Merge pull request #120 from Wimmics/release-4.4.0

Release 4.4.0

Author: remiceres

.gitignore

@@ -88,4 +88,10 @@ nb-configuration.xml
 ## logs
 ##############################
 log/
-log.txt
+log.txt
+corese-server/SSL_SERVER_PID
+
+##############################
+## test
+##############################
+earl-report-test.ttl

.gitlab-ci.yml

@@ -1,16 +1,48 @@
-<!-- markdownlint-disable MD024 -->
 # Corese Changelog
 
-## Unreleased
+## 4.4.0 – 2021/03/30 – Storage update
 
 ### Added
 
-- Support for [RDF*](https://w3c.github.io/rdf-star/cg-spec/2021-07-01.html) (beta)
-- Support for [SPARQL*](https://w3c.github.io/rdf-star/cg-spec/2021-07-01.html) (beta)
+- Storage Systems in Corese:
+  - Integration of Jena TDB1.
+  - Integration of Corese Graph.
+  - Integration of RDF4J Model.
+  - [More information can be found here](https://github.com/Wimmics/corese/blob/master/docs/storage/Configuring%20and%20Connecting%20to%20Different%20Storage%20Systems%20in%20Corese.md).
+- Beta support for RDF\* and SPARQL\* ([Community Group Report 17 December 2021](https://w3c.github.io/rdf-star/cg-spec/2021-12-17.html)).
+- Corese Command-Line Interface (Beta):
+  - `convert`: Convert RDF files between different serialization formats.
+  - `sparql`: Execute SPARQL queries on files.
+  - `owlProfile`: Check OWL profiles on files.
+  - `ldscript`: Run LDSCRIPT files.
+- Corese-Python interface (Beta):
+  - [Use the Corese-library with Python](https://github.com/Wimmics/corese/blob/master/docs/corese-python/Corese-library%20with%20Python.md).
+  - [Use the Corese-server with Python](https://github.com/Wimmics/corese/blob/master/docs/corese-python/Corese-server%20with%20Python.md).
+- Undo/Redo support added to Corese GUI ([Pull Request #97](https://github.com/Wimmics/corese/pull/97) thanks to [@alaabenfatma](https://github.com/alaabenfatma)).
+
+### Changes
+
+- Updated Jetty server library to version 11.0.8.
+- Code clean-up, correction, and commenting for improved readability and maintenance.
 
 ### Fixed
 
-- Encoding error with Windows when exporting graphs from Corese-Gui.
+- Fixed an encoding error when loading a file whose path contains a space in Corese-GUI
+- Fixed encoding error with Windows when exporting graphs from Corese-GUI.
+- Fixed SPARQL engine bug where it was impossible to load a named graph that contains a non-empty RDF list.
+- Fixed issue with "rdf:" not found when sending a federated query to Fuseki. See [issue #114](https://github.com/Wimmics/corese/issues/114).
+- Fixed non-standard JSON format on query timeout. See [issue #113](https://github.com/Wimmics/corese/issues/113).
+- Fixed inconsistent status of the OWL and Rules checkboxes in Corese-GUI that was not updated during reload. See [issue #110](https://github.com/Wimmics/corese/issues/110).
+- Fixed the rule engine that was implementing optimizations incompatible with the `owl:propertyChainAxiom` rule. See [issue #110](https://github.com/Wimmics/corese/issues/110).
+
+### Security
+
+- Bumped testng from 7.3.0 to 7.7.1. See [pull request #118](https://github.com/Wimmics/corese/pull/118).
+- Bumped jsoup from 1.14.2 to 1.15.3 in /corese-server. See [pull request #101](https://github.com/Wimmics/corese/pull/101).
+- Bumped junit from 4.11 to 4.13.1 in /corese-storage. See [pull request #98](https://github.com/Wimmics/corese/pull/98).
+- Bumped xercesImpl from 2.12.0 to 2.12.2. See [pull request #92](https://github.com/Wimmics/corese/pull/92).
+- Bumped gremlin-core from 3.2.3 to 3.6.2.
+- Bumped Jetty server to 11.0.14.
 
