/**
* {@inheritDoc}
*/
public function load(ObjectManager $om)
{
$om = $this->container->get('vib.doctrine.registry')->getManagerForClass('VIB\\FliesBundle\\Entity\\Stock');
$vm = $this->container->get('vib.doctrine.registry')->getManagerForClass('VIB\\FliesBundle\\Entity\\Vial');
$om->disableAutoAcl();
$vm->disableAutoAcl();
$user = $this->getReference('user');
$stock_1 = new Stock();
$stock_1->setName('stock 1');
$stock_1->setGenotype('yw');
$om->persist($stock_1);
$om->flush();
$om->createACL($stock_1, $user);
$vm->createACL($stock_1->getVials(), $user);
$this->addReference('stock_1', $stock_1);
$stock_2 = new Stock();
$stock_2->setName('stock 2');
$stock_2->setGenotype('yw;Sp/CyO');
$om->persist($stock_2);
$om->flush();
$om->createACL($stock_2, $user);
$vm->createACL($stock_2->getVials(), $user);
$this->addReference('stock_2', $stock_2);
$admin = $this->getReference('admin');
$stock_3 = new Stock();
$stock_3->setName('stock 3');
$stock_3->setGenotype('yw;;Tm2/Tm6');
$om->persist($stock_3);
$om->flush();
$om->createACL($stock_3, $admin);
$vm->createACL($stock_3->getVials(), $admin);
$this->addReference('stock_3', $stock_3);
$stock_4 = new Stock();
$stock_4->setName('stock 4');
$stock_4->setGenotype('yw/Fm7');
$om->persist($stock_4);
$om->flush();
$om->createACL($stock_4, $admin);
$vm->createACL($stock_4->getVials(), $admin);
$this->addReference('stock_4', $stock_4);
$om->enableAutoAcl();
$vm->enableAutoAcl();
}
public function crossParentNameProvider()
{
$stock = new Stock();
$stock->setGenotype('test genotype');
$stock->setName('test stock');
$stockVial = new StockVial();
$stockVial->setStock($stock);
$injection = new InjectionVial();
$injection->setTargetStock($stock);
$injection->setConstructName('test');
return array(array(new FakeCrossVial(), null, 'test'), array(new FakeCrossVial(), $stockVial, 'test parent'), array(new FakeCrossVial(), $injection, 'test parent'), array(new FakeCrossVial(), new CrossVial(), 'test'));
}
protected function execute(InputInterface $input, OutputInterface $output)
{
$filename = $input->getArgument('csv');
$file = fopen($filename, 'r');
$logfilename = $input->getArgument('logfile');
$logfile = fopen($logfilename, 'w');
$listfilename = $input->getArgument('listfile');
$importlist = array();
if ($listfilename) {
$listfile = fopen($listfilename, 'r');
if ($listfile) {
while ($data = fgetcsv($listfile, 0, "\t")) {
$importlist[] = $data[0];
}
}
}
$dialog = $this->getHelperSet()->get('dialog');
$this->container = $this->getApplication()->getKernel()->getContainer();
$connection = $this->container->get('database_connection');
$om = $this->container->get('vib.doctrine.registry')->getManagerForClass('VIB\\CoreBundle\\Entity\\Entity');
$vm = $this->container->get('vib.doctrine.registry')->getManagerForClass('VIB\\FliesBundle\\Entity\\StockVial');
$om->disableAutoAcl();
$vm->disableAutoAcl();
$stocks = array();
$stock_register = array();
$vials = array();
if ($file) {
while ($data = fgetcsv($file, 0, "\t")) {
$trim = " \t\n\r\v\"";
$owner_name = trim($data[0], $trim);
$stock_name = trim($data[1], $trim);
$stock_genotype = trim($data[2], $trim);
$creator_name = trim($data[4], $trim);
$stock_notes = trim($data[5], $trim);
$stock_vendor = trim($data[6], $trim);
$stock_vendor_id = trim($data[7], $trim);
$stock_info_url = str_replace(" ", "", trim($data[8], $trim));
$stock_verified = trim($data[9], $trim) == "yes" ? true : false;
$stock_vials_size = trim($data[10], $trim);
$stock_vials_size = $stock_vials_size == "" ? 'medium' : $stock_vials_size;
$stock_vials_number = (int) trim($data[11], $trim);
$stock_vials_number = $stock_vials_number <= 0 ? 1 : $stock_vials_number;
$stock_vials_food = trim($data[12], $trim);
