Mentions légales du service

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  • rules/integraal
  • ulliana/integraal
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.gitignore
Edit View file @ 0955fe49
......@@ -88,3 +88,4 @@ tatooinetmp.conf
# ctags file
tags
build.xml
/integraal/integraal-explanation/gsat.gcnf
integraal/Test Results - ExternalOntologyTest.xml 0 → 100644
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This diff is collapsed.
integraal/integraal-all/pom.xml
Edit View file @ 0955fe49
......@@ -94,36 +94,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven-shade-plugin-version}</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>jar-with-dependencies</shadedClassifierName>
<finalName>integraal-with-dependencies</finalName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/module-info.*</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/**/*.class</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
......
integraal/integraal-api/pom.xml
Edit View file @ 0955fe49
......@@ -118,79 +118,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven-shade-plugin-version}</version>
<executions>
<execution>
<id>build-integraal-commander</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>
fr.boreal.api.integraal_commander.InteGraalCommander</mainClass>
</transformer>
</transformers>
<finalName>integraal-commander</finalName>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>jar-with-dependencies</shadedClassifierName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/module-info.*</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/**/*.class</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>build-integraal-cli</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>
fr.boreal.api.integraal_repl.IGRepl</mainClass>
</transformer>
</transformers>
<finalName>integraal-cli</finalName>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>jar-with-dependencies</shadedClassifierName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/module-info.*</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/**/*.class</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
......
integraal/integraal-api/src/main/java/fr/boreal/api/integraal_repl/IGCommands.java
Edit View file @ 0955fe49
......@@ -86,7 +86,7 @@ public class IGCommands {
* Prints the substitutions from the iterator.
*
* @param subIt The iterator of substitutions containing the query results.
* @param vars The variables to print; this provides the order of the variables
* @param varsOrder The variables to print; this provides the order of the variables
* @param writer The DlgpWriter object used to write the results.break;
* @param max The maximum number of substitutions to print.
*/
......
integraal/integraal-component/src/test/java/test/factbase_loader/FactbaseLoadingWithComponentTest.java 0 → 100644
Edit View file @ 0955fe49
package test.factbase_loader;
import fr.boreal.component_builder.AlgorithmParameters;
import fr.boreal.component_builder.InputDataScenario;
import fr.boreal.component_builder.components.FactBaseLoaderFromFile;
import fr.boreal.configuration.keywords.InteGraalKeywords;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.RuleBase;
import fr.boreal.model.kb.impl.RuleBaseImpl;
import fr.boreal.model.query.api.Query;
import fr.boreal.storage.builder.StorageBuilder;
import org.junit.Test;
import org.junit.jupiter.api.Assertions;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
/**
*
*/
public class FactbaseLoadingWithComponentTest {
/**
* Helper method to retrieve the absolute path of a resource in the test/resources folder.
*
* @param relativePath The relative path to the resource.
* @return The absolute Path object of the resource.
* @throws URISyntaxException If the path syntax is incorrect.
*/
private Path getAbsoluteResourcePath(String relativePath) throws URISyntaxException {
return Paths.get(ClassLoader.getSystemResource(relativePath).toURI());
}
/**
* @throws URISyntaxException
*/
@Test
public void testSetFactbasePaths() throws URISyntaxException {
InputDataScenario scenario = new InputDataScenario("TestScenario");
// Get absolute paths using the helper method
String[] paths = {
getAbsoluteResourcePath("factbase/test_factbase.rls").toString()
};
scenario.setFactbasePaths(paths);
var param = new AlgorithmParameters("test in memory storage", InteGraalKeywords.Algorithms.KB_CHASE);
var fb = FactBaseLoaderFromFile.getFactbaseFor(scenario, param);
System.out.println(fb);
Assertions.assertTrue(fb.size()==2);
}
}
integraal/integraal-component/src/test/java/test/InputDataScenarioTest.java → integraal/integraal-component/src/test/java/test/input_data_scenario_object/InputDataScenarioTest.java
Edit View file @ 0955fe49
package test;
package test.input_data_scenario_object;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
......@@ -11,6 +11,9 @@ import java.util.Arrays;
import java.util.Collection;
import java.util.Optional;
import fr.boreal.component_builder.AlgorithmParameters;
import fr.boreal.component_builder.components.FactBaseLoaderFromFile;
import fr.boreal.configuration.keywords.InteGraalKeywords;
import org.junit.Test;
import fr.boreal.component_builder.InputDataScenario;
......
integraal/integraal-component/src/test/resources/factbase/test_factbase.rls
Edit View file @ 0955fe49
@source p[2]: load-csv("./test_factbase2.csv") .
