Removed old views handlers that are no longer needed thanks to the new system where all chado tables are integrated

tripal_views/tripal_views.views.inc

@@ -90,9 +90,6 @@ function tripal_views_views_handlers() {
       'views_handler_field_node_optional' => array(
         'parent' => 'views_handler_field_node',
       ),
-      'views_handler_field_cvterm_name' => array(
-        'parent' => 'views_handler_field',
-      ),
       'views_handler_field_chado_tf_boolean' => array(
         'parent' => 'views_handler_field_boolean',
       ),
@@ -102,9 +99,6 @@ function tripal_views_views_handlers() {
       'views_handler_filter_chado_boolean' => array(
         'parent' => 'views_handler_filter_boolean_operator',
       ),
-      'views_handler_field_chado_rel_by_type' => array(
-        'parent' => 'views_handler_field_prerender_list',
-      ),
       'views_handler_field_dbxref_accession_link' => array(
         'parent' => 'views_handler_field',
       ),

tripal_views/views/handlers/views_handler_argument_stockprop_id.inc

@@ -1,76 +0,0 @@
-<?php
-
-/**
- * @file
- * Allows a stock property in the path to be used to filter a view
- *
- * @ingroup tripal_stock
- * @ingroup views_argument_handlers
- */
-class views_handler_argument_stockprop_id extends views_handler_argument_string {
-
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-    unset($form['glossary']);
-    unset($form['limit']);
-    unset($form['add_table']);
-    unset($form['require_value']);
-
-    //get options & display as options
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM cvterm cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM stockprop)");
-    tripal_db_set_active($previous_db);
-    $types = array();
-    while ($r = db_fetch_object($result)) {
-      $types[$r->type_id] = $r->name;
-    }
-    $form['stockprop_type_id'] = array(
-      '#type' => 'radios',
-      '#title' => t('Property Types'),
-      '#options' => $types,
-      '#default_value' => $this->options['stockprop_type_id'],
-      '#required' => TRUE,
-      '#description' => t('Select the type of property represented by this argument.'),
-    );
-
-    $operators = 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)'),
-    );
-    $form['operator'] = array(
-      '#type' => 'radios',
-      '#title' => 'Operator',
-      '#description' => t('Specify how to compare the argument with the property values.'),
-      '#options' => $operators,
-      '#default_value' => $this->options['operator'],
-      '#required' => TRUE,
-    );
-  }
-
-  /**
-   * Build the query based upon the formula
-   */
-  function query() {
-    $argument = $this->argument;
-    if (!empty($this->options['transform_dash'])) {
-      $argument = strtr($argument, '-', ' ');
-    }
-
-    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->options['stockprop_type_id'] . ")";
-    }
-    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->options['stockprop_type_id'] . ")";
-    }
-    else {
-      $new_where_sql = "stock.stock_id IN (SELECT stockprop.stock_id FROM stockprop "
-              . "WHERE stockprop.type_id=" . $this->options['stockprop_type_id'] . " AND stockprop.value" . $this->options['operator'] . "'" . $argument . "')";
-    }
-    $this->query->add_where($this->options['group'], $new_where_sql);
-  }
-
-}

tripal_views/views/handlers/views_handler_field_chado_rel_by_type.inc

@@ -1,212 +0,0 @@
-<?php
-
-/**
- * @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
- */
-class views_handler_field_chado_rel_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // 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
-    $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, $this->table));
-    tripal_db_set_active($previous_db);
-    if (!$exists->bool) {
-      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;
-    }
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['rel_type_ids'] = array('default' => array());
-    $options['rel_display_options'] = array('default' => array('subject', 'type', 'object'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    if ($this->broken) {
-      $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',
-        ),
-      );
-    }
-    else {
-      $form['rel_display_parts'] = array(
-        '#type' => 'checkboxes',
-        '#title' => t('Display Relationship Parts'),
-        '#description' => t('Check each part of the relationship you want displayed where the part '
-          .'of a relationship are: [Subject] [Relationship Type] [Object]. '
-          .'For example, with the relationship Sarah is the maternal parent of Fred '
-          .'if you checked only Object then "Fred" would be displayed.'),
-        '#options' => array(
-          'subject' => 'Subject',
-          'type' => 'Relationship Type',
-          'object' => 'Object',
-        ),
-        '#default_value' => array($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'
-          .' 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',
-        ),
-        '#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);
-      while ($r = db_fetch_object($resource)) {
-        $options[ $r->type_id ] = $r->name;
-      }
-      $form['rel_type_ids'] = array(
-        '#type' => 'checkboxes',
-        '#title' => t('Relationship Types'),
-        '#options' => $options,
-        '#default_value' => $this->options['rel_type_ids'],
-      );
-    }
-  }
-
-  /**
-   * Add this term to the query
-   */
-  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 . " "
-        ."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) . ") ";
-      $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);
-          $r->{$chado_id} = $r->subject_id;
-          $this->view->result[$key]->{$this->aliases['relationships']}[] = clone $r;
-        }
-        if (in_array($r->object_id, $chado_ids)) {
-          $key = array_search($r->object_id, $chado_ids);
-          $r->{$chado_id} = $r->object_id;
-          $this->view->result[$key]->{$this->aliases['relationships']}[] = clone $r;
-        }
-      }
-
-    }
-
-    // add relationships to this field
-    foreach ($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 $relationship) {
-          // perform filtering------
-          //type
-          if (!empty($this->options['rel_type_ids'])) {
-            if (!in_array($relationship->type_id, $relationships2keep)) {
-              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/', $this->options['rel_display_rels'])) {
-            if ($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};
-          $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['subject_id'] = $relationship->subject_id;
-          $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['subject_name'] = $relationship->subject_name;
-          $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['object_id'] = $relationship->object_id;
-          $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['object_name'] = $relationship->object_name;
-          $this->items[$relationship->{$chado_id}][$relationship->{$chado_relationship_id}]['type_id'] = $relationship->type_id;
-          $this->items[$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[] = $item['subject_name'];
-    }
-    if ($this->options['rel_display_parts']['type']) {
-      $text[] = $item['type_name'];
-    }
-    if ($this->options['rel_display_parts']['object']) {
-      $text[] = $item['object_name'];
-    }
-
-    return implode(' ', $text);
-  }
-}

