| Class | 81 |Description | 82 |
|---|---|
| drugOrder | 86 |
87 | This example is taken from Owlready paper: https://www.archives-ouvertes.fr/hal-01592746/document
88 | To compare difference in the number of lines of code written with OWL-API and OWLOOP-API
89 | |
90 |
| Class | 81 |Description | 82 |
|---|---|
| addAxioms | 86 |
87 | An example to illustrate how to add axioms to an ontology.
88 | |
89 |
| Class | 81 |Description | 82 |
|---|---|
| useDescriptorBuildMethod | 86 |
87 | An example to illustrate how to 'build()' method of a descriptor.
88 | |
89 |
| Class | 81 |Description | 82 |
|---|---|
| RemoveAxioms | 86 |
87 | An example to illustrate how to remove axioms from an ontology.
88 | |
89 |
33 | 34 | 35 | -------------------------------------------------------------------------------- /docs/package-list: -------------------------------------------------------------------------------- 1 | it.emarolab.owloop.articleExamples.drugOrderExample 2 | it.emarolab.owloop.articleExamples.example1 3 | it.emarolab.owloop.articleExamples.example2 4 | it.emarolab.owloop.articleExamples.example3 5 | it.emarolab.owloop.articleExamples.exampleDescriptors 6 | it.emarolab.owloop.core 7 | it.emarolab.owloop.descriptor.construction.descriptorEntitySet 8 | it.emarolab.owloop.descriptor.construction.descriptorExpression 9 | it.emarolab.owloop.descriptor.construction.descriptorGround 10 | it.emarolab.owloop.descriptor.utility.classDescriptor 11 | it.emarolab.owloop.descriptor.utility.dataPropertyDescriptor 12 | it.emarolab.owloop.descriptor.utility.individualDescriptor 13 | it.emarolab.owloop.descriptor.utility.objectPropertyDescriptor 14 | it.emarolab.owloop.descriptorDebugging 15 | -------------------------------------------------------------------------------- /docs/script.js: -------------------------------------------------------------------------------- 1 | function show(type) 2 | { 3 | count = 0; 4 | for (var key in methods) { 5 | var row = document.getElementById(key); 6 | if ((methods[key] & type) != 0) { 7 | row.style.display = ''; 8 | row.className = (count++ % 2) ? rowColor : altColor; 9 | } 10 | else 11 | row.style.display = 'none'; 12 | } 13 | updateTabs(type); 14 | } 15 | 16 | function updateTabs(type) 17 | { 18 | for (var value in tabs) { 19 | var sNode = document.getElementById(tabs[value][0]); 20 | var spanNode = sNode.firstChild; 21 | if (value == type) { 22 | sNode.className = activeTableTab; 23 | spanNode.innerHTML = tabs[value][1]; 24 | } 25 | else { 26 | sNode.className = tableTab; 27 | spanNode.innerHTML = "" + tabs[value][1] + ""; 28 | } 29 | } 30 | } 31 | -------------------------------------------------------------------------------- /gitRepoResources/NotesDuringDevelopment.txt: -------------------------------------------------------------------------------- 1 | ######################################################## 2 | 3 | Notes taken during development of this (OWLOOP) project. 4 | 5 | ######################################################## 6 | 7 | This document is mainly for keeping track on how we overcome some critical/common problems when we find them. 8 | Because as you know, when we leave the code for a week or two, and come back to it, we forget how we made it. :) 9 | 10 | Moreover, this document can also be used to note ideas for future development, and the prerequisites that can bring them to life. 11 | 12 | The structure for tracking the problems is as follows: 13 | 14 | [Date - Author] 15 | [Problem] 16 | [Fix] 17 | 18 | The structure for tracking the ideas is as follows: 19 | 20 | [Date - Author] 21 | [Idea] 22 | [Prerequisites] 23 | 24 | ################################################################################################################ 25 | 26 | [Date - Author] 21/05/2019 - Syed Yusha Kareem 27 | [Problem] Axioms do not get removed, if some are added by hand in protege and others added from the code. To delete something, need to delete everything (i.e, IndividualExpressionAxioms). 