common_reports_api package

Subpackages

• common_reports_api.tests package
  • Submodules
  • common_reports_api.tests.test_common_reports_api module
    • test_autogenerate_common_report()
    • test_families_data_all_download()
    • test_families_data_all_download_no_permissions()
    • test_families_data_download()
    • test_families_data_download_no_permissions()
    • test_families_tags_download()
    • test_families_tags_download_errors_on_bad_body()
    • test_family_counters()
    • test_family_counters_download()
    • test_variant_reports()
    • test_variant_reports_full()
    • test_variant_reports_has_permissions()
    • test_variant_reports_permissions()
  • Module contents

Submodules

common_reports_api.common_reports_helper module

class common_reports_api.common_reports_helper.BaseCommonReportsHelper

Bases: GPFTool

Base class for common reports helper

abstract get_common_report() → dict[str, Any] | None

Load and return common report for a study.

abstract get_family_counter_list(group_name: str, counter_id: int) → Any

Return family counters as list.

abstract get_family_counter_tsv(group_name: str, counter_id: int) → list[str]

Return family counters as tsv file.

abstract get_family_data_tsv() → list[str]

Return family counters as tsv file.

abstract get_filtered_family_data_tsv(data: dict) → list[str]

Return family counters as tsv file.

abstract get_full_common_report() → dict[str, Any] | None

Load and return full common report for a study.

class common_reports_api.common_reports_helper.CommonReportsHelper(study: WDAEStudy)

Bases: BaseCommonReportsHelper

Build enrichment tool test.

get_common_report() → dict[str, Any] | None

Load and return common report for a study.

get_family_counter_list(group_name: str, counter_id: int) → Any

Return family counters as list.

get_family_counter_tsv(group_name: str, counter_id: int) → list[str]

Return family counters as tsv file.

get_family_data_tsv() → list[str]

Return family counters as tsv file.

get_filtered_family_data_tsv(data: dict) → list[str]

Return family counters as tsv file.

get_full_common_report() → dict[str, Any] | None

Load and return full common report for a study.

static make_tool(study: WDAEAbstractStudy) → GPFTool | None

common_reports_api.urls module

common_reports_api.views module

class common_reports_api.views.FamiliesDataDownloadView

Bases: QueryBaseView, DatasetAccessRightsView

Families data download view class.

get(_request: Request, dataset_id: str) → Response | StreamingHttpResponse

Return full family data for a specified study.

post(request: Request, dataset_id: str) → Response | StreamingHttpResponse

Return full family data for a specified study and tags.

class common_reports_api.views.FamilyCounterDownloadView

Bases: QueryBaseView, DatasetAccessRightsView

Family counters download view class.

post(request: Request) → Response | StreamingHttpResponse

Return family couters for a specified study and group name.

class common_reports_api.views.FamilyCounterListView

Bases: QueryBaseView, DatasetAccessRightsView

Family couters list view class.

post(request: Request) → Response

Return family counters for specified study and group name.

class common_reports_api.views.VariantReportsFullView

Bases: QueryBaseView, DatasetAccessRightsView

Variants report full view class.

get(_request: Request, common_report_id: str) → Response

Return full variant report when requested.

class common_reports_api.views.VariantReportsView

Bases: QueryBaseView

Variant reports view class.

get(_request: Request, common_report_id: str) → Response

Return a variant report when requested.

common_reports_api.views.create_common_reports_helper(gpf_instance: WGPFInstance, study: WDAEAbstractStudy) → BaseCommonReportsHelper

Create an pheno browser helper for the given dataset.

Module contents