Returns the static model of the specified AR class.
| public static model ( $className = __CLASS__ ) : ProtectedFile | ||
| return | ProtectedFile | the static model class |
public function actionCrop($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 $report;
}
public function actionThumbnail($id, $dimensions, $name)
{
if (!($file = ProtectedFile::model()->findByPk($id))) {
throw new CHttpException(404, "File not found");
}
if (!($thumbnail = $file->getThumbnail($dimensions, true))) {
throw new CHttpException(404, "Thumbnail not available");
}
header('Content-Type: ' . $file->mimetype);
header('Expires: 0');
header('Cache-Control: must-revalidate');
header('Content-Length: ' . $thumbnail['size']);
ob_clean();
flush();
readfile($thumbnail['path']);
}
/**
* 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();
}
$transaction->rollback();
}
}
public function getDecryptedSignature($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 $image_data;
}
}
}
return false;
}
/**
* Trawl an existing OE database and find all files that match the given
* pattern. A pattern MUST be specified.
*
* If no pattern is specified, all images that match the standard humphrey
* image size are processed.
*/
public function actionRedact($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, $file);
}
}
}
/**
* removes the compressed file association for this collection. Should be called when the files for it are
* changed so that a new compressed file is created when needed.
*
* will also call the delete function on the protected file itself to remove orphaned files
*/
protected function cleanCompressedFile()
{
// note we have to work on the file id not the relation
if ($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
}
}
}
}