28 | [Fix] 29 | 30 | /* 31 | QUICK THOUGHTS: 32 | 33 | // Regarding the use of readExpressionAxioms() 34 | 35 | 36 | d1.addObject( "hasProp1", "X"); 37 | d1.addObject( "hasProp2", "X"); 38 | d1.writeExpressionAxioms(); 39 | 40 | FullIndividualDesc d1 = new FullIndividualDesc("Robot1", ontoref); 41 | d1.readExpressionAxioms(); //at this point the descriptor reads all knowledge 42 | System.out.println( " 11 " + d1); 43 | 44 | FullIndividualDesc d2 = new FullIndividualDesc("Robot1", ontoref); 45 | d2.addObject( "hasProp1"); 46 | d2.addObject( "hasProp2"); 47 | d2.readExpressionAxioms(); //at this point the descriptor reads only particular knowledge 48 | System.out.println( " 22 " + d2); 49 | */ 50 | 51 | 52 | /* 53 | We need ..OWLRefCreated.. to make an ontology which does not exist 54 | We need ..OWLRefFromFile.. to interact with an ontology which already exists 55 | From the ..OWLRefCreated.. file we can write/save in both ways (ontoref.save(), descriptor.save(path)) and CAN-READ in both ways (same descriptor, new descriptor). 56 | From the ..OWLRefFromFile.. we can write/save in one way (descriptor.save(path)) and CAN-READ in both ways (same descriptor, new descriptor). 57 | SynchronizeReasoner() to be in sync with the latest state of the ontology (else the descriptor reads the state of the ontology, when it was instantiated) 58 | readExpressionAxioms(), when called for the first time, reads all (asserted and inferred) axioms because when the descriptor is initialized, syncOnto() is called. 59 | With newOWLReferenceFromFileWithPellet(), decriptor.saveOntology(path), IS WORKING 60 | With newOWLReferenceFromFileWithPellet(), ontoRef.saveOntology(path), IS WORKING 61 | TODO: [Make developer's life easier] Make ontoRef.saveOntology() work with newOWLReferenceFromFileWithPellet() 62 | Its nice to (sync and save) after writing something to the ontology. 63 | */ 64 | 65 | /* 66 | Regarding mandatory usage of OWLReferencesContainer from aMOR 67 | 68 | Note that: First and foremost it is important to instantiate an object such that we load ontology into memory (An in-memory representation - Abstract Syntax Tree). 69 | To do this aMOR provides a class called OWLReferencesContainer that initializes the ontology by loading it into memory and gives an OWLReference object. 70 | */ 71 | 72 | /* 73 | UNEXPECTED BEHAVIOUR AND THEIR FIXES 74 | 75 | (If) Ontology is not updated properly 76 | (Then) Try using writeAxiomsReasonReadAxioms() 77 | 78 | (If) Descriptor's internal state is not updating properly 79 | (Then) Make AMORLogging(True) and check is there is an error (because the ontology could be inconsistent) 80 | 81 | (If) OWLReferences object 'ontoRef' is instantiated with newOWLReferenceFromFileWithPellet() and ontoRef.saveOntology() is not saving axioms to .owl file 82 | (Then) Provide file-path, i.e., ontoRef.saveOntology(ontoRef.getFilePath()) 83 | */ 84 | 85 | TODO [Find out] what is the use of ontoRef.getReasonerExplainer(); -------------------------------------------------------------------------------- /gitRepoResources/images/add_axioms_and_view_in_protege.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheEngineRoom-UniGe/OWLOOP/1e1a8e48407098361a4656d1ba0bad0cbe535775/gitRepoResources/images/add_axioms_and_view_in_protege.gif -------------------------------------------------------------------------------- /gitRepoResources/images/classesAssertedInferred.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheEngineRoom-UniGe/OWLOOP/1e1a8e48407098361a4656d1ba0bad0cbe535775/gitRepoResources/images/classesAssertedInferred.png -------------------------------------------------------------------------------- /gitRepoResources/images/d_methods.png: 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/gitRepoResources/images/unige_ter_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheEngineRoom-UniGe/OWLOOP/1e1a8e48407098361a4656d1ba0bad0cbe535775/gitRepoResources/images/unige_ter_logo.png -------------------------------------------------------------------------------- /gradlew: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | ############################################################################## 4 | ## 5 | ## Gradle start up script for UN*X 6 | ## 7 | ############################################################################## 8 | 9 | # Attempt to set APP_HOME 10 | # Resolve links: $0 may be a link 11 | PRG="$0" 12 | # Need this for relative symlinks. 