simphony/simphony-osp

Error when installing ontologies (wrong encoding)

kysrpex opened this issue · 0 comments

From a comment on issue #558:

I just ran into this issue again with @eich-2020 on his windows machine
He is using the latest OSP-core (v3.5.5) with rdflib v5.0.0. We attempted to upgrade rdflib, but OSP-core now has a constraint that it should be lower than v6, so that is not an option

The traceback is the following (produced when running pico install on this file.

INFO 2021-08-02 12:11:47,533 [osp.core.ontology.installation]: Will install the following namespaces: ['emmo']
INFO 2021-08-02 12:11:47,539 [osp.core.ontology.namespace_registry]: Loading namespaces emmo, http://emmo.info/emmo#.
ERROR 2021-08-02 12:11:47,865 [osp.core.pico]: An Exception occurred during installation.
Traceback (most recent call last):
  File "C:\Anaconda3\lib\site-packages\osp\core\pico.py", line 65, in install_from_terminal
    ontology_installer.install(args.files)
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\installation.py", line 35, in install
    self.install(files, self.get_new_packages, False)
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\installation.py", line 151, in _install
    self.namespace_registry.load_parser(parser)
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\namespace_registry.py", line 375, in load_parser
    ontology = Ontology(from_parser=parser)
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\ontology.py", line 120, in __init
    self._ontology_graph = deepcopy(parser.graph)
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\parser\owl\parser.py", line 87, in graph
    self._graph = self._read_ontology_graph(self._yaml_config,
  File "C:\Anaconda3\lib\site-packages\osp\core\ontology\parser\owl\parser.py", line 209, in _read_ontology_graph
    graph.parse(file_like,
  File "C:\Anaconda3\lib\site-packages\rdflib\graph.py", line 1078, in parse
    parser.parse(source, self, *args)
  File "C:\Anaconda3\lib\site-packages\rdflib\plugins\parsers\rdfxml.py", line 579, in parse
    self._parser.parse(source)
  File "C:\Anaconda3\lib\xml\sax\expatreader.py", line 111, in parse
    xmlreader.IncrementalParser.parse(self, source)
  File "C:\Anaconda3\lib\xml\sax\xmlreader.py", line 126, in parse
    buffer = file.read(self._bufsize)
  File "C:\Anaconda3\lib\encodings\cp1252.py", line 23, in decode
    return codecs.charmap_decode(input,self.errors,decoding_table)[0]
UnicodeDecodeError: 'charmap' codec can't decode byte 0x81 in position 16461: character maps to <undefined>
ERROR 2021-08-02 12:11:47,898 [osp.core.pico]: Consider running 'pico --log-level debug install ...'