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datamanagertest.php
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datamanagertest.php
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<?php
gc_enable();
$dataset = new Dataset();
$form = $this->createForm('AppBundle\Form\DatasetType', $dataset);
$form->handleRequest($request);
$em = $this->getDoctrine()->getManager();
$query = $em->createQuery(
"SELECT ds
FROM AppBundle:Dataset ds"
);
$dataset_array = $query->getResult();
$delete_dataset_array = array();
foreach($dataset_array as $dataset){
$id = $dataset->getId();
$year = $dataset->getYear();
$author = $dataset->getAuthor();
$delete_dataset_array[$id] = "$author ($year)";
}
$defaultData = array('message' => 'Type your message here');
$delete_form = $this->createFormBuilder($defaultData)
->add('dataset_to_delete', ChoiceType::class, array(
'choices' => $delete_dataset_array))->getForm();
$delete_form->handleRequest($request);
///$handle = fopen("C:\\Users\\Miles\\Desktop\\test\\test.txt", "w");
//stats for data upload
$interactions_added = 0;
$new_proteins_added = 0;
$new_identifier_added = 0;
$new_organisms_added = 0;
$new_datasets_added = 0;
$new_domain_added = 0;
if ($delete_form->isSubmitted() && $delete_form->isValid()) {
$dataset_id = $delete_form->get('dataset_to_delete')->getData();
self::deleteData($dataset_id);
return $this->redirectToRoute('data_manager');
}
if ($form->isSubmitted() && $form->isValid()) {
/** @var Symfony\Component\HttpFoundation\File\UploadedFile $file */
$file = $data_File->getDataFile();
$fileName = $file->getClientOriginalName();
$file->move(
$this->container->getParameter('data_file_directory'),
$fileName
);
$data_File->setDataFile($fileName);
$upload_dir = $this->get('kernel')->getRootDir() . '/../web/uploads/data/';
$filepath = $upload_dir . $fileName;
$handle = fopen($filepath , "r");
$form_data = $form->getData();
$file_type = $form_data->getFileType();
$file_row = 0;
while ($file_data = fgetcsv($handle, 0, "\t"))
{
//skip header
if($file_row < 1){ $file_row++; continue; }
try{
//variable for each mitab coloumn
list ($interactor_A_id, $interactor_B_id, $alt_interactor_A_id, $alt_interactor_B_id, $interactor_A_alias, $interactor_B_alias, $interaction_detection_method,
$publication_first_author, $publication_identifier, $taxid_interactor_A, $taxid_interactor_B, $interaction_type, $source_database,
$interaction_identifier, $confidence_value, $expansion_method, $biological_role_interactor_A, $biological_role_interactor_B,
$experimental_role_interactor_A, $experimental_role_interactor_B, $type_interactor_A, $type_interactor_B, $xref_interactor_A,
$xref_interactor_B, $interaction_xref, $annotation_interactor_A, $annotation_interactor_B, $interaction_annotation, $host_organism,
$interaction_parameter, $creation_date, $update_date, $checksum_interactor_A, $checksum_interactor_B, $interaction_checksum,
$negative, $feature_interactor_A, $feature_interactor_B, $stoichiometry_interactor_A, $stoichiometry_interactor_B,
$identification_method_participant_A, $identification_method_participant_B) = $file_data;
$doctrine_manager = $this->getDoctrine()->getManager();
$doctrine_manager->getConfiguration()->setSQLLogger(null);
if(self::isNewInteraction($interactor_A_id, $interactor_B_id) == true){
//Domain
$domain = self::domainHandler($feature_interactor_A);
//Organism
$organism_array = self::organismHandler($taxid_interactor_A, $taxid_interactor_B, $doctrine_manager);
$organism_A_array = $organism_array[0];
$organism_B_array = $organism_array[1];
$organism_AB_array = $organism_array[2];
//Protein
$protein_A_array = self::proteinHandler($interactor_A_id, $doctrine_manager);
$protein_A = $protein_A_array[0];
$identifier_A_protein = $protein_A_array[1];
$links_array_A = $protein_A_array[2];
if($identifier_A_protein){
$identifier_A_protein->setProtein($protein_A);
}
$protein_B_array = self::proteinHandler($interactor_B_id, $doctrine_manager);
$protein_B = $protein_B_array[0];
$identifier_B_protein = $protein_B_array[1];
$links_array_B = $protein_B_array[2];
if($identifier_B_protein){
$identifier_B_protein->setProtein($protein_B);
}
//Interaction
$interaction = self::interactionHandler($feature_interactor_B, $confidence_value);
//Alt Interactor
$alt_interactor_array = self::alt_interactorHandler($alt_interactor_A_id, $alt_interactor_B_id);
//Aliases
$alias_interactor_array = self::aliasHandler($interactor_A_alias, $interactor_B_alias);
//Support Information
$support_informations_array = self::support_informationHandler($interaction_parameter);
$support_information_array = '';
$interaction_support_information_array = '';
if($support_informations_array){
$support_information_array = $support_informations_array[0];
$interaction_support_information_array = $support_informations_array[1];
}
//Dataset
$dataset = self::datasetHandler($publication_identifier, $publication_first_author);
foreach ($organism_AB_array as $organism_AB){
if(self::assertRelationshipExistsProteinOrganism($protein_A, $organism_AB) == false){
$organism_AB->addProtein($protein_A);
$protein_A->addOrganism($organism_AB);
}
if($domain){