13 | while [ -h "$PRG" ] ; do 14 | ls=`ls -ld "$PRG"` 15 | link=`expr "$ls" : '.*-> \(.*\)$'` 16 | if expr "$link" : '/.*' > /dev/null; then 17 | PRG="$link" 18 | else 19 | PRG=`dirname "$PRG"`"/$link" 20 | fi 21 | done 22 | SAVED="`pwd`" 23 | cd "`dirname \"$PRG\"`/" >/dev/null 24 | APP_HOME="`pwd -P`" 25 | cd "$SAVED" >/dev/null 26 | 27 | APP_NAME="Gradle" 28 | APP_BASE_NAME=`basename "$0"` 29 | 30 | # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. 31 | DEFAULT_JVM_OPTS="" 32 | 33 | # Use the maximum available, or set MAX_FD != -1 to use that value. 34 | MAX_FD="maximum" 35 | 36 | warn ( ) { 37 | echo "$*" 38 | } 39 | 40 | die ( ) { 41 | echo 42 | echo "$*" 43 | echo 44 | exit 1 45 | } 46 | 47 | # OS specific support (must be 'true' or 'false'). 48 | cygwin=false 49 | msys=false 50 | darwin=false 51 | nonstop=false 52 | case "`uname`" in 53 | CYGWIN* ) 54 | cygwin=true 55 | ;; 56 | Darwin* ) 57 | darwin=true 58 | ;; 59 | MINGW* ) 60 | msys=true 61 | ;; 62 | NONSTOP* ) 63 | nonstop=true 64 | ;; 65 | esac 66 | 67 | CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar 68 | 69 | # Determine the Java command to use to start the JVM. 70 | if [ -n "$JAVA_HOME" ] ; then 71 | if [ -x "$JAVA_HOME/jre/sh/java" ] ; then 72 | # IBM's JDK on AIX uses strange locations for the executables 73 | JAVACMD="$JAVA_HOME/jre/sh/java" 74 | else 75 | JAVACMD="$JAVA_HOME/bin/java" 76 | fi 77 | if [ ! -x "$JAVACMD" ] ; then 78 | die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME 79 | 80 | Please set the JAVA_HOME variable in your environment to match the 81 | location of your Java installation." 82 | fi 83 | else 84 | JAVACMD="java" 85 | which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 86 | 87 | Please set the JAVA_HOME variable in your environment to match the 88 | location of your Java installation." 89 | fi 90 | 91 | # Increase the maximum file descriptors if we can. 92 | if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then 93 | MAX_FD_LIMIT=`ulimit -H -n` 94 | if [ $? -eq 0 ] ; then 95 | if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then 96 | MAX_FD="$MAX_FD_LIMIT" 97 | fi 98 | ulimit -n $MAX_FD 99 | if [ $? -ne 0 ] ; then 100 | warn "Could not set maximum file descriptor limit: $MAX_FD" 101 | fi 102 | else 103 | warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" 104 | fi 105 | fi 106 | 107 | # For Darwin, add options to specify how the application appears in the dock 108 | if $darwin; then 109 | GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" 110 | fi 111 | 112 | # For Cygwin, switch paths to Windows format before running java 113 | if $cygwin ; then 114 | APP_HOME=`cygpath --path --mixed "$APP_HOME"` 115 | CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` 116 | JAVACMD=`cygpath --unix "$JAVACMD"` 117 | 118 | # We build the pattern for arguments to be converted via cygpath 119 | ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` 120 | SEP="" 121 | for dir in $ROOTDIRSRAW ; do 122 | ROOTDIRS="$ROOTDIRS$SEP$dir" 123 | SEP="|" 124 | done 125 | OURCYGPATTERN="(^($ROOTDIRS))" 126 | # Add a user-defined pattern to the cygpath arguments 127 | if [ "$GRADLE_CYGPATTERN" != "" ] ; then 128 | OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" 129 | fi 130 | # Now convert the arguments - kludge to limit ourselves to /bin/sh 131 | i=0 132 | for arg in "$@" ; do 133 | CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` 134 | CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option 135 | 136 | if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition 137 | eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` 138 | else 139 | eval `echo args$i`="\"$arg\"" 140 | fi 141 | i=$((i+1)) 142 | done 143 | case $i in 144 | (0) set -- ;; 145 | (1) set -- "$args0" ;; 146 | (2) set -- "$args0" "$args1" ;; 147 | (3) set -- "$args0" "$args1" "$args2" ;; 148 | (4) set -- "$args0" "$args1" "$args2" "$args3" ;; 149 | (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; 150 | (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; 151 | (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; 152 | (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; 153 | (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; 154 | esac 155 | fi 156 | 157 | # Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules 158 | function splitJvmOpts() { 159 | JVM_OPTS=("$@") 160 | } 161 | eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS 162 | JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME" 163 | 164 | # by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong 165 | if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then 166 | cd "$(dirname "$0")" 167 | fi 168 | 169 | exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@" 170 | -------------------------------------------------------------------------------- /gradlew.bat: -------------------------------------------------------------------------------- 1 | @if "%DEBUG%" == "" @echo off 2 | @rem ########################################################################## 3 | @rem 4 | @rem Gradle startup script for Windows 5 | @rem 6 | @rem ########################################################################## 7 | 8 | @rem Set local scope for the variables with windows NT shell 9 | if "%OS%"=="Windows_NT" setlocal 10 | 11 | set DIRNAME=%~dp0 12 | if "%DIRNAME%" == "" set DIRNAME=. 13 | set APP_BASE_NAME=%~n0 14 | set APP_HOME=%DIRNAME% 15 | 16 | @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. 17 | set DEFAULT_JVM_OPTS= 18 | 19 | @rem Find java.exe 20 | if defined JAVA_HOME goto findJavaFromJavaHome 21 | 22 | set JAVA_EXE=java.exe 23 | %JAVA_EXE% -version >NUL 2>&1 24 | if "%ERRORLEVEL%" == "0" goto init 25 | 26 | echo. 27 | echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 28 | echo. 29 | echo Please set the JAVA_HOME variable in your environment to match the 30 | echo location of your Java installation. 31 | 32 | goto fail 33 | 34 | :findJavaFromJavaHome 35 | set JAVA_HOME=%JAVA_HOME:"=% 36 | set JAVA_EXE=%JAVA_HOME%/bin/java.exe 37 | 38 | if exist "%JAVA_EXE%" goto init 39 | 40 | echo. 41 | echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 42 | echo. 43 | echo Please set the JAVA_HOME variable in your environment to match the 44 | echo location of your Java installation. 45 | 46 | goto fail 47 | 48 | :init 49 | @rem Get command-line arguments, handling Windows variants 50 | 51 | if not "%OS%" == "Windows_NT" goto win9xME_args 52 | 53 | :win9xME_args 54 | @rem Slurp the command line arguments. 55 | set CMD_LINE_ARGS= 56 | set _SKIP=2 57 | 58 | :win9xME_args_slurp 59 | if "x%~1" == "x" goto execute 60 | 61 | set CMD_LINE_ARGS=%* 62 | 63 | :execute 64 | @rem Setup the command line 65 | 66 | set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar 67 | 68 | @rem Execute Gradle 69 | "%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% 70 | 71 | :end 72 | @rem End local scope for the variables with windows NT shell 73 | if "%ERRORLEVEL%"=="0" goto mainEnd 74 | 75 | :fail 76 | rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of 77 | rem the _cmd.exe /c_ return code! 78 | if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 79 | exit /b 1 80 | 81 | :mainEnd 82 | if "%OS%"=="Windows_NT" endlocal 83 | 84 | :omega 85 | -------------------------------------------------------------------------------- /lib/amor-2.2.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheEngineRoom-UniGe/OWLOOP/1e1a8e48407098361a4656d1ba0bad0cbe535775/lib/amor-2.2.jar -------------------------------------------------------------------------------- /lib/owloop-2.