tripal_views/views/handlers/views_handler_field_chado_relationship_all.inc

@@ -1,105 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler for terms.
- */
-class views_handler_field_chado_relationship_all extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-  }
-
-  function query() {
-    // not sure why this is needed since nothing is added to the query...
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['relationships'] = 'relationships';
-    $this->aliases['primary_id'] = $this->view->base_table . '_id';
-    $this->field_alias = $this->aliases['primary_id'];
-    $relationship_tablename = $this->view->base_table . '_relationship';
-    $this->aliases['relationship_primary_id'] = $relationship_tablename  .  '_id';
-    $table_desc = module_invoke_all('chado_' . $relationship_tablename . '_schema');
-    foreach ($table_desc['foreign keys'][$this->view->base_table]['columns'] as $k => $v) {
-      if (preg_match('/subject/', $k)) {
-        $subject_id = $k;
-      }
-      if (preg_match('/object/', $k)) {
-        $object_id = $k;
-      }
-    }
-    $this->aliases['subject_id'] = $subject_id;
-    $this->aliases['object_id'] = $object_id;
-
-    //Add values for all if possible
-    if (!$this->view->result[0]->relationships) {
-      //get base table primary keys
-      $primary_ids = array();
-      foreach ($this->view->result as $row_num => $row) {
-        $primary_ids[$row_num] = $row->{$this->aliases['primary_id']};
-      }
-
-      //generate results from db
-      $sql = "SELECT " . $relationship_tablename . ".*, cvterm.name as type_name, "
-          ."subject_parent.name as subject_name, object_parent.name as object_name "
-          ."FROM " . $relationship_tablename . " "
-          ."LEFT JOIN " . $this->view->base_table . " subject_parent ON "
-            . $relationship_tablename . "." . $subject_id . "=subject_parent." . $this->aliases['primary_id'] . " "
-          ."LEFT JOIN " . $this->view->base_table . " object_parent ON "
-            . $relationship_tablename . "." . $object_id . "=object_parent." . $this->aliases['primary_id'] . " "
-          ."LEFT JOIN cvterm cvterm ON "
-            . $relationship_tablename . ".type_id = cvterm.cvterm_id "
-          ."WHERE " . $relationship_tablename . "." . $subject_id . " IN (" . implode(',', $primary_ids) . ") "
-          ."OR " . $relationship_tablename . "." . $object_id . " IN (" . implode(',', $primary_ids) . ") ";
-      $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql);
-      tripal_db_set_active($previous_db);
-
-      //add results to views results
-      while ($r = db_fetch_object($resource)) {
-        if (in_array($r->{$subject_id}, $primary_ids)) {
-          $key = array_search($r->{$subject_id}, $primary_ids);
-          $r->{$this->aliases['primary_id']} = $r->{$subject_id};
-          $this->view->result[$key]->relationships[] = clone $r;
-        }
-        if (in_array($r->{$object_id}, $primary_ids)) {
-          $key = array_search($r->{$object_id}, $primary_ids);
-          $r->{$this->aliases['primary_id']} = $r->{$object_id};
-          $this->view->result[$key]->relationships[] = clone $r;
-        }
-      } //end of while
-    }// end of if add values
-
-    //for each stock in this view page, add the values
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['relationships']})) {
-
-        // all relationships including the current stock
-        $relationships = $result->{$this->aliases['relationships']};
-        foreach ($relationships as $relationship) {
-          // Add relationship to the list of items to be rendered
-          // Note: $this->aliases['primary_id'] = base table primary key
-
-          $elements = array(
-            $this->aliases['primary_id'] => $relationship->{$this->aliases['primary_id']},
-            $this->aliases['relationship_primary_id'] => $relationship->{$this->aliases['relationship_primary_id']},
-            'subject_id' => $relationship->{$this->aliases['subject_id']},
-            'subject_name' => $relationship->subject_name,
-            'object_id' => $relationship->{$this->aliases['object_id']},
-            'object_name' => $relationship->object_name,
-            'type_id' => $relationship->type_id,
-            'type_name' => $relationship->type_name,
-          );
-          $this->items[$relationship->{$this->aliases['primary_id']}][$relationship->{$this->aliases['relationship_primary_id']}] = $elements;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    return $item['subject_name'] . ' ' . $item['type_name'] . ' ' . $item['object_name'];
-  }
-
-}
-

tripal_views/views/handlers/views_handler_field_chado_relationship_by_type.inc

@@ -1,166 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler for terms.
- */
-class views_handler_field_chado_relationship_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // 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
-    $this->display_type = TRUE;
-
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['stockrel_type_ids'] = array('default' => array());
-    $options['stockrel_display_options'] = array('default' => array('subject', 'type', 'object'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['stockrel_display_parts'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Display Relationship Parts'),
-      '#description' => t('Check each part of the relationship you want displayed where the part '
-        .'of a relationship are: \<Subject\> \<Relationship Type\> \<Object\>. '
-        .'For example, with the relationship Sarah is the maternal parent of Fred '
-        .'if you checked only Object then "Fred" would be displayed.'),
-      '#options' => array(
-        'subject' => 'Subject',
-        'type' => 'Relationship Type',
-        'object' => 'Object',
-      ),
-      '#default_value' => array($this->options['stockrel_display_parts']['subject'], $this->options['stockrel_display_parts']['type'], $this->options['stockrel_display_parts']['object']),
-    );
-
-    $form['stockrel_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 stock, '
-        .'if you selected "Current Stock is the Object" only Sarah is the maternal parent of Fred'
-        .' would be displayed.'),
-      '#options' => array(
-        'subject' => 'Current Stock is the Subject',
-        'object' => 'Current Stock is the Object',
-        'all' => 'Current Stock is the Subject and/or Object',
-      ),
-      '#default_value' => $this->options['stockrel_display_rels'],
-    );
-
-    $options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
-    $form['stockrel_type_ids'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Relationship Types'),
-      '#options' => $options,
-      '#default_value' => $this->options['stockrel_type_ids'],
-    );
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['relationships'] = 'relationships';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['relationships']})) {
-
-        // all relationships including the current stock
-        $relationships = $result->{$this->aliases['relationships']};
-        foreach ($relationships as $relationship) {
-          // perform filtering------
-          //type
-          if (!empty($this->options['stockrel_type_ids'])) {
-            $relationships2keep = array_filter($this->options['stockrel_type_ids']);
-            if (!in_array($relationship->type_id, $relationships2keep)) {
-              continue;
-            }
-          }
-
-          //"Display Relationships Where" criteria
-          if (preg_match('/subject/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->subject_id) {
-              continue;
-            }
-          }
-          elseif (preg_match('/object/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->object_id) {
-              continue;
-            }
-          }
-
-          // Add relationship to the list of items to be rendered
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_id'] = $relationship->stock_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_relationship_id'] = $relationship->stock_relationship_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_id'] = $relationship->subject_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_name'] = $relationship->subject_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_id'] = $relationship->object_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_name'] = $relationship->object_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_id'] = $relationship->type_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_name'] = $relationship->type_name;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    $text = array();
-
-    // Render Parts
-    if ($this->options['stockrel_display_parts']['subject']) {
-      $text[] = $item['subject_name'];
-    }
-    if ($this->options['stockrel_display_parts']['type']) {
-      $text[] = $item['type_name'];
-    }
-    if ($this->options['stockrel_display_parts']['object']) {
-      $text[] = $item['object_name'];
-    }
-
-    return implode(' ', $text);
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = t('Relationship ID');
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = t('Subject ID');
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = t('Subject Name');
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = t('Object ID');
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = t('Object Name');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('Type ID');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('Type Name');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = $item['stock_relationship_id'];
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = $item['subject_id'];
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = $item['subject_name'];
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = $item['object_id'];
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = $item['object_name'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-
-  }
-}
-

tripal_views/views/handlers/views_handler_field_chado_relationship_by_type.inc.orig

@@ -1,173 +0,0 @@
-<?php
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_field_chado_relationship_by_type.inc
-=======
-/**
- * @file
- * @todo Add file header description
- */
->>>>>>> 6.x-0.4-dev:tripal_natural_diversity/views/handlers/views_handler_field_chado_relationship_by_type.inc
-
-/**
- * @file
- * Field handler for terms.
- */
-class views_handler_field_chado_relationship_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // 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
-    $this->display_type = TRUE;
-
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['stockrel_type_ids'] = array('default' => array());
-    $options['stockrel_display_options'] = array('default' => array('subject', 'type', 'object'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['stockrel_display_parts'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Display Relationship Parts'),
-      '#description' => t('Check each part of the relationship you want displayed where the part '
-        .'of a relationship are: \<Subject\> \<Relationship Type\> \<Object\>. '
-        .'For example, with the relationship Sarah is the maternal parent of Fred '
-        .'if you checked only Object then "Fred" would be displayed.'),
-      '#options' => array(
-        'subject' => 'Subject',
-        'type' => 'Relationship Type',
-        'object' => 'Object',
-      ),
-      '#default_value' => array($this->options['stockrel_display_parts']['subject'], $this->options['stockrel_display_parts']['type'], $this->options['stockrel_display_parts']['object']),
-    );
-
-    $form['stockrel_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 stock, '
-        .'if you selected "Current Stock is the Object" only Sarah is the maternal parent of Fred'
-        .' would be displayed.'),
-      '#options' => array(
-        'subject' => 'Current Stock is the Subject',
-        'object' => 'Current Stock is the Object',
-        'all' => 'Current Stock is the Subject and/or Object',
-      ),
-      '#default_value' => $this->options['stockrel_display_rels'],
-    );
-
-    $options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
-    $form['stockrel_type_ids'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Relationship Types'),
-      '#options' => $options,
-      '#default_value' => $this->options['stockrel_type_ids'],
-    );
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['relationships'] = 'relationships';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['relationships']})) {
-
-        // all relationships including the current stock
-        $relationships = $result->{$this->aliases['relationships']};
-        foreach ($relationships as $relationship) {
-          // perform filtering------
-          //type
-          if (!empty($this->options['stockrel_type_ids'])) {
-            $relationships2keep = array_filter($this->options['stockrel_type_ids']);
-            if (!in_array($relationship->type_id, $relationships2keep)) {
-              continue;
-            }
-          }
-
-          //"Display Relationships Where" criteria
-          if (preg_match('/subject/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->subject_id) {
-              continue;
-            }
-          }
-          elseif (preg_match('/object/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->object_id) {
-              continue;
-            }
-          }
-
-          // Add relationship to the list of items to be rendered
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_id'] = $relationship->stock_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_relationship_id'] = $relationship->stock_relationship_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_id'] = $relationship->subject_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_name'] = $relationship->subject_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_id'] = $relationship->object_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_name'] = $relationship->object_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_id'] = $relationship->type_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_name'] = $relationship->type_name;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    $text = array();
-
-    // Render Parts
-    if ($this->options['stockrel_display_parts']['subject']) {
-      $text[] = $item['subject_name'];
-    }
-    if ($this->options['stockrel_display_parts']['type']) {
-      $text[] = $item['type_name'];
-    }
-    if ($this->options['stockrel_display_parts']['object']) {
-      $text[] = $item['object_name'];
-    }
-
-    return implode(' ', $text);
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = t('Relationship ID');
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = t('Subject ID');
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = t('Subject Name');
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = t('Object ID');
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = t('Object Name');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('Type ID');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('Type Name');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = $item['stock_relationship_id'];
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = $item['subject_id'];
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = $item['subject_name'];
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = $item['object_id'];
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = $item['object_name'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-
-  }
-}
-

