updated package names

.gitlab-ci.yml

@@ -3,11 +3,6 @@ image: maven:3.6.2-jdk-8
 build:
   stage: build
   script:
-    - git clone https://github.com/sparql-generate/sparql-generate.git
-    - cd sparql-generate
-    - cd sparql-generate-parent
-    - mvn install -Pskip
-    - cd ../..
     - mvn package
   artifacts:
     paths:

pom.xml

@@ -3,9 +3,9 @@
 	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>fr.emse.gitlab.saref</groupId>
+	<groupId>fr.mines-stetienne.ci.saref</groupId>
 	<artifactId>saref-pipeline</artifactId>
-	<version>1.0-SNAPSHOT</version>
+	<version>1.0</version>
 	<packaging>jar</packaging>
 
 	<name>SAREF-Pipeline</name>
@@ -65,7 +65,7 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<project.scm.id>git</project.scm.id>
-		<sparql-generate.version>2.0-SNAPSHOT</sparql-generate.version>
+		<sparql-generate.version>2.0.0</sparql-generate.version>
 	</properties>
 
 	<dependencies>
@@ -139,17 +139,17 @@
 			<version>3.13.0</version>
 		</dependency>
 		<dependency>
-			<groupId>fr.emse.ci</groupId>
+			<groupId>fr.mines-stetienne.ci.sparql-generate</groupId>
 			<artifactId>sparql-generate-xml</artifactId>
 			<version>${sparql-generate.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>fr.emse.ci</groupId>
+			<groupId>fr.mines-stetienne.ci.sparql-generate</groupId>
 			<artifactId>sparql-generate-markdown</artifactId>
 			<version>${sparql-generate.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>fr.emse.ci</groupId>
+			<groupId>fr.mines-stetienne.ci.sparql-generate</groupId>
 			<artifactId>sparql-generate-jena</artifactId>
 			<version>${sparql-generate.version}</version>
 		</dependency>

src/main/java/fr/emse/gitlab/saref/CLIExecution.java → src/main/java/fr/mines_stetienne/ci/saref/CLIExecution.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import java.io.Console;
 import java.io.File;
@@ -40,7 +40,7 @@ import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import fr.emse.gitlab.saref.SAREFPipeline.Mode;
+import fr.mines_stetienne.ci.saref.SAREFPipeline.Mode;
 
 /**
  *

src/main/java/fr/emse/gitlab/saref/Main.java → src/main/java/fr/mines_stetienne/ci/saref/Main.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import java.awt.Desktop;
 import java.awt.GraphicsEnvironment;
@@ -37,10 +37,10 @@ import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import fr.emse.gitlab.saref.SAREFPipeline.Mode;
-import fr.emse.gitlab.saref.gui.MainFrame;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.tests.TestSuites;
+import fr.mines_stetienne.ci.saref.SAREFPipeline.Mode;
+import fr.mines_stetienne.ci.saref.gui.MainFrame;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.tests.TestSuites;
 
 /**
  *

src/main/java/fr/emse/gitlab/saref/SAREF.java → src/main/java/fr/mines_stetienne/ci/saref/SAREF.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -40,11 +40,11 @@ import org.apache.jena.atlas.RuntimeIOException;
 import org.apache.jena.riot.Lang;
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.entities.SAREFCore;
-import fr.emse.gitlab.saref.entities.SAREFExtension;
-import fr.emse.gitlab.saref.entities.SAREFNamedGraph;
-import fr.emse.gitlab.saref.entities.SAREFProject;
-import fr.emse.gitlab.saref.entities.SAREFVersionName;
+import fr.mines_stetienne.ci.saref.entities.SAREFCore;
+import fr.mines_stetienne.ci.saref.entities.SAREFExtension;
+import fr.mines_stetienne.ci.saref.entities.SAREFNamedGraph;
+import fr.mines_stetienne.ci.saref.entities.SAREFProject;
+import fr.mines_stetienne.ci.saref.entities.SAREFVersionName;
 