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TheEngineRoom-UniGe/OWLOOP/1e1a8e48407098361a4656d1ba0bad0cbe535775/lib/owloop-2.1.jar -------------------------------------------------------------------------------- /settings.gradle: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2017 Luca Buoncompagni, Syed Yusha Kareem. 3 | * 4 | * Licensed under the GNU GENERAL PUBLIC LICENSE, Version 3.0. 5 | * You may obtain a copy of the License at https://www.gnu.org/licenses/gpl-3.0.en.html 6 | * 7 | * Unless required by applicable law or agreed to in writing, software 8 | * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT 9 | * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the 10 | * License for the specific language governing permissions and limitations under 11 | * the License. 12 | */ 13 | 14 | rootProject.name = 'owloop' 15 | -------------------------------------------------------------------------------- /src/main/java/it/emarolab/owloop/descriptor/construction/descriptorEntitySet/Classes.java: -------------------------------------------------------------------------------- 1 | package it.emarolab.owloop.descriptor.construction.descriptorEntitySet; 2 | 3 | import it.emarolab.owloop.core.Axiom; 4 | import org.semanticweb.owlapi.model.OWLClass; 5 | 6 | import java.util.Collection; 7 | 8 | /** 9 | * An extension of {@link DescriptorEntitySet.EntitySetBase} for {@link OWLClass}. 10 | *
11 | * It represent the {@link Axiom.EntitySet} which contains OWL-Classes. 12 | *
13 | * 14 | *15 | *
12 | * It represents a set of OWL-DataProperties and related OWL-Literals, as a collection of {@link DataLinks}. 13 | *
14 | * 15 | *16 | *
11 | * It represent the {@link Axiom.EntitySet} which contains OWL-DataProperties. 12 | *
13 | * 14 | *15 | *
11 | * It represents the {@link Axiom.EntitySet} which contains OWL-Individuals. 12 | *
13 | * 14 | *15 | *
11 | * It represent the {@link Axiom.EntitySet} which contains OWL-literals. 12 | *
13 | * 14 | *15 | *
12 | * It represents a set of OWL-ObjectProperties and related OWL-Individuals, as a collection of {@link ObjectLinks}. 13 | *
14 | * 15 | *16 | *
11 | * It represent the {@link Axiom.EntitySet} which contains OWL-ObjectProperties. 12 | *
13 | * 14 | *15 | *
11 | * It represent the {@link Axiom.EntitySet} which contains OWL-Restrictions. 12 | *
13 | * 14 | *15 | *
12 | *
13 | *
12 | *
12 | *
23 | *
22 | *
23 | *
22 | *
23 | *
23 | *
23 | *
24 | *
23 | *
22 | *
16 | *
17 | *
17 | *
13 | *
8 | * Extends LocationClassDesc. 9 | *
10 | * Adds some-restriction on the concept "CORRIDOR", i.e, CORRIDOR hasDoor some DOOR. 11 | * Furthermore, adds min-cardinality-restriction, i.e., CORRIDOR hasDoor min 2 DOOR. 12 | * 13 | *14 | *
21 | *
20 | * Doing build() with this Descriptor returns the descriptor of type {@link DefSubClassDesc}. 21 | *
22 | * See {@link FullClassDesc} for an example of a 'compound' Class Descriptor that implements all ConceptExpressions. 23 | * 24 | *25 | *
8 | * Extends DefClassDesc. 9 | *
10 | * Adds some-restriction on the concept "LOCATION", i.e, LOCATION hasDoor some DOOR 11 | * 12 | *13 | *
19 | * Doing build() with this Descriptor returns another descriptor of type {@link FullObjectPropertyDesc}. 20 | *
21 | * See {@link FullIndividualDesc} for an example of a 'compound' Individual Descriptor that implements all IndividualExpressions. 22 | * 23 | *24 | *
8 | * Extends LocationClassDesc. 9 | *
10 | * Adds some-restriction on the concept "ROOM", i.e, ROOM hasDoor some DOOR. 11 | * Furthermore, adds max-cardinality-restriction, i.e., ROOM hasDoor max 1 DOOR. 12 | * 13 | *14 | *
20 | * Doing build() with this Descriptor returns another descriptor of type {@link DefSubClassDesc}. 21 | *
22 | * 23 | * See {@link FullIndividualDesc} for an example of a 'compound' Individual Descriptor that implements all IndividualExpressions. 24 | * 25 | *26 | *