tripal_galaxy.module

<?php

/**
 * @file
 * The module for for the tripal_galaxy module.
 */

require 'theme/tripal_galaxy.theme.inc';
require 'api/tripal_galaxy.api.inc';
require 'includes/tripal_galaxy.form_elements.inc';
require 'includes/tripal_galaxy.webform.inc';
require 'includes/tripal_galaxy.results.inc';

/**
 * Implements hook_init().
 */
function tripal_galaxy_init() {
  global $user;

  $library = libraries_detect('blend4php');
  if (user_access('administer galaxy', $user)) {
    if (!$library) {
      drupal_set_message(t('The blend4php library is not installed. The Galaxy module requires it.'), 'warning');
    }
  }
}

/**
 * Implements hook_libraries_info().
 */
function tripal_galaxy_libraries_info() {

  // A very simple library. No changing APIs (hence, no versions), no variants.
  // Expected to be extracted into 'sites/all/libraries/simple'.
  $libraries['blend4php'] = [
    'name' => 'blend4php',
    'vendor url' => 'https://github.com/galaxyproject/blend4php',
    'download url' => 'https://github.com/galaxyproject/blend4php',
    'version arguments' => [
      'file' => 'version.txt',
      'pattern' => '/^(.*)$/',
      'lines' => 1,
    ],
    'files' => [
      'php' => [
        'galaxy.inc',
      ],
    ],
  ];

  return $libraries;
}

/**
 * Implements hook_permissions().
 *
 * Set the permission types that this module uses.
 */
function tripal_galaxy_permission() {
  return [
    'use galaxy' => [
      'title' => t('Execute Published Galaxy Workflows'),
      'description' => t('Allows a user to submit a published workflow for execution on a remote Galaxy Instance'),
    ],
    'administer galaxy' => [
      'title' => t('Administer Galaxy'),
      'description' => t('Allows a user to configure site-wide default Galaxy instances.'),
    ],
  ];
}

/**
 * Implements hook_menu().
 *
 * Specifies menu items and URLs used by this module.
 */
function tripal_galaxy_menu() {
  $items = [];

  // EXPLANATION: all extension modules should have an administrative menu item
  // with the path set to 'admin/tripal/extension/[module name]'.
  $items['admin/tripal/extension/galaxy'] = [
    'title' => 'Galaxy',
    'description' => 'Integrate workflows from a remote Galaxy instance with this Tripal site',
    'page callback' => 'tripal_galaxy_admin_home',
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_NORMAL_ITEM,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Edit Galaxy.
  $items['admin/tripal/extension/galaxy/edit/%'] = [
    'description' => 'Edit a galaxy instance',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_configuration_form',
      5,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_configuration_form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Test Galaxy.
  $items['admin/tripal/extension/galaxy/test/%'] = [
    'description' => 'Test a galaxy instance',
    'page callback' => 'tripal_galaxy_admin_test_server',
    'page arguments' => [
      5,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Disable workflows for this Galaxy.
  $items['admin/tripal/extension/galaxy/disable/%'] = [
    'description' => 'Disable all workflows for this galaxy server',
    'page callback' => 'tripal_galaxy_admin_disable_workflows',
    'page arguments' => [
      5,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Enable workflows for this Galaxy.
  $items['admin/tripal/extension/galaxy/enable/%'] = [
    'description' => 'Enable all workflows for this galaxy server',
    'page callback' => 'tripal_galaxy_admin_enable_workflows',
    'page arguments' => [
      5,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Add Galaxy.
  $items['admin/tripal/extension/galaxy/add'] = [
    'description' => 'Add a galaxy server instance',
    'title' => 'Add Galaxy Instance',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_configuration_form',
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_ACTION,
    'file' => 'includes/tripal_galaxy.admin_configuration_form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  $items['admin/tripal/extension/galaxy/delete/%'] = [
    'description' => 'Delete a galaxy server instance',
    'title' => 'Delete Galaxy Instance',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_delete_galaxy_instance_form',
      5,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_configuration_form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Available Workflows.
  $items['admin/tripal/extension/galaxy/workflows'] = [
    'title' => 'Workflows',
    'description' => 'Lists the available Workflows of the user',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_workflows_form',
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_TASK,
    'file' => 'includes/tripal_galaxy.admin_workflow_form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 5,
  ];
  // Add Workflows.
  $items['admin/tripal/extension/galaxy/workflows/add'] = [
    'title' => 'Add Workflows',
    'description' => 'Add workflows to the site given the remote galaxy instance',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_add_workflow_form',
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_ACTION,
    'file' => 'includes/tripal_galaxy.admin_workflow_form_add.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  // Remove Workflows.
  $items['admin/tripal/extension/galaxy/workflows/remove/%'] = [
    'description' => 'Remove a workflow from site',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_confirm_remove_workflow_form',
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  // Disable Workflows.
  $items['admin/tripal/extension/galaxy/workflows/disable/%'] = [
    'description' => 'Disable this workflow',
    'page callback' => 'tripal_galaxy_admin_disable_workflow',
    'page arguments' => [
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  // Enable Workflows.
  $items['admin/tripal/extension/galaxy/workflows/enable/%'] = [
    'description' => 'Enable this workflow',
    'page callback' => 'tripal_galaxy_admin_enable_workflow',
    'page arguments' => [
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  $items['admin/tripal/extension/galaxy/workflows/settings/%'] = [
    'description' => 'Settings for the workflow',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_workflow_settings_form',
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];


