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Source code for galaxy.tool_util.ontologies.ontology_data
from collections import defaultdict
from typing import (
cast,
Dict,
List,
NamedTuple,
Optional,
Tuple,
)
from galaxy.tool_util.biotools import BiotoolsMetadataSource
from galaxy.tool_util.parser import (
ToolSource,
XrefDict,
)
from galaxy.util.resources import resource_string
def _multi_dict_mapping(content: str) -> Dict[str, List[str]]:
mapping: Dict[str, List[str]] = {}
for x in content.splitlines():
if x.startswith("#"):
continue
key, value = cast(Tuple[str, str], tuple(x.split("\t")))
mapping.setdefault(key, []).append(value)
return mapping
def _read_ontology_data_text(filename: str) -> str:
return resource_string(__package__, filename)
BIOTOOLS_MAPPING_FILENAME = "biotools_mappings.tsv"
EDAM_OPERATION_MAPPING_FILENAME = "edam_operation_mappings.tsv"
EDAM_TOPIC_MAPPING_FILENAME = "edam_topic_mappings.tsv"
BIOTOOLS_MAPPING_CONTENT = _read_ontology_data_text(BIOTOOLS_MAPPING_FILENAME)
BIOTOOLS_MAPPING: Dict[str, List[str]] = defaultdict(list)
for line in BIOTOOLS_MAPPING_CONTENT.splitlines():
if not line.startswith("#"):
tool_id, xref = line.split("\t")
BIOTOOLS_MAPPING[tool_id].append(xref)
EDAM_OPERATION_MAPPING_CONTENT = _read_ontology_data_text(EDAM_OPERATION_MAPPING_FILENAME)
EDAM_OPERATION_MAPPING: Dict[str, List[str]] = _multi_dict_mapping(EDAM_OPERATION_MAPPING_CONTENT)
EDAM_TOPIC_MAPPING_CONTENT = _read_ontology_data_text(EDAM_TOPIC_MAPPING_FILENAME)
EDAM_TOPIC_MAPPING: Dict[str, List[str]] = _multi_dict_mapping(EDAM_TOPIC_MAPPING_CONTENT)
[docs]class OntologyData(NamedTuple):
xrefs: List[XrefDict]
edam_operations: Optional[List[str]]
edam_topics: Optional[List[str]]
[docs]def biotools_reference(xrefs):
for xref in xrefs:
if xref["reftype"] == "bio.tools":
return xref["value"]
return None
[docs]def legacy_biotools_external_reference(all_ids: List[str]) -> List[str]:
for tool_id in all_ids:
if tool_id in BIOTOOLS_MAPPING:
return BIOTOOLS_MAPPING[tool_id]
return []
[docs]def expand_ontology_data(
tool_source: ToolSource, all_ids: List[str], biotools_metadata_source: Optional[BiotoolsMetadataSource]
) -> OntologyData:
xrefs = tool_source.parse_xrefs()
has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
if not has_biotools_reference:
for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
if legacy_biotools_ref is not None:
xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
edam_operations = tool_source.parse_edam_operations()
edam_topics = tool_source.parse_edam_topics()
for tool_id in all_ids:
if tool_id in EDAM_OPERATION_MAPPING:
edam_operations = EDAM_OPERATION_MAPPING[tool_id]
break
for tool_id in all_ids:
if tool_id in EDAM_TOPIC_MAPPING:
edam_topics = EDAM_TOPIC_MAPPING[tool_id]
break
has_missing_data = len(edam_operations) == 0 or len(edam_topics) == 0
if has_missing_data:
biotools_reference_str = biotools_reference(xrefs)
if biotools_reference_str and biotools_metadata_source:
biotools_entry = biotools_metadata_source.get_biotools_metadata(biotools_reference_str)
if biotools_entry:
edam_info = biotools_entry.edam_info
if len(edam_operations) == 0:
edam_operations = edam_info.edam_operations
if len(edam_topics) == 0:
edam_topics = edam_info.edam_topics
return OntologyData(
xrefs,
edam_operations,
edam_topics,
)