Public Member Functions | |
| form ($form, &$form_state) | |
| formValidate ($form, &$form_state) | |
| run () | |
| getLandmarkTypeID ($landmark_name) | |
| postRun () | |
| formSubmit ($form, &$form_state) | |
| insert_cvterm ($term, $options=[]) | |
 Public Member Functions inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| __construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection) | |
| getChadoConnection () | |
| addAnalysis ($form, &$form_state) | |
| Public Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase | |
| __construct (array $configuration, $plugin_id, $plugin_definition) | |
| describeUploadFileFormat () | |
| setJob ($job) | |
| createImportJob ($run_args, $file_details=[]) | |
| load ($import_id) | |
| submitJob () | |
| prepareFiles () | |
| cleanFile () | |
| getArguments () | |
Additional Inherited Members | |
| Static Public Member Functions inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| static | create (ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition) |
| Protected Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase | |
| setTotalItems ($total_items) | |
| addItemsHandled ($num_handled) | |
| setItemsHandled ($total_handled) | |
| setInterval ($interval) | |
| Protected Attributes inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase | |
| $chado_schema_main | |
| $messenger = NULL | |
| $connection | |
| Protected Attributes inherited from Drupal\tripal\TripalImporter\TripalImporterBase | |
| $job | |
| $logger | |
| $arguments | |
| $import_id | |
| $is_prepared | |
| $messenger = NULL | |
| $reported | |
| $plugin_id | |
| $plugin_definition | |
Detailed Description
GFF3 Importer implementation of the TripalImporterBase.
@TripalImporter( id = "chado_gff3_loader", label = @Translation("Chado GFF3 File Loader"), description = @Translation("Import a GFF3 file into Chado"), file_types = {"gff","gff3", "txt"}, upload_description = @Translation("Please provide a plain text, tab-delimited file following the <a target='_blank' href='https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md'>GFF3 Specification</a>. It is expected that all landmark features are associated with the same organism and that the type (column 3) are sequence ontology terms."), upload_title = @Translation("GFF3 File"), use_analysis = True, require_analysis = True, button_text = @Translation("Import GFF3 file"), file_upload = True, file_remote = True, file_local = True, file_required = True, )
Member Function Documentation
◆ form()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::form | ( | $form, | |
| & | $form_state | ||
| ) |
{Provides form elements to be added to the loader form.These form elements are added after the file uploader section that is automaticaly provided by the TripalImporter.
- Parameters
-
array $form The form array definition. \Drupal\Core\Form\FormStateInterface $form_state The form state object.
- Returns
- array A new form array definition.
Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.
◆ formSubmit()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::formSubmit | ( | $form, | |
| & | $form_state | ||
| ) |
{Handles submission of the form elements.The form elements provided in the implementation of the form() function can be used for special submit if needed.
- Parameters
-
array $form The form array definition. \Drupal\Core\Form\FormStateInterface $form_state The form state object.
Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.
◆ formValidate()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::formValidate | ( | $form, | |
| & | $form_state | ||
| ) |
Handles validation of the form elements.The form elements provided in the implementation of the form() function should be validated using this function.
- Parameters
-
array $form The form array definition.* \Drupal\Core\Form\FormStateInterface $form_state The form state object.
Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.
◆ getLandmarkTypeID()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::getLandmarkTypeID | ( | $landmark_name | ) |
This looks up the landmark type_id by utilizing the landmark_types associate array cached values and then checks the landmark_types_type_ids associate array cached values.
◆ postRun()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::postRun | ( | ) |
{Performs the import.}
Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.
◆ run()
| Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::run | ( | ) |
Performs the import.
Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.
The documentation for this class was generated from the following file:
- tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php
