/**
* @Route("/protocol/{protocol_id}/monitoring/{monitoring_action_id}", name="protocol_new_monitoring_that_not_amendment")
* @Template()
*/
public function monitoringCreateThatNotAmendmentAction($protocol_id, $monitoring_action_id)
{
$output = array();
$request = $this->getRequest();
$session = $request->getSession();
$translator = $this->get('translator');
$em = $this->getDoctrine()->getManager();
$user = $this->get('security.token_storage')->getToken()->getUser();
$util = new Util($this->container, $this->getDoctrine());
$protocol_repository = $em->getRepository('Proethos2ModelBundle:Protocol');
$monitoring_action_repository = $em->getRepository('Proethos2ModelBundle:MonitoringAction');
$upload_type_repository = $em->getRepository('Proethos2ModelBundle:UploadType');
$submission_upload_repository = $em->getRepository('Proethos2ModelBundle:SubmissionUpload');
$user_repository = $em->getRepository('Proethos2ModelBundle:User');
// getting the current submission
$protocol = $protocol_repository->find($protocol_id);
$output['protocol'] = $protocol;
if (!$protocol) {
throw $this->createNotFoundException($translator->trans('No protocol found'));
}
if (!$protocol->getMainSubmission()->isOwner($user)) {
throw $this->createNotFoundException($translator->trans('You don\'t have access to do this'));
}
$monitoring_action = $monitoring_action_repository->find($monitoring_action_id);
$output['monitoring_action'] = $monitoring_action;
$submission = $protocol->getMainSubmission();
$output['submission'] = $submission;
$upload_types = $upload_type_repository->findByStatus(true);
$output['upload_types'] = $upload_types;
if (!$monitoring_action) {
throw $this->createNotFoundException($translator->trans('Monitoring action does not exist'));
}
// checking if was a post request
if ($this->getRequest()->isMethod('POST')) {
// getting post data
$post_data = $request->request->all();
$file = $request->files->get('new-atachment-file');
if (!empty($file)) {
if (!isset($post_data['new-atachment-type']) or empty($post_data['new-atachment-type'])) {
$session->getFlashBag()->add('error', $translator->trans("Field 'new-atachment-type' is required."));
return $output;
}
$upload_type = $upload_type_repository->find($post_data['new-atachment-type']);
if (!$upload_type) {
throw $this->createNotFoundException($translator->trans('No upload type found'));
return $output;
}
$submission_upload = new SubmissionUpload();
$submission_upload->setSubmission($submission);
$submission_upload->setUploadType($upload_type);
$submission_upload->setUser($user);
$submission_upload->setFile($file);
$submission_upload->setSubmissionNumber($submission->getNumber());
$submission_upload->setIsMonitoringAction(true);
$em = $this->getDoctrine()->getManager();
$em->persist($submission_upload);
$em->flush();
$submission->addAttachment($submission_upload);
$em = $this->getDoctrine()->getManager();
$em->persist($submission);
$em->flush();
$session->getFlashBag()->add('success', $translator->trans("File uploaded with sucess."));
return $this->redirectToRoute('protocol_new_monitoring_that_not_amendment', array('protocol_id' => $protocol_id, 'monitoring_action_id' => $monitoring_action_id), 301);
}
if (isset($post_data['delete-attachment-id']) and !empty($post_data['delete-attachment-id'])) {
$submission_upload = $submission_upload_repository->find($post_data['delete-attachment-id']);
if ($submission_upload) {
$em->remove($submission_upload);
$em->flush();
$session->getFlashBag()->add('success', $translator->trans("File removed with sucess."));
return $output;
}
}
// checking required files
foreach (array('monitoring-action', 'justification') as $field) {
if (!isset($post_data[$field]) or empty($post_data[$field])) {
$session->getFlashBag()->add('error', $translator->trans("Field '%field%' is required.", array("%field%" => $field)));
return $output;
}
}
foreach ($protocol->getMainSubmission()->getAttachments() as $submission_upload) {
$submission_upload->setIsMonitoringAction(false);
$em->persist($submission_upload);
$em->flush();
}
$protocol->setMonitoringAction($monitoring_action);
$em->persist($protocol);
$em->flush();
// setting the Rejected status
$protocol->setStatus("S");
$protocol->setUpdatedIn(new \DateTime());
// setting protocool history
$message = $translator->trans("New amendment submited by");
$message .= ' "' . $user . '" ';
$message .= $translator->trans("with this justification:");
$message .= ' "' . $post_data['justification'] . '"';
$protocol_history = new ProtocolHistory();
$protocol_history->setProtocol($protocol);
$protocol_history->setMessage($message);
$em->persist($protocol_history);
$em->flush();
// sending email
$baseurl = $request->getScheme() . '://' . $request->getHttpHost() . $request->getBasePath();