 ## 4.3.0 – 2021/01/18 – RDF4J Update
 
@@ -19,7 +51,7 @@
 - Graphical editor for SHACL file in Corese-GUI.
 - Graphical editor for TURTLE file in Corese-GUI.
 - Save graph option un Corese-GUI.
-- New type of graph [´CoreseModel´](https://notes.inria.fr/s/OB038LBLV#) implementing the [RDF4J](https://rdf4j.org/) [model API](https://rdf4j.org/javadoc/latest/).
+- New type of graph [´CoreseModel´](https://github.com/Wimmics/corese/blob/master/docs/rdf4j/RDF4J%20API%20in%20Corese.md) implementing the [RDF4J](https://rdf4j.org/) [model API](https://rdf4j.org/javadoc/latest/).
 - `DataManager` API to allows to connect the Corese SPARQL engine with other triple storage stucture.
 - Implement a `DataManager` for RDF4J.
 

.gitmodules

@@ -1,4 +1,5 @@
 <!-- markdownlint-configure-file { "MD004": { "style": "consistent" } } -->
+
 <!-- markdownlint-disable MD033 -->
 
 #
@@ -17,29 +18,31 @@ Corese is a software platform implementing and extending the standards of the Se
 Corese implement W3C standards [RDF](https://www.w3.org/RDF/), [RDFS](https://www.w3.org/2001/sw/wiki/RDFS), [SPARQL1.1 Query & Update](https://www.w3.org/2001/sw/wiki/SPARQL), [OWL RL](https://www.w3.org/2005/rules/wiki/OWLRL), [SHACL](https://www.w3.org/TR/shacl/) …
 It also implements extensions like [STTL SPARQL](https://files.inria.fr/corese/doc/sttl.html), [SPARQL Rule](https://files.inria.fr/corese/doc/rule.html) and [LDScript](https://files.inria.fr/corese/doc/ldscript.html).
 
-There are three versions of Corese:
+There are several interfaces for Corese:"
 
 - **Corese-library:** Java library to process RDF data and use Corese features via an API.
 - **Corese-server:** Tool to easily create, configure and manage SPARQL endpoints.
 - **Corese-gui:** Graphical interface that allows an easy and visual use of Corese features.
+- **Corese-Python (beta):** Python wrapper for accessing and manipulating RDF data with Corese features using py4j.
+- **Corese-Command (beta):** Command Line Interface for Corese that allows users to interact with Corese features from the terminal.
 
 ## Download and install
 
 ### Corese-library
 
-- Download from [maven-central](https://search.maven.org/search?q=g:fr.inria.corese)
+- Download from [maven-central](https://central.sonatype.com/namespace/fr.inria.corese)
 
 ```xml
 <dependency>
     <groupId>fr.inria.corese</groupId>
     <artifactId>corese-core</artifactId>
-    <version>4.3.0</version>
+    <version>4.4.0</version>
 </dependency>
 
 <dependency>
     <groupId>fr.inria.corese</groupId>
     <artifactId>corese-rdf4j</artifactId>
-    <version>4.3.0</version>
+    <version>4.4.0</version>
 </dependency>
 ```
 
@@ -58,9 +61,8 @@ docker run --name my-corese \
 - Download [Corese-server jar file](https://project.inria.fr/corese/download/).
 
 ```sh
-# Replace ${VERSION} with the desired version number (e.g: 4.3.0)
-wget "files.inria.fr/corese/distrib/corese-server-${VERSION}.jar"
-java -jar "corese-server-${VERSION}.jar"
+wget "files.inria.fr/corese/distrib/corese-server-4.4.0.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-server-4.4.0.jar"
 ```
 
 Documentation: [Getting Started With Corese-server](https://notes.inria.fr/s/SoyFglO_1#)
@@ -70,9 +72,26 @@ Documentation: [Getting Started With Corese-server](https://notes.inria.fr/s/Soy
 - Download [Corese-gui jar file](https://project.inria.fr/corese/download/).
 
 ```sh
-# Replace ${VERSION} with the desired version number (e.g: 4.3.0)
-wget "files.inria.fr/corese/distrib/corese-gui-${VERSION}.jar"
-java -jar "corese-gui-${VERSION}.jar"
+wget "files.inria.fr/corese/distrib/corese-gui-4.4.0.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-gui-4.4.0.jar"
+```
+
+### Corese-Python (beta)
+
+- Download [Corese-python jar file](https://project.inria.fr/corese/download/).
+
+```sh
+wget "files.inria.fr/corese/distrib/corese-library-python-4.4.0.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-library-python-4.4.0.jar"
+```
+
+### Corese-Command (beta)
+
+- Download [Corese-command jar file](https://project.inria.fr/corese/download/).
+
+```sh
+wget "files.inria.fr/corese/distrib/corese-command-4.4.0.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-command-4.4.0.jar"
 ```
 
