form_utils.inc

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<?php

function tpps_dynamic_list(array &$form, array &$form_state, $id, array $repeat, array $options = array()) {
  $label = $options['label'] ?? $id;
  $parents = $options['parents'] ?? array();
  $number_parents = $parents;
  array_push($number_parents, $id, 'number');
  $up = $options['up'] ?? "Add $label";
  $down = $options['down'] ?? "Remove $label";
  $name_suffix = $options['name_suffix'] ?? "";
  $default = $options['default'] ?? 0;
  $minimum = $options['minimum'] ?? $default;
  $fieldset_title = $options['title'] ?? "$label information:";
  $button_callback = $options['callback'] ?? "tpps_{$id}_callback";
  $list_wrapper = $options['wrapper'] ?? "$id-wrapper";
  $sub_keys = $options['substitute_keys'] ?? array();
  $sub_fields = $options['substitute_fields'] ?? array();
  $replace_pattern = $options['replacement_pattern'] ?? '/!num/';
  $alt_buttons = $options['alternative_buttons'] ?? array();
  $button_weights = $options['button_weights'] ?? array();

  $element = array(
    '#type' => 'fieldset',
    '#tree' => TRUE,
    '#title' => "<div class=\"fieldset-title\">$fieldset_title</div>",
    '#collapsible' => $options['collapsible'] ?? TRUE,
    '#prefix' => "<div id=\"$list_wrapper\">",
    '#suffix' => '</div>',
    'add' => array(
      '#type' => 'button',
      '#button_type' => 'button',
      '#value' => $up,
      '#name' => $up . $name_suffix,
      '#ajax' => array(
        'wrapper' => $list_wrapper,
        'callback' => $button_callback,
      ),
      '#weight' => $button_weights[$up] ?? NULL,
    ),
    'remove' => array(
      '#type' => 'button',
      '#button_type' => 'button',
      '#value' => $down,
      '#name' => $down . $name_suffix,
      '#ajax' => array(
        'wrapper' => $list_wrapper,
        'callback' => $button_callback,
      ),
      '#weight' => $button_weights[$down] ?? NULL,
    ),
  );

  $number_options = array();
  foreach ($alt_buttons as $button => $inc_value) {
    $element[$button] = array(
      '#type' => 'button',
      '#button_type' => 'button',
      '#value' => $button,
      '#name' => $button . $name_suffix,
      '#ajax' => array(
        'wrapper' => $list_wrapper,
        'callback' => $button_callback,
      ),
      '#weight' => $button_weights[$button] ?? NULL,
    );
    $number_options[$button . $name_suffix] = $inc_value;
  }

  $number = tpps_get_ajax_number($form_state, $number_parents, $up . $name_suffix, $down . $name_suffix, $default, $minimum, $number_options);

  $element['number'] = array(
    '#type' => 'hidden',
    '#value' => $number,
  );

  for ($i = 1; $i <= $number; $i++) {
    $instance = $repeat;
    foreach ($sub_fields as $field) {
      if (!is_array($field)) {
        $instance[$field] = preg_replace($replace_pattern, $i, $repeat[$field]);
      }
      else {
        $new_value = preg_replace($replace_pattern, $i, drupal_array_get_nested_value($repeat, $field));
        drupal_array_set_nested_value($instance, $field, $new_value);
      }
    }
    foreach ($sub_keys as $key) {
      $value = drupal_array_get_nested_value($instance, $key);
      drupal_array_set_nested_value($instance, $key, NULL);
      $new_key = array();
      foreach ($key as $key_item) {
        $new_key[] = preg_replace($replace_pattern, $i, $key_item);
      }
      drupal_array_set_nested_value($instance, $new_key, $value);
    }
    $element[$i] = $instance;
  }

  $element_parents = $parents;
  array_push($element_parents, $id);
  drupal_array_set_nested_value($form, $element_parents, $element);
}

function tpps_get_ajax_number(array &$state, array $parents, $up, $down, $default = 0, $minimum = 0, array $options = array()) {
  // Get page number.
  $page = $state['stage'] ?? '';

  // Check form_state values, update if necessary.
  $value_parents = $parents;
  // If the triggering element is an upload/remove file button, then the
  // form_state['values'] array will not be loaded correctly, so we will need
  // to use the 'complete form' array instead.
  $button_name = $state['triggering_element']['#name'] ?? '';
  if (preg_match('/^.*_(upload|remove)_button$/', $button_name)) {
    array_unshift($value_parents, 'complete form');
    $val = drupal_array_get_nested_value($state, $value_parents);
    if (isset($val['#type']) and $val['#type'] == 'hidden') {
      array_push($value_parents, '#value');
    }
  }
  else {
    array_unshift($value_parents, 'values');
  }
  $val = drupal_array_get_nested_value($state, $value_parents);
  if (isset($val) and array_key_exists($button_name, $options)) {
    $increment = $options[$button_name];
    $new_val = $val;
    if (is_int($increment)) {
      $new_val = $val + $increment;
      if ($new_val < $minimum) {
        $new_val = $minimum;
      }
    }
    if (is_string($increment) and function_exists($increment)) {
      $new_val = $increment($button_name, $val);
    }
    drupal_array_set_nested_value($state, $value_parents, $new_val);
  }
  elseif (isset($val) and $button_name == $up) {
    drupal_array_set_nested_value($state, $value_parents, $val + 1);
  }
  elseif (isset($val) and $button_name == $down and $val > $minimum) {
    drupal_array_set_nested_value($state, $value_parents, $val - 1);
  }
  $val = drupal_array_get_nested_value($state, $value_parents);
  if (isset($val)) {
    return $val;
  }