$stock_vials_food = $stock_vials_food == "" ? 'standard' : $stock_vials_food;
$test = $om->getRepository('VIB\\FliesBundle\\Entity\\Stock')->findOneByName($stock_name);
if (!in_array($stock_name, $stock_register) && $creator_name == "" && null === $test) {
if ($stock_vendor != "" && $stock_vendor_id != "") {
$output->write("Querying FlyBase for " . $stock_name . ": ");
$stock_data = $this->getStockData($stock_vendor, $stock_vendor_id);
if (count($stock_data) == 1) {
$stock_genotype = $stock_data[0]['stock_genotype'];
$stock_info_url = $stock_data[0]['stock_link'];
$output->writeln("success");
} elseif (count($stock_data) != 1) {
$output->writeln("failed");
}
}
$stock = new Stock();
$stock->setName($stock_name);
$stock->setGenotype($stock_genotype);
$stock->setNotes($stock_notes);
$stock->setVendor($stock_vendor);
$stock->setVendorId($stock_vendor_id);
$stock->setInfoURL($stock_info_url);
$stock->setVerified($stock_verified);
for ($i = 0; $i < $stock_vials_number - 1; $i++) {
$vial = new StockVial();
$stock->addVial($vial);
}
$stock_vials = $stock->getVials();
foreach ($stock_vials as $vial) {
$vial->setSize($stock_vials_size);
$vial->setFood($stock_vials_food);
}
$stock_register[] = $stock_name;
$stocks[$owner_name][$stock_name] = $stock;
} else {
$vials[$owner_name][$stock_name]['size'] = $stock_vials_size;
$vials[$owner_name][$stock_name]['number'] = $stock_vials_number;
$vials[$owner_name][$stock_name]['food'] = $stock_vials_food;
}
}
}
$connection->beginTransaction();
foreach ($stocks as $user_name => $user_stocks) {
try {
$user = $this->container->get('user_provider')->loadUserByUsername($user_name);
} catch (UsernameNotFoundException $e) {
$user = null;
}
if ($user instanceof UserInterface) {
$output->writeln("Adding stocks for user " . $user_name . ":");
$userStocks = new ArrayCollection();
$userVials = new ArrayCollection();
foreach ($user_stocks as $stock_name => $stock) {
$om->persist($stock);
$userStocks->add($stock);
$userVials->add($stock->getVials());
$output->write(".");
fprintf($logfile, "%s\n", $stock->getName());
}
$om->flush();
$output->writeln("");
$output->write("Creating ACLs...");
$om->createACL($userStocks, $user);
$vm->createACL($userVials, $user);
$output->writeln(" done");
} else {
$output->writeln("<error>User " . $user_name . " does not exits. Skipping!</error>");
}
}
foreach ($vials as $user_name => $user_vials) {
try {
$user = $this->container->get('user_provider')->loadUserByUsername($user_name);
} catch (UsernameNotFoundException $e) {
$user = null;
}
if ($user instanceof UserInterface) {
$output->writeln("Adding vials for user " . $user_name . ":");
$userVials = new ArrayCollection();
foreach ($user_vials as $stock_name => $stock_vials) {
$stock = $om->getRepository('VIB\\FliesBundle\\Entity\\Stock')->findOneByName($stock_name);
if ($stock instanceof Stock) {
$stockVials = new ArrayCollection();
for ($i = 0; $i < $stock_vials['number']; $i++) {
$vial = new StockVial();
$stock->addVial($vial);
$stockVials->add($vial);
$userVials->add($vial);
}
foreach ($stockVials as $vial) {
$vial->setSize($stock_vials['number']);
$vial->setFood($stock_vials['number']);
$vm->persist($vial);
}
$output->write(".");
} else {
$output->write("?");
}
}
$output->writeln("");
$vm->flush();
$vm->createACL($userVials, $user);
} else {
$output->writeln("<error>User " . $user_name . " does not exits. Skipping!</error>");
}
}
$message = 'Stocks and vials have been created. Commit?';
if ($dialog->askConfirmation($output, '<question>' . $message . '</question>', true)) {
$connection->commit();
} else {
$connection->rollback();
$connection->close();
}
$om->enableAutoAcl();
$vm->enableAutoAcl();
}