tripal_views/views/handlers/views_handler_field_cvterm_name.inc

@@ -1,66 +0,0 @@
-<?php
-
-/**
- * @file
- * @ingroup views_field_handlers
- * @ingroup tripal_core
- */
-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)) {
-
-      //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;
-      $cvterm_join['alias'] = $this->table . '_cvterm';
-      $cvterm_join['relationship'] = $this->table;
-
-      $cvterm_join['join'] = clone($this->query->table_queue[$this->table]['join']);
-      $cvterm_join['join']->table = 'cvterm';
-      $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;
-      $cvterm_join['join']->definition['left_field'] = 'type_id';
-
-      $this->query->table_queue[$cvterm_join['alias']] = $cvterm_join;
-
-      // add to table--------------------------------------------------
-      $this->query->tables[$this->view->base_table][$this->table . '_cvterm'] = array(
-        'count' => 1,
-        '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');
-      $this->add_additional_fields();
-      $this->aliases['name'] = $field_alias;
-
-    }
-  }
-
-  /**
-   * Ensure that the type/cvterm name is rendered
-   */
-  function render($values) {
-    return $values->{$this->aliases['name']};
-  }
-
-}

tripal_views/views/handlers/views_handler_field_stock_dbxref_all.inc

@@ -1,88 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all database references for a given stock to be displayed in a single cell
- *
- * This handler only deals with database references joined to the stock through stock_dbxref. For
- * the database reference joined to the stock by stock.dbxref_id simply join to the dbxref table.
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stock_dbxref_all extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['dbxref'] = 'dbxref';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['dbxref']})) {
-
-        // all dbxrefs including the current stock
-        $dbxrefs = $result->{$this->aliases['dbxref']};
-        foreach ($dbxrefs as $dbxref) {
-          // Add dbxref to the list of items to be rendered
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['stock_id'] = $dbxref->stock_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['stock_dbxref_id'] = $dbxref->stock_dbxref_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['dbxref_id'] = $dbxref->dbxref_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['is_current'] = $dbxref->is_current;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['db_id'] = $dbxref->db_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['db_name'] = $dbxref->db_name;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['urlprefix'] = $dbxref->urlprefix;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['accession'] = $dbxref->accession;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['version'] = $dbxref->version;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['description'] = $dbxref->description;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    if (!empty($item['urlprefix'])) {
-      return l($item['accession'], $item['urlprefix'] . $item['accession']) . ' (' . $item['db_name'] . ')';
-    }
-    else {
-      return $item['accession'] . ' (' . $item['db_name'] . ')';
-    }
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_dbxref_id' . ']'] = t('Stock Database Reference ID');
-    $tokens['[' . $this->options['id'] . '-dbxref_id' . ']'] = t('Database Reference ID');
-    $tokens['[' . $this->options['id'] . '-is_current' . ']'] = t('Is Current');
-    $tokens['[' . $this->options['id'] . '-db_id' . ']'] = t('Database ID');
-    $tokens['[' . $this->options['id'] . '-db_name' . ']'] = t('Database Name');
-    $tokens['[' . $this->options['id'] . '-urlprefix' . ']'] = t('URL Prefix');
-    $tokens['[' . $this->options['id'] . '-accession' . ']'] = t('Accession');
-    $tokens['[' . $this->options['id'] . '-version' . ']'] = t('Version');
-    $tokens['[' . $this->options['id'] . '-description' . ']'] = t('Description');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_dbxref_id' . ']'] = $item['stock_dbxref_id'];
-    $tokens['[' . $this->options['id'] . '-dbxref_id' . ']'] =  $item['dbxref_id'];
-    $tokens['[' . $this->options['id'] . '-is_current' . ']'] = $item['is_current'];
-    $tokens['[' . $this->options['id'] . '-db_id' . ']'] = $item['db_id'];
-    $tokens['[' . $this->options['id'] . '-db_name' . ']'] = $item['db_name'];
-    $tokens['[' . $this->options['id'] . '-urlprefix' . ']'] = $item['urlprefix'];
-    $tokens['[' . $this->options['id'] . '-accession' . ']'] = $item['accession'];
-    $tokens['[' . $this->options['id'] . '-version' . ']'] = $item['version'];
-    $tokens['[' . $this->options['id'] . '-description' . ']'] = $item['description'];
-  }
-}
-

tripal_views/views/handlers/views_handler_field_stock_dbxref_by_type.inc

@@ -1,161 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all database references of a specified db for a given stock to be
- * displayed in a single cell.
- *
- * This handler only deals with database references joined to the stock through stock_dbxref. For
- * the database reference joined to the stock by stock.dbxref_id simply join to the dbxref table.
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stock_dbxref_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // 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
-    $this->display_type = TRUE;
-
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['stockprop_type_ids'] = array('default' => array());
-    $options['display_options'] = array('default' => array('accession', 'db_name', 'link'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['display_options'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Display DB Reference Parts'),
-      '#description' => t('Check each part of the database reference you want displayed where the parts '
-        ."of a database relationship are: \<Accession\> (\<Datbase Name\>). You can also specify whether the accession "
-        .'should be linked to the record in the database by checking "Link to External Record".'),
-      '#options' => array(
-        'accession' => 'Accession',
-        'db_name' => 'Database Name',
-        'link' => 'Link to External Record',
-      ),
-      '#default_value' => array($this->options['display_options']['accession'], $this->options['display_options']['db_name'], $this->options['display_options']['link']),
-    );
-
-    $db_options = tripal_db_get_db_options();
-    $db_options[0] = 'Select a Database';
-    ksort($db_options);
-    $form['db_ids'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Database'),
-      '#options' => $db_options,
-      '#default_value' => $this->options['db_ids'],
-    );
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['dbxref'] = 'dbxref';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['dbxref']})) {
-
-        // all dbxrefs including the current stock
-        $dbxrefs = $result->{$this->aliases['dbxref']};
-        foreach ($dbxrefs as $dbxref) {
-
-          // perform filtering
-          if (!empty($this->options['db_ids'])) {
-            $dbs2keep = array_filter($this->options['db_ids']);
-            if (!in_array($dbxref->db_id, $dbs2keep)) {
-              continue;
-            }
-          }
-
-          // Add dbxref to the list of items to be rendered
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['stock_id'] = $dbxref->stock_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['stock_dbxref_id'] = $dbxref->stock_dbxref_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['dbxref_id'] = $dbxref->dbxref_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['is_current'] = $dbxref->is_current;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['db_id'] = $dbxref->db_id;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['db_name'] = $dbxref->db_name;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['urlprefix'] = $dbxref->urlprefix;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['accession'] = $dbxref->accession;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['version'] = $dbxref->version;
-          $this->items[$dbxref->stock_id][$dbxref->stock_dbxref_id]['description'] = $dbxref->description;        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    $text = array();
-    if ($this->options['display_options']['link']) {
-      if ($this->options['display_options']['accession']) {
-        $text[] = l(t($item['accession']), $item['urlprefix'] . $item['accession']);
-      }
-      else {
-        $text[] = l(t('External Record'), $item['urlprefix'] . $item['accession']);
-      }
-    }
-    else {
-      if ($this->options['display_options']['accession']) {
-        $text[] = $item['accession'];
-      }
-    }
-
-
-    if ($this->options['display_options']['db_name']) {
-      $text[] = $item['db_name'];
-    }
-
-    if (sizeof($text) > 1) {
-      return $text[0] . ' (' . $text[1] . ')';
-    }
-    else {
-      return $text[0];
-    }
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_dbxref_id' . ']'] = t('Stock Database Reference ID');
-    $tokens['[' . $this->options['id'] . '-dbxref_id' . ']'] = t('Database Reference ID');
-    $tokens['[' . $this->options['id'] . '-is_current' . ']'] = t('Is Current');
-    $tokens['[' . $this->options['id'] . '-db_id' . ']'] = t('Database ID');
-    $tokens['[' . $this->options['id'] . '-db_name' . ']'] = t('Database Name');
-    $tokens['[' . $this->options['id'] . '-urlprefix' . ']'] = t('URL Prefix');
-    $tokens['[' . $this->options['id'] . '-accession' . ']'] = t('Accession');
-    $tokens['[' . $this->options['id'] . '-version' . ']'] = t('Version');
-    $tokens['[' . $this->options['id'] . '-description' . ']'] = t('Description');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_dbxref_id' . ']'] = $item['stock_dbxref_id'];
-    $tokens['[' . $this->options['id'] . '-dbxref_id' . ']'] =  $item['dbxref_id'];
-    $tokens['[' . $this->options['id'] . '-is_current' . ']'] = $item['is_current'];
-    $tokens['[' . $this->options['id'] . '-db_id' . ']'] = $item['db_id'];
-    $tokens['[' . $this->options['id'] . '-db_name' . ']'] = $item['db_name'];
-    $tokens['[' . $this->options['id'] . '-urlprefix' . ']'] = $item['urlprefix'];
-    $tokens['[' . $this->options['id'] . '-accession' . ']'] = $item['accession'];
-    $tokens['[' . $this->options['id'] . '-version' . ']'] = $item['version'];
-    $tokens['[' . $this->options['id'] . '-description' . ']'] = $item['description'];
-  }
-}
-

