tripal/tripal_stock/tripal_stock.views.inc

<?php

/**
 *  @file
 *  This file contains the basic functions for views integration of
 *  chado/tripal stock tables. Supplementary functions can be found in
 *  ./views/
 *
 *  Documentation on views integration can be found at
 *  http://views2.logrus.com/doc/html/index.html.
 */

/**
 * @defgroup tripal_stock_views Stock Views Integration
 * @ingroup views
 * @ingroup tripal_stock
 */

/**
 * Implements hook_views_data(): Describe chado/tripal tables & fields to views
 *
 * @return array
 *   A data array which follows the structure outlined in the
 *   views2 documentation for this hook. Essentially, it's an array of table
 *   definitions keyed by chado/tripal table name. Each table definition
 *   includes basic details about the table, fields in that table and
 *   relationships between that table and others (joins)
 *
 * @ingroup tripal_stock_views
 */
function tripal_stock_views_data()  {
  $data = array();

  if (module_exists('tripal_views')) {
    $tablename = 'stock';
    if (!tripal_views_is_integrated($tablename, 9)) {
      $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE);

      // Add in node relationships if chado is in the same db as drupal
      if (tripal_core_chado_schema_exists()) {
        $integrations = tripal_views_add_node_relationship_to_chado_table_integration($table_integration_array);
        foreach ($integrations as $integration) {
          tripal_views_integration_add_entry($integration);
        }
      }
      else {
        tripal_views_integration_add_entry($table_integration_array);
      }
    }

    $tablename = 'stockcollection';
    if (!tripal_views_is_integrated($tablename, 9)) {
      $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE);
      tripal_views_integration_add_entry($table_integration_array);
    }

    $tables = array(
      'stock_cvterm',
      'stock_dbxref',
      'stock_genotype',
      'stock_pub',
      'stock_relationship',
      'stock_relationship_pub',
      'stockcollection_stock',
      'stockcollectionprop',
      'stockprop',
      'stockprop_pub'
    );
    foreach ($tables as $tablename) {
      if (!tripal_views_is_integrated($tablename, 9)) {
        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE);
        tripal_views_integration_add_entry($table_integration_array);
      }
    }
  }

  return $data;
}

/**
 * Implements hook_views_handlers()
 *
 * Purpose: Register all custom handlers with views
 *   where a handler describes either "the type of field",
 *   "how a field should be filtered", "how a field should be sorted"
 *
 * @return array
 *   An array of handler definitions
 *
 * @ingroup tripal_stock_views
 */
function tripal_stock_views_handlers() {
  return array(
  'info' => array(
    'path' => drupal_get_path('module', 'tripal_stock') . '/views/handlers',
  ),
  'handlers' => array(
    'views_handler_field_computed_stock_nid' => array(
      'parent' => 'views_handler_field_numeric',
    ),
  'views_handler_field_stockprop_by_type' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_field_stockprop_all' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_field_stockrel_by_type' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_field_stockrel_all' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_field_stock_dbxref_by_type' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_field_stock_dbxref_all' => array(
    'parent' => 'views_handler_field_prerender_list',
    ),
  'views_handler_filter_stockprop_id' => array(
    'parent' => 'views_handler_filter',
    ),
  'views_handler_filter_stock_dbxref_id' => array(
    'parent' => 'views_handler_filter',
    ),
  'views_handler_filter_stock_relationship_id' => array(
    'parent' => 'views_handler_filter',
    ),
  'views_handler_argument_stockprop_id' => array(
    'parent' => 'views_handler_argument_string',
    ),
  ),
  );
}

/**
 * Implementation of hook_views_data_alter().
 */
function tripal_stock_views_data_alter(&$data) {

  if ( !(is_array($db_url) and array_key_exists('chado', $db_url)) ) {

    // Add featuer relationship to node
    $data['node']['stock_chado_nid'] = array(
      'group' => 'Stock',
      'title' => 'Stock Node',
      'help' => 'Links Chado Stock Fields/Data to the Nodes in the current View.',
      'real field' => 'nid',
      'relationship' => array(
        'handler' => 'views_handler_relationship',
        'title' => t('Node => Chado'),
        'label' => t('Node => Chado'),
        'real field' => 'nid',
        'base' => 'chado_stock',
        'base field' => 'nid'
      ),
    );
  }

