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dennisvangPatrickDekkerHealthRI
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PatrickDekkerHealthRI
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Remove rdf4j-generator-maven-plugin dependency (#719)
* cherry-pick fix: remove rdf4j-generator (#715) * fix: remove rdf4j-generator * fix: checkstyle warnings on DATACITE,FDP, R3D generate classes and remove SCHEMAORG * cherry-pick: Clean up vocabulary classes (#717) * remove unused WebAccessControl vocabulary * rename vocabulary.Sio to SIO and use util.ValueFactoryHelper.i for consistency * remove unused terms from DATACITE vocabulary and refactor for consistency * remove unused terms from R3D vocabulary and refactor for consistency * remove unused terms from FDP vocabulary and refactor for consistency --------- Co-authored-by: Patrick Dekker <168626347+PatrickDekkerHealthRI@users.noreply.github.com>
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+124
-107
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‎pom.xml

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@@ -71,7 +71,6 @@
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<plugin.coveralls.version>4.3.0</plugin.coveralls.version>
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<plugin.javax_xml_bind.version>2.3.1</plugin.javax_xml_bind.version>
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<plugin.git_commit_id.version>9.0.2</plugin.git_commit_id.version>
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<plugin.rdf4j_generator.version>0.2.0</plugin.rdf4j_generator.version>
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<plugin.checkstyle.version>3.6.0</plugin.checkstyle.version>
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<plugin.spotbugs.version>4.9.3.0</plugin.spotbugs.version>
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</properties>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>com.github.kburger</groupId>
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<artifactId>rdf4j-generator-maven-plugin</artifactId>
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<version>${plugin.rdf4j_generator.version}</version>
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<executions>
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<execution>
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<goals>
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<goal>generate</goal>
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</goals>
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</execution>
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</executions>
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<configuration>
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<package>org.fairdatapoint.vocabulary</package>
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<addGeneratedAnnotation>false</addGeneratedAnnotation>
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<vocabularies>
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<vocabulary>
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<url>https://sparontologies.github.io/datacite/current/datacite.ttl</url>
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<prefix>datacite</prefix>
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</vocabulary>
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<vocabulary>
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<url>https://raw.githubusercontent.com/re3data/ontology/master/r3dOntology.ttl</url>
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</vocabulary>
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<vocabulary>
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<url>https://raw.githubusercontent.com/FAIRDataTeam/FDP-O/v1.1/fdp-ontology.owl</url>
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<namespace>https://w3id.org/fdp/fdp-o#</namespace>
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<prefix>fdp</prefix>
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</vocabulary>
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<vocabulary>
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<url>https://raw.githubusercontent.com/schemaorg/schemaorg/main/data/releases/3.4/schema.ttl</url>
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<namespace>http://schema.org/</namespace>
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<prefix>schemaOrg</prefix>
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</vocabulary>
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</vocabularies>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>

‎src/main/java/org/fairdatapoint/entity/metadata/MetadataSetter.java

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import org.fairdatapoint.vocabulary.DCAT3;
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import org.fairdatapoint.vocabulary.FDP;
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import org.fairdatapoint.vocabulary.Sio;
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import org.fairdatapoint.vocabulary.SIO;
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import org.eclipse.rdf4j.model.IRI;
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import org.eclipse.rdf4j.model.Literal;
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import org.eclipse.rdf4j.model.Model;
@@ -122,12 +122,12 @@ public static void setPublisher(Model metadata, IRI uri, Agent publisher) {
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}
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public static void setMetrics(Model metadata, IRI uri, List<Metric> metrics) {
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metadata.remove(null, Sio.IS_ABOUT, null);
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metadata.remove(null, Sio.REFERS_TO, null);
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metadata.remove(null, SIO.IS_ABOUT, null);
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metadata.remove(null, SIO.REFERS_TO, null);
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metrics.forEach(metric -> {
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metadata.add(uri, Sio.REFERS_TO, metric.getUri());
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metadata.add(metric.getUri(), Sio.IS_ABOUT, metric.getMetricType());
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metadata.add(metric.getUri(), Sio.REFERS_TO, metric.getValue());
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metadata.add(uri, SIO.REFERS_TO, metric.getUri());
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metadata.add(metric.getUri(), SIO.IS_ABOUT, metric.getMetricType());
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metadata.add(metric.getUri(), SIO.REFERS_TO, metric.getValue());
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});
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}
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‎src/main/java/org/fairdatapoint/vocabulary/DATACITE.java

