Migration of BATS to ICE

org.eclipse.ice.bats/.gitignore

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+
+# Created by https://www.toptal.com/developers/gitignore/api/java,eclipse
+# Edit at https://www.toptal.com/developers/gitignore?templates=java,eclipse
+
+### Eclipse ###
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
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+.recommenders
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+# External tool builders
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+# Locally stored "Eclipse launch configurations"
+*.launch
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+*.pydevproject
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+# CDT-specific (C/C++ Development Tooling)
+.cproject
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+# CDT- autotools
+.autotools
+
+# Java annotation processor (APT)
+.factorypath
+
+# PDT-specific (PHP Development Tools)
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# Tern plugin
+.tern-project
+
+# TeXlipse plugin
+.texlipse
+
+# STS (Spring Tool Suite)
+.springBeans
+
+# Code Recommenders
+.recommenders/
+
+# Annotation Processing
+.apt_generated/
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+# Scala IDE specific (Scala & Java development for Eclipse)
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+# Uncomment this line if you wish to ignore the project description file.
+# Typically, this file would be tracked if it contains build/dependency configurations:
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+*.class
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+*.log
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+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+# End of https://www.toptal.com/developers/gitignore/api/java,eclipse
+
+target

org.eclipse.ice.bats/README.md

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+# BATS
+
+BATS, the Basic Artifact Tracking System (BATS), is a simple data management service for managing scientific data.
+
+BATS is a standalone maven package that can be used within or outside of ICE.
+
+BATS leverages [Apache Jena](https://jena.apache.org/index.html) to create [RDF Models](https://jena.apache.org/tutorials/rdf_api.html) and connects to [Apache Jena Fuseki](https://jena.apache.org/documentation/fuseki2/index.html) to publish these models.
+
+
+
+## Build Instructions
+
+### Prerequisites
+
+BATS requires a full installation of Docker for building, executing, and storing images.
+
+
+### Using Maven
+
+Building the package can be performed like most other maven packages, where the end result is a jar file that can be included as a dependency
+Due to the integration tests requiring a [Apache Jene Fuseki](https://jena.apache.org/documentation/fuseki2/index.html) server,
+we need to first build the image using the Dockerfile located in `src/main/docker/Dockerfile`.
+A test Fuseki container will be started and stopped during the tests using the [fabric8io docker-maven-plugin](https://dmp.fabric8.io/)
+(GitHub repo link [here](https://github.com/fabric8io/docker-maven-plugin)
+
+```
+$ mvn clean docker:build install
+```
+
+This installs the jar file to the local repository in `~/.m2`. It is also possible to build the package without installing by running
+
+```
+$ mvn clean docker:build verify
+```
+
+In both cases one can skip the tests by including `-DskipTests` in your build. 
+
+## BATS API
+
+Below are examples of a few general use cases for the BATS API
+
+### Upload a new DataSet
+
+One can create a connection to a Fuseki server to upload a [Dataset](https://jena.apache.org/documentation/javadoc/arq/org/apache/jena/query/Dataset.html), or a collection of named graphs (called [Models](https://jena.apache.org/documentation/javadoc/jena/org/apache/jena/rdf/model/Model.html) in Apache Jena).
+
+Here we upload a new, empty Dataset called `my-new-dataset`
+to our Fuseki server `http://my-fuseki-server.org:3030`.
+
+The upload takes place when we issue the `.create()` method
+for "creating" the data on the server.
+
+```
+import org.eclipse.ice.bats.DataSet;
+
+DataSet dataset = new DataSet();
+dataset.setName("my-new-dataset");
+dataset.setHost("http://my-fuseki-server.org");
+dataset.setPort(3030);
+dataset.create();
+```
+
+### Upload a new RDF Model to a DataSet
+
+We can also add a RDF [Model](https://jena.apache.org/documentation/javadoc/jena/org/apache/jena/rdf/model/Model.html) in Apache Jena,
+to the Dataset on the Fuseki server as follows:
+
+```
+import org.eclipse.ice.bats.DataSet;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+
+DataSet dataset = new DataSet();
+dataset.setName("my-new-dataset");
+dataset.setHost("http://my-fuseki-server.org");
+dataset.setPort(3030);
+
+Model model = ModelFactory.createDefaultModel();
+dataset.updateModel("my-model", model);
+```
+
+### Pull a RDF Model from a DataSet
+
+Following the previous example for uploading a RDF Model,
+we can pull that same model using the following:
+
+```
+import org.eclipse.ice.bats.DataSet;
+import org.apache.jena.rdf.model.Model;
+
+DataSet dataset = new DataSet();
+dataset.setName("my-new-dataset");
+dataset.setHost("http://my-fuseki-server.org");
+dataset.setPort(3030);
+
+Model model = dataset.getModel("my-model");
+```
+
+### Get "raw" Jena Dataset
+
+Sometimes we require the "raw" Jena dataset.
+We can use the following to pull this dataset and check if it is "null"
+
+```
+import org.eclipse.ice.bats.DataSet;
+import org.apache.jena.query.Dataset;
+
+DataSet dataset = new DataSet();
+dataset.setName("my-new-dataset");
+dataset.setHost("http://my-fuseki-server.org");
+dataset.setPort(3030);
+
+Dataset rawDataset = dataset.getJenaDataset();
+if ( rawDataset == null ) {
+    throw new Exception("DataSet Not Found");
+}
+```
+
+## How BATS got its name
+
+Jay Jay Bilings had a discussion with his daughter, 17 months old at the time, about her favorite animal.
+She picked the moose, but since that is already taken by several projects, they settled on her second favorite animal, the bat.
+The name was then back-ronymed out of it.

