diff --git a/.gitignore b/.gitignore
index 7e511a4f71a14e36b90af9746b481a88cde92475..7d13785b01f085c0a5135689f6dc8ee6643986c1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,6 @@
lib
out
/output/
-target
\ No newline at end of file
+target
+.gradle
+build
\ No newline at end of file
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000000000000000000000000000000000000..24b9d60c164e93e9971794c574e221f9bf119ed6
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,49 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This project uses @Incubating APIs which are subject to change.
+ */
+
+plugins {
+ id 'java'
+ id 'maven-publish'
+}
+
+repositories {
+ mavenLocal()
+ maven {
+ url = uri('https://repo.maven.apache.org/maven2/')
+ }
+}
+
+dependencies {
+ implementation 'org.deeplearning4j:deeplearning4j-core:1.0.0-M1.1'
+ implementation 'org.nd4j:nd4j-native-platform:1.0.0-M1.1'
+ implementation 'com.fasterxml.jackson.core:jackson-core:2.12.1'
+ implementation 'com.fasterxml.jackson.core:jackson-annotations:2.12.1'
+ implementation 'com.fasterxml.jackson.core:jackson-databind:2.12.1'
+ implementation 'commons-codec:commons-codec:1.15'
+ implementation 'org.slf4j:slf4j-nop:1.7.36'
+ implementation 'org.apache.jena:apache-jena-libs:4.4.0'
+ implementation 'org.apache.commons:commons-text:1.9'
+ implementation 'net.sourceforge.argparse4j:argparse4j:0.9.0'
+
+ //https://gitlab.inria.fr/moex/alignapi/-/releases
+ implementation files('lib/align.jar')
+ implementation files('lib/alignsvc.jar')
+ implementation files('lib/ontowrap.jar')
+ implementation files('lib/procalign.jar')
+}
+
+group = 'org.example'
+version = '1.0-SNAPSHOT'
+description = 'CanardE'
+java.sourceCompatibility = JavaVersion.VERSION_18
+
+publishing {
+ publications {
+ maven(MavenPublication) {
+ from(components.java)
+ }
+ }
+}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 0000000000000000000000000000000000000000..249e5832f090a2944b7473328c07c9755baa3196
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 0000000000000000000000000000000000000000..ae04661ee733431762e7ccf8ab9b7409ed44960c
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
new file mode 100755
index 0000000000000000000000000000000000000000..a69d9cb6c20655813e44515156e7253a2a239138
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,240 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+# Gradle start up script for POSIX generated by Gradle.
+#
+# Important for running:
+#
+# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+# noncompliant, but you have some other compliant shell such as ksh or
+# bash, then to run this script, type that shell name before the whole
+# command line, like:
+#
+# ksh Gradle
+#
+# Busybox and similar reduced shells will NOT work, because this script
+# requires all of these POSIX shell features:
+# * functions;
+# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+# * compound commands having a testable exit status, especially «case»;
+# * various built-in commands including «command», «set», and «ulimit».
+#
+# Important for patching:
+#
+# (2) This script targets any POSIX shell, so it avoids extensions provided
+# by Bash, Ksh, etc; in particular arrays are avoided.
+#
+# The "traditional" practice of packing multiple parameters into a
+# space-separated string is a well documented source of bugs and security
+# problems, so this is (mostly) avoided, by progressively accumulating
+# options in "$@", and eventually passing that to Java.
+#
+# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+# see the in-line comments for details.
+#
+# There are tweaks for specific operating systems such as AIX, CygWin,
+# Darwin, MinGW, and NonStop.
+#
+# (3) This script is generated from the Groovy template
+# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# within the Gradle project.
