Horizontal example: usercase_ontology.owl

[lukas-koschmieder]

I'm trying to reproduce the horizontal example on my computer.

Where do I find the ontology (../vertical/usercase_ontology.owl) referenced in the very first step?

https://github.com/emmo-repo/EMMO-python/blob/b8e2d1017dc795e1788ff9548192e09f50ca5472/demo/horizontal/step1_generate_metadata.py#L29

There is no such file nowhere in the repository. Am I supposed to use ../vertical/demo.owl instead (the result of the vertical example)? Am asking because if I do use it, step1_generate_metadata.py produces the following error.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/owlready2/driver.py in parse(self, f, format, delete_existing_triples, default_base)
    153               if not line.endswith("\n"): line = "%s\n" % line
--> 154               s,p,o = splitter.split(line[:-3], 2)
    155 

ValueError: not enough values to unpack (expected 3, got 2)

The above exception was the direct cause of the following exception:

OwlReadyOntologyParsingError              Traceback (most recent call last)
/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/ontology.py in _load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, **kwargs)
    561             elif resolved_url.startswith(web_protocol):
--> 562                 return super().load(
    563                     only_local=only_local,

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/owlready2/namespace.py in load(self, only_local, fileobj, reload, reload_if_newer, url, **args)
    954         try:
--> 955           new_base_iri = self.graph.parse(fileobj, default_base = self.base_iri, **args)
    956         except OwlReadyOntologyParsingError:

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/owlready2/driver.py in parse(self, f, format, delete_existing_triples, default_base)
    187         if current_line:
--> 188           raise OwlReadyOntologyParsingError("NTriples parsing error (or unrecognized file format) in %s, line %s." % (getattr(f, "name", getattr(f, "url", "???")), current_line)) from e
    189         else:

OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl, line 9.

During handling of the above exception, another exception occurred:

KeyError                                  Traceback (most recent call last)
/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/rdflib/plugin.py in get(name, kind)
    123     try:
--> 124         p: Plugin[PluginT] = _plugins[(name, kind)]
    125     except KeyError:

KeyError: ('text/plain', <class 'rdflib.parser.Parser'>)

During handling of the above exception, another exception occurred:

PluginException                           Traceback (most recent call last)
/tmp/ipykernel_3270962/3122766218.py in <module>
     28 )
     29 onto = get_ontology(ontopath)
---> 30 onto.load()
     31 
     32 

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/ontology.py in load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, emmo_based, **kwargs)
    423         if self.loaded:
    424             return self
--> 425         self._load(
    426             only_local=only_local,
    427             filename=filename,

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/ontology.py in _load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, **kwargs)
    569             else:
    570                 with open(resolved_url, "rb") as handle:
--> 571                     return super().load(
    572                         only_local=only_local,
    573                         fileobj=handle,

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/owlready2/namespace.py in load(self, only_local, fileobj, reload, reload_if_newer, url, **args)
   1004 
   1005     # Load imported ontologies
-> 1006     imported_ontologies = [self.world.get_ontology(self._unabbreviate(abbrev_iri)).load() for abbrev_iri in self.world._get_obj_triples_sp_o(self.storid, owl_imports)]
   1007     self._imported_ontologies._set(imported_ontologies)
   1008 

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/owlready2/namespace.py in <listcomp>(.0)
   1004 
   1005     # Load imported ontologies
-> 1006     imported_ontologies = [self.world.get_ontology(self._unabbreviate(abbrev_iri)).load() for abbrev_iri in self.world._get_obj_triples_sp_o(self.storid, owl_imports)]
   1007     self._imported_ontologies._set(imported_ontologies)
   1008 

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/ontology.py in load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, emmo_based, **kwargs)
    423         if self.loaded:
    424             return self
--> 425         self._load(
    426             only_local=only_local,
    427             filename=filename,

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/ontology.py in _load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, **kwargs)
    592             with tempfile.TemporaryDirectory() as handle:
    593                 output = os.path.join(handle, os.path.basename(resolved_url))
--> 594                 convert_imported(
    595                     input_ontology=resolved_url,
    596                     output_ontology=output,

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/ontopy/utils.py in convert_imported(input_ontology, output_ontology, input_format, output_format, url_from_catalog, catalog_file)
    564 
    565     graph = Graph()
--> 566     graph.parse(input_ontology, format=fmt)
    567     graph.serialize(destination=output_ontology, format=output_format)
    568     recur(graph, outext)

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/rdflib/graph.py in parse(self, source, publicID, format, location, file, data, **args)
   1253                 format = "turtle"
   1254                 could_not_guess_format = True
-> 1255         parser = plugin.get(format, Parser)()
   1256         try:
   1257             # TODO FIXME: Parser.parse should have **kwargs argument.

