studies.tests package

Submodules

studies.tests.test_pheno_measures_columns module

studies.tests.test_pheno_measures_columns.test_pheno_measure_genotype_browser_columns(admin_client: Client, t4c8_wgpf_instance: WGPFInstance) → None[source]
studies.tests.test_pheno_measures_columns.test_study_with_phenotype_data(t4c8_wgpf_instance: WGPFInstance) → None[source]

studies.tests.test_query_transformer_family_tags module

studies.tests.test_query_transformer_family_tags.test_transform_and_mode_family_tags_kwargs(t4c8_wgpf_instance: WGPFInstance, t4c8_study_1_wrapper: WDAEStudy) → None[source]
studies.tests.test_query_transformer_family_tags.test_transform_complex_family_tags_kwargs(t4c8_wgpf_instance: WGPFInstance, t4c8_study_1_wrapper: WDAEStudy) → None[source]
studies.tests.test_query_transformer_family_tags.test_transform_deselected_family_tags_kwargs(t4c8_wgpf_instance: WGPFInstance, t4c8_study_1_wrapper: WDAEStudy) → None[source]
studies.tests.test_query_transformer_family_tags.test_transform_or_mode_family_tags_kwargs(t4c8_wgpf_instance: WGPFInstance, t4c8_study_1_wrapper: WDAEStudy) → None[source]
studies.tests.test_query_transformer_family_tags.test_transform_selected_family_tags_kwargs(t4c8_wgpf_instance: WGPFInstance, t4c8_study_1_wrapper: WDAEStudy) → None[source]

studies.tests.test_query_transformer_present_in_child_and_parent module

studies.tests.test_query_transformer_present_in_child_and_parent.test_attributes_query_roles() → None[source]
studies.tests.test_query_transformer_present_in_child_and_parent.test_transform_present_in_child_and_present_in_parent(present_in_child: set[str], present_in_parent: set[str], inheritance: list[Inheritance], roles: list[Role], accepted: bool) → None[source]
studies.tests.test_query_transformer_present_in_child_and_parent.test_transform_present_in_child_and_present_in_parent_inheritance(present_in_child: set[str], present_in_parent: set[str], accepted: list[int], rejected: list[int], expected_query: str) → None[source]
studies.tests.test_query_transformer_present_in_child_and_parent.test_transform_present_in_child_and_present_in_parent_roles(present_in_child: set[str], present_in_parent: set[str], accepted: list[int], rejected: list[int], expected_query: str) → None[source]

studies.tests.test_response_transformer_columns module

studies.tests.test_response_transformer_columns.fv1(t4c8_study_1: GenotypeData) → FamilyVariant[source]
studies.tests.test_response_transformer_columns.fv2(t4c8_study_1: GenotypeData) → FamilyVariant[source]
studies.tests.test_response_transformer_columns.phenotype_person_sets(t4c8_study_1: GenotypeData) → PersonSetCollection[source]
studies.tests.test_response_transformer_columns.test_inheritance_type_column(fv2: FamilyVariant) → None[source]
studies.tests.test_response_transformer_columns.test_is_denovo(fv2: FamilyVariant) → None[source]
studies.tests.test_response_transformer_columns.test_phenotype_attr_columns(fv1: FamilyVariant, phenotype_person_sets: PersonSetCollection, column: str, expected: list[str]) → None[source]
studies.tests.test_response_transformer_columns.test_special_attr_columns(fv1: FamilyVariant, column: str, expected: Any) → None[source]
studies.tests.test_response_transformer_columns.test_special_attrs_formatting(t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, t4c8_study_1_wrapper: WDAEStudy) → None[source]

studies.tests.test_study_config_genotype_browser_columns module

studies.tests.test_study_config_genotype_browser_columns.gpf_fixture(tmp_path_factory: TempPathFactory) → GPFInstance[source]
studies.tests.test_study_config_genotype_browser_columns.test_genotype_browser_download_columns_default(trio_study: GenotypeData) → None[source]
studies.tests.test_study_config_genotype_browser_columns.test_genotype_browser_download_columns_ext(trio_study: GenotypeData, gpf_fixture: GPFInstance) → None[source]
studies.tests.test_study_config_genotype_browser_columns.test_genotype_browser_preview_columns_default(trio_study: GenotypeData) → None[source]
studies.tests.test_study_config_genotype_browser_columns.test_genotype_browser_preview_columns_ext(trio_study: GenotypeData, gpf_fixture: GPFInstance) → None[source]
studies.tests.test_study_config_genotype_browser_columns.test_study_wrapper_download_columns_ext(trio_study: GenotypeData, gpf_fixture: GPFInstance) → None[source]
studies.tests.test_study_config_genotype_browser_columns.test_study_wrapper_preview_columns_ext(trio_study: GenotypeData, gpf_fixture: GPFInstance) → None[source]
studies.tests.test_study_config_genotype_browser_columns.trio_study(tmp_path_factory: TempPathFactory, gpf_fixture: GPFInstance) → GenotypeData[source]

