/**
* 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);
}
/**
* 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);
}