galaxy.tool_util.biotools package

class galaxy.tool_util.biotools.BiotoolsMetadataSource[source]

Bases: object

get_biotools_metadata(biotools_reference: str) → Optional[BiotoolsEntry][source]

Return a BiotoolsEntry if available.

class galaxy.tool_util.biotools.BiotoolsMetadataSourceConfig[source]

Bases: object

use_api: bool = False
content_directory: Optional[str] = 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]) → Optional[str][source]

galaxy.tool_util.biotools.source module

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

Bases: object

get_biotools_metadata(biotools_reference: str) → Optional[BiotoolsEntry][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) → Optional[BiotoolsEntry][source]

Return a BiotoolsEntry if available.

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

Bases: object

backend: Dict[str, Optional[str]] = {}
get(key: str, createfunc: Callable[[], Optional[str]])[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) → Optional[BiotoolsEntry][source]

Return a BiotoolsEntry if available.

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

Bases: BiotoolsMetadataSource

__init__(use_api=False, cache=None, content_directory: Optional[str] = None)[source]
get_biotools_metadata(biotools_reference: str) → Optional[BiotoolsEntry][source]

Return a BiotoolsEntry if available.

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

Bases: object

use_api: bool = False
content_directory: Optional[str] = None
cache = None
galaxy.tool_util.biotools.source.get_biotools_metadata_source(metadata_source_config: BiotoolsMetadataSourceConfig) → BiotoolsMetadataSource[source]