Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.tool_util.biotools package

class galaxy.tool_util.biotools.BiotoolsMetadataSource[source]

Bases: object

get_biotools_metadata(biotools_reference: str) → BiotoolsEntry | None[source]: Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.BiotoolsMetadataSourceConfig[source]

Bases: object

use_api: bool = False

content_directory: str | None = None

cache = None

galaxy.tool_util.biotools.get_biotools_metadata_source(metadata_source_config: BiotoolsMetadataSourceConfig) → BiotoolsMetadataSource[source]

class galaxy.tool_util.biotools.ParsedBiotoolsEntry[source]

Bases: object

Provide XML wrapper relevant entities from a bio.tool entry - topics and operations.

biotoolsID: str

edam_topics: List[str]

edam_operations: List[str]

Submodules

galaxy.tool_util.biotools.interface module

class galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry[source]

Bases: object

Provide XML wrapper relevant entities from a bio.tool entry - topics and operations.

biotoolsID: str

edam_topics: List[str]

edam_operations: List[str]

class galaxy.tool_util.biotools.interface.BiotoolsEntry[source]

Bases: object

Parse the RAW entries of interest for Galaxy from a bio.tools entry.

biotoolsID: str

topic: List[dict]

function: List[dict]

static from_json(from_json: Dict[str, Any]) → BiotoolsEntry[source]

property edam_info: ParsedBiotoolsEntry

galaxy.tool_util.biotools.interface.simplify_edam_dicts(a_list: List[Dict[str, str]])[source]

galaxy.tool_util.biotools.interface.simplify_edam_dict(as_dict: Dict[str, str]) → str | None[source]

galaxy.tool_util.biotools.source module

class galaxy.tool_util.biotools.source.BiotoolsMetadataSource[source]

Bases: object

get_biotools_metadata(biotools_reference: str) → BiotoolsEntry | None[source]: Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.source.GitContentBiotoolsMetadataSource(content_directory)[source]

Bases: BiotoolsMetadataSource

Parse entries from a repository clone of https://github.com/bio-tools/content.

__init__(content_directory)[source]

get_biotools_metadata(biotools_reference: str) → BiotoolsEntry | None[source]: Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.source.InMemoryCache[source]

Bases: object

backend: Dict[str, str | None] = {}

get(key: str, createfunc: Callable[[], str | None])[source]

class galaxy.tool_util.biotools.source.ApiBiotoolsMetadataSource(cache=None)[source]

Bases: BiotoolsMetadataSource

Parse entries from bio.tools API.

__init__(cache=None)[source]

get_biotools_metadata(biotools_reference: str) → BiotoolsEntry | None[source]: Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.source.CascadingBiotoolsMetadataSource(use_api=False, cache=None, content_directory: str | None = None)[source]

Bases: BiotoolsMetadataSource

__init__(use_api=False, cache=None, content_directory: str | None = None)[source]

get_biotools_metadata(biotools_reference: str) → BiotoolsEntry | None[source]: Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.source.BiotoolsMetadataSourceConfig[source]

Bases: object

use_api: bool = False

content_directory: str | None = None

cache = None

galaxy.tool_util.biotools.source.get_biotools_metadata_source(metadata_source_config: BiotoolsMetadataSourceConfig) → BiotoolsMetadataSource[source]