zmap_expression.module

<?php
/**
 * Notice: Install R-base and ape package before use this module.
 */
require_once 'includes/zmap_expression_input_geneids.form.inc';
require_once 'api/zmap_expression.api.inc';

/**
 * Implements hook_menu.
 */
function zmap_expression_menu()
{
    $items['zmap_expression/pop'] = array(
        'title' => 'ZEAMAP Gene Expression',
        'page callback' => 'zmap_expression_search',
        'page arguments' => array(1),
        'access arguments' => array('access content'),
        'type' => MENU_NORMAL_ITEM,
    );

    $items['zmap_expression/ref'] = array(
        'title' => 'ZEAMAP Gene Expression',
        'page callback' => 'zmap_expression_search',
        'page arguments' => array(1),
        'access arguments' => array('access content'),
        'type' => MENU_NORMAL_ITEM,
    );

    $items['zmap_expression/search/result/etype/%/geneids/%/samples/%'] = array(
        'title' => 'ZEAMAP Gene Expression',
        'page callback' => 'zmap_expression_search_result',
        'page arguments' => array(4, 6, 8),
        'access arguments' => array('access content'),
        'type' => MENU_CALLBACK,
    );

    $items['zmap_expression/search/result/downloadtsv/%'] = array(
        'title' => 'ZEAMAP Gene Expression',
        'page callback' => 'zmap_expression_search_result_downloadtsv',
        'page arguments' => array(4),
        'access arguments' => array('access content'),
        'type' => MENU_CALLBACK,
    );

    //api retrive tissues
    $items['api/expression/%/samples'] = array(
        'page callback' => 'zmap_expression_api_retrive_samples',
        'page arguments' => array(2),
        'access arguments' => array('access content'),
        'type' => MENU_CALLBACK,
    );
    //api retrive format geneids
    $items['api/gene/geneids/%'] = array(
        'page callback' => 'zmap_expression_api_retrive_geneids',
        'page arguments' => array(3),
        'access arguments' => array('access content'),
        'type' => MENU_CALLBACK,
    );
    //api retrive expression media data for selected samples and geneids
    $items['api/exp_gene/type/%/samples/%/geneids/%'] = array(
        'page callback' => 'zmap_expression_api_retrive_media_data',
        'page arguments' => array(3, 5, 7),
        'access arguments' => array('access content'),
        'type' => MENU_CALLBACK,
    );

    return $items;
}

function zmap_expression_search($arg)
{
    $arg = trim($arg, '#');
    $path = drupal_get_path('module', 'zmap_expression');
    drupal_add_js($path.'/theme/js/jquery-3.2.1.min.js');
    drupal_add_js($path.'/theme/js/zmap_expression_form.js');
    drupal_add_css($path.'/theme/css/zmap_expression_search_form.css', array('group' => CSS_DEFAULT, 'every_page' => false));

    return theme('zmap_expression_search', array('type' => $arg));
}

function zmap_expression_search_result($etype, $geneids, $samples)
{
    $path = drupal_get_path('module', 'zmap_expression');
	//add css
    drupal_add_css($path.'/theme/css/bootstrap.min.css', array('group' => CSS_DEFAULT, 'every_page' => false));
    drupal_add_css($path.'/theme/css/all.css', array('group' => CSS_DEFAULT, 'every_page' => false));
    drupal_add_css($path.'/theme/css/select2.min.css', array('group' => CSS_DEFAULT, 'every_page' => false));
    drupal_add_css($path.'/theme/css/dendrogram.css', array('group' => CSS_DEFAULT, 'every_page' => false));
    drupal_add_css($path.'/theme/css/expressMap.css', array('group' => CSS_DEFAULT, 'every_page' => false));
	
    //add js
    drupal_add_js($path.'/theme/js/jquery-3.2.1.min.js');
    drupal_add_js($path.'/theme/js/select2.full.min.js');
    drupal_add_js($path.'/theme/js/popper.min.js');
    drupal_add_js($path.'/theme/js/bootstrap.min.js');
    drupal_add_js($path.'/theme/js/FileSaver.min.js');
    drupal_add_js($path.'/theme/js/expression-map.bundle.min.js');

    return theme('zmap_expression_search_result', array('etype' => $etype, 'geneids' => $geneids, 'samples' => $samples));
}

/**
 * Implements hook_theme.
 */
function zmap_expression_theme()
{
    $path = drupal_get_path('module', 'zmap_expression');
    $theme = array(
        'zmap_expression_search' => array(
            'variables' => array('type' => null),
            'template' => 'zmap_expression_search',
            'path' => "$path/theme",
        ),
        'zmap_expression_search_result' => array(
            'template' => 'zmap_expression_search_result',
            'path' => "$path/theme",
        ),
    );

    return $theme;
}

/**
 * download search result tsv file.
 */
function zmap_expression_search_result_downloadtsv($filename)
{
    $files_dir = variable_get('file_public_path', conf_path().'/files');
    $path = $files_dir.'/zmap_expression_search_result/'.$filename;
    $file_size = filesize($path);
    $buffer = 1024;
    $count = 0;
    if (file_exists($path)) {
        header('Content-type:application/octet-stream');
        header('Accept-Ranges:bytes');
        header("Accept-Length:$file_size");
        header('Content-Disposition:attachment;filename='.$filename);
        $fp = fopen($path, 'r');
        while (!feof($fp) && $count < $file_size) {
            $contents = fread($fp, $buffer);
            $count += $buffer;
            echo $contents;
        }
        fclose($fp);
    } else {
        drupal_not_fount();
    }
}