 ## Compilation from source
@@ -82,7 +101,21 @@ Download source code and compile.
 ```shell
 git clone "https://github.com/Wimmics/corese.git"
 cd corese
-mvn -Dmaven.test.skip=true package
+mvn clean -Dmaven.test.skip=true package
+```
+
+## How to cite Corese
+
+```bibtex
+@misc{corese,
+    author = {Corby, Olivier and Ceres, Rémi and Demairy, Erwan and Song, Fuqi and Bottollier, Virginie and Savoie, Olivier},
+    title = {{Corese: Semantic Web Factory}},
+    howpublished = {\url{https://project.inria.fr/corese/}},
+    version = {4.4.0},
+    institution = {Inria},
+    abstract = {{Software platform implementing and extending the standards of the Semantic Web.}},
+    url = {https://github.com/Wimmics/corese}
+}
 ```
 
 ## Contributions and discussions
@@ -93,6 +126,7 @@ We welcome everyone to contribute to [issue reports](https://github.com/Wimmics/
 ## General informations
 
 - [Corese website](https://project.inria.fr/corese)
+- [Documentation](https://project.inria.fr/corese/documentation/)
 - [Source code](https://github.com/Wimmics/corese)
 - [Corese server demo](http://corese.inria.fr/)
 - [Changelog](https://github.com/Wimmics/corese/blob/master/CHANGELOG.md)

CHANGELOG.md

@@ -9,8 +9,8 @@
   </parent>
 
   <groupId>fr.inria.corese</groupId>
-  <artifactId>corese-cli</artifactId>
-  <name>corese-cli</name>
+  <artifactId>corese-command</artifactId>
+  <name>corese-command</name>
 
   <dependencies>
 
@@ -60,7 +60,7 @@
               <shadedClassifierName>jar-with-dependencies</shadedClassifierName>
               <transformers>
                 <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                  <mainClass>fr.inria.corese.cli.App</mainClass>
+                  <mainClass>fr.inria.corese.command.App</mainClass>
                 </transformer>
                 <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
               </transformers>

Jenkinsfile

@@ -0,0 +1,28 @@
+package fr.inria.corese.command;
+
+import fr.inria.corese.command.programs.Convert;
+import fr.inria.corese.command.programs.LDScript;
+import fr.inria.corese.command.programs.Profile;
+import fr.inria.corese.command.programs.Sparql;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+
+/**
+ * Hello world!
+ */
+@Command(name = "Corese-command", version = "4.4.0", mixinStandardHelpOptions = true, subcommands = {
+        Convert.class, Sparql.class, Profile.class, LDScript.class,
+})
+public final class App implements Runnable {
+
+    public static void main(String[] args) {
+        int exitCode = new CommandLine(new App()).execute(args);
+        System.exit(exitCode);
+    }
+
+    @Override
+    public void run() {
+        // Print usage
+        CommandLine.usage(new App(), System.out);
+    }
+}

README.md

@@ -1,15 +1,15 @@
-package fr.inria.corese.cli.programs;
+package fr.inria.corese.command.programs;
 
 import java.nio.file.Path;
 
-import fr.inria.corese.cli.utils.GraphUtils;
-import fr.inria.corese.cli.utils.format.InputFormat;
-import fr.inria.corese.cli.utils.format.OutputFormat;
+import fr.inria.corese.command.utils.GraphUtils;
+import fr.inria.corese.command.utils.format.InputFormat;
+import fr.inria.corese.command.utils.format.OutputFormat;
 import fr.inria.corese.core.Graph;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Parameters;
 
-@Command(name = "convert", version = "4.3.0", description = "Convert an RDF file between different serialization formats.", mixinStandardHelpOptions = true)
+@Command(name = "convert", version = "4.4.0", description = "Convert an RDF file between different serialization formats.", mixinStandardHelpOptions = true)
 public class Convert implements Runnable {
 
     @Parameters(paramLabel = "INPUT_FORMAT", description = "Input file format."

corese-cli/src/main/java/fr/inria/corese/cli/App.java

@@ -1,4 +1,4 @@
-package fr.inria.corese.cli.programs;
+package fr.inria.corese.command.programs;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
@@ -10,7 +10,7 @@
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Parameters;
 
-@Command(name = "ldscript", version = "4.3.0", description = "Run an LDSCRIPT file.", mixinStandardHelpOptions = true)
+@Command(name = "ldscript", version = "4.4.0", description = "Run an LDSCRIPT file.", mixinStandardHelpOptions = true)
 public class LDScript implements Runnable {
 
     @Parameters(paramLabel = "INPUT", description = "LDScript file to run.")