nd_genotypes.module

<?php
/**
 * @file
 * Contains general functionality for this module.
 */

require_once('api/nd_genotypes.api.inc');

require_once('includes/nd_genotypes.mview.inc');
require_once('includes/nd_genotypes.mview.sync.inc');
require_once('includes/nd_genotypes.form_elements.inc');

require_once('includes/nd_genotypes.fields.inc');

require_once('includes/nd_genotypes.genotype_matrix.inc');
require_once('includes/nd_genotypes.genotype_matrix.download.inc');

/**
 * Implements hook_menu().
 */
function nd_genotypes_menu() {

  // Administration.
  $items['admin/tripal/extension/nd_genotypes'] = array(
    'title' => 'Natural Diversity Genotypes',
    'description' => 'Provides an interface for genotypes and the experiments that generate them.',
    'access arguments' => array('administer tripal'),
    'page callback' => 'nd_genotypes_admin_landing_page',
    'file' => 'includes/nd_genotypes.admin.inc'
  );

  $items['admin/tripal/extension/nd_genotypes/settings'] = array(
    'title' => 'Settings',
    'type' => MENU_LOCAL_TASK,
    'page callback' => 'drupal_get_form',
    'page arguments' => array('nd_genotypes_admin_settings'),
    'access arguments' => array('administer tripal'),
    'weight' => 0,
    'file' => 'includes/nd_genotypes.admin.inc'
  );

  $items['admin/tripal/extension/nd_genotypes/sync'] = array(
    'title' => 'Sync',
    'type' => MENU_LOCAL_TASK,
    'page callback' => 'drupal_get_form',
    'page arguments' => array('nd_genotypes_admin_sync_mviews'),
    'access arguments' => array('administer tripal'),
    'weight' => 2,
    'file' => 'includes/nd_genotypes.admin.inc'
  );

  $items['admin/tripal/extension/nd_genotypes/help'] = array(
    'title' => 'Help',
    'type' => MENU_LOCAL_TASK,
    'page callback' => 'theme',
    'page arguments' => array('nd_genotypes__help'),
    'access arguments' => array('administer tripal'),
    'weight' => 4
  );

  // For auto-complete of germplasm that had been genotyped.
  $items['tripal_ajax/nd_genotypes/genotyped_germplasm/name_to_id/%/only'] = array(
    'title' => 'Germplasm Genotyped AJAX',
    'type' => MENU_CALLBACK,
    'page callback' => 'nd_genotypes_lookup_germplasm_name_callback',
    'page arguments' => array(4), //arg is partition
    'access arguments' => array('access content'),
    'weight' => 4
  );

  // For autocomplete of sequence backbone names.
  $items['tripal_ajax/nd_genotypes/genotyped_backbones/name_to_id/%/only'] = array(
    'title' => 'Backbones Genotyped AJAX',
    'type' => MENU_CALLBACK,
    'page callback' => 'nd_genotypes_lookup_backbone_name_callback',
    'page arguments' => array(4), //arg is partition
    'access arguments' => array('access content'),
    'weight' => 4
  );

  // For autocomplete of project names.
  $items['tripal_ajax/nd_genotypes/project/name'] = array(
    'title' => 'Projects AJAX',
    'type' => MENU_CALLBACK,
    'page callback' => 'nd_genotypes_lookup_project_name_callback',
    'access arguments' => array('access content'),
    'weight' => 4
  );

  // Add Marker x Germplasm Matrix links (1/organism synced)
  $sql = "
    SELECT *
      FROM {organism} O
    ORDER BY O.genus, O.species
  ";
  $orgs = chado_query($sql);
  foreach ($orgs as $organism) {

    // @PARTITION: We use the partition to determine if the mview tables are available
    // for this organism before making the page available.
    $partition = $organism->genus;
    if (ndg_mview_tables_exist($partition)) {

      $items['chado/genotype/' . $organism->genus] = array(
        'title' => $organism->genus . ' Genotypes',
        'description' => 'Marker by Germplasm Genotypes Search for ' . $organism->genus . ' species.',
        'page callback' => 'nd_genotype_matrix_page',
        'page arguments' => array($organism->genus),
        //'page callback' => 'drupal_get_form',
        //'page arguments' => array('nd_genotypes_matrix_filter_form', $organism->genus),
        'access arguments' => array('access nd_genotypes'),
        'type' => MENU_NORMAL_ITEM,
        'file' => 'includes/nd_genotypes.genotype_matrix.inc',
      );

