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Source code for galaxy.tool_util.biotools.interface

import re
from typing import Any, Dict, List, Optional

TERM_PATTERN = re.compile(r"https?://edamontology.org/(.*)")

[docs]class ParsedBiotoolsEntry: """Provide XML wrapper relevant entities from a bio.tool entry - topics and operations.""" biotoolsID: str edam_topics: List[str] edam_operations: List[str]
[docs]class BiotoolsEntry: """Parse the RAW entries of interest for Galaxy from a bio.tools entry.""" biotoolsID: str topic: List[dict] function: List[dict]
[docs] @staticmethod def from_json(from_json: Dict[str, Any]) -> 'BiotoolsEntry': entry = BiotoolsEntry() entry.biotoolsID = from_json["biotoolsID"] entry.topic = from_json["topic"] entry.function = from_json["function"] return entry
@property def edam_info(self) -> ParsedBiotoolsEntry: parsed = ParsedBiotoolsEntry() parsed.biotoolsID = self.biotoolsID parsed.edam_topics = list(set(simplify_edam_dicts(self.topic))) operations = [] for function in self.function: if "operation" in function: operations.extend(simplify_edam_dicts(function["operation"])) parsed.edam_operations = list(set(operations)) return parsed
[docs]def simplify_edam_dicts(a_list: List[Dict[str, str]]): terms = [] for term in map(simplify_edam_dict, a_list): if term: terms.append(term) return terms
[docs]def simplify_edam_dict(as_dict: Dict[str, str]) -> Optional[str]: uri = as_dict["uri"] match = TERM_PATTERN.match(uri) if match: return match.group(1) else: # TODO: log problem... return None