It seems there's an error with the disjointness operator in CogniPy.

The following assertions result with an inconsistency detected in the ontology:

Anything either 
  is a second-name,
  is a first-name or
  is a last-name
  or-something-else.

First-Name-1 is a first-name.
First-Name-1 is a last-name.

While the following assertions does not:

Anything either 
  is a first-name or
  is a last-name
  or-something-else.

First-Name-1 is a first-name.
First-Name-1 is a last-name.

I tried the examples in a cognipy installation under Ubuntu. At first it seemed that everything works as expected, but suddenly I started to receive the following error:

Traceback (most recent call last):
  File "check_consistency.py", line 28, in <module>
    printReasoningInfo(onto)
  File "check_consistency.py", line 15, in printReasoningInfo
    info=onto.reasoningInfo()
  File "/usr/local/lib/python3.7/dist-packages/cognipy/ontology.py", line 299, in reasoningInfo
    self.super_concepts_of("a thing")
  File "/usr/local/lib/python3.7/dist-packages/cognipy/ontology.py", line 179, in super_concepts_of
    return cognipy_call(self._uid, "GetSuperConceptsOf", cnl, direct)
  File "/usr/local/lib/python3.7/dist-packages/cognipy/interop.py", line 71, in cognipy_call
    raise translate_exception(json.loads(js))
Exception: [

  "InvalidOperationException",
  {
    "ClassName": "System.InvalidOperationException",
    "Message": "The reasoner is not initialized. You need to call Load... before calling this method.",
    "Data": null,
    "InnerException": null,

    "HelpURL": null,

    "StackTraceString": "  at CogniPy.CogniPySvr.get_reasoner () [0x00008] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at CogniPy.CogniPySvr.Materialize () [0x0001b] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at CogniPy.CogniPySvr.GetSuperConceptsOf (System.String cnlName, System.Boolean direct) [0x00000] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at (wrapper managed-to-native) System.Reflection.RuntimeMethodInfo.InternalInvoke(System.Reflection.RuntimeMethodInfo,object,object[],System.Exception&)\n  at System.Reflection.RuntimeMethodInfo.Invoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x0006a] in <533173d24dae460899d2b10975534bb0>:0 ",
    "RemoteStackTraceString": null,
    "RemoteStackIndex": 0,
    "ExceptionMethod": null,
    "HResult": -2146233079,
    "Source": "CogniPyLib"
  }
]

My python version is 3.7.12 and mono version is 6.12.0.122. I will submit a Dockerfile which will allow to reproduce the error.

Update: example.tar.gz

Bumps Newtonsoft.Json from 12.0.3 to 13.0.1.

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Please refer to below ontology:

Something is a human if-and-only-if-it-either is a child, is an old-man, is a middle-aged-man or is a young-man.
Jan is a child.
Jan is an old-man.

After loading it, reasoner doesn't catch the inconsistency - the reasoningInfo() function returns no problems.

Providing path to non-existing encnl file the error is:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "venv/lib/python3.6/site-packages/cognipy/ontology.py", line 104, in __init__
    modalCheck, passParamsAsCnl, stop_on_error)
  File "venv/lib/python3.6/site-packages/cognipy/interop.py", line 71, in cognipy_call
    raise translate_exception(json.loads(js))
Exception: [

  "IllegalArgumentException",

  {

    "ClassName": "java.lang.IllegalArgumentException",

    "Message": "URI is not absolute",

    "Data": null,

    "InnerException": null,

    "HelpURL": null,

    "StackTraceString": "  at CogniPy.CogniPySvr.Load (CogniPy.ReferenceManager+WhatToLoad whatToLoad, System.String contentToLoad, CogniPy.CNL.DL.Paragraph impliAst, System.Boolean throwOnException, System.Boolean loadAnns, System.Boolean materialize, System.Boolean modalChecker) [0x00057] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at CogniPy.CogniPySvr.LoadCnl (System.String filename, CogniPy.CNL.DL.Paragraph impliAst, System.Boolean throwOnException, System.Boolean loadAnns, System.Boolean materialize, System.Boolean modalChecker) [0x00000] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at CogniPy.CogniPySvr.LoadCnl (System.String filename, System.Boolean loadAnnotations, System.Boolean materialize, System.Boolean modalChecker, System.Boolean throwOnError) [0x00000] in <f8783c48f78341ba843524fd57b41eb3>:0 \n  at (wrapper managed-to-native) System.Reflection.MonoMethod:InternalInvoke (System.Reflection.MonoMethod,object,object[],System.Exception&)\n  at System.Reflection.MonoMethod.Invoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00038] in <8f2c484307284b51944a1a13a14c0266>:0 ",

    "RemoteStackTraceString": null,

    "RemoteStackIndex": 0,

    "ExceptionMethod": null,

    "HResult": -2146233088,

    "Source": "CogniPyLib",

    "$0": {

      "$0": {

        "type": "java.lang.IllegalArgumentException, IKVM.OpenJDK.Core, Version=8.1.5717.0, Culture=neutral, PublicKeyToken=13235d27fcbfff58",

        "sig": null

      },

      "$1": {

        "$0": {

          "type": "java.lang.RuntimeException, IKVM.OpenJDK.Core, Version=8.1.5717.0, Culture=neutral, PublicKeyToken=13235d27fcbfff58",

          "sig": null

        },

        "$1": {

          "$0": {

            "type": "java.lang.Exception, IKVM.OpenJDK.Core, Version=8.1.5717.0, Culture=neutral, PublicKeyToken=13235d27fcbfff58",

