| $all_orgs | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| $arguments | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $bundle_type_id | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | protected |
| $chado_schema_main (defined in Drupal\tripal_chado\TripalImporter\ChadoImporterBase) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | protected |
| $connection (defined in Drupal\tripal_chado\TripalImporter\ChadoImporterBase) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | protected |
| $fileretriever (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $import_id | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $is_prepared | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $job | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $logger (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $messenger (defined in Drupal\tripal_chado\TripalImporter\ChadoImporterBase) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | protected |
| $phylotree | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| $plugin_definition (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $plugin_id (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $publish_manager (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $rank_cvterm_id | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| $reported (defined in Drupal\tripal\TripalImporter\TripalImporterBase) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| $tree | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| __construct(array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection, ?Messenger $messenger=NULL, ?TripalLogger $logger=NULL, ?TripalFileRetriever $fileretriever=NULL, ?TripalBackendPublishManager $publish_manager=NULL,) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| Drupal::tripal::TripalImporter::TripalImporterBase::__construct(array $configuration, $plugin_id, $plugin_definition, ?Messenger $messenger=NULL, ?TripalLogger $logger=NULL, ?TripalFileRetriever $fileretriever=NULL, ?TripalBackendPublishManager $publish_manager=NULL,) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| addAnalysis($form, &$form_state) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| addBundleTypeProperty(string $pkey, int $record_id, string $property_table, string $termIdSpace, string $termAccession, string $value='', ?int $rank=NULL) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | protected |
| addItemsHandled($num_handled) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| addOrganismNode($organism, $root_taxon=NULL) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| addTaxonomyNode(&$tree, $node, $lineage_elements) (defined in Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| cleanFile() | Drupal\tripal\TripalImporter\TripalImporterBase | |
| create(ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition,) | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | static |
| createImportJob($run_args, $file_details=[]) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| describeUploadFileFormat() | Drupal\tripal\TripalImporter\TripalImporterBase | |
| form($form, &$form_state) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | |
| formSubmit($form, &$form_state) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | |
| formValidate($form, &$form_state) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | |
| getArguments() | Drupal\tripal\TripalImporter\TripalImporterBase | |
| getChadoConnection() | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| getPhylonode(int $phylotree_id, int $organism_id) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| initTree($tree_name) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| load($import_id) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| postRun() | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| prepareFiles() | Drupal\tripal\TripalImporter\TripalImporterBase | |
| queryPhylonode(int $phylotree_id, string $node_name, bool &$lineage_good, array &$lineage_nodes) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| rebuildTree($root_taxon=NULL) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| rebuildTreeOrganismLineage($organism, $root_taxon, &$tree, &$lineage_good) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| removeTree($tree_name) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| retrieveLineage($root_taxon=NULL) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| rollbackTransaction(string $stage) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| run() | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | |
| setArguments(array $arguments) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| setInterval($interval) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| setItemsHandled($total_handled) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| setJob($job) | Drupal\tripal\TripalImporter\TripalImporterBase | |
| setTotalItems($total_items) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
| startTransactions() | Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| submitJob() | Drupal\tripal\TripalImporter\TripalImporterBase | |
| trimLineage($lineage, $root_taxon=NULL) | Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator | protected |
| xmlIsValid(string $xml) | Drupal\tripal\TripalImporter\TripalImporterBase | protected |