  // Admin submission report.
  $items['admin/tripal/extension/galaxy/workflows/report/%'] = [
    'title' => 'Workflow Submission Details',
    'description' => 'The report for a submitted workflow.',
    'page callback' => 'tripal_galaxy_submission_admin_report',
    'page arguments' => [
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  //
  // USER SUBMITTED WORKFLOW JOBS
  //
  // User submission report.
  $items['user/%/galaxy-jobs/%'] = [
    'title' => 'Analysis Results',
    'description' => 'The results for a submitted analysis.',
    'page callback' => 'tripal_galaxy_submission_user_report',
    'page arguments' => [
      3,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.user.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  // User report page.
  $items['user/%/galaxy-jobs/%/results'] = [
    'title' => 'Workflow Submission Files',
    'description' => 'The files from a submitted workflow.',
    'page callback' => '',
    'page arguments' => [
      3,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 10,
  ];

  // Usage.
  $items['admin/tripal/extension/galaxy/usage'] = [
    'title' => 'Usage',
    'description' => 'View Usage of Galaxy Workflows',
    'page callback' => 'tripal_galaxy_admin_usage_page',
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_TASK,
    'file' => 'includes/tripal_galaxy.admin_usage.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 20,
  ];

  //
  // SITE-WIDE FILES
  // .
  $items['admin/tripal/extension/galaxy/files'] = [
    'title' => 'Files',
    'description' => 'Files available site-wide for workflows.',
    'page callback' => 'tripal_galaxy_admin_manage_files',
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_TASK,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 40,
  ];
  $items['admin/tripal/extension/galaxy/files/add'] = [
    'title' => 'Add a New File',
    'description' => 'Files available site-wide for workflows.',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_add_file_form',
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_ACTION,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];
  $items['admin/tripal/extension/galaxy/files/disable/%'] = [
    'description' => "Disable a file.",
    'page callback' => 'tripal_galaxy_admin_disable_file',
    'page arguments' => [
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];
  $items['admin/tripal/extension/galaxy/files/enable/%'] = [
    'description' => "Enable a file.",
    'page callback' => 'tripal_galaxy_admin_enable_file',
    'page arguments' => [
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];
  $items['admin/tripal/extension/galaxy/files/edit/%'] = [
    'title' => 'Edit File Details',
    'description' => "Edit a site-wide file.",
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_edit_file_form',
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];
  $items['admin/tripal/extension/galaxy/files/delete/%'] = [
    'title' => 'Delete File',
    'description' => "Deletes a site-wide file.",
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_delete_file_form',
      6,
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_CALLBACK,
    'file' => 'includes/tripal_galaxy.admin_files.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];

  $items['galaxy/proxy/%'] = [
    'title' => 'Results Viewer',
    'page callback' => 'tripal_galaxy_stream_url_proxy',
    'page arguments' => [
      2,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
  ];
  $items['galaxy/viewer/%'] = [
    'title' => 'Results Viewer',
    'page callback' => 'tripal_galaxy_results_viewer_page',
    'page arguments' => [
      2,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
  ];
  $items['galaxy/viewer-full/%'] = [
    'title' => 'Results Viewer',
    'page callback' => 'tripal_galaxy_results_viewer_full_page',
    'page arguments' => [
      2,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
  ];
  $items['galaxy/download/%'] = [
    'title' => 'Download',
    'page callback' => 'tripal_galaxy_results_download',
    'page arguments' => [
      2,
    ],
    'access arguments' => [
      'use galaxy',
    ],
    'type' => MENU_CALLBACK,
  ];

  // SETTINGS
  // Available Workflows.
  $items['admin/tripal/extension/galaxy/settings'] = [
    'title' => 'Settings',
    'description' => 'Galaxy Settings',
    'page callback' => 'drupal_get_form',
    'page arguments' => [
      'tripal_galaxy_admin_settings_form',
    ],
    'access arguments' => [
      'administer galaxy',
    ],
    'type' => MENU_LOCAL_TASK,
    'file' => 'includes/tripal_galaxy.admin_settings_form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
    'weight' => 50,
  ];
  return $items;
}

/**
 * Implements hook_menu_alter().
 */
function tripal_galaxy_menu_alter(&$items) {
  $items['node/%webform_menu/webform/export-workflow'] = [
    'title' => 'Export',
    'page callback' => 'export_tripal_galaxy_workflow',
    'page arguments' => [
      1,
    ],
    'access arguments' => [
      'access content',
    ],
    'weight' => 9,
    'type' => MENU_LOCAL_TASK,
  ];
  $items['node/%webform_menu/webform/import-workflow'] = [
    'title' => 'Import',
    'page callback' => 'import_tripal_galaxy_workflow',
    'page arguments' => [
      1,
    ],
    'access arguments' => [
      'access content',
    ],
    'weight' => 10,
    'type' => MENU_LOCAL_TASK,
    'file' => 'includes/tripal_galaxy.import_webform.form.inc',
    'file path' => drupal_get_path('module', 'tripal_galaxy'),
  ];
}

/**
 * Implements hook_views_api().
 *
 * This hook tells drupal that there is views
 * support for for this module which then automatically includes the
 * tripal_db.views.inc where all the views integration code is found.
 *
 * @ingroup
 * tripal_galaxy
 */
function tripal_galaxy_views_api() {
  return [
    'api' => 3.0,
  ];
}