tripal_views/views/handlers/views_handler_field_stockprop_all.inc

@@ -1,68 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all properties for a given stock to be displayed in a single cell
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stockprop_all extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['properties'] = 'properties';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['properties']})) {
-
-        // all properties for the current stock
-        $properties = $result->{$this->aliases['properties']};
-        foreach ($properties as $property) {
-          // Add property to the list of items to be rendered
-          $this->items[$property->stock_id][$property->stockprop_id]['stock_id'] = $property->stock_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['stockprop_id'] = $property->stockprop_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['type_id'] = $property->type_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['type_name'] = check_plain($property->type_name);
-          $this->items[$property->stock_id][$property->stockprop_id]['value'] = check_plain($property->value);
-          $this->items[$property->stock_id][$property->stockprop_id]['rank'] = $property->rank;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    return $item['value'] . ' (' . $item['type_name'] . ')';
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stockprop_id' . ']'] = t('The Property ID.');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('The Property Type ID.');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('The Property Type.');
-    $tokens['[' . $this->options['id'] . '-value' . ']'] = t('The Value of the Property.');
-    $tokens['[' . $this->options['id'] . '-rank' . ']'] = t('The Rank of the Property.');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stockprop_id' . ']'] = $item['stockprop_id'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-    $tokens['[' . $this->options['id'] . '-value' . ']'] = $item['value'];
-    $tokens['[' . $this->options['id'] . '-rank' . ']'] = $item['rank'];
-  }
-}
-

tripal_views/views/handlers/views_handler_field_stockprop_by_type.inc

@@ -1,138 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all properties of a specified type for a given stock to be displayed in a
- * single cell
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stockprop_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['stockprop_type_ids'] = array('default' => array());
-    $options['stockprop_display_options'] = array('default' => array('type', 'value'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['stockprop_display_options'] = array(
-      '#prefix' => '<div><div id="edit-options-display_options">',
-      '#suffix' => '</div></div>',
-      '#type' => 'checkboxes',
-      '#title' => t('Display Relationship Parts'),
-      '#description' => t('Check each part of the property you want displayed where the parts '
-        .'of a property are: <type> and <value>. '
-        .'For example, with the property temperature 54 degrees Celcius the type=temperature and the value=54 degrees Celcius. '
-        .'Thus, if you checked only value then "54 degrees Celcius" would be displayed.'),
-      '#options' => array(
-        'type' => 'Type',
-        'value' => 'Value',
-      ),
-      '#default_value' => array($this->options['stockprop_display_options']['type'], $this->options['stockprop_display_options']['value']),
-    );
-
-    $options = tripal_cv_get_cvterm_options( variable_get('chado_stock_prop_types_cv', 'null') );
-    $form['stockprop_type_ids'] = array(
-      '#prefix' => '<div><div id="edit-options-stockprop_type_ids">',
-      '#suffix' => '</div></div>',
-      '#type' => 'checkboxes',
-      '#title' => t('Property Types'),
-      '#options' => $options,
-      '#default_value' => $this->options['stockprop_type_ids'],
-    );
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['properties'] = 'properties';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['properties']})) {
-
-        // all properties for the current stock
-        $properties = $result->{$this->aliases['properties']};
-        foreach ($properties as $property) {
-          // perform filtering
-          if (!empty($this->options['stockprop_type_ids'])) {
-            $types2keep = array_filter($this->options['stockprop_type_ids']);
-            if (!in_array($property->type_id, $types2keep)) {
-              continue;
-            }
-          }
-
-          // Add property to the list of items to be rendered
-          $this->items[$property->stock_id][$property->stockprop_id]['stock_id'] = $property->stock_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['stockprop_id'] = $property->stockprop_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['type_id'] = $property->type_id;
-          $this->items[$property->stock_id][$property->stockprop_id]['type_name'] = check_plain($property->type_name);
-          $this->items[$property->stock_id][$property->stockprop_id]['value'] = check_plain($property->value);
-          $this->items[$property->stock_id][$property->stockprop_id]['rank'] = $property->rank;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    $text = array();
-
-    if ($this->options['stockprop_display_options']['value']) {
-      if ($item['value']) {
-        $text[] =  $item['value'];
-      }
-      else {
-        //display checkmark image
-        $image_path = drupal_get_path('module', 'tripal_core') . '/images/checkmark.gif';
-        $text[] = '<img border="0" src="' . url($image_path) . '" alt="checkmark" />';
-      }
-    }
-    if ($this->options['stockprop_display_options']['type']) {
-      $text[] = $item['type_name'];
-    }
-
-    if (sizeof($text) > 1) {
-      return $text[0] . ' (' . $text[1] . ')';
-    }
-    else {
-      return $text[0];
-    }
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stockprop_id' . ']'] = t('The Property ID.');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('The Property Type ID.');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('The Property Type.');
-    $tokens['[' . $this->options['id'] . '-value' . ']'] = t('The Value of the Property.');
-    $tokens['[' . $this->options['id'] . '-rank' . ']'] = t('The Rank of the Property.');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stockprop_id' . ']'] = $item['stockprop_id'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-    $tokens['[' . $this->options['id'] . '-value' . ']'] = $item['value'];
-    $tokens['[' . $this->options['id'] . '-rank' . ']'] = $item['rank'];
-  }
-}
-

tripal_views/views/handlers/views_handler_field_stockrel_all.inc

@@ -1,75 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all relationships for a given stock to be displayed in a single cell
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stockrel_all extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['relationships'] = 'relationships';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['relationships']})) {
-
-        // all relationships including the current stock
-        $relationships = $result->{$this->aliases['relationships']};
-        foreach ($relationships as $relationship) {
-          // Add relationship to the list of items to be rendered
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_id'] = $relationship->stock_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_relationship_id'] = $relationship->stock_relationship_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_id'] = $relationship->subject_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_name'] = $relationship->subject_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_id'] = $relationship->object_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_name'] = $relationship->object_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_id'] = $relationship->type_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_name'] = $relationship->type_name;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    return $item['subject_name'] . ' ' . $item['type_name'] . ' ' . $item['object_name'];
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = t('Relationship ID');
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = t('Subject ID');
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = t('Subject Name');
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = t('Object ID');
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = t('Object Name');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('Type ID');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('Type Name');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = $item['stock_relationship_id'];
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = $item['subject_id'];
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = $item['subject_name'];
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = $item['object_id'];
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = $item['object_name'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-
-  }
-}
-

