Revision 9260
Added by Jing Tao about 9 years ago
test/edu/ucsb/nceas/metacat/annotation/DatapackageSummarizerTest.java | ||
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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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* |
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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.annotation; |
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import java.io.ByteArrayInputStream; |
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import java.io.InputStream; |
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import java.math.BigInteger; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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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 java.util.Vector; |
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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.service.exceptions.NotFound; |
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import org.dataone.service.types.v1.Identifier; |
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import org.dataone.service.types.v1.ObjectFormatIdentifier; |
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import org.dataone.service.types.v1.Session; |
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import org.dataone.service.types.v2.SystemMetadata; |
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import edu.ucsb.nceas.metacat.DBUtil; |
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import edu.ucsb.nceas.metacat.DocumentImpl; |
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import edu.ucsb.nceas.metacat.IdentifierManager; |
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException; |
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import edu.ucsb.nceas.metacat.dataone.D1NodeServiceTest; |
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import edu.ucsb.nceas.metacat.dataone.MNodeService; |
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import edu.ucsb.nceas.metacat.replication.ReplicationService; |
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import edu.ucsb.nceas.metacat.util.DocumentUtil; |
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public class DatapackageSummarizerTest extends D1NodeServiceTest { |
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private static final String ANNOTATION_TEST_DOC = "test/eml-sample-annotation.xml"; |
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/** |
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* constructor for the test |
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*/ |
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public DatapackageSummarizerTest(String name) { |
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super(name); |
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} |
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/** |
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* Establish a testing framework by initializing appropriate objects |
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*/ |
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public void setUp() throws Exception { |
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super.setUp(); |
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} |
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/** |
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* Release any objects after tests are complete |
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*/ |
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public void tearDown() { |
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} |
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/** |
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* Create a suite of tests to be run together |
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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 DatapackageSummarizerTest("testGenerateAnnotations")); |
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// suite.addTest(new DatapackageSummarizerTest("testGenerateAnnotation")); |
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// suite.addTest(new DatapackageSummarizerTest("testStandaloneAnnotation")); |
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suite.addTest(new DatapackageSummarizerTest("