$url = $baseurl . $this->generateUrl('protocol_show_protocol', array("protocol_id" => $protocol->getId()));
$recipients = array();
foreach ($user_repository->findAll() as $secretary) {
if (in_array("secretary", $secretary->getRolesSlug())) {
$recipients[] = $secretary;
}
}
foreach ($recipients as $recipient) {
$message = \Swift_Message::newInstance()->setSubject("[proethos2] " . $translator->trans("A new monitoring action has been submitted."))->setFrom($util->getConfiguration('committee.email'))->setTo($recipient->getEmail())->setBody($translator->trans("Hello!") . "<br>" . "<br>" . $translator->trans("A new monitoring action has been submitted. Access the link below for more details") . ":" . "<br>" . "<br>{$url}" . "<br>" . "<br>" . $translator->trans("Regards") . "," . "<br>" . $translator->trans("Proethos2 Team"), 'text/html');
$send = $this->get('mailer')->send($message);
}
$session->getFlashBag()->add('success', $translator->trans("Amendment submitted with success!"));
return $this->redirectToRoute('crud_investigator_protocol_list', array(), 301);
}
return $output;
}
/**
* @Route("/submission/new/{submission_id}/seventh", name="submission_new_seventh_step")
* @Template()
*/
public function SeventhStepAction($submission_id)
{
$output = array();
$request = $this->getRequest();
$session = $request->getSession();
$translator = $this->get('translator');
$em = $this->getDoctrine()->getManager();
$user = $this->get('security.token_storage')->getToken()->getUser();
$util = new Util($this->container, $this->getDoctrine());
$submission_repository = $em->getRepository('Proethos2ModelBundle:Submission');
$upload_type_repository = $em->getRepository('Proethos2ModelBundle:UploadType');
$user_repository = $em->getRepository('Proethos2ModelBundle:User');
// getting the current submission
$submission = $submission_repository->find($submission_id);
$output['submission'] = $submission;
if (!$submission or $submission->getIsSended()) {
throw $this->createNotFoundException($translator->trans('No submission found'));
}
$allow_to_edit_submission = true;
$user = $this->get('security.token_storage')->getToken()->getUser();
// if current user is not owner, check the team
if ($user != $submission->getOwner()) {
$allow_to_edit_submission = false;
foreach ($submission->getTeam() as $team_member) {
// if current user = some team member, than it allows to edit
if ($user == $team_member) {
$allow_to_edit_submission = true;
}
}
}
if (!$allow_to_edit_submission) {
throw $this->createNotFoundException($translator->trans('No submission found'));
}
// Revisions
$revisions = array();
$final_status = true;
$text = $translator->trans('Team') . " (" . count($submission->getTeam()) + 1 . " " . $translator->trans('member(s)') . ")";
$item = array('text' => $text, 'status' => true);
$revisions[] = $item;
// $text = $translator->trans('Files Submited') . " (" . count($submission->getAttachments()) . " " . $translator->trans('files(s)') . ")";
// $item = array('text' => $text, 'status' => true);
// if(count($submission->getAttachments()) == 0) {
// $item = array('text' => $text, 'status' => false);
// $final_status = false;
// }
// $revisions[] = $item;
$text = $translator->trans('Abstract');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getAbstract())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Keywords');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getKeywords())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Introduction');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getIntroduction())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Justification');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getJustification())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Goals');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getGoals())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Study Design');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getStudyDesign())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Gender');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getGender())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Minimum Age');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getMinimumAge())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Maximum Age');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getMaximumAge())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Inclusion Criteria');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getInclusionCriteria())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Exclusion Criteria');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getExclusionCriteria())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Inicial