tripal_blast.module

<?php
/**
 * @file
 * .module file of Tripal BLAST.
 */

use Drupal\Core\Url;
use \Drupal\Core\Link;
use Drupal\Core\Render\Markup;

/**
 * Implements hook_theme().
 * Used by Tripal BLAST UI page.
 *
 * @see templates in /templates
 */
function tripal_blast_theme($existing, $type, $theme, $path) {

  // Links rendered as a markup for the template file.
  // Query type + programs route.
  $blast_programs = [
    'blastn'  => ['nucleotide', 'nucleotide'],
    'blastx'  => ['nucleotide', 'protein'],
    'tblastn' => ['protein', 'nucleotide'],
    'blastp'  => ['protein', 'protein']
  ];
  $route_ui = 'tripal_blast.blast_program';
  $links_ui = [];

  foreach($blast_programs as $name => $param) {
    list($query, $db) = $param;
    $links_ui[ 'link_' . $name ] = Link::createFromRoute(
      t($name),
      $route_ui,
      ['query' => $query, 'db' => $db]
    );
  }

  $context_links = [
    // MISC/ADMIN.
    'link_config' => '#',
    'link_jobs'    => '#',
    'link_nodeadd'  => '#',
    'link_dbadd'     => '#',
    'link_dbfields'   => '#',
  ];

  // Recent jobs table: Note this is not BLAST program specific.
  $recent_jobs = \Drupal::service('tripal_blast.job_service')
    ->jobsCreateTable();

  // Pass rendered links as variables and make available in the template file.
  $variables = [
    // Tripal BLAST UI page.
    'theme-tripal-blast-ui' => [
      'variables' => [
        'context_links' => $links_ui,
        'recent_jobs' => $recent_jobs
      ],
      'template'  => 'template-tripal-blast-ui',
    ],
    // Tripal BLAST Configuration page.
    // Tripal BLAST Help page.
    'theme-tripal-blast-help' => [
      'variables' => ['context_links' => $context_links],
      'template'  => 'template-tripal-blast-help',
    ],
    // Tripal BLAST messages.
    'theme-tripal-blast-message' => [
      'variables' => ['data' => []],
      'template' => 'template-tripal-blast-message'
    ],
    // Tripal BLAST Report Pending.
    'theme-tripal-blast-report-pending' => [
      'variables' => ['data' => []],
      'template' => 'template-tripal-blast-report-pending'
    ],
    // Tripal BLAST Show Report.
    'theme-tripal-blast-show-report' => [
      'variables' => ['report' => []],
      'template' => 'template-tripal-blast-show-report'
    ]
  ];

  return $variables;
}

/**
 * Run BLAST (should be called from the command-line)
 *
 * @param $program
 *   Which BLAST program to run (ie: 'blastn', 'tblastn', tblastx', 'blastp','blastx')
 * @param $query
 *   The full path and filename of the query FASTA file
 * @param $database
 *   The full path and filename prefix (excluding .nhr, .nin, .nsq, etc.)
 * @param $output_filestub
 *   The filename (not including path) to give the results. Should not include file type suffix
 * @param $options
 *   An array of additional option where the key is the name of the option used by
 *   BLAST (ie: 'num_alignments') and the value is relates to this particular
 *   BLAST job (ie: 250)
 */
function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $options, $job_id = NULL) {
  $output_file = $output_filestub . '.asn';
  $output_file_xml = $output_filestub . '.xml';
  $output_file_tsv = $output_filestub . '.tsv';
  $output_file_html = $output_filestub . '.html';
  $output_file_gff = $output_filestub . '.gff';

  print "\nExecuting $program\n\n";
  print "Query: $query\n";
  print "Database: $database\n";
  print "Results File: $output_file\n";

  print "Options:\n";

  // Allow administrators to use an absolute path for these commands.
  // Defaults to using $PATH.
  $blast_path = \Drupal::config('tripal_blast.settings')
    ->get('tripal_blast_config_general.path');

  $blast_threads = \Drupal::config('tripal_blast.settings')
    ->get('tripal_blast_config_general.threads');

  // Strip the extension off the BLAST target
  $suffix = ['.ndb', '.nhr', '.nin', '.not', '.nsq', '.ntf', '.nto',
    '.pdb', '.phr', '.pin', '.pot', '.psq', '.ptf', '.pto'];

