dataset_upload.module

<?php
function dataset_upload_menu() {
  $items['dataset_upload/form'] = array(
    'title' => t('Dataset upload form'),
    'page callback' => 'dataset_upload_form',
    'access arguments' => array('access content'),
    'access callback' => TRUE,
    'description' => t('Dataset uplaod and validation form'),
    'type' => MENU_CALLBACK,
  );
  return $items;
}

//only logged user can submit the dataset
function ask_for_login($calling_uri) {
  global $user; 
  if (!($user->uid)) {
    $dest = drupal_get_destination();
    drupal_set_message(t('You need to login or register to validate and upload your dataset'), 'error');
    drupal_goto('user/login', array('query' => $calling_uri));
  }
}

function dataset_upload_form() {
  ask_for_login(drupal_get_destination()); 
  return drupal_get_form('dataset_upload_multipage_form');
}

function dataset_upload_multipage_form($form, $form_state) {
  // Display page 2 if $form_state['storage']['page_two'] is set
  if (isset($form_state['storage']['page_two'])) {
    return dataset_upload_multipage_form_page_two($form, $form_state);
  }

  $form = array();
  $form['creation'] = array(
    '#type' => 'fieldset',
    //'#title' => t('File validation'),
    '#description' => t('Before you upload your dataset make sure you have validated it against the IOOS compliance checker. This service is provided by this portal. 
                         Your dataset will be checked against CF-1.6 and ACDD-1.3 standards. <br> If your dataset is not compliant it will not be accepted for upload 
                         and your submission will fail.'),
  );

  $form['creation']['file'] = array(
    '#type' => 'managed_file',
    '#title' => t('Upload Your File'),
    //'#required' => TRUE,
    '#upload_validators' => array(
      'file_validate_extensions' => array('nc'),
      // IMPORTANT for allowing file upload: 
      // this works only when changing the /etc/php5/apache2/php.ini post_max_size and filesize in apache
      'file_validate_size' => array(200 * 1024 * 1024),
    ),
    '#upload_location' => 'public://dataset_upload_folder/',
  );
  //$form += dataset_upload_add_submit_buttons($form_state);
  $form['next'] = array(
    '#type' => 'submit',
    '#value' => 'Next >>',
  );
  $form['#validate'][] = 'dataset_upload_multipage_p1_validate';
  return $form;
}

function dataset_upload_multipage_p1_validate($form, &$form_state) {
 //only validates page1
 //if (isset($form_state['storage']['page_two'])) {
 //   return;
 // }
  $fname = $form['creation']['file'];
  $fid = $fname["#file"]->fid;
  $uri = $fname["#file"]->uri;  //public://dataset_upload_folder/t.nc   
  $path = explode("://", $uri)[1];  //dataset_upload_folder/t.nc
  $name = explode("dataset_upload_folder/", $uri)[1]; //t.nc
  $fdir = drupal_realpath('public://'); // /var/www/multisite/sites/mysite/files

  //pass filename
  $form_state['dataset_fid'] = $fname["#file"]->fid;
  $form_state['dataset_fname'] = $fname["#file"]->filename;


  //define cf output
  $ex_out_cf = $fdir.'/dataset_upload_folder/'.$name.'_cf.html';
  //define acdd output
  $ex_out_acdd = $fdir.'/dataset_upload_folder/'.$name.'_acdd.html';
  //define nc_to_mmd output
  $ex_out_nctommd = $fdir.'/dataset_upload_folder/'.$name.'.xml';

  //Run the compliant checker
  exec('compliance-checker -v --format=html --output='.$ex_out_cf.' --test=cf:1.6 '.$fdir.'/'.$path, $out, $status1);
  exec('compliance-checker -v --format=html --output='.$ex_out_acdd.' --test=acdd '.$fdir.'/'.$path, $out, $status2);
  //$status = $status1 + $status2; 
  //$ex_out = file_get_contents($ex_out_cf).file_get_contents($ex_out_acdd);
  $status = $status1; 
  $ex_out = file_get_contents($ex_out_cf);

