Warning

This document is for an old release 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]