+#
+# You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+ APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
+ [ -h "$app_path" ]
+do
+ ls=$( ls -ld "$app_path" )
+ link=${ls#*' -> '}
+ case $link in #(
+ /*) app_path=$link ;; #(
+ *) app_path=$APP_HOME$link ;;
+ esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+ echo "$*"
+} >&2
+
+die () {
+ echo
+ echo "$*"
+ echo
+ exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD=$JAVA_HOME/jre/sh/java
+ else
+ JAVACMD=$JAVA_HOME/bin/java
+ fi
+ if [ ! -x "$JAVACMD" ] ; then
+ die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+ fi
+else
+ JAVACMD=java
+ which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+# * args from the command line
+# * the main class name
+# * -classpath
+# * -D...appname settings
+# * --module-path (only if needed)
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+ APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+ CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+ JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+ # Now convert the arguments - kludge to limit ourselves to /bin/sh
+ for arg do
+ if
+ case $arg in #(
+ -*) false ;; # don't mess with options #(
+ /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
+ [ -e "$t" ] ;; #(
+ *) false ;;
+ esac
+ then
+ arg=$( cygpath --path --ignore --mixed "$arg" )
+ fi
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
+ done
+fi
+
+# Collect all arguments for the java command;
+# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+# shell script including quotes and variable substitutions, so put them in
+# double quotes to make sure that they get re-expanded; and
+# * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+ "-Dorg.gradle.appname=$APP_BASE_NAME" \
+ -classpath "$CLASSPATH" \
+ org.gradle.wrapper.GradleWrapperMain \
+ "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+ die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+# set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+ printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+ xargs -n1 |
+ sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+ tr '\n' ' '
+ )" '"$@"'
+
+exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
new file mode 100644
index 0000000000000000000000000000000000000000..53a6b238d414d91c30c5644c82393d27416fbbe6
--- /dev/null
+++ b/gradlew.bat
@@ -0,0 +1,91 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
+@rem ##########################################################################
+@rem
+@rem Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%"=="" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if %ERRORLEVEL% equ 0 goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if %ERRORLEVEL% equ 0 goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 4349fcd61e9617101af90e526d344bab2aebe391..0000000000000000000000000000000000000000
--- a/pom.xml
+++ /dev/null
@@ -1,107 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <groupId>org.example</groupId>
- <artifactId>CanardE</artifactId>
- <version>1.0-SNAPSHOT</version>
-
- <properties>
- <maven.compiler.source>18</maven.compiler.source>
- <maven.compiler.target>18</maven.compiler.target>
- </properties>
-
- <dependencies>
- <dependency>
- <groupId>org.deeplearning4j</groupId>
- <artifactId>deeplearning4j-core</artifactId>
- <version>1.0.0-M1.1</version>
- </dependency>
- <dependency>
- <groupId>org.nd4j</groupId>
- <artifactId>nd4j-native-platform</artifactId>
- <version>1.0.0-M1.1</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-core</artifactId>
- <version>2.12.1</version>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-annotations</artifactId>
- <version>2.12.1</version>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>2.12.1</version>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>fr.inrialpes.exmo</groupId>
- <artifactId>procalign</artifactId>
- <version>4.9</version>
- <exclusions>
- <exclusion>
- <artifactId>log4j-core</artifactId>
- <groupId>org.apache.logging.log4j</groupId>
- </exclusion>
- </exclusions>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/procalign.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>fr.inrialpes.exmo.</groupId>
- <artifactId>ontowrap</artifactId>
- <version>4.9</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/ontowrap.jar</systemPath>
- </dependency>
- <dependency>
- <groupId>org.semanticweb.owl.align</groupId>
- <artifactId>align</artifactId>
- <version>4.9</version>
- <scope>system</scope>
- <systemPath>${project.basedir}/lib/align.jar</systemPath>
- </dependency>
-
-
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>1.15</version>
- </dependency>
-
-
- <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-nop -->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-nop</artifactId>
- <version>1.7.36</version>
- </dependency>
-
-
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>apache-jena-libs</artifactId>
- <type>pom</type>
- <version>4.4.0</version>
- </dependency>
-
-
- <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-text -->
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>commons-text</artifactId>
- <version>1.9</version>
- </dependency>
-
-
- </dependencies>
-
-</project>
\ No newline at end of file
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 0000000000000000000000000000000000000000..0542fd49fefc736ab0d0cc2f97541a7c77fdd168
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,7 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This project uses @Incubating APIs which are subject to change.