tripal_views/views/handlers/views_handler_field_stockrel_by_type.inc

@@ -1,170 +0,0 @@
-<?php
-
-/**
- * @file
- * Field handler allowing all relationships of a specified type for a given stock to be displayed in
- * a single cell
- *
- * @ingroup tripal_stock
- * @ingroup views_field_handlers
- */
-class views_handler_field_stockrel_by_type extends views_handler_field_prerender_list {
-  function init(&$view, $options) {
-    parent::init($view, $options);
-
-    // 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
-    $this->display_type = TRUE;
-
-  }
-
-  function option_definition() {
-    $options = parent::option_definition();
-    $options['stockrel_type_ids'] = array('default' => array());
-    $options['stockrel_display_options'] = array('default' => array('subject', 'type', 'object'));
-    return $options;
-  }
-
-  /**
-   * Provide "link to term" option.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['stockrel_display_parts'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Display Relationship Parts'),
-      '#description' => t('Check each part of the relationship you want displayed where the part '
-        .'of a relationship are: \<Subject\> \<Relationship Type\> \<Object\>. '
-        .'For example, with the relationship Sarah is the maternal parent of Fred '
-        .'if you checked only Object then "Fred" would be displayed.'),
-      '#options' => array(
-        'subject' => 'Subject',
-        'type' => 'Relationship Type',
-        'object' => 'Object',
-      ),
-      '#default_value' => array($this->options['stockrel_display_parts']['subject'], $this->options['stockrel_display_parts']['type'], $this->options['stockrel_display_parts']['object']),
-    );
-
-    $form['stockrel_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 stock, '
-        .'if you selected "Current Stock is the Object" only Sarah is the maternal parent of Fred'
-        .' would be displayed.'),
-      '#options' => array(
-        'subject' => 'Current Stock is the Subject',
-        'object' => 'Current Stock is the Object',
-        'all' => 'Current Stock is the Subject and/or Object',
-      ),
-      '#default_value' => $this->options['stockrel_display_rels'],
-    );
-
-    $options = tripal_cv_get_cvterm_options( variable_get('chado_stock_relationship_cv', 'null') );
-    $form['stockrel_type_ids'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Relationship Types'),
-      '#options' => $options,
-      '#default_value' => $this->options['stockrel_type_ids'],
-    );
-  }
-
-  /**
-   * Add this term to the query
-   */
-  function query() {
-    $this->add_additional_fields();
-  }
-
-  function pre_render($values) {
-    $this->aliases['relationships'] = 'relationships';
-    $this->aliases['stock_id'] = 'stock_id';
-    $this->field_alias = $this->aliases['stock_id'];
-
-    //for each stock in this view page
-    foreach ($values as $result) {
-      if (!empty($result->{$this->aliases['relationships']})) {
-
-        // all relationships including the current stock
-        $relationships = $result->{$this->aliases['relationships']};
-        foreach ($relationships as $relationship) {
-          // perform filtering------
-          //type
-          if (!empty($this->options['stockrel_type_ids'])) {
-            $relationships2keep = array_filter($this->options['stockrel_type_ids']);
-            if (!in_array($relationship->type_id, $relationships2keep)) {
-              continue;
-            }
-          }
-
-          //"Display Relationships Where" criteria
-          if (preg_match('/subject/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->subject_id) {
-              continue;
-            }
-          }
-          elseif (preg_match('/object/', $this->options['stockrel_display_rels'])) {
-            if ($relationship->stock_id != $relationship->object_id) {
-              continue;
-            }
-          }
-
-          // Add relationship to the list of items to be rendered
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_id'] = $relationship->stock_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['stock_relationship_id'] = $relationship->stock_relationship_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_id'] = $relationship->subject_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['subject_name'] = $relationship->subject_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_id'] = $relationship->object_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['object_name'] = $relationship->object_name;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_id'] = $relationship->type_id;
-          $this->items[$relationship->stock_id][$relationship->stock_relationship_id]['type_name'] = $relationship->type_name;
-        }
-      }
-    }
-  }
-
-  function render_item($count, $item) {
-    $text = array();
-
-    // Render Parts
-    if ($this->options['stockrel_display_parts']['subject']) {
-      $text[] = $item['subject_name'];
-    }
-    if ($this->options['stockrel_display_parts']['type']) {
-      $text[] = $item['type_name'];
-    }
-    if ($this->options['stockrel_display_parts']['object']) {
-      $text[] = $item['object_name'];
-    }
-
-    return implode(' ', $text);
-  }
-
-  function document_self_tokens(&$tokens) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = t('The Stock ID.');
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = t('Relationship ID');
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = t('Subject ID');
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = t('Subject Name');
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = t('Object ID');
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = t('Object Name');
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = t('Type ID');
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = t('Type Name');
-  }
-
-  function add_self_tokens(&$tokens, $item) {
-    $tokens['[' . $this->options['id'] . '-stock_id' . ']'] = $item['stock_id'];
-    $tokens['[' . $this->options['id'] . '-stock_relationship_id' . ']'] = $item['stock_relationship_id'];
-    $tokens['[' . $this->options['id'] . '-subject_id' . ']'] = $item['subject_id'];
-    $tokens['[' . $this->options['id'] . '-subject_name' . ']'] = $item['subject_name'];
-    $tokens['[' . $this->options['id'] . '-object_id' . ']'] = $item['object_id'];
-    $tokens['[' . $this->options['id'] . '-object_name' . ']'] = $item['object_name'];
-    $tokens['[' . $this->options['id'] . '-type_id' . ']'] = $item['type_id'];
-    $tokens['[' . $this->options['id'] . '-type_name' . ']'] = $item['type_name'];
-
-  }
-}
-

tripal_views/views/handlers/views_handler_field_type_name.inc

@@ -1,16 +0,0 @@
-<?php
-
-/**
- * @file
- * @ingroup views_field_handlers
- * @ingroup tripal_core
- */
-class views_handler_field_type_name extends views_handler_field {
-  function construct() {
-    parent::construct();
-  }
-
-  function render($values) {
-    return $values->property_type_name;
-  }
-}