studies.tests.test_study_group_person_sets_queries module

studies.tests.test_study_group_person_sets_queries.dataset(wgpf_fixture: WGPFInstance, study_1: WDAEStudy, study_2: WDAEStudy) → WDAEStudyGroup[source]
studies.tests.test_study_group_person_sets_queries.gpf_fixture(request: FixtureRequest, tmp_path_factory: TempPathFactory) → GPFInstance[source]
studies.tests.test_study_group_person_sets_queries.query_transformer(wgpf_fixture: WGPFInstance) → QueryTransformer[source]
studies.tests.test_study_group_person_sets_queries.response_transformer(wgpf_fixture: WGPFInstance) → ResponseTransformer[source]
studies.tests.test_study_group_person_sets_queries.study_1(wgpf_fixture: WGPFInstance) → WDAEStudy[source]
studies.tests.test_study_group_person_sets_queries.study_2(wgpf_fixture: WGPFInstance) → WDAEStudy[source]
studies.tests.test_study_group_person_sets_queries.test_dataset_person_sets_queries(dataset: WDAEStudy, query_transformer: QueryTransformer, response_transformer: ResponseTransformer, psc_query: PSCQuery, count: int) → None[source]
studies.tests.test_study_group_person_sets_queries.test_dataset_simple(dataset: WDAEStudyGroup) → None[source]
studies.tests.test_study_group_person_sets_queries.wgpf_fixture(gpf_fixture: GPFInstance) → WGPFInstance[source]

studies.tests.test_study_query_request module

studies.tests.test_study_query_request.test_query_request_simple(admin_client: Client, t4c8_wgpf_instance: WGPFInstance) → None[source]

studies.tests.test_study_wrapper module

studies.tests.test_study_wrapper.test_is_group_dataset(t4c8_wgpf_instance: WGPFInstance) → None[source]
studies.tests.test_study_wrapper.test_is_group_study(t4c8_wgpf_instance: WGPFInstance) → None[source]
studies.tests.test_study_wrapper.test_t4c8_dataset(t4c8_dataset: GenotypeData) → None[source]
studies.tests.test_study_wrapper.test_t4c8_study_1(t4c8_study_1: GenotypeData) → None[source]
studies.tests.test_study_wrapper.test_t4c8_study_2(t4c8_study_2: GenotypeData) → None[source]

studies.tests.test_study_wrapper_queries module

studies.tests.test_study_wrapper_queries.test_query_all_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer) → None[source]
studies.tests.test_study_wrapper_queries.test_query_complex_query(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer) → None[source]
studies.tests.test_study_wrapper_queries.test_query_effect_types_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, effect_types: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_family_filters(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer) → None[source]
studies.tests.test_study_wrapper_queries.test_query_family_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, family_ids: list[str] | None, count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_gene_scores(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, option: dict, count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_gene_scores_formatting(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, float_format: str, float_val: str) → None[source]
studies.tests.test_study_wrapper_queries.test_query_inheritance_types(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer) → None[source]
studies.tests.test_study_wrapper_queries.test_query_limit_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, max_variants_count: int | None, count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_person_filters(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer) → None[source]
studies.tests.test_study_wrapper_queries.test_query_present_in_child(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, options: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_present_in_parent(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, options: dict, count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_present_in_parent_and_present_in_child(t4c8_study_2_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, present_in_child: list[str], present_in_parent: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_present_in_parent_and_present_in_child_and_phenotypes(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, present_in_child: list[str], present_in_parent: list[str], phenotypes: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_regions_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, regions: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_sexes_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, sexes: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_study_filters(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, query: dict, count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_query_unique_family_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, mocker: MockerFixture) → None[source]
studies.tests.test_study_wrapper_queries.test_query_variant_type_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, variant_type: list[str], count: int) → None[source]
studies.tests.test_study_wrapper_queries.test_study_2_query_inheritance_variants(t4c8_study_1_wrapper: WDAEStudy, t4c8_query_transformer: QueryTransformer, t4c8_response_transformer: ResponseTransformer, inheritance_type: str, count: int) → None[source]

Module contents