Source code for sbmlsim.model.model_resources

"""Model resources.

Interacting with model resources to retrieve models.
This currently includes BioModels, but can easily be extended to other models.
import re
from dataclasses import dataclass
from pathlib import Path
from typing import Dict, Optional, Union

import requests
from sbmlutils import log

[docs]logger = log.get_logger(__name__)
[docs]class Source: """Class for keeping track of the resolved sources."""
[docs] source: str
[docs] path: Optional[Path] = None # if source is a path
[docs] content: Optional[str] = None # if source is something which has to be resolved
[docs] def is_path(self) -> bool: """Check if the source is a Path.""" return self.path is not None
[docs] def is_content(self) -> bool: """Check if the source is Content.""" return self.content is not None
[docs] def to_dict(self) -> Dict[str, Optional[str]]: """Convert to dict. Used for serialization. """ return { "source": str(self.source), "path": str(self.path) if self.path else None, "content": str(self.content), }
[docs] def from_source( cls, source: Union["Source", str, Path], base_dir: Path = None ) -> "Source": """Resolve the source string.""" if isinstance(source, Source): return source path: Optional[Path] = None content: Optional[str] = None if isinstance(source, str): if is_urn(source): content = model_from_urn(source) elif is_http(source): content = model_from_url(url=source) # is path if content is None: if base_dir: path = Path(base_dir) / Path(source) else: # uses current working dir as base_dir path = Path(source).resolve() path = path.resolve() if not path.exists(): raise IOError( f"Path '{path}' for model source '{source}' " f"does not exist." ) return Source(source, path, content)
[docs]def is_urn(source: str) -> bool: """Check if urn source.""" return source.lower().startswith("urn")
[docs]def is_http(source: str) -> bool: """Check if http source.""" return source.lower().startswith("http")
[docs]def model_from_urn(urn: str) -> str: """Get model string from given URN.""" logger.debug(f"Loading model from urn: {urn}") if "biomodel" in urn: mid = parse_biomodels_mid(urn) content = model_from_biomodels(mid) else: raise ValueError(f"Unkown URN for model: {urn}") return content
[docs]def model_from_url(url: str) -> str: """Get model string from given URL. Handles redirects of the download page. :param url: :return: """ # check for special case of old biomodel urls if url.startswith(""): mid = parse_biomodels_mid(url) logger.error( f"Use of deprecated biomodels URL '{url}'," f"use updated url instead: " f"'{mid}?filename={mid}_url.xml'" ) return model_from_biomodels(mid) response = requests.get(url, allow_redirects=True) response.raise_for_status() model_str = response.content # bytes array in py3 return str(model_str.decode("utf-8"))
# --- BioModels ---
[docs]def parse_biomodels_mid(text: str) -> str: """Parse biomodel id from string.""" pattern = r"((BIOMD|MODEL)\d{10})|(BMID\d{12})" match =, text) if match: mid = else: raise ValueError(f"Biomodel id pattern '{pattern}' not found in string: 'text'") return mid
[docs]def model_from_biomodels(mid: str) -> str: """Get SBML string from given BioModels identifier. :param mid: biomodels id :return: SBML string """ # query file information url = f"{mid}?format=json" r = requests.get(url) r.raise_for_status() # query main file json = r.json() try: filename = json["files"]["main"][0]["name"] url = ( f"{mid}?filename={filename}" ) except (TypeError, KeyError) as err: logger.error( f"Filename of 'main' file could not be resolved from response: " f"'{json}'" ) raise err return model_from_url(url)