tripal_eutils.module

<?php

/**
 * @file
 * Tripal Eutils module file.
 */

require_once 'includes/EUtilsFactoryInterface.inc';
require_once 'includes/resources/EUtilsResource.inc';
require_once 'includes/resources/EUtilsRequest.inc';
require_once 'includes/resources/EFetch.inc';
require_once 'includes/resources/ESearch.inc';
require_once 'includes/resources/ESummary.inc';
require_once 'includes/resources/EUtils.inc';
require_once 'includes/resources/EFTP.inc';

// Connects to NCBI to fetch the current biosample property list hosted.
require_once 'includes/resources/BiosamplePropertyLookup.inc';

// Parsers.  Convert XML into keyed arrays.
require_once 'includes/xml_parsers/EUtilsXMLParserFactory.inc';
require_once 'includes/xml_parsers/EUtilsParserInterface.inc';
require_once 'includes/xml_parsers/EUtilsBioSampleParser.inc';
require_once 'includes/xml_parsers/EUtilsBioProjectParser.inc';
require_once 'includes/xml_parsers/EUtilsAssemblyParser.inc';
require_once 'includes/xml_parsers/EUtilsPubmedParser.inc';

// Repositories. Handling DB operations.
require_once 'includes/repositories/EUtilsRepositoryFactory.inc';
require_once 'includes/repositories/EUtilsRepository.inc';
require_once 'includes/repositories/EUtilsBioSampleRepository.inc';
require_once 'includes/repositories/EUtilsBioProjectRepository.inc';
require_once 'includes/repositories/EUtilsAssemblyRepository.inc';
require_once 'includes/repositories/EUtilsPubmedRepository.inc';

// Repository helpers.  Assist with looking up terms.
require_once 'includes/TagMapper.inc';

// Formatters.
require_once 'includes/formatters/EUtilsFormatter.inc';
require_once 'includes/formatters/EUtilsFormatterFactory.inc';
require_once 'includes/formatters/EUtilsBioSampleFormatter.inc';
require_once 'includes/formatters/EUtilsBioProjectFormatter.inc';
require_once 'includes/formatters/EUtilsAssemblyFormatter.inc';

/**
 * Implements hook_menu().
 */
function tripal_eutils_menu() {

  // Admin can configure which emails get sent out, more stuff?
  // Set site-wide admin settings.
  $items['admin/tripal/tripal_eutils'] = [
    'title' => 'Tripal EUtils settings',
    'page callback' => 'drupal_get_form',
    'file' => 'includes/tripal_eutils_admin_settings.form.inc',
    'access arguments' => ['access tripal_eutils admin'],
    'page arguments' => ['tripal_eutils_admin_settings_form'],
  ];

  return $items;
}

/**
 * Implements hook_permission().
 */
function tripal_eutils_permission() {

  return [
    'access tripal_eutils admin' => [
      'title' => t('Submit NCBI Accessions directly via admin form'),
    ],
  ];

}

/**
 * Runs the EUtils class to create the records for an NCBI entry.
 *
 * @param string $db
 *   The database name (eg, biosample, assembly or bioproject).
 * @param string $accession
 *   The numeric accession, or accessions separated by delimiter of comma, semicolon, or space.
 * @param bool $create_linked_records
 *   Whether to create linked records or not.
 */
function tripal_eutils_create_records(string $db, string $accession, bool $create_linked_records, $job = NULL) {
  $accs = preg_split('/[,; ]+/', trim($accession));
  foreach ($accs as $acc) {
    $attempts = 3;
    $success = false;
    while ((!$success) and ($attempts)) {
      try {

        $eutils = new EUtils($create_linked_records, $job);
        $eutils->get($db, $acc);
        $success = true;
      }
      catch (Exception $exception) {

        $message = $exception->getMessage();
        // Distinguish between download error and SQL error, e.g. from reloading same assembly twice.
        // Download error: "ERROR Could not make request: Status: 400"
        // SQL error: "SQLSTATE[25P02]: In failed sql transaction: 7 ERROR:  current transaction is aborted, commands ignored until end of transaction block"
        if (preg_match('/SQL/', $message)) {
          $attempts = 1;
        }
        if ($attempts > 1) {
          tripal_report_error('tripal_eutils', TRIPAL_WARNING, 'Download error, retrying '.$message, [], ['print' => TRUE, 'job' => $job]);
          sleep(1);
        }
        else {
          tripal_report_error('tripal_eutils', TRIPAL_ERROR, $message, [], ['print' => TRUE, 'job' => $job]);
        }
      }
      $attempts--;
    }
  }
}