handler_field_chado_rel_by_type.inc

@@ -1,7 +1,8 @@
 <?php
 
 /**
- * Field handler allowing all relationships of a specified type for a given chado entity to be displayed in 
+ * @file
+ * Field handler allowing all relationships of a specified type for a given chado entity to be displayed in
  * a single cell
  *
  * @ingroup views_field_handlers
@@ -12,18 +13,18 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
 
     // Boolean to determine whether
     //    TRUE =>  value (property type)      -more than one property type displayed
-    //    FALSE => or just value is rendered  -only 1 porperty type is displayed    
+    //    FALSE => or just value is rendered  -only 1 porperty type is displayed
     $this->display_type = TRUE;
 
     $this->chado_type = $this->table;
-    
+
     // Check that this chado type has a <chado type>_relationship table
     $sql = "SELECT true as bool FROM pg_tables WHERE tablename='%s_relationship'";
     $previous_db = tripal_db_set_active('chado');
-    $exists = db_fetch_object(db_query($sql,$this->table));
+    $exists = db_fetch_object(db_query($sql, $this->table));
     tripal_db_set_active($previous_db);
     if (!$exists->bool) {
-      drupal_set_message('The Relationship by Type handler cannot be used with this table since the '.$this->table.'_relationship table doesn\'t exist', 'error');
+      drupal_set_message(t('The Relationship by Type handler cannot be used with this table since the %table_relationship table doesn\'t exist', array('%table' => $this->table)), 'error');
       $this->broken = TRUE;
     }
   }
@@ -31,7 +32,7 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
   function option_definition() {
     $options = parent::option_definition();
     $options['rel_type_ids'] = array('default' => array());
-    $options['rel_display_options'] = array('default' => array('subject','type','object'));
+    $options['rel_display_options'] = array('default' => array('subject', 'type', 'object'));
     return $options;
   }
 
@@ -45,10 +46,11 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
       $form = array(
         'broken' => array(
           '#type' => 'item',
-          '#value' => 'The Relationship by Type handler cannot be used with this table since the '.$this->table.'_relationship table doesn\'t exist',
+          '#value' => 'The Relationship by Type handler cannot be used with this table since the ' . $this->table . '_relationship table doesn\'t exist',
         ),
       );
-    } else {    
+    }
+    else {
       $form['rel_display_parts'] = array(
         '#type' => 'checkboxes',
         '#title' => t('Display Relationship Parts'),
@@ -63,29 +65,29 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
         ),
         '#default_value' => array($this->options['rel_display_parts']['subject'], $this->options['rel_display_parts']['type'], $this->options['rel_display_parts']['object']),
       );
-      
+
       $form['rel_display_rels'] = array(
         '#type' => 'radios',
         '#title' => t('Display Relationships Where'),
         '#description' => t('Only relationships where the selected criteria is met will be shown. '
           .'The parts of a relationship are: [Subject] [Relationship Type] [Object]. '
           .'For example, with the relationships Sarah is the maternal parent of Fred and '
-          .'Fred is the paternal_parent of Max where Fred is the current '.$this->chado_type.', '
-          .'if you selected "Current '.$this->chado_type.' is the Object" only Sarah is the maternal parent of Fred'
+          .'Fred is the paternal_parent of Max where Fred is the current ' . $this->chado_type . ', '
+          .'if you selected "Current ' . $this->chado_type . ' is the Object" only Sarah is the maternal parent of Fred'
           .' would be displayed.'),
         '#options' => array(
-          'subject' => 'Current '.$this->chado_type.' is the Subject',
-          'object' => 'Current '.$this->chado_type.' is the Object',
-          'all' => 'Current '.$this->chado_type.' is the Subject and/or Object',
+          'subject' => 'Current ' . $this->chado_type . ' is the Subject',
+          'object' => 'Current ' . $this->chado_type . ' is the Object',
+          'all' => 'Current ' . $this->chado_type . ' is the Subject and/or Object',
         ),
         '#default_value' => $this->options['rel_display_rels'],
       );
-      
+
       $options = array();
       $sql = 'SELECT rel.type_id, cvt.name FROM %s_relationship rel LEFT JOIN cvterm cvt ON cvt.cvterm_id=rel.type_id GROUP BY rel.type_id,cvt.name';
       $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql,$this->table);
-      tripal_db_set_active($previous_db);      
+      $resource = db_query($sql, $this->table);
+      tripal_db_set_active($previous_db);
       while ($r = db_fetch_object($resource)) {
         $options[ $r->type_id ] = $r->name;
       }
@@ -104,36 +106,36 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
   function query() {
     $this->add_additional_fields();
   }
-  
+
   function pre_render($values) {
     $this->aliases['relationships'] = $this->chado_type . '_relationships';
     $chado_id = $this->table . '_id';
     $chado_relationship_id = $this->table . '_relationship_id';
     $this->aliases[$chado_id] = $chado_id;
     $this->field_alias = $this->aliases[$chado_id];
-    
+
     //check if relationships added to results, if not then add
     if (empty( $this->view->result[0]->{$this->aliases['relationships']} )) {
-      
+
       // retrieve the chado_id for each record in the views current page
       $chado_ids = array();
       foreach ($this->view->result as $row_num => $row) {
         $chado_ids[$row_num] = $row->{$chado_id};
       }
-      
+
       // Add relationships to the view results
       $sql = "SELECT rel.*, cvterm.name as type_name, "
         ."subject.name as subject_name, object.name as object_name "
-        ."FROM ".$this->table."_relationship rel "
-        ."LEFT JOIN ".$this->table." subject ON rel.subject_id=subject.".$chado_id." "
-        ."LEFT JOIN ".$this->table." object ON rel.object_id=object.".$chado_id." "
+        ."FROM " . $this->table . "_relationship rel "
+        ."LEFT JOIN " . $this->table . " subject ON rel.subject_id=subject." . $chado_id . " "
+        ."LEFT JOIN " . $this->table . " object ON rel.object_id=object." . $chado_id . " "
         ."LEFT JOIN cvterm cvterm ON rel.type_id = cvterm.cvterm_id "
-        ."WHERE rel.subject_id IN (".implode(',',$chado_ids).") "
-        ."OR rel.object_id IN (".implode(',',$chado_ids).") ";
+        ."WHERE rel.subject_id IN (" . implode(',', $chado_ids) . ") "
+        ."OR rel.object_id IN (" . implode(',', $chado_ids) . ") ";
       $previous_db = tripal_db_set_active('chado');
       $resource = db_query($sql);
       tripal_db_set_active($previous_db);
-    
+
       while ($r = db_fetch_object($resource)) {
         if (in_array($r->subject_id, $chado_ids)) {
           $key = array_search($r->subject_id, $chado_ids);
@@ -148,14 +150,14 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
       }
 
