pheno_tool_api package

Subpackages

• pheno_tool_api.tests package
  • Submodules
  • pheno_tool_api.tests.test_pheno_tool_api module
    • test_pheno_tool_api_permissions()
    • test_pheno_tool_download_valid_request()
    • test_pheno_tool_view_cnv_on_non_cnv_study()
    • test_pheno_tool_view_family_ids_filter()
    • test_pheno_tool_view_missense()
    • test_pheno_tool_view_missing_dataset()
    • test_pheno_tool_view_missing_measure()
    • test_pheno_tool_view_na_values()
    • test_pheno_tool_view_normalize()
    • test_pheno_tool_view_pheno_filter()
    • test_pheno_tool_view_query_no_limit()
    • test_pheno_tool_view_valid_request()
  • pheno_tool_api.tests.test_pheno_tool_view_class_static_methods module
    • test_pheno_tool_view_align_na_results_invalid()
    • test_pheno_tool_view_align_na_results_valid()
    • test_pheno_tool_view_build_report_description()
    • test_pheno_tool_view_get_result_by_sex()
  • Module contents

Submodules

pheno_tool_api.adapter module

class pheno_tool_api.adapter.PhenoToolAdapter(study: WDAEStudy)

Bases: PhenoToolAdapterBase

Adapter for PhenoTool class.

static align_na_results(results: list[dict[str, Any]]) → None

Align NA results.

build_report_description(measure_id: str, normalize_by: Any) → str

Build a description for a report.

calc_by_effect(measure_id: str, effect: str, people_variants: Counter, *, person_ids: list[str] | None = None, family_ids: list[str] | None = None, normalize_by: list[dict[str, str]] | None = None) → dict[str, Any]

Run the base pheno tool calc on given variant counts.

calc_variants(query_data: dict[str, Any]) → dict[str, Any]

Run pheno tool on given data.

get_result_by_sex(result: dict[str, PhenoResult], sex: str) → dict[str, Any]

static make_tool(study: WDAEAbstractStudy) → GPFTool | None

produce_download(query_data: dict[str, Any], query_transformer: QueryTransformer) → Generator[str, None, None]

Produce columns for download.

class pheno_tool_api.adapter.PhenoToolAdapterBase

Bases: GPFTool

Base class for pheno tool adapters.

abstract calc_variants(query_data: dict[str, Any]) → dict[str, Any]

Return pheno tool result for given variants.

abstract produce_download(query_data: dict[str, Any], query_transformer: QueryTransformer) → Generator[str, None, None]

Produce columns for download.

pheno_tool_api.urls module

pheno_tool_api.views module

class pheno_tool_api.views.PhenoToolDownload

Bases: PhenoToolView, DatasetAccessRightsView

Pheno tool download view.

post(request: Request) → Response | StreamingHttpResponse

Pheno tool download.

class pheno_tool_api.views.PhenoToolInstruments

Bases: QueryBaseView, DatasetAccessRightsView

View for returning instruments and their measures.

get(request: Request) → Response

Get instruments and their measures.

measure_to_json(measure: Measure) → dict

class pheno_tool_api.views.PhenoToolMeasure

Bases: QueryBaseView, DatasetAccessRightsView

View for returning single measure info.

get(request: Request) → Response

Get measure info.

class pheno_tool_api.views.PhenoToolMeasures

Bases: QueryBaseView, DatasetAccessRightsView

View for returning multiple measures info.

get(request: Request) → Response

Get measures info.

class pheno_tool_api.views.PhenoToolPeopleValues

Bases: QueryBaseView, DatasetAccessRightsView

View for returning person phenotype data.

post(request: Request) → Response

Return people values.

class pheno_tool_api.views.PhenoToolView

Bases: QueryBaseView

View for returning pheno tool results.

static get_result_by_sex(result: dict[str, PhenoResult], sex: str) → dict[str, Any]

post(request: Request) → Response | StreamingHttpResponse

Return pheno tool results based on POST request.

Module contents