     $items['chado/genotype/' . $organism->genus . '/csv'] = array(
       'title' => 'Download Genotypes: CSV',
       'page callback' => 'trpdownload_download_page',
       'page arguments' => array('genotype_matrix_csv', 4),
       'access arguments' => array('download nd_genotype_matrix'),
       'type' => MENU_CALLBACK,
      );

      $items['chado/genotype/' . $organism->genus . '/hapmap'] = array(
       'title' => 'Download Genotypes: HAPMAP',
       'page callback' => 'trpdownload_download_page',
       'page arguments' => array('genotype_matrix_hapmap', 4),
       'access arguments' => array('download nd_genotype_matrix'),
       'type' => MENU_CALLBACK,
      );

      // JSON Callback: Number of results for genotype matrix.
     $items['chado/genotype/' . $organism->genus . '/num_results.json'] = array(
       'title' => 'Number of Results',
       'page callback' => 'nd_genotypes_count_genotype_matrix_results_callback',
       'page arguments' => array(2,4),
       'access arguments' => array('access nd_genotypes'),
       'type' => MENU_CALLBACK,
      );

      // JSON Callback: Number of results for genotype matrix.
     $items['chado/genotype/' . $organism->genus . '/num_variants.json'] = array(
       'title' => 'Number of Results',
       'page callback' => 'nd_genotypes_count_genotype_matrix_variants_callback',
       'page arguments' => array(2,4),
       'access arguments' => array('access nd_genotypes'),
       'type' => MENU_CALLBACK,
      );
    }
  }


  return $items;
}

/**
 * Register any theme functions/templates for this module.
 * Implements hook_theme().
 */
function nd_genotypes_theme($existing, $type, $theme, $path) {
  $items = array();

  // Help Page
  // @todo: Update this page.
  $items['nd_genotypes__help'] = array(
    'template' => 'nd_genotypes--help',
    'path' => "$path/theme/templates",
  );

  // This is used for the "Germplasm" filter on the genotype matrix form.
  // It's a custom form element that lets you select multiple germplasm to be filtered on.
  $items['multiple_organism_stock'] = array(
    'render element' => 'element',
  );

  $items['pairwise_compare_germplasm'] = array(
    'render element' => 'element'
  );

  // This template executes the query as well as building the genotype matrix table.
  // The filter form is in nd_genotypes_matrix_filter_form().
  $items['nd_genotype_matrix'] = array(
    'template' => 'nd_genotypes.genotype_matrix',
    'path' => $path . '/theme/templates/',
  );

  return $items;
}

/**
 * Implements hook_permission().
 */
function nd_genotypes_permission() {
  return array(
    'access nd_genotypes' => array(
      'title' => t('Access ND Genotypes.'),
      'description' => t('Provides access to the genotype matrix page and Genotype/Sequence panes on feature pages.'),
    ),
    'download nd_genotype_matrix' => array(
      'title' => t('Download Genotypes.'),
      'description' => t('Allows bulk download of genotypes through the genotype matrix page.'),
    ),
  );
}

/**
 * Simple function to render the genotype matrix based on the template file.
 */
function nd_genotype_matrix_page($genus) {

  // @PARTITION: This is where the partition is set for the genotype matrix. From here
  // if is carried throughout the rest of the functions.
  global $base_url;
  $vars = array('genus' => $genus, 'partition' => strtolower($genus),
    'baseUrl' => $base_url . '/chado/genotype/' . $genus);

  // Add the CSS.
  drupal_add_css(drupal_get_path('module', 'nd_genotypes') . '/theme/css/nd_genotype_matrix.css');

  // Add the JS to add result counts via AJAX.
  drupal_add_js('misc/ajax.js');
  drupal_add_js(drupal_get_path('module', 'nd_genotypes') . '/theme/js/genotypeMatrixGetResultCounts.js');
  drupal_add_js(array('NDgenotypes' => $vars), 'setting');

  // Save the query paramters.
  $vars['q'] = drupal_get_query_parameters();

  // Process the query paramters to determine the defaults for the filter form
  // as well as to isolate the values that are needed to retrieve the data.
  nd_genotypes_process_query_parameters($vars);

