Public Member Functions | |
| testGFFImporterSimpleTest () | |
 Public Member Functions inherited from Drupal\Tests\tripal\Functional\TripalTestBrowserBase | |
| createTripalTerm ($values, $idspace_plugin_id, $vocab_plugin_id) | |
| createTripalContent ($values=[]) | |
| createTripalContentType ($values=[]) | |
Additional Inherited Members | |
| Public Attributes inherited from Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase | |
| const | SCHEMA_NAME_ONLY = 0 |
| const | CREATE_SCHEMA = 1 |
| const | INIT_DUMMY = 2 |
| const | INIT_CHADO_EMPTY = 3 |
| const | INIT_CHADO_DUMMY = 4 |
| const | PREPARE_TEST_CHADO = 5 |
| Protected Member Functions inherited from Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase | |
| setUp () | |
| Protected Attributes inherited from Drupal\Tests\tripal\Functional\TripalTestBrowserBase | |
| $defaultTheme = 'stark' | |
| Static Protected Attributes inherited from Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase | |
| static | $modules = ['tripal', 'tripal_biodb', 'tripal_chado'] |
| Static Protected Attributes inherited from Drupal\Tests\tripal\Functional\TripalTestBrowserBase | |
| static | $modules = ['tripal'] |
Detailed Description
Tests for the GFF3Importer class
@group TripalImporter @group ChadoImporter @group GFF3Importer
Member Function Documentation
◆ testGFFImporterSimpleTest()
| Drupal\Tests\tripal_chado\Functional\GFF3ImporterTest::testGFFImporterSimpleTest | ( | ) |
Confirm basic GFF importer functionality.
@group gff
Run the GFF loader on gff_duplicate_ids.gff for testing.
This tests whether the GFF loader detects duplicate IDs which makes a GFF file invalid since IDs should be unique. The GFF loader should throw and exception which this test checks for
Run the GFF loader on gff_tag_unescaped_character.gff for testing.
This tests whether the GFF loader adds IDs that contain a comma. The GFF loader should allow it
Run the GFF loader on gff_invalidstartend.gff for testing.
This tests whether the GFF loader fixes start end values
Run the GFF loader on gff_phase_invalid_character.gff for testing.
This tests whether the GFF loader interprets the phase values correctly for CDS rows when a character outside of the range 0,1,2 is specified.
Run the GFF loader on gff_phase_invalid_number.gff for testing.
This tests whether the GFF loader interprets the phase values correctly for CDS rows when a number outside of the range 0,1,2 is specified.
Test that when checked, when phase is specified for CDS
@TODO Add a skip protein option. Test that when checked, implicit proteins are not created, but that they are created when unchecked.
Run the GFF loader on gff_rightarrow_ids.gff for testing.
This tests whether the GFF loader fails if ID contains arrow >. It should not fail.
Run the GFF loader on gff_score.gff for testing.
This tests whether the GFF loader interprets the score values
Run the GFF loader on gff_seqid_invalid_character.gff for testing. Seqids seem to also be called landmarks within GFF loader. This tests whether the GFF loader has any issues with characters like single quotes.
Run the GFF loader on gff_strand_invalid.gff for testing.
This tests whether the GFF loader interprets the strand values
Run the GFF loader on gff_strand.gff for testing.
This tests whether the GFF loader interprets the strand values
Run the GFF loader on gff_tag_parent_verification.gff for testing.
This tests whether the GFF loader adds Parent attributes The GFF loader should allow it
Run the GFF loader on gff_tagvalue_encoded_character.gff for testing.
This tests whether the GFF loader adds IDs that contain encoded character. The GFF loader should allow it
Run the GFF loader on gff_tagvalue_comma_character.gff for testing.
This tests whether the GFF loader adds tag values contain comma seperation character. The GFF loader should allow it
Run the GFF loader on gff_tagvalue_comma_character.gff for testing.
This tests whether the GFF loader adds tag values containing encoded comma character. The GFF loader should allow it
Run the GFF loader on gff_1380_landmark_test.gff for testing.
This tests whether the GFF loader adds landmarks directly from the GFF file character. The GFF loader should allow it
Run the GFF loader on Citrus GFF3 for testing.
This tests whether the GFF loader adds Citrus data character. The GFF loader should allow it
The documentation for this class was generated from the following file:
- tripal_chado/tests/src/Functional/Plugin/GFF3ImporterTest.php
