submissions.inc

Go to the documentation of this file.

<?php

function tpps_load_submission($accession, $state = TRUE) {
  $result = db_select('tpps_submission', 's')
    ->fields('s')
    ->condition('accession', $accession)
    ->range(0, 1)
    ->execute()->fetchObject();

  if ($result) {
    if ($state) {
      return unserialize($result->submission_state);
    }
    return $result;
  }

  // Search for alternative accessions.
  $query = db_select('tpps_submission', 's');
  $query->join('tpps_submission_dbxref', 's_dbx', 's.tpps_submission_id = s_dbx.tpps_submission_id');
  $query->join('chado.dbxref', 'dbx', 'dbx.dbxref_id = s_dbx.dbxref_id');
  $query->fields('s');
  $query->condition('dbx.accession', $accession);
  $query->condition('s.status', 'Approved');
  $query->range(0, 1);
  $query = $query->execute();
  $result = $query->fetchObject();

  if ($result) {
    if ($state) {
      return unserialize($result->submission_state);
    }
    return $result;
  }

  // Provide legacy support for older TPPS submissions.
  global $user;
  $state = variable_get('tpps_incomplete_' . $user->mail . $accession, NULL);
  if (!empty($state)) {
    return $state;
  }
  else {
    return variable_get('tpps_complete_' . $user->mail . $accession, NULL);
  }
}

function tpps_load_submission_multiple(array $conditions = array(), $state = TRUE) {
  $submissions = array();
  $query = db_select('tpps_submission', 's')
    ->fields('s');

  if (!empty($conditions)) {
    foreach ($conditions as $key => $cond) {
      if (!empty($cond)) {
        if (!is_array($cond)) {
          $query->condition($key, $cond);
        }
        else {
          $or = db_or();
          foreach ($cond as $item) {
            $or->condition($key, $item);
          }
          $query->condition($or);
        }
      }
    }
  }

  $results = $query->execute();
  while (($result = $results->fetchObject())) {
    if ($state) {
      $submissions[] = unserialize($result->submission_state);
      continue;
    }
    $submissions[] = $result;
  }
  return $submissions;
}

function tpps_create_submission(array $state, $uid) {
  $values = array(
    'uid' => $uid,
    'status' => 'Incomplete',
    'accession' => $state['accession'],
    'dbxref_id' => $state['dbxref_id'],
    'submission_state' => serialize($state),
  );

  db_insert('tpps_submission')
    ->fields($values)
    ->execute();

  if ((!isset($state['tpps_type']) or $state['tpps_type'] != 'tppsc')) {
    tpps_submission_add_tag($state['accession'], 'TPPS');
  }
  else {
    tpps_submission_add_tag($state['accession'], 'TPPSc');
  }
}

function tpps_change_tgdr_number($old_accession, $new_accession, TripalJob $job = NULL) {
  $job->logMessage('[INFO] Clearing database for study ' . $old_accession);
  $job->setInterval(1);
  // Clear the db of all data for the old study accession
  tpps_submission_clear_db($old_accession);

  $job->logMessage('[INFO] Alter submission state data from ' . $old_accession . ' to ' . $new_accession);
  // Update the form state data for the study
  $submission = tpps_load_submission($old_accession, FALSE);
  $state = unserialize($submission->submission_state);

  $job->logMessage('Original submission data for ' . $old_accession);
  $job->logMessage(print_r($state, true));

  // Update the TGDR with the new_accession
  // First encode to JSON before string replacement
  $state_json = json_encode($state);

  // Now replace the old accession with the new accession
  $state_json = str_replace($old_accession,$new_accession,$state_json);

  // Now convert JSON back to an array
  $state = json_decode($state_json,true);



  $job->logMessage('New submission data for ' . $new_accession);
  $job->logMessage(print_r($state, true));

  // This function will not work here because it tries to update
  // a non existing TGDR (the new one has not been created as yet)
  // The update SQL after this, will make it exist because
  // it renames the old tgdr number to the new tgdr number
  // So instead of this function tpps_update_submission, manually do it
  // tpps_update_submission($state);

  $options['status'] = 'Approved';
  $state['updated'] = time();
  $options['submission_state'] = serialize($state);

  db_update('tpps_submission')
    ->fields($options)
    ->condition('accession', $old_accession)
    ->execute();  


