experimenthub package

Submodules

experimenthub.record module

class experimenthub.record.ExperimentHubRecord(ehub_id, title, species, taxonomy_id, genome, description, url, release_date, preparer_dataclass)[source]

Bases: object

Container for a single ExperimentHub entry.

__annotations__ = {'description': 'Optional[str]', 'ehub_id': 'str', 'genome': 'Optional[str]', 'preparer_dataclass': 'Optional[str]', 'release_date': 'Optional[date]', 'species': 'Optional[str]', 'taxonomy_id': 'Optional[str]', 'title': 'str', 'url': 'str'}
__dataclass_fields__ = {'description': Field(name='description',type='Optional[str]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'ehub_id': Field(name='ehub_id',type='str',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'genome': Field(name='genome',type='Optional[str]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'preparer_dataclass': Field(name='preparer_dataclass',type='Optional[str]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'release_date': Field(name='release_date',type='Optional[date]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'species': Field(name='species',type='Optional[str]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'taxonomy_id': Field(name='taxonomy_id',type='Optional[str]',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'title': Field(name='title',type='str',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD), 'url': Field(name='url',type='str',default=<dataclasses._MISSING_TYPE object>,default_factory=<dataclasses._MISSING_TYPE object>,init=True,repr=True,hash=None,compare=True,metadata=mappingproxy({}),kw_only=False,_field_type=_FIELD)}
__dataclass_params__ = _DataclassParams(init=True,repr=True,eq=True,order=False,unsafe_hash=False,frozen=True,match_args=True,kw_only=False,slots=False,weakref_slot=False)
__delattr__(name)

Implement delattr(self, name).

__eq__(other)

Return self==value.

__hash__()

Return hash(self).

__init__(ehub_id, title, species, taxonomy_id, genome, description, url, release_date, preparer_dataclass)
__match_args__ = ('ehub_id', 'title', 'species', 'taxonomy_id', 'genome', 'description', 'url', 'release_date', 'preparer_dataclass')
__repr__()

Return repr(self).

__setattr__(name, value)

Implement setattr(self, name, value).

description: Optional[str]
ehub_id: str
classmethod from_db_row(row)[source]

Build a record from a database query row.

Expected row format: (id, title, species, taxonomyid, genome, description, full_url, date_added, rdataclass)

Return type:

ExperimentHubRecord

genome: Optional[str]
preparer_dataclass: Optional[str]
release_date: Optional[date]
species: Optional[str]
taxonomy_id: Optional[str]
title: str
url: str

experimenthub.registry module

class experimenthub.registry.ExperimentHubRegistry(cache_dir=None, force=False)[source]

Bases: object

Registry for ExperimentHub resources.

SUPPORTED_EXTENSIONS = '.rds'
SUPPORTED_R_CLASSES = {'character', 'data frame', 'data.frame', 'dataframe', 'dframe', 'genomicranges', 'granges', 'int', 'iranges', 'list', 'matrix', 'multiassayexperiment', 'numeric', 'rangedSummarizedexperiment', 'singlecellexperiment', 'summarizedexperiment', 'vector'}
__init__(cache_dir=None, force=False)[source]

Initialize the ExperimentHub registry.

Parameters:

  • cache_dir (Union[str, Path, None]) – Directory for the BiocFileCache database and cached files. If None, defaults to “~/.cache/experimenthub_bfc”.

  • force (bool) – If True, force re-download of the ExperimentHub metadata database.

download(ehub_id, force=False)[source]

Download and cache the resource file.

Return type:

str

get_record(ehub_id)[source]

Get the metadata record for a given ExperimentHub ID.

Return type:

ExperimentHubRecord

list_ids()[source]

List all available ExperimentHub IDs (e.g., ‘EH1’, ‘EH123’).

Return type:

List[str]

load(ehub_id, force=False)[source]

Load the resource using rds2py.

Return type:

Any

search(query)[source]

Search for resources matching the query string.

Return type:

List[ExperimentHubRecord]

Module contents