form_utils.inc File Reference

Go to the source code of this file.

Functions
	tpps_dynamic_list (array &$form, array &$form_state, $id, array $repeat, array $options=array())
	tpps_form_state_info (array &$new, array &$old)
	tpps_get_ajax_number (array &$state, array $parents, $up, $down, $default=0, $minimum=0, array $options=array())
	tpps_get_ajax_value (array &$state, array $parents, $default=NULL, $file_name="")
	tpps_pre_validate ($accession, $fid, $org_num, $job=NULL)
	tpps_pre_validate_init ($accession=NULL)
	tpps_pre_validate_status ($accession=NULL, $jid=NULL)
	tpps_preserve_valid_file (array &$form_state, $fid, $org_num=NULL, $prefix=NULL)

Detailed Description

Defines useful functions to be used with the TPPS form.

Definition in file form_utils.inc.

Function Documentation

tpps_dynamic_list()

tpps_dynamic_list	(	array &	$form,
		array &	$form_state,
			$id,
		array	$repeat,
		array	$options = array()
	)

Creates a dynamic list fieldset complete with add/remove buttons and ajax.

This function accepts a form object, form state object, an id, and a field to repeat, and creates a fieldset with buttons to add/remove items from the list. This function also supports a variety of additional options, which can be specified in the $options array. The list will be inserted at $form[$id], unless parents are specified in the options, in which case the list will be inserted at $form[...$parents][$id].

Parameters

array	$form	The form array that the new list will be generated for.
array	$form_state	The form state array of the provided form.
string	$id	The id of the dynamic list.
array	$repeat	The field to repeat.
array	$options	Additional options.

Definition at line 29 of file form_utils.inc.

                                                                                                           {
  $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);
}

tpps_form_state_info()

tpps_form_state_info	(	array &	$new,
		array &	$old
	)

Migrates necessary information from the old form state to the new one.

This function is usually only called from tpps_main().

Parameters

array	$new	The new form state to be populated.
array	$old	The old form state with the old information.

Definition at line 290 of file form_utils.inc.

                                                        {
  $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;
}

tpps_get_ajax_number()

tpps_get_ajax_number	(	array &	$state,
		array	$parents,
			$up,
			$down,
			$default = 0,
			$minimum = 0,
		array	$options = array()
	)

Retrieves the value of the number of a tpps_dynamic_list fieldset.

This function first checks the values of the form state, then the saved_values, and finally returns the default if it cannot find the number. This function also accepts an optional $options array, which contains alternative increment values, or functions which return a new number. This can be useful for adding buttons to a dynamic list such as "Add 5 of x".

Parameters

array	$state	The state of the form.
array	$parents	The parents leading to the list number.
string	$up	The #name of the button to increase the list number.
string	$down	The #name of the button to decrease the list number.
int	$default	The default number if the number does not exist.
int	$minimum	The minimum number we are allowed to reach.
array	$options	Optional additional increment values.

Returns

int The ajax number of the dynamic list, or the default number.

Definition at line 157 of file form_utils.inc.

                                                                                                                               {
  // 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;
}

tpps_get_ajax_value()

tpps_get_ajax_value	(	array &	$state,
		array	$parents,
			$default = NULL,
			$file_name = ""
	)

Retrieves the value of a field that may have been altered through ajax.

This function first checks the 'complete form' of the form state, then the saved_values, and finally returns the default if it cannot find the value. If the value we are trying to reach is part of a TPPS managed_file, then we can also pass the file name in order to find saved_values such as 'file-columns', or 'file-no-header'.

Parameters

array	$state	The state of the form.
array	$parents	The parents leading to the list number.
mixed	$default	The default value to return.
string	$file_name	Optional - the name of the file.

Returns

mixed The value of the specified field, or the default value.

Definition at line 236 of file form_utils.inc.

                                                                                              {
  $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;
}

tpps_pre_validate()

tpps_pre_validate	(		$accession,
			$fid,
			$org_num,
			$job = NULL
	)

Executes a TPPS pre-validation job.

Parameters

string	$accession	The accession of the submission being pre-validated.
int	$fid	The id of the file to be pre-validated.
int	$org_num	The organism number that this file is associated with.
mixed	$job	The TripalJob object of the current job.

Definition at line 451 of file form_utils.inc.

                                                                    {
  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);
  }
}

tpps_pre_validate_init()

tpps_pre_validate_init

(

$accession = NULL

)

Initializes TPPS VCF file pre-validation jobs.

This function also requires that the body of the pre-validation request contains the file ids of all of the VCF files that need to be pre-validated.

Parameters

string

$accession

The accession of the submission to pre-validate.

Definition at line 349 of file form_utils.inc.

                                                   {
  $state = tpps_load_submission($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);
}

tpps_pre_validate_status()

tpps_pre_validate_status	(		$accession = NULL,
			$jid = NULL
	)

Check the status of a TPPS pre-validation job.

Parameters

string	$accession	The accession of the submission being pre-validated.
int	$jid	The id of the pre-validation job.

Definition at line 424 of file form_utils.inc.

                                                                  {
  $job = tripal_get_job($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);
}

tpps_preserve_valid_file()

tpps_preserve_valid_file	(	array &	$form_state,
			$fid,
			$org_num = NULL,
			$prefix = NULL
	)

If there have been no form errors, then the file is valid, so preserve it.

Also adds the standardized name and fid to the submission state file_info.

Parameters

array	$form_state	The form state being validated.
int	$fid	The Drupal file ID.
mixed	$org_num	The species number to get the species name from the form state array.
mixed	$prefix	The standardized file name prefix.

Definition at line 328 of file form_utils.inc.

                                                                                             {
  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}";
    }
  }
}