@source q[2]: load-csv("./test_factbase3.csv") .
integraal/integraal-component/src/test/resources/factbase/test_factbase2.csv
Edit View file @ 0955fe49
a, b
\ No newline at end of file
integraal/integraal-component/src/test/resources/factbase/test_factbase3.csv 0 → 100644
Edit View file @ 0955fe49
c, d
\ No newline at end of file
integraal/integraal-configuration/src/main/java/fr/boreal/configuration/keywords/InteGraalKeywords.java
Edit View file @ 0955fe49
......@@ -350,7 +350,8 @@ public enum InteGraalKeywords {
/**
* GRD Scheduler
*/
GRD
GRD,
BY_PREDICATE
}
/**
......
integraal/integraal-explanation/clauses_SAT4J.txt 0 → 100644
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This diff is collapsed.
integraal/integraal-explanation/dockerfile 0 → 100644
Edit View file @ 0955fe49
# Use an official Python image with Debian-based OS
FROM python:3.9-slim
# Set working directory
WORKDIR /usr/local/bin
# Install system dependencies
RUN apt-get update -y && apt-get install -y \
git \
build-essential \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
# Clone and build MARCO
RUN git clone https://github.com/liffiton/MARCO && \
cd MARCO/src/pyminisolvers && make && \
cd /usr/local/bin && mv ./MARCO/* .
# Ensure MARCO-MUS directory exists and move MARCO files
RUN mkdir -p /usr/local/bin/MARCO-MUS && \
mv /usr/local/bin/marco.py /usr/local/bin/MARCO-MUS/ && \
chmod +x /usr/local/bin/MARCO-MUS/marco.py
# Set environment variables for MARCO
ENV PATH="/usr/local/bin/MARCO-MUS:${PATH}"
ENV PYTHONPATH="/usr/local/bin/src:${PYTHONPATH}"
# Debugging step: Verify MARCO installation
RUN echo "===== Checking MARCO Installation =====" && \
ls -l /usr/local/bin/MARCO-MUS/ && \
echo "===== Checking Python Installation =====" && \
which python3 && python3 --version
# Test MARCO Execution inside Docker
RUN /usr/local/bin/MARCO-MUS/marco.py --help || echo "MARCO execution failed"
# Set MARCO as the default command
ENTRYPOINT ["python", "/usr/local/bin/MARCO-MUS/marco.py"]
integraal/integraal-explanation/pom.xml
Edit View file @ 0955fe49
......@@ -17,9 +17,15 @@
<description>Facilities for explaining answers to queries</description>
<dependencies>
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>5.7.1</version> <!-- or the latest version -->
</dependency>
<dependency>
<groupId>${groupId}</groupId>
<artifactId>integraal-model</artifactId>
<version>${revision}</version>
</dependency>
<dependency>
<groupId>${groupId}</groupId>
......@@ -49,6 +55,19 @@
<groupId>${groupId}</groupId>
<artifactId>integraal-component</artifactId>
</dependency>
<dependency>
<groupId>org.ow2.sat4j</groupId>
<artifactId>org.ow2.sat4j.pb</artifactId>
<version>2.3.6</version>
</dependency>
<dependency>
<groupId>org.ow2.sat4j</groupId>
<artifactId>org.ow2.sat4j.pom</artifactId>
<version>2.3.6</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
......@@ -64,11 +83,35 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ow2.sat4j</groupId>
<artifactId>org.ow2.sat4j.sat</artifactId>
<version>2.3.6</version>
</dependency>
<dependency>
<groupId>org.ow2.sat4j</groupId>
<artifactId>org.ow2.sat4j.core</artifactId>
<version>2.3.6</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
<groupId>fr.lirmm.graphik</groupId>
<artifactId>integraal-model</artifactId>
</dependency>
</dependencies>
</dependencies>
<build>
<testResources>
<testResource>
<directory>src/test/resources</directory>
<excludes>
<exclude>**/*</exclude>
</excludes>
