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Commit 63b19c82 authored by Stephane Dervaux's avatar Stephane Dervaux
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Merge branch '0.9.8.2'

parents c19a29f8 90fa7675
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pom.xml
+ 1
− 1
View file @ 63b19c82
......@@ -6,7 +6,7 @@
<groupId>fr.inrae.po2engine</groupId>
<artifactId>PO2Engine</artifactId>
<version>0.9.8.1</version>
<version>0.9.8.2</version>
<packaging>jar</packaging>
<properties>
......
src/main/java/fr/inrae/po2engine/model/Data.java
+ 166
− 1
View file @ 63b19c82
......@@ -5,7 +5,10 @@ import fr.inrae.po2engine.cloudexception.CantWriteException;
import fr.inrae.po2engine.cloudexception.LocalLockException;
import fr.inrae.po2engine.cloudexception.NotLoginException;
import fr.inrae.po2engine.externalTools.CloudConnector;
import fr.inrae.po2engine.externalTools.JenaTools;
import fr.inrae.po2engine.externalTools.RDF4JTools;
import fr.inrae.po2engine.model.dataModel.GeneralFile;
import fr.inrae.po2engine.model.dataModel.ItineraryFile;
import fr.inrae.po2engine.model.dataModel.MaterialsMethodsFile;
import fr.inrae.po2engine.model.dataModel.ProjectFile;
import fr.inrae.po2engine.model.partModel.MaterialMethodPart;
......@@ -17,15 +20,21 @@ import javafx.beans.property.DoubleProperty;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.util.Pair;
import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
import org.apache.commons.compress.archivers.zip.ZipFile;
import org.apache.commons.compress.utils.IOUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.http.auth.AuthenticationException;
import org.apache.jena.graph.Graph;
import org.apache.jena.graph.GraphMaker;
import org.apache.jena.graph.impl.SimpleGraphMaker;
import org.apache.jena.ontology.OntClass;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFWriter;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.vocabulary.SKOS;
import org.apache.logging.log4j.LogManager;
......@@ -34,6 +43,8 @@ import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.apache.poi.xssf.usermodel.XSSFRow;
import org.apache.poi.xssf.usermodel.XSSFSheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.json.JSONArray;
import org.json.JSONObject;
import java.io.*;
......@@ -207,7 +218,13 @@ public class Data extends OntoData{
// }
public void setGraphModel(Graph graphModel) {
this.graphModel = graphModel;
this.dataModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, ModelFactory.createModelForGraph(graphModel));
}
public OntModel createDataModel() {
if(this.graphModel != null) {
this.dataModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, ModelFactory.createModelForGraph(graphModel));
}
return this.dataModel;
}
public Graph getGraphModel() {
......@@ -745,4 +762,152 @@ public class Data extends OntoData{
this.materialMethodFile.getMethodPart().add(mPart);
}
}
public Boolean publish(JSONObject listPath) {
if(!listPath.keySet().contains("file_onto") || !listPath.keySet().contains("file_data") || !listPath.keySet().contains("onto_name")) {
return false;
}
String projectName = "";
String repoLabel = "";
projectName = this.getProjectFile().getNameProperty().getValue();
repoLabel = "repository for project " + projectName + "-- Ontology used : " + listPath.getString("onto_name");
String projectID = Tools.normalize(projectName);
try {
RDF4JTools.createOrClearRepository(repoLabel, projectID);
RDF4JTools.upload(projectID, "http://opendata.inra.fr/ontology/" + projectID, new FileInputStream(listPath.getString("file_onto")), RDFFormat.TURTLE);
RDF4JTools.upload(projectID, "http://opendata.inra.fr/data/" + projectID, new FileInputStream(listPath.getString("file_data")), RDFFormat.TURTLE);
} catch (IOException e) {
e.printStackTrace();
return false;
}
try {
RDF4JTools.setFreeReadRepository(projectID, isPublic());
} catch (AuthenticationException | IOException e) {
e.printStackTrace();
return false;
}
if (this.getGroup() != null && !this.getGroup().isEmpty()) {
try {
String groupName = Tools.normalize(this.getGroup());
RDF4JTools.replaceGraph(groupName, "http://opendata.inra.fr/data/" + projectID, new FileInputStream(listPath.getString("file_data")), "http://opendata.inra.fr/ontology/ontology", new FileInputStream(listPath.getString("file_onto")), RDFFormat.TURTLE);
RDF4JTools.setFreeReadRepository(groupName, isPublic());
} catch (IOException | AuthenticationException e) {
e.printStackTrace();
}
}
CloudConnector.addLog(this, "published");
RDF4JTools.initRepositotyInfos(this);
return true;
}
public JSONObject semantize(Pair<GeneralFile, ArrayList<ItineraryFile>> process, Ontology onto) throws IOException {
Tools.addProgress(ProgressPO2.PUBLISH, "Loading core ontology");
JSONObject mess = new JSONObject();
JSONArray error = new JSONArray();
JSONArray listMessages = new JSONArray();
mess.put("listMessages", listMessages);
mess.put("error", error);
if(!this.isLoaded().get()) {
error.put("data not loaded");
}
if(this.isModified()) {
error.put("data not saved");
}
if(onto == null) {
error.put("ontology is null");
}
if(!onto.isLoaded().get()) {
error.put("ontology not loaded");
}