}

/**
 * Implements hook_views_pre_render
 *
 * Purpose: Intercepts the view after the query has been executed
 *   All the results are stored in $view->result
 *   Looking up the NID here ensures the query is only executed once
 *   for all stocks in the table.
 *
 * @todo add if !<chado/drupal same db> around NID portion
 *
 * @ingroup tripal_stock_views
 */
function tripal_stock_views_pre_render  (&$view) {
  if (preg_match('/stock/', $view->base_table)) {

    //-----Node IDs---------------------------------------------
    // @see tripal_core.views.inc, tripal_core_add_node_ids_to_view()

    // retrieve the stock_id for each record in the views current page
    $stock_ids = array();
    foreach ($view->result as $row_num => $row) {
      $stock_ids[$row_num] = $row->stock_id;
    }

    if (sizeof($stock_ids)) {

      //-----Properties------------------------------------------
      $field_names = array_keys($view->field);
      //if any property fields are in the current view
      $property_field_names = preg_grep('/properties/', $field_names);
      if (!empty($property_field_names)) {
        $sql = "SELECT stockprop.*, cvterm.name as type_name FROM {stockprop} "
          ."INNER JOIN cvterm cvterm ON stockprop.type_id=cvterm.cvterm_id "
          ."WHERE stockprop.stock_id IN (" . implode(',', $stock_ids) . ")";
        $previous_db = tripal_db_set_active('chado');
        $resource = db_query($sql);
        tripal_db_set_active($previous_db);

        $view->result[$key]->properties = array();
        while ($r = db_fetch_object($resource)) {
          $key = array_search($r->stock_id, $stock_ids);
          $view->result[$key]->properties[] = $r;
        }
      }

      //-----Relationships----------------------------------------
      //if any relationship fields are in the current view
      $relationship_field_names = preg_grep('/relationships/', $field_names);
      if (!empty($relationship_field_names)) {
        $sql = "SELECT stock_relationship.*, cvterm.name as type_name, "
          ."subject_stock.name as subject_name, object_stock.name as object_name "
          ."FROM stock_relationship "
          ."LEFT JOIN stock subject_stock ON stock_relationship.subject_id=subject_stock.stock_id "
          ."LEFT JOIN stock object_stock ON stock_relationship.object_id=object_stock.stock_id "
          ."LEFT JOIN cvterm cvterm ON stock_relationship.type_id = cvterm.cvterm_id "
          ."WHERE stock_relationship.subject_id IN (" . implode(',', $stock_ids) . ") "
          ."OR stock_relationship.object_id IN (" . implode(',', $stock_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, $stock_ids)) {
            $key = array_search($r->subject_id, $stock_ids);
            $r->stock_id = $r->subject_id;
            $view->result[$key]->relationships[] = clone $r;
          }
          if (in_array($r->object_id, $stock_ids)) {
            $key = array_search($r->object_id, $stock_ids);
            $r->stock_id = $r->object_id;
            $view->result[$key]->relationships[] = clone $r;
          }
        }
      }

      //-----DB References--------------------------------------------
      //if any dbxref fields are in the current view
      $dbxref_field_names = preg_grep('/dbxref/', $field_names);
      if (!empty($dbxref_field_names)) {
        $sql = "SELECT stock_dbxref.*, dbxref.db_id, db.name as db_name, db.urlprefix, "
          ."dbxref.accession, dbxref.version, dbxref.description "
          ."FROM stock_dbxref "
          ."LEFT JOIN dbxref dbxref ON stock_dbxref.dbxref_id=dbxref.dbxref_id "
          ."LEFT JOIN db db ON dbxref.db_id=db.db_id "
          ."WHERE stock_dbxref.stock_id IN (" . implode(',', $stock_ids) . ")";
        $previous_db = tripal_db_set_active('chado');
        $resource = db_query($sql);
        tripal_db_set_active($previous_db);

        $view->result[$key]->dbxref = array();
        while ($r = db_fetch_object($resource)) {
          $key = array_search($r->stock_id, $stock_ids);
          $view->result[$key]->dbxref[] = $r;
        }
      }

