Tripal Stock: Views related bug fixes plus new stock relationships views filter

tripal_stock/tripal_stock.views.inc

@@ -86,6 +86,9 @@ function tripal_stock_views_handlers() {
      'views_handler_filter_stock_dbxref_id' => array(
      	'parent' => 'views_handler_filter',
      ),
+     'views_handler_filter_stock_relationship_id' => array(
+     	'parent' => 'views_handler_filter',
+     ),
      'views_handler_argument_stockprop_id' => array(
      	'parent' => 'views_handler_argument_string',
      ),

tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc

@@ -0,0 +1,296 @@
+<?php
+
+class views_handler_filter_stock_relationship_id extends views_handler_filter {
+
+	function query () {
+	  if ($this->value) {
+	  
+      // get variable position
+      if ($this->options['fixed_position'] == 'subject_id') {
+        $this->options['variable_position'] = 'object_id';
+      } else {
+        $this->options['variable_position'] = 'subject_id';
+      }
+        
+	    // determine if just checking presence
+	    if (preg_match('/NULL/', $this->operator)) {
+          $where = 'stock.stock_id IN ('
+            .'SELECT '.$this->options['variable_position'].' FROM stock_relationship '
+            .'WHERE '.$this->options['fixed_position'].' '.$this->operator.' AND type_id = '.$this->options['type']
+          .')';
+          $this->query->add_where($this->options['group'], $where);	      
+	    } else {
+        
+        // determine whether regex was requested
+        if ($this->operator == '~') {
+          $search_options = array('regex_columns' => array('name','uniquename'));
+          $this->operator = '=';
+        } elseif ($this->operator == '!~') {
+          $search_options = array('regex_columns' => array('name','uniquename'));
+          $this->operator = '!=';
+        } else {
+          $search_options = array();
+        }
+        
+        // get fixed stock id(s)
+        $fixed_stock = tripal_core_chado_select('stock',array('stock_id'),array('uniquename' => $this->value), $search_options);
+        $fixed_stock_ids = array();
+        if ($fixed_stock[0]->stock_id) {
+          $fixed_stock_ids[] = $fixed_stock[0]->stock_id;
+        } else {
+          $fixed_stock = tripal_core_chado_select('stock',array('stock_id'),array('name' => $this->value), $search_options);
+          if (sizeof($fixed_stock) > 1) {
+            foreach ($fixed_stock as $s) {
+              $fixed_stock_ids[] = $s->stock_id;
+            }
+          } elseif (sizeof($fixed_stock) == 1) {
+            $fixed_stock_ids[] = $fixed_stock[0]->stock_id;
+          }
+        }
+        
+        // determine operator
+        if ($this->operator == '=' && sizeof($fixed_stock_ids) > 1) {
+          $this->operator = 'IN';
+        } elseif ($this->operator == '!=' && sizeof($fixed_stock_ids) > 1) {
+          $this->operator = 'NOT IN';
+        }
+        
+        //generate where
+        if (sizeof($fixed_stock_ids) == 1) {
+          $where = 'stock.stock_id IN ('
+            .'SELECT '.$this->options['variable_position'].' FROM stock_relationship '
+            .'WHERE '.$this->options['fixed_position'].' '.$this->operator.' '.$fixed_stock_ids[0].' AND type_id = '.$this->options['type']
+          .')';
+          $this->query->add_where($this->options['group'], $where);
+        } elseif (sizeof($fixed_stock_ids) > 1) {
+          $where = 'stock.stock_id IN ('
+            .'SELECT '.$this->options['variable_position'].' FROM stock_relationship '
+            .'WHERE '.$this->options['fixed_position'].' '.$this->operator.' ('.implode(', ',$fixed_stock_ids).') AND type_id = '.$this->options['type']
+          .')';
+          $this->query->add_where($this->options['group'], $where);
+        } else {
+          drupal_set_message('No stock with the name or uniquename '.$this->value.' was found -No filtering done.','error');
+        }
+      } //end of not just checking presence
+    }
+	}
+	
+  function options_form(&$form, &$form_state) {
+  	
+    if ($this->can_expose()) {
+      $this->show_expose_button($form, $form_state);
+    }
+
+  	$instructions = 'This filter allows you to enter a stock, the position of that stock in the '
+  		.'relationship and relationship type and only stocks with a relationship of the type described '
+  		.'will be shown. For example, if you want all stocks where Fred is_paternal_parent_of, then '
+  		.'you would enter Fred as the value, select is_paternal_parent_of as the Relationship Type '
+  		.'and subject as the Fixed Position.';
+  	$form['instructions'] = array(
+  		'#type' => 'item',
+  		'#value' => t($instructions)
+  	);
+  	
+    $form['op_val_start'] = array('#value' => '<div class="clear-block">');
+
+    // left side
+    
+    $this->types_form($form, $form_state);
+		$form['type']['#prefix'] = '<div class="views-left-50">';
+		$form['type']['#suffix'] = '</div>';
+
+    $this->show_operator_form($form, $form_state);
+    $form['operator']['#prefix'] = '<div class="views-right-50">';
+		$form['operator']['#suffix'] = '</div>';
+		
+		$this->show_value_form($form, $form_state);
+		$form['value']['#prefix'] = '<div class="views-right-50">';
+		$form['value']['#suffix'] = '</div>';
+		
+    // right side
+
+
+    $this->fixed_position_form($form, $form_state);
+    $form['fixed_position']['#prefix'] = '<div class="views-right-50">';
+    $form['fixed_position']['#suffix'] = '</div>';
+
+		
+    if ($this->can_expose()) {
+      $this->show_expose_form($form, $form_state);
+    }
+    
+    $form['op_val_start'] = array('#value' => '</div>');
+
+  }
+
+  function value_form(&$form, &$form_state) {