+ */
+
+rootProject.name = 'CanardE'
diff --git a/src/main/java/irit/complex/ComplexAlignmentGeneration.java b/src/main/java/irit/complex/ComplexAlignmentGeneration.java
index a748ed09e0560f71f624ee96ecce57dd6d5f23e0..8c7acc0fbf7eeb523f34f1441233fa5368397d90 100755
--- a/src/main/java/irit/complex/ComplexAlignmentGeneration.java
+++ b/src/main/java/irit/complex/ComplexAlignmentGeneration.java
@@ -8,16 +8,19 @@ import irit.dataset.DatasetManager;
import irit.output.OutputManager;
import irit.resource.IRI;
import irit.resource.Resource;
-import irit.similarity.EmbeddingManager;
import irit.sparql.exceptions.IncompleteSubstitutionException;
import irit.sparql.SparqlProxy;
import irit.sparql.query.exception.SparqlEndpointUnreachableException;
import irit.sparql.query.exception.SparqlQueryMalFormedException;
import irit.sparql.query.select.SparqlSelect;
+import net.sourceforge.argparse4j.ArgumentParsers;
+import net.sourceforge.argparse4j.impl.Arguments;
+import net.sourceforge.argparse4j.inf.ArgumentParser;
+import net.sourceforge.argparse4j.inf.ArgumentParserException;
+import net.sourceforge.argparse4j.inf.Namespace;
import org.apache.jena.rdf.model.RDFNode;
import java.io.IOException;
-import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
import java.util.concurrent.*;
@@ -26,140 +29,120 @@ import java.util.concurrent.*;
public class ComplexAlignmentGeneration {
- public static void main(String[] args) throws SparqlEndpointUnreachableException, SparqlQueryMalFormedException, ExecutionException, InterruptedException, IncompleteSubstitutionException {
+ public static void main(String[] args) throws SparqlEndpointUnreachableException, SparqlQueryMalFormedException, ExecutionException, InterruptedException, IncompleteSubstitutionException, IOException {
- System.out.println("===============================================================================");
- System.out.println("CanardE");
- System.out.println("===============================================================================");
- String datasets = args[0];
- String needs = args[1];
- String embeddings = args[2];
- String source = args[3];
- String target = args[4];
- String range = args[5];
+ ArgumentParser parser = buildArgumentParser();
- Set<String> stringSet = Set.of(source, target);
-
- Map<String, String> ds = new HashMap<>();
try {
- Files.walk(Paths.get(datasets), 1).forEach(path -> {
- if (!path.toString().endsWith(".ttl") && !stringSet.contains(path.getFileName().toString())) return;
- ds.put(path.getFileName().toString().split("_")[0], path.toString());
- });
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
+ Namespace res = parser.parseArgs(args);
+ String source = res.get("source");
+ String target = res.get("target");
+ String cqa = res.get("cqa");
+ String range = res.get("range");
+ String output = res.get("output");
+ boolean silent = res.get("silent");
+ int maxMatches = res.get("maxMatches");
- System.out.println("Found " + ds.size() + " datasets.");
+ String sourceName = getFileName(source);
+ String targetName = getFileName(target);
- Map<String, String> nd = new HashMap<>();
- Map<String, List<SparqlSelect>> cqas = new HashMap<>();
- try {
- Files.walk(Paths.get(needs), 1).forEach(path -> {
- String ont = path.getFileName().toString();
- if (!ds.containsKey(ont)) return;