     }
-    
+
     // add relationships to this field
     foreach ($this->view->result as $result) {
       if (!empty($result->{$this->aliases['relationships']})) {
         $relationships2keep = array_filter($this->options['rel_type_ids']);
-        
+
         // all relationships including the current chado guy
-        foreach ($result->{$this->aliases['relationships']} as $relationship) {      
+        foreach ($result->{$this->aliases['relationships']} as $relationship) {
           // perform filtering------
           //type
           if (!empty($this->options['rel_type_ids'])) {
@@ -163,18 +165,19 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
               continue;
             }
           }
-          
+
           //"Display Relationships Where" criteria
           if (preg_match('/subject/', $this->options['rel_display_rels'])) {
             if ($relationship->{$chado_id} != $relationship->subject_id) {
               continue;
-            }      
-          } elseif (preg_match('/object/', $this->options['rel_display_rels'])) {
+            }
+          }
+          elseif (preg_match('/object/', $this->options['rel_display_rels'])) {
             if ($relationship->{$chado_id} != $relationship->object_id) {
               continue;
             }
           }
-          
+
           // Add relationship to the list of items to be rendered
           $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}][$chado_id] = $relationship->{$chado_id};
           $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}][$chado_relationship_id] = $relationship->{$chado_relationship_id};
@@ -186,13 +189,13 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
           $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['type_name'] = $relationship->type_name;
         }
       }
-    } 
-    
+    }
+
   }
 
   function render_item($count, $item) {
     $text = array();
-    
+
     // Render Parts
     if ($this->options['rel_display_parts']['subject']) {
       $text[] = $item['subject_name'];
@@ -203,7 +206,7 @@ class views_handler_field_chado_rel_by_type extends views_handler_field_prerende
     if ($this->options['rel_display_parts']['object']) {
       $text[] = $item['object_name'];
     }
-    
+
     return implode(' ', $text);
   }
 }

tripal_views/views/handlers/views_handler_field_chado_tf_boolean.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * A handler to provide proper displays for booleans.
  *
  * Allows for display of true/false, yes/no, on/off.
@@ -28,11 +29,11 @@ class views_handler_field_chado_tf_boolean extends views_handler_field_boolean {
     }
 
     if (isset($this->formats[$this->options['type']])) {
-      return preg_match('/t/',$value) ? $this->formats[$this->options['type']][0] : $this->formats[$this->options['type']][1];
+      return preg_match('/t/', $value) ? $this->formats[$this->options['type']][0] : $this->formats[$this->options['type']][1];
     }
     else {
       return preg_match('/t/', $value) ? $this->formats['yes-no'][0] : $this->formats['yes-no'][1];
     }
   }
-  
+
 }

tripal_views/views/handlers/views_handler_field_cvterm_name.inc

@@ -1,8 +1,7 @@
-<?php 
-// $Id$
+<?php
 
 /**
- *
+ * @file
  * @ingroup views_field_handlers
  * @ingroup tripal_core
  */
@@ -12,16 +11,16 @@ class views_handler_field_cvterm_name extends views_handler_field {
    * Add join to the cvterm table and cvterm.name field to the query
    */
   function query() {
-      
+
     // if this table isn't a base table
     // if it is this can be done by describing a join between base table and cvterm
-    if (!preg_match('/^'.$this->view->base_table.'$/', $this->table)) {
+    if (!preg_match('/^' . $this->view->base_table . '$/', $this->table)) {
 
       //Want to add join: LEFT JOIN cvterm nd_experimentprop_cvterm ON nd_experimentprop.type_id = nd_experimentprop_cvterm.cvterm_id
-      //===============================================================      
+      //===============================================================
 
       $this->query->ensure_table($this->table);
-      
+
       // add to table_queue--------------------------------------------
       $cvterm_join['table'] = 'cvterm';
       $cvterm_join['num'] = 1;
@@ -33,7 +32,7 @@ class views_handler_field_cvterm_name extends views_handler_field {
       $cvterm_join['join']->field = 'cvterm_id';
       $cvterm_join['join']->left_table = $this->table;
       $cvterm_join['join']->left_field = 'type_id';
-      
+
       $cvterm_join['join']->definition['table'] = 'cvterm';
       $cvterm_join['join']->definition['field'] = 'cvterm_id';
       $cvterm_join['join']->definition['left_table'] = $this->table;
@@ -42,26 +41,26 @@ class views_handler_field_cvterm_name extends views_handler_field {
       $this->query->table_queue[$cvterm_join['alias']] = $cvterm_join;
 
       // add to table--------------------------------------------------
-      $this->query->tables[$this->view->base_table][$this->table.'_cvterm'] = array(
+      $this->query->tables[$this->view->base_table][$this->table . '_cvterm'] = array(
         'count' => 1,
-        'alias' => $this->table.'_cvterm',
-      );    
+        'alias' => $this->table . '_cvterm',
+      );
 
       //Want to add field: nd_experimentprop_cvterm.name as nd_experimentprop_type
       //===============================================================
-      $field_alias = $this->table.'_cvterm_name';
-      $this->query->add_field($this->table.'_cvterm', 'name');
+      $field_alias = $this->table . '_cvterm_name';
+      $this->query->add_field($this->table . '_cvterm', 'name');
       $this->add_additional_fields();
-      $this->aliases['name'] = $field_alias;  
-      
+      $this->aliases['name'] = $field_alias;
+
     }
   }
-  
+
   /**
    * Ensure that the type/cvterm name is rendered
    */
- function render($values) { 
-   return $values->{$this->aliases['name']}; 
- }
-  
+  function render($values) {
+    return $values->{$this->aliases['name']};
+  }
+
 }

tripal_views/views/handlers/views_handler_field_dbxref_accession_link.inc

@@ -1,42 +1,47 @@
 <?php
 
 /**
+ * @file
+ * Used for a custom field so that field can render the database reference link
  *
  * @ingroup views_field_handlers
  * @ingroup tripal_core
  */
 class views_handler_field_dbxref_accession_link extends views_handler_field {
- function construct() {
-   parent::construct();
-   $this->additional_fields['accession'] = 'accession';
-   $this->additional_fields['db_id'] = 'db_id';
-
- }
-
- function query() { 
-   $this->ensure_my_table();
-   $this->add_additional_fields(); 
- }
-
- function render($values) { 
-
-   $accession = $values->{$this->aliases['accession']}; 
-   $db_id = $values->{$this->aliases['db_id']};
-
-   if (!empty($db_id) AND !empty($accession)) {
-     $previous_db = tripal_db_set_active('chado');
-     $result = db_fetch_object(db_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
-     tripal_db_set_active($previous_db);   
-     $urlprefix = $result->urlprefix;
-
-     if (!empty($urlprefix)) {
-       $accession_link = $urlprefix . $accession;
-       return($accession_link); 
-     } else {
-       return $accession;
-     }
-   } else {
-     return $accession;
-   }
- } 
-} 
+  function construct() {
+    parent::construct();
+
+    $this->additional_fields['accession'] = 'accession';
+    $this->additional_fields['db_id'] = 'db_id';
+
+  }
+
+  function query() {
+    $this->ensure_my_table();
+    $this->add_additional_fields();
+  }
+
+  function render($values) {
+
+    $accession = $values->{$this->aliases['accession']};
+    $db_id = $values->{$this->aliases['db_id']};
+
+    if (!empty($db_id) AND !empty($accession)) {
+      $previous_db = tripal_db_set_active('chado');
+      $result = db_fetch_object(db_query('SELECT urlprefix FROM db WHERE db_id=%d', $db_id));
+      tripal_db_set_active($previous_db);
+      $urlprefix = $result->urlprefix;
+
+      if (!empty($urlprefix)) {
+        $accession_link = $urlprefix . $accession;
+        return $accession_link;
+      }
+      else {
+        return $accession;
+      }
+    }
+    else {
+      return $accession;
+    }
+  }
+}