/**
 * Implements hook_theme().
 *
 * We need to let drupal know about our theme functions and their arguments.
 * We create theme functions to allow users of the module to customize the
 * look and feel of the output generated in this module @ingroup tripal_galaxy.
 */
function tripal_galaxy_theme($existing, $type, $theme, $path) {
  $items = [
    'html__galaxy__viewer_full' => [
      'template' => 'html--galaxy--viewer-full',
      'render element' => 'html',
      'base hook' => 'html',
      'path' => drupal_get_path('module', 'tripal_galaxy') . "/theme/templates",
    ],
    'page__galaxy__viewer_full' => [
      'template' => 'page--galaxy--viewer-full',
      'render element' => 'page',
      'base hook' => 'page',
      'path' => drupal_get_path('module', 'tripal_galaxy') . "/theme/templates",
    ],
    'tripal_galaxy_admin_add_workflow_form_rows' => [
      'render element' => 'form',
    ],
    'tripal_galaxy_admin_workflows_form_rows' => [
      'render element' => 'form',
    ],
  ];
  return $items;
}

/**
 * Implements hook_form_alter().
 *
 * Add a submit handler to the client webform form.
 */
function tripal_galaxy_form_webform_client_form_alter(&$form, &$form_state, $form_id) {
  $node = $form['#node'];
  $workflow = db_select('tripal_galaxy_workflow', 'tgw')->fields('tgw')
    ->condition('nid', $node->nid)
    ->execute()
    ->fetchObject();
  if ($workflow and $workflow->status == 'Altered') {
    drupal_set_message('Unfortunately, this wokflow is deprecated and no longer
        available for submissions.', 'error');
    tripal_set_message('This form is disabled because the workflow was
        altered on the remote Galaxy Instance and may be out of sync
        with this web form.  If you want to continue to offer this workflow
        to your site visitors, you will need to ' . l(t('add the workflow'), 'admin/tripal/extension/galaxy/workflows') . ' again as a new web form on this site.', TRIPAL_ERROR);
    $form['actions']['next']['#disabled'] = TRUE;
  }
  else {
    if ($workflow and $workflow->status == 'disabled') {
      drupal_set_message('Unfortunately, this wokflow is disabled and no longer
        avaliable for submissions.', 'error');
      tripal_set_message('This form is disabled you may ' . l(t('enable the workflow here'), 'admin/tripal/extension/galaxy') . '.', TRIPAL_ERROR);
      $form['actions']['next']['#disabled'] = TRUE;
    }
  }

  // Check if this particular webform really is a galaxy webform
  // At each 'turn of the page' of the particular webform this is being called.
  if ($form['#node']->webform['components'][1]['form_key'] == 'galaxy_webform') {
    $form['#submit'][] = 'tripal_galaxy_webform_client_form_submit';
  }
}

/**
 * Submit function for the webform_client_form.
 */
function tripal_galaxy_webform_client_form_submit($form, &$form_state) {
  global $user;


  // Don't do anything if the webform isn't finished being filled out.
  if ($form_state['webform_completed'] != TRUE) {
    return;
  }
  try {

    // Get the submissinon ID.
    $wf_sid = $form_state['storage']['details']['sid'];

    // Get the Galaxy server workflow ID from the form then
    // lookup our internal galaxy workflow ID.
    $workflow_id = $form['#node']->webform['components'][1]['extra']['workflow_id'];
    $workflow = db_select('tripal_galaxy_workflow', 'tgw')->fields('tgw')
      ->condition('workflow_id', $workflow_id)
      ->execute()
      ->fetchObject();

    // Create the workflow submission.
    $tg_workflow = tripal_galaxy_init_submission($workflow, $user);

    // Linker table.
    $data = [
      'wf_sid' => $wf_sid,
      'tg_sid' => $tg_workflow,
    ];
    drupal_write_record('tripal_galaxy_webform', $data);

    // For any files that were uploaded we want to set the usage for those
    // so that they are mapped to the correct submission.
    foreach ($form_state['values']['submitted'] as $cid => $component) {
      if (is_array($component) and array_key_exists('existing', $component)) {
        $fids = [];
        if(array_key_exists('existing', $component) and $component['existing']) {
          $fids = explode('|', $component['existing']);
        }
        if(array_key_exists('site_wide', $component) and $component['site_wide']) {
          $fids = explode('|', $component['site_wide']);
        }
        if(array_key_exists('data_collection', $component) and $component['data_collection']) {
          $fids = explode('|', $component['data_collection']);
        }
        $keys = preg_grep('/^submitted_.*$/', array_keys($component));
        $uploaded_key = array_shift($keys);
        if ($uploaded_key and $component[$uploaded_key]) {
          $fids = explode('|', $component[$uploaded_key]);
        }
        if ($fids) {
          foreach ($fids as $fid) {
            $file = file_load($fid);
            file_usage_add($file, 'tripal_galaxy', 'submission', $tg_workflow);
          }
        }
      }
    }