/opt/aixvipmap/2107/conda/envs/emmo/lib/python3.9/site-packages/rdflib/plugin.py in get(name, kind)
    124         p: Plugin[PluginT] = _plugins[(name, kind)]
    125     except KeyError:
--> 126         raise PluginException("No plugin registered for (%s, %s)" % (name, kind))
    127     return p.getClass()
    128 

PluginException: No plugin registered for (text/plain, <class 'rdflib.parser.Parser'>)

[jesper-friis]

Hi Lukas. Yes, the intention is to run the horizontal demo based on the ontology generated by the vertical demo. When testing it, I am able to reproduce the same errors as you see. These demos were created during in the CSA project which ended in 2019 and clearly need an update.

[markdoerr]

Hej Jesper (@jesper-friis ) I have same issue with a small - self-generated ontology (just adding some classes into a newly generated ontology, like in the vertical demo) . When I try to import my exported ontology (oso_mesurement-v0.0.1.owl), like:

from ontopy import get_ontology

onto = get_ontology('oso_mesurement-v0.0.1.owl')
onto.load()

I get a similar error (s.below). Shall I open a new issue for that, since it is not directly related to the vertical demo ?

lib/python3.10/site-packages/ontopy/ontology.py:587: UserWarning: Recovering from Owlready2 parsing error... might be deprecated
  warnings.warn(
Output exceeds the [size limit](command:workbench.action.openSettings?[). Open the full output data [in a text editor](command:workbench.action.openLargeOutput?5578c98f-ebe8-42fd-b088-959533a21acc)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/py3venv/lara/lib/python3.10/site-packages/owlready2/driver.py:154, in BaseSubGraph.parse(self, f, format, delete_existing_triples, default_base)
    153 if not line.endswith("\n"): line = "%s\n" % line
--> 154 s,p,o = splitter.split(line[:-3], 2)
    156 if   s.startswith("<"): s = s[1:-1]

ValueError: not enough values to unpack (expected 3, got 2)

The above exception was the direct cause of the following exception:

OwlReadyOntologyParsingError              Traceback (most recent call last)
File ~/py3venv/lara/lib/python3.10/site-packages/ontopy/ontology.py:562, in Ontology._load(self, only_local, filename, format, reload, reload_if_newer, url_from_catalog, catalog_file, **kwargs)
    561 elif resolved_url.startswith(web_protocol):
--> 562     return super().load(
    563         only_local=only_local,
    564         reload=reload,
    565         reload_if_newer=reload_if_newer,
    566         **kwargs,
    567     )
    569 else:

File ~/py3venv/lara/lib/python3.10/site-packages/owlready2/namespace.py:955, in Ontology.load(self, only_local, fileobj, reload, reload_if_newer, url, **args)
    954 try:
--> 955   new_base_iri = self.graph.parse(fileobj, default_base = self.base_iri, **args)
...
    125 except KeyError:
--> 126     raise PluginException("No plugin registered for (%s, %s)" % (name, kind))
    127 return p.getClass()

PluginException: No plugin registered for (text/plain, <class 'rdflib.parser.Parser'>)

[jesper-friis]

@markdoerr, you might have to provide a format argument to load(). Since the file extension is .owl, EMMontoPy assumes by default rdf/xml format.

[markdoerr]

Tak, @jesper-friis , for the hint - the current default format of ontopy.onotogy.load() is set to 'None' . Maybe one should write a few words about the formats in the ontopy documentation ? A few days ago, I installed EMMOntoPy on a new machine and am working now with turtle flies, like you do in your domain-atomistic ontology and everything is magically working (though the interface to ontopy or owlready2 is quite brittle - I have a lot of trouble there). I did not have to specify the format in load(), if I work with turtle/ttl files. @lukas-koschmieder : for a working example, see https://gitlab.com/opensourcelab/scientificdata/ontologies/openscienceontology/measurements