 /**
 *
@@ -70,6 +70,7 @@ public class SAREF {
 	public static final String NAME_SOURCES = "sources";
 	public static final String NAME_SOURCES_PORTAL = "portal";
 
+	public static final boolean IGNORE_OOPS = true;
 	
 	// project acronym
 	public static final String REGEX_ACRONYM_VAR = "acronym";

src/main/java/fr/emse/gitlab/saref/SAREFCredentialsProvider.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFCredentialsProvider.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 public interface SAREFCredentialsProvider {
 	

src/main/java/fr/emse/gitlab/saref/SAREFErrorLogger.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFErrorLogger.java

@@ -23,17 +23,17 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import java.util.Arrays;
 import java.util.ResourceBundle;
 
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.managers.DatasetManager;
-import fr.emse.gitlab.saref.managers.OntologyManager;
-import fr.emse.gitlab.saref.managers.SiteManager;
-import fr.emse.gitlab.saref.managers.SourcesManager;
+import fr.mines_stetienne.ci.saref.managers.DatasetManager;
+import fr.mines_stetienne.ci.saref.managers.OntologyManager;
+import fr.mines_stetienne.ci.saref.managers.SiteManager;
+import fr.mines_stetienne.ci.saref.managers.SourcesManager;
 
 public abstract class SAREFErrorLogger {
 

src/main/java/fr/emse/gitlab/saref/SAREFPipeline.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFPipeline.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import java.io.File;
 import java.io.IOException;
@@ -41,12 +41,12 @@ import org.apache.log4j.PatternLayout;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import fr.emse.gitlab.saref.managers.DatasetManager;
-import fr.emse.gitlab.saref.managers.OntologyManager;
-import fr.emse.gitlab.saref.managers.SiteManager;
-import fr.emse.gitlab.saref.managers.SourcesManager;
-import fr.emse.gitlab.saref.tests.TestSuites;
-import fr.emse.gitlab.saref.tests.TestSuitesAppender;
+import fr.mines_stetienne.ci.saref.managers.DatasetManager;
+import fr.mines_stetienne.ci.saref.managers.OntologyManager;
+import fr.mines_stetienne.ci.saref.managers.SiteManager;
+import fr.mines_stetienne.ci.saref.managers.SourcesManager;
+import fr.mines_stetienne.ci.saref.tests.TestSuites;
+import fr.mines_stetienne.ci.saref.tests.TestSuitesAppender;
 
 public class SAREFPipeline {
 

src/main/java/fr/emse/gitlab/saref/SAREFPipelineException.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFPipelineException.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 /**
 *

src/main/java/fr/emse/gitlab/saref/SAREFRepositoryErrorLogger.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFRepositoryErrorLogger.java

-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.entities.SAREFProject;
-import fr.emse.gitlab.saref.entities.SAREFRepository;
+import fr.mines_stetienne.ci.saref.entities.SAREFProject;
+import fr.mines_stetienne.ci.saref.entities.SAREFRepository;
 
 public class SAREFRepositoryErrorLogger extends SAREFErrorLogger {
 	

src/main/java/fr/emse/gitlab/saref/SAREFRepositoryVersionErrorLogger.java → src/main/java/fr/mines_stetienne/ci/saref/SAREFRepositoryVersionErrorLogger.java

-package fr.emse.gitlab.saref;
+package fr.mines_stetienne.ci.saref;
 
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.entities.SAREFProject;
-import fr.emse.gitlab.saref.entities.SAREFRepository;
-import fr.emse.gitlab.saref.entities.SAREFVersion;
-import fr.emse.gitlab.saref.entities.SAREFVersionName;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.entities.SAREFProject;
+import fr.mines_stetienne.ci.saref.entities.SAREFRepository;
+import fr.mines_stetienne.ci.saref.entities.SAREFVersion;
+import fr.mines_stetienne.ci.saref.entities.SAREFVersionName;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 public class SAREFRepositoryVersionErrorLogger extends SAREFErrorLogger {
 	

src/main/java/fr/emse/gitlab/saref/checkers/AbstractChecker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/AbstractChecker.java

