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galaxy.webapps.base package

Submodules

galaxy.webapps.base.api module

class galaxy.webapps.base.api.GalaxyFileResponse(path: str | os.PathLike[str], status_code: int = 200, headers: Mapping[str, str] | None = None, media_type: str | None = None, background: BackgroundTask | None = None, filename: str | None = None, stat_result: stat_result | None = None, method: str | None = None, content_disposition_type: str = 'attachment')

Bases: FileResponse

Augments starlette FileResponse with x-accel-redirect/x-sendfile and byte-range handling.

nginx_x_accel_redirect_base: str | None = None

apache_xsendfile: bool | None = None

__init__(path: str | os.PathLike[str], status_code: int = 200, headers: Mapping[str, str] | None = None, media_type: str | None = None, background: BackgroundTask | None = None, filename: str | None = None, stat_result: stat_result | None = None, method: str | None = None, content_disposition_type: str = 'attachment') → None

galaxy.webapps.base.api.add_sentry_middleware(app: FastAPI) → None

galaxy.webapps.base.api.get_error_response_for_request(request: Request, exc: MessageException) → JSONResponse

galaxy.webapps.base.api.add_exception_handler(app: FastAPI) → None

class galaxy.webapps.base.api.AccessLoggingMiddleware

Bases: Plugin

key: str = 'access_line'

async process_request(request)

Runs always on request.

Extracts value from header by default.

async enrich_response(response) → None

Runs always on response.

Does nothing by default.

galaxy.webapps.base.api.add_raw_context_middlewares(app: FastAPI)

galaxy.webapps.base.api.add_request_id_middleware(app: FastAPI)

galaxy.webapps.base.api.include_all_package_routers(app: FastAPI, package_name: str)

galaxy.webapps.base.controller module

Contains functionality needed in every web interface

exception galaxy.webapps.base.controller.HTTPBadRequest(detail=None, headers=None, comment=None, body_template=None, json_formatter=None, **kw)

Bases: HTTPClientError, HTTPBadRequest

explanation = 'The server could not comply with the request since it is either malformed or otherwise incorrect.'

class galaxy.webapps.base.controller.SharableMixin

Bases: object

Mixin for a controller that manages an item that can be shared.

manager: Any = None

serializer: Any = None

slug_builder = <galaxy.managers.sharable.SlugBuilder object>

set_slug_async(trans, id, new_slug)

share(trans, id=None, email='', **kwd)

Handle sharing an item with a particular user.

display_by_username_and_slug(trans, username, slug, **kwargs)

Display item by username and slug.

get_item(trans, id)

Return item based on id.

galaxy.webapps.base.controller.sort_by_attr(seq, attr)

Sort the sequence of objects by object’s attribute Arguments: seq - the list or any sequence (including immutable one) of objects to sort. attr - the name of attribute to sort by

galaxy.webapps.base.controller.url_for(*args, **kwargs) → str

Tries to resolve the URL using the routes module.

This only works in a WSGI app so a deprecation message is returned when running an ASGI app.

class galaxy.webapps.base.controller.UsesExtendedMetadataMixin

Bases: SharableItemSecurityMixin

Mixin for getting and setting item extended metadata.

get_item_extended_metadata_obj(trans, item)

Given an item object (such as a LibraryDatasetDatasetAssociation), find the object of the associated extended metadata

set_item_extended_metadata_obj(trans, item, extmeta_obj, check_writable=False)

unset_item_extended_metadata_obj(trans, item, check_writable=False)

create_extended_metadata(trans, extmeta)

Create/index an extended metadata object. The returned object is not associated with any items

delete_extended_metadata(trans, item)

class galaxy.webapps.base.controller.UsesFormDefinitionsMixin

Bases: object

Mixin for controllers that use Galaxy form objects.

get_all_forms(trans, all_versions=False, filter=None, form_type='All')

Return all the latest forms from the form_definition_current table if all_versions is set to True. Otherwise return all the versions of all the forms from the form_definition table.

save_widget_field(trans, field_obj, widget_name, **kwd)

get_form_values(trans, user, form_definition, **kwd)

Returns the name:value dictionary containing all the form values

class galaxy.webapps.base.controller.UsesTagsMixin

Bases: SharableItemSecurityMixin

set_tags_from_list(trans, item, new_tags_list, user=None)

get_user_tags_used(trans, user=None)

Return a list of distinct ‘user_tname:user_value’ strings that the given user has used.

user defaults to trans.user. Returns an empty list if no user is given and trans.user is anonymous.

galaxy.webapps.base.webapp module

class galaxy.webapps.base.webapp.WebApplication(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None)

Bases: WebApplication

Base WSGI application instantiated for all Galaxy webapps.

A web application that:

• adds API and UI controllers by scanning given directories and importing all modules found there.

• has a security object.

• builds mako template lookups.