  $job->logMessage('[INFO] Update tpps_submission table study ' . $old_accession . ' to ' . $new_accession);
  // Now change the accession number in the tpps_submission table
  $transaction = db_transaction();
  try {
    chado_query('UPDATE tpps_submission SET accession = :new_accession WHERE accession = :old_accession', array(
      ':new_accession' => $new_accession,
      ':old_accession' => $old_accession
    )); 
  }
  catch (\Exception $e) {
    $transaction->rollback();
    throw $e;
  }

  $job->logMessage('Completed! The next job in the queue should reimport the study data for ' . $new_accession);
}

function tpps_update_submission(array $state, array $options = array()) {
  if (empty($options['status']) and !empty($state['status'])) {
    $options['status'] = $state['status'];
  }
  $state['updated'] = time();
  $options['submission_state'] = serialize($state);

  
  // dpm($options);
  // dpm($state['accession']);
  

  db_update('tpps_submission')
    ->fields($options)
    ->condition('accession', $state['accession'])
    ->execute();
}

function tpps_delete_submission($accession, $redirect = TRUE) {
  global $user;
  $submission = tpps_load_submission($accession, FALSE);
  $dbxref_id = $submission->dbxref_id;
  $state = unserialize($submission->submission_state);
  db_delete('tpps_submission')
    ->condition('accession', $accession)
    ->execute();
  if (empty($state['saved_values']['frontpage']['use_old_tgdr'])) {
    db_delete('chado.dbxref')
      ->condition('dbxref_id', $dbxref_id)
      ->execute();
  }
  if ($redirect) {
    drupal_goto("user/{$user->uid}/tpps");
  }
}

function tpps_submission_add_alternative_accession(array $state, $alt_accession) {
  $tpps_local_db = variable_get('tpps_local_db');
  if (!is_array($alt_accession)) {
    $alt_accession = array($alt_accession);
  }

  $state_id = tpps_load_submission($state['accession'], FALSE)->tpps_submission_id;

  // Remove the existing alternative accessions.
  db_delete('tpps_submission_dbxref')
    ->condition('tpps_submission_id', $state_id)
    ->execute();

  foreach ($alt_accession as $acc) {
    $dbx = chado_select_record('dbxref', array('*'), array(
      'db_id' => $tpps_local_db->db_id,
      'accession' => $acc,
    ));
    $dbxref_id = current($dbx)->dbxref_id ?? NULL;

    if (empty($dbxref_id)) {
      $dbx = chado_insert_record('dbxref', array(
        'db_id' => $tpps_local_db->db_id,
        'accession' => $acc,
      ));
      $dbxref_id = $dbx['dbxref_id'];
    }

    db_insert('tpps_submission_dbxref')
      ->fields(array(
        'tpps_submission_id' => $state_id,
        'dbxref_id' => $dbxref_id,
      ))
      ->execute();
  }
}

function tpps_submission_tag_manage() {

  $query = db_select('tpps_tag', 't')
    ->fields('t')
    ->execute();

  $rows = array();
  while (($result = $query->fetchObject())) {
    $color = !empty($result->color) ? $result->color : 'white';
    $edit_link = $result->static ? "" : "<a href=\"tpps-tag/edit/{$result->tpps_tag_id}\">edit</a>";
    $rows[$result->tpps_tag_id] = array(
      "<span class=\"tag\" style=\"background-color:$color\"><span class=\"tag-text\">{$result->name}</span></span>",
      $result->name,
      $color,
      $edit_link,
    );
  }

  ksort($rows);

  $vars = array(
    'header' => array(
      'Tag',
      'Name',
      'Color',
      '',
    ),
    'rows' => $rows,
    'attributes' => array(
      'class' => array('view'),
      'id' => 'tpps_table_display',
    ),
    'caption' => '',
    'colgroups' => NULL,
    'sticky' => FALSE,
    'empty' => '',
  );

  $output = theme('table', $vars);

  drupal_add_js(drupal_get_path('module', 'tpps') . TPPS_JS_PATH);
  drupal_add_css(drupal_get_path('module', 'tpps') . TPPS_CSS_PATH);

  return $output;
}

function tpps_submission_tag_create(array $form, array &$form_state) {
  // This will add the color picker to the TPPS submission tags edit-color
  // field id.
  drupal_add_js('https://cdnjs.cloudflare.com/ajax/libs/tinyColorPicker/1.1.1/jqColorPicker.min.js', 'external');
  drupal_add_js(drupal_get_path('module', 'tpps') . '/js/tag_colorpicker.js');

