Ontology to KB export, TBox/ABox modifications, unit tests, ontology interface usage examples

.gitignore

@@ -1,3 +1,4 @@
 *.pyc
+.ipynb_checkpoints/
 docs/html/*
 docs/latex/*

.travis.yml

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+sudo: required
+
+language: python
+
+before_install:
+    # Install ROS
+  - sudo sh -c 'echo "deb http://packages.ros.org/ros/ubuntu xenial main" > /etc/apt/sources.list.d/ros-latest.list'
+  - sudo curl -sSL 'http://keyserver.ubuntu.com/pks/lookup?op=get&search=0xC1CF6E31E6BADE8868B172B4F42ED6FBAB17C654' | sudo apt-key add -
+  - sudo apt-get update
+  - sudo apt-get install -y --no-install-recommends ros-kinetic-ros-base 
+  - sudo rosdep init
+  - rosdep update
+  - sudo apt install -y --no-install-recommends python-rosinstall python-rosinstall-generator python-wstool build-essential python-catkin-tools ros-kinetic-roslint
+  - sudo pip install catkin_pkg empy
+  - source /opt/ros/kinetic/setup.bash
+    # Install RDFLib
+  - sudo pip install rdflib
+
+install:
+  - cd ../ && mkdir -p catkin_ws/src
+  - cp -r mas_knowledge_base catkin_ws/src/
+  - cd catkin_ws && catkin init && cd src && catkin build
+  - source ../devel/setup.bash
+  - cd mas_knowledge_base
+
+stages:
+  - test
+
+jobs:
+  include:
+    - stage: test
+      script:
+        - python common/tests/ontology_query_interface_unit_tests.py

common/assertions/test_apartment.yaml

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+class_assertions:
+    Male: [Alex, Sushant]
+    Female: [Argentina]
+    Room: [RopodLab, atWorkLab]
+    Chair: [AlexChair, ArgentinaChair, SushantChair]
+    HighTable: [RopodWorkDesk, atWorkDesk]
+property_assertions:
+    defaultLocation:
+        AlexChair: RopodLab
+        ArgentinaChair: RopodLab
+        SushantChair: RopodLab
+        RopodWorkDesk: RopodLab
+        atWorkDesk: atWorkLab
+    locatedAt:
+        AlexChair: RopodLab
+        ArgentinaChair: RopodLab
+        SushantChair: atWorkLab
+        RopodWorkDesk: RopodLab
+        atWorkDesk: atWorkLab
+    nextTo:
+        AlexChair: RopodWorkDesk
+        ArgentinaChair: RopodWorkDesk
+        SushantChair: atWorkDesk

common/definitions/test_apartment.yaml

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+class_definitions:
+    Person: []
+    Male: [Person]
+    Female: [Person]
+    Chair: [Furniture]
+    HighTable: [Furniture]
+property_definitions:
+    nextTo:
+        domain: [None, Object]
+        range: [None, Object]
+        type: SymmetricProperty
+    age:
+        domain: [None, Person]
+        range: [xsd, integer]
+        type: None

