public function testImportEventIsSettableUponCreation()
{
$import = Mockery::mock('DAG\\Component\\Resource\\Model\\Import');
$subject = Mockery::mock('DAG\\Bundle\\ResourceBundle\\Import\\ResourceInterface')->shouldReceive('isSubject')->zeroOrMoreTimes()->andReturn(true)->getMock();
$target = Mockery::mock('DAG\\Bundle\\ResourceBundle\\Import\\ResourceInterface')->shouldReceive('isTarget')->zeroOrMoreTimes()->andReturn(true)->getMock();
$event = new ImportEvent($subject, $target, $import);
$this->assertSame($import, $event->getImport());
}
/**
* Converts record array into actual target entity.
*
* @param ImportEvent $event
*/
public function convert(ImportEvent $event)
{
$importer = $event->getImporter();
if (!('sample' == $importer->getSubject() && 'cpd_genetic_results' == $importer->getName())) {
return;
}
$records = $event->getRecords();
$repo = $event->getTarget()->getRepository();
$prototype = $this->prototypeProvider->getPrototypeByName('genetic-results');
$fields['cpd-id'] = $prototype->getFieldByName('genetic-results-cpd-id');
$fields['gene-id'] = $prototype->getFieldByName('genetic-results-gene-id');
$fields['gene'] = $prototype->getFieldByName('genetic-results-gene');
$fields['variant-detected'] = $prototype->getFieldByName('genetic-results-variant-detected');
$fields['variant-categorization'] = $prototype->getFieldByName('genetic-results-variant-categorization');
$fields['cdna-change'] = $prototype->getFieldByName('genetic-results-cdna-change');
$fields['mutation-type-cdna'] = $prototype->getFieldByName('genetic-results-mutation-type-cdna');
$fields['mutation-type-protein'] = $prototype->getFieldByName('genetic-results-mutation-type-protein');
$fields['variant-alias'] = $prototype->getFieldByName('genetic-results-variant-alias');
$fields['genetic-test-version-id'] = $prototype->getFieldByName('genetic-results-genetic-test-version-id');
$fields['transcript-id'] = $prototype->getFieldByName('genetic-results-transcript-id');
$fields['position'] = $prototype->getFieldByName('genetic-results-position');
$fields['genotype'] = $prototype->getFieldByName('genetic-results-genotype');
$fields['fdp'] = $prototype->getFieldByName('genetic-results-fdp');
$fields['frd'] = $prototype->getFieldByName('genetic-results-frd');
$fields['fad'] = $prototype->getFieldByName('genetic-results-fad');
$fields['faf'] = $prototype->getFieldByName('genetic-results-faf');
$fields['exon-id'] = $prototype->getFieldByName('genetic-results-exon-id');
$fields['exon'] = $prototype->getFieldByName('genetic-results-exon');
$sources = array();
foreach ($records as $key => $record) {
$source = new Source();
$source->setPatient($record['patient']);
$source->setSourceDate($record['activity_date']);
$source->setAmount(1);
$sample = new Sample();
$sample->setPrototype($prototype);
$sample->setPatient($record['patient']);
$source->addSample($sample);
if (array_key_exists('diagnosis', $record)) {
$sample->setDiagnosis($record['diagnosis']);
}
foreach ($fields as $key => $field) {
$fieldValue = new FieldValue();
$fieldValue->setField($field);
$fieldValue->setValue($record[str_replace('genetic_results_', '', str_replace('-', '_', $field->getName()))]);
$sample->addField($fieldValue);
}
$sources[$record['pk_id']] = $source;
unset($records[$key]);
}
$event->setRecords($sources);
}
/**
* Convert.
*
* @param array $records
* @return void
*/
public function convert(ImportEvent $event)
{
$records = $event->getRecords();
$flattened = array();
foreach ($records as $key => $value) {
foreach ($value as $possibleObject) {
if (is_object($possibleObject) && !$possibleObject instanceof Resource && !$possibleObject instanceof DateTime) {
$flattened[] = $possibleObject;
}
}
unset($records[$key]);
}
$event->setRecords($flattened);
}
/**
* Initialize the import object.