tripal_views/views/handlers/views_handler_filter_stock_dbxref_id.inc

@@ -1,245 +0,0 @@
-<?php
-
-/**
- * @file
- * Allows stocks to be filtered by associated database reference accession
- *
- * @ingroup tripal_stock
- * @ingroup views_filter_handlers
- */
-class views_handler_filter_stock_dbxref_id extends views_handler_filter {
-
-  function init(&$view, $options) {
-    parent::init($view, $options);
-    $this->db = $this->options['db'];
-  }
-
-  function options_form(&$form, &$form_state) {
-    if ($this->can_expose()) {
-      $this->show_expose_button($form, $form_state);
-    }
-
-    $form['op_val_start'] = array('#value' => '<div class="clear-block">');
-
-    $this->types_form($form, $form_state);
-
-    $this->show_operator_form($form, $form_state);
-    $form['operator']['#prefix'] = '<div class="views-right-70">';
-    $this->show_value_form($form, $form_state);
-    $form['op_val_end'] = array('#value' => '</div>');
-
-    if ($this->can_expose()) {
-      $this->show_expose_form($form, $form_state);
-    }
-
-  }
-
-  function query() {
-    $this-> db = array_filter($this->db);
-
-    if (preg_match('/IS NOT NULL/', $this->options['operator'])) {
-      $new_where_sql = "stock.stock_id IN "
-      ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
-      $this->query->add_where($this->options['group'], $new_where_sql);
-    }
-    elseif (preg_match('/IS NULL/', $this->options['operator'])) {
-      $new_where_sql = "stock.stock_id NOT IN "
-      ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
-      $this->query->add_where($this->options['group'], $new_where_sql);
-    }
-    else {
-      if (!empty($this->value)) {
-        $new_where_sql = "stock.stock_id IN "
-          ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id "
-          ."AND dbxref.db_id IN (" . implode(', ', $this->db) . ") AND dbxref.accession" . $this->operator . "'" . $this->value . "')";
-        $this->query->add_where($this->options['group'], $new_where_sql);
-      }
-    }
-  }
-
-  /////////// Form Parts/////////////////////////
-  function types_form(&$form, &$form_state) {
-
-    $db_options = tripal_db_get_db_options();
-    ksort($db_options);
-    $form['db'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Databases'),
-      '#options' => $db_options,
-      '#default_value' => $this->db,
-      '#prefix' => '<div class="views-left-30">',
-      '#suffix' => '</div>',
-    );
-
-  }
-
-  function value_form(&$form, &$form_state) {
-    parent::value_form($form, $form_state);
-
-    $form['value'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Accession'),
-      '#default_value' => $this->value,
-    );
-  }
-
-  function operator_options() {
-    return array(
-      '=' => t('Is equal to'),
-      '!=' => t('Is not equal to'),
-      '~' => t('Contains'),
-      '!~' => t('Does not contain'),
-      'IS NOT NULL' => t('Is Present (Not Empty)'),
-      'IS NULL' => t('Is Absent (Empty)'),
-    );
-  }
-
- /**
-  * Render our chunk of the exposed filter form when selecting
-  */
-  function exposed_form(&$form, &$form_state) {
-    if (empty($this->options['exposed'])) {
-      return;
-    }
-
-    if (!empty($this->options['expose']['use_type']) && !empty($this->options['expose']['type'])) {
-      $type = $this->options['expose']['type'];
-      $form[$type] = array(
-        '#type' => 'select',
-        '#title' => t('Database References'),
-        '#options' => $this->type_options(),
-        '#default_value' => $this->type,
-      );
-
-      if (isset($form[$type]['#title'])) {
-        unset($form[$type]['#title']);
-      }
-    }
-
-    if (!empty($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, &$form_state) {
-    if (!empty($form['type']['#type'])) {
-      $form['expose']['use_type'] = array(
-        '#type' => 'checkbox',
-        '#title' => t('Unlock Database Reference'),
-        '#description' => t('When checked, the Database Reference will be exposed to the user'),
-        '#default_value' => !empty($this->options['expose']['use_type']),
-      );
-      $form['expose']['type'] = array(
-        '#type' => 'textfield',
-        '#default_value' => $this->options['expose']['type'],
-        '#title' => t('Database Reference identifier'),
-        '#size' => 40,
-        '#description' => t('This will appear in the URL after the ? to identify this Database Reference.'),
-        '#process' => array('views_process_dependency'),
-        '#dependency' => array(
-          'edit-options-expose-use-type' => array(1)
-        ),
-      );
-    }
-    else {
-      $form['expose']['type'] = array(
-        '#type' => 'value',
-        '#value' => '',
-      );
-    }
-
-    $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_views/views/handlers/views_handler_filter_stock_dbxref_id.inc.orig

@@ -1,258 +0,0 @@
-<?php
-
-/**
- * @file
- * Allows stocks to be filtered by associated database reference accession
- *
- * @ingroup tripal_stock
- * @ingroup views_filter_handlers
- */
-class views_handler_filter_stock_dbxref_id extends views_handler_filter {
-
-  function init(&$view, $options) {
-    parent::init($view, $options);
-    $this->db = $this->options['db'];
-  }
-
-  function options_form(&$form, &$form_state) {
-    if ($this->can_expose()) {
-      $this->show_expose_button($form, $form_state);
-    }
-
-    $form['op_val_start'] = array('#value' => '<div class="clear-block">');
-
-    $this->types_form($form, $form_state);
-
-    $this->show_operator_form($form, $form_state);
-    $form['operator']['#prefix'] = '<div class="views-right-70">';
-    $this->show_value_form($form, $form_state);
-    $form['op_val_end'] = array('#value' => '</div>');
-
-    if ($this->can_expose()) {
-      $this->show_expose_form($form, $form_state);
-    }
-
-  }
-
-  function query() {
-    $this-> db = array_filter($this->db);
-
-    if (preg_match('/IS NOT NULL/', $this->options['operator'])) {
-      $new_where_sql = "stock.stock_id IN "
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_dbxref_id.inc
-      ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
-=======
-      . "(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_dbxref_id.inc
-      $this->query->add_where($this->options['group'], $new_where_sql);
-    }
-    elseif (preg_match('/IS NULL/', $this->options['operator'])) {
-      $new_where_sql = "stock.stock_id NOT IN "
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_dbxref_id.inc
-      ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
-=======
-      . "(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id AND dbxref.db_id IN (" . implode(', ', $this->db) . "))";
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_dbxref_id.inc
-      $this->query->add_where($this->options['group'], $new_where_sql);
-    }
-    else {
-      if (!empty($this->value)) {
-        $new_where_sql = "stock.stock_id IN "
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_dbxref_id.inc
-          ."(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id "
-          ."AND dbxref.db_id IN (" . implode(', ', $this->db) . ") AND dbxref.accession" . $this->operator . "'" . $this->value . "')";
-=======
-          . "(SELECT stock_dbxref.stock_id FROM stock_dbxref, dbxref WHERE stock_dbxref.dbxref_id=dbxref.dbxref_id "
-          . "AND dbxref.db_id IN (" . implode(', ', $this->db) . ") AND dbxref.accession" . $this->operator . "'" . $this->value . "')";
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_dbxref_id.inc
-        $this->query->add_where($this->options['group'], $new_where_sql);
-      }
-    }
-  }
-
-  /////////// Form Parts/////////////////////////
-  function types_form(&$form, &$form_state) {
-
-    $db_options = tripal_db_get_db_options();
-    ksort($db_options);
-    $form['db'] = array(
-      '#type' => 'checkboxes',
-      '#title' => t('Databases'),
-      '#options' => $db_options,
-      '#default_value' => $this->db,
-      '#prefix' => '<div class="views-left-30">',
-      '#suffix' => '</div>',
-    );
-
-  }
-
-  function value_form(&$form, &$form_state) {
-    parent::value_form($form, $form_state);
-
-    $form['value'] = array(
-      '#type' => 'textfield',
-      '#title' => t('Accession'),
-      '#default_value' => $this->value,
-    );
-  }
-
-  function operator_options() {
-    return array(
-      '=' => t('Is equal to'),
-      '!=' => t('Is not equal to'),
-      '~' => t('Contains'),
-      '!~' => t('Does not contain'),
-      'IS NOT NULL' => t('Is Present (Not Empty)'),
-      'IS NULL' => t('Is Absent (Empty)'),
-    );
-  }
-
- /**
-  * Render our chunk of the exposed filter form when selecting
-  */
-  function exposed_form(&$form, &$form_state) {
-    if (empty($this->options['exposed'])) {
-      return;
-    }
-
-    if (!empty($this->options['expose']['use_type']) && !empty($this->options['expose']['type'])) {
-      $type = $this->options['expose']['type'];
-      $form[$type] = array(
-        '#type' => 'select',
-        '#title' => t('Database References'),
-        '#options' => $this->type_options(),
-        '#default_value' => $this->type,
-      );
-
-      if (isset($form[$type]['#title'])) {
-        unset($form[$type]['#title']);
-      }
-    }
-
-    if (!empty($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, &$form_state) {
-    if (!empty($form['type']['#type'])) {
-      $form['expose']['use_type'] = array(
-        '#type' => 'checkbox',
-        '#title' => t('Unlock Database Reference'),
-        '#description' => t('When checked, the Database Reference will be exposed to the user'),
-        '#default_value' => !empty($this->options['expose']['use_type']),
-      );
-      $form['expose']['type'] = array(
-        '#type' => 'textfield',
-        '#default_value' => $this->options['expose']['type'],
-        '#title' => t('Database Reference identifier'),
-        '#size' => 40,
-        '#description' => t('This will appear in the URL after the ? to identify this Database Reference.'),
-        '#process' => array('views_process_dependency'),
-        '#dependency' => array(
-          'edit-options-expose-use-type' => array(1)
-        ),
-      );
-    }
-    else {
-      $form['expose']['type'] = array(
-        '#type' => 'value',
-        '#value' => '',
-      );
-    }
-
-    $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_views/views/handlers/views_handler_filter_stock_relationship_id.inc