            "sig": null

          },

          "$1": {

            "$0": {

              "type": "java.lang.Throwable, IKVM.OpenJDK.Core, Version=8.1.5717.0, Culture=neutral, PublicKeyToken=13235d27fcbfff58",

              "sig": null

            },

            "$1": "Ljava/lang/Throwable;",

            "$2": "Ljava/lang/String;",

            "$3": "[Ljava/lang/StackTraceElement;",

            "$4": "Ljava/util/List;",

            "$5": null,

            "$data": "FAFyASgAE2phdmEubGFuZy5UaHJvd2FibGXVxjUnOXe4ywMABEwABWNhdXNlARBMAA1kZXRhaWxNZXNzYWdlAQ1bAApzdGFja1RyYWNlARdMABRzdXBwcmVzc2VkRXhjZXB0aW9ucwIA"

          },

          "$data": "FAFyASAAE2phdmEubGFuZy5FeGNlcHRpb27Q/R8+GjscxAIAAAEA"

        },

        "$data": "FAFyAScAGmphdmEubGFuZy5SdW50aW1lRXhjZXB0aW9unl8GRwo0g+UCAAABAA=="

      },

      "$data": "FAFyAS8AImphdmEubGFuZy5JbGxlZ2FsQXJndW1lbnRFeGNlcHRpb261iXPTfWaPvAIAAAEA"

    },

    "$2": "URI is not absolute",

    "$3": [],

    "$4": [],

    "$data": "CgUA"

  }

]

To reproduce (on Ubuntu):

onto = Ontology("cnl/file","nonexisting.encnl")

Both owls produces same issue: https://sites.google.com/site/ontoworks/ontologies/DSA_04092015.owl?attredirects=0&d=1 https://www.isibang.ac.in/~bisu/ontology/instOntology.owl

Names of methods suggests that you can insert/delete any CNL yet if you insert/delete incorrect cnl like subsumption in attached pic error occures. Maybe output can be prettier?

Bumps Newtonsoft.Json from 12.0.3 to 13.0.2.

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Using

onto = Ontology("cnl/file","hello.encnl",stop_on_error=True)

Works with

%%writefile hello.encnl
Kas is something.

Errors with

%%writefile hello.encnl
K9s is something.

---------------------------------------------------------------------------
ParseException                            Traceback (most recent call last)
Input In [3], in <cell line: 1>()
----> 1 onto = Ontology("cnl/file","hello.encnl",stop_on_error=True)

File /opt/conda/lib/python3.10/site-packages/cognipy/ontology.py:103, in Ontology.__init__(self, source, arg, verbose, evaluator, graph_attribute_formatter, stop_on_error)
    101 self._uid = cognipy_create()
    102 if source == "cnl/file":
--> 103     cognipy_call(self._uid, "LoadCnl", arg, loadAnnotations,
    104                  modalCheck, passParamsAsCnl, stop_on_error)
    105 elif source == "cnl/string":
    106     cognipy_call(self._uid, "LoadCnlFromString", arg,
    107                  loadAnnotations, modalCheck, passParamsAsCnl, stop_on_error)

File /opt/conda/lib/python3.10/site-packages/cognipy/interop.py:76, in cognipy_call(uid, cmd, *args)
     74 js="\r\n".join(ja)
     75 if fl.strip()=='@exception':
---> 76     raise translate_exception(json.loads(js))
     77 return json.loads(js)

ParseException: {'Errors': [{'Line': 0, 'Column': 0, 'Pos': 0, 'Context': 'K9s is something.\n', 'Hint': 'K^9s is something.'}]}

(running in a jupyther/minimal image with mono added)

BTW there's a similar issue with assertions on relations.

Both these work:

No first-name is pesel-num. Every first-name connects-with nothing-but thing that is a pesel-num. First-Name-6 is a first-name. First-Name-7 is a first-name. First-Name-6 connects-with First-Name-7. Causes error.

No first-name is last-name. Every first-name connects-with nothing-but thing that is a last-name. First-Name-6 is a first-name. First-Name-7 is a first-name. First-Name-6 connects-with First-Name-7. Causes error too.

But:

No first-name is last-name. No first-name is pesel-num. Every first-name connects-with nothing-but thing that is a last-name and-or pesel-num. First-Name-6 is a first-name. First-Name-7 is a first-name. First-Name-6 connects-with First-Name-7. Does not cause an error.

@apohllo

Author apohllo commented 4 days ago The RDF/OWL conversions are as follows, for the first type of assertion:

<rdfs:subClassOf>
  <owl:Restriction>
    <owl:onProperty rdf:resource="http://www.cognitum.eu/onto#connectsWith" />
    <owl:allValuesFrom rdf:resource="http://www.cognitum.eu/onto#lastName" />
  </owl:Restriction>
</rdfs:subClassOf>

and for the second type:

<rdfs:subClassOf>
  <owl:Restriction>
    <owl:onProperty rdf:resource="http://www.cognitum.eu/onto#connectsWith" />
    <owl:allValuesFrom>
      <owl:Class>
        <owl:unionOf rdf:parseType="Collection">
          <rdf:Description rdf:about="http://www.cognitum.eu/onto#lastName" />
          <rdf:Description rdf:about="http://www.cognitum.eu/onto#peselNum" />
        </owl:unionOf>
      </owl:Class>
    </owl:allValuesFrom>
  </owl:Restriction>
</rdfs:subClassOf>

Fluent Editor is using 'utf-8-sig' encoding and it needs to be used when opening these files e.g.: '''onto=Ontology("cnl/string",'\n'.join(open(fn,"rt",encoding='utf-8-sig').read() for fn in ["data/sample-data.encnl"]))''' Please update documentation and examples