recruitment estimated date');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getRecruitmentInitDate())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Interventions');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getInterventions())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Primary Outcome');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getPrimaryOutcome())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Funding Source');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getFundingSource())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Primary Sponsor');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getPrimarySponsor())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Bibliography');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getBibliography())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$text = $translator->trans('Scientific Contact');
$item = array('text' => $text, 'status' => true);
if (empty($submission->getSscientificContact())) {
$item = array('text' => $text, 'status' => false);
$final_status = false;
}
$revisions[] = $item;
$output['revisions'] = $revisions;
$output['final_status'] = $final_status;
// checking if was a post request
if ($this->getRequest()->isMethod('POST')) {
// getting post data
$post_data = $request->request->all();
if ($final_status) {
if ($post_data['accept-terms'] == 'on') {
// gerando um novo pdf
try {
$html = $this->renderView('Proethos2CoreBundle:NewSubmission:showPdf.html.twig', $output);
$pdf = $this->get('knp_snappy.pdf');
// setting margins
$pdf->getInternalGenerator()->setOption('margin-top', '50px');
$pdf->getInternalGenerator()->setOption('margin-bottom', '50px');
$pdf->getInternalGenerator()->setOption('margin-left', '20px');
$pdf->getInternalGenerator()->setOption('margin-right', '20px');
// adding pdf to tmp file
$filepath = "/tmp/" . date("Y-m-d") . "-submission.pdf";
file_put_contents($filepath, $pdf->getOutputFromHtml($html));
$submission_number = count($submission->getProtocol()->getSubmission());
$upload_type = $upload_type_repository->findOneBy(array("slug" => "protocol"));
// send tmp file to upload class and save
$pdfFile = new SubmissionUpload();
$pdfFile->setSubmission($submission);
$pdfFile->setSimpleFile($filepath);
$pdfFile->setUploadType($upload_type);
$pdfFile->setUser($user);
$pdfFile->setSubmissionNumber($submission->getNumber());
$em->persist($pdfFile);
$em->flush();
} catch (\RuntimeException $e) {
$session->getFlashBag()->add('error', $translator->trans('Problems generating PDF. Please contact the administrator.'));
return $output;
}
// updating protocol and setting status
$protocol = $submission->getProtocol();
$protocol->setStatus("S");
$protocol->setDateInformed(new \DateTime());
$protocol->setUpdatedIn(new \DateTime());
$em->persist($protocol);
$em->flush();
$submission->setIsSended(true);
$em->persist($submission);
$em->flush();
$protocol_history = new ProtocolHistory();
$protocol_history->setProtocol($protocol);
$protocol_history->setMessage($translator->trans("Submission of protocol."));
$em->persist($protocol_history);
$em->flush();
if ($protocol->getMonitoringAction()) {
// sending email
$baseurl = $request->getScheme() . '://' . $request->getHttpHost() . $request->getBasePath();
$url = $baseurl . $this->generateUrl('protocol_show_protocol', array("protocol_id" => $protocol->getId()));
$recipients = array();
foreach ($user_repository->findAll() as $secretary) {
if (in_array("secretary", $secretary->getRolesSlug())) {
$recipients[] = $secretary;
}
}
foreach ($recipients as $recipient) {
$message = \Swift_Message::newInstance()->setSubject("[proethos2] " . $translator->trans("A new monitoring action has been submitted."))->setFrom($util->getConfiguration('committee.email'))->setTo($recipient->getEmail())->setBody($translator->trans("Hello!") . "<br>" . "<br>" . $translator->trans("A new monitoring action has been submitted. Access the link below for more details") . ":" . "<br>" . "<br>{$url}" . "<br>" . "<br>" . $translator->trans("Regards") . "," . "<br>" . $translator->trans("Proethos2 Team"), 'text/html');
$send = $this->get('mailer')->send($message);
}
$session->getFlashBag()->add('success', $translator->trans("Amendment submitted with success!"));
} else {
$session->getFlashBag()->add('success', $translator->trans("Protocol submitted with sucess!"));
}
return $this->redirectToRoute('protocol_show_protocol', array('protocol_id' => $protocol->getId()), 301);
} else {
$session->getFlashBag()->add('error', $translator->trans("You must accept the terms and conditions."));
}
} else {
$session->getFlashBag()->add('error', $translator->trans('You have pending reviews.'));
}
}
return $output;
}