@@ -23,13 +23,13 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.SAREFRepositoryVersionErrorLogger;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.SAREFRepositoryVersionErrorLogger;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 public abstract class AbstractChecker extends SAREFRepositoryVersionErrorLogger {
 	

src/main/java/fr/emse/gitlab/saref/checkers/AbstractClauseChecker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/AbstractClauseChecker.java

@@ -23,16 +23,16 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.slf4j.Logger;
 
-import fr.emse.gitlab.saref.SAREF;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 public abstract class AbstractClauseChecker extends AbstractChecker {
 

src/main/java/fr/emse/gitlab/saref/checkers/AbstractShaclChecker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/AbstractShaclChecker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.InputStream;
 import java.io.StringWriter;
@@ -51,10 +51,10 @@ import org.topbraid.jenax.util.JenaUtil;
 import org.topbraid.shacl.validation.ValidationUtil;
 import org.topbraid.shacl.vocabulary.SH;
 
-import fr.emse.gitlab.saref.SAREF;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.vocabs.SHACL;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.vocabs.SHACL;
 
 public abstract class AbstractShaclChecker extends AbstractClauseChecker {
 

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_2_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_2_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -39,8 +39,8 @@ import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.2: Structure of the SAREF project version directory

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_3_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_3_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -43,11 +43,11 @@ import com.opencsv.CSVParserBuilder;
 import com.opencsv.CSVReader;
 import com.opencsv.CSVReaderBuilder;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.GenerateRDFaManager;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.utils.Languages;
-import fr.emse.gitlab.saref.vocabs.VTC;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.GenerateRDFaManager;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.utils.Languages;
+import fr.mines_stetienne.ci.saref.vocabs.VTC;
 
 /**
  * Checks TS 103 673 Clause 9.3: Ontology requirements

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_1_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_1_Checker.java

@@ -23,15 +23,15 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.utils.Languages;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.utils.Languages;
 
 /**
  * Checks TS 103 673 Clause 9.4.1: The ontology directory

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_2_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_2_Checker.java

@@ -23,17 +23,17 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.util.HashMap;
 import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import fr.emse.gitlab.saref.SAREF;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.entities.SAREFExtension;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.entities.SAREFExtension;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.2: Prefixes declaration

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_3_1_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_3_1_Checker.java

@@ -23,13 +23,13 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.entities.SAREFVersion;
-import fr.emse.gitlab.saref.entities.SAREFVersionName;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.vocabs.SHACL;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.entities.SAREFVersion;
+import fr.mines_stetienne.ci.saref.entities.SAREFVersionName;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.vocabs.SHACL;
 
 /**
  * Checks TS 103 673 Clause 9.4.3.1: Ontology IRI and Ontology Version IRI

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_3_2_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_3_2_Checker.java

@@ -23,12 +23,12 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
-import fr.emse.gitlab.saref.SAREF;
-import fr.emse.gitlab.saref.SAREFPipeline.Mode;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.SAREFPipeline.Mode;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.3.2: Documentation metadata

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_3_3_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_3_3_Checker.java

@@ -23,10 +23,10 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.3.3: Creators and contributors

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_3_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_3_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ResIterator;
@@ -31,8 +31,8 @@ import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.vocabulary.OWL2;
 import org.apache.jena.vocabulary.RDF;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.3: The ontology declaration

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_4_1_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_4_1_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -35,9 +35,9 @@ import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.vocabulary.OWL2;
 import org.apache.jena.vocabulary.RDF;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.entities.SAREFTerm;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.entities.SAREFTerm;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.4.1: Term IRI

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_4_2_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_4_2_Checker.java