    $args = [$tg_workflow];
    $includes = [];
    $job_id = tripal_add_job("Galaxy Workflow #" . $tg_workflow, 'tripal_galaxy',
      'tripal_galaxy_invoke_webform_submission', $args, $user->uid, 10, $includes,
      $ignore_duplicates = FALSE);
    if ($job_id) {
      drupal_set_message(t('Your job is successfully submitted to the job queue! You will be notified by email when your job begins and completes.'));
    }
    else {
      drupal_set_message(t('Your analysis workflow was successfully submitted, but the job could not be added. Please contact the site administrator to report this issue.', 'warning'));
    }
  }
  catch (Exception $e) {
    drupal_set_message(t('Could not complete workflow submission.  Please contact the web site administrator to report this issue.'), 'error');
    watchdog_exception('tripal_galaxy', $e);
  }

  drupal_goto('user/' . $user->uid . '/galaxy-jobs');
}

/**
 * Implements hook_webform_component_info().
 *
 * Describes new components for webforms that Galaxy workflows will use.
 */
function tripal_galaxy_webform_component_info() {
  $components = [];
  $components['BDSS_file'] = [
    'label' => t('BDSS File'),
    'description' => t('Allows multiple paths (URL, upload, Tripal web services) that a file may be attached.'),
    'features' => [
      'csv' => TRUE,
      'email' => FALSE,
      'email_address' => FALSE,
      'email_name' => FALSE,
      'required' => FALSE,
      'title_display' => FALSE,
      'title_inline' => FALSE,
      'conditional' => TRUE,
      'group' => FALSE,
      'spam_analysis' => FALSE,
      'attachment' => FALSE,
      'conditional_action_set' => TRUE,
    ],
    'file' => 'includes/components/tripal_galaxy.BDSS_file.inc',
  ];
  $components['galaxy_sfile'] = [
    'label' => t('File'),
    'description' => t('Provides a single file for a Galaxy input.'),
    'features' => [
      'csv' => TRUE,
      'email' => FALSE,
      'email_address' => FALSE,
      'email_name' => FALSE,
      'required' => FALSE,
      'title_display' => FALSE,
      'title_inline' => FALSE,
      'conditional' => TRUE,
      'group' => FALSE,
      'spam_analysis' => FALSE,
      'attachment' => FALSE,
      'conditional_action_set' => TRUE,
    ],
    'file' => 'includes/components/tripal_galaxy.galaxy_sfile.inc',
  ];
  $components['galaxy_sflist'] = [
    'label' => t('List Files'),
    'description' => t('Provides a list of files for a Galaxy input.'),
    'features' => [
      'csv' => TRUE,
      'email' => FALSE,
      'email_address' => FALSE,
      'email_name' => FALSE,
      'required' => FALSE,
      'title_display' => FALSE,
      'title_inline' => FALSE,
      'conditional' => TRUE,
      'group' => FALSE,
      'spam_analysis' => FALSE,
      'attachment' => FALSE,
      'conditional_action_set' => TRUE,
    ],
    'file' => 'includes/components/tripal_galaxy.galaxy_sflist.inc',
  ];
  $components['galaxy_pflist'] = [
    'label' => t('List of Paired Files'),
    'description' => t('Provides a list of paired files for a Galaxy input.'),
    'features' => [
      'csv' => TRUE,
      'email' => FALSE,
      'email_address' => FALSE,
      'email_name' => FALSE,
      'required' => FALSE,
      'title_display' => FALSE,
      'title_inline' => FALSE,
      'conditional' => TRUE,
      'group' => FALSE,
      'spam_analysis' => FALSE,
      'attachment' => FALSE,
      'conditional_action_set' => TRUE,
    ],
    'file' => 'includes/components/tripal_galaxy.galaxy_pflist.inc',
  ];
  $components['fixed_value'] = [
    'label' => t('Fixed Value'),
    'description' => t('A fixed value set by the workflow programmer.'),
    'features' => [
      'csv' => TRUE,
      'email' => FALSE,
      'email_address' => FALSE,
      'email_name' => FALSE,
      'required' => FALSE,
      'title_display' => FALSE,
      'title_inline' => FALSE,
      'conditional' => TRUE,
      'group' => FALSE,
      'spam_analysis' => FALSE,
      'attachment' => FALSE,
      'conditional_action_set' => TRUE,
    ],
    'file' => 'includes/components/tripal_galaxy.fixed_value.inc',
  ];
  return $components;
}

/**
 * Webform submission presave function.
 */
function tripal_galaxy_webform_submission_presave($node, &$submission) {

  // Iterate through the components being submitted and remove non
  // needed elements added by our galaxy form elements.
  foreach ($submission->data as $cid => $data) {
    $component = db_select('webform_component', 'wc')->fields('wc', [
      'type',
      'form_key',
    ])
      ->condition('cid', $cid)
      ->execute()
      ->fetchObject();

    if ($component->type == 'galaxy_sfile') {
      unset($submission->data[$cid]['uploader_fset']);
      unset($submission->data[$cid]['existing_fset']);
      unset($submission->data[$cid]['site_wide_fset']);

