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/**
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* '$RCSfile$'
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* Copyright: 2010 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* Purpose: To test the Access Controls in metacat by JUnit
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*
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* '$Author:$'
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* '$Date:$'
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* '$Revision:$'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat.dataone;
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import gov.loc.repository.bagit.Bag;
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import gov.loc.repository.bagit.BagFactory;
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import gov.loc.repository.bagit.BagFile;
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import gov.loc.repository.bagit.Manifest;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileReader;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.UnsupportedEncodingException;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import junit.framework.Test;
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import junit.framework.TestSuite;
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import org.apache.commons.io.IOUtils;
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import org.dataone.client.v1.itk.DataPackage;
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import org.dataone.client.v2.formats.ObjectFormatCache;
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import org.dataone.configuration.Settings;
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import org.dataone.ore.ResourceMapFactory;
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import org.dataone.service.util.TypeMarshaller;
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import org.dataone.service.exceptions.IdentifierNotUnique;
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import org.dataone.service.exceptions.InsufficientResources;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.exceptions.SynchronizationFailed;
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import org.dataone.service.exceptions.UnsupportedType;
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import org.dataone.service.types.v1.AccessPolicy;
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import org.dataone.service.types.v1.AccessRule;
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import org.dataone.service.types.v1.Checksum;
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import org.dataone.service.types.v1.DescribeResponse;
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import org.dataone.service.types.v1.Event;
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import org.dataone.service.types.v1.Identifier;
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import org.dataone.service.types.v2.Log;
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import org.dataone.service.types.v2.Node;
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import org.dataone.service.types.v1.NodeReference;
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import org.dataone.service.types.v1.ObjectFormatIdentifier;
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import org.dataone.service.types.v1.ObjectList;
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import org.dataone.service.types.v1.Permission;
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import org.dataone.service.types.v1.Person;
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import org.dataone.service.types.v1.Session;
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import org.dataone.service.types.v1.Subject;
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import org.dataone.service.types.v1.SubjectInfo;
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import org.dataone.service.types.v2.SystemMetadata;
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import org.dspace.foresite.ResourceMap;
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import org.jibx.runtime.JiBXException;
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import org.junit.After;
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import org.junit.Before;
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/**
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* A JUnit test to insert a resource map into metacat with PROV relationships
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*
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* @author lwalker 08-15-2014
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*
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*/
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public class InsertORETest extends D1NodeServiceTest {
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/**
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* Set up the test fixtures
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*
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* @throws Exception
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*/
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@Before
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public void setUp() throws Exception {
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super.setUp();
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// set up the configuration for d1client
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Settings.getConfiguration().setProperty("D1Client.cnClassName", MockCNode.class.getName());
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}
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/**
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* Remove the test fixtures
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*/
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@After
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public void tearDown() {
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}
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/**
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* Build the test suite
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* @return
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*/
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public static Test suite() {
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TestSuite suite = new TestSuite();
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suite.addTest(new InsertORETest("initialize"));
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// Insert test
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suite.addTest(new InsertORETest("testInsertORE"));
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return suite;
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}
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/**
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* Constructor for the tests
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*
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* @param name - the name of the test
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*/
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public InsertORETest(String name) {
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super(name);
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}
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/**
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* Initial blank test
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*/
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public void initialize() {
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assertTrue(1 == 1);
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}
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public void testInsertORE() {
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printTestHeader("testInsertORE");
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try {
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//Create the predicate URIs and NS
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String provNS = "http://www.w3.org/ns/prov#";
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String wasDerivedFromURI = provNS + "wasDerivedFrom";
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String usedURI = provNS + "used";
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String wasGeneratedByURI = provNS + "wasGeneratedBy";
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String generatedURI = provNS + "generated";
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String wasInformedByURI = provNS + "wasInformedBy";
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Long uniqueNum = System.currentTimeMillis();
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// construct the ORE package
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Identifier resourceMapId = new Identifier();
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resourceMapId.setValue("package." + uniqueNum + ".1");
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DataPackage dataPackage = new DataPackage(resourceMapId);
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//Metadata
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Identifier metadataId = new Identifier();
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metadataId.setValue("meta." + uniqueNum + ".1");
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//Data
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List<Identifier> dataIds = new ArrayList<Identifier>();
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Identifier dataId = new Identifier();
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dataId.setValue("data." + uniqueNum + ".1");
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Identifier imgId = new Identifier();
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imgId.setValue("img." + uniqueNum + ".1");
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Identifier drawActivityId = new Identifier();
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drawActivityId.setValue("drawActivity." + uniqueNum + ".1");
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Identifier composeActivityId = new Identifier();
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composeActivityId.setValue("composeActivity." + uniqueNum + ".1");
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//Create the primary (external) resources identifiers
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Identifier primaryDataId = new Identifier();
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primaryDataId.setValue("primaryData.1.1");
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Identifier primaryDataId2 = new Identifier();
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primaryDataId2.setValue("primaryData.2.1");
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dataIds.add(dataId);
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dataIds.add(imgId);
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dataIds.add(drawActivityId);
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dataIds.add(composeActivityId);
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//Create lists of the items to use in the triples
