pheno_browser_api package

Subpackages

• pheno_browser_api.tests package
  • Submodules
  • pheno_browser_api.tests.test_pheno_browser_api module
    • test_anonymous_instruments_allowed()
    • test_anonymous_measures_allowed()
    • test_download()
    • test_download_all_instruments()
    • test_download_all_instruments_specific_measures()
    • test_download_specific_measures()
    • test_instruments()
    • test_instruments_missing_dataset_id()
    • test_instruments_missing_dataset_id_forbidden()
    • test_measure_details()
    • test_measures()
    • test_measures_count()
    • test_measures_info()
    • test_pheno_browser_api_permissions()
  • Module contents

Submodules

pheno_browser_api.pheno_browser_helper module

class pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper

Bases: GPFTool

Base class for pheno browser helpers.

abstract get_count(data: dict[str, Any]) → int

Return measure count for request.

abstract get_image(image_path: str) → tuple[bytes | None, str | None]

Get image by path.

abstract get_instruments() → list[str]

Get instruments.

abstract get_measure_description(measure_id: str) → dict[str, Any]

Get measures description.

abstract get_measure_ids(data: dict[str, Any]) → Generator[str, None, None]

Get measure ids.

abstract get_measures_info() → dict[str, Any]

Get measures info.

abstract measures_count_status(data: dict[str, Any]) → str

Get measure ids count status.

abstract search_measures(data: dict[str, Any]) → list[dict[str, Any]]

Search measures.

exception pheno_browser_api.pheno_browser_helper.CountError

Bases: Exception

class pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper(study: WDAEStudy)

Bases: BasePhenoBrowserHelper

Build enrichment tool test.

get_count(data: dict[str, Any]) → int

Return measure count for request.

get_image(image_path: str) → tuple[bytes | None, str | None]

Get image by path.

get_instruments() → list[str]

Get instruments.

get_measure_description(measure_id: str) → dict[str, Any]

Get measures description.

get_measure_ids(data: dict[str, Any]) → Generator[str, None, None]

Get measure ids.

get_measures_info() → dict[str, Any]

Get measures info.

static make_tool(study: WDAEAbstractStudy) → GPFTool | None

measures_count_status(data: dict[str, Any]) → str

Get measure ids count status.

search_measures(data: dict[str, Any]) → list[dict[str, Any]]

Search measures.

pheno_browser_api.urls module

pheno_browser_api.views module

class pheno_browser_api.views.PhenoImagesView

Bases: QueryBaseView, DatasetAccessRightsView

Remote pheno images view.

get(_request: Request, pheno_id: str | None, image_path: str | None) → Response | HttpResponse

Return raw image data from a remote GPF instance.

class pheno_browser_api.views.PhenoInstrumentsView

Bases: QueryBaseView

Phenotype instruments view.

get(request: Request) → Response

Get phenotype instruments.

class pheno_browser_api.views.PhenoMeasureDescriptionView

Bases: QueryBaseView

Phenotype measures description view.

get(request: Request) → Response

Get pheno measures description.

class pheno_browser_api.views.PhenoMeasuresCount

Bases: QueryBaseView, DatasetAccessRightsView

Phenotype measure search count view.

get(request: Request) → Response

Return a CSV file stream for measures.

class pheno_browser_api.views.PhenoMeasuresDownload

Bases: QueryBaseView, DatasetAccessRightsView

Phenotype measure downloads view.

get(request: Request) → Response

Return a CSV file stream for measures.

head(request: Request) → Response

Return a status code validating if measures can be downloaded.

class pheno_browser_api.views.PhenoMeasuresInfoView

Bases: QueryBaseView

Phenotype measures info view.

get(request: Request) → Response

Get pheno measures info.

class pheno_browser_api.views.PhenoMeasuresView

Bases: QueryBaseView

Phenotype measures view.

get(request: Request) → Response

Get pheno measures pages.

pheno_browser_api.views.create_pheno_browser_helper(gpf_instance: WGPFInstance, study: WDAEAbstractStudy) → BasePhenoBrowserHelper

Create an pheno browser helper for the given dataset.

Module contents