tripal_views/views/handlers/views_handler_field_node_optional.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Field handler to provide simple renderer that allows linking to a node.
  *
  * @ingroup views_field_handlers
@@ -15,12 +16,12 @@ class views_handler_field_node_optional extends views_handler_field_node {
       $this->additional_fields['language'] = array('table' => 'node', 'field' => 'language');
     }
   }
-  
+
   /**
    * Add chado_* and *_node alias'd left joins to the table
    */
   function query() {
-    
+
     // Check what we have (ie: current table? node table? )
     $chado_table = 'chado_' . $this->table;
     foreach ($this->query->table_queue as $table_def) {
@@ -28,21 +29,21 @@ class views_handler_field_node_optional extends views_handler_field_node {
       if ($table_def['table'] == $this->table) {
         $this_table_alias = $table_def['alias'];
       }
-      
+
       // check is node joined to #this->table
       if ($table_def['table'] == $chado_table) {
         $node_table_alias = $table_def['alias'];
       }
     }
-    
+
     // First: Add the main field-----------------------------------------------
     if (!$this_table_alias) {
       $this_table_alias = $this->ensure_my_table();
     }
-    $field_alias = $this->query->add_field($this_table_alias, $this->real_field); 
+    $field_alias = $this->query->add_field($this_table_alias, $this->real_field);
     $this->aliases[ $this->real_field ] = $field_alias;
     $this->field_alias = $field_alias;
-    
+
     // Second: Add nid field and Joins if necessary----------------------------
     // Add node join if needed
     if (!$node_table_alias) {
@@ -50,18 +51,18 @@ class views_handler_field_node_optional extends views_handler_field_node {
       $def['field'] = $this->table . '_id';
       $def['left_table'] = $this_table_alias;
       $def['left_field'] = $this->table . '_id';
-      
+
       $join = new views_join();
       $join->definition = $def;
       $join->construct();
       $join->adjusted = TRUE;
-    
+
       $node_table_alias = $this->query->add_relationship($def['table'], $join, $def['table']);
     }
-    
+
     // Finally Add Field
-    $field_alias = $this->query->add_field($node_table_alias, 'nid'); 
-    $this->aliases['nid'] = $field_alias;   
+    $field_alias = $this->query->add_field($node_table_alias, 'nid');
+    $this->aliases['nid'] = $field_alias;
 
   }
 
@@ -71,7 +72,7 @@ class views_handler_field_node_optional extends views_handler_field_node {
    * Data should be made XSS safe prior to calling this function.
    */
   function render_link($data, $values) {
-    if (!empty($this->options['link_to_node']) && $data !== NULL && $data !== '') {  
+    if (!empty($this->options['link_to_node']) && $data !== NULL && $data !== '') {
       if (!empty($values->{$this->aliases['nid']})) {
         $this->options['alter']['make_link'] = TRUE;
         $this->options['alter']['path'] = "node/" . $values->{$this->aliases['nid']};
@@ -84,11 +85,13 @@ class views_handler_field_node_optional extends views_handler_field_node {
             unset($this->options['alter']['language']);
           }
         }
-      } else {
+      }
+      else {
         $this->options['alter']['make_link'] = FALSE;
-        $this->options['alter']['path'] = "";        
+        $this->options['alter']['path'] = "";
       }
     }
+
     return $data;
   }
 }

tripal_views/views/handlers/views_handler_field_readable_date.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * A handler to provide proper displays for dates.
  *
  * @ingroup views_field_handlers
@@ -56,7 +57,7 @@ class views_handler_field_readable_date extends views_handler_field {
     if (in_array($format, array('custom', 'raw time ago', 'time ago', 'raw time span', 'time span'))) {
       $custom_format = $this->options['custom_date_format'];
     }
-    
+
     if (!$value) {
       return theme('views_nodate');
     }

tripal_views/views/handlers/views_handler_field_type_name.inc

@@ -1,16 +1,16 @@
 <?php
 
 /**
- *
+ * @file
  * @ingroup views_field_handlers
  * @ingroup tripal_core
  */
 class views_handler_field_type_name extends views_handler_field {
- function construct() {
-   parent::construct();
- }
+  function construct() {
+    parent::construct();
+  }
 
- function render($values) { 
-   return $values->property_type_name;
- } 
-} 
+  function render($values) {
+    return $values->property_type_name;
+  }
+}

tripal_views/views/handlers/views_handler_filter_chado_boolean.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Purpose: This handler provides a TRUE/FALSE or YES/NO select for chado fields
  *  of type boolean (includes both 0/1 and t/f booleans)
  *
@@ -10,17 +11,14 @@
 class views_handler_filter_chado_boolean extends views_handler_filter_boolean_operator {
  /**
   * Checks if this field uses 0/1 or t/f
+  * @todo Implement LIMIT 1 functionality for tripal_core_chado_select().
   */
   function init(&$view, $options) {
     parent::init($view, $options);
-    
-    $sql = 'SELECT '.$this->field.' FROM '.$this->table.' LIMIT 1';
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_fetch_object(db_query($sql));
-    tripal_db_set_active($previous_db);
-    
+
+    $results = tripal_core_chado_select($this->table, array($this->field), array());
     $this->boolean_type_tf = FALSE;
-    if (preg_match('/[tf]/', $result->{$this->field})) {
+    if (preg_match('/[tf]/', $results[0]->{$this->field})) {
       $this->boolean_type_tf = TRUE;
     }
 
@@ -46,8 +44,9 @@ class views_handler_filter_chado_boolean extends views_handler_filter_boolean_op
       // Provide a fallback if the above didn't set anything.
       if (!isset($this->value_options)) {
         $this->value_options = array('t' => t('True'), 'f' => t('False'));
-      }    
-    } else { //end of t/f boolean
+      }
+    }
+    else { //end of t/f boolean
       if (isset($this->definition['type'])) {
         if ($this->definition['type'] == 'yes-no') {
           $this->value_options = array(1 => t('Yes'), 0 => t('No'));
@@ -70,19 +69,22 @@ class views_handler_filter_chado_boolean extends views_handler_filter_boolean_op
     $where = "$this->table_alias.$this->real_field ";
 
     if ($this->boolean_type_tf) {
-      if (preg_match('/f/',$this->value)) {
+      if (preg_match('/f/', $this->value)) {
         $where .= "= 'f'";
-      } else {
+      }
+      else {
         $where .= "= 't'";
       }
-      $this->query->add_where($this->options['group'], $where);    
-    } else {
+      $this->query->add_where($this->options['group'], $where);
+    }
+    else {
       if (empty($this->value)) {
         $where .= '= 0';
         if ($this->accept_null) {
           $where = '(' . $where . " OR $this->table_alias.$this->real_field IS NULL)";
         }
-      } else {
+      }
+      else {
         $where .= '<> 0';
       }
       $this->query->add_where($this->options['group'], $where);

tripal_views/views/handlers/views_handler_filter_chado_select_cvterm_name.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Purpose: This Handler provides a select list for the type field
  *
  *  NOTE: This handler only works when applied to the type_id field in the base_table of
@@ -12,56 +13,63 @@
 class views_handler_filter_chado_select_cvterm_name extends views_handler_filter_string {
 
