The followings are the available columns in table 'protected_file':
/**
* create a new protected file object which has properties that can be used for writing an actual file to
*
* @param string $name
* @return ProtectedFile
*/
public static function createForWriting($name)
{
$file = new ProtectedFile();
$file->name = $name;
$file->generateUID();
$path = $file->getFilePath();
if (!file_exists($path)) {
if (!@mkdir($path, 0755, true)) {
throw new Exception("{$path} could not be created: permission denied");
}
}
return $file;
}
public function actionCrop($dims = '1328x560,776x864')
{
$dimensions = explode(',', $dims);
$xy = explode('x', $dimensions[0]);
$wh = explode('x', $dimensions[1]);
$src_x = $xy[0];
$src_y = $xy[1];
$dest_w = $wh[0];
$dest_h = $wh[1];
// find all cropped images in ophinvisualfields_field_measurement->cropped_image_id:
$fields = OphInVisualfields_Field_Measurement::model()->findAll();
foreach ($fields as $field) {
$full = ProtectedFile::model()->findByPk($field->image_id);
$cropped = ProtectedFile::model()->findByPk($field->cropped_image_id);
// if the value isnt set, move on
if (!$full || !$cropped) {
continue;
}
// next step, take image_id and open image:
if (file_exists($full->getPath())) {
$src = imagecreatefromgif($full->getPath());
$dest = imagecreatetruecolor($dest_w, $dest_h);
imagecopy($dest, $src, 0, 0, $src_x, $src_y, $dest_w, $dest_h);
imagegif($dest, $cropped->getPath());
echo 'patient: ' . $field->getPatientMeasurement()->patient->hos_num . ', path: ' . $cropped->getPath() . PHP_EOL;
// Reset sizes
$full->size = filesize($full->getPath());
$full->save();
$cropped->size = filesize($cropped->getPath());
$cropped->save();
}
}
}
public static function fromFhir($fhirObject)
{
$report = parent::fromFhir($fhirObject);
$patient = \Patient::model()->find('id=?', array($report->patient_id));
$report->patient_id = $patient->id;
$eye = 'Right';
if ($report->eye == 'L') {
$eye = 'Left';
} elseif ($report->eye == 'B') {
$eye = 'Both';
}
$report->eye_id = \Eye::model()->find('name=:name', array(':name' => $eye))->id;
if (isset($fhirObject->xml_file_data)) {
$report->xml_file_data = base64_decode($fhirObject->xml_file_data);
}
$title = $report->file_reference;
if (\ProtectedFile::model()->find('name = ?', array($title))) {
throw new EverythingsFine("Duplicate filename: {$title} (patient ID {$report->patient_id})");
}
$protected_file = \ProtectedFile::createForWriting($title);
$protected_file->name = $title;
file_put_contents($protected_file->getPath(), base64_decode($report->image_scan_data));
$protected_file->mimetype = 'image/gif';
$protected_file->save();
$cropped_file = \ProtectedFile::createForWriting($title);
// all content is base64 encoded, so decode it:
file_put_contents($cropped_file->getPath(), base64_decode($report->image_scan_crop_data));
$cropped_file->mimetype = 'image/gif';
$cropped_file->name = $title;
$cropped_file->save();
$report->scanned_field_id = $protected_file->id;
$report->scanned_field_crop_id = $cropped_file->id;
return $report;
}
public function actionImport()
{
echo "<h1>Importing files:</h1>";
foreach (glob(Yii::app()->basePath . '/data/test/*') as $src_file) {
$file = ProtectedFile::createFromFile($src_file);
if (!$file->save()) {
throw new CException('Cannot save file' . print_r($file->getErrors(), true));
}
unlink($src_file);
echo "<p>Imported " . $file->uid . ' - ' . $file->name . "</p>";
}
echo "<p>Done!</p>";
}
/**
* abstraction to process FileCollection form.
*
* @param OphCoTherapyapplication_FileCollection $model
* @param string $audit_type
*/
protected function processFileCollectionForm($model, $audit_type = 'create')
{
$model->attributes = $_POST['OphCoTherapyapplication_FileCollection'];
// validate the model
$model->validate();
$transaction = Yii::app()->getDb()->beginTransaction();
// slightly complex rollback process because of files being copied into the protected file store
// we want to be able to roll this back as well as the db process.
try {
$pf_ids = $this->processFileCollectionFileUpload($model, $_FILES['OphCoTherapyapplication_FileCollection_files']);
if (!count($model->getErrors())) {
if ($model->save()) {
// because this might be an update, we get the current files on the model so that we don't remove files
// from it
$curr_pf_ids = array();
foreach ($model->files as $file) {
$curr_pf_ids[] = $file->id;
}
$model->updateFiles(array_merge($curr_pf_ids, $pf_ids));
Audit::add('admin', $audit_type, $model->id, null, array('module' => 'OphCoTherapyapplication', 'model' => 'OphCoTherapyapplication_FileCollection'));
Yii::app()->user->setFlash('success', 'File Collection created');
$transaction->commit();
$this->redirect(array('viewfilecollections'));
}
}
// clear out any protected files that might have been created.