*
* Figure out criteria to use...
*
* @param ImportEvent $event
*/
public function initialize(ImportEvent $event)
{
$import = $event->getImport();
$history = $event->getHistory();
$importer = $event->getImporter();
$criteria = array();
if (empty($history)) {
$criteria = $this->criteria->setParams($this->criteria->retrieveDefault());
}
if (empty($criteria)) {
$criteria = $this->criteria->setParams($this->criteria->calculate($history));
}
$import->setImporter($importer->getName());
$import->setCriteria($criteria->retrieve());
}
/**
* Converts record array into actual target entity.
*
* @param ImportEvent $event
*/
public function convert(ImportEvent $event)
{
$importer = $event->getImporter();
if (!('sample' === $importer->getSubject() && 'hmtb_specimens_collection' === $importer->getName())) {
return;
}
$records = $event->getRecords();
$repo = $event->getTarget()->getRepository();
$prototype = $this->prototypeProvider->getPrototypeByName('specimen-collection');
$fields['sample-type'] = $prototype->getFieldByName('hmtb-sample-type');
$fields['restricted'] = $prototype->getFieldByName('hmtb-restricted');
$fields['subtype'] = $prototype->getFieldByName('hmtb-subtype');
$fields['total-sum-vials-remaining'] = $prototype->getFieldByName('hmtb-total-sum-vials-remaining');
$fields['blasts'] = $prototype->getFieldByName('hmtb-blasts');
$fields['ct-cyle'] = $prototype->getFieldByName('hmtb-ct-cycle');
$fields['ct-study-day'] = $prototype->getFieldByName('hmtb-ct-study-day');
$fields['ct-peak-through'] = $prototype->getFieldByName('hmtb-ct-peak-through');
$fields['ct-time-post-drug'] = $prototype->getFieldByName('hmtb-ct-time-post-drug');
$fields['ct-time-post-drug-unit'] = $prototype->getFieldByName('hmtb-ct-time-post-drug-unit');
$fields['ct-treatment-relation-time'] = $prototype->getFieldByName('hmtb-ct-treatment-relation-time');
$fields['when-modified'] = $prototype->getFieldByName('hmtb-when-modified');
$sources = array();
foreach ($records as $key => $record) {
$source = new Source();
$source->setPatient($record['patient']);
$source->setSourceDate($record['activity_date']);
$source->setAmount(1);
$sample = new Sample();
$sample->setPrototype($prototype);
$sample->setAmount(1);
$sample->setPatient($record['patient']);
$source->addSample($sample);
foreach ($fields as $key => $field) {
if (method_exists($field, 'getName')) {
$fieldValue = new FieldValue();
$fieldValue->setField($field);
$fieldValue->setSample($sample);
$fieldValue->setValue($record[str_replace('hmtb_', '', str_replace('-', '_', $field->getName()))]);
$sources[$record['identifier'] . $field->getName()] = $fieldValue;
}
}
$sources[$record['identifier']] = $source;
unset($records[$key]);
}
$event->setRecords($sources);
}
/**
* Converts record array into actual target entity.