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/**
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* The MIT License
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* Copyright © 2016-2024 FAIR Data Team
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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package org.fairdatapoint.vocabulary;
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import org.eclipse.rdf4j.model.IRI;
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import static org.fairdatapoint.util.ValueFactoryHelper.i;
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public final class DATACITE {
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public static final String NAMESPACE = "http://purl.org/spar/datacite/";
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public static final IRI IDENTIFIER = i(NAMESPACE + "Identifier");
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}

‎src/main/java/org/fairdatapoint/vocabulary/FDP.java

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/**
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* The MIT License
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* Copyright © 2016-2024 FAIR Data Team
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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package org.fairdatapoint.vocabulary;
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import org.eclipse.rdf4j.model.IRI;
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import static org.fairdatapoint.util.ValueFactoryHelper.i;
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public final class FDP {
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public static final String NAMESPACE = "https://w3id.org/fdp/fdp-o#";
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public static final IRI FAIRDATAPOINT = i(NAMESPACE + "FAIRDataPoint");
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public static final IRI FDPSOFTWAREVERSION = i(NAMESPACE + "fdpSoftwareVersion");
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public static final IRI METADATACATALOG = i(NAMESPACE + "metadataCatalog");
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public static final IRI METADATAIDENTIFIER = i(NAMESPACE + "metadataIdentifier");
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public static final IRI METADATAISSUED = i(NAMESPACE + "metadataIssued");
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public static final IRI METADATAMODIFIED = i(NAMESPACE + "metadataModified");
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public static final IRI METADATASERVICE = i(NAMESPACE + "MetadataService");
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}

‎src/main/java/org/fairdatapoint/vocabulary/R3D.java

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/**
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* The MIT License
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* Copyright © 2016-2024 FAIR Data Team
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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package org.fairdatapoint.vocabulary;
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import org.eclipse.rdf4j.model.IRI;
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import static org.fairdatapoint.util.ValueFactoryHelper.i;
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public final class R3D {
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public static final String NAMESPACE = "http://www.re3data.org/schema/3-0#";
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public static final IRI COUNTRY = i(NAMESPACE + "country");
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public static final IRI DATACATALOG = i(NAMESPACE + "dataCatalog");
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public static final IRI REPOSITORY = i(NAMESPACE + "Repository");
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public static final IRI REPOSITORYIDENTIFIER = i(NAMESPACE + "repositoryIdentifier");
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}

‎src/main/java/org/fairdatapoint/vocabulary/Sio.java renamed to ‎src/main/java/org/fairdatapoint/vocabulary/SIO.java

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package org.fairdatapoint.vocabulary;
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import org.eclipse.rdf4j.model.IRI;
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import org.eclipse.rdf4j.model.ValueFactory;
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import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
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import static org.fairdatapoint.util.ValueFactoryHelper.i;
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/**
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* Semanticscience Integrated Ontology
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* @version 0.1
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* @since 2018-01-17
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*/
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public class Sio {
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public class SIO {
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public static final ValueFactory VF = SimpleValueFactory.getInstance();
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public static final String PREFIX = "sio";
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public static final String NAMESPACE = "http://semanticscience.org/resource/";
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public static final IRI REFERS_TO = VF.createIRI(NAMESPACE + "SIO_000628");
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public static final IRI IS_ABOUT = VF.createIRI(NAMESPACE + "SIO_000332");
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public static final IRI IS_ABOUT = i(NAMESPACE + "SIO_000332");
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public static final IRI REFERS_TO = i(NAMESPACE + "SIO_000628");
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}

‎src/main/java/org/fairdatapoint/vocabulary/WebAccessControl.java

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