helium_exporter.module

<?php

/**
 * @file
 * The main functionality for this module.
 */

// Include general API and helper functions.
module_load_include('inc', 'helium_exporter', 'api/helium_exporter.api');

 /**
  * Implements hook_menu().
  */
function helium_exporter_menu() {
  // Download Data.
  $items['helium-exporter'] = array(
    'title' => t(''),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('helium_exporter_form'),
    'access arguments' => array('access helium_exporter'),
    'file' => 'includes/helium_exporter.form.inc',
    'type' => MENU_NORMAL_ITEM,
  );
  
  // Configure Helium Exporter.
  $items['admin/tripal/extension/helium_exporter/configure'] = array(
    'title' => t('Helium Exporter Configuration'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('helium_exporter_settings_form'),
    'access arguments' => array('administer tripal'),
    'file' => 'includes/helium_exporter_settings.form.inc',
    'type' => MENU_NORMAL_ITEM,
  );

  // Tripal Download Implementation.
  $items['helium/exporter/download'] = array(
    'title' => 'Helium Exporter Download',
    'page callback' => 'trpdownload_download_page',
    'page arguments' => array('helium_exporter_download'),
    'access arguments' => array('access helium_exporter'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_permission().
 */
function helium_exporter_permission() {
  return array(
    'access helium_exporter' => array(
      'title' => t('Access Helium Export Page'),
    )
  );
}

/**
 * Implements hook_theme().
 */
function helium_exporter_theme($existing, $type, $theme, $path) {
  $items['helium_exporter_form'] = array(
    'render element' => 'form',
    'template' => 'helium_exporter_page',
    'path' => $path . '/theme',
  );

  return $items;
}

/**
 * Implement hook_preprocess_HOOK().
 */
function helium_exporter_preprocess_helium_exporter_form(&$variables, $hook) {
  $path = drupal_get_path('module', 'helium_exporter');
 
  // Attach script and style.
  drupal_add_css($path . '/theme/css/style-helium-exporter-page.css');    
  drupal_add_js($path . '/theme/script/script-helium-exporter-page.js', array('type' => 'file', 'scope' => 'footer'));
  
  // Attach library autocomplete:
  drupal_add_library('system', 'ui.autocomplete');

  // Define template variables.
  $variables['path_module'] = $GLOBALS['base_url'] . '/' . $path;

  $config = variable_get('helium_exporter_pedigree_relations');
  $is_configured = ($config == '0') ? FALSE : TRUE;
  $variables['is_configured'] = $is_configured; 

  // Help url configuration.
  $help_url = variable_get('helium_exporter_help_url');
  $variables['help_url'] = trim($help_url);

  $variables['helium_resource'] = array(
    'download' => 'https://github.com/cardinalb/helium-docs/wiki/Download-Helium',
    'information' => 'https://github.com/cardinalb/helium-docs/wiki',
    'help' => 'https://github.com/cardinalb/helium-docs/wiki/Data-Formats',
    'web-base' => 'https://helium.hutton.ac.uk', 
  );
}

// TRIPAL DOWNLOAD API IMPLEMENTATION

/**
 * Implements hook_register_tripaldownload_type().
 */
function helium_exporter_register_trpdownload_type() {
  $types = array();

  // The key is the machine name of my download type.
  $types['helium_exporter_download'] = array(
    // A human readable name to show in an administrative interface one day.
    'type_name' => 'Helium Exporter Data Download',
    // A human readable description of the format.
    'format' => '',
    // An array of functions that the API will use to customize your experience.
    'functions' => array(
      // The function that tripal jobs will call to generate the file.
      'generate_file' => 'helium_exporter_trpdownload_generate_file',
      // OPTIONAL: provide a summary to the user on the download page.
      'summarize' => 'helium_exporter_trpdownload_summarize_download',
      // OPTIONAL: determine your own filename.
      'get_filename' => 'helium_exporter_trpdownload_get_filename',
      // OPTIONAL: Change the file suffix (defaults to .txt)
      'get_file_suffix' => 'helium_exporter_trpdownload_get_suffix',
      // OPTIONAL: determine the human-readable format based on a function.
      'get_format' => 'helium_exporter_trpdownload_get_readable_format',
    ),
  );

  return $types;
}

/**
 * Generate a readable and unique filename for the file to be generated.
 */
function helium_exporter_trpdownload_get_filename($vars) {
  // Filename.
  $filename = 'He_pedigree_' . date('YMd') .'_'. time();

  return $filename;
}

/**
 * determine the human-readable format based on a function.
 */
function helium_exporter_trpdownload_get_readable_format($vars) {
  $format = 'Helium (.helium)';
  
  return $format;
}

/**
 * Determine the file suffix for the file to be generated.
 */
function helium_exporter_trpdownload_get_suffix($vars) {
  return 'helium';
}