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List<Identifier> dataIdList = new ArrayList<Identifier>();
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dataIdList.add(dataId);
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List<Identifier> activityIdList = new ArrayList<Identifier>();
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activityIdList.add(drawActivityId);
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List<Identifier> composeActivityIdList = new ArrayList<Identifier>();
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composeActivityIdList.add(composeActivityId);
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List<Identifier> primaryDataIdList = new ArrayList<Identifier>();
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primaryDataIdList.add(primaryDataId);
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primaryDataIdList.add(primaryDataId2);
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//---- isDocumentedBy/documents ----
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dataPackage.insertRelationship(metadataId, dataIds);
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//---- wasDerivedFrom ----
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dataPackage.insertRelationship(dataId, primaryDataIdList, provNS, wasDerivedFromURI);
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dataPackage.insertRelationship(imgId, dataIdList, provNS, wasDerivedFromURI);
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//---- wasGeneratedBy ----
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dataPackage.insertRelationship(imgId, activityIdList, provNS, wasGeneratedByURI);
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dataPackage.insertRelationship(dataId, composeActivityIdList, provNS, wasGeneratedByURI);
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//---- wasInformedBy ----
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dataPackage.insertRelationship(drawActivityId, composeActivityIdList, provNS, wasInformedByURI);
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//---- used ----
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dataPackage.insertRelationship(drawActivityId, dataIdList, provNS, usedURI);
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dataPackage.insertRelationship(composeActivityId, primaryDataIdList, provNS, usedURI);
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//Create the resourceMap
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ResourceMap resourceMap = dataPackage.getMap();
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assertNotNull(resourceMap);
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String rdfXml = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
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assertNotNull(rdfXml);
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Session session = getTestSession();
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InputStream object = null;
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SystemMetadata sysmeta = null;
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// save the data objects (data just contains their ID)
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InputStream dataObject1 = new ByteArrayInputStream(dataId.getValue().getBytes("UTF-8"));
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sysmeta = createSystemMetadata(dataId, session.getSubject(), dataObject1);
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MNodeService.getInstance(request).create(session, dataId, dataObject1, sysmeta);
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// second data file
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InputStream dataObject2 = new ByteArrayInputStream(imgId.getValue().getBytes("UTF-8"));
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sysmeta = createSystemMetadata(imgId, session.getSubject(), dataObject2);
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MNodeService.getInstance(request).create(session, imgId, dataObject2, sysmeta);
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// third data file
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InputStream dataObject3 = new ByteArrayInputStream(drawActivityId.getValue().getBytes("UTF-8"));
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sysmeta = createSystemMetadata(drawActivityId, session.getSubject(), dataObject3);
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MNodeService.getInstance(request).create(session, drawActivityId, dataObject3, sysmeta);
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// fourth data file
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InputStream dataObject4 = new ByteArrayInputStream(composeActivityId.getValue().getBytes("UTF-8"));
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sysmeta = createSystemMetadata(composeActivityId, session.getSubject(), dataObject4);
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MNodeService.getInstance(request).create(session, composeActivityId, dataObject4, sysmeta);
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// metadata file
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String testfile = "test/eml-sample.xml";
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InputStream metadataObject = new FileInputStream(testfile);
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sysmeta = createSystemMetadata(metadataId, session.getSubject(), null);
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sysmeta.setFormatId(ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.1.0").getFormatId());
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MNodeService.getInstance(request).create(session, metadataId, metadataObject, sysmeta);
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// save the ORE object
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object = new ByteArrayInputStream(rdfXml.getBytes("UTF-8"));
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sysmeta = createSystemMetadata(resourceMapId, session.getSubject(), object);
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sysmeta.setFormatId(ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId());
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Identifier pid = MNodeService.getInstance(request).create(session, resourceMapId, object, sysmeta);
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// get the package we uploaded
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InputStream bagStream = MNodeService.getInstance(request).getPackage(session, null, pid);
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File bagFile = File.createTempFile("bagit.", ".zip");
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IOUtils.copy(bagStream, new FileOutputStream(bagFile));
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BagFactory bagFactory = new BagFactory();
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Bag bag = bagFactory.createBag(bagFile);
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Iterator<Manifest> manifestIter = bag.getTagManifests().iterator();
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while (manifestIter.hasNext()) {
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String filepath = manifestIter.next().getFilepath();
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BagFile entryFile = bag.getBagFile(filepath);
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InputStream result = entryFile.newInputStream();
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// check ORE
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if (filepath.contains(resourceMapId.getValue())) {
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object.reset();
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assertTrue(object.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, object));
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}
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// check metadata
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if (filepath.contains(metadataId.getValue())) {
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metadataObject.reset();
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assertTrue(metadataObject.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, metadataObject));
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}
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if (filepath.contains(dataId.getValue())) {
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dataObject1.reset();
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assertTrue(dataObject1.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, dataObject1));
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}
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if (filepath.contains(imgId.getValue())) {
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dataObject2.reset();
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assertTrue(dataObject2.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, dataObject2));
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}
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if (filepath.contains(drawActivityId.getValue())) {
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dataObject3.reset();
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assertTrue(dataObject3.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, dataObject3));
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}
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if (filepath.contains(composeActivityId.getValue())) {
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dataObject4.reset();
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assertTrue(dataObject4.available() > 0);
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assertTrue(result.available() > 0);
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assertTrue(IOUtils.contentEquals(result, dataObject4));
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}
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}
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// clean up
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bagFile.delete();
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// test the ORE lookup
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List<Identifier> oreIds = MNodeService.getInstance(request).lookupOreFor(metadataId, true);
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assertTrue(oreIds.contains(resourceMapId));
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System.out.println("************** The package is: ***********");
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for(Identifier objectId : oreIds){
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System.out.println(objectId.getValue());
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}
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System.out.println("***********************************************");
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} catch (Exception e) {
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e.printStackTrace();
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fail("Unexpected error: " + e.getMessage());
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}
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}
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}
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