- nd.put(ont, path.toString());
-
-
- try {
- Files.walk(path, 1).forEach(path1 -> {
- if (Files.isDirectory(path1)) return;
- Scanner squery = null;
- try {
- squery = new Scanner(path1);
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
-
- String query = squery.useDelimiter("\\Z").next();
- SparqlSelect sq = new SparqlSelect(query);
- cqas.computeIfAbsent(ont, s -> new ArrayList<>()).add(sq);
- squery.close();
- });
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
+ List<SparqlSelect> sparqlSelects = SparqlSelect.load(cqa);
+ List<Float> rangeList = parseRange(range);
- });
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
+ DatasetManager.getInstance().load(sourceName, source);
+ DatasetManager.getInstance().load(targetName, target);
- for (String s : ds.keySet()) {
- if (nd.containsKey(s)) continue;
- System.out.println("⚠️ Not found CQAs for " + s + ".");
+
+ run(sourceName, targetName, sparqlSelects, rangeList, maxMatches, false, output);
+
+
+ } catch (ArgumentParserException e) {
+ parser.handleError(e);
}
- System.out.println("Needs loaded.");
+ }
- System.out.println("Loading embeddings.");
- Map<String, String[]> embs = new HashMap<>();
- try {
- Files.walk(Paths.get(embeddings), 1).forEach(path -> {
- if (Files.isDirectory(path)) return;
- String f = path.getFileName().toString();
- String[] split = f.split("[_.]");
+ public static ArgumentParser buildArgumentParser() {
+ ArgumentParser parser = ArgumentParsers.newFor("Canard").build()
+ .description("Complex alignment generator.");
- if (split[1].equals("n")) embs.computeIfAbsent(split[0], s -> new String[2])[0] = path.toString();
- else if (split[1].equals("e")) embs.computeIfAbsent(split[0], s -> new String[2])[1] = path.toString();
+ parser.addArgument("source")
+ .type(String.class)
+ .required(true)
+ .help("Source ontology.");
- });
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
+ parser.addArgument("target")
+ .type(String.class)
+ .required(true)
+ .help("Target ontology.");
+ parser.addArgument("cqa")
+ .type(String.class)
+ .required(true)
+ .help("CQA folder.");
- embs.forEach((name, paths) -> {
- try {
- EmbeddingManager.load(paths[0], paths[1]);
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
- });
+ parser.addArgument("--range")
+ .type(String.class)
+ .setDefault("0.8")
+ .help("Threshold range.");
+ parser.addArgument("--output")
+ .type(String.class)
+ .setDefault("output")
+ .help("Output folder.");
- ds.forEach((name, path) -> {
- DatasetManager.getInstance().load(name, path);
- });
+ parser.addArgument("--embedding")
+ .type(String.class)
+ .help("Path to embeddings.");
+ parser.addArgument("--silent")
+ .type(Boolean.class)
+ .action(Arguments.storeConst())
+ .setConst(true)
+ .setDefault(false)
+ .help("Disable console output.");
- List<String[]> datasetArgs = new ArrayList<>();
+ parser.addArgument("--maxMatches")
+ .type(Integer.class)
+ .setDefault(10)
+ .help("Max Matches.");
- ds.forEach((s, s2) -> {
- if (source != null && !source.startsWith(s)) return;
- ds.forEach((s1, s21) -> {
- if (s.equals(s1)) return;
- if (target != null && !target.startsWith(s1)) return;
- datasetArgs.add(new String[]{s, s1});
- });
- });
+ return parser;
+ }
+ public static String getFileName(String path) {
+ String[] split = Paths.get(path).getFileName().toString().split("\\.");