</testResource>
</testResources>
</build>
</project>
\ No newline at end of file
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/InternalDLGPParser.java 0 → 100644
Edit View file @ 0955fe49
package fr.boreal.explanation;
import fr.boreal.explanation.kb_gri.explainers.static_gri.FactSupportExplainer_KBGRI;
import fr.boreal.explanation.kb_gri.explainers.static_gri.KBSupportExplainer_KBGRI;
import fr.boreal.io.api.ParseException;
import fr.boreal.io.dlgp.DlgpParser;
import fr.boreal.model.kb.api.FactBase;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.kb.api.RuleBase;
import fr.boreal.model.kb.impl.KnowledgeBaseImpl;
import fr.boreal.model.kb.impl.RuleBaseImpl;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.logicalElements.factory.api.PredicateFactory;
import fr.boreal.model.logicalElements.factory.api.TermFactory;
import fr.boreal.model.logicalElements.factory.impl.SameObjectPredicateFactory;
import fr.boreal.model.logicalElements.factory.impl.SameObjectTermFactory;
import fr.boreal.model.rule.api.FORule;
import fr.boreal.storage.natives.SimpleInMemoryGraphStore;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Set;
public class InternalDLGPParser {
public InternalDLGPParser(File datalogProgrammeFile, File factsFile, File query_file) throws FileNotFoundException {
PredicateFactory predicateFactory = SameObjectPredicateFactory.instance();
TermFactory termFactory = SameObjectTermFactory.instance();
RuleBase rb = ParserForDLGP.parseRB(datalogProgrammeFile);
FactBase fb = ParserForDLGP.parseFB(datalogProgrammeFile);
KnowledgeBase kb = new KnowledgeBaseImpl(fb,rb);
Collection<Atom> queryAtoms = ParserForDLGP.parseQueries(query_file);
FactSupportExplainer_KBGRI explainer;
explainer = new FactSupportExplainer_KBGRI(kb);
for (Atom queryAtom : queryAtoms) {
Set<FactBase> explanations = explainer.getAllExplanations(queryAtom);
if (explanations.isEmpty()) {
throw new RuntimeException("No explanations found for " + queryAtom);
}
}
}
public static class ParserForDLGP {
public static KnowledgeBase parseKB(File dlgpFile) throws FileNotFoundException {
FactBase fb = new SimpleInMemoryGraphStore();
Collection<FORule> rules = new ArrayList<FORule>();
int ruleLabelNb = 0;
try (DlgpParser dlgp_parseur = new DlgpParser(dlgpFile)) {
while (dlgp_parseur.hasNext()) {
try {
Object result = dlgp_parseur.next();
if (result instanceof Atom) {
fb.add((Atom)result);
} else if (result instanceof FORule) {
((FORule) result).setLabel("r"+ruleLabelNb++);
rules.add((FORule)result);
}
} catch (ParseException e) {
throw new RuntimeException(
String.format("Error with the file %s ", dlgpFile),
e);
}
}
}
RuleBase rb = new RuleBaseImpl(rules);
KnowledgeBase kb = new KnowledgeBaseImpl(fb, rb);
return kb;
}
public static FactBase parseFB(File dlgpFile) throws FileNotFoundException {
FactBase fb = new SimpleInMemoryGraphStore();
try (DlgpParser dlgp_parseur = new DlgpParser(dlgpFile)) {
while (dlgp_parseur.hasNext()) {
try {
Object result = dlgp_parseur.next();
if (result instanceof Atom) {
fb.add((Atom)result);
}
} catch (ParseException e) {
throw new RuntimeException(
String.format("Error with the file %s ", dlgpFile),
e);
}
}
}
return fb;
}
public static RuleBase parseRB(File dlgpFile) throws FileNotFoundException {
Collection<FORule> rules = new ArrayList<FORule>();
try (DlgpParser dlgp_parseur = new DlgpParser(dlgpFile)) {
while (dlgp_parseur.hasNext()) {
try {
Object result = dlgp_parseur.next();if (result instanceof FORule) {