• generates GalaxyWebTransactions.

injection_aware: bool = False

__init__(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None) → None

Create a new web application object. To actually connect some controllers use add_controller and add_route. Call finalize_config when all controllers and routes have been added and __call__ to handle a request (WSGI style).

build_apispec()

Traverse all route paths starting with “api” and create an APISpec instance.

create_mako_template_lookup(galaxy_app, name)

handle_controller_exception(e, trans, method, **kwargs)

Allow handling of exceptions raised in controller methods.

make_body_iterable(trans, body)

transaction_chooser(environ, galaxy_app: BasicSharedApp, session_cookie: str)

add_ui_controllers(package_name, app)

Search for UI controllers in package_name and add them to the webapp.

add_api_controllers(package_name, app)

Search for UI controllers in package_name and add them to the webapp.

galaxy.webapps.base.webapp.config_allows_origin(origin_raw, config)

galaxy.webapps.base.webapp.url_builder(*args, **kwargs) → str

Wrapper around the WSGI version of the function for reversing URLs.

class galaxy.webapps.base.webapp.GalaxyWebTransaction(environ: Dict[str, Any], app: BasicSharedApp, webapp: WebApplication, session_cookie: str | None = None)

Bases: DefaultWebTransaction, ProvidesHistoryContext

Encapsulates web transaction specific state for the Galaxy application (specifically the user’s “cookie” session and history)

__init__(environ: Dict[str, Any], app: BasicSharedApp, webapp: WebApplication, session_cookie: str | None = None) → None

property app

Provide access to the Galaxy app object.

property url_builder

Provide access to Galaxy URLs (if available).

Parameters:

qualified (bool) – if True, the fully qualified URL is returned, else a relative URL is returned (default False).

set_cors_allow(name=None, value=None)

set_cors_origin(origin=None)

set_cors_headers()

Allow CORS requests if configured to do so by echoing back the request’s ‘Origin’ header (if any) as the response header ‘Access-Control-Allow-Origin’

Preflight OPTIONS requests to the API work by routing all OPTIONS requests to a single method in the authenticate API (options method), setting CORS headers, and responding OK.

NOTE: raising some errors (such as httpexceptions), will remove the header (e.g. client will get both CORS error and 404 inside that)

get_user()

Return the current user if logged in or None.

set_user(user)

Set the current user.

property user

Return the current user if logged in or None.

get_cookie(name='galaxysession')

Convenience method for getting a session cookie

set_cookie(value, name='galaxysession', path='/', age=90, version='1')

property cookie_path

check_user_library_import_dir(user)

user_checks(user)

This could contain more checks around a user upon login

handle_user_login(user)

Login a new user (possibly newly created)

• do some ‘system’ checks (if any) for this user

• create a new session

• associate new session with user

• if old session had a history and it was not associated with a user, associate it with the new session, otherwise associate the current session’s history with the user

• add the disk usage of the current session to the user’s total disk usage

handle_user_logout(logout_all=False)

Logout the current user:

• invalidate the current session

• create a new session with no user associated

get_galaxy_session()

Return the current galaxy session

get_history(create=False, most_recent=False)

Load the current history.

• If that isn’t available, we find the most recently updated history.

• If that isn’t available, we get or create the default history.

Transactions will not always have an active history (API requests), so None is a valid response.

set_history(history)

property history

Provide access to the user’s current history model object.

Return type:

Optional[galaxy.model.History]

get_or_create_default_history()

Gets or creates a default history and associates it with the current session.

get_most_recent_history()

Gets the most recently updated history.

new_history(name=None)

Create a new history and associate it with the current session and its associated user (if set).

template_context

Property that replaces itself with a calculated value the first time it is used.

set_message(message, type=None)

Convenience method for setting the ‘message’ and ‘message_type’ element of the template context.

get_message()

Convenience method for getting the ‘message’ element of the template context.

show_message(message, type='info', refresh_frames=None, cont=None, use_panels=False, active_view='')

Convenience method for displaying a simple page with a single message.

type: one of “error”, “warning”, “info”, or “done”; determines the

type of dialog box and icon displayed with the message

refresh_frames: names of frames in the interface that should be

refreshed when the message is displayed

show_error_message(message, refresh_frames=None, use_panels=False, active_view='')

Convenience method for displaying an error message. See show_message.

show_ok_message(message, refresh_frames=None, use_panels=False, active_view='')

Convenience method for displaying an ok message. See show_message.

show_warn_message(message, refresh_frames=None, use_panels=False, active_view='')

Convenience method for displaying an warn message. See show_message.

property session_csrf_token

check_csrf_token(payload)

fill_template(filename, **kwargs)

Fill in a template, putting any keyword arguments on the context.

fill_template_mako(filename, template_lookup=None, **kwargs)

qualified_url_for_path(path)

galaxy.webapps.base.webapp.create_new_session(trans, prev_galaxy_session=None, user_for_new_session=None)

Create a new GalaxySession for this request, possibly with a connection to a previous session (in prev_galaxy_session) and an existing user (in user_for_new_session).

Caller is responsible for flushing the returned session.

galaxy.webapps.base.webapp.default_url_path(path)

galaxy.webapps.base.webapp.build_url_map(app, global_conf, **local_conf)