      // If we have a data collection then we need to copy the files out
      // of the data collection and into the Galaxy files.
      if (array_key_exists('data_collection_fset', $submission->data[$cid]) and $submission->data[$cid]['data_collection_fset']['data_collection']) {
        $fid = $submission->data[$cid]['data_collection_fset']['data_collection'];
        $file = file_load($fid);
        $site_dir = tripal_galaxy_get_files_dir();
        if (!$site_dir) {
          drupal_set_message('Could not access the data collection to the directory on the server for storing this file.  This analysis may not execute correctly.', 'error');
        }
        else {
          $file = file_copy($file, $site_dir . '/' . $file->filename);
          if (!$file) {
            drupal_set_message('Could not copy the data collection to the directory on the server for storing this file.  This analysis may not execute correctly.', 'error');
          }
          else {
            $submission->data[$cid]['data_collection'] = $file->fid;
          }
        }
      }
    }
    unset($submission->data[$cid]['data_collection_fset']);
    if ($component->type == 'galaxy_pfile') {
      unset($submission->data[$cid]['uploader_fset']);
      unset($submission->data[$cid]['existing_fset']);
      unset($submission->data[$cid]['site_wide_fset']);
    }
    if ($component->type == 'galaxy_pflist') {
      unset($submission->data[$cid]['uploader_fset']);
      unset($submission->data[$cid]['existing_fset']);
    }
    if ($component->type == 'galaxy_sflist') {
      unset($submission->data[$cid]['uploader_fset']);
      unset($submission->data[$cid]['existing_fset']);
    }
  }
}


/**
 * Retrieves the workflow submission report for an admin user.
 *
 * @param int $sid
 *   The webform submission ID.
 */
function tripal_galaxy_submission_admin_report($sid) {

  // Set the breadcrumb.
  $breadcrumb = [];
  $breadcrumb[] = l(t('Home'), '<front>');
  $breadcrumb[] = l(t('Administration'), 'admin');
  $breadcrumb[] = l(t('Tripal'), 'admin/tripal');
  $breadcrumb[] = l(t('Extensions'), 'admin/tripal/extension');
  $breadcrumb[] = l(t('Galaxy'), 'admin/tripal/extension/galaxy');
  $breadcrumb[] = l(t('Job Queue'), 'admin/tripal/extension/galaxy/job-queue');
  drupal_set_breadcrumb($breadcrumb);

  return tripal_galaxy_workflow_report($sid);
}

/**
 * Implements hook_cron().
 */
function tripal_galaxy_cron() {
  $args = [];

  // We only want to execute the following tasks on a specific interval. The
  // cron may be set to run every 30 minutes but some of our Galaxy
  // housekeeping activities only need to run every day at least.  If the
  // tripal_galaxy_cron_last variable has never been used before we'll set
  // a default to just 1 second over the $hours_between_runs.
  $hours_between_runs = variable_get('tripal_galaxy_cron_hours', 24);
  $last_execution = variable_get('tripal_galaxy_cron_last', time() - ($hours_between_runs * 60 * 60 + 1));
  $next_execution = $last_execution + ($hours_between_runs * 60 * 60);

  if (time() > $next_execution) {
    try {
      tripal_galaxy_check_servers();
    }
    catch (Exception $e) {
      drupal_set_message($e->getMessage(), 'error');
      drupal_set_message(t('Cannot disable the workflows'), 'error');
      watchdog_exception('tripal_galaxy', $e);
      return;
    }

    // Remove old histories from the remote tripal server.
    try {
      tripal_galaxy_delete_expired_histories();
    }
    catch (Exception $e) {
      watchdog_exception('tripal_galaxy', $e);
      return;
    }
    variable_set('tripal_galaxy_cron_last', time());
  }
}

/**
 * Checks the remote Galaxy servers to make sure they are up and running.
 */
function tripal_galaxy_check_servers() {
  // Retrieve the list of galaxy servers
  $sql = "SELECT * FROM {tripal_galaxy}";
  $results = db_query($sql);

  while ($result = $results->fetchObject()) {
    $server_status = tripal_galaxy_test_connection(['galaxy_id' => $result->galaxy_id,]);
    if ($server_status === FALSE) {

      // Update status in the db.
      db_update('tripal_galaxy')->fields(['serverstatus' => 'unavailable'])
        ->condition('galaxy_id', $result->galaxy_id, '=')
        ->execute();

      // Put a message on the dashboard.
      $title = t('Galaxy Server %servername was unreachable when tested at %time', [
        '%server' => $result->servername,
        '%time' => format_date(time()),
      ]);
      $details = t('Galaxy Server %servername was unreachable when tested at %time. Please check the server status. If the server is down you may disable the workflows associated with that server by going to the Tripal Galaxy admin page.', [
        '%server' => $result->servername,
        '%time' => format_date(time()),
      ]);
      $actions['Disable Server\'s Workflows'] = 'admin/tripal/extension/galaxy/disable/' . $result->galaxy_id;
      $type = 'Tripal Galaxy';
      $submitter_id = 'tripal_galaxy' . $result->servername . time();
      tripal_add_notification($title, $details, $type, $actions, $submitter_id);
    }
    else {
      if ($server_status === TRUE) {
        db_update('tripal_galaxy')->fields(['serverstatus' => 'available',])
          ->condition('galaxy_id', $result->galaxy_id, '=')
          ->execute();

        // Make sure no notification is up about the server being down.
        $submitter_id = 'tripal_galaxy' . $result->servername;
        $note = db_select('tripal_admin_notfications', 'tan')->fields('tan')
          ->condition('submitter_id', $submitter_id, '=')
          ->execute()
          ->fetchAll();
        if ($note) {
          db_delete('tripal_admin_notfications')
            ->condition('submitter_id', $submitter_id)
            ->execute();
        }
      }
    }
  }
}