+ return split[0];
+ }
- String[] split = range.split(":");
- List<Float> ths = new ArrayList<>();
+ public static List<Float> parseRange(String range) {
+ List<Float> ranges = new ArrayList<>();
+ String[] split = range.split(":");
- for (float th = Float.parseFloat(split[0]); th <= Float.parseFloat(split[1]); th += Float.parseFloat(split[2])) {
- ths.add(th);
- }
+ float start = Float.parseFloat(split[0]);
+ float end = start;
+ float step = 0.1f;
- String output = "output";
+ if (split.length > 1) end = Float.parseFloat(split[1]);
+ if (split.length > 2) start = Float.parseFloat(split[2]);
- for (String[] datasetArg : datasetArgs) {
- run(datasetArg[0], datasetArg[1], cqas.get(datasetArg[0]), ths, 10, false, output);
+ for (; start < end; start += step) {
+ ranges.add(start);
}
-
+ return ranges;
}
public static void run(String sourceEndpoint, String targetEndpoint, List<SparqlSelect> queries, List<Float> th, int maxMatches, boolean reassess, String outputPath) throws SparqlEndpointUnreachableException, SparqlQueryMalFormedException, ExecutionException, InterruptedException, IncompleteSubstitutionException {
+
OutputManager outputManager = new OutputManager();
outputManager.initOutputEdoal(sourceEndpoint, targetEndpoint, th, outputPath);
@@ -293,10 +276,8 @@ public class ComplexAlignmentGeneration {
}
}
-// System.out.println("Number of correspondences found (" + threshold + "): " + output.size());
if (reassess) {
- System.out.println("Reassessing similarity");
for (SubgraphForOutput s : output) {
s.reassessSimilarityWithCounterExamples(sourceEndpoint, targetEndpoint, sq);
}
diff --git a/src/main/java/irit/complex/answer/SingleAnswer.java b/src/main/java/irit/complex/answer/SingleAnswer.java
index e1ad15174033685d9e034b99e13ad3a90f4a3c05..b37e5dc79198a2117d5e74fcdc41412bb6247524 100755
--- a/src/main/java/irit/complex/answer/SingleAnswer.java
+++ b/src/main/java/irit/complex/answer/SingleAnswer.java
@@ -56,15 +56,6 @@ public class SingleAnswer extends Answer {
HashSet<String> queryLabels = query.getLabels();
- INDArray zeros = Nd4j.zeros(DataType.DOUBLE, EmbeddingManager.embshape);
-
- for (String queryLabel : queryLabels) {
- zeros = zeros.add(EmbeddingManager.get(queryLabel));
- }
-
- zeros = zeros.div(queryLabels.size());
-
-
double maxSim = -1;
Triple bestTriple = new Triple();
@@ -81,10 +72,9 @@ public class SingleAnswer extends Answer {
for (Triple t : iri.getTriples()) {
double similarity = 0;
-// t.retrieveIRILabels(targetEndpoint);
-// t.retrieveTypes(targetEndpoint);
-// similarity += t.compareLabel(queryLabels, similarityThreshold, targetEndpoint);
- similarity += t.compareSim(zeros, similarityThreshold);
+ t.retrieveIRILabels(targetEndpoint);
+ t.retrieveTypes(targetEndpoint);
+ similarity += t.compareLabel(queryLabels, similarityThreshold, targetEndpoint);
if (similarity > maxSim) {
maxSim = similarity;
diff --git a/src/main/java/irit/similarity/EmbeddingManager.java b/src/main/java/irit/similarity/EmbeddingManager.java
index 9fd0e8417c760693c332653bc5da24df6627af8c..aa627efc5872ce2168070e64742c0e5c178b935c 100644
--- a/src/main/java/irit/similarity/EmbeddingManager.java
+++ b/src/main/java/irit/similarity/EmbeddingManager.java
@@ -1,5 +1,6 @@
package irit.similarity;
+import org.apache.commons.text.similarity.LevenshteinDistance;
