Merge pull request #185 from ashleycaselli/53-shaclinfersh-hangs-when…

…-ttl-contains-some-specific-owlimports 53 shaclinfersh hangs when ttl contains some specific owlimports
TopQuadrant · Jan 11, 2025 · 49170c2 · 49170c2
2 parents 486da09 + c0e31bc
commit 49170c2
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diff --git a/.docker/Dockerfile b/.docker/Dockerfile
@@ -14,6 +14,8 @@ LABEL org.opencontainers.image.version=${VERSION}
 
 # BUILD STAGE 1: install minimal Java environment + curl & zip for SHACL API
 
+RUN apk add --no-cache binutils maven curl zip
+
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
          --add-modules java.base,java.compiler,java.desktop,java.management,java.naming,java.net.http,java.rmi,java.scripting,java.security.jgss,java.security.sasl,java.sql,java.xml.crypto,jdk.unsupported \
@@ -23,16 +25,14 @@ RUN $JAVA_HOME/bin/jlink \
          --compress=2 \
          --output /javaruntime
 
-RUN apk add maven curl zip
-
 # Compile with maven, extract binaries and copy into image
 COPY . /app
 RUN mvn versions:set -DnewVersion=${VERSION} && mvn package -Dmaven.test.skip=true
 RUN unzip target/shacl-${VERSION}-bin.zip -d /app/
 
 # BUILD STAGE 2: keep only Java and SHACL
 
-FROM alpine:3.20.3
+FROM alpine:3.21.2
 
 ARG VERSION
 

diff --git a/.docker/entrypoint.sh b/.docker/entrypoint.sh
@@ -23,6 +23,14 @@ PARAMETER:
 		input to be validated (only .ttl format supported)
 	-shapesfile /data/myshapes.ttl [OPTIONAL]
 		shapes for validation (only .ttl format supported)
+    -maxiterations 1 [OPTIONAL] - default is 1
+        iteratively applies the inference rules until the maximum number of iterations is reached (or no new triples are inferred)
+    -validateShapes [OPTIONAL]
+        in case you want to include the metashapes (from the tosh namespace in particular)
+    -addBlankNodes [OPTIONAL]
+        adds the blank nodes to the validation report
+    -noImports [OPTIONAL]
+        disables the import of external ontologies
 EOF
 	exit 1
 fi

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -39,11 +39,11 @@ jobs:
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@49b3bc8e6bdd4a60e6116a5414239cba5943d3cf # v3.2.0
+        uses: docker/setup-qemu-action@53851d14592bedcffcf25ea515637cff71ef929a # v3.3.0
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3.7.1
+        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3.8.0
 
       # inspired by https://github.com/reloc8/action-latest-release-version
       - name: Get release version
@@ -76,7 +76,7 @@ jobs:
 
       - name: Build and push Docker image for x86 and arm64
         id: build
-        uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75 # v6.9.0
+        uses: docker/build-push-action@b32b51a8eda65d6793cd0494a773d4f6bcef32dc # v6.11.0
         with:
           file: .docker/Dockerfile
           push: true
@@ -93,7 +93,7 @@ jobs:
           digest="${{ steps.build.outputs.digest }}"
           touch "/tmp/digests/${digest#sha256:}"     
       - name: Upload digest
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
+        uses: actions/upload-artifact@65c4c4a1ddee5b72f698fdd19549f0f0fb45cf08 # v4.6.0
         with:
           name: digests-${{ matrix.package }}
           path: /tmp/digests/*
@@ -131,7 +131,7 @@ jobs:
             merge-multiple: true
 
         - name: Set up Docker Buildx
-          uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3.7.1
+          uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3.8.0
 
         - name: Extract metadata (tags, labels) for Docker
           id: meta

diff --git a/.github/workflows/maven-test-pr.yml b/.github/workflows/maven-test-pr.yml
@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       - name: Set up JDK
-        uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4.5.0
+        uses: actions/setup-java@7a6d8a8234af8eb26422e24e3006232cccaa061b # v4.6.0
         with:
           distribution: ${{ matrix.distribution }}
           java-version: ${{ matrix.java }}

diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ The binary distribution is:
 
 `https://repo1.maven.org/maven2/org/topbraid/shacl/*VER*/shacl-*VER*-bin.zip`.
 
-Two command line utilities are included: shaclvalidate (performs constraint validation) and shaclinfer (performs SHACL rule inferencing).
+Two command line utilities are included: `shaclvalidate` (performs constraint validation) and `shaclinfer` (performs SHACL rule inferencing).
 
 To use them, set up your environment similar to https://jena.apache.org/documentation/tools/ (note that the SHACL download includes Jena).
 