+    parent::value_form($form, $form_state);
+
+		$form['value'] = array(
+			'#type' => 'textfield',
+			'#title' => ($this->options['label']) ? $this->options['label'] : t('Stock Name'),
+			'#default_value' => $this->value,
+			'#size' => 40,
+		);
+    	
+  }
+
+  function type_options () {
+
+    $previous_db = tripal_db_set_active('chado');
+    $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM cvterm cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM stock_relationship)");
+    tripal_db_set_active($previous_db);
+
+    $types = array();
+    while ($r = db_fetch_object($result)) { $types[$r->type_id] = $r->name; }
+    
+    return $types;
+  }
+  
+  function types_form(&$form, &$form_state) {
+  	
+    $form['type'] = array(
+      '#type' => count($options) < 10 ? 'radios' : 'select',
+      '#title' => t('Relationship Types'),
+      '#options' => $this->type_options(),
+      '#default_value' => $this->options['type'],
+    );
+
+  }
+  
+  function fixed_position_form (&$form, &$form_state) {
+  
+  	$form['fixed_position'] = array(
+  		'#type' => 'radios',
+  		'#title' => 'Position of Stock to Filter on',
+  		'#description' => t('Where a relationship consists of a subject type object, this field indicates '
+  			.'what position in the relationship remains fixed (is the stock entered as the value).'),
+  		'#options' => array(
+  			'subject_id' => 'Subject',
+  			'object_id' => 'Object'
+  		),
+  		'#default_value' => ($this->options['fixed_position']) ? $this->options['fixed_position'] : 'subject_id',
+  	);
+  	
+  }
+
+  function operator_options() {
+    return array(
+      '=' => t('Is equal to'),
+      '!=' => t('Is not equal to'),
+      '~' => t('Contains'),
+      '!~' => t('Does not contain'),
+      'IS NOT NULL' => t('Is Present (Not Empty)'),
+      'IS NULL' => t('Is Absent (Empty)'),
+    );
+  }
+
+ /**
+  * Render our chunk of the exposed filter form when selecting
+  */
+  function exposed_form(&$form, &$form_state) {
+    if (empty($this->options['exposed'])) {
+      return;
+    }
+
+    if (!empty($this->options['expose']['use_operator']) && !empty($this->options['expose']['operator'])) {
+      $operator = $this->options['expose']['operator'];
+      $this->operator_form($form, $form_state);
+      $form[$operator] = $form['operator'];
+
+      if (isset($form[$operator]['#title'])) {
+        unset($form[$operator]['#title']);
+      }
+
+      $this->exposed_translate($form[$operator], 'operator');
+
+      unset($form['operator']);
+    }
+
+    if (!empty($this->options['expose']['identifier'])) {
+      $value = $this->options['expose']['identifier'];
+      $this->value_form($form, $form_state);
+      $form[$value] = $form['value'];
+
+      if (isset($form[$value]['#title']) && !empty($form[$value]['#type']) && $form[$value]['#type'] != 'checkbox') {
+        unset($form[$value]['#title']);
+      }
+
+      $this->exposed_translate($form[$value], 'value');
+
+      if (!empty($form['#type']) && ($form['#type'] == 'checkboxes' || ($form['#type'] == 'select' && !empty($form['#multiple'])))) {
+        unset($form[$value]['#default_value']);
+      }
+
+      if (!empty($form['#type']) && $form['#type'] == 'select' && empty($form['#multiple'])) {
+        $form[$value]['#default_value'] = 'All';
+      }
+
+      if ($value != 'value') {
+        unset($form['value']);
+      }
+    }
+  }
+
+  function expose_form_left(&$form, &$form_state) {
+    $form['expose']['label'] = array(
+      '#type' => 'textfield',
+      '#default_value' => $this->options['expose']['label'],
+      '#title' => t('Label'),
+      '#size' => 40,
+    );
+
+    $form['expose']['identifier'] = array(
+      '#type' => 'textfield',
+      '#default_value' => $this->options['expose']['identifier'],
+      '#title' => t('Filter identifier'),
+      '#size' => 40,
+      '#description' => t('This will appear in the URL after the ? to identify this filter. Cannot be blank.'),
+    );
+    
+  }
+
+  function expose_form_right(&$form, &$form_state) {
+
+    $form['expose']['identifier'] = array(
+      '#type' => 'textfield',
+      '#default_value' => $this->options['expose']['identifier'],
+      '#title' => t('Filter identifier'),
+      '#size' => 40,
+      '#description' => t('This will appear in the URL after the ? to identify this filter. Cannot be blank.'),
+    );
+
+    if (!empty($form['operator']['#type'])) {
+      $form['expose']['use_operator'] = array(
+        '#type' => 'checkbox',
+        '#title' => t('Unlock operator'),
+        '#description' => t('When checked, the operator will be exposed to the user'),
+        '#default_value' => !empty($this->options['expose']['use_operator']),
+      );
+      $form['expose']['operator'] = array(
+        '#type' => 'textfield',
+        '#default_value' => $this->options['expose']['operator'],
+        '#title' => t('Operator identifier'),
+        '#size' => 40,
+        '#description' => t('This will appear in the URL after the ? to identify this operator.'),
+        '#process' => array('views_process_dependency'),
+        '#dependency' => array(
+          'edit-options-expose-use-operator' => array(1)
+        ),
+      );
+    }
+    else {
+      $form['expose']['operator'] = array(
+        '#type' => 'value',
+        '#value' => '',
+      );
+    }
+    
+    $form['expose']['optional'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Optional'),
+      '#description' => t('This exposed filter is optional and will have added options to allow it not to be set.'),
+      '#default_value' => $this->options['expose']['optional'],
+    );
+  }
+}

tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc

@@ -58,12 +58,15 @@ class views_handler_filter_stockprop_id extends views_handler_filter {
 	function query () {
 		if (preg_match('/IS NOT NULL/', $this->options['operator'])) {
 			$new_where_sql = "stock.stock_id IN (SELECT stockprop.stock_id FROM stockprop WHERE stockprop.type_id=".$this->type.")";
+			$this->query->add_where($this->options['group'], $new_where_sql);
 		} elseif (preg_match('/IS NULL/', $this->options['operator'])) {
 			$new_where_sql = "stock.stock_id NOT IN (SELECT stockprop.stock_id FROM stockprop WHERE stockprop.type_id=".$this->type.")";
-		} else {
+			$this->query->add_where($this->options['group'], $new_where_sql);
+		} elseif ($this->value) {
 			$new_where_sql = "stock.stock_id IN (SELECT stockprop.stock_id FROM stockprop WHERE stockprop.type_id=".$this->type." AND stockprop.value".$this->operator."'".$this->value."')";
+			$this->query->add_where($this->options['group'], $new_where_sql);
 		}
-		$this->query->add_where($this->options['group'], $new_where_sql);
+		
 	}
 	
   function types_form(&$form, &$form_state) {

tripal_stock/views/stock.views.inc

@@ -158,10 +158,10 @@ function retrieve_stock_views_data() {
 
   //Field: is_obsolete (boolean t/f)
   $data['stock']['is_obsolete'] = array(
-    'title' => t('Is Obsolete'),
+    'title' => t('Is Obsolete?'),
     'help' => t('A yes/no field indicating whether a given stock is obsolete or not.'),
     'field' => array(
-      'handler' => 'views_handler_field',
+      'handler' => 'views_handler_field_chado_tf_boolean',
       'click sortable' => TRUE,
     ),
     'filter' => array(
@@ -221,6 +221,9 @@ function retrieve_stock_views_data() {
       'help' => t('Display a given type of relationships including the current stock.'),
       'handler' => 'views_handler_field_stockrel_by_type',
     ),
+    'filter' => array(
+    	'handler' => 'views_handler_filter_stock_relationship_id'
+    ),
   );
 
 	//Calculated Field: stock relationships (ALL)