    } //if there are stocks
  } //if we're dealing with a stock view
}

/**
 *
 * @ingroup tripal_stock_views
 */
function tripal_stock_views_default_views() {
  $views = array();

  if (!module_exists('tripal_views')) {
    return $views;
  }

  // Main default view
  $view = new view;
  $view->name = 'stock_listing';
  $view->description = 'This view lists all stocks by default.';
  $view->tag = 'chado default';
  $view->base_table = 'stock';
  $view->core = 0;
  $view->api_version = '2';
  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
  $handler = $view->new_display('default', 'Defaults', 'default');
  $handler->override_option('fields', array(
    'uniquename' => array(
      'label' => 'Unique Name',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'link_to_node' => 1,
      'exclude' => 0,
      'id' => 'uniquename',
      'table' => 'stock',
      'field' => 'uniquename',
      'relationship' => 'none',
    ),
    'name_2' => array(
      'label' => 'Name',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'link_to_node' => 1,
      'exclude' => 0,
      'id' => 'name_2',
      'table' => 'stock',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'name' => array(
      'label' => 'Type',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'exclude' => 0,
      'id' => 'name',
      'table' => 'cvterm',
      'field' => 'name',
      'relationship' => 'none',
    ),
    'common_name' => array(
      'label' => 'Organism',
      'alter' => array(
        'alter_text' => 0,
        'text' => '',
        'make_link' => 0,
        'path' => '',
        'link_class' => '',
        'alt' => '',
        'prefix' => '',
        'suffix' => '',
        'target' => '',
        'help' => '',
        'trim' => 0,
        'max_length' => '',
        'word_boundary' => 1,
        'ellipsis' => 1,
        'html' => 0,
        'strip_tags' => 0,
      ),
      'empty' => '',
      'hide_empty' => 0,
      'empty_zero' => 0,
      'link_to_node' => 1,
      'exclude' => 0,
      'id' => 'common_name',
      'table' => 'organism',
      'field' => 'common_name',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('sorts', array(
    'common_name' => array(
      'order' => 'ASC',
      'id' => 'common_name',
      'table' => 'organism',
      'field' => 'common_name',
      'relationship' => 'none',
    ),
    'uniquename' => array(
      'order' => 'ASC',
      'id' => 'uniquename',
      'table' => 'stock',
      'field' => 'uniquename',
      'relationship' => 'none',
    ),
  ));
  $handler->override_option('filters', array(
    'common_name' => array(
      'operator' => '=',
      'value' => array(),
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'common_name_op',
        'identifier' => 'organism_common_name',
        'label' => 'Organism',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'common_name',
      'table' => 'organism',
      'field' => 'common_name',
      'relationship' => 'none',
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'search_results' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => FALSE,
      'expose' => array(
        'operator' => FALSE,
        'label' => '',
      ),
      'id' => 'search_results',
      'table' => 'views',
      'field' => 'search_results',
      'relationship' => 'none',
      'apply_button' => 'Show',
      'no_results_text' => 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.',
    ),
    'type_id' => array(
      'operator' => '=',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'type_id_op',
        'identifier' => 'type_id',
        'label' => 'Type',
        'remember' => 0,
      ),
      'case' => 1,
      'id' => 'type_id',
      'table' => 'stock',
      'field' => 'type_id',
      'relationship' => 'none',
      'values_form_type' => 'select',
      'multiple' => 1,
      'optional' => 0,
      'show_all' => 0,
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
    'name' => array(
      'operator' => 'contains',
      'value' => '',
      'group' => '0',
      'exposed' => TRUE,
      'expose' => array(
        'use_operator' => 0,
        'operator' => 'name_op',
        'identifier' => 'name',
        'label' => 'Name Contains',
        'remember' => 0,
      ),
      'case' => 0,
      'id' => 'name',
      'table' => 'stock',
      'field' => 'name',
      'relationship' => 'none',
      'agg' => array(
        'records_with' => 1,
        'aggregates_with' => 1,
      ),
    ),