org.eclipse.ice.bats/pom.xml

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+<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.eclipse.ice</groupId>
+    <artifactId>org.eclipse.ice.bats</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+    <name>Eclipse ICE BATS</name>
+    <description>Basic Artifact Tracking System</description>
+
+    <properties>
+      <java.version>11</java.version>
+      <maven.compiler.source>11</maven.compiler.source>
+      <maven.compiler.target>11</maven.compiler.target>
+      <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <build>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-failsafe-plugin</artifactId>
+          <version>2.22.1</version>
+          <executions>
+            <execution>
+              <goals>
+                <goal>integration-test</goal>
+                <goal>verify</goal>
+              </goals>
+            </execution>
+          </executions>
+        </plugin>
+
+        <plugin>
+          <groupId>io.fabric8</groupId>
+          <artifactId>docker-maven-plugin</artifactId>
+          <version>0.34.1</version>
+          <configuration>
+            <images>
+              <image>
+                <name>bats-fuseki:latest</name>
+                <build>
+                  <contextDir>${project.basedir}/src/main/docker</contextDir>
+                  <dockerFile>Dockerfile.fuseki</dockerFile>
+                </build>
+                <run>
+                  <ports>
+                    <port>3030:3030</port>
+                  </ports>
+                  <volumes>
+                    <bind>
+                      <volume>/opt/fuseki-TDB:/data/TDB</volume>
+                    </bind>
+                  </volumes>
+                  <network>
+                    <mode>host</mode>
+                  </network>
+                  <wait>
+                    <url>http://localhost:3030</url>
+                  </wait>
+                </run>
+              </image>
+            </images>
+          </configuration>
+          <executions>
+            <execution>
+              <id>prepare-fuseki-database</id>
+              <phase>pre-integration-test</phase>
+              <goals>
+                <goal>start</goal>
+              </goals>
+            </execution>
+            <execution>
+              <id>remove-fuseki-database</id>
+              <phase>post-integration-test</phase>
+              <goals>
+                <goal>stop</goal>
+              </goals>
+            </execution>
+          </executions>
+        </plugin>
+
+      </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>apache-jena-libs</artifactId>
+            <type>pom</type>
+            <version>3.7.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.topbraid</groupId>
+            <artifactId>shacl</artifactId>
+            <version>1.1.0</version>
+        </dependency>
+
+        <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core -->
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <version>2.11.2</version>
+        </dependency>
+
+    </dependencies>
+</project>

org.eclipse.ice.bats/src/main/docker/Dockerfile.fuseki

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+FROM openjdk:11.0.1-jre
+
+# Specify Fuseki variables
+ARG FUSEKI_VERSION=3.16.0
+ARG FUSEKI_NAME=apache-jena-fuseki
+ARG FUSEKI_DOWNLOAD_FILE=$FUSEKI_NAME-$FUSEKI_VERSION.tar.gz
+
+# Install Fuseki
+RUN wget https://www-us.apache.org/dist/jena/binaries/$FUSEKI_DOWNLOAD_FILE && \
+    tar -xzvf $FUSEKI_DOWNLOAD_FILE && \
+    mv $FUSEKI_NAME-$FUSEKI_VERSION /opt/$FUSEKI_NAME && \
+    mkdir -p /opt/$FUSEKI_NAME/run/configuration
+
+# Expose the Fuseki port
+EXPOSE 3030
+
+# Execute Fuseki from the installation directory
+WORKDIR /opt/apache-jena-fuseki
+ENTRYPOINT ["./fuseki-server"]
+