  // Actually query whatever storage method you are currently using and retrieve the
  // data needed for the current page of the matrix.
  // Currently there is only one backend supported (postgresql: chado) so we will just
  // use it but things have been set-up this way to facilitate use of other backends
  // in the future as needed or desired.
  // ASSUMPTION: the following function should return a Variant X Germplasm Grid stored
  // in a 'data' associative array and a list of variant details in a 'variants'
  // associative array.
  if ($_SERVER['REQUEST_METHOD'] =='GET') {
    nd_genotypes_retrive_matrix_postgresql($vars);
  }

  return theme('nd_genotype_matrix', $vars);
}

/**
 * Auto-complete: Look-up names of germplasm genotyped.
 */
function nd_genotypes_lookup_germplasm_name_callback($partition, $string = "") {
  $matches = array();

  if (!empty($partition) AND trim($string) AND ndg_mview_tables_exist($partition)) {
    $result = ndg_mview_query($partition, '
      SELECT germplasm_name
      FROM {mview_ndg_germplasm_genotyped} m
      WHERE partition = :partition AND germplasm_name ~* :query
      LIMIT 10
    ', array(':query' => $string, ':partition' => $partition))->fetchCol();
    foreach ($result as $name) {
      $matches[$name] = $name;
    }
  }

  drupal_json_output($matches);
}

/**
 * Auto-complete: Look-up names of backbones genotyped.
 */
function nd_genotypes_lookup_backbone_name_callback($partition, $string = "") {
  $matches = array();
  if (!empty($partition) AND trim($string) AND ndg_mview_tables_exist($partition)) {
    $result = ndg_mview_query($partition, '
      SELECT srcfeature_name as name
      FROM {mview_ndg_variants} m
      WHERE srcfeature_name ~* :query
      GROUP BY srcfeature_name
      LIMIT 10
    ', array(':query' => $string))->fetchCol();
    foreach ($result as $name) {
      $matches[$name] = $name;
    }
  }

  drupal_json_output($matches);
}

/**
 * Auto-complete: Look-up names of  projects.
 */
function nd_genotypes_lookup_project_name_callback($string = '') {
  $matches = array();
  if (trim($string)) {
    $result = chado_query('
      SELECT name
      FROM {project} p
      WHERE name ~* :query
      LIMIT 10
    ', array(':query' => $string))->fetchCol();
    foreach ($result as $name) {
      $matches[$name] = $name;
    }
  }

  drupal_json_output($matches);
}

/**
 * JSON Callback: Returns the number of results for a given genotype matrix.
 *
 * The genotype matrix is specified in the query parameters ($_GET). This we processs it
 * just as we do when building the matrix but instead of limiting the query to the given
 * page, we count the entire resultset.
 *
 * This callback is used in the genotype matrix to asynchronously fill in the number of results.
 * @see theme/js/genotypeMatrixGetResultCount.js
 */
function nd_genotypes_count_genotype_matrix_results_callback($partition = '', $type = 'ajax') {

  // @PARTITION: This is where the partition is set for the genotype matrix. From here
  // if is carried throughout the rest of the functions.
  $vars = array('genus' => $partition, 'partition' => $partition);
  if (!ndg_mview_tables_exist($partition)) {
    return FALSE;
  }

  // Save the query paramters.
  $vars['q'] = drupal_get_query_parameters();

  // Process the query paramters to determine the defaults for the filter form
  // as well as to isolate the values that are needed to retrieve the data.
  nd_genotypes_process_query_parameters($vars);

  // Compile all the parameters we will use when grabbing the calls so that we can restrict
  // the variant list to those that will have data once we do retrieve the calls.
  $query_args = $vars['query_args'];
  $call = $variant = $call_args = $variant_args = $variant_joins = array();