  /**
-	* Executed when the field is added
-	* Determine which cv to limit the cvterms to
-	*/
+  * Executed when the field is added
+  * Determine which cv to limit the cvterms to
+  */
   function init(&$view, $options) {
     parent::init($view, $options);
-  	
-  	if ($this->options['show_all']) {
-        $cv_id = variable_get('chado_'.$this->view->base_table.'_cv', null);
-        if ($cv_id) {
-          $results = tripal_core_chado_select('cvterm',array('cvterm_id','name'), array('cv_id'=>$cv_id));	
-          if (empty($results)) { $results = array(); }
-          foreach ($results as $c) {
-            $cvterms[$c->cvterm_id] = $c->name;
-          }    	
-        } else {
-          //get a list of cvs currently used
-          if ($this->view->base_table == 'cvterm') {
-            $sql = 'SELECT distinct(cv.cv_id) FROM '.$this->view->base_table
-              .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';	
-          } else {
-            $sql = 'SELECT distinct(cv.cv_id) FROM '.$this->view->base_table
-              .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id='.$this->view->base_table.'.type_id '
-              .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
-          }
-          $previous_db = tripal_db_set_active('chado');
-          $resource = db_query($sql);
-          tripal_db_set_active($previous_db);
-          $cvterms = array();
-          while ( $r = db_fetch_object($resource) ) {
-            $results = tripal_core_chado_select('cvterm',array('cvterm_id','name'), array('cv_id'=>$r->cv_id));	
-            if (empty($results)) { $results = array(); }
-            foreach ($results as $c) {
-              $cvterms[$c->cvterm_id] = $c->name;
-            }
-          }
-        }// end of if variable not defined
-    
-    } else {
-        $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(type_id) FROM %s)";
+
+    if ($this->options['show_all']) {
+      $cv_id = variable_get('chado_' . $this->view->base_table . '_cv', NULL);
+      if ($cv_id) {
+        $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
+        if (empty($results)) {
+          $results = array();
+        }
+        foreach ($results as $c) {
+          $cvterms[$c->cvterm_id] = $c->name;
+        }
+      }
+      else {
+        //get a list of cvs currently used
+        if ($this->view->base_table == 'cvterm') {
+          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+            .' LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+        }
+        else {
+          $sql = 'SELECT distinct(cv.cv_id) FROM ' . $this->view->base_table
+            .' LEFT JOIN cvterm cvterm ON cvterm.cvterm_id=' . $this->view->base_table . '.type_id '
+            .'LEFT JOIN cv cv ON cv.cv_id=cvterm.cv_id';
+        }
         $previous_db = tripal_db_set_active('chado');
-        $resource = db_query($sql, $this->view->base_table);
+        $resource = db_query($sql);
         tripal_db_set_active($previous_db);
         $cvterms = array();
         while ( $r = db_fetch_object($resource) ) {
-          $cvterms[$r->cvterm_id] = $r->name;
-        }        
+          $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
+          if (empty($results)) {
+            $results = array();
+          }
+          foreach ($results as $c) {
+            $cvterms[$c->cvterm_id] = $c->name;
+          }
+        }
+      }// end of if variable not defined
+
+    }
+    else {
+      $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(type_id) FROM %s)";
+      $previous_db = tripal_db_set_active('chado');
+      $resource = db_query($sql, $this->view->base_table);
+      tripal_db_set_active($previous_db);
+      $cvterms = array();
+      while ( $r = db_fetch_object($resource) ) {
+        $cvterms[$r->cvterm_id] = $r->name;
+      }
     }
     //sort cvterms by name (case insensitive)
     natcasesort($cvterms);
-    
+
     //add to this handler
     $this->cvterm_options = $cvterms;
   }
@@ -74,7 +82,7 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
 
     $form['values_form_type'] = array(
       '#type' => 'radios',
-      '#title' => 'Filter Type',
+      '#title' => t('Filter Type'),
       '#options' => array(
         'textfield' => 'Text Field',
         'select' => 'Drop-Down Box',
@@ -95,90 +103,95 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
       '#description' => t('Adds --Any-- to the available options.'),
       '#default_value' => (isset($this->options['optional'])) ? $this->options['optional'] : TRUE,
     );
-    
+
     $form['show_all'] = array(
       '#type' => 'checkbox',
-      '#title' => 'Show All Terms',
+      '#title' => t('Show All Terms'),
       '#description' => 'Otherwise only cvterms used in the base table will be used'
     );
   }
-  
+
  /**
   * Alters the query so that WHERE cvterm.cvterm_id=212 is used
   */
   function query() {
     $this->ensure_table;
-    
+
     if ($this->options['multiple']) {
       // Remove any if it's there
       unset($this->value['All']);
-      
+
       if (sizeof($this->value)) {
         $holders = array();
         foreach ($this->value as $v) {
-          if (preg_match('/^[\d\.]+$/',$v)) {
+          if (preg_match('/^[\d\.]+$/', $v)) {
             $holders[] = '%d';
-          } else {
+          }
+          else {
             $holders[] = "'%s'";
           }
         }
-        $where = "cvterm.cvterm_id IN (".implode(", ",$holders).")";
+        $where = "cvterm.cvterm_id IN (" . implode(", ", $holders) . ")";
       }
-    } else {
+    }
+    else {
       if (preg_match('/^\d+$/', $this->value)) {
         $where = 'cvterm.cvterm_id=%d';
-      } else {
+      }
+      else {
         $where = "cvterm.name" . $this->operator . "'%s'";
       }
     }
-    
+
     if ($where) {
       $this->query->add_where($this->options['group'], $where, $this->value);
     }
   }
-  
+
  /**
   * Defines the value field in both the views filter options form
   *   and the exposed form
   */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
-    
+
     if (preg_match('/select/', $this->options['values_form_type'])) {
       // Get Options
       if ($this->options['optional']) {
-        $options['<select '.$this->table.'>'] = '--None--';
+        $options['<select ' . $this->table . '>'] = '--None--';
         $options['All'] = '--Any--';
       }
       $max_length = 40;
       foreach ($this->cvterm_options as $cvterm_id => $cvterm_name) {
-        if (strlen($cvterm_name) > $max_length) {
-          $options[$cvterm_id] = substr($cvterm_name,0,$max_length) . '...';
-        } else {
-          $options[$cvterm_id] = $cvterm_name;    
+        if (drupal_strlen($cvterm_name) > $max_length) {
+          $options[$cvterm_id] = drupal_substr($cvterm_name, 0, $max_length) . '...';
+        }
+        else {
+          $options[$cvterm_id] = $cvterm_name;
         }
       }
-      
+
       if (empty($options)) {
         $options[0] = '';
       }
-      
+
       //Select List
       $form['value'] = array(
           '#type' => 'select',
-          '#title' => $this->options['label'],
+          '#title' => t('%label', array('%label' => $this->options['label'])),
           '#options' => $options,
           '#default_value' => $this->value,
       );
-      
+
       if ($this->options['multiple']) {
         $form['value']['#multiple'] = TRUE;
       }
-    
-    } else {
+
+    }
+    else {
       $form['value'] = array(
         '#type' => 'textfield',
-        '#title' => $this->options['label'],
+        '#title' => t('%label', array('%label' => $this->options['label'])),
         '#default_value' => $this->value,
       );
     }
@@ -242,7 +255,7 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
         'values' => 1,
       ),
     );
-    
+
     return $operators;
   }
 }

tripal_views/views/handlers/views_handler_filter_chado_select_string.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Purpose: This Handler provides a generic select list for any chado field that is a string
  *  The select list includes all distinct values for that field.
  *
@@ -14,14 +15,14 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
 