  $form['name'] = array(
    '#type' => 'textfield',
    '#title' => t('Name'),
    '#description' => t('The name of the new tag'),
    '#required' => TRUE,
    '#prefix' => '<a href="/tpps-tag">Back to TPPS Submission Tags page</a>',
  );

  $form['color'] = array(
    '#type' => 'textfield',
    '#title' => t('Color'),
    '#description' => t('The color of the new tag. Can be the name of a color, like "red" or "blue", or can be a hexidecimal color like "#FFFFFF" or "#A2C32F". Hexidecimal colors must start with the "#" character.'),
    '#required' => TRUE,
    '#suffix' => '<div id="color-picker"><a>Toggle Color Picker</a></div>',
  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => t('Submit'),
  );

  return $form;
}

function tpps_submission_tag_create_validate(&$form, &$form_state) {
  $result = db_select('tpps_tag', 't')
    ->fields('t')
    ->condition('name', $form_state['values']['name'], 'ILIKE')
    ->range(0, 1)
    ->execute()->fetchObject();
  if (!empty($result)) {
    form_set_error('name', t("A tag already exists with this name. Please select a different name or use the existing tag."));
  }
}

function tpps_submission_tag_create_submit($form, &$form_state) {
  db_insert('tpps_tag')
    ->fields(array(
      'name' => $form_state['values']['name'],
      'color' => $form_state['values']['color'],
    ))
    ->execute();
  drupal_goto('tpps-tag');
}

function tpps_submission_tag_edit(array $form, array &$form_state, $tag_id = NULL) {
  if (empty($tag_id)) {
    drupal_goto('tpps-tag');
  }

  $tag = db_select('tpps_tag', 't')
    ->fields('t')
    ->condition('tpps_tag_id', $tag_id)
    ->range(0, 1)
    ->execute()->fetchObject();

  if (empty($tag) or $tag->static) {
    drupal_goto('tpps-tag');
  }

  $form = tpps_submission_tag_create($form, $form_state);

  $form['name']['#default_value'] = $tag->name;
  $form['color']['#default_value'] = $tag->color;

  $form['id'] = array(
    '#type' => 'hidden',
    '#value' => $tag_id,
  );

  return $form;
}

function tpps_submission_tag_edit_validate(&$form, &$form_state) {
  $result = db_select('tpps_tag', 't')
    ->fields('t')
    ->condition('name', $form_state['values']['name'], 'ILIKE')
    ->condition('tpps_tag_id', $form_state['values']['id'], '!=')
    ->range(0, 1)
    ->execute()->fetchObject();
  if (!empty($result)) {
    form_set_error('name', t("A tag already exists with this name. Please select a different name or use the existing tag."));
  }
}

function tpps_submission_tag_edit_submit($form, &$form_state) {
  db_update('tpps_tag')
    ->fields(array(
      'name' => $form_state['values']['name'],
      'color' => $form_state['values']['color'],
    ))
    ->condition('tpps_tag_id', $form_state['values']['id'])
    ->execute();
  drupal_goto('tpps-tag');
}

function tpps_submission_get_tags($accession) {
  $query = db_select('tpps_submission_tag', 'st');
  $query->join('tpps_submission', 's', 's.tpps_submission_id = st.tpps_submission_id');
  $query->join('tpps_tag', 't', 't.tpps_tag_id = st.tpps_tag_id');
  $query->fields('t');
  $query->condition('s.accession', $accession);
  $query = $query->execute();
  $results = array();
  while (($result = $query->fetchObject())) {
    $results[$result->tpps_tag_id] = array(
      'id' => $result->tpps_tag_id,
      'name' => $result->name,
      'color' => $result->color,
      'static' => $result->static,
    );
  }
  return $results;
}

function tpps_submission_clear_default_tags($accession) {
  $tags = array(
    'Genotype',
    'Phenotype',
    'Environment',
  );
  foreach ($tags as $tag) {
    tpps_submission_remove_tag($accession, $tag);
  }
}

function tpps_submission_add_remove_tag($type, $accession, $tag) {
  $result = db_select('tpps_tag', 't')
    ->fields('t')
    ->condition('tpps_tag_id', $tag)
    ->range(0, 1)
    ->execute()->fetchObject();

  if ($result->static) {
    drupal_goto('tpps-tag');
  }

  if ($type == 'add') {
    tpps_submission_add_tag($accession, $tag);
  }
  if ($type == 'remove') {
    tpps_submission_remove_tag($accession, $tag);
  }
}

function tpps_submission_add_tag($accession, $tag) {
  if (gettype($tag) == 'string') {
    $id = tpps_get_tag_id($tag);
    if (!empty($id)) {
      $tag = $id;
    }
  }