if(self::assertRelationshipExistsDomainOrganism($domain, $organism_AB) == false){
$domain->addOrganism($organism_AB);
$organism_AB->addDomain($domain);
}
}
if(self::assertRelationshipExistsProteinOrganism($protein_B, $organism_AB) == false){
$organism_AB->addProtein($protein_B);
$protein_B->addOrganism($organism_AB);
}
$doctrine_manager->persist($organism_AB);
}
foreach ($organism_A_array as $organism_A){
if(self::assertRelationshipExistsProteinOrganism($protein_A, $organism_A) == false){
$organism_A->addProtein($protein_A);
$protein_A->addOrganism($organism_A);
}
if($domain){
if(self::assertRelationshipExistsDomainOrganism($domain, $organism_A) == false){
$domain->addOrganism($organism_A);
$organism_A->addDomain($domain);
}
}
$doctrine_manager->persist($organism_A);
}
foreach ($organism_B_array as $organism_B){
if(self::assertRelationshipExistsProteinOrganism($protein_B, $organism_B) == false){
$organism_B->addProtein($protein_B);
$protein_B->addOrganism($organism_B);
}
$doctrine_manager->persist($organism_B);
}
if($support_information_array){
foreach ($support_information_array as $support_information){
$doctrine_manager->persist($support_information);
}
}
if($interaction_support_information_array){
foreach ($interaction_support_information_array as $interaction_support_information){
$interaction->addInteractionSupportInformation($interaction_support_information);
$interaction_support_information->setInteraction($interaction);
$doctrine_manager->persist($interaction_support_information);
}
}
if($identifier_A_protein){
$doctrine_manager->persist($identifier_A_protein);
}
if($identifier_B_protein){
$doctrine_manager->persist($identifier_B_protein);
}
$alt_interactor_A_array = $alt_interactor_array[0];
foreach ($alt_interactor_A_array as $alt_interactor_A){
$alt_interactor_A->setProtein($protein_A);
$doctrine_manager->persist($alt_interactor_A);
}
$alt_interactor_B_array = $alt_interactor_array[1];
foreach ($alt_interactor_B_array as $alt_interactor_B){
$alt_interactor_B->setProtein($protein_B);
$doctrine_manager->persist($alt_interactor_B);
}
$alias_interactor_A_array = $alias_interactor_array[0];
foreach ($alias_interactor_A_array as $alias_interactor_A){
$alias_interactor_A->setProtein($protein_A);
$doctrine_manager->persist($alias_interactor_A);
}
$alias_interactor_B_array = $alias_interactor_array[1];
foreach ($alias_interactor_B_array as $alias_interactor_B){
$alias_interactor_B->setProtein($protein_B);
$doctrine_manager->persist($alias_interactor_B);
}
if($links_array_A){
foreach ($links_array_A as $link_A){
$doctrine_manager->persist($link_A);
}
}
if($links_array_B){
foreach ($links_array_B as $link_B){
$doctrine_manager->persist($link_B);
}
}
if($dataset){
$dataset->addInteraction($interaction);
$interaction->addDataset($dataset);
$doctrine_manager->persist($dataset);
}
$interaction->setInteractorA($protein_A);
$interaction->setInteractorB($protein_B);
if($domain != null){
$interaction->setDomain($domain);
$domain->setProtein($protein_A);
$doctrine_manager->persist($domain);
}
$doctrine_manager->persist($interaction);
$doctrine_manager->flush();
$doctrine_manager->clear();
gc_collect_cycles();
}elseif(self::isNewDatasetFromPublicationIdentifier($publication_identifier) == false){
$interaction = self::getInteractionByIds($interactor_A_id, $interactor_B_id);
$dataset = self::getDatasetByPublicationIdentifier($publication_identifier);
if(self::assertRelationshipExistsInteractionDataset($interaction, $dataset) == false){
$dataset->addInteraction($interaction);
$interaction->addDataset($dataset);
$doctrine_manager->persist($dataset);
$doctrine_manager->persist($interaction);
$doctrine_manager->flush();
$doctrine_manager->clear();
gc_collect_cycles();
}
}elseif(self::isNewDatasetFromPublicationIdentifier($publication_identifier) == true){
$interaction = self::getInteractionByIds($interactor_A_id, $interactor_B_id);
$dataset = self::datasetHandler($publication_identifier, $publication_first_author);
$dataset->addInteraction($interaction);
$interaction->addDataset($dataset);
$doctrine_manager->persist($dataset);
$doctrine_manager->persist($interaction);
$doctrine_manager->flush();
$doctrine_manager->clear();
gc_collect_cycles();
}
}catch(Exception $e) {
}
}
}
$admin_settings = $this->getDoctrine()
->getRepository('AppBundle:Admin_Settings')
->find(1);
$footer = $admin_settings->getFooter();
$main_color_scheme = $admin_settings->getMainColorScheme();
$header_color_scheme = $admin_settings->getHeaderColorScheme();
$logo_color_scheme = $admin_settings->getLogoColorScheme();
$button_color_scheme = $admin_settings->getButtonColorScheme();
$short_title = $admin_settings->getShortTitle();
$title = $admin_settings->getTitle();
return $this->render('data_manager.html.twig', array(
'delete_form' => $delete_form->createView(),
'form' => $form->createView(),
'dataset_array' => $dataset_array,
'footer' => $footer,
'main_color_scheme' => $main_color_scheme,
'header_color_scheme' => $header_color_scheme,
'logo_color_scheme' => $logo_color_scheme,
'button_color_scheme' => $button_color_scheme,
'short_title' => $short_title,
'title' => $title
));