tripal/tripal/includes/tripal.importer.inc

<?php


/**
 * Build the form for a TripalImporter implementation.
 */
function tripal_get_importer_form($form, &$form_state, $class) {
  global $user;

  tripal_load_include_importer_class($class);

  $form['importer_class'] = [
    '#type' => 'value',
    '#value' => $class,
  ];

  if ((array_key_exists('file_upload', $class::$methods) and $class::$methods['file_upload'] == TRUE) or
    (array_key_exists('file_local', $class::$methods) and $class::$methods['file_local'] == TRUE) or
    (array_key_exists('file_remote', $class::$methods) and $class::$methods['file_remote'] == TRUE)) {
    $form['file'] = [
      '#type' => 'fieldset',
      '#title' => t($class::$upload_title),
      '#description' => t($class::$upload_description),
      '#weight' => -15,
    ];
  }

  if (array_key_exists('file_upload', $class::$methods) and $class::$methods['file_upload'] == TRUE) {

    $existing_files = tripal_get_user_uploads($user->uid, $class::$file_types);
    if (count($existing_files) > 0) {
      $fids = [0 => '--Select a file--'];
      foreach ($existing_files as $fid => $file) {
        $fids[$fid] = $file->filename . ' (' . tripal_format_bytes($file->filesize) . ') ';
      }
      $form['file']['file_upload_existing'] = [
        '#type' => 'select',
        '#title' => t('Existing Files'),
        '#description' => t('You may select a file that is already uploaded.'),
        '#options' => $fids,
      ];
    }
    $form['file']['file_upload'] = [
      '#type' => 'html5_file',
      '#title' => '',
      '#description' => 'Remember to click the "Upload" button below to send ' .
        'your file to the server.  This interface is capable of uploading very ' .
        'large files.  If you are disconnected you can return, reload the file and it ' .
        'will resume where it left off.  Once the file is uploaded the "Upload ' .
        'Progress" will indicate "Complete".  If the file is already present on the server ' .
        'then the status will quickly update to "Complete".',
      '#usage_type' => 'tripal_importer',
      '#usage_id' => 0,
      '#allowed_types' => $class::$file_types,
      '#cardinality' => $class::$cardinality,
    ];
  }

  if (array_key_exists('file_local', $class::$methods) and $class::$methods['file_local'] == TRUE) {
    $form['file']['file_local'] = [
      '#title' => t('Server path'),
      '#type' => 'textfield',
      '#maxlength' => 5120,
      '#description' => t('If the file is local to the Tripal server please provide the full path here.'),
    ];
  }
  if (array_key_exists('file_remote', $class::$methods) and $class::$methods['file_remote'] == TRUE) {
    $form['file']['file_remote'] = [
      '#title' => t('Remote path'),
      '#type' => 'textfield',
      '#maxlength' => 5102,
      '#description' => t('If the file is available via a remote URL please provide the full URL here.  The file will be downloaded when the importer job is executed.'),
    ];
  }

  if ($class::$use_analysis) {
    // get the list of analyses
    $sql = "SELECT * FROM {analysis} ORDER BY name";
    $org_rset = chado_query($sql);
    $analyses = [];
    $analyses[''] = '';
    while ($analysis = $org_rset->fetchObject()) {
      $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
    }
    $form['analysis_id'] = [
      '#title' => t('Analysis'),
      '#type' => t('select'),
      '#description' => t('Choose the analysis to which the uploaded data will be associated. ' .
        'Why specify an analysis for a data load?  All data comes from some place, even if ' .
        'downloaded from a website. By specifying analysis details for all data imports it ' .
        'provides provenance and helps end user to reproduce the data set if needed. At ' .
        'a minimum it indicates the source of the data.'),
      '#required' => $class::$require_analysis,
      '#options' => $analyses,
      '#weight' => -14,
    ];
  }

  // Retrieve the forms from the custom TripalImporter class
  // for this loader.
  $importer = new $class();
  $element = [];
  $element_form = $importer->form($element, $form_state);
  // Quick check to make sure we had an array returned so array_merge() works.
  if (!is_array($element_form)) {
    $element_form = arry();
  }

  // Merge the custom form with our default one.
  // This way, the custom TripalImporter can use the #weight property
  // to change the order of their elements in reference to the default ones.
  $form = array_merge($form, $element_form);

  $form['button'] = [
    '#type' => 'submit',
    '#value' => t($class::$button_text),
    '#weight' => 10,
  ];
  return $form;
}