  $tags = tpps_submission_get_tags($accession);
  if (!array_key_exists($tag, $tags)) {
    db_insert('tpps_submission_tag')
      ->fields(array(
        'tpps_submission_id' => tpps_load_submission($accession, FALSE)->tpps_submission_id,
        'tpps_tag_id' => $tag,
      ))
      ->execute();
  }
}

function tpps_submission_remove_tag($accession, $tag) {
  if (gettype($tag) == 'string') {
    $id = tpps_get_tag_id($tag);
    if (!empty($id)) {
      $tag = $id;
    }
  }
  db_delete('tpps_submission_tag')
    ->condition('tpps_submission_id', tpps_load_submission($accession, FALSE)->tpps_submission_id)
    ->condition('tpps_tag_id', $tag)
    ->execute();
}

function tpps_get_tag_id($name) {
  $result = db_select('tpps_tag', 't')
    ->fields('t', array('tpps_tag_id'))
    ->condition('name', $name)
    ->range(0, 1)
    ->execute()->fetchObject();

  if ($result) {
    return $result->tpps_tag_id;
  }
  return FALSE;
}

function tpps_submission_rename_files($accession) {
  $state = tpps_load_submission($accession);
  if (!empty($state['file_info'])) {
    $state['files'] = array();
    foreach ($state['file_info'] as $page_files) {
      foreach ($page_files as $fid => $name) {
        $state['files'][] = $fid;
        if ($name === '#NO_RENAME') {
          continue;
        }
        $old_file = file_load($fid);
        if ($old_file->uri[0] != '/') {
          $old_path = file_create_url($old_file->uri);
          // Prepare new file_name.
          $file_load = file_load($fid);
          $new_filename = $accession .'_'.$name . "." . tpps_get_path_extension($file_load->uri);
          if (!preg_match('/^(.*\/)(.*)$/', $new_name, $matches)) {
            preg_match('/^(.*\/).*$/', $file->uri, $matches);
            $new_filename = $matches[1] . $new_filename;
          }
          // Check if file already exists then return that file.
          if ($new_filename != '') {
            $result = db_query('SELECT f.fid
            FROM {file_managed} f WHERE f.uri = :uri', array(':uri' => $new_filename));
            $record = $result->fetchObject();
          }
          
          if(isset($record)) {
            $file = file_load($record->fid);
          }
          else {
            $file = tpps_rename_file($fid, "{$accession}_{$name}");
            $file->status = FILE_STATUS_PERMANENT;
            $file = file_save($file);
          }
          
          $new_path = file_create_url($file->uri);
          chado_update_record('projectprop', array(
            'project_id' => $state['ids']['project_id'],
            'value' => $old_path,
          ), array(
            'value' => $new_path,
          ));
        }
        if (!empty($state['revised_files'][$fid])) {
          $rev_fid = $state['revised_files'][$fid];
          $state['files'][] = $rev_fid;
          $file = tpps_rename_file($rev_fid, "{$accession}_{$name}_revised");
          $file->status = FILE_STATUS_PERMANENT;
          file_save($file);
        }
      }
    }
    tpps_update_submission($state);
  }
}

function tpps_submission_clear_db($accession) {
  $state = tpps_load_submission($accession);
  $state['file_rank'] = 0;
  $project_id = $state['ids']['project_id'] ?? NULL;
  if (empty($project_id)) {
    return FALSE;
  }
  if (empty($accession)) {
    throw new Exception('Accession cannot be empty');
  }