import org.nd4j.linalg.api.buffer.DataType;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.factory.Nd4j;
@@ -32,18 +33,7 @@ public class EmbeddingManager {
public static double getSim(String s1, String s2){
- INDArray n1 = embs1.get(s1);
- INDArray n2 = embs1.get(s2);
-
- if (n1 == null){
- n1 = Nd4j.zeros(DataType.DOUBLE, embshape);
- }
-
- if (n2 == null){
- n2 = Nd4j.zeros(DataType.DOUBLE, embshape);
- }
-
- return Transforms.cosineSim(n1, n2);
+ return LevenshteinDistance.getDefaultInstance().apply(s1, s2) / (float) Math.max(s1.length(), s2.length());
}
private static Map<String, INDArray> loadEmbs(String n1, String e1) throws IOException {
diff --git a/src/main/java/irit/sparql/query/select/SparqlSelect.java b/src/main/java/irit/sparql/query/select/SparqlSelect.java
index 74e6c2fe7d19b3425b5c792ebc095ee96c53f154..6d3a2530a7dca5a3683cae754898f9b2fc8dcd51 100755
--- a/src/main/java/irit/sparql/query/select/SparqlSelect.java
+++ b/src/main/java/irit/sparql/query/select/SparqlSelect.java
@@ -3,12 +3,13 @@ package irit.sparql.query.select;
import irit.resource.IRI;
import irit.sparql.query.SparqlQuery;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Map;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-
+import java.util.stream.Collectors;
public class SparqlSelect extends SparqlQuery {
@@ -20,12 +21,12 @@ public class SparqlSelect extends SparqlQuery {
mainQuery = mainQuery.trim().replaceAll("SELECT", "select").replaceAll("WHERE", "where").replaceAll("\n", " ");
selectFocus = new ArrayList<>();
Pattern pattern = Pattern.compile("""
- select[ \t
- distncDISTNC]+(\\?[A-Za-z\\d_-]+)[ \t
- ]+(\\?*[A-Za-z\\d_-]*[ \t
- ]*)where[ \t
- ]*\\{(.+)}[ \t
- ]*$""");
+ select[ \t
+ distncDISTNC]+(\\?[A-Za-z\\d_-]+)[ \t
+ ]+(\\?*[A-Za-z\\d_-]*[ \t
+ ]*)where[ \t
+ ]*\\{(.+)}[ \t
+ ]*$""");
Matcher matcher = pattern.matcher(mainQuery);
while (matcher.find()) {
selectFocus.add(matcher.group(1).trim());
@@ -34,12 +35,12 @@ public class SparqlSelect extends SparqlQuery {
}
where = matcher.group(3).trim();
setAggregate();
- }
+ }
Pattern pattern2 = Pattern.compile("""
- select([ \t
- distncDISTNC]+\\?[A-Za-z\\d_-]+[ \t
- ]+\\?*[A-Za-z\\d_-]*[ \t
- ]*)where""");
+ select([ \t
+ distncDISTNC]+\\?[A-Za-z\\d_-]+[ \t
+ ]+\\?*[A-Za-z\\d_-]*[ \t
+ ]*)where""");
Matcher matcher2 = pattern2.matcher(mainQuery);
if (matcher2.find()) {
select = matcher2.group(1);
@@ -48,6 +49,26 @@ public class SparqlSelect extends SparqlQuery {
}
+
+ public static List<SparqlSelect> load(String path) throws IOException {
+ List<SparqlSelect> sparqlSelects;
+ try (var walk = Files.walk(Paths.get(path), 1)) {
+ sparqlSelects = walk
+ .filter(path1 -> !Files.isDirectory(path1))
+ .map(path1 -> {
+ try {
+ return Files.readString(path1);
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+ })
+ .map(SparqlSelect::new).toList();
+
+ }
+ return sparqlSelects;
+
+ }
+
public String getSelect() {
return select;
}
@@ -93,11 +114,10 @@ public class SparqlSelect extends SparqlQuery {
}
-
- public HashSet<String> getLabels(){
+ public HashSet<String> getLabels() {
HashSet<String> queryLabels = new HashSet<>();
- for (Map.Entry<String, IRI> iri : getIRIList().entrySet()){
+ for (Map.Entry<String, IRI> iri : getIRIList().entrySet()) {
queryLabels.addAll(iri.getValue().getLabels());
}
return queryLabels;