$criteria = new CDbCriteria();
$criteria->addInCondition('id', $pf_ids);
foreach (ProtectedFile::model()->findAll($criteria) as $pf) {
$pf->delete();
}
// if we've got this far, something is amiss
$transaction->rollback();
} catch (Exception $e) {
Yii::log('OphCoTherapyapplication_FileCollection creation error: ' . $e->getMessage(), 'error');
Yii::app()->user->setFlash('error', 'An unexpected error has occurred');
// clear out any protected files that might have been created.
$criteria = new CDbCriteria();
$criteria->addInCondition('id', $pf_ids);
foreach (ProtectedFile::model()->findAll($criteria) as $pf) {
$pf->delete();
}
$transaction->rollback();
}
}
/**
* main method to run the command for file collection creation.
*
* @TODO: look for a summary text file to include.
* @TODO: search for existing file collections and update instead of adding.
*
* @param array $args
*
* @return int|void
*/
public function run($args)
{
if (!count($args) == 1) {
$this->usageError('missing source path argument');
}
if (!is_readable($args[0])) {
$this->usageError('cannot read specified source path ' . $args[0]);
}
$base_path = $args[0];
// read directory structure into data
$file_list = $this->buildFileList($base_path, './');
$file_ext_regexp = implode('|', $this->file_extensions);
$sets = array();
// determine the file collections to be created
foreach ($file_list as $fname => $details) {
if (preg_match('/' . $file_ext_regexp . '$/', $fname)) {
$path = str_replace(DIRECTORY_SEPARATOR, ' - ', dirname($fname));
if (!@$sets[$path]) {
$summary_text = $this->summary_text_default;
$summary_filepath = $base_path . dirname($fname) . DIRECTORY_SEPARATOR . $this->summary_filename;
if ($this->summary_filename && file_exists($summary_filepath)) {
// read the summary text in from the file
$summary_text = file_get_contents($summary_filepath);
}
$sets[$path] = array('summary' => $summary_text, 'files' => array($details));
} else {
$sets[$path]['files'][] = $details;
}
}
}
$created = 0;
$modified = 0;
// iterate through and create the file collections.
foreach ($sets as $set_name => $set_details) {
$created_flag = false;
$transaction = Yii::app()->getDb()->beginTransaction();
$pf_list = array();
$pf_ids = array();
try {
foreach ($set_details['files'] as $details) {
$pf = ProtectedFile::createFromFile($details['source']);
if ($pf->save()) {
$pf_ids[] = $pf->id;
$pf_list[] = $pf;
} else {
foreach ($pf_list as $pf) {
$pf->delete();
}
break;
}
}
// update the existing file collection if there is one
$criteria = new CDbCriteria();
$criteria->addCondition('name = :nm');
$criteria->params = array(':nm' => $set_name);
if (!($fc = OphCoTherapyapplication_FileCollection::model()->find($criteria))) {
$fc = new OphCoTherapyapplication_FileCollection();
$fc->name = $set_name;
$created_flag = true;
}
$fc->summary = $set_details['summary'];
if (!$fc->validate()) {
echo "unexpected validation error with file collection\n";
var_dump($fc->getErrors());
$transaction->rollback();
} else {
if ($fc->save()) {
$fc->updateFiles($pf_ids);
Audit::add('admin', 'create', $fc->id, null, array('module' => 'OphCoTherapyapplication', 'model' => 'OphCoTherapyapplication_FileCollection'));
$transaction->commit();
$created_flag ? $created++ : $modified++;
} else {
foreach ($pf_list as $pf) {
$pf->delete();
}
$transaction->rollback();
}
}
} catch (Exception $e) {
echo $e->getMessage();
foreach ($pf_list as $pf) {
$pf->delete();
}
$transaction->rollback();
}
}
echo 'Processing complete, ' . $created . ' collections created, ' . $modified . " collections updated\n";
}
public function getDecryptedSignature($signature_pin)
{
if ($signature_pin) {
if ($this->signature_file_id) {
$signature_file = ProtectedFile::model()->findByPk($this->signature_file_id);
$image_data = base64_decode($this->decryptSignature(file_get_contents($signature_file->getPath()), md5(md5($this->id) . $this->generateUniqueCodeWithChecksum($this->getUniqueCode()) . $signature_pin)));
if (strlen($image_data) > 100) {
return $image_data;
}
}
}
return false;
}
/**
* Store the PDF as a ProtectedFile in the system
*
* @return ProtectedFile
* @throws Exception
*/
public function storePDF()
{
$pf = ProtectedFile::createFromFile($this->outDir . '/' . $this->outFile);
$pf->save();
$this->cleanUp();
return $pf;
}
/**
* Trawl an existing OE database and find all files that match the given
* pattern. A pattern MUST be specified.
