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]