if(onto.isModified()) {
error.put("ontology not saved");
}
if(error.length() > 0) {
Tools.delProgress(ProgressPO2.PUBLISH);
return mess;
}
mess.put("onto_name", onto.getName().get());
Tools.updateProgress(ProgressPO2.PUBLISH, "Loading core ontology");
OntModel coreModel = JenaTools.ReadCoreModel();
String PO2_domain = null;
OntModel dataModel = null;
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Loading domain ontology");
logger.debug("Chargement de la domaine ontologie : " + onto.getName().get());
OntModel domainModel = JenaTools.ReadModel(onto.getOntologyFile().getAbsolutePath());
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Settings NameSpaces");
if(domainModel != null) {
logger.debug("creating data model");
GraphMaker gm = new SimpleGraphMaker();
Graph dataGraph = gm.createGraph("http://www.testnom.com");
this.setCoreModel(coreModel);
this.setDomainModel(domainModel);
this.setGraphModel(dataGraph);
dataModel = this.createDataModel();
dataModel.setNsPrefix("domain", this.getDOMAIN_NS());
dataModel.setNsPrefix("core", this.getCORE_NS());
dataModel.setNsPrefix("", this.getDATA_NS());
dataModel.setNsPrefix("time", "http://www.w3.org/2006/time#");
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Semantization", 0.0);
File tempFile = this.getProjectFile().publish(coreModel, domainModel, dataModel, listMessages, process);
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Merge of graphs", -1.0);
// fusion core && domain
Model unionModel = coreModel.union(domainModel);
File tempDomain = File.createTempFile("pref", "ttl");
FileOutputStream output = new FileOutputStream(tempDomain);
RDFWriter ontologyWriter = unionModel.getWriter("TTL");
ontologyWriter.write(unionModel, output, null);
output.flush();
mess.put("file_onto", tempDomain.getAbsolutePath());
mess.put("file_data", tempFile.getAbsolutePath());
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
Tools.delProgress(ProgressPO2.PUBLISH);
return mess;
}
}
src/main/java/fr/inrae/po2engine/model/Ontology.java
+ 88
− 0
View file @ 63b19c82
......@@ -6,6 +6,7 @@ import fr.inrae.po2engine.cloudexception.LocalLockException;
import fr.inrae.po2engine.cloudexception.NotLoginException;
import fr.inrae.po2engine.externalTools.CloudConnector;
import fr.inrae.po2engine.externalTools.JenaTools;
import fr.inrae.po2engine.externalTools.RDF4JTools;
import fr.inrae.po2engine.utils.ProgressPO2;
import fr.inrae.po2engine.utils.Tools;
import javafx.collections.FXCollections;
......@@ -14,9 +15,15 @@ import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
import org.apache.commons.compress.archivers.zip.ZipFile;
import org.apache.commons.compress.utils.IOUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.http.auth.AuthenticationException;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.RDFWriter;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.json.JSONArray;
import org.json.JSONObject;
import java.io.*;
import java.net.URISyntaxException;
......@@ -405,4 +412,85 @@ public class Ontology extends OntoData{
return listScale;
}
public Boolean publish(JSONObject listPath) {
if(!listPath.keySet().contains("file_onto")) {
return false;
}
String repoLabel = "repository for ontology " + this.getName().get();
String projectID = Tools.normalize(this.getName().get());
try {
RDF4JTools.createOrClearRepository(repoLabel, projectID);
} catch (IOException e) {
e.printStackTrace();
return false;
}
try {
RDF4JTools.upload(projectID, "http://opendata.inra.fr/ontology/" + projectID, new FileInputStream(listPath.getString("file_onto")), RDFFormat.TURTLE);
RDF4JTools.setFreeReadRepository(projectID, isPublic());
} catch (AuthenticationException | IOException e) {
e.printStackTrace();
return false;
}
CloudConnector.addLog(this, "published");
RDF4JTools.initRepositotyInfos(this);
return true;
}
public JSONObject semantize() throws IOException {
Tools.addProgress(ProgressPO2.PUBLISH, "Loading core ontology");
JSONObject mess = new JSONObject();
JSONArray error = new JSONArray();
mess.put("error", error);
JSONArray listMessages = new JSONArray();
mess.put("listMessages", listMessages);
if(!this.isLoaded().get()) {
error.put("ontology not loaded");
}
if(this.isModified()) {
error.put("ontology not saved");
}
if(error.length() > 0) {
Tools.delProgress(ProgressPO2.PUBLISH);
return mess;
}
OntModel coreModel = JenaTools.ReadCoreModel();
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Loading domain ontology");
OntModel domainModel = JenaTools.ReadModel(ontologyFile.getAbsolutePath());
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.updateProgress(ProgressPO2.PUBLISH, "Settings NameSpaces");
Model unionModel = coreModel.union(domainModel);
File tempDomain = File.createTempFile("pref", "ttl");
FileOutputStream output = new FileOutputStream(tempDomain);
RDFWriter ontologyWriter = unionModel.getWriter("TTL");
ontologyWriter.write(unionModel, output, null);
output.flush();
mess.put("file_onto", tempDomain.getAbsolutePath());
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
Tools.delProgress(ProgressPO2.PUBLISH);
return mess;
}
}
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