*
* If no pattern is specified, all images that match the standard humphrey
* image size are processed.
*/
public function actionRedact($pattern = null)
{
$criteria = new CDbCriteria();
if ($pattern != null) {
$criteria->condition = 'name like :name';
$criteria->params = array(':name' => $pattern);
} else {
echo 'You MUST specify a file pattern to match.';
}
$files = ProtectedFile::model()->findAll($criteria);
// we can't really filter images, except on size - for now just
// assume the count is half the amount when taking thumbnails into
// consideration
echo count($files) / 2 . ' files found for modification.';
if ($files) {
foreach ($files as $file) {
if (file_exists($file->getPath())) {
$this->anonymiseTif($file->getPath());
} else {
echo 'Could not transform file; ' . $file->getPathName() . ' does not exist.' . PHP_EOL;
}
}
}
}
public function actionImport($importDir, $archiveDir, $errorDir, $dupDir, $interval = 'PT45M', $pasImport = false)
{
$this->importDir = $this->checkSeparator($importDir);
$this->archiveDir = $this->checkSeparator($archiveDir);
$this->errorDir = $this->checkSeparator($errorDir);
$this->dupDir = $this->checkSeparator($dupDir);
$this->interval = $interval;
$fhirMarshal = Yii::app()->fhirMarshal;
$eventType = EventType::model()->find('class_name=:class_name', array(':class_name' => 'OphInVisualfields'));
if (!$eventType) {
echo 'Cannot find OphInVisualfields event type, cannot continue' . PHP_EOL;
die;
}
echo 'Processing FMES files...' . PHP_EOL;
$filenames = glob($this->importDir . '/*.fmes');
echo count($filenames) . " files to process\n";
foreach ($filenames as $file) {
try {
$basename = basename($file);
echo $basename . PHP_EOL;
// First check the file has not already been imported:
$field = file_get_contents($file);
$fieldObject = $fhirMarshal->parseXml($field);
if ($protected_file = ProtectedFile::model()->find('name=:name', array(':name' => $fieldObject->file_reference))) {
echo '- ProtectedFile exists (' . $protected_file->id . ')' . PHP_EOL;
$this->move($this->dupDir, $file);
continue;
}
// Extract the patient number
$matches = array();
preg_match('/__OE_PATIENT_ID_([0-9]*)__/', $field, $matches);
if (count($matches) < 2) {
echo '- Failed to extract patient ID' . PHP_EOL;
$this->move($this->errorDir, $file);
continue;
}
$match = str_pad($matches[1], 7, '0', STR_PAD_LEFT);
// Fetch the patient
if ($pasImport) {
$model = new Patient(null);
$model->hos_num = $match;
$results = $model->search()->getData();
$patient = reset($results);
} else {
$patient = Patient::model()->find('hos_num=:hos_num', array(':hos_num' => $match));
}
if (!$patient) {
echo "- Failed to find patient ({$match})" . PHP_EOL;
$this->move($this->errorDir, $file);
continue;
}
$pid = $patient->id;
$field = preg_replace('/__OE_PATIENT_ID_([0-9]*)__/', $pid, $field);
// Convert to measurement
$resource_type = 'MeasurementVisualFieldHumphrey';
$service = Yii::app()->service->getService($resource_type);
$fieldObject = $fhirMarshal->parseXml($field);
$tx = Yii::app()->db->beginTransaction();
$ref = $service->fhirCreate($fieldObject);
$tx->commit();
$refId = $ref->getId();
$measurement = OphInVisualfields_Field_Measurement::model()->findByPk($refId);
$study_datetime = $measurement->study_datetime;
// Check for existing legacy events
if (!($episode = Episode::model()->find('legacy = 1 AND patient_id = :patient_id', array(':patient_id' => $pid)))) {
echo '- No legacy episode found, creating...';
$episode = new Episode();
$episode->legacy = 1;
$episode->patient_id = $pid;
$episode->save();
echo 'done' . PHP_EOL;
// As there are no previous legacy events, we can create a new event
$this->newEvent($episode, $eventType, $measurement);
$this->move($this->archiveDir, $file);
} else {
// There is a legacy episode, so there may be unmatched legacy field events
$criteria = new CdbCriteria();
$criteria->condition = 'event_type_id = :event_type_id and t.deleted = 0 and ep.deleted = 0 and ep.legacy = 1 and ep.patient_id = :patient_id';
$criteria->join = 'join episode ep on ep.id = t.episode_id';
$criteria->order = 't.event_date desc';
$criteria->params = array(':patient_id' => $pid, ':event_type_id' => $eventType->id);
if ($this->interval) {
// we're looking for all events that are bound to a legacy episode,
// for the given patient, looking for the last created test -
// this accounts for multiple tests per eye - the implication
// being that the newest test overrides the last test for the same eye
// (e.g. when a mistake is made and the test is re-ran):
// Base time on interval defined by user, a narrow time slot that the test falls within
$startCreatedTime = new DateTime($study_datetime);
$endCreatedTime = new DateTime($study_datetime);
$startCreatedTime->sub(new DateInterval($this->interval));
$endCreatedTime->add(new DateInterval($this->interval));
$criteria->condition .= ' AND t.event_date >= STR_TO_DATE("' . $startCreatedTime->format('Y-m-d H:i:s') . '", "%Y-%m-%d %H:%i:%s") AND t.event_date <= STR_TO_DATE("' . $endCreatedTime->format('Y-m-d H:i:s') . '", "%Y-%m-%d %H:%i:%s")';
}
// Of events, there can only be one or none:
// FIXME: This can return multiple events, so how do we choose?
