gpf_instance package

Subpackages

• gpf_instance.tests package
  • Submodules
  • gpf_instance.tests.test_genome_view module
    • test_genome_hg19()
    • test_genome_hg38()
    • test_genome_other()
  • gpf_instance.tests.test_version_api module
    • mock_instance()
    • test_get_gpf_version()
    • test_gpf_about_description()
    • test_gpf_main_description()
    • test_update_gpf_about_description_anonymous()
    • test_update_gpf_main_description_anonymous()
  • gpf_instance.tests.test_wgpf_instance module
    • test_get_common_report()
    • test_get_common_report_nonexistant()
    • test_get_genotype_data()
    • test_get_genotype_data_config()
    • test_get_genotype_data_config_nonexistant()
    • test_get_genotype_data_ids()
    • test_get_genotype_data_nonexistant()
    • test_get_wdae_wrapper()
    • test_get_wdae_wrapper_nonexistant()
    • test_make_wdae_wrapper()
  • Module contents

Submodules

gpf_instance.apps module

Provides class for configuing WDAE Django application.

class gpf_instance.apps.WDAEConfig(app_name, app_module)

Bases: AppConfig

Configure WDAE django application.

name = 'gpf_instance'

ready() → None

Override this method in subclasses to run code when Django starts.

gpf_instance.extension module

class gpf_instance.extension.GPFExtensionBase(instance: Any)

Bases: object

Base class for GPF extensions.

GPF extensions can handle adding new studies and support for various GPF tools to an instance.

abstract get_studies() → list[WDAEAbstractStudy]

abstract get_studies_ids() → list[str]

get_tool(study: WDAEAbstractStudy, tool_id: str) → GPFTool | None

setup() → None

class gpf_instance.extension.GPFTool(tool_id: str)

Bases: object

Base class for implementing GPF tools.

GPF tools are classes which interact with studies to provide data.

abstract static make_tool(study: WDAEAbstractStudy) → GPFTool | None

property tool_id: str

gpf_instance.gpf_instance module

Provides wdae GPFInstance class.

gpf_instance.gpf_instance.get_wgpf_instance(config_filename: str | Path | None = None, **kwargs: Any) → WGPFInstance

Load and return a WGPFInstance.

gpf_instance.urls module

gpf_instance.views module

class gpf_instance.views.AboutDescriptionView

Bases: MarkdownFileView

Provide fetching and editing the main application description.

CONTENT_ID = 'instance_about'

get(_request: Request) → Response

Collect the application description.

class gpf_instance.views.DescriptionView

Bases: MarkdownFileView

Provide fetching and editing the main application description.

CONTENT_ID = 'instance_description'

get(_request: Request) → Response

Collect the application description.

class gpf_instance.views.GenomeView

Bases: QueryBaseView

Provide genome build

get(_: Request) → Response

class gpf_instance.views.MarkdownFileView

Bases: QueryBaseView

Provide fetching and editing markdown files.

CONTENT_ID = 'placeholder_id'

get(_request: Request) → Response

Collect the application description.

post(request: Request) → Response

Overwrite the application description.

gpf_instance.views.get_about_etag(_request: Request, **_kwargs: dict[str, Any]) → str | None

gpf_instance.views.get_description_etag(_request: Request, **_kwargs: dict[str, Any]) → str | None

gpf_instance.views.version(request, *args, **kwargs)

Get GPF version.

Module contents