cognitum-octopus / cognipy Goto Github PK

In-memory Graph Database and Knowledge Graph with Natural Language Interface, compatible with Pandas

Home Page: https://cognitum-octopus.github.io/cognipy/

License: Other

C# 36.03% Batchfile 0.04% Python 0.56% JavaScript 0.12% Prolog 35.54% Smarty 0.15% Makefile 0.01% CSS 0.01% Jupyter Notebook 27.42% Smalltalk 0.14%

owl jena rl-reasoner rdf graph-algorithms pandas python elk controlled-natural-language natural-language-interface graph memory-graph-database knowledge-graph sparql dataframe jupyter

cognipy's Issues

Research on testrunner for the project

Add progress bar for reasoning

FluentEditor is using encoding='utf-8-sig'

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

Investigate FIBO OoM error

Complete methods descriptions

Reasoner loading error under Ubuntu - BOM and CR/LF problem

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

Manage ontology format when translating from/to CNL

Add Profile selection and validation (start from RL)

delete_instance

Ontology.delete_instance() behaviour

Handle n-ary relations in CNL with : by, at , with

Sometimes we need to use n-ary relations e.g.:

Prime is a number with a specific-property.
Chart-101 presents information about Cat from 2001 until 2012.

Export of modalities to OWL

Currently modalities are not exported to OWL

UnicodeEncodeError

https://www.isibang.ac.in/~bisu/ontology/mod-ontology-09092016.owl

load ontology with Ontology constructor
use draw_graph() method

ValueError: To many values to unpack

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

Misleading error message

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")

Research on the CNL Edit control implementation so it can use CodeMirror instead of ipywidgets.TextArea

Currently, CNL Edit uses ipywidgets. This has many limitations including problems with JupyterLab which is the future of the data-science. We need to investigate the best approach and start working on it.

Update the OWL API version

TODO annotations_for_subject method in ontology

Add initial unitary test for the ontology class

ParseException for `K9s is something.`

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)

setup cognipy landing page on github pages. Make documentation as a subfolder

insert_cnl, delete_cnl methods output

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?

Ontology constructor execution takes forever when uri is invalid.

TODO setup_function method in Ontology.py

RDF -> CNL -> RDF causes annotations to disappear

NumberFormatException

when loading http://krr-nas.cs.ox.ac.uk/ontologies/lib/BioPAX/biopax-level2/biopax-example-ecocyc-glycolysis/v1.0/00007.owl

TODO constrains_for_subject method in ontology

Disjoint union inconsistency not being detected by reasoner

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.

Clean up CogniPySvr class

Analyze code in CogniPySvr class in terms of unused/untested methods since it's most exposed class to a user

ExpactError

Error occures when following ontology is loaded https://www.cs.upc.edu/~loliva/OntoWAWO+.owl and trying to do draw_graph().

serialization error

If X connects-to something that connects-to Y then Y follows X.
follows->followed

Add support for uncountables

Nothing but workclass
instead of
nothing but workclasses

Add tests for the rest of the Ontology class methods

RiotException

when loading http://krr-nas.cs.ox.ac.uk/ontologies/lib/BAMS/neuron-ontology/2009-10-28/00006.owl

Problem with the disjointness assertion

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.

Union in range of the role

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>

cognitum-octopus / cognipy Goto Github PK

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