  // Check saved values.
  $saved_value_parents = $parents;
  array_unshift($saved_value_parents, 'saved_values', $page);
  $saved_val = drupal_array_get_nested_value($state, $saved_value_parents);
  if (isset($saved_val)) {
    return $saved_val;
  }

  // Found nothing, return default.
  return $default;
}

function tpps_get_ajax_value(array &$state, array $parents, $default = NULL, $file_name = "") {
  $page = $state['stage'];
  $value_parents = $parents;
  array_unshift($value_parents, 'values');
  $element = drupal_array_get_nested_value($state, $value_parents);
  if (isset($element['#type']) and $element['#type'] != 'fieldset') {
    array_push($value_parents, '#value');
  }
  $val = drupal_array_get_nested_value($state, $value_parents);
  if (isset($val)) {
    return $val;
  }

  $complete_parents = $parents;
  array_unshift($complete_parents, 'complete form');
  $element = drupal_array_get_nested_value($state, $complete_parents);
  if (isset($element['#type']) and $element['#type'] != 'fieldset') {
    array_push($complete_parents, '#value');
  }
  $val = drupal_array_get_nested_value($state, $complete_parents);
  if (isset($val)) {
    return $val;
  }

  $saved_value_parents = $parents;
  if (!empty($file_name)) {
    $saved_value_parents = array();
    $last = '';
    foreach ($parents as $item) {
      if ($last == $file_name) {
        $item = "$file_name-$item";
      }
      $last = $item;
      if ($item == $file_name) {
        continue;
      }
      $saved_value_parents[] = $item;
    }
  }
  array_unshift($saved_value_parents, 'saved_values', $page);
  $saved_val = drupal_array_get_nested_value($state, $saved_value_parents);
  return $saved_val ?? $default;
}

function tpps_form_state_info(array &$new, array &$old) {
  $new['saved_values'] = $old['saved_values'];
  $new['stage'] = $old['stage'];
  $new['accession'] = $old['accession'];
  $new['dbxref_id'] = $old['dbxref_id'];
  $new['stats'] = $old['stats'] ?? NULL;
  $new['ids'] = $old['ids'] ?? NULL;
  $new['tpps_type'] = $old['tpps_type'] ?? NULL;
  $new['file_info'] = $old['file_info'] ?? NULL;
  $new['status'] = $old['status'] ?? NULL;
  $new['updated'] = $old['updated'] ?? time();
  $new['created'] = $old['created'] ?? NULL;
  $new['approved'] = $old['approved'] ?? NULL;
  $new['completed'] = $old['completed'] ?? NULL;
  $new['loaded'] = $old['loaded'] ?? NULL;
  $new['submitting_uid'] = $old['submitting_uid'] ?? NULL;
  $new['job_id'] = $old['job_id'] ?? NULL;
  $new['revised_files'] = $old['revised_files'] ?? NULL;
  $new['admin_comments'] = $old['admin_comments'] ?? NULL;
  $new['alternative_accessions'] = $old['alternative_accessions'] ?? NULL;
  $new['data'] = $old['data'] ?? NULL;
  $new['phenotypes_edit'] = $old['phenotypes_edit'] ?? NULL;
}

function tpps_preserve_valid_file(array &$form_state, $fid, $org_num = NULL, $prefix = NULL) {
  if (!form_get_errors()) {
    $file = file_load($fid);
    file_usage_add($file, 'tpps', 'tpps_project', substr($form_state['accession'], 4));

    if (!empty($org_num) and !empty($prefix)) {
      $species = implode('_', explode(' ', $form_state['saved_values'][TPPS_PAGE_1]['organism'][$org_num]['name']));
      $form_state['file_info'][TPPS_PAGE_3][$file->fid] = "{$prefix}_{$species}";
    }
  }
}

function tpps_pre_validate_init($accession = NULL) {
  $state = tpps_load_submission($accession);
  if (empty($accession) or empty($state)) {
    drupal_json_output("Submission could not be loaded from accession");
    return;
  }
  $params = drupal_get_query_parameters(NULL, array());
  $vcfs = $params['vcfs'] ?? NULL;
  if (!is_array($vcfs) or empty($vcfs)) {
    drupal_json_output("No VCF file ids were provided");
    return;
  }

  global $user;
  $state['vcf_replace'] = array();
  foreach ($vcfs as $org_num => $fid) {
    if (!file_load($fid)) {
      if (!is_string($fid)) {
        drupal_json_output("Could not load one or more VCFs from file ID");
        return;
      }
      elseif (!file_exists($fid)) {
        drupal_json_output("One or more VCF local paths was invalid");
        return;
      }
      else {
        $existing_files = file_load_multiple(FALSE, array('uri' => $fid));
        if (!empty($existing_files)) {
          $file = current($existing_files);
        }
        else {
          $file = new stdClass();
          $file->fid = NULL;
          $file->uri = $fid;
          $file->filename = drupal_basename($fid);
          $file->filemime = file_get_mimetype($file->uri);
          $file->uid = $user->uid;
          $file->status = 0;
          $file = file_save($file);
        }