     $form['values_form_type'] = array(
       '#type' => 'radios',
-      '#title' => 'Filter Type',
+      '#title' => t('Filter Type'),
       '#options' => array(
         'textfield' => 'Text Field',
         'select' => 'Drop-Down Box',
       ),
       '#default_value' => ($this->options['values_form_type']) ? $this->options['values_form_type'] : 'select',
     );
-    
+
     $form['multiple'] = array(
       '#type' => 'checkbox',
       '#title' => t('Select Multiple'),
@@ -35,7 +36,7 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
       '#description' => t('Adds --Any-- to the available options.'),
       '#default_value' => (isset($this->options['optional'])) ? $this->options['optional'] : TRUE,
     );
- 
+
     $form['max_length'] = array(
       '#type' => 'textfield',
       '#title' => t('Max Width'),
@@ -43,23 +44,26 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
       '#default_value' => (isset($this->options['max_length'])) ? $this->options['max_length'] : 40,
 
     );
-    
+
   }
-  
+
  /**
   * Defines the value field in both the views filter options form
   *   and the exposed form
   */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
-    
+
     if (preg_match('/textfield/', $this->options['values_form_type'])) {
       $form['value'] = array(
         '#type' => 'textfield',
-        '#title' => $this->options['label'],
+        '#title' => t('%label', array('%label' => $this->options['label'])),
         '#default_value' => $this->value,
-      );    
-    } else {
+      );
+
+    }
+    else {
+
       // Get Options
       if ($this->options['optional']) {
         //$options['<select '.$this->table.'>'] = '--None--';
@@ -68,27 +72,28 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
       $sql = "SELECT $this->field FROM $this->table ORDER BY $this->field ASC";
       $previous_db = tripal_db_set_active('chado');  // use chado database
       $results = db_query($sql);
-      tripal_db_set_active($previous_db);  // now use drupal database 
+      tripal_db_set_active($previous_db);  // now use drupal database
       $max_length = $this->options['max_length'];
-      if(!$max_length){
-         $max_length = 40;
+      if (!$max_length) {
+        $max_length = 40;
       }
-      while($r = db_fetch_object($results)){
-        if (strlen($r->{$this->field}) > $max_length) {
-          $options[$r->{$this->field}] = substr($r->{$this->field},0,$max_length) . '...';
-        } else {
-          $options[$r->{$this->field}] = $r->{$this->field};    
+      while ($r = db_fetch_object($results)) {
+        if (drupal_strlen($r->{$this->field}) > $max_length) {
+          $options[$r->{$this->field}] = drupal_substr($r->{$this->field}, 0, $max_length) . '...';
+        }
+        else {
+          $options[$r->{$this->field}] = $r->{$this->field};
         }
       }
-      
+
       //Select List
       $form['value'] = array(
           '#type' => 'select',
-          '#title' => $this->options['label'],
+          '#title' => t('%label', array('%label' => $this->options['label'])),
           '#options' => $options,
           '#default_value' => $this->value,
       );
-      
+
       if ($this->options['multiple']) {
         $form['value']['#multiple'] = TRUE;
       }
@@ -131,7 +136,7 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
   *
   */
   function query() {
-  
+
     $this->ensure_my_table();
     $field = "$this->table_alias.$this->real_field";
     $upper = $this->case_transform();
@@ -139,25 +144,28 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
     if ($this->options['multiple']) {
       // Remove any if it's there
       unset($this->value['All']);
-      
+
       if (sizeof($this->value)) {
         $holders = array();
         foreach ($this->value as $v) {
-          if (preg_match('/^[\d\.]+$/',$v)) {
+          if (preg_match('/^[\d\.]+$/', $v)) {
             $holders[] = '%d';
-          } else {
+          }
+          else {
             $holders[] = "'%s'";
           }
         }
-        $where = "$field IN (".implode(", ",$holders).")";
+        $where = "$field IN (" . implode(", ", $holders) . ")";
         $this->query->add_where($this->options['group'], $where, $this->value);
       }
-    } else {
-  
+    }
+    else {
+
       // Deal with All/Any as value
       if (preg_match('/All/', $this->value)) {
-        // Don't do anything    
-      } else {
+        // Don't do anything
+      }
+      else {
         $info = $this->operators();
         if (!empty($info[$this->operator]['method'])) {
           $this->{$info[$this->operator]['method']}($field, $upper);

tripal_views/views/handlers/views_handler_filter_file_upload.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Purpose: This Handler provides a file upload field by extending the
  * views_handler_filter object.
  *
@@ -8,26 +9,16 @@
  */
 class views_handler_filter_file_upload extends views_handler_filter {
 
-  function init(&$view,$options){
-     parent::init($view,$options);
-
-  }
-
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-  }
-
   /**
-  * Defines the value field in both the views filter options form
-  *   and the exposed form
-  */
+   * Defines the value field in both the views filter options form
+   *   and the exposed form
+   */
   function value_form(&$form, &$form_state) {
     parent::value_form($form, $form_state);
 
     $this->value_form = array(
        '#type' => 'file_upload_combo',
-       '#title' => $this->options['expose']['label'],
+       '#title' => t('%label', array('%label' => $this->options['expose']['label'])),
        '#default_value' => $this->value,
        '#multiple' => FALSE,
        '#description' => t('Provide search values for %label. Please place each search
@@ -37,9 +28,9 @@ class views_handler_filter_file_upload extends views_handler_filter {
   }
 
   /**
-  * Ensures the upload field gets rendered when the filter is exposed. It also
-  * changes the form type from a GET to a POST so that file uploads will work.
-  */
+   * Ensures the upload field gets rendered when the filter is exposed. It also
+   * changes the form type from a GET to a POST so that file uploads will work.
+   */
   function exposed_form(&$form, &$form_state) {
 
     // don't do anything if the form isn't exposed.
@@ -64,69 +55,74 @@ class views_handler_filter_file_upload extends views_handler_filter {
     }
 