/**
 * Checks the status of non completed workflows.
 *
 * This function is meant to be added by cron and run by the TripalJob's system.
 *
 * @param TripalJob $job
 *   An instance of a TripalJob object.
 */
function tripal_galaxy_check_status(TripalJob $job = NULL) {
  // Update the status of running workflows.
  $query = db_select('tripal_galaxy_workflow_submission', 'tgws');
  $query->fields('tgws', [
    'sid',
  ]);
  $query->condition('tgws.status', [
    'Error',
    'Completed',
  ], 'NOT IN');
  $submissions = $query->execute();
  foreach ($submissions as $submission) {
    tripal_galaxy_check_submission_status($submission->sid);
  }

  // Update the status of the workflows to see if any of them were
  // changed on the galaxy server. If os then that means the workflow we
  // currently have may not work.
  $workflows = db_select('tripal_galaxy_workflow', 'tgw')->fields('tgw')->execute();
  $queue = DrupalQueue::get('check_workflow_status');
  while ($workflow = $workflows->fetchObject()) {
    $queue->createItem($workflow);
  }
}

/**
 * Implements hook_mail().
 */
function tripal_galaxy_mail($key, &$message, $params) {
  $site_name = variable_get('site_name', 'Drupal');
  $submission = $params['submission'];
  $title = $params['title'];

  $workflow = $submission->workflow;
  $email_text = tripal_galaxy_get_email_text($workflow);

  switch ($key) {
    case 'submission-started':
      $email_text = tripal_galaxy_untokenize_email_text($submission, 'invoke');
      $message['subject'] = $email_text['subject'];
      $message['body'] = $email_text['body'];
      break;

    case 'submission-ended':
      $email_text = tripal_galaxy_untokenize_email_text($submission, 'success');
      $message['subject'] = $email_text['subject'];
      $message['body'] = $email_text['body'];
      break;

    case 'submission-failed':
      $email_text = tripal_galaxy_untokenize_email_text($submission, 'failure');
      $message['subject'] = $email_text['subject'];
      $message['body'] = $email_text['body'];
      break;
  }
}

/**
 * Replaces tokens in the email text.
 */
function tripal_galaxy_untokenize_email_text($submission, $type) {
  $message = tripal_galaxy_get_email_text($submission->workflow);
  $new_message = [];
  $new_message['subject'] = tripal_galaxy_untokenize_email_line($submission, $message[$type]['subject']);
  $new_message['body'] = [];
  foreach ($message[$type]['body'] as $line) {
    $new_message['body'][] = tripal_galaxy_untokenize_email_line($submission, $line);
  }
  return $new_message;
}

/**
 * A helper function for tripal_galaxy_untokenize_email_text().
 */
function tripal_galaxy_untokenize_email_line($submission, $line) {
  $user = user_load($submission->uid);
  $line = preg_replace('/\[site_name\]/', variable_get('site_name'), $line);
  $line = preg_replace('/\[workflow_title\]/', $submission->node_title ? $submission->node_title : $submission->workflow->workflow_name, $line);
  $line = preg_replace('/\[submission_init\]/', $submission->submit_date ? format_date($submission->submit_date) : '', $line);
  $line = preg_replace('/\[submission_start\]/', $submission->start_time ? format_date($submission->start_time) : '', $line);
  $line = preg_replace('/\[submission_end\]/', $submission->end_time ? format_date($submission->end_time) : '', $line);
  $line = preg_replace('/\[submission_status\]/', $submission->status, $line);
  $line = preg_replace('/\[user_name\]/', $user->name, $line);
  $line = preg_replace('/\[jobs_link\]/', url('/user/' . $user->uid . '/galaxy-jobs', ['absolute' => TRUE]), $line);
  $line = preg_replace('/\[results_link\]/', url('/user/' . $user->uid . '/galaxy-jobs/'. $submission->sid, ['absolute' => TRUE]), $line);

  return $line;
}


/**
 * Retrieves the email content defaults.
 */
function tripal_galaxy_get_email_text($workflow) {

  // Set the defaults.
  $email_text = [
    'success' => [
      'subject' => 'Your job at [site_name] has completed',
      'body' => [
        "You recently submitted a job titled: [workflow_title].",
        "This job has completed.",
        "You may view results of this job at [results_link].",
        "Thank you.",
      ],
      'no_email' => 0
    ],
    'failure' => [
      'subject' => 'Your job at [site_name] has failed',
      'body' => [
        "You recently submitted a job titled: [workflow_title].",
        "This job has failed.",
        "You may view error reports for this job at [jobs_link].",
        "Thank you.",
      ],
      'no_email' => 0
    ],
    'invoke' => [
      'subject' => 'Your job at [site_name] has started',
      'body' => [
        "You recently submitted a job titled: [workflow_title].",
        "This job has started.",
        "You may check the status of all your submitted jobs at [jobs_link].",
        "Thank you.",
      ],
      'no_email' => 0
    ],
  ];

  // Check the settings for the failure email.
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_failure_subject');
  if ($value) {
    $email_text['failure']['subject'] = $value;
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_failure_body');
  if ($value) {
    $email_text['failure']['body'] = explode("\n", $value);
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'no_failure_email');
  if ($value) {
    $email_text['failure']['no_email'] = $value;
  }