  $database = str_replace($suffix, '', $database);

  // Check that the database exists before trying to execute the job.
  if (!(file_exists($database . '.nsq') OR file_exists($database . '.psq'))) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST database (ie: @db). Please ensure you have supplied the absolute path not including the file format endings.",
      ['@db' => $database],
      ['print' => TRUE]
    );

    return FALSE;
  }

  // The BLAST executeable.
  $program = $blast_path . $program;
  if (!file_exists($program)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST executable (ie: /usr/bin/blastn). This can be changed in the admin settings; you supplied: @command",
      ['@command' => $program],
      ['print' => TRUE]
    );

    return FALSE;
  }

  // The blast db formatter executable.
  $blast_formatter_command = $blast_path . 'blast_formatter';
  if (!file_exists($blast_formatter_command)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to find the BLAST Formatter executable (ie: /usr/bin/blast_formatter). This can be changed in the admin settings; you supplied: @command",
      ['@command' => $blast_formatter_command],
      ['print' => TRUE]
    );

    return FALSE;
  }

  // Note: all variables are escaped (adds single quotes around their values) for security reasons.
  $blast_cmd = escapeshellarg($program) . ' -query ' . escapeshellarg($query) . ' -db ' . escapeshellarg($database) . ' -out ' . escapeshellarg($output_file) . ' -outfmt=11';
  if (!empty($options)) {
    foreach ($options as $opt => $val) {
      $val = trim($val);
      if (!empty($val)) {
        print "\t$opt: $val\n";
        // We want to escape all the option values since they were supplied via
        // user input. These values should also have been checked in the
        // advanced form _validate functions but this adds an extra layer of
        // protection.
        $blast_cmd .= ' -' . escapeshellarg($opt) . ' ' . escapeshellarg($val);
      }
    }
  }

  // Setting the value of threads by admin page
  $blast_cmd .= ' -num_threads ' . escapeshellarg($blast_threads);

  print "\nExecuting the following BLAST command:\n" . $blast_cmd . "\n";

  system($blast_cmd);

  if (!file_exists($output_file)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "BLAST did not complete successfully as is implied by the lack of output file (%file). The command run was @command",
      ['%file' => $output_file, '@command' => $blast_cmd],
      ['print' => TRUE]
    );

    return FALSE;
  }

  print "\nGenerating additional download formats...\n";

  print "\tXML\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 5 -out ' . escapeshellarg($output_file_xml);
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);

  if (!file_exists($output_file_xml)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "Unable to convert BLAST ASN.1 archive to XML (%archive => %file).",
      ['%archive' => $output_file, '%file' => $output_file_xml],
      ['print' => TRUE]
    );
  }

  print "\tTab-delimited\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 7 -out ' . escapeshellarg($output_file_tsv);
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);

  if (!file_exists($output_file_tsv)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST ASN.1 archive to Tabular Output (%archive => %file).",
      ['%archive' => $output_file, '%file' => $output_file_tsv],
      ['print' => TRUE]
    );
  }

  print "\tGFF\n";
  $job_service = \Drupal::service('tripal_blast.job_service');
  $job_service->jobsConvertTSVtoGFF3($output_file_tsv,$output_file_gff);

  if (!file_exists($output_file_gff)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST Tabular Output to GFF Output (%archive => %file).",
      ['%archive' => $output_file, '%file' => $output_file_gff],
      ['print' => TRUE]
    );
  }

  print "\tHTML (includes alignments)\n";
  $format_cmd = escapeshellarg($blast_formatter_command) . ' -archive ' . escapeshellarg($output_file) . ' -outfmt 0 -out ' . escapeshellarg($output_file_html) . ' -html';
  print "\t\tExecuting $format_cmd\n\n";
  system($format_cmd);

  if (!file_exists($output_file_tsv)) {
    tripal_report_error(
      'blast_ui',
      TRIPAL_WARNING,
      "Unable to convert BLAST ASN.1 archive to HTML Output (%archive => %file).",
      ['%archive' => $output_file, '%file' => $output_file_html],
      ['print' => TRUE]
    );
  }

  print "\nDone!\n";
}