   }
+
   /**
    *  Validates the input form
    */
   function exposed_validate(&$form, &$form_state) {
      //dpm($form_state);
   }
+
   /**
    *
    */
   function query() {
-     $this->ensure_my_table();
-     $field = "$this->table.$this->real_field";
-
-     // get the form element value
-     $value = $this->value[0];
-
-     // the form element value has sub values, so get those
-     $items =  $value['items'];
-     $file_path = $value['file_path'];
-
-     $holders = array();
-     $values = array();
-
-     // get the file upload content if one has been provided
-     if($file_path){
-        $fh = fopen($file_path,'r');
-        while($line = fgets($fh)){
-           $items = trim($line);
-
-           // remove extra spaces and new lines
-           $items = preg_replace("/\s+,/",",",$items);
-           $items = preg_replace("/\s+\n/","\n",$items);
-           $items = preg_replace("/,\n/","\n",$items);
-
-           // add the values from this line to the values[] array
-           $vals = preg_split("/[\n,]+/",$items);
-           $values = array_merge($values,$vals);
-        }
-     }
-     // if a file upload has not been provided then use the value in the textarea
-     if($items){
+    $this->ensure_my_table();
+    $field = "$this->table.$this->real_field";
+
+    // get the form element value
+    $value = $this->value[0];
+
+    // the form element value has sub values, so get those
+    $items =  $value['items'];
+    $file_path = $value['file_path'];
+
+    $holders = array();
+    $values = array();
+
+    // get the file upload content if one has been provided
+    if ($file_path) {
+      $fh = fopen($file_path, 'r');
+      while ($line = fgets($fh)) {
+        $items = trim($line);
 
         // remove extra spaces and new lines
-        $items = preg_replace("/\s+,/",",",$items);
-        $items = preg_replace("/\s+\n/","\n",$items);
-        $items = preg_replace("/,\n/","\n",$items);
-
-        // in the event the user uploaded a file and provided items in the
-        // textbox then we need to merge these two lists
-        $vals = preg_split("/[\n,]+/",$items);
-        $values = array_merge($values,$vals);
-     }
-     // iterate through all of the values and generate the corresponding
-     // sprintf style holders
-     for($i = 0 ; $i < count($values); $i++){
-        $values[$i] = trim($values[$i]);
-        $holders[] = "'%s'";
-     }
-     // if we have any values supplied then update the where clause for
-     // the views query
-     if(count($holders) > 0){
-        $where = "$field IN (".implode(", ",$holders).")";
-        $this->query->add_where($this->options['group'], $where, $values);
-     }
+        $items = preg_replace("/\s+,/", ",", $items);
+        $items = preg_replace("/\s+\n/", "\n", $items);
+        $items = preg_replace("/,\n/", "\n", $items);
+
+        // add the values from this line to the values[] array
+        $vals = preg_split("/[\n,]+/", $items);
+        $values = array_merge($values, $vals);
+      }
+    }
+
+    // if a file upload has not been provided then use the value in the textarea
+    if ($items) {
+
+      // remove extra spaces and new lines
+      $items = preg_replace("/\s+,/", ",", $items);
+      $items = preg_replace("/\s+\n/", "\n", $items);
+      $items = preg_replace("/,\n/", "\n", $items);
+
+      // in the event the user uploaded a file and provided items in the
+      // textbox then we need to merge these two lists
+      $vals = preg_split("/[\n,]+/", $items);
+      $values = array_merge($values, $vals);
+    }
+
+    // iterate through all of the values and generate the corresponding
+    // sprintf style holders
+    for ($i = 0 ; $i < count($values); $i++) {
+      $values[$i] = trim($values[$i]);
+      $holders[] = "'%s'";
+    }
+
+    // if we have any values supplied then update the where clause for
+    // the views query
+    if (count($holders) > 0) {
+      $where = "$field IN (" . implode(", ", $holders) . ")";
+      $this->query->add_where($this->options['group'], $where, $values);
+    }
   }
 }

tripal_views/views/handlers/views_handler_filter_no_results.inc

@@ -1,5 +1,11 @@
 <?php
 
+/**
+ * @file
+ * This filter ensures that when a page is first loaded, there are no results (ie: the
+ * query is not run). This imitates an advanced search form allowing users to fist
+ * enter other filter values and then retrieve results.
+ */
 class views_handler_filter_no_results extends views_handler_filter {
 
   /**
@@ -8,12 +14,12 @@ class views_handler_filter_no_results extends views_handler_filter {
   function can_expose() {
     return FALSE;
   }
-  
+
   /**
    * Defines the options form (form available to admin when they add a field to a view)
    */
   function options_form(&$form, &$form_state) {
-    
+
     $form['msg'] = array(
       '#type' => 'item',
       '#value' => t('This filter ensures that when the page is first loaded, there are no results '
@@ -22,56 +28,56 @@ class views_handler_filter_no_results extends views_handler_filter {
         .'large number of results if left unfiltered since it removes the long load time before '
         .'even allowing users the ability to filter down the results.')
     );
-    
+
     $form['apply_button'] = array(
       '#type' => 'textfield',
       '#title' => 'Apply Button Text',
       '#default_value' => isset($this->options['apply_button']) ? $this->options['apply_button'] : 'Search'
     );
-    
+
     $form['no_results_text'] = array(
       '#type' => 'textarea',
       '#title' => 'Header Text before Search',
       '#description' => 'This text will replace the no results text when the view is first loaded (before the user clicks Apply/Search)',
       '#default_value' => isset($this->options['no_results_text']) ? $this->options['no_results_text'] : ''
     );
-    
+
   }
-  
+
   function query() {
     global $base_url;
-    
+
     if (empty($this->view->exposed_input)) {
       $this->view->executed = TRUE;
-      
+
       $jquery_loaded = FALSE;
-      
+
       // If set, change the no_results text
       if (!empty($this->options['apply_button'])) {
         if (!$jquery_loaded) {
-          drupal_set_html_head('<script type="text/javascript" src="'.$base_url.'/misc/jquery.js"></script>');
+          drupal_set_html_head('<script type="text/javascript" src="' . $base_url . '/misc/jquery.js"></script>');
           $jquery_loaded = TRUE;
         }
         $javascript = '<script type="text/javascript">'."\n"
           ."$(document).ready(function(){\n"
-          ."  $('div.view-empty').html('".addslashes($this->options['no_results_text'])."');\n"
+          ."  $('div.view-empty').html('" . addslashes($this->options['no_results_text']) . "');\n"
           ."});\n"
           .'</script>'."\n";
         drupal_set_html_head($javascript);
       }
     }
-    
+
     // Set the Apply button text
     if (!empty($this->options['apply_button'])) {
       if (!$jquery_loaded) {
-        drupal_set_html_head('<script type="text/javascript" src="'.$base_url.'/misc/jquery.js"></script>');
+        drupal_set_html_head('<script type="text/javascript" src="' . $base_url . '/misc/jquery.js"></script>');
         $jquery_loaded = TRUE;
       }
       $javascript = '<script type="text/javascript">'."\n"
         ."$(document).ready(function(){\n"
-        ."  $('div.views-submit-button').html(".'"'."<input type='submit' id='edit-submit-all-analysis' value='".$this->options['apply_button']."' class='form-submit'>".'"'.");\n"
+        ."  $('div.views-submit-button').html(" . '"' . "<input type='submit' id='edit-submit-all-analysis' value='" . $this->options['apply_button'] . "' class='form-submit'>" . '"' . ");\n"
         ."});\n"
-        .'</script>'."\n";
+        .'</script>' . "\n";
       drupal_set_html_head($javascript);
     }
   }

tripal_views/views/handlers/views_handler_join_chado_aggregator.inc

@@ -1,6 +1,7 @@
 <?php
 
 /**
+ * @file
  * Handler to allow joins between records via a linking table
  *
  * Example Usage:
@@ -21,7 +22,7 @@ class views_handler_join_chado_aggregator extends views_join {
   // the call to constructors upstream where appropriate.
   function construct($table = NULL, $left_table = NULL, $left_field = NULL, $field = NULL, $extra = array(), $type = 'LEFT', $added = NULL) {
     parent::construct($table, $left_table, $left_field, $field, $extra, $type);
-    
+
     // Determine the postgresql version
     $postgresql_version = pg_version();
     $this->postgresql_version = $postgresql_version['client'];
@@ -42,33 +43,33 @@ class views_handler_join_chado_aggregator extends views_join {
 