@@ -1,317 +0,0 @@
-<?php
-
-/**
- * @file
- * Filter stocks via stock_relationships
- */
-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(t('No stock with the name or uniquename %value was found -No filtering done.', array('%value' => $this->value)), 'error');
-        }
-      } //end of not just checking presence
-    }
-  }
-
-  function options_form(&$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, $form_state);
-
-    if ($this->options['label']) {
-      $label = $this->options['label'];
-    }
-    else {
-      $label = 'Stock Name';
-    }
-    $form['value'] = array(
-      '#type' => 'textfield',
-      '#title' => t('%label', array('%label' => $label)),
-      '#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_views/views/handlers/views_handler_filter_stock_relationship_id.inc.orig

@@ -1,355 +0,0 @@
-<?php
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- * @file
- * Filter stocks via stock_relationships
- */
-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 ('
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_relationship_id.inc
-            .'SELECT ' . $this->options['variable_position'] . ' FROM stock_relationship '
-            .'WHERE ' . $this->options['fixed_position'] . ' ' . $this->operator . ' AND type_id = ' . $this->options['type']
-          .')';
-=======
-            . 'SELECT ' . $this->options['variable_position'] . ' FROM {stock_relationship} '
-            . 'WHERE ' . $this->options['fixed_position'] . ' ' . $this->operator . ' AND type_id = ' . $this->options['type']
-          . ')';
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc
-          $this->query->add_where($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 ('
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_relationship_id.inc
-            .'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']
-          .')';
-=======
-            . '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']
-          . ')';
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc
-          $this->query->add_where($this->options['group'], $where);
-        }
-        elseif (sizeof($fixed_stock_ids) > 1) {
-          $where = 'stock.stock_id IN ('
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_relationship_id.inc
-            .'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(t('No stock with the name or uniquename %value was found -No filtering done.', array('%value' => $this->value)), 'error');
-=======
-            . '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(t('No stock with the name or uniquename %value was found -No filtering done.',  array('%value' => $this->value ), 'error'));
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc
-        }
-      } //end of not just checking presence
-    }
-  }
-
-  function options_form(&$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, $form_state);
-
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_relationship_id.inc
-    if (!$this->options['label']) {
-      $label = 'Stock Name';
-    }
-    else {
-      $label = $this->options['label'];
-=======
-    if ($this->options['label']) {
-      $label = $this->options['label'];
-    }
-    else {
-      $label = 'Stock Name';
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc
-    }
-    $form['value'] = array(
-      '#type' => 'textfield',
-      '#title' => t('%label', array('%label' => $label)),
-      '#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)) {
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stock_relationship_id.inc
-      $types[$r->type_id] = $r->name;
-    }
-=======
-    $types[$r->type_id] = $r->name; }
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stock_relationship_id.inc
-
-    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_views/views/handlers/views_handler_filter_stockprop_id.inc

@@ -1,295 +0,0 @@
-<?php
-
-/**
- * @file
- * Allows stocks to be filtered by proeprty values
- *
- * @ingroup tripal_stock
- * @ingroup views_filter_handlers
- */
-class views_handler_filter_stockprop_id extends views_handler_filter {
-
-  function init(&$view, $options) {
-    parent::init($view, $options);
-    $this->type = $this->options['type'];
-  }
-
-  function options_form(&$form, &$form_state) {
-    if ($this->can_expose()) {
-      $this->show_expose_button($form, $form_state);
-    }
-
-    $form['op_val_start'] = array('#value' => '<div class="clear-block">');
-
-    $this->types_form($form, $form_state);
-
-    $this->show_operator_form($form, $form_state);
-    $form['operator']['#prefix'] = '<div class="views-right-70">';
-    $this->show_value_form($form, $form_state);
-    $form['op_val_end'] = array('#value' => '</div>');
-
-    if ($this->can_expose()) {
-      $this->show_expose_form($form, $form_state);
-    }
-
-  }
-
-  function options_validate(&$form, &$form_state) {
-    parent::options_validate($form, $form_state);
-
-    if (preg_match('/NULL/', $form_state['values']['options']['operator'])) {
-      $value = $form_state['values']['options']['value'];
-      if (!empty($value)) {
-        drupal_set_message(t('The Value (%value) will be IGNORED when the Operator is set to "Is Present" or Is Absent".', array('%value' => $value)), 'warning');
-      }
-    }
-    else {
-      $value = $form_state['values']['options']['value'];
-      if (empty($value)) {
-        form_error($form['value'], t('Value required. The value will be used in conjunction with the operator. For example, if the '
-           .'operator="Is equal to" and the value="2010" then only properties with a value of 2010 and the type specified will be displayed.'));
-      }
-    }
-
-    if (empty($form_state['values']['options']['type'])) {
-      drupal_set_message(t('No Property Type was choosen. As such, any property type whose value %op %value will be displayed.',
-        array('%op' => $form_state['values']['options']['operator'], '%value' => $form_state['values']['options']['value'])), 'warning');
-    }
-  }
-
-  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 . ")";
-      $this->query->add_where($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'], $new_where_sql);
-    }
-
-  }
-
-  function types_form(&$form, &$form_state) {
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM {cvterm} cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM {stockprop})");
-    tripal_db_set_active($previous_db);
-
-    $types = array();
-    while ($r = db_fetch_object($result)) {
-      $types[$r->type_id] = $r->name;
-    }
-
-    $form['type'] = array(
-      '#type' => count($options) < 10 ? 'radios' : 'select',
-      '#title' => t('Property Types'),
-      '#options' => $types,
-      '#default_value' => $this->type,
-      '#prefix' => '<div class="views-left-30">',
-      '#suffix' => '</div>',
-    );
-
-  }
-
-  function value_form(&$form, &$form_state) {
-    parent::value_form($form, $form_state);
-
-    if ($this->options['expose']['display_type'] == 'select') {
-
-      // Get options
-      $previous_db = tripal_db_set_active('chado');
-      $resource = db_query("SELECT value FROM stockprop WHERE type_id=" . $this->type . " ORDER BY value");
-      tripal_db_set_active($previous_db);
-      while ($r = db_fetch_object($resource)) {
-        $options[$r->value] = $r->value;
-      }
-      $form['value'] = array(
-        '#type' => 'select',
-        '#title' => t('%label', array('%label' => $this->options['label'])),
-        '#options' => $options,
-        '#default_value' => $this->value,
-      );
-    }
-    else {
-      $form['value'] = array(
-        '#type' => 'textfield',
-        '#title' => t('Value'),
-        '#default_value' => $this->value,
-      );
-    }
-  }
-
-  function operator_options() {
-    return array(
-      '=' => t('Is equal to'),
-      '!=' => t('Is not equal to'),
-      '~' => t('Contains'),
-      '!~' => t('Does not contain'),
-      'IS NOT NULL' => t('Is Present (Not Empty)'),
-      'IS NULL' => t('Is Absent (Empty)'),
-    );
-  }
-
- /**
-  * Render our chunk of the exposed filter form when selecting
-  */
-  function exposed_form(&$form, &$form_state) {
-    if (empty($this->options['exposed'])) {
-      return;
-    }
-
-    if (!empty($this->options['expose']['use_type']) && !empty($this->options['expose']['type'])) {
-      $type = $this->options['expose']['type'];
-      $form[$type] = array(
-        '#type' => 'select',
-        '#title' => t('Property Types'),
-        '#options' => $this->type_options(),
-        '#default_value' => $this->type,
-      );
-
-      if (isset($form[$type]['#title'])) {
-        unset($form[$type]['#title']);
-      }
-    }
-
-    if (!empty($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.'),
-    );
-
-    $form['expose']['display_type'] = array(
-      '#type' => 'radios',
-      '#default_value' => $this->options['expose']['display_type'],
-      '#title' => t('Display Type'),
-      '#description' => t('This will change the form item type of the exposed value form. ie: it can be used to let the user select the property value from a select box rather than a textfield.'),
-      '#options' => array(
-        'textfield' => 'Text Field',
-        'select' => 'Drop Down',
-      ),
-    );
-  }
-
-  function expose_form_right(&$form, &$form_state) {
-    if (!empty($form['type']['#type'])) {
-      $form['expose']['use_type'] = array(
-        '#type' => 'checkbox',
-        '#title' => t('Unlock Property Type'),
-        '#description' => t('When checked, the property type will be exposed to the user'),
-        '#default_value' => !empty($this->options['expose']['use_type']),
-      );
-      $form['expose']['type'] = array(
-        '#type' => 'textfield',
-        '#default_value' => $this->options['expose']['type'],
-        '#title' => t('Property Type identifier'),
-        '#size' => 40,
-        '#description' => t('This will appear in the URL after the ? to identify this property type.'),
-        '#process' => array('views_process_dependency'),
-        '#dependency' => array(
-          'edit-options-expose-use-type' => array(1)
-        ),
-      );
-    }
-    else {
-      $form['expose']['type'] = array(
-        '#type' => 'value',
-        '#value' => '',
-      );
-    }
-
-    $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_views/views/handlers/views_handler_filter_stockprop_id.inc.orig

