tripal_test.info

package = Tripal Download API Test
name = Test Download API
description = Provides an api for creating download pages. Uses tripal Jobs to generate files and provides a progress bar to users.
version = 7.x-0.x
core = 7.x

dependencies[] = tripal_core
dependencies[] = trpdownload_api

tripal_test.module

<?php
  /**
   * @file
   * Provides some examples showing how module developers could use the
   * Tripal Download API.
   */

  /**
   * Implements hook_register_trpdownload_type().
   */
  function tripal_test_register_trpdownload_type() {
	$types = array();

	$types['organism_csv'] = array(
	  'type_name' => 'Organism CSV',
	  'format' => 'Comma-separated Values',
	  'functions' => array(
		'generate_file' => 'tripal_test_organism_csv_generate_file',
	  ),
	);

	return $types;
  }

  /**
   * Implements hook_menu().
   */
  function tripal_test_menu() {
	$items = array();

	$items['chado/organism/csv'] = array(
	  'title' => 'Download Features: CSV',
	  'page callback' => 'trpdownload_download_page',
	  'page arguments' => array('organism_csv', 3),
	  'access arguments' => array('access content'),
	  'type' => MENU_CALLBACK,
	);

	return $items;

  }

//  /**
//   * Generates a file listing feature in CSV.
//   *
//   * @param $variables
//   *   An associative array of parameters including:
//   *     - q: all the query paramters.
//   *     - site_safe_name: a sanitized version of your site name for use in variables & filenames.
//   *     - type_info: an array of info for the download type.
//   *     - suffix: the file format suffix.
//   *     - filename: the filename of the file to generate not including path.
//   *     - fullpath: the full path and filename of the file to generate.
//   *     - format_name: a human-readable description of the format.
//   * @param $job_id
//   *   The ID of the tripal job executing this function ;-).
//   */
//
  function tripal_test_organism_csv_generate_file($variables, $job_id = NULL) {

	// Create the file and ready it for writting to.
	$filepath = variable_get('trpdownload_fullpath', '') . $variables['filename'];
	drush_print("File: " . $filepath);
	$FILE = fopen($filepath, 'w') or die ('Uable to create file to write to');

	// Add header to the file.
	fputcsv($FILE, array(
	  'Genus',
	  'Species',
	  'Scientific Name',
	  'Common Name',
	  'Abbreviation'
	));

	// Determine which where criteria to include based on what is in query parameters.
	$where = array('true');
	$where_args = array();
	// feature.name
	if (isset($variables['q']['common_name']) AND !empty($variables['q']['common_name'])) {
	  $where[] = "organism.common_name ~ :common_name";
	  $where_args[':common_name'] = $variables['q']['common_name'];
	}
	// feature.uniquename
	if (isset($variables['q']['genus']) AND !empty($variables['q']['genus'])) {
	  $where[] = "organism.genus ~ :genus";
	  $where_args[':uniquename'] = $variables['q']['uniquename'];
	}
	// feature.type_id
	if (isset($variables['q']['species']) AND !empty($variables['q']['species'])) {
	  $where[] = "organism.species = :species";
	  $where_args[':species'] = $variables['q']['species'];
	}
//	// organism.common_name
//	if (isset($variables['q']['organism'])
//	  AND !empty($variables['q']['organism'])
//	  AND $variables['q']['organism']!= 'All') {
//	  $where[] = "organism.common_name = :organism";
//	  $where_args[':organism'] = $variables['q']['organism'];
//	}
//
	// Query copied from the views interface with where arguments determined above.
	$query = "SELECT organism.genus AS organism_genus, organism.species AS organism_species, organism.common_name AS organism_common_name, organism.abbreviation AS organism_abbreviation FROM 
{organism} organism 
LEFT JOIN [chado_organism] chado_organism ON organism.organism_id = chado_organism.organism_id 
LEFT JOIN [node] node_chado_organism ON chado_organism.nid = node_chado_organism.nid 
LEFT JOIN [node] node ON chado_organism.nid = node.nid 
WHERE " . implode(' AND ', $where) ." 
ORDER BY organism_genus ASC, organism_species ASC OFFSET 0";



//    SELECT
//      feature.uniquename AS feature_uniquename,
//      feature.name AS feature_name,
//      cvterm.name AS cvterm_name,
//      organism.common_name AS organism_common_name,
//      feature.seqlen AS feature_seqlen,
//      feature.is_obsolete AS feature_is_obsolete
//    FROM
//      {feature} feature
//      LEFT JOIN [chado_feature] chado_feature ON feature.feature_id = chado_feature.feature_id
//      LEFT JOIN [node] node_chado_feature ON chado_feature.nid = node_chado_feature.nid
//      LEFT JOIN {organism} organism ON feature.organism_id = organism.organism_id
//      LEFT JOIN {cvterm} cvterm ON feature.type_id = cvterm.cvterm_id
//      WHERE " . implode(' AND ', $where) ."
//      ORDER BY organism.common_name ASC, cvterm.name ASC, feature.name ASC";

	// Determine the total number of lines resulting from the query
	// for tracking progress.
	$count_query = preg_replace('/SELECT.*FROM/s', 'SELECT count(*) as num_lines FROM', $query);
	$count_query = preg_replace('/ORDER BY .*$/', '', $count_query);
	$total_lines = chado_query($count_query, $where_args)->fetchField();
	drush_print('Total Lines: '.$total_lines);

	// Execute the original query to get the results.
	$resource = chado_query($query, $where_args);
//
	// For each db result write a CSV line to the file.
	$cur_line = 0;
	foreach ($resource as $row) {

	  // Output the progress.
	  $cur_line++;
	  $percent = $cur_line/$total_lines * 100;
	  if ($percent%5 == 0) {
		drush_print(round($percent,2).'% Complete.');
		db_query('UPDATE {tripal_jobs} SET progress=:percent WHERE job_id=:id',
		  array(':percent' => round($percent), ':id' => $job_id));
	  }

	  // Don't forget to write the line to the file ;-).
	  fputcsv($FILE, (array)$row );
	}

	// Finally, close the file.
	fclose($FILE);
  }