/**
* {@inheritdoc}
*/
public function run(OptionsResolverInterface $resolver)
{
$records = array();
$localRecords = $this->localSource->execute();
$results = $this->cpdSource->execute();
$cachedMrns = array();
foreach ($results as $key => $result) {
$result = array_change_key_case($result, CASE_LOWER);
$mrn = $result['patient'];
try {
if (!isset($cachedMrns[$mrn])) {
$result['previous_record'] = $this->provider->getPatientByMRN($mrn);
$cachedMrns[$mrn] = $result['previous_record'];
} else {
$result['previous_record'] = $cachedMrns[$mrn];
}
} catch (PatientNotFoundException $e) {
unset($result, $results[$key]);
continue;
}
$record['identifier'] = $result['pk_id'];
$result['import_description'] = sprintf('%s genetic results on the %s.', $result['cpd_id'], $result['patient']);
$record = $resolver->resolve($result);
if ($record['patient'] && $record['genetic_test_version_id'] == '2' && !in_array($record['pk_id'], $localRecords)) {
$records[] = $record;
}
unset($results[$key]);
}
unset($cachedMrns, $localRecords);
return $records;
}
/**
* Merge a source
*
* @param SourceInterface $source
*/
public function mergeSource(SourceInterface $source)
{
if (array_key_exists($source->sourceId(), $this->sources)) {
unset($this->sources[$source->sourceId()]);
} else {
$this->newSources[$source->sourceId()] = $source;
}
$this->sources[$source->sourceId()] = $source;
}
/**
* @param SourceInterface $source
* @return bool
*/
public function equals(SourceInterface $source)
{
if (!$source instanceof FileSource) {
return false;
}
if ($this->path !== $source->getPath()) {
return false;
}
if ($this->line !== $source->getLine()) {
return false;
}
if ($this->column !== $source->getColumn()) {
return false;
}
return true;
}
public function match(SourceInterface $source)
{
if (!$source instanceof CliSource) {
return false;
}
if (count($this->specificationParts) == 0) {
return array();
}
$argvParts = $source->getArguments();
$curArgvPart = array_shift($argvParts);
$parameters = array();
foreach ($this->specificationParts as $i => $specPart) {
switch ($specPart[0]) {
case self::PART_WORD:
if ($specPart[1] != $curArgvPart) {
return false;
} else {
$curArgvPart = array_shift($argvParts);
continue;
}
break;
case self::PART_PARAMETER:
$parameterName = ltrim(rtrim($specPart[1], '?'), ':');
$parameters[$parameterName] = null;
if ($curArgvPart == '' && substr($specPart[1], -1) != '?') {
return false;
}
$parameters[$parameterName] = $curArgvPart;
$curArgvPart = array_shift($argvParts);
break;
case self::PART_OPTION:
$optionName = substr($specPart[1], 1);
$parameters[$optionName] = array();
while ($curArgvPart[0] == '-') {
$parameters[$optionName][] = $curArgvPart;
$curArgvPart = array_shift($argvParts);
}
break;
}
}
return $parameters;
}
/**
* {@inheritdoc}
*/
public function setSource(SourceInterface $source)
{
$this->setOption('source', $source->getMachineName());
return $this->addObject($source);
}
/**
* @param TokenInterface $token
* @return UserInterface
*/
public function getUser(TokenInterface $token)
{
return $this->source->findByPK($token->userPK());
}
/**
* Adds another source to the list of words.
*
* @param SourceInterface $source
* @return self
*/
public function addSource(SourceInterface $source)
{
$this->words = array_merge($this->words, $source->getWords());
return $this;
}
/**
* Set the source of this layer.
*
* @param SourceInterface $source
* The source object.
*/
public function setSource(SourceInterface $source)
{
/* @var Source $source */
$this->setOption('source', $source->getMachineName());
}