     // Create the table SQL (used in join) -------
     // query creating one-to-one table using array_agg
-    $table_desc = module_invoke_all('chado_'.$this->definition['table'].'_schema');
+    $table_desc = module_invoke_all('chado_' . $this->definition['table'] . '_schema');
     $select_fields[ $this->definition['table'] ] = $table_desc['fields'];
-    
+
     // Add joins to tables with a foreign key in this table
     // (ie: add join to cvterm if this table has a type_id
     $joins = array();
-    foreach($table_desc['foreign keys'] as $defn) {
+    foreach ($table_desc['foreign keys'] as $defn) {
       if ($defn['table'] != $this->left_table) {
-        foreach( $defn['columns'] as $left => $right) {
+        foreach ( $defn['columns'] as $left => $right) {
           $left = $this->definition['table'] .'.'. $left;
-          $right = $defn[table] .'.'. $right;
+          $right = $defn['table'] .'.'. $right;
           $joins[] = "LEFT JOIN $defn[table] $defn[table] ON $left=$right";
         }
-        
+
         // Fields to be selected from joined table
-        $join_table = module_invoke_all('chado_'.$defn['table'].'_schema');
+        $join_table = module_invoke_all('chado_' . $defn['table'] . '_schema');
         $select_fields[ $defn['table'] ] = $join_table['fields'];
-      } 
+      }
     }
-    
+
     // Determine Order BY's for aggregates
     $order_by = array();
     foreach ($this->sort as $s) {
-      $order_by[] = $s['table'].'.'.$s['field'].' '.$s['order'];
+      $order_by[] = $s['table'] . '.' . $s['field'] . ' ' . $s['order'];
     }
-    
-    
+
+
     // Fields to be selected
     foreach ($select_fields as $table => $table_fields) {
       foreach ($table_fields as $fname => $f) {
@@ -76,43 +77,46 @@ class views_handler_join_chado_aggregator extends views_join {
         if ($table != $this->definition['table']) {
           $alias = $table .'_';
         }
-        
+
         if ($fname != $this->definition['field']) {
           // Add sort to aggregate field if postgreSQL 9.0+
           if ($this->postgresql_9up && !empty($order_by)) {
-            $fields[] = 'array_agg('.$table.'.'.$fname.' ORDER BY '.implode(',',$order_by).') as '.$alias.$fname;
-          } else {
-            $fields[] = 'array_agg('.$table.'.'.$fname.') as '.$alias.$fname;
+            $fields[] = 'array_agg(' . $table . '.' . $fname . ' ORDER BY ' . implode(',', $order_by) . ') as ' . $alias . $fname;
+          }
+          else {
+            $fields[] = 'array_agg(' . $table . '.' . $fname . ') as ' . $alias . $fname;
           }
-          $composite_field_parts[] = "'".$alias.$fname."::' ||".$table.'.'.$fname;
-        } else {
+          $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
+        }
+        else {
           $fields[] = $fname;
-          $composite_field_parts[] = "'".$alias.$fname."::' ||".$table.'.'.$fname;
+          $composite_field_parts[] = "'" . $alias . $fname . "::' ||" . $table . '.' . $fname;
         }
       }
     }
-    
-    // composite field 
+
+    // composite field
     // (combines all other fields before aggregating)
     // Add sort to aggregate field if postgreSQL 9.0+
     if ($this->postgresql_9up && !empty($order_by)) {
-      $composite_field = "array_agg('{'||".implode(" || ',' || ",$composite_field_parts)."||'}' ORDER BY ".implode(',',$order_by).") as all";
-    } else {
-      $composite_field = "array_agg('{'||".implode(" || ',' || ",$composite_field_parts)."||'}') as all";
+      $composite_field = "array_agg('{'||" . implode(" || ',' || ", $composite_field_parts) . "||'}' ORDER BY " . implode(',', $order_by) . ") as all";
+    }
+    else {
+      $composite_field = "array_agg('{'||" . implode(" || ',' || ", $composite_field_parts) . "||'}') as all";
     }
     $fields[] = $composite_field;
-    
+
     // SQL to use in the join
-    $sql = 'SELECT '.implode(', ',$fields)
-      .' FROM '.$this->definition['table']
-      .' '.implode(' ',$joins);
- 
+    $sql = 'SELECT ' . implode(', ', $fields)
+      .' FROM ' . $this->definition['table']
+      .' ' . implode(' ', $joins);
+
     if (!empty($this->filter)) {
-      $sql .= ' WHERE '.implode(', ', $this->filter);
+      $sql .= ' WHERE ' . implode(', ', $this->filter);
     }
-    
-    $sql .= ' GROUP BY '.$this->definition['field'];
-    
+
+    $sql .= ' GROUP BY ' . $this->definition['field'];
+
     // Create the join (full SQL) ----------------
     $output[] = $this->create_single_join(
       $query,
@@ -128,41 +132,47 @@ class views_handler_join_chado_aggregator extends views_join {
       ),
       'LEFT'
     );
-    
-    return implode("\n",$output);
+
+    return implode("\n", $output);
   }
-  
+
   /**
    * Creates SQL for a single join based on parameters
-   * Join will be: <type> JOIN (<query creating one-to-one table using array_agg>) <table alias> 
+   * Join will be: <type> JOIN (<query creating one-to-one table using array_agg>) <table alias>
    *                  ON <qualified left field>=<qualified right field>
    */
-  function create_single_join (&$query, $right_spec, $left_spec, $join_type) {
-    
+  function create_single_join(&$query, $right_spec, $left_spec, $join_type) {
+
     if ($right_spec['table']) {
       $right = $query->get_table_info($right_spec['table']);
-      if (!$right['alias']) { $right['alias'] = $right_spec['table']; }
+      if (!$right['alias']) {
+        $right['alias'] = $right_spec['table'];
+      }
       $right_field = "$right[alias].$right_spec[field]";
 
       if ($right_spec['is_drupal']) {
-        $right_table = '{'.$right_spec['table'].'}';
-      } else {
+        $right_table = '{' . $right_spec['table'] . '}';
+      }
+      else {
         $right_table = $right_spec['table'];
       }
-    }   
+    }
 
     if ($left_spec['table']) {
       $left = $query->get_table_info($left_spec['table']);
-      if (!$left['alias']) { $left['alias'] = $left_spec['table']; }
+      if (!$left['alias']) {
+        $left['alias'] = $left_spec['table'];
+      }
       $left_field = "$left[alias].$left_spec[field]";
-    } else {
+    }
+    else {
       // This can be used if left_field is a formula or something. It should be used only *very* rarely.
       $left_field = $this->left_spec['field'];
     }
-    
+
     $output = " $join_type JOIN ($right_spec[table_sql]) $right[alias] ON $left_field = $right_field";
-     
+
     return $output;
   }
- 
+
 }

tripal_views/views/handlers/views_handler_join_chado_through_linking.inc

@@ -1,9 +1,10 @@
 <?php
 
-module_load_include('inc','views','includes/base');
-module_load_include('inc','views','includes/handlers');
+module_load_include('inc', 'views', 'includes/base');
+module_load_include('inc', 'views', 'includes/handlers');
 
