divseek_search.module

<?php

/**
 * @file
 * General functions relating to this module.
 * This file will not include the searches themselves.
 */
require_once 'includes/GermplasmAccessionSearch.inc';
require_once 'includes/TraitSearch.inc';
require_once 'includes/GeneticMapSearch.inc';
require_once 'includes/TraitQtlMarkerSearch.inc';
require_once 'includes/GeneticMarkerSearch.inc';
require_once 'includes/form_elements.inc';
require_once 'includes/mviews.inc';

/**
 * Implement hook_chado_custom_search().
 *
 * This hook simply lists the machine name of the searches so that we can find
 * the info hook. We've done this for performance reasons.
 */
function divseek_search_chado_custom_search() {
  $searches = [];

  $searches['GermplasmAccessionSearch'] = 'Germplasm Accessions';
  $searches['TraitSearch'] = 'Phenotypic Traits';
  $searches['GeneticMapSearch'] = 'Genetic Maps';
  $searches['TraitQtlMarkerSearch'] = 'Trait QTL Marker Discovery Tool';
  $searches['GeneticMarkerSearch'] = 'Genetic Markers';

  return $searches;
}

/**
 * Implements hook_menu().
 */
function divseek_search_menu() {
  $items = [];

  $items['data/divseeksearch/trait/heatmap/%/%'] =  array(
    'title' => t('Heatmap Trait data'),
    'page callback' => 'divseek_search_get_heatmap_data',
    'page arguments' => [4, 5],
    'access arguments' => array('access content'),
    'file' => 'includes/heatmap_callbacks.inc',
  );

  return $items;
}

/**
 * Implements hook_theme().
 */
function divseek_search_theme() {
  return array(
    'divseek_search_inline_form_element' => array(
      'render element' => 'element',
    ),
  );
}

function divseek_search_flush_caches() {
  divseek_search_mview_phenotype_means();
  divseek_search_cache_options();
}

/**
 * Save options used in search form using variable_get/set().
 */
function divseek_search_cache_options() {
  $sql= "SELECT value, value
    FROM chado.featureprop
    WHERE type_id IN (
        SELECT cvterm_id FROM chado.cvterm WHERE name='marker_type'
    )
    AND feature_id IN (
        SELECT feature_id FROM chado.feature WHERE type_id IN (
            SELECT cvterm_id FROM chado.cvterm WHERE name='genetic_marker'
        )
    )
    GROUP BY value";
  $options = chado_query($sql)->fetchAllKeyed(0,0);
  variable_set('divseek_search_marker_types', serialize($options));
}

/**
 * Alter the Genotype Matrix.
 */
function divseek_search_form_nd_genotypes_matrix_filter_form_alter(&$form, &$form_state, $form_id) {
  $form['#attached']['css'][] = drupal_get_path('module', 'divseek_search') . '/css/genotype-matrix.css';
}