  $stocks_sql = "SELECT stock_id FROM chado.project_stock WHERE project_id = $project_id";
  chado_query("UPDATE chado.project_dbxref SET is_current = FALSE WHERE project_id = $project_id");
  chado_query("DELETE FROM chado.project_organism WHERE project_id = $project_id");
  chado_query("DELETE FROM chado.project_pub WHERE project_id = $project_id");
  chado_query("DELETE FROM chado.projectprop WHERE project_id = $project_id");
  db_query("DELETE FROM public.tpps_project_file_managed WHERE project_id = $project_id");
  chado_query("DELETE FROM chado.phenotype_cvterm WHERE phenotype_id IN (SELECT phenotype_id from chado.stock_phenotype WHERE stock_id in ($stocks_sql))");
  chado_query("DELETE FROM chado.phenotype_to_synonym WHERE phenotype_id IN (SELECT phenotype_id FROM chado.stock_phenotype WHERE stock_id IN ($stocks_sql))");
  chado_query("DELETE FROM chado.phenotype WHERE phenotype_id IN (SELECT phenotype_id FROM chado.stock_phenotype WHERE stock_id IN ($stocks_sql))");
  chado_query("DELETE FROM chado.genotype_call WHERE project_id = $project_id");
  chado_query("DELETE FROM chado.stock_genotype WHERE stock_id IN ($stocks_sql)");
  chado_query("DELETE FROM chado.stock_phenotype WHERE stock_id IN ($stocks_sql)");
  chado_query("DELETE FROM chado.stock WHERE stock_id IN ($stocks_sql)");
  chado_query("DELETE FROM chado.phenotype WHERE uniquename LIKE '" . $accession ."-%';");
  echo "FINISHED DB CLEAR DELETES\n";

  // Force delete stock just in case by study accession name
  // Make sure to ensure $accession is properly populated before doing this
  if(strpos($accession,'TGDR') !== FALSE && strlen($accession) >= 7) {
    chado_query("DELETE FROM chado.stock WHERE uniquename LIKE :accession", [
      ':accession' => $accession . '%'
    ]);
  }

  $state['ids'] = array('project_id' => $project_id);
  tpps_update_submission($state);
  return TRUE;
}

function tpps_submission_update_all_stats(array &$form_state) {
  for ($i = 1; $i <= 4; $i++) {
    $form_state['values'] = $form_state['saved_values'][$i];
    $form_state['stage'] = $i;
    tpps_submission_update_stats($form_state);
  }
}

function tpps_submission_update_stats(array &$form_state) {
  switch ($form_state['stage']) {
    case TPPS_PAGE_1:
      $form_state['stats']['author_count'] = $form_state['values']['publication']['secondaryAuthors']['number'] + 1;
      if (!empty($form_state['values']['publication']['secondaryAuthors']['check'])) {
        $form_state['stats']['author_count'] = tpps_file_len($form_state['values']['publication']['secondaryAuthors']['file']);
      }

      $form_state['stats']['species_count'] = $form_state['values']['organism']['number'];
      break;

    case TPPS_PAGE_2:
      if (empty($form_state['tpps_type']) or $form_state['tpps_type'] == 'tpps') {
        $start = new DateTime("{$form_state['values']['StartingDate']['year']}-{$form_state['values']['StartingDate']['month']}");
        $end = new DateTime("{$form_state['values']['EndingDate']['year']}-{$form_state['values']['EndingDate']['month']}");
        $dur = date_diff($start, $end);
        $form_state['stats']['duration'] = $dur->format('%y years %m months');
      }
      break;

    case TPPS_PAGE_3:
      $form_state['stats']['tree_count'] = 0;
      for ($i = 1; $i <= $form_state['stats']['species_count']; $i++) {
        $form_state['stats']['tree_count'] += tpps_file_len($form_state['values']['tree-accession']["species-$i"]['file']);
        $form_state['stats']['tree_count'] += $form_state['values']['tree-accession']["species-$i"]['file-no-header'];
        if ($form_state['stats']['species_count'] == 1 or empty($form_state['values']['tree-accession']['check'])) {
          break;
        }
      }
      break;

    case TPPS_PAGE_4:
      $form_state['stats']['phenotype_count'] = 0;
      $form_state['stats']['unique_phenotypes'] = 0;
      for ($i = 1; $i <= $form_state['stats']['species_count']; $i++) {
        $phenotype = $form_state['values']["organism-$i"]['phenotype'] ?? NULL;
        $form_state['stats']['unique_phenotypes'] += $phenotype['phenotypes-meta']['number'] ?? 0;
        if (!empty($phenotype['file']) and file_load($phenotype['file'])) {
          $rows = tpps_file_len($phenotype['file']) + !empty($phenotype['file-no-header']);
          if ($phenotype['format'] == 0) {
            $phenotype_file_name_cols = $phenotype['file-groups']['Phenotype Data']['0'];
            $form_state['stats']['phenotype_count'] += $rows * count($phenotype_file_name_cols);
          }
          else {
            $form_state['stats']['phenotype_count'] += $rows;
          }