@@ -1,340 +0,0 @@
-<?php
-
-/**
- * @file
- * Allows stocks to be filtered by proeprty values
- *
- * @ingroup tripal_stock
- * @ingroup views_filter_handlers
- */
-class views_handler_filter_stockprop_id extends views_handler_filter {
-
-  function init(&$view, $options) {
-    parent::init($view, $options);
-    $this->type = $this->options['type'];
-  }
-
-  function options_form(&$form, &$form_state) {
-    if ($this->can_expose()) {
-      $this->show_expose_button($form, $form_state);
-    }
-
-    $form['op_val_start'] = array('#value' => '<div class="clear-block">');
-
-    $this->types_form($form, $form_state);
-
-    $this->show_operator_form($form, $form_state);
-    $form['operator']['#prefix'] = '<div class="views-right-70">';
-    $this->show_value_form($form, $form_state);
-    $form['op_val_end'] = array('#value' => '</div>');
-
-    if ($this->can_expose()) {
-      $this->show_expose_form($form, $form_state);
-    }
-
-  }
-
-  function options_validate(&$form, &$form_state) {
-    parent::options_validate($form, $form_state);
-
-    if (preg_match('/NULL/', $form_state['values']['options']['operator'])) {
-      $value = $form_state['values']['options']['value'];
-      if (!empty($value)) {
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-        drupal_set_message(t('The Value (%value) will be IGNORED when the Operator is set to "Is Present" or Is Absent".', array('%value' => $value)), 'warning');
-=======
-        drupal_set_message(t('The Value %value will be IGNORED when the Operator is set to "Is Present" or Is Absent". ', array('%value' => $value), 'warning'));
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-      }
-    }
-    else {
-      $value = $form_state['values']['options']['value'];
-      if (empty($value)) {
-        form_error($form['value'], t('Value required. The value will be used in conjunction with the operator. For example, if the '
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-           .'operator="Is equal to" and the value="2010" then only properties with a value of 2010 and the type specified will be displayed.'));
-=======
-           . 'operator="Is equal to" and the value="2010" then only properties with a value of 2010 and the type specified will be displayed.'));
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-      }
-    }
-
-    if (empty($form_state['values']['options']['type'])) {
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-      drupal_set_message(t('No Property Type was choosen. As such, any property type whose value %op %value will be displayed.',
-        array('%op' => $form_state['values']['options']['operator'], '%value' => $form_state['values']['options']['value'])), 'warning');
-=======
-      drupal_set_message('No Property Type was choosen. As such, any property type whose value '
-                 . $form_state['values']['options']['operator'] . ' ' . $form_state['values']['options']['value'] . ' will be displayed', 'warning');
-    }
-  }
-
-  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);
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-    }
-    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 . ")";
-      $this->query->add_where($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);
-    }
-
-  }
-
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-  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 . ")";
-      $this->query->add_where($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'], $new_where_sql);
-    }
-
-  }
-
-=======
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-  function types_form(&$form, &$form_state) {
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_query("SELECT cvt.cvterm_id as type_id, cvt.name FROM {cvterm} cvt WHERE cvt.cvterm_id IN (SELECT type_id FROM {stockprop})");
-    tripal_db_set_active($previous_db);
-
-    $types = array();
-    while ($r = db_fetch_object($result)) {
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-      $types[$r->type_id] = $r->name;
-    }
-=======
-    $types[$r->type_id] = $r->name; }
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-
-    $form['type'] = array(
-      '#type' => count($options) < 10 ? 'radios' : 'select',
-      '#title' => t('Property Types'),
-      '#options' => $types,
-      '#default_value' => $this->type,
-      '#prefix' => '<div class="views-left-30">',
-      '#suffix' => '</div>',
-    );
-
-  }
-
-  function value_form(&$form, &$form_state) {
-    parent::value_form($form, $form_state);
-
-    if ($this->options['expose']['display_type'] == 'select') {
-
-      // Get options
-      $previous_db = tripal_db_set_active('chado');
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-      $resource = db_query("SELECT value FROM stockprop WHERE type_id=" . $this->type . " ORDER BY value");
-      tripal_db_set_active($previous_db);
-=======
-      $resource = db_query("SELECT value FROM {stockprop} WHERE type_id=" . $this->type . " ORDER BY value");
-     tripal_db_set_active($previous_db);
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-      while ($r = db_fetch_object($resource)) {
-        $options[$r->value] = $r->value;
-      }
-      $form['value'] = array(
-        '#type' => 'select',
-<<<<<<< HEAD:tripal_views/views/handlers/views_handler_filter_stockprop_id.inc
-        '#title' => t('%label', array('%label' => $this->options['label'])),
-=======
-        '#title' => t('%label', array('%title' => $this->options['label'])),
->>>>>>> 6.x-0.4-dev:tripal_stock/views/handlers/views_handler_filter_stockprop_id.inc
-        '#options' => $options,
-        '#default_value' => $this->value,
-      );
-    }
-    else {
-      $form['value'] = array(
-        '#type' => 'textfield',
-        '#title' => t('Value'),
-        '#default_value' => $this->value,
-      );
-    }
-  }
-
-  function operator_options() {
-    return array(
-      '=' => t('Is equal to'),
-      '!=' => t('Is not equal to'),
-      '~' => t('Contains'),
-      '!~' => t('Does not contain'),
-      'IS NOT NULL' => t('Is Present (Not Empty)'),
-      'IS NULL' => t('Is Absent (Empty)'),
-    );
-  }
-
- /**
-  * Render our chunk of the exposed filter form when selecting
-  */
-  function exposed_form(&$form, &$form_state) {
-    if (empty($this->options['exposed'])) {
-      return;
-    }
-
-    if (!empty($this->options['expose']['use_type']) && !empty($this->options['expose']['type'])) {
-      $type = $this->options['expose']['type'];
-      $form[$type] = array(
-        '#type' => 'select',
-        '#title' => t('Property Types'),
-        '#options' => $this->type_options(),
-        '#default_value' => $this->type,
-      );
-
-      if (isset($form[$type]['#title'])) {
-        unset($form[$type]['#title']);
-      }
-    }
-
-    if (!empty($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.'),
-    );
-
-    $form['expose']['display_type'] = array(
-      '#type' => 'radios',
-      '#default_value' => $this->options['expose']['display_type'],
-      '#title' => t('Display Type'),
-      '#description' => t('This will change the form item type of the exposed value form. ie: it can be used to let the user select the property value from a select box rather than a textfield.'),
-      '#options' => array(
-        'textfield' => 'Text Field',
-        'select' => 'Drop Down',
-      ),
-    );
-  }
-
-  function expose_form_right(&$form, &$form_state) {
-    if (!empty($form['type']['#type'])) {
-      $form['expose']['use_type'] = array(
-        '#type' => 'checkbox',
-        '#title' => t('Unlock Property Type'),
-        '#description' => t('When checked, the property type will be exposed to the user'),
-        '#default_value' => !empty($this->options['expose']['use_type']),
-      );
-      $form['expose']['type'] = array(
-        '#type' => 'textfield',
-        '#default_value' => $this->options['expose']['type'],
-        '#title' => t('Property Type identifier'),
-        '#size' => 40,
-        '#description' => t('This will appear in the URL after the ? to identify this property type.'),
-        '#process' => array('views_process_dependency'),
-        '#dependency' => array(
-          'edit-options-expose-use-type' => array(1)
-        ),
-      );
-    }
-    else {
-      $form['expose']['type'] = array(
-        '#type' => 'value',
-        '#value' => '',
-      );
-    }
-
-    $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'],
-    );
-  }
-
-
-}