/**
* @return string
*/
public function getCollectionPath()
{
$institutionPath = $this->getPath() . '/' . $this->collection->getInstitution()->getInstitutioncode() . '/';
UtilityService::createDir($institutionPath, $this->userGroup);
$collectionPath = $institutionPath . $this->collection->getCollectioncode();
return UtilityService::createDir($collectionPath, $this->userGroup);
}
/**
* @param Collection $collection
* @param QueryBuilder $qb
* @param array $catalogNumbers
* @param string $alias
*/
protected function setSpecimenCodesWhereClause(Collection $collection, QueryBuilder &$qb, $catalogNumbers, $alias = 's')
{
$qb->andWhere(sprintf('%s.institutioncode = :institutionCode', $alias))->andWhere(sprintf('%s.collectioncode = :collectionCode', $alias))->andWhere($qb->expr()->in(sprintf('%s.catalognumber', $alias), ':catalogNumbers'))->setParameters(['institutionCode' => $collection->getInstitution()->getInstitutioncode(), 'collectionCode' => $collection->getCollectioncode(), 'catalogNumbers' => $catalogNumbers]);
}
/**
* @param Collection $collection
* @param array|string $catalogNumbers
* @return array
* @throws \Doctrine\ORM\NonUniqueResultException
*/
public function findBestTaxonsByCatalogNumbers(Collection $collection, $catalogNumbers)
{
if (!is_array($catalogNumbers)) {
$catalogNumbers = [$catalogNumbers];
}
$rsm = new ResultSetMapping();
$rsm->addScalarResult('scientificname', 'scientificname');
$rsm->addScalarResult('scientificnameauthorship', 'scientificnameauthorship');
$rsm->addScalarResult('catalognumber', 'catalognumber');
$nativeSqlTaxon = '
WITH FirstIDentified AS (
SELECT First_Value(t.taxonid) OVER (PARTITION BY catalognumber ORDER BY identificationverifstatus) First,
t.taxonid, t.scientificname, t.scientificnameauthorship,
s.catalognumber
FROM Taxons t
JOIN Determinations d ON t.taxonid = d.taxonid
JOIN Specimens s on d.occurrenceid = s.occurrenceid
WHERE s.collectioncode = :collectionCode AND
s.catalognumber IN (:catalogNumbers)
)
SELECT catalognumber, scientificname, scientificnameauthorship FROM FirstIdentified
WHERE taxonid = First
';
$this->getEntityManager()->getConnection()->setFetchMode(\PDO::FETCH_ASSOC);
$results = $this->getEntityManager()->getConnection()->executeQuery($nativeSqlTaxon, ['collectionCode' => $collection->getCollectioncode(), 'catalogNumbers' => $catalogNumbers], ['catalogNumbers' => Connection::PARAM_STR_ARRAY])->fetchAll();
$formattedResult = [];
if (count($results)) {
foreach ($results as $values) {
$formattedResult[$values['CATALOGNUMBER']] = Taxon::toString($values['SCIENTIFICNAME'], $values['SCIENTIFICNAMEAUTHORSHIP']);
}
}
return $formattedResult;
}
public function checkUserRight(User $user, Collection $collection)
{
if (!$user->isManagerFor($collection->getCollectioncode())) {
throw new AccessDeniedException($this->translator->trans('access.denied.wrongPermission', [], 'exceptions'));
}
}
private function setLogFilePath()
{
$now = new \DateTime();
$logFilePath = sprintf($this->getContainer()->getParameter('export_path') . '/' . $this->logFileTemplate, $this->collection->getInstitution()->getInstitutioncode(), $this->collection->getCollectioncode(), $now->format('d-m-Y-H-i-s'));
$this->logFile = new \SplFileObject($logFilePath, 'w+');
}
/**
* @param Collection $collection
* @return $this
* @throws \Exception
*/
public function setCollection(Collection $collection)
{
$this->collection = $collection;
$this->collectionCode = $collection->getCollectioncode();
if (is_null($this->collection)) {
throw new \Exception('Can\'t found the collection with collectionCode = ' . $this->collectionCode);
} else {
$this->diffHandler = new DiffHandler($this->user->getDataDirPath(), $this->collection, $this->userGroup);
//if (!$this->getDiffHandler()->shouldSearchDiffs()) {
$this->selectedSpecimensHandler = new SelectedSpecimensHandler($this->diffHandler->getCollectionPath(), $this->userGroup);
$data = $this->getDiffHandler()->getDiffsFile()->getData();
$data['selectedSpecimens'] = $this->selectedSpecimensHandler->getData();
$this->sessionHandler = new SessionHandler($this->sessionManager, $this->genericEntityManager, $data);
$this->getSessionHandler()->init($this->getDiffHandler(), $this->collectionCode);
//}
}
return $this;
}