/**
 * Create summary.
 */
function helium_exporter_trpdownload_summarize_download($vars) { 
  $code = '';
  foreach($vars['q'] as $j => $m) {
    if ($j == 'code') {
      $code = $m;
      break;
    }
  }
  
  $code = base64_decode($code);
  parse_str($code, $values);

  $path = file_directory_temp() . '/';
  $He_file =  $path . $values['he'];
  $querystring = file_get_contents($He_file);
  unset($values);
  parse_str($querystring, $values);

  $path = variable_get('trpdownload_relpath');
  $file_link = l($values['f'], file_create_url($path) .  '/' . $values['f'], 
    array('attributes' => array('target' => '_blank', 'download' => $values['f']))
  );

  $file_icon = theme_image(array(
    'path' => drupal_get_path('module','trpdownload_api').'/theme/icons/file_generic.128.png',
    'alt' => 'download environment data file',
    'attributes' => array()
  ));

  $output = '<div style="position: absolute; left: 0; width: 100%; margin-top: 90px; padding: 10px;">
    <div style="margin: 0 20px 0 0;">
      <div class="download-pane" style="margin: 0 20px;">'

       . $file_icon .

       '<div class="inner-pane file">
          <h2>File:</h2>
          <div class="file-link">' . $file_link . '</div>
          <div class="file-format">Format: Helium (.helium)</div>
        </div>
      </div>
    </div>
  </div>';

  // Link to download a different set.
  $exporter = l('Go back Helium Exporter', '/helium-exporter');

  return 'Download Pedigree and Categorical Data <br />' . $exporter . $output;
}

/**
 * Function callback: generate .helum file.
 */
function helium_exporter_trpdownload_generate_file($vars, $job_id = NULL) {
  // Use this character to separate entries in a string.
  $delimiter = '+';

  $code = '';
  foreach($vars['q'] as $j => $m) {
    if ($j == 'code') {
      $code = $m;
      break;
    }
  }
  
  // User selected values parsed from the querystring.
  $code = base64_decode($code);
  parse_str($code, $values);

  $path = file_directory_temp() . '/';
  $He_file =  $path . $values['he'];
  $querystring = file_get_contents($He_file);
  unset($values);

  parse_str($querystring, $values);
  
  $experiment = $values['e'];
  // Get experiment assets to match traits and germplasm only
  // belonging to the same experiment.
  $experiment_assets = helium_exporter_get_experiment_assets($experiment);
  // Germplasm and traits selected.
  $germplasm  = explode(' ', $values['g']);
  $traits     = explode(' ', $values['t']);
  // Source directory for files.
  $path_tripal_download = variable_get('trpdownload_fullpath');
  // Lineage option.
  $lineage = $values['l'];
  
  // PEDIGREE:
  $file_pedigree = $path_tripal_download . $vars['filename'];
  $FILE = fopen($file_pedigree, 'w') or die ('Unable to read file to write pedigree to.');
  
  // Write metadata about this file in the header followed
  // by column headers.
  $header = '# heliumInput = PEDIGREE : ' . $experiment_assets['experiment'];
  fwrite($FILE, $header . "\n");
  fputcsv($FILE, array('LineName', 'Parent', 'ParentType'), "\t");
  
  // Datapoints that will map to every column headers.
  // For each germplasm selected, fetch pedigree information.
  $rows = [];
  foreach($germplasm as $line) {
    // Get selections of etc. and parents.
    $relations = helium_exporter_get_parents($line, $lineage);
    foreach($relations as $rel) {
      fputcsv($FILE, $rel, "\t");
    }
  }
  
  fclose($FILE); 

  // CATEGORICAL/PHENOTYPES:
  $file_phenotypes = file_create_url($path_tripal_download . $values['f']);
  $FILE = fopen($file_phenotypes, 'w') or die ('Unable to read file to write phenotypes to.');
  
  // Write metadata about this file in the header followed
  // by column headers.
  $header = '# heliumInput = PHENOTYPE : ' . $experiment_assets['experiment'];
  fwrite($FILE, $header . "\n");
  $phenotypes = helium_exporter_get_phenotypes($experiment, $traits, $germplasm);
  if ($phenotypes) {
    fputcsv($FILE, $phenotypes['headers'], "\t");
    foreach($phenotypes['rows'] as $data) {
      fputcsv($FILE, $data, "\t");
    }
  }

  fclose($FILE); 
}