$events = Event::model()->findAll($criteria);
if (count($events) == 1) {
echo '- Found existing event (' . $events[0]->id . ')' . PHP_EOL;
$element = Element_OphInVisualfields_Image::model()->find('event_id = :event_id', array(':event_id' => $events[0]->id));
$side = strtolower($measurement->eye->name);
if ($existing = $element->{"{$side}_field"}) {
if ($measurement->study_datetime > $existing->study_datetime) {
echo "Newer than existing measurement on {$side}, overwriting\n";
$element->{"{$side}_field_id"} = $measurement->id;
$unattached = $existing;
} else {
echo "Older than existing measurement on {$side}, ignoring\n";
$unattached = $measurement;
}
// Add dummy reference for the unattached measurement
$ref = new MeasurementReference();
$ref->patient_measurement_id = $unattached->getPatientMeasurement()->id;
$ref->save();
} else {
echo "No existing measurement on {$side}, adding\n";
$element->{"{$side}_field_id"} = $measurement->id;
}
$element->save();
$this->move($this->archiveDir, $file);
} elseif (count($events) > 1) {
echo '- Found more than one matching event, cannot attach' . PHP_EOL;
$this->move($this->errorDir, $file);
} else {
// No events in match window, so we create a new one
$this->newEvent($episode, $eventType, $measurement);
$this->move($this->archiveDir, $file);
}
}
} catch (Exception $ex) {
echo $ex . PHP_EOL;
if (@$tx && $tx->active) {
echo '- rolling back tx' . PHP_EOL;
$tx->rollback();
}
$this->move($this->errorDir, $file);
}
}
}
/**
* create the PDF file as a ProtectedFile for the given side.
*
* @param CController $controller
* @param array $template_data
* @param string $side
*
* @throws Exception
*
* @return ProtectedFile|null
*/
protected function createAndSavePdfForSide(CController $controller, array $template_data, $side)
{
if ($html = $this->getPDFContentForSide($controller, $template_data, $side)) {
$html = '<link rel="stylesheet" type="text/css" href="' . $controller->assetPath . '/css/print.css" />' . "\n" . $html;
$this->event->lock();
if (!$this->event->hasPDF('therapy_application')) {
$wk = new WKHtmlToPDF();
$wk->setDocuments(1);
$wk->setDocRef($this->event->docref);
$wk->setPatient($this->event->episode->patient);
$wk->setBarcode($this->event->barcodeHTML);
$wk->generatePDF($this->event->imageDirectory, 'event', 'therapy_application', $html, false, false);
}
$this->event->unlock();
if (@$_GET['html']) {
return Yii::app()->end();
}
$pfile = ProtectedFile::createForWriting('ECForm - ' . $side . ' - ' . $template_data['patient']->hos_num . '.pdf');
if (!@copy($this->event->getPDF('therapy_application'), $pfile->getPath())) {
throw new Exception('Unable to write to file: ' . $pfile->getPath());
}
if (!$pfile->save()) {
throw new Exception('Unable to save file: ' . print_r($pfile->errors, true));
}
return $pfile;
}
return;
}
/**
* removes the compressed file association for this collection. Should be called when the files for it are
* changed so that a new compressed file is created when needed.
*
* will also call the delete function on the protected file itself to remove orphaned files
*/
protected function cleanCompressedFile()
{
// note we have to work on the file id not the relation
if ($id = $this->zipfile_id) {
$this->zipfile_id = null;
if ($this->save()) {
$pf = ProtectedFile::model()->findByPk($id);
try {
$pf->delete();
} catch (Exception $e) {
// ignore this exception as it's because the compressed file is referenced elsewhere
}
}
}
}