  // Sequence Ranges:
  // First get the arguements. There must always be a backbone and fmin even if the user
  // did not provide one.
  if (isset($query_args['start_backbone'])) {
    if (isset($query_args['start_pos'])) {
      $variant_args[':sbackbone'] = $query_args['start_backbone'];
      $variant_args[':sfmin'] = (int) $query_args['start_pos'];
    }
    else {
      $variant_args[':sbackbone'] = $query_args['start_backbone'];
      $variant_args[':sfmin'] = 1;
    }
    unset($query_args['start_backbone'], $query_args['start_pos']);
  }
  if (isset($query_args['end_backbone'])) {
    if (isset($query_args['end_pos'])) {
      $variant_args[':ebackbone'] = $query_args['end_backbone'];
      $variant_args[':efmin'] = (int) $query_args['end_pos'];
    }
    else {
      $variant_args[':ebackbone'] = $query_args['end_backbone'];
      // @TODO: Switch to bigints then change this value to match the largest bigint.
      $variant_args[':efmin'] = 2147483645;
    }
    unset($query_args['end_backbone'], $query_args['end_pos']);
  }
  // Now add the query where condition.
  if (isset($variant_args[':sbackbone']) AND isset($variant_args[':ebackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) BETWEEN ROW(:sbackbone, :sfmin) AND ROW(:ebackbone,:efmin)';
  }
  elseif (isset($variant_args[':sbackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) >= ROW(:sbackbone, :sfmin)';
  }
  elseif (isset($variant_args[':ebackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) <= ROW(:ebackbone, :efmin)';
  }

  // Variant Type:
  if (isset($query_args['variant_type'])) {
    $variant[] = 'variant_type=:variant_type';
    $variant_args[':variant_type'] = $query_args['variant_type'];
    unset($query_args['variant_type']);
  }

  // Variant Name:
  $variant_name_filter = FALSE;
  if (isset($query_args['variant_name'])) {
    $variant[] = "variant_name IN (VALUES('" . implode("'), ('", $query_args['variant_name']) . "'))";
    //$variant_args[':variant_names'] = $query_args['variant_name'];
    unset($query_args['variant_name']);
    $variant_name_filter = TRUE;
  }
  elseif (isset($query_args['variant_name_list'])) {
    $list_json = db_query('SELECT list FROM {ndg_matrix_variant_user_lists} WHERE list_id=:id',
      array(':id' => $query_args['variant_name_list']))->fetchField();
    $list = json_decode($list_json);
    $variant[] = "variant_name IN (VALUES('" . implode("'), ('", $list) . "'))";
  }

  // Polymorphic:
  $polymorphic_filter = FALSE;
  if (isset($query_args['polymorphic'])
    AND is_numeric($query_args['polymorphic']['first'])
    AND is_numeric($query_args['polymorphic']['second'])) {
      if (!$variant_name_filter) {
        $variant_joins[] = "LEFT JOIN (
            SELECT a.variant_id, a.allele_call=b.allele_call as monomorphic
            FROM {mview_ndg_calls} a, {mview_ndg_calls} b
            WHERE a.variant_id=b.variant_id AND a.germplasm_id=:poly1 AND b.germplasm_id=:poly2
          ) p ON p.variant_id=v.variant_id ";
        $variant_args[':poly1'] = $query_args['polymorphic']['first'];
        $variant_args[':poly2'] = $query_args['polymorphic']['second'];
        $variant[] = "p.monomorphic IS FALSE";
      }
      $polymorphic_filter = TRUE;
  }

  // Germplasm:
  if (isset($query_args['germplasm_id']) AND !empty($query_args['germplasm_id'])) {
    $call[] = 'germplasm_id IN (:germplasm_ids)';
    $call_args[':germplasm_ids'] = $query_args['germplasm_id'];
    unset($query_args['germplasm_id']);
  }
  else {
    return FALSE;
  }

  // Project:
  if (isset($query_args['project_id']) AND !empty($query_args['project_id'])) {
    if (sizeof($query_args['project_id']) == 1) {
      $call[] = 'project_id = :project_id';
    }
    else {
      $call[] = 'project_id IN (:project_id)';
    }
    $call_args[':project_id'] = $query_args['project_id'];
  }

  // Marker Type:
  if (isset($query_args['marker_type'])) {
    $call[] = 'marker_type = :marker_type';
    $call_args[':marker_type'] = $query_args['marker_type'];
  }

  // Now determine the query for the variants.
  $sql = "SELECT count(v.variant_id) \n"
       . "FROM {mview_ndg_variants} v \n"
       . implode("\n", $variant_joins)
       . "WHERE \n";

  // Add in conditions on the variants table.
  if ($variant) {
    $sql .= implode("\n  AND ",$variant) . "\n  AND ";
  }