  // Check the settings for the success email.
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_success_subject');
  if ($value) {
    $email_text['success']['subject'] = $value;
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_success_body');
  if ($value) {
    $email_text['success']['body'] = explode("\n", $value);
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'no_success_email');
  if ($value) {
    $email_text['success']['no_email'] = $value;
  }

  // Check the settings for the invocation email.
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_invoke_subject');
  if ($value) {
    $email_text['invoke']['subject'] = $value;
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'email_invoke_body');
  if ($value) {
    $email_text['invoke']['body'] = explode("\n", $value);
  }
  $value = tripal_galaxy_get_workflow_setting($workflow, 'no_invoke_email');
  if ($value) {
    $email_text['invoke']['no_email'] = $value;
  }
  return $email_text;
}

/**
 *  Adds a new setting for the workflow.
 */
function tripal_galaxy_get_workflow_setting($workflow, $setting_name) {

  $value = db_select('tripal_galaxy_workflow_settings', 'tgws')
    ->fields('tgws', ['value'])
    ->condition('workflow_id', $workflow->galaxy_workflow_id)
    ->condition('setting_name', $setting_name)
    ->execute()
    ->fetchField();
  return $value;
}

/**
 *  Adds a new setting for the workflow.
 */
function tripal_galaxy_add_workflow_setting($workflow, $setting_name, $value) {

  // The primary keys is set if this is an update.
  $pkeys = [];

  // Create the object for inserting/updating the table.
  $setting = new stdClass();
  $setting->workflow_id = $workflow->galaxy_workflow_id;
  $setting->setting_name = $setting_name;
  $setting->value = $value;

  // Before adding the setting, make sure it doesn't already exists. If so
  // then this is an update.
  $setting_id = db_select('tripal_galaxy_workflow_settings', 'tgws')
    ->fields('tgws', ['setting_id'])
    ->condition('workflow_id', $workflow->galaxy_workflow_id)
    ->condition('setting_name', $setting_name)
    ->execute()
    ->fetchField();
  if ($setting_id) {
    $pkeys = 'setting_id';
    $setting->setting_id = $setting_id;
  }
  $success = drupal_write_record('tripal_galaxy_workflow_settings', $setting, $pkeys);
  if ($success === FALSE) {
    throw new Exception('Could not save setting' . $setting_name);
  }

}

/**
 * Sends an email to the user when a Galaxy job starts.
 *
 * @param int $sid
 *   The Submission ID of the job.
 */
function tripal_galaxy_send_submission_start_mail(int $sid) {
  $submission = tripal_galaxy_get_submission($sid);

  // If the email should not be sent then just return.
  $no_send = tripal_galaxy_get_workflow_setting($submission->workflow, 'no_invoke_email');
  if ($no_send) {
    return;
  }

  $user = user_load($submission->uid);
  $module = 'tripal_galaxy';
  $key = 'submission-started';

  // Specify 'to' and 'from' addresses.
  $to = $user->mail;
  $from = variable_get('site_mail', 'admin@localhost.localdomain');

  // "params" loads in additional context for email content completion in
  // hook_mail(). In this case, we want to pass in the values the user entered
  // into the form, which include the message body in $form_values['message'].
  $params = [
    'submission' => $submission,
    'title' => $submission->webform_title ? $submission->webform_title : $submission->workflow_title,
  ];

  // The language of the e-mail.
  $language = language_default();

  // Whether or not to automatically send the mail when drupal_mail() is called.
  $send = TRUE;

  // Send the mail, and check for success. Note that this does not guarantee
  // message delivery; only that there were no PHP-related issues encountered
  // while sending.
  $result = drupal_mail($module, $key, $to, $language, $params, $from, $send);
  if ($result['result'] != TRUE) {
    watchdog('tripal_galaxy',
      'There was a problem sending your message and it was not sent.', [], WATCHDOG_ERROR);
  }
}

/**
 * Sends an email to the user when a Galaxy job ends.
 *
 * @param int $sid
 *   The Submission ID of the job.
 */
function tripal_galaxy_send_submission_ended_mail(int $sid) {

  $submission = tripal_galaxy_get_submission($sid);

  // If the email should not be sent then just return.
  $no_send = tripal_galaxy_get_workflow_setting($submission->workflow, 'no_success_email');
  if ($no_send) {
    return;
  }

  $user = user_load($submission->uid);
  $module = 'tripal_galaxy';
  $key = 'submission-ended';

  // Specify 'to' and 'from' addresses.
  $to = $user->mail;
  $from = variable_get('site_mail', 'admin@localhost.localdomain');

  // "params" loads in additional context for email content completion in
  // hook_mail(). In this case, we want to pass in the values the user entered
  // into the form, which include the message body in $form_values['message'].
  $params = [
    'submission' => $submission,
    'title' => $submission->webform_title ? $submission->webform_title : $submission->workflow_title,
  ];

  // The language of the e-mail.
  $language = language_default();

  // Whether or not to automatically send the mail when drupal_mail() is called.
  $send = TRUE;

