Source code for galaxy.tool_util.biotools.interface

import re
from typing import (
    Any,
)

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.get("topic", [])
        entry.function = from_json.get("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]) -> str | None:
    uri = as_dict["uri"]
    if match := TERM_PATTERN.match(uri):
        return match.group(1)
    else:
        # TODO: log problem...
        return None