          if (!empty($phenotype['metadata']) and file_load($phenotype['metadata'])) {
            $form_state['stats']['unique_phenotypes'] += tpps_file_len($phenotype['metadata']) + !empty($phenotype['metadata-no-header']);
          }

          continue;
        }
        if (!empty($phenotype['iso']) and file_load($phenotype['iso'])) {
          $headers = tpps_file_headers($phenotype['iso']);
          while (($k = array_search(NULL, $headers))) {
            unset($headers[$k]);
          }
          $num_unique_columns = count(array_unique($headers)) - 1;
          $rows = tpps_file_len($phenotype['iso']);
          $form_state['stats']['phenotype_count'] += $rows * $num_unique_columns;
        }
      }
      break;

    default:
      break;
  }
}

function tpps_submission_edit_publication(array $form, array &$form_state, $accession = NULL) {
  global $base_url;
  $state = tpps_load_submission($accession);

  $form['accession'] = array(
    '#type' => 'hidden',
    '#value' => $accession,
  );

  $form['status'] = array(
    '#type' => 'select',
    '#title' => t('Publication Status'),
    '#options' => array(
      0 => t('- Select -'),
      'In Preparation or Submitted' => t('In Preparation or Submitted'),
      'In Press' => t('In Press'),
      'Published' => t('Published'),
    ),
    '#default_value' => $state['saved_values'][TPPS_PAGE_1]['publication']['status'],
    '#required' => TRUE,
    '#prefix' => "<a href=\"$base_url/tpps/details/$accession\">Back to TPPS Details Page</a>",
  );

  $year_options = array(0 => '- Select -');
  for ($i = 1990; $i <= date('Y'); $i++) {
    $year_options[$i] = "$i";
  }

  $form['year'] = array(
    '#type' => 'select',
    '#title' => t('Year of Publication'),
    '#options' => $year_options,
    '#description' => t('If your publication has not been published yet, please choose the expected year of publication.'),
    '#default_value' => $state['saved_values'][TPPS_PAGE_1]['publication']['year'],
    '#required' => TRUE,
  );

  $form['journal'] = array(
    '#type' => 'textfield',
    '#title' => t('Journal'),
    '#autocomplete_path' => 'tpps/autocomplete/journal',
    '#default_value' => $state['saved_values'][TPPS_PAGE_1]['publication']['journal'],
    '#required' => TRUE,
  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => t('Submit'),
  );

  return $form;
}

function tpps_submission_edit_publication_validate(&$form, &$form_state) {
  if (empty($form_state['values']['status'])) {
    form_set_error('status', t('Publication Status: field is required.'));
  }
  if (empty($form_state['values']['year'])) {
    form_set_error('year', t('Publication Year: field is required.'));
  }
}

function tpps_submission_edit_publication_submit($form, &$form_state) {
  $accession = $form_state['values']['accession'];
  $state = tpps_load_submission($accession);
  $submit_job = FALSE;

  if ($state['saved_values'][TPPS_PAGE_1]['publication']['status'] != $form_state['values']['status']) {
    $state['saved_values'][TPPS_PAGE_1]['publication']['status'] = $form_state['values']['status'];
    $submit_job = TRUE;
  }

  if ($state['saved_values'][TPPS_PAGE_1]['publication']['year'] != $form_state['values']['year']) {
    $state['saved_values'][TPPS_PAGE_1]['publication']['year'] = $form_state['values']['year'];
    $submit_job = TRUE;
  }

  if ($state['saved_values'][TPPS_PAGE_1]['publication']['journal'] != $form_state['values']['journal']) {
    $state['saved_values'][TPPS_PAGE_1]['publication']['journal'] = $form_state['values']['journal'];
    $submit_job = TRUE;
  }

  if ($submit_job) {
    module_load_include('php', 'tpps', 'forms/submit/submit_all');

    $includes = array();
    $includes[] = module_load_include('php', 'tpps', 'forms/submit/submit_all');
    $includes[] = module_load_include('inc', 'tpps', 'includes/file_parsing');
    $args = array($accession);
    $jid = tripal_add_job("Update Publication Information - $accession", 'tpps', 'tpps_submit_all', $args, $state['submitting_uid'], 10, $includes, TRUE);
    $state['job_id'] = $jid;
    tpps_update_submission($state);
  }
}