pheno_browser_api package

Submodules

pheno_browser_api.pheno_browser_helper module

class pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper[source]

Bases: GPFTool

Base class for pheno browser helpers.

abstractmethod get_count(data: dict[str, Any]) → int[source]: Return measure count for request.

abstractmethod get_image(image_path: str) → tuple[bytes | None, str | None][source]: Get image by path.

abstractmethod get_instruments() → list[str][source]: Get instruments.

abstractmethod get_measure_description(measure_id: str) → dict[str, Any][source]: Get measures description.

abstractmethod get_measure_ids(data: dict[str, Any]) → Generator[str, None, None][source]: Get measure ids.

abstractmethod get_measures_info() → dict[str, Any][source]: Get measures info.

abstractmethod measures_count_status(data: dict[str, Any]) → str[source]: Get measure ids count status.

abstractmethod search_measures(data: dict[str, Any]) → list[dict[str, Any]][source]: Search measures.

exception pheno_browser_api.pheno_browser_helper.CountError[source]: Bases: Exception

class pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper(study: WDAEStudy)[source]

Bases: BasePhenoBrowserHelper

Build enrichment tool test.

get_count(data: dict[str, Any]) → int[source]: Return measure count for request.

get_image(image_path: str) → tuple[bytes | None, str | None][source]: Get image by path.

get_instruments() → list[str][source]: Get instruments.

get_measure_description(measure_id: str) → dict[str, Any][source]: Get measures description.

get_measure_ids(data: dict[str, Any]) → Generator[str, None, None][source]: Get measure ids.

get_measures_info() → dict[str, Any][source]: Get measures info.

static make_tool(study: WDAEAbstractStudy) → GPFTool | None[source]

measures_count_status(data: dict[str, Any]) → str[source]: Get measure ids count status.

search_measures(data: dict[str, Any]) → list[dict[str, Any]][source]: Search measures.

pheno_browser_api.urls module

pheno_browser_api.views module

class pheno_browser_api.views.PhenoImagesView[source]

Bases: QueryBaseView, DatasetAccessRightsView

Remote pheno images view.

get(_request: Request, pheno_id: str | None, image_path: str | None) → Response | HttpResponse[source]: Return raw image data from a remote GPF instance.

class pheno_browser_api.views.PhenoInstrumentsView[source]

Bases: QueryBaseView

Phenotype instruments view.

get(request: Request) → Response[source]: Get phenotype instruments.

class pheno_browser_api.views.PhenoMeasureDescriptionView[source]

Bases: QueryBaseView

Phenotype measures description view.

get(request: Request) → Response[source]: Get pheno measures description.

class pheno_browser_api.views.PhenoMeasuresCount[source]

Bases: QueryBaseView, DatasetAccessRightsView

Phenotype measure search count view.

get(request: Request) → Response[source]: Return a CSV file stream for measures.

class pheno_browser_api.views.PhenoMeasuresDownload[source]

Bases: QueryBaseView, DatasetAccessRightsView

Phenotype measure downloads view.

get(request: Request) → Response[source]: Return a CSV file stream for measures.

head(request: Request) → Response[source]: Return a status code validating if measures can be downloaded.

class pheno_browser_api.views.PhenoMeasuresInfoView[source]

Bases: QueryBaseView

Phenotype measures info view.

get(request: Request) → Response[source]: Get pheno measures info.

class pheno_browser_api.views.PhenoMeasuresView[source]

Bases: QueryBaseView

Phenotype measures view.

get(request: Request) → Response[source]: Get pheno measures pages.

pheno_browser_api.views.create_pheno_browser_helper(gpf_instance: WGPFInstance, study: WDAEAbstractStudy) → BasePhenoBrowserHelper[source]: Create an pheno browser helper for the given dataset.

pheno_browser_api package

Submodules

pheno_browser_api.pheno_browser_helper module

pheno_browser_api.urls module

pheno_browser_api.views module

Module contents