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Commit 07840057 authored by Guilherme Henrique's avatar Guilherme Henrique
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changed to gradle

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.gitignore
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View file @ 07840057
......@@ -2,4 +2,6 @@
lib
out
/output/
target
\ No newline at end of file
target
.gradle
build
\ No newline at end of file
build.gradle 0 → 100644
+ 49
− 0
View file @ 07840057
/*
* 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)
}
}
}
gradle/wrapper/gradle-wrapper.jar 0 → 100644
+ 0
− 0
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File added
gradle/wrapper/gradle-wrapper.properties 0 → 100644
+ 5
− 0
View file @ 07840057
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
gradlew 0 → 100755
+ 240
− 0
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#!/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 "$JAVACMD" "$@"
gradlew.bat 0 → 100644
+ 91
− 0
View file @ 07840057
@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
pom.xml deleted 100644 → 0
+ 0
− 107
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<?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
settings.gradle 0 → 100644
+ 7
− 0
View file @ 07840057
/*
* This file was generated by the Gradle 'init' task.
*
* This project uses @Incubating APIs which are subject to change.
*/
rootProject.name = 'CanardE'
src/main/java/irit/complex/ComplexAlignmentGeneration.java
+ 82
− 101
View file @ 07840057
......@@ -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);
}
......
src/main/java/irit/complex/answer/SingleAnswer.java
+ 3
− 13
View file @ 07840057
......@@ -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;
......
src/main/java/irit/similarity/EmbeddingManager.java
+ 2
− 12
View file @ 07840057
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 {
......
src/main/java/irit/sparql/query/select/SparqlSelect.java
+ 38
− 18
View file @ 07840057
......@@ -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;
......
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