  // Add in conditions on the call table.
  $sql .= "EXISTS ( \n"
       . "    SELECT true \n"
       . "    FROM {mview_ndg_calls} call \n"
       . "    WHERE \n"
       . "      " . implode("\n      AND ", $call) .  "\n"
       . "      AND call.variant_id=v.variant_id\n"
       . "  ) \n";

  if ($polymorphic_filter AND $variant_name_filter) {
    $subsql = str_replace('SELECT count(v.variant_id)', 'SELECT v.variant_id', $sql);
    $sql = "SELECT count(v.variant_id) FROM (\n"
      . $subsql . ") v \n"
      . "LEFT JOIN (
            SELECT a.variant_id, a.allele_call=b.allele_call as monomorphic
            FROM {mview_ndg_calls} a, {mview_ndg_calls} b
            WHERE a.variant_id=b.variant_id AND a.germplasm_id=:poly1 AND b.germplasm_id=:poly2
          ) p ON p.variant_id=v.variant_id \n"
      . "WHERE p.monomorphic IS FALSE \n";
      $variant_args[':poly1'] = $query_args['polymorphic']['first'];
      $variant_args[':poly2'] = $query_args['polymorphic']['second'];
  }


  $args = array_merge($call_args, $variant_args);
  $count = ndg_mview_query($vars['partition'], $sql, $args)->fetchField();

  drupal_json_output(array(
    'raw' => $count,
    'formatted' => number_format($count),
  ));
}

/**
 * JSON Callback: Returns the number of variants for a given genotype matrix.
 *
 * The genotype matrix is specified in the query parameters ($_GET). We still process the
 * query arguements the same but this time the query we build needs to group by variant_id.
 *
 * This callback is used in the genotype matrix to asynchronously fill in the number of variants.
 * @see theme/js/genotypeMatrixGetResultCount.js
 */
function nd_genotypes_count_genotype_matrix_variants_callback($partition = '', $type = 'ajax') {

  // @PARTITION: This is where the partition is set for the genotype matrix. From here
  // if is carried throughout the rest of the functions.
  $vars = array('genus' => $partition, 'partition' => $partition);

  // Save the query paramters.
  $vars['q'] = drupal_get_query_parameters();

  // Process the query paramters to determine the defaults for the filter form
  // as well as to isolate the values that are needed to retrieve the data.
  nd_genotypes_process_query_parameters($vars);

  // Compile all the parameters we will use when grabbing the calls so that we can restrict
  // the variant list to those that will have data once we do retrieve the calls.
  $query_args = $vars['query_args'];
  $call = $variant = $call_args = $variant_args = $variant_joins = array();

  // Sequence Ranges:
  // First get the arguements. There must always be a backbone and fmin even if the user
  // did not provide one.
  if (isset($query_args['start_backbone'])) {
    if (isset($query_args['start_pos'])) {
      $variant_args[':sbackbone'] = $query_args['start_backbone'];
      $variant_args[':sfmin'] = (int) $query_args['start_pos'];
    }
    else {
      $variant_args[':sbackbone'] = $query_args['start_backbone'];
      $variant_args[':sfmin'] = 1;
    }
    unset($query_args['start_backbone'], $query_args['start_pos']);
  }
  if (isset($query_args['end_backbone'])) {
    if (isset($query_args['end_pos'])) {
      $variant_args[':ebackbone'] = $query_args['end_backbone'];
      $variant_args[':efmin'] = (int) $query_args['end_pos'];
    }
    else {
      $variant_args[':ebackbone'] = $query_args['end_backbone'];
      // @TODO: Switch to bigints then change this value to match the largest bigint.
      $variant_args[':efmin'] = 2147483645;
    }
    unset($query_args['end_backbone'], $query_args['end_pos']);
  }
  // Now add the query where condition.
  if (isset($variant_args[':sbackbone']) AND isset($variant_args[':ebackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) BETWEEN ROW(:sbackbone, :sfmin) AND ROW(:ebackbone,:efmin)';
  }
  elseif (isset($variant_args[':sbackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) >= ROW(:sbackbone, :sfmin)';
  }
  elseif (isset($variant_args[':ebackbone'])) {
    $variant[] = 'ROW(v.srcfeature_name, v.fmin) <= ROW(:ebackbone, :efmin)';
  }

  // Variant Type:
  if (isset($query_args['variant_type'])) {
    $variant[] = 'variant_type=:variant_type';
    $variant_args[':variant_type'] = $query_args['variant_type'];
    unset($query_args['variant_type']);
  }