  //decide what to do according to the compliance checker exit status.
  if($status !==0){
     //if the cf-checker fails then give message and remove submission file also from DB. 
     form_set_error('file','Your dataset is not following the netCDF/CF-1.6 and ACDD-1.3 standards. Your submission can not proceed. <br> 
     Check your dataset and correct the errors before making a new submission.');
     //do not show the checker output for the upload module. The user has to go back to the validation link and see the output there. 
     $file_notsaved = file_load($fid);
     file_delete($file_notsaved);
  }else{
     drupal_set_message(t("Your dataset is compliant with CF and ACDD standards. The submission can now proceed."), 'status');
     exec('/usr/local/bin/nc_to_mmd.pl --output='.$ex_out_nctommd.' '.$fdir.'/'.$path, $out_nctommd, $status_nctommd);
     //get xml file content
     $xml_content = file_get_contents($ex_out_nctommd); // this is a string from gettype 
     //get xml object iterator 
     $xml = new SimpleXmlIterator($xml_content);
     //get xml object iterator with mmd namespaces
     $xml_wns = $xml->children($xml->getNamespaces(true)['mmd']);

     // extract mmd to the last child
     function depth_mmd($prefix, $iterator) {
        $kv_a = array();
        foreach ($iterator as $k => $v) {
           if ($iterator->hasChildren()) {
              $kv_a = array_merge($kv_a, depth_mmd($prefix . ' ' . $k, $v));
           } else {
              //add mmd keys and values to form_state to be passed to the second page. 
              $kv_a[] = array($prefix . ' ' . $k, (string)$v);
           }
        }
        return $kv_a; //this function returms an array of arrys
     }

     $form_state['metadata'] = depth_mmd("", $xml_wns);

  }

  //remove validation files
  if(file_exists($ex_out_cf)){
     file_unmanaged_delete($ex_out_cf);
  }
  if(file_exists($ex_out_acdd)){
     file_unmanaged_delete($ex_out_acdd);
  }

  return $form;
}

// New function created to help make the code more manageable
function dataset_upload_multipage_form_page_two($form, &$form_state) {

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

  $form['dsfid'] = array(
    '#type' => 'fieldset',
    '#description' => 'Your dataset: "' . $form_state['dataset_fname'] . '" has the metadata as reported in the following tabel. Please make sure they are correct before
                     confirming your submission. If the metadata are not correct, cancel your submission, correct your information and proceed with a new submission.',
  );


  $header = array('Metadata Key', 'Metadata value');
  $rows = $form_state['metadata'];

  $form['table'] = array(
    '#markup' => theme('table', array('header'=>$header, 'rows'=>$rows)),
  );


  $form['review'] = array(
    '#type' => 'submit',
    '#value' => 'Confirm',
  );
  $form['clear'] = array(
    '#type' => 'submit',
    '#value' => 'Cancel Submission',
    '#validate' => array('dataset_upload_multipage_form_clear'),
  );


  return $form;
}

function dataset_upload_multipage_form_clear($form, $form_state) {
  drupal_set_message(t('Your dataset upload has been cancelled'),'warning');
  $form_state['storage']['page_one_values'] = $form_state['values'];

// need to delete records from folder and DB
  $file_notsaved = file_load($form_state['dataset_fid']);
  file_delete($file_notsaved);

  unset ($form_state['values']);  
  unset ($form_state['storage']); 
  $form_state['rebuild'] = TRUE;
  $form_state['redirect'] = ''; // Redirects the user.
}

function dataset_upload_multipage_form_submit($form, &$form_state) {
  // Handle page 1 submissions
  if ($form_state['clicked_button']['#id'] == 'edit-next') {
    $form_state['storage']['page_two'] = TRUE; // We set this to determine
                                               // which elements to display
                                               // when the page reloads.
    // Values below in the $form_state['storage'] array are saved
    // to carry forward to subsequent pages in the form.
    $form_state['storage']['page_one_values'] = $form_state['values'];
    $form_state["rebuild"] = TRUE;   // Added
  }elseif ($form_state['clicked_button']['#id'] == 'edit-clear'){
    unset ($form_state['storage']); 
  }else {
    drupal_set_message(t('Your dataset and related info have been submitted.'),'status');
    $form_state['redirect'] = ''; // Redirects the user.
    unset ($form_state['storage']); 
  }
}

function dataset_upload_add_submit_buttons($form_state) {
  $buttons = array();
  // Display 'Prev' button on all steps excluding first.
  if ($form_state['storage']['step'] > 1) {
    $buttons['prev'] = array(
      '#type' => 'submit',
      '#value' => 'Prev',
    );
  }
  // Display 'Next' button on all steps excluding last.
  if ($form_state['storage']['step'] < 3) {
    $buttons['next'] = array(
      '#type' => 'submit',
      '#value' => 'Next',
    );
  }
  // Display 'Finish' button on the last step.
  if ($form_state['storage']['step'] == 3) {
    $buttons['finish'] = array(
      '#type' => 'submit',
      '#value' => 'Confirm',
    );
  }
  return $buttons;
}