@@ -72,17 +72,13 @@ export SHACLROOT=/home/holger/shacl/shacl-1.4.3-bin/shacl-1.4.3/bin
 export PATH=$SHACLROOT:$PATH 
 ```
 
-Both tools take the following parameters, for example:
+After setting up the environment, you can run the command line utilities (i.e. validation) using the following command:
 
-`shaclvalidate.bat -datafile myfile.ttl -shapesfile myshapes.ttl`
+- Windows: `shaclvalidate.bat -datafile myfile.ttl -shapesfile myshapes.ttl`
 
-where `-shapesfile` is optional and falls back to using the data graph as shapes graph.
-Add -validateShapes in case you want to include the metashapes (from the tosh namespace in particular).
+- Linux/Unix: `shaclvalidate.sh -datafile myfile.ttl -shapesfile myshapes.ttl`
 
-For the shaclinfer tool, you can use the `-maxiterations` argument to apply SHACL rule inferencing multiple times; this will add inferred results back to the data graph to see if further triples can be inferred.
-The tool will iterate until either (a) the maximum number of iterations is reached, or (b) no new triples are inferred. The flag is optional and defaults to `1` (single iteration).
-
-Currently only Turtle (.ttl) files are supported.
+Both tools (Windows, Linux) take the parameters described in the [Dockerfile Usage](#dockerfile-usage) section. **Currently, only Turtle (.ttl) files are supported.**
 
 The tools print the validation report or the inferences graph to the output screen.
 
@@ -113,15 +109,23 @@ Any other command after `ghcr.io/topquadrant/shacl:1.4.3` will print the followi
 Please use this docker image as follows:
 docker run -v /path/to/data:/data ghcr.io/topquadrant/shacl:1.4.3 [COMMAND] [PARAMETERS]
 COMMAND:
-	validate 
-		to run validation
-	infer
-		to run rule inferencing
+    validate 
+        to run validation
+    infer
+        to run rule inferencing
 PARAMETERS:
-	-datafile /data/myfile.ttl [MANDATORY]
-		input to be validated (only .ttl format supported)
-	-shapesfile /data/myshapes.ttl [OPTIONAL]
-		shapes for validation (only .ttl format supported)
+    -datafile /data/myfile.ttl [MANDATORY]
+        input to be validated (only .ttl format supported)
+    -shapesfile /data/myshapes.ttl [OPTIONAL]
+        shapes for validation (only .ttl format supported)
+    -maxiterations 1 [OPTIONAL] - default is 1
+        iteratively applies the inference rules until the maximum number of iterations is reached (or no new triples are inferred)
+    -validateShapes [OPTIONAL]
+        in case you want to include the metashapes (from the tosh namespace in particular)
+    -addBlankNodes [OPTIONAL]
+        adds the blank nodes to the validation report
+    -noImports [OPTIONAL]
+        disables the import of external ontologies
 ```
 