rules.add((FORule)result);
}
} catch (ParseException e) {
throw new RuntimeException(
String.format("Error with the file %s ", dlgpFile),
e);
}
}
}
RuleBase rb = new RuleBaseImpl(rules);
return rb;
}
public static Collection<Atom> parseQueries(File dlgpFile) throws FileNotFoundException {
try (DlgpParser dlgp_parseur = new DlgpParser(dlgpFile)) {
Collection<Atom> queryAtoms = new ArrayList<Atom>();
while (dlgp_parseur.hasNext()) {
try {
Object result = dlgp_parseur.next();
if (result instanceof Atom) {
queryAtoms.add((Atom)result);
}
} catch (ParseException e) {
throw new RuntimeException(
String.format("Error with the file %s ", dlgpFile),
e);
}
}
return queryAtoms;
}
}
}
}
\ No newline at end of file
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/api/AtomicQueryExplanationEnumerator.java deleted 100644 → 0
View file @ 60f50132
package fr.boreal.explanation.api;
import fr.boreal.model.formula.api.FOFormulaConjunction;
import fr.boreal.model.kb.api.KnowledgeBase;
import fr.boreal.model.logicalElements.api.Atom;
import fr.boreal.model.query.api.Query;
import java.util.Arrays;
import java.util.Set;
/**
* Interface for an explainer which supports only ground atomic queries (expressed as atoms).
*
* @param <ExplanationType> the type of the (set of) explanations which is returned by the enumerator
*/
public interface AtomicQueryExplanationEnumerator<ExplanationType extends Object> {
/**
* Checks if an atom can be explained
*
* @param query
* @return true iff the query contains only constants and literals
*/
default boolean canExplain(KnowledgeBase kb, Atom query) {
var queryOK = Arrays.stream(query.getTerms()).allMatch(term -> term.isConstant() || term.isLiteral());
// check that all rules body and head are conjunctions
// TODO : check more in depth that the FOFormulaConjunction contains only atoms
// TODO : check that in the the data (be careful of federations) there are only constants and literals
// TODO : check that in the rules there are no functional terms
var rulesOK = true;
for (var r : kb.getRuleBase().getRules()) {
// rules must have a label
if (r.getLabel() == null || r.getLabel().isBlank()) {
throw new RuntimeException("rule label is empty: " + r);
}
if (!(r.getBody() instanceof FOFormulaConjunction || r.getBody() instanceof Atom)) {
rulesOK = false;
break;
}
if (!(r.getHead() instanceof FOFormulaConjunction || r.getHead() instanceof Atom)) {
rulesOK = false;
break;
}
}
return queryOK && rulesOK;
}
/**
*
* @param query
* @return the set of explanations for the query on the current KB
*/
Set<ExplanationType> explain(Atom query);
}
integraal/integraal-explanation/src/main/java/fr/boreal/explanation/api/encoders/GSATEncoder_GRI.java 0 → 100644
Edit View file @ 0955fe49
package fr.boreal.explanation.api.encoders;
import fr.boreal.model.logicalElements.api.Atom;
import java.util.Set;
import java.util.function.Predicate;
/**
* Computes at GSAT encoding of the GRI and the Query for GMUS enumeration
* @param <DataStructureType> the data structure holding the GRI
* @param <QueryType> the query type
*/
public interface GSATEncoder_GRI<DataStructureType, QueryType> {
/**
*
* @param filteredGRI
* @param query
* @param belongsToInitialFactbase
* @return at GSAT encoding of the filteredGRI and the Query for GMUS enumeration
*/
GSATEncodingResult_GRI encode(DataStructureType filteredGRI, QueryType query, Predicate<Atom> belongsToInitialFactbase);
}