        $vcfs[$org_num] = $file->fid;
        $state['vcf_replace'][$org_num] = $file->fid;
      }
    }
  }
  if (empty($state['vcf_replace'])) {
    unset($state['vcf_replace']);
  }

  $state['vcf_val_errors'] = array();
  $state['vcf_validated'] = FALSE;
  tpps_update_submission($state);

  $jobs = array();
  foreach ($vcfs as $org_num => $fid) {
    $includes = array();
    $includes[] = module_load_include('inc', 'tpps', 'includes/form_utils');
    $includes[] = module_load_include('inc', 'tpps', 'includes/file_parsing');
    $args = array($accession, $fid, $org_num);
    $jobs[] = tripal_add_job("{$accession} Pre-validate VCF {$fid}", 'tpps', 'tpps_pre_validate', $args, $user->uid, 10, $includes, TRUE);
  }
  drupal_get_messages('status', TRUE);

  drupal_json_output($jobs);
}

function tpps_pre_validate_status($accession = NULL, $jid = NULL) {
  $job = tripal_get_job($jid);

  if ($job->status == 'Completed') {
    $state = tpps_load_submission($accession);
    $job->val_errors = $state['vcf_val_errors'] ?? array();
    if (empty($job->val_errors)) {
      $state['vcf_validated'] = TRUE;
      tpps_update_submission($state);
    }
  }

  drupal_json_output($job);
}

function tpps_pre_validate($accession, $fid, $org_num, $job = NULL) {
  if (empty($job)) {
    return;
  }
  $job->logMessage("[INFO] TGDR Accession: $accession");
  $job->logMessage("[INFO] VCF File ID: $fid");
  $job->logMessage("[INFO] Organism Number: $org_num");
  $vcf_file = file_load($fid);
  if (!$vcf_file) {
    $job->logMessage("[ERROR] VCF File failed to load", array(), TRIPAL_ERROR);
    return;
  }
  $job->logMessage("[INFO] VCF File Location: {$vcf_file->uri}");

  $state = tpps_load_submission($accession);
  if (empty($state['saved_values'][TPPS_PAGE_3]['tree-accession']['check'])) {
    $species_index = 'species-1';
  }
  else {
    $species_index = "species-$org_num";
  }
  $tree_accession_file = $state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file'];
  $id_col_accession_name = $state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file-groups']['Tree Id']['1'];
  $accession_ids = tpps_parse_file_column($tree_accession_file, $id_col_accession_name);

  $job->logMessage("[INFO] Extracting VCF archive...");
  $location = tpps_get_location($vcf_file->uri);
  $job->logMessage("[INFO] Opening $location...");
  $vcf_content = gzopen($location, 'r');
  $stocks = array();
  while (($vcf_line = gzgets($vcf_content)) !== FALSE) {
    if (preg_match('/#CHROM/', $vcf_line)) {
      $vcf_line = explode("\t", $vcf_line);
      for ($j = 9; $j < count($vcf_line); $j++) {
        $stocks[] = trim($vcf_line[$j]);
      }
      break;
    }
  }

  $state_errors = $state['vcf_val_errors'] ?? array();
  if (count($stocks) == 0) {
    $message = "unable to parse Plant Identifiers. The format of your VCF file must be invalid";
    $job->logMessage("[ERROR] $message", array(), TRIPAL_ERROR);
    $state_errors[] = "Genotype VCF File: $message";
  }
  else {
    $missing_plants = array();
    foreach ($stocks as $stock_id) {
      if (array_search($stock_id, $accession_ids) === FALSE) {
        $missing_plants[] = $stock_id;
      }
    }
    if (count($missing_plants) > 0) {
      $missing_plants = implode(', ', $missing_plants);
      $message = "We found Plant Identifiers in your VCF file that were not present in your accession file. Please either add these plants to your accession file or remove them from your VCF file. The missing plants are: {$missing_plants}.";
      $job->logMessage("[ERROR] $message", array(), TRIPAL_ERROR);
      $state_errors[] = "Genotype VCF File: $message";
    }
  }

  if (empty($state_errors)) {
    $job->logMessage("[INFO] VCF Validated successfully - no errors!");
  }
  else {
    $state['vcf_val_errors'] = $state_errors;
    tpps_update_submission($state);
  }
}