← Về thư mục
- PathSanitisingTests · class · L67-L110 — class PathSanitisingTests(unittest.TestCase)
- test_ordinary_paths_pass_through_unchanged · method · L68-L73 — def test_ordinary_paths_pass_through_unchanged(self) -> None
- test_empty_and_none_fall_back_to_the_default · method · L75-L81 — def test_empty_and_none_fall_back_to_the_default(self) -> None
- test_shell_metacharacters_are_refused · method · L83-L98 — def test_shell_metacharacters_are_refused(self) -> None
- test_parent_directory_segments_are_refused · method · L100-L104 — def test_parent_directory_segments_are_refused(self) -> None
- test_a_dotdot_substring_inside_a_name_is_allowed · method · L106-L110 — def test_a_dotdot_substring_inside_a_name_is_allowed(self) -> None: # Only whole segments are parent references;
a..b.bam is a filename.
- PathListTests · class · L113-L132 — class PathListTests(unittest.TestCase)
- test_space_separated_values_are_split_and_validated · method · L114-L118 — def test_space_separated_values_are_split_and_validated(self) -> None
- test_an_empty_list_is_refused · method · L120-L122 — def test_an_empty_list_is_refused(self) -> None
- test_one_bad_entry_rejects_the_whole_list · method · L124-L126 — def test_one_bad_entry_rejects_the_whole_list(self) -> None
- test_quoting_cannot_smuggle_a_space_into_a_single_path · method · L128-L132 — def test_quoting_cannot_smuggle_a_space_into_a_single_path(self) -> None: # shlex.split honours the quotes, but sanitize_path then rejects the # space -- the two layers have to agree, not just the first.
- PositiveIntTests · class · L135-L148 — class PositiveIntTests(unittest.TestCase)
- test_integers_and_integer_strings_are_accepted · method · L136-L138 — def test_integers_and_integer_strings_are_accepted(self) -> None
- test_zero_negative_and_non_numeric_are_refused · method · L140-L148 — def test_zero_negative_and_non_numeric_are_refused(self) -> None
- ShellQuotingTests · class · L151-L167 — class ShellQuotingTests(unittest.TestCase)
- test_values_are_quoted_for_bash · method · L152-L154 — def test_values_are_quoted_for_bash(self) -> None
- test_arrays_quote_each_element · method · L156-L159 — def test_arrays_quote_each_element(self) -> None
- test_relative_run_hints_are_prefixed_so_bash_finds_them · method · L161-L167 — def test_relative_run_hints_are_prefixed_so_bash_finds_them(self) -> None
- GeneratedScriptTests · class · L170-L209 — class GeneratedScriptTests(unittest.TestCase)
- _generate · method · L173-L177 — def _generate(self, workflow: str) -> str
- test_every_advertised_workflow_has_a_generator · method · L179-L180 — def test_every_advertised_workflow_has_a_generator(self) -> None
- test_generated_scripts_parse_as_bash · method · L182-L195 — def test_generated_scripts_parse_as_bash(self) -> None
- test_generated_scripts_fail_fast · method · L197-L202 — def test_generated_scripts_fail_fast(self) -> None
- test_parameters_reach_the_script_quoted · method · L204-L209 — def test_parameters_reach_the_script_quoted(self) -> None
- FileValidationTests · class · L212-L315 — class FileValidationTests(unittest.TestCase)
- test_missing_file_is_reported_not_raised · method · L213-L216 — def test_missing_file_is_reported_not_raised(self) -> None
- test_bam_index_is_found_under_either_naming_convention · method · L218-L237 — def test_bam_index_is_found_under_either_naming_convention(self) -> None
- test_tiny_bigwig_is_flagged_as_suspicious · method · L239-L250 — def test_tiny_bigwig_is_flagged_as_suspicious(self) -> None
- test_well_formed_bed_passes_and_counts_regions · method · L252-L264 — def test_well_formed_bed_passes_and_counts_regions(self) -> None
- test_bed_rejects_too_few_columns_bad_types_and_inverted_ranges · method · L266-L280 — def test_bed_rejects_too_few_columns_bad_types_and_inverted_ranges(self) -> None
- test_comment_only_bed_is_treated_as_empty · method · L282-L288 — def test_comment_only_bed_is_treated_as_empty(self) -> None
- test_validate_files_aggregates_across_types · method · L290-L310 — def test_validate_files_aggregates_across_types(self) -> None
- test_no_files_means_nothing_to_report · method · L312-L315 — def test_no_files_means_nothing_to_report(self) -> None