@@ -23,14 +23,14 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import org.apache.jena.rdf.model.Resource;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.entities.SAREFTerm;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.vocabs.SHACL;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.entities.SAREFTerm;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.vocabs.SHACL;
 
 /**
  * Checks TS 103 673 Clause 9.4.4.2: Documentation metadata

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_4_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_4_Checker.java

@@ -23,10 +23,10 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4.4: Term declarations

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_5_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_5_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -31,10 +31,8 @@ import java.net.SocketTimeoutException;
 import java.util.ArrayList;
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
 import java.util.stream.Collectors;
 
-import fr.emse.gitlab.saref.managers.ThemisManager;
 import org.apache.jena.rdf.model.Model;
 import org.semanticweb.owl.explanation.api.Explanation;
 import org.semanticweb.owl.explanation.api.ExplanationGenerator;
@@ -46,19 +44,20 @@ import org.semanticweb.owlapi.profiles.violations.UseOfDefinedDatatypeInDatatype
 import org.semanticweb.owlapi.profiles.violations.UseOfDefinedDatatypeInLiteral;
 import org.semanticweb.owlapi.profiles.violations.UseOfUndeclaredDatatype;
 import org.semanticweb.owlapi.profiles.violations.UseOfUnknownDatatype;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.OntologyManager;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.OntologyManager;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.managers.ThemisManager;
 import okhttp3.MediaType;
 import okhttp3.OkHttpClient;
 import okhttp3.Request;
 import okhttp3.RequestBody;
 import okhttp3.Response;
-import org.semanticweb.owlapi.reasoner.TimeOutException;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
 
 /**
  * Checks TS 103 673 Clause 9.4.5: OWL Profile, Consistency, and Satisfiability
@@ -130,6 +129,9 @@ public class Clause_9_4_5_Checker extends AbstractClauseChecker {
 	}
 
 	public void checkOops() throws Exception {
+		if(SAREF.IGNORE_OOPS) {
+			return;
+		}
 
 		ByteArrayOutputStream out = new ByteArrayOutputStream();
 		String onto = "";

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_4_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_4_Checker.java

@@ -23,12 +23,12 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.4: The Ontology specification

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_5_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_5_Checker.java

@@ -23,7 +23,7 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -50,12 +50,12 @@ import com.opencsv.CSVParserBuilder;
 import com.opencsv.CSVReader;
 import com.opencsv.CSVReaderBuilder;
 
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.GenerateRDFaManager;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
-import fr.emse.gitlab.saref.managers.ThemisManager;
-import fr.emse.gitlab.saref.utils.Languages;
-import fr.emse.gitlab.saref.vocabs.VTC;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.GenerateRDFaManager;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.managers.ThemisManager;
+import fr.mines_stetienne.ci.saref.utils.Languages;
+import fr.mines_stetienne.ci.saref.vocabs.VTC;
 import okhttp3.MediaType;
 import okhttp3.OkHttpClient;
 import okhttp3.Request;

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_6_1_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_6_1_Checker.java

@@ -23,16 +23,16 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.util.stream.Collectors;
 
-import fr.emse.gitlab.saref.SAREF;
-import fr.emse.gitlab.saref.SAREFPipelineException;
-import fr.emse.gitlab.saref.managers.RepositoryManager;
+import fr.mines_stetienne.ci.saref.SAREF;
+import fr.mines_stetienne.ci.saref.SAREFPipelineException;
+import fr.mines_stetienne.ci.saref.managers.RepositoryManager;
 
 /**
  * Checks TS 103 673 Clause 9.6.1: The examples directory

src/main/java/fr/emse/gitlab/saref/checkers/Clause_9_6_2_Checker.java → src/main/java/fr/mines_stetienne/ci/saref/checkers/Clause_9_6_2_Checker.java

@@ -23,20 +23,20 @@
  * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED 
  * OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-package fr.emse.gitlab.saref.checkers;
+package fr.mines_stetienne.ci.saref.checkers;
 
 import java.util.HashMap;
 import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;