*
* @param ImportEvent $event
*/
public function convert(ImportEvent $event)
{
$records = $event->getRecords();
$prototype = $this->prototypeProvider->getPrototypeByName('ridic-dose');
$fields = array();
$fields['0'] = $prototype->getFieldByName('0');
$fields['first-treatment'] = $prototype->getFieldByName('first-treatment');
$fields['last-treatment'] = $prototype->getFieldByName('last-treatment');
$fields['course-ser'] = $prototype->getFieldByName('course-ser');
$fields['course-serv'] = $prototype->getFieldByName('course-serv');
$fields['course-id'] = $prototype->getFieldByName('course-id');
$fields['hup-mrn'] = $prototype->getFieldByName('hup-mrn');
$fields['attending-npi'] = $prototype->getFieldByName('attending-npi');
$fields['treatment-intent'] = $prototype->getFieldByName('treatment-intent');
$fields['department-ser'] = $prototype->getFieldByName('department-ser');
$fields['pcam-yn'] = $prototype->getFieldByName('pcam-yn');
$fields['pah-yn'] = $prototype->getFieldByName('pah-yn');
$fields['chh-yn'] = $prototype->getFieldByName('chh-yn');
$fields['dh-yn'] = $prototype->getFieldByName('dh-yn');
$fields['vf-yn'] = $prototype->getFieldByName('vf-yn');
$fields['first-treatment-dt'] = $prototype->getFieldByName('first-treatment-dt');
$fields['last-treatment-dt'] = $prototype->getFieldByName('last-treatment-dt');
$fields['days-elapsed'] = $prototype->getFieldByName('days-elapsed');
$fields['days-treated'] = $prototype->getFieldByName('days-treated');
$fields['first-treatment-modality'] = $prototype->getFieldByName('first-treatment-modality');
$fields['linac-yn'] = $prototype->getFieldByName('linac-yn');
$fields['proton-yn'] = $prototype->getFieldByName('proton-yn');
$fields['conformal-yn'] = $prototype->getFieldByName('conformal-yn');
$fields['imrt-yn'] = $prototype->getFieldByName('imrt-yn');
$fields['arc-yn'] = $prototype->getFieldByName('arc-yn');
$fields['rapid-arc-yn'] = $prototype->getFieldByName('rapid-arc-yn');
$fields['stereotactic-yn'] = $prototype->getFieldByName('stereotactic-yn');
$fields['tbi-yn'] = $prototype->getFieldByName('tbi-yn');
$fields['single-scattering-yn'] = $prototype->getFieldByName('single-scattering-yn');
$fields['double-scattering-yn'] = $prototype->getFieldByName('double-scattering-yn');
$fields['uniform-scanning-yn'] = $prototype->getFieldByName('uniform-scanning-yn');
$fields['pbs-yn'] = $prototype->getFieldByName('pbs-yn');
$fields['electron-static-yn'] = $prototype->getFieldByName('electron-static-yn');
$fields['hdtse-yn'] = $prototype->getFieldByName('hdtse-yn');
$fields['cyberknife-yn'] = $prototype->getFieldByName('cyberknife-yn');
$fields['ref-point-serv'] = $prototype->getFieldByName('ref-point-serv');
$fields['ref-point-id'] = $prototype->getFieldByName('ref-point-id');
$fields['rx-total-dose'] = $prototype->getFieldByName('rx-total-dose');
$fields['rx-daily-dose'] = $prototype->getFieldByName('rx-daily-dose');
$fields['rx-session-dose'] = $prototype->getFieldByName('rx-session-dose');
$fields['rx-fraction'] = $prototype->getFieldByName('rx-fraction');
$fields['treated-total-dose'] = $prototype->getFieldByName('treated-total-dose');
$fields['treated-fractions'] = $prototype->getFieldByName('treated-fractions');
$fields['icd9-code'] = $prototype->getFieldByName('icd9-code');
$fields['dx-desc'] = $prototype->getFieldByName('dx-desc');
$fields['ref-point-ser'] = $prototype->getFieldByName('ref-point-ser');
$fields['rx-fractions'] = $prototype->getFieldByName('rx-fractions');
$fields['patient-ser'] = $prototype->getFieldByName('patient-ser');
$activities = array();
foreach ($records as $key => $record) {
$activity = new Activity();
$activity->setPatient($record['patient']);
$activity->setActivityDate($record['activity_date']);
$activity->setPrototype($prototype);
foreach ($fields as $key => $field) {
if (method_exists($field, 'getName')) {
$fieldValue = new FieldValue();
$fieldValue->setField($field);
$fieldValue->setActivity($activity);
$fieldValue->setValue($record[str_replace('-', '_', $field->getName())]);
$activities[$record['identifier'] . $field->getName()] = $fieldValue;
}
}
$activities[$record['identifier']] = $activity;
unset($records[$key]);
}
$event->setRecords($activities);
}
/**
* Disable SQL logger.
*
* @param ImportEvent $event
*/
public function disableSQLLog(ImportEvent $event)
{
$event->getTarget()->getManager()->getConnection()->getConfiguration()->setSQLLogger(null);
}