  ));
  $handler->override_option('access', array(
    'type' => 'perm',
    'perm' => 'access chado_stock content',
  ));
  $handler->override_option('cache', array(
    'type' => 'none',
  ));
  $handler->override_option('title', 'Stocks');
  $handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
  $handler->override_option('header_format', '2');
  $handler->override_option('header_empty', 0);
  $handler->override_option('empty', 'No stocks match the supplied criteria.');
  $handler->override_option('empty_format', '1');
  $handler->override_option('items_per_page', 50);
  $handler->override_option('use_pager', '1');
  $handler->override_option('style_plugin', 'table');
  $handler->override_option('style_options', array(
    'grouping' => '',
    'override' => 1,
    'sticky' => 0,
    'order' => 'asc',
    'columns' => array(
      'uniquename' => 'uniquename',
      'name_2' => 'name_2',
      'name' => 'name',
      'common_name' => 'common_name',
      'all_dbxref' => 'all_dbxref',
      'all_properties' => 'all_properties',
      'all_relationships' => 'all_relationships',
    ),
    'info' => array(
      'uniquename' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'name_2' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'common_name' => array(
        'sortable' => 1,
        'separator' => '',
      ),
      'all_dbxref' => array(
        'separator' => '',
      ),
      'all_properties' => array(
        'separator' => '',
      ),
      'all_relationships' => array(
        'separator' => '',
      ),
    ),
    'default' => '-1',
  ));
  $default_handler = $handler;
  $handler = $view->new_display('page', 'Page', 'page_1');
  $handler->override_option('path', 'chado/stocks');
  $handler->override_option('menu', array(
    'type' => 'normal',
    'title' => 'Stocks',
    'description' => 'A stock is the physical entities, either living or preserved, held by collections and can be globally identified by the combination of organism, uniquename and stock type.',
    'weight' => '10',
    'name' => 'navigation',
  ));
  $handler->override_option('tab_options', array(
    'type' => 'none',
    'title' => '',
    'description' => '',
    'weight' => 0,
    'name' => 'navigation',
  ));
  // Add code specific to a local chado installation
  // NOTE: Edit $handler above to $default_handler for the default display
  if (tripal_core_chado_schema_exists()) {
    // Add nid field
    $fields = $view->get_items('field', 'default');
    $new_fields = array(
      'nid' => array(
        'label' => 'Nid',
        'alter' => array(
          'alter_text' => 0,
          'text' => '',
          'make_link' => 0,
          'path' => '',
          'absolute' => 0,
          'link_class' => '',
          'alt' => '',
          'rel' => '',
          'prefix' => '',
          'suffix' => '',
          'target' => '',
          'help' => '',
          'trim' => 0,
          'max_length' => '',
          'word_boundary' => 1,
          'ellipsis' => 1,
          'html' => 0,
          'strip_tags' => 0,
        ),
        'empty' => '',
        'hide_empty' => 0,
        'empty_zero' => 0,
        'hide_alter_empty' => 1,
        'link_to_node' => 0,
        'exclude' => 1,
        'id' => 'nid',
        'table' => 'node',
        'field' => 'nid',
        'relationship' => 'none',
      )
    );
    $fields = $new_fields + $fields;
    // Change analysis.name to have a link to the node
    $fields['name_2']['alter']['make_link'] = 1;
    $fields['name_2']['alter']['path'] = 'node/[nid]';
    $default_handler->override_option('fields', $fields);
    // Adds stock => Node relationship
    $default_handler->override_option('relationships', array(
      'nid' => array(
        'label' => 'Stock to Node',
        'required' => 0,
        'id' => 'nid',
        'table' => 'chado_stock',
        'field' => 'nid',
        'relationship' => 'none',
      ),
    ));
    // Only show records with published nodes
    $filters = $view->get_items('filter', 'default');
    $filters['status'] = array(
      'operator' => '=',
      'value' => '1',
      'group' => '0',
      'exposed' => FALSE,
      'expose' => array(
        'operator' => FALSE,
        'label' => '',
      ),
      'id' => 'status',
      'table' => 'node',
      'field' => 'status',
      'relationship' => 'none',
    );
    $default_handler->override_option('filters', $filters);
  }
  $views[$view->name] = $view;

  return $views;
}