  // Variant Name:
  $variant_name_filter = FALSE;
  if (isset($query_args['variant_name'])) {
    $variant[] = "variant_name IN (VALUES('" . implode("'), ('", $query_args['variant_name']) . "'))";
    //$variant_args[':variant_names'] = $query_args['variant_name'];
    unset($query_args['variant_name']);
    $variant_name_filter = TRUE;
  }
  elseif (isset($query_args['variant_name_list'])) {
    $list_json = db_query('SELECT list FROM {ndg_matrix_variant_user_lists} WHERE list_id=:id',
      array(':id' => $query_args['variant_name_list']))->fetchField();
    $list = json_decode($list_json);
    $variant[] = "variant_name IN (VALUES('" . implode("'), ('", $list) . "'))";
  }

  // Polymorphic:
  $polymorphic_filter = FALSE;
  if (isset($query_args['polymorphic'])
    AND is_numeric($query_args['polymorphic']['first'])
    AND is_numeric($query_args['polymorphic']['second'])) {
      if (!$variant_name_filter) {
        $variant_joins[] = "LEFT JOIN (
            SELECT a.variant_id, a.allele_call=b.allele_call as monomorphic
            FROM {mview_ndg_calls} a, {mview_ndg_calls} b
            WHERE a.variant_id=b.variant_id AND a.germplasm_id=:poly1 AND b.germplasm_id=:poly2
          ) p ON p.variant_id=v.variant_id ";
        $variant_args[':poly1'] = $query_args['polymorphic']['first'];
        $variant_args[':poly2'] = $query_args['polymorphic']['second'];
        $variant[] = "p.monomorphic IS FALSE";
      }
      $polymorphic_filter = TRUE;
  }

  // Germplasm:
  if (isset($query_args['germplasm_id']) AND !empty($query_args['germplasm_id'])) {
    $call[] = 'germplasm_id IN (:germplasm_ids)';
    $call_args[':germplasm_ids'] = $query_args['germplasm_id'];
    unset($query_args['germplasm_id']);
  }
  else {
    return FALSE;
  }

  // Project:
  if (isset($query_args['project_id']) AND !empty($query_args['project_id'])) {
    if (sizeof($query_args['project_id']) == 1) {
      $call[] = 'project_id = :project_id';
    }
    else {
      $call[] = 'project_id IN (:project_id)';
    }
    $call_args[':project_id'] = $query_args['project_id'];
  }

  // Marker Type:
  if (isset($query_args['marker_type'])) {
    $call[] = 'marker_type = :marker_type';
    $call_args[':marker_type'] = $query_args['marker_type'];
  }

  // Now determine the query for the variants.
  $sql = "SELECT v.variant_id, v.variant_name \n"
       . "FROM {mview_ndg_variants} v \n"
       . implode("\n", $variant_joins)
       . "WHERE \n";

  // Add in conditions on the variants table.
  if ($variant) {
    $sql .= implode("\n  AND ",$variant) . "\n  AND ";
  }

  // Add in conditions on the call table.
  $sql .= "EXISTS ( \n"
       . "    SELECT true \n"
       . "    FROM {mview_ndg_calls} call \n"
       . "    WHERE \n"
       . "      " . implode("\n      AND ", $call) .  "\n"
       . "      AND call.variant_id=v.variant_id\n"
       . "  ) \n";

  if ($polymorphic_filter AND $variant_name_filter) {
    $sql = "SELECT v.variant_id, v.variant_name FROM (\n"
      . $sql . ") v \n"
      . "LEFT JOIN (
            SELECT a.variant_id, a.allele_call=b.allele_call as monomorphic
            FROM {mview_ndg_calls} a, {mview_ndg_calls} b
            WHERE a.variant_id=b.variant_id AND a.germplasm_id=:poly1 AND b.germplasm_id=:poly2
          ) p ON p.variant_id=v.variant_id \n"
      . "WHERE p.monomorphic IS FALSE \n";
      $variant_args[':poly1'] = $query_args['polymorphic']['first'];
      $variant_args[':poly2'] = $query_args['polymorphic']['second'];
  }


  $count_sql = "SELECT count(distinct variant_name) FROM (" . $sql . " GROUP BY v.variant_id, v.variant_name) t";
  $args = array_merge($call_args, $variant_args);
  $count = ndg_mview_query($vars['partition'], $count_sql, $args)->fetchField();

  drupal_json_output(array(
    'raw' => $count,
    'formatted' => number_format($count),
  ));

}