 /**
+ * @file
  * Handler to allow joins between records via a linking table
  *
  * Example Usage:
@@ -20,10 +21,10 @@ module_load_include('inc','views','includes/handlers');
           'left_field' => 'feature_id',
           'field' => 'analysis_id',
           'handler' => 'views_handler_join_chado_through_linking'
-        ); 
+        );
  *   @endcode
  *
- * NOTE: If the right table is in the drupal schema rather then the chado schema 
+ * NOTE: If the right table is in the drupal schema rather then the chado schema
  *  (ie: node, chado_feature) then add the following to the above join description:
  *  @code
     'table_is_drupal' => TRUE
@@ -40,7 +41,7 @@ class views_handler_join_chado_through_linking extends views_join {
   function construct($table = NULL, $left_table = NULL, $left_field = NULL, $field = NULL, $extra = array(), $type = 'LEFT', $added = NULL) {
     parent::construct($table, $left_table, $left_field, $field, $extra, $type);
   }
-  
+
   /**
    * Creates SQL for both joins table => linking_table and linking_table => left_table
    * NOTE: Uses fields in definition as passed in from hook_views_data join definition
@@ -62,7 +63,7 @@ class views_handler_join_chado_through_linking extends views_join {
       ),
       'LEFT'
     );
-    
+
     $joins[] = $this->create_single_join(
       $query,
       array(
@@ -76,40 +77,46 @@ class views_handler_join_chado_through_linking extends views_join {
       ),
       'LEFT'
     );
-    
-    $output .= implode("\n",$joins);
+
+    $output .= implode("\n", $joins);
     return $output;
   }
-  
+
   /**
    * Creates SQL for a single join based on parameters
    */
-  function create_single_join (&$query, $right_spec, $left_spec, $join_type) {
-    
+  function create_single_join(&$query, $right_spec, $left_spec, $join_type) {
+
     if ($right_spec['table']) {
       $right = $query->get_table_info($right_spec['table']);
-      if (!$right['alias']) { $right['alias'] = $right_spec['table']; }
+      if (!$right['alias']) {
+        $right['alias'] = $right_spec['table'];
+      }
       $right_field = "$right[alias].$right_spec[field]";
 
       if ($right_spec['is_drupal']) {
-        $right_table = '{'.$right_spec['table'].'}';
-      } else {
+        $right_table = '{' . $right_spec['table'] . '}';
+      }
+      else {
         $right_table = $right_spec['table'];
       }
-    }   
+    }
 
     if ($left_spec['table']) {
       $left = $query->get_table_info($left_spec['table']);
-      if (!$left['alias']) { $left['alias'] = $left_spec['table']; }
+      if (!$left['alias']) {
+        $left['alias'] = $left_spec['table'];
+        }
       $left_field = "$left[alias].$left_spec[field]";
-    } else {
+    }
+    else {
       // This can be used if left_field is a formula or something. It should be used only *very* rarely.
       $left_field = $this->left_spec['field'];
     }
-    
+
     $output = " $join_type JOIN $right_table $right[alias] ON $left_field = $right_field";
-     
+
     return $output;
   }
- 
+
 }

tripal_views/views_data_export/plugins/tripal_views_plugin_style_export_fasta.inc

@@ -20,7 +20,7 @@ class tripal_views_plugin_style_export_fasta extends views_data_export_plugin_st
   function option_definition() {
     $options = parent::option_definition();
 
-  
+
     return $options;
   }
 

tripal_views/views_data_export/theme/tripal_views_data_export.theme.inc

@@ -1,17 +1,29 @@
 <?php
 
+/**
+ * @file
+ * Contains template preprocessing functions
+ */
+
+/**
+ * Preprocess the variables for the FASTA views data export -body template
+ *   - replace the field tokens in the fasta record definition lines
+ *
+ * @param $vars
+ *   The variables available to the template
+ */
 function template_preprocess_views_data_export_fasta_body(&$vars) {
-   _views_data_export_header_shared_preprocess($vars);
-   _views_data_export_body_shared_preprocess($vars);
-   $defline_tpl = $vars['options']['defline_fields'];
+  _views_data_export_header_shared_preprocess($vars);
+  _views_data_export_body_shared_preprocess($vars);
+  $defline_tpl = $vars['options']['defline_fields'];
 
-   // iterate through the rows and replace the field tokens with values
-   // to generate the definition line
-   foreach ($vars['themed_rows'] as $i => $fields) {
-      $defline = $defline_tpl;
-      foreach ($fields as $key => $value) {
-         $defline = preg_replace("/\[$key\]/",$value,$defline);
-      }
-      $vars['themed_rows'][$i]['defline'] = $defline;
-   }
+  // iterate through the rows and replace the field tokens with values
+  // to generate the definition line
+  foreach ($vars['themed_rows'] as $i => $fields) {
+    $defline = $defline_tpl;
+    foreach ($fields as $key => $value) {
+      $defline = preg_replace("/\[$key\]/", $value, $defline);
+    }
+    $vars['themed_rows'][$i]['defline'] = $defline;
+  }
 }

tripal_views/views_data_export/theme/views-data-export-fasta-body.tpl.php

@@ -1,19 +1,36 @@
 <?php
+
+/**
+ * @file
+ * Renders the body portion of a FASTA views data export
+ */
+
 //print_r($themed_rows);
+
+// print the first FASTA record header
+// this is needed due to the order of the fields
 print $defline;
+
+// foreach row in the views table
 foreach ($themed_rows as $index => $fields) {
-   $defline = array();
-   $residues = '';
-   foreach ($fields as $key => $value) {
-     if (strcmp($key,'residues')==0)b{
-        $residues = wordwrap($value, 60, "\r\n", true);
-     }
-     if (strcmp($key,'defline')==0) {
-        $defline = $value;
-     }
-   }
-   print ">$defline\r\n";
-   print "$residues\r\n";
+  $defline = array();
+  $residues = '';
+  foreach ($fields as $key => $value) {
+
+    // wrap the sequence
+    if (strcmp($key, 'residues') == 0) {
+      $residues = wordwrap($value, 60, "\r\n", TRUE);
+    }
+
+    // set the FASTA header
+    if (strcmp($key, 'defline') == 0) {
+      $defline = $value;
+    }
+  }
+
+  // print the FASTA record
+  print ">$defline\r\n";
+  print "$residues\r\n";
 }
 
 

tripal_views/views_data_export/theme/views-data-export-fasta-footer.tpl.php

@@ -1,5 +1,7 @@
 <?php
 
 /**
+ * @file
+ * Renders the footer of a FASTA views data export
  * FASTA files don't have a footer.
  */

tripal_views/views_data_export/theme/views-data-export-fasta-header.tpl.php

@@ -1,5 +1,7 @@
 <?php
 
 /**
+ * @file
+ * Renders the header of a FASTA views data export
  * FASTA files don't have a header.
  */