/**
 * Validate function for the tripal_get_importer_form form().
 */
function tripal_get_importer_form_validate($form, &$form_state) {

  $class = $form_state['values']['importer_class'];
  tripal_load_include_importer_class($class);

  $file_local = NULL;
  $file_upload = NULL;
  $file_remote = NULL;
  $file_existing = NULL;

  // Get the form values for the file.
  if (array_key_exists('file_local', $class::$methods) and $class::$methods['file_local'] == TRUE) {
    $file_local = trim($form_state['values']['file_local']);
    // If the file is local make sure it exists on the local filesystem.
    if ($file_local) {
      // check to see if the file is located local to Drupal
      $file_local = trim($file_local);
      $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $file_local;
      if (!file_exists($dfile)) {
        // if not local to Drupal, the file must be someplace else, just use
        // the full path provided
        $dfile = $file_local;
      }
      if (!file_exists($dfile)) {
        form_set_error('file_local', t("Cannot find the file on the system. Check that the file exists or that the web server has permissions to read the file."));
      }
    }
  }
  if (array_key_exists('file_upload', $class::$methods) and $class::$methods['file_upload'] == TRUE) {
    $file_upload = trim($form_state['values']['file_upload']);
    if (array_key_exists('file_upload_existing', $form_state['values']) and $form_state['values']['file_upload_existing']) {
      $file_existing = $form_state['values']['file_upload_existing'];
    }
  }
  if (array_key_exists('file_remote', $class::$methods) and $class::$methods['file_remote'] == TRUE) {
    $file_remote = trim($form_state['values']['file_remote']);
  }

  // The user must provide at least an uploaded file or a local file path.
  if ($class::$file_required == TRUE and !$file_upload and !$file_local and !$file_remote and !$file_existing) {
    form_set_error('file_local', t("You must provide a file."));
  }

  // Now allow the loader to do validation of it's form additions.
  $importer = new $class();
  $importer->formValidate($form, $form_state);
}

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

  $run_args = $form_state['values'];
  $class = $form_state['values']['importer_class'];
  tripal_load_include_importer_class($class);

  // Remove the file_local and file_upload args. We'll add in a new
  // full file path and the fid instead.
  unset($run_args['file_local']);
  unset($run_args['file_upload']);
  unset($run_args['file_upload_existing']);
  unset($run_args['form_build_id']);
  unset($run_args['form_token']);
  unset($run_args['form_id']);
  unset($run_args['op']);
  unset($run_args['button']);

  $file_local = NULL;
  $file_upload = NULL;
  $file_remote = NULL;
  $file_existing = NULL;

  // Get the form values for the file.
  if (array_key_exists('file_local', $class::$methods) and $class::$methods['file_local'] == TRUE) {
    $file_local = trim($form_state['values']['file_local']);
  }
  if (array_key_exists('file_upload', $class::$methods) and $class::$methods['file_upload'] == TRUE) {
    $file_upload = trim($form_state['values']['file_upload']);
    if (array_key_exists('file_upload_existing', $form_state['values']) and $form_state['values']['file_upload_existing']) {
      $file_existing = trim($form_state['values']['file_upload_existing']);
    }
  }
  if (array_key_exists('file_remote', $class::$methods) and $class::$methods['file_remote'] == TRUE) {
    $file_remote = trim($form_state['values']['file_remote']);
  }


  // Sumbit a job for this loader.
  $fname = '';
  $fid = NULL;
  $file_details = [];
  if ($file_existing) {
    $file_details['fid'] = $file_existing;
  }
  elseif ($file_local) {
    $fname = preg_replace("/.*\/(.*)/", "$1", $file_local);
    $file_details['file_local'] = $file_local;
  }
  elseif ($file_upload) {
    $file_details['fid'] = $file_upload;
  }
  elseif ($file_remote) {
    $file_details['file_remote'] = $file_remote;
  }
  try {

    // Now allow the loader to do its own submit if needed.
    $importer = new $class();
    $importer->formSubmit($form, $form_state);
    // If the formSubmit made changes to the $form_state we need to update the
    // $run_args info.
    if ($run_args !== $form_state['values']) {
      $run_args = $form_state['values'];
    }

    // If the importer wants to rebuild the form for some reason then let's
    // not add a job.
    if (array_key_exists('rebuild', $form_state) and $form_state['rebuild'] == TRUE) {
      return;
    }

    $importer->create($run_args, $file_details);
    $importer->submitJob();

  } catch (Exception $e) {
    drupal_set_message('Cannot submit import: ' . $e->getMessage(), 'error');
  }
}