  // Send the mail, and check for success. Note that this does not guarantee
  // message delivery; only that there were no PHP-related issues encountered
  // while sending.
  $result = drupal_mail($module, $key, $to, $language, $params, $from, $send);

  if ($result['result'] != TRUE) {
    db_update('tripal_galaxy_workflow_submission')->fields(array(
      'email' => 'SENT',
    ))
      ->condition('sid', $sid)
      ->execute();
    watchdog('tripal_galaxy', 'There was a problem sending your message and it was not sent.', [], WATCHDOG_ERROR);
  }
  else {
    db_update('tripal_galaxy_workflow_submission')->fields([
      'email' => 'SENT',
    ])
      ->condition('sid', $sid)
      ->execute();
  }
}

/**
 * Sends an email to the user when a Galaxy job failes.
 *
 * @param int $sid
 *   The Submission ID of the job.
 */
function tripal_galaxy_send_submission_failed_mail($sid) {
  $submission = tripal_galaxy_get_submission($sid);

  // If the email should not be sent then just return.
  $no_send = tripal_galaxy_get_workflow_setting($submission->workflow, 'no_failure_email');
  if ($no_send) {
    return;
  }

  $user = user_load($submission->uid);
  $module = 'tripal_galaxy';
  $key = 'submission-failed';

  // Specify 'to' and 'from' addresses.
  $to = $user->mail;
  $from = variable_get('site_mail', 'admin@localhost.localdomain');

  // "params" loads in additional context for email content completion in
  // hook_mail(). In this case, we want to pass in the values the user entered
  // into the form, which include the message body in $form_values['message'].
  $params = [
    'submission' => $submission,
    'title' => $submission->webform_title ? $submission->webform_title : $submission->workflow_title,
  ];

  // The language of the e-mail.
  $language = language_default();

  // Whether or not to automatically send the mail when drupal_mail() is called.
  $send = TRUE;

  // Send the mail, and check for success. Note that this does not guarantee
  // message delivery; only that there were no PHP-related issues encountered
  // while sending.
  $result = drupal_mail($module, $key, $to, $language, $params, $from, $send);
  if ($result['result'] != TRUE) {
    watchdog('tripal_galaxy', 'There was a problem sending your message and it was not sent.', [], WATCHDOG_ERROR);
  }
  else {
    db_update('tripal_galaxy_workflow_submission')->fields([
      'email' => 'SENT',
    ])
      ->condition('sid', $sid)
      ->execute();
  }
}

/**
 * Implements hook_handle_uploaded_file().
 */
function tripal_galaxy_handle_uploaded_file($file, $type) {
  global $user;

  // Split the type into a node ID and form_key.
  list ($id, $form_key) = explode('-', $type);
}



/**
 * Exports a Galaxy workflow webform.
 *
 * @param object $node
 *   A page callback to export galaxy webform as a json file.
 */
function export_tripal_galaxy_workflow($node) {
  $webform = json_encode($node->webform);

  drupal_add_http_header('Content-Type', 'application/json');
  drupal_add_http_header('Content-Disposition', 'attachment; filename="webform-' . $node->type . '-' . $node->nid . '.json";');
  drupal_add_http_header('Content-Length', sprintf('%u', strlen($webform)));

  print($webform);

  exit();
}

/**
 * Imports a Galaxy webform.
 *
 * @param object $node
 *   The Drupal node for the submission.
 */
function import_tripal_galaxy_workflow($node) {
  if (count($node->webform['components']) < 1) {
    drupal_set_message('This is not a valid Galaxy webform. This action only works for Galaxy webform.', 'warning');
    return '';
  }

  if (isset($node->webform['components'][1])) {
    if ($node->webform['components'][1]['form_key'] != 'galaxy_webform') {
      drupal_set_message('This is not a valid Galaxy webform. This action only works for Galaxy webform.', 'warning');
      return '';
    };
  }

  // Store nid and workflow id.
  $workflow_and_node_ids = [
    'nid' => $node->nid,
    'workflow_id' => $node->webform['components'][1]['extra']['workflow_id'],
  ];
  $build_page = [
    'json_markup' => [
      '#markup' => '<h1>Replace Galaxy Webform</h1><p>Import a well-annotated Galaxy webform in JSON format
        to replace this original Galaxy webform.</p>',
    ],
    'form' => drupal_get_form('galaxy_webform_import_form', $workflow_and_node_ids),
  ];

  return $build_page;
}

/**
 * Implements hook_node_access().
 */
function tripal_galaxy_node_access($node, $op, $account = NULL) {
  if (property_exists($node, 'webform')) {
    if (!empty($node->webform['components'])) {
      $component = current($node->webform['components']);
      if ($component['form_key'] === 'galaxy_webform') {
        return user_access('use galaxy', $account) ? NODE_ACCESS_ALLOW : NODE_ACCESS_DENY;
      }
    }
  }

  return NODE_ACCESS_IGNORE;
}

/**
 * Implements hook_views_pre_render().
 *
 * Hook views pre render to hide the 'View Results', 'Re-Run', and
 * 'View Details' links in the user workflow listing found on
 * /user/#/galaxy-jobs.
 */
function tripal_galaxy_views_pre_render(&$view) {
  if ($view->name == 'galaxy_usage') {
    if (isset($view->result[0]) and $view->result[0]->tripal_galaxy_workflow_submission_status == 'deleted') {
      $view->field['ctools_dropdown']->options['fields']['nothing_2'] = NULL;
      $view->field['ctools_dropdown']->options['fields']['nothing_3'] = NULL;
      $view->field['ctools_dropdown']->options['fields']['nothing'] = NULL;
    }
  }
}