Open Zethson opened 3 months ago
3.66.0 still works.
{ "name": "KeyError", "message": "'{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource'", "stack": "--------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[2], line 1 ----> 1 ont = bt.base.ExperimentalFactor(source=\"efo\", version=\"3.67.0\") File ~/PycharmProjects/bionty/bionty/base/entities/_experimentalfactor.py:32, in ExperimentalFactor.__init__(self, organism, source, version, **kwargs) 25 def __init__( 26 self, 27 organism: Optional[Literal[\"all\"]] = None, (...) 30 **kwargs, 31 ) -> None: ---> 32 super().__init__( 33 organism=organism, 34 source=source, 35 version=version, 36 include_id_prefixes={\"efo\": [\"EFO\", \"http://www.ebi.ac.uk/efo/\"]}, 37 **kwargs, 38 ) File ~/PycharmProjects/bionty/bionty/base/_public_ontology.py:99, in PublicOntology.__init__(self, source, version, organism, include_id_prefixes, **kwargs) 96 self.include_id_prefixes = include_id_prefixes 98 # df is only read into memory at the init to improve performance ---> 99 df = self._load_df() 100 # self._df has no index 101 if df.index.name is not None: File ~/PycharmProjects/bionty/bionty/base/_public_ontology.py:304, in PublicOntology._load_df(self) 302 if not self._url.endswith(\"parquet\"): 303 if not self._local_parquet_path.exists(): --> 304 df = self.to_pronto().to_df( 305 source=self.source, include_id_prefixes=self.include_id_prefixes 306 ) 307 df.to_parquet(self._local_parquet_path) 309 # Loading the parquet file resets the index File ~/PycharmProjects/bionty/bionty/base/entities/_experimentalfactor.py:50, in ExperimentalFactor.to_pronto(self) 41 \"\"\"The Pronto Ontology object. 42 43 See: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html 44 \"\"\" 45 self._download_ontology_file( 46 localpath=self._local_ontology_path, # type:ignore 47 url=self._url, # type:ignore 48 md5=self._md5, # type:ignore 49 ) ---> 50 onto = Ontology( 51 handle=self._local_ontology_path, # type:ignore 52 prefix=\"http://www.ebi.ac.uk/efo/\", 53 ) 54 # TODO: fix 55 onto.__setattr__(\"efo_to_df\", efo_to_df) File ~/PycharmProjects/bionty/bionty/base/_ontology.py:33, in Ontology.__init__(self, handle, import_depth, timeout, threads, prefix) 31 self._prefix = prefix 32 warnings.filterwarnings(\"ignore\", category=pronto.warnings.ProntoWarning) ---> 33 super().__init__( 34 handle=handle, import_depth=import_depth, timeout=timeout, threads=threads 35 ) File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pronto/ontology.py:283, in Ontology.__init__(self, handle, import_depth, timeout, threads) 281 for cls in BaseParser.__subclasses__(): 282 if cls.can_parse(typing.cast(str, self.path), buffer): --> 283 cls(self).parse_from(_handle) # type: ignore 284 break 285 else: File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pronto/parsers/rdfxml.py:117, in RdfXMLParser.parse_from(self, handle, threads) 115 self._extract_annotation_property(prop, curies) 116 for class_ in tree.iterfind(_NS[\"owl\"][\"Class\"]): --> 117 self._extract_term(class_, curies) 118 for axiom in tree.iterfind(_NS[\"owl\"][\"Axiom\"]): 119 self._process_axiom(axiom, curies) File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pronto/parsers/rdfxml.py:399, in RdfXMLParser._extract_term(self, elem, curies) 397 termdata.xrefs.add(Xref(text)) 398 else: --> 399 termdata.xrefs.add(Xref(attrib[_NS[\"rdf\"][\"resource\"]])) 400 except ValueError: 401 pass KeyError: '{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource'" }
Reported upstream: https://github.com/EBISPOT/efo/issues/2264
3.66.0 still works.
Reported upstream: https://github.com/EBISPOT/efo/issues/2264