 If you'd like to build the image locally in an `x86` architecture, use:
@@ -134,4 +138,4 @@ If your architecture is `arm`, use:
 
 ```
 docker build -f .docker/Dockerfile -t ghcr.io/topquadrant/shacl:1.4.3 --build-arg VERSION=1.4.3 --build-arg ARCH_BASE=amazoncorretto:11-alpine3.18-jdk .
-```
+```
diff --git a/pom.xml b/pom.xml
@@ -70,8 +70,8 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <ver.jena>5.2.0</ver.jena>
     <ver.junit>4.13.2</ver.junit>
-    <ver.slf4j>1.7.36</ver.slf4j>
-    <ver.log4j2>2.20.0</ver.log4j2>
+    <ver.slf4j>2.0.16</ver.slf4j>
+    <ver.log4j2>2.24.3</ver.log4j2>
     <java.version>17</java.version>
   </properties>
 
@@ -99,7 +99,7 @@
     <!-- Require a logging implementation -->
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
-      <artifactId>log4j-slf4j-impl</artifactId>
+      <artifactId>log4j-slf4j2-impl</artifactId>
       <version>${ver.log4j2}</version>
       <optional>true</optional>
     </dependency>
@@ -210,7 +210,7 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-javadoc-plugin</artifactId>
-            <version>3.11.1</version>
+            <version>3.11.2</version>
             <executions>
               <execution>
                 <id>attach-javadocs</id>

diff --git a/src/main/java/org/topbraid/shacl/tools/AbstractTool.java b/src/main/java/org/topbraid/shacl/tools/AbstractTool.java
@@ -16,11 +16,6 @@
  */
 package org.topbraid.shacl.tools;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
 import org.apache.jena.ontology.OntDocumentManager;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.ontology.OntModelSpec;
@@ -34,78 +29,78 @@
 import org.topbraid.shacl.vocabulary.SH;
 import org.topbraid.shacl.vocabulary.TOSH;
 
+import java.io.*;
+
 class AbstractTool {
 
-	private final static String DATA_FILE = "-datafile";
-
-	private final static String SHAPES_FILE = "-shapesfile";
-
-	private final static String MAX_ITERATIONS = "-maxiterations";
-
-
-	private OntDocumentManager dm = new OntDocumentManager();
-
-	private OntModelSpec spec = new OntModelSpec(OntModelSpec.OWL_MEM);
-
-
-	AbstractTool() {
-
-		InputStream shaclTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/shacl.ttl");
-		Model shacl = JenaUtil.createMemoryModel();
-		shacl.read(shaclTTL, SH.BASE_URI, FileUtils.langTurtle);
-		shacl.add(SystemTriples.getVocabularyModel());
-		dm.addModel(SH.BASE_URI, shacl);
-
-		InputStream dashTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/dash.ttl");
-		Model dash = JenaUtil.createMemoryModel();
-		dash.read(dashTTL, SH.BASE_URI, FileUtils.langTurtle);
-		dm.addModel(DASH.BASE_URI, dash);
-
-		InputStream toshTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/tosh.ttl");
-		Model tosh = JenaUtil.createMemoryModel();
-		tosh.read(toshTTL, SH.BASE_URI, FileUtils.langTurtle);
-		dm.addModel(TOSH.BASE_URI, tosh);
-
-		spec.setDocumentManager(dm);
-	}
-
-	protected int getMaxIterations(String[] args) {
-		for(int i = 0; i < args.length - 1; i++) {
-			if(MAX_ITERATIONS.equals(args[i])) {
-				return Integer.parseInt(args[i + 1]);
-			}
-		}
-		return 1;
-	}
-
-	protected Model getDataModel(String[] args) throws IOException {
-		for(int i = 0; i < args.length - 1; i++) {
-			if(DATA_FILE.equals(args[i])) {
-				String dataFileName = args[i + 1];
-				OntModel dataModel = ModelFactory.createOntologyModel(spec);
-				File file = new File(dataFileName);
-				String lang = FileUtils.langTurtle;
-				dataModel.read(new FileInputStream(file), "urn:x:base", lang);
-				return dataModel;
-			}
-		}
-		System.err.println("Missing -datafile, e.g.: -datafile myfile.ttl");
-		System.exit(0);
-		return null;
-	}
-
-
-	protected Model getShapesModel(String[] args) throws IOException {
-		for(int i = 0; i < args.length - 1; i++) {
-			if(SHAPES_FILE.equals(args[i])) {
-				String fileName = args[i + 1];
-				OntModel model = ModelFactory.createOntologyModel(spec);
-				File file = new File(fileName);
-				String lang = FileUtils.langTurtle;
-				model.read(new FileInputStream(file), "urn:x:base", lang);
-				return model;
-			}
-		}
-		return null;
-	}
-}
+    private final static String DATA_FILE = "-datafile";
+
+    private final static String SHAPES_FILE = "-shapesfile";
+
+    private final static String MAX_ITERATIONS = "-maxiterations";
+
+    protected final OntDocumentManager dm = new OntDocumentManager();
+
+    private OntModelSpec spec = new OntModelSpec(OntModelSpec.OWL_MEM);
+
+
+    AbstractTool() {
+
+        InputStream shaclTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/shacl.ttl");
+        Model shacl = JenaUtil.createMemoryModel();
+        shacl.read(shaclTTL, SH.BASE_URI, FileUtils.langTurtle);
+        shacl.add(SystemTriples.getVocabularyModel());
+        dm.addModel(SH.BASE_URI, shacl);
+
+        InputStream dashTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/dash.ttl");
+        Model dash = JenaUtil.createMemoryModel();
+        dash.read(dashTTL, SH.BASE_URI, FileUtils.langTurtle);
+        dm.addModel(DASH.BASE_URI, dash);
+
+        InputStream toshTTL = SHACLSystemModel.class.getResourceAsStream("/rdf/tosh.ttl");
+        Model tosh = JenaUtil.createMemoryModel();
+        tosh.read(toshTTL, SH.BASE_URI, FileUtils.langTurtle);
+        dm.addModel(TOSH.BASE_URI, tosh);
+
+        spec.setDocumentManager(dm);
+    }
+
+    protected int getMaxIterations(String[] args) {
+        for (int i = 0; i < args.length - 1; i++) {
+            if (MAX_ITERATIONS.equals(args[i])) {
+                return Integer.parseInt(args[i + 1]);
+            }
+        }
+        return 1;
+    }
+
+    protected Model getDataModel(String[] args) throws IOException {
+        for (int i = 0; i < args.length - 1; i++) {
+            if (DATA_FILE.equals(args[i])) {
+                return getModel(args, i);
+            }
+        }
+        System.err.println("Missing -datafile, e.g.: -datafile myfile.ttl");
+        System.exit(0);
+        return null;
+    }
+
+    protected Model getShapesModel(String[] args) throws IOException {
+        for (int i = 0; i < args.length - 1; i++) {
+            if (SHAPES_FILE.equals(args[i])) {
+                return getModel(args, i);
+            }
+        }
+        return null;
+    }
+
+    private Model getModel(String[] args, int i) throws FileNotFoundException {
+        String fileName = args[i + 1];
+        OntModel dataModel = ModelFactory.createOntologyModel(spec);
+        File file = new File(fileName);
+        String lang = FileUtils.langTurtle;
+        dataModel.read(new FileInputStream(file), "urn:x:base", lang);
+        return dataModel;
+    }
+
+}