common/mas_knowledge_utils/abox_yaml_loader.py

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+import yaml
+import argparse
+import os
+from mas_knowledge_utils.ontology_query_interface import OntologyQueryInterface
+
+class ABoxYAMLLoader:
+    '''Updates an ontology with class and property assertions 
+    that are specified in a yaml file.
+
+    Constructor arguments:
+    @param ontology_file -- full URL of an ontology file (of the form file://<absolute-path>)
+    @param ontology_class_prefix -- class prefix of the items in the given ontology
+    @param assertions_file -- absolute-path to the yaml file containing assertions
+    @param verbose -- boolean to enable debug console logging, which is disabled by default.
+
+    @author Sushant Chavan
+    @contact [email protected]
+
+    '''
+    def __init__(self, ontology_file, ontology_class_prefix, assertions_file, verbose=False):
+        self.ontology_if = OntologyQueryInterface(ontology_file=ontology_file,
+                                    class_prefix=ontology_class_prefix, verbose=verbose)
+        self.class_assertions = None
+        self.property_assertions = None
+        self.verbose = verbose
+
+        self.__load_assertions(assertions_file)
+
+    def update_ontology(self, export_path):
+        '''Inserts the class and property assertions and updates/exports the ontology.
+
+        Keyword arguments:
+        export_path -- string representing the filepath (of the form file://<absolute-path>)
+                       if the ontology has to be exported to a new file. 
+                       If it is 'None', the loaded ontology will be updated with the assertions
+
+        '''
+        self.process_class_assertions()
+        self.process_property_assertions()
+        self.export_ontology(export_path)
+
+    def process_class_assertions(self):
+        '''Inserts the class assertions into the loaded ontology.
+
+        '''
+        if self.class_assertions is None:
+            return
+
+        for class_name in self.class_assertions.keys():
+            instance_names = self.class_assertions[class_name]
+            for instance_name in instance_names:
+                self.ontology_if.insert_class_assertion(class_name, instance_name)
+                self.__verbose("Inserting class assertion: {0}, {1}".format(
+                               class_name, instance_name))
+
+    def process_property_assertions(self):
+        '''Inserts the property assertions into the loaded ontology.
+
+        '''
+        if self.property_assertions is None:
+            return
+
+        for property_name in self.property_assertions.keys():
+            for subj, obj in self.property_assertions[property_name].items():
+                self.ontology_if.insert_property_assertion(property_name, (subj, obj))
+                self.__verbose("Inserting property assertion: {0}, {1}, {2}".format(
+                               subj, property_name, obj))
+
+    def export_ontology(self, export_path):
+        '''Updates/exports the ontology.
+
+        Keyword arguments:
+        export_path -- string representing the filepath (of the form file://<absolute-path>)
+                       if the ontology has to be exported to a new file. 
+                       If it is 'None', the loaded ontology will be updated with the assertions
+
+        '''
+        if export_path is None:
+            # Overwrite the existing ontology file with the updated ontology
+            self.__verbose("No export filepath specified. Updating the loaded ontology.")
+            self.ontology_if.update()
+        else:
+            # Save the updated ontology at the given file location
+            self.__verbose("Exporting the ontology to {0}".format(export_path))
+            self.ontology_if.export(export_path)
+
+    def __load_assertions(self, assertions_file):
+        '''Loads the class and property assertions as two separate
+        dictionaries from the yaml file
+
+        Keyword arguments:
+        assertions_file -- absolute-path to the yaml file containing assertions
+
+        '''
+        assertions = None
+        with open(assertions_file, 'r') as f:
+            assertions = yaml.load(f, Loader=yaml.FullLoader)
+
+        if assertions is None:
+            raise Exception("Could not load the assertion file!")
+        else:
+            self.class_assertions = assertions['class_assertions']
+            self.property_assertions = assertions['property_assertions']
+
+    def __verbose(self, content):
+        '''Console debug logger to print the content along with the
+        '[ABoxYAMLLoader]' tag only if the self.verbose flag is set
+
+        Keyword arguments:
+        @param content -- string representing the content to be printed
+
+        '''
+        if self.verbose:
+            print("[ABoxYAMLLoader] {0}".format(content))
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('asserts', type=str, 
+                        help="Name of the yaml file containing the assertions \
+                              (eg.: apartment_asserts)")
+    parser.add_argument('-o', '--ontology', type=str, action='store', 
+                        help="Filename of the ontology (default: apartment_go_2019)",
+                        default='apartment_go_2019')
+    parser.add_argument('-c', '--class-prefix', type=str, action='store', 
+                        help="class prefix (or namespace) of the items in the \
+                              given ontology (default: apartment)",
+                        default='apartment')
+    parser.add_argument('-e', '--export-file', type=str, action='store', 
+                        help="Filename for exporting the updated ontology \
+                              (eg.: apartment_go_2019_updated). If not \
+                               specified, the loaded ontology will be updated.",
+                        default=None)
+    parser.add_argument('-v', '--verbose', action='store_true',
+                        help="Enable debug console logs")
+
+    args = parser.parse_args()
+
+    script_dir = os.path.abspath(os.path.dirname(__file__))
+    ontology_dir = os.path.join(os.path.dirname(script_dir), "ontology")
+    assertions_dir = os.path.join(os.path.dirname(script_dir), "assertions")
+
+    ontology_file_path = "file://" + os.path.join(ontology_dir, args.ontology + ".owl")
+    assertions_file_path = os.path.join(assertions_dir, args.asserts + ".yaml")
+
+    export_file_path = None
+    if args.export_file is not None:
+        export_file_path = "file://" + os.path.join(ontology_dir, args.export_file + ".owl")
+
+    loader = ABoxYAMLLoader(ontology_file_path, args.class_prefix, 
+                            assertions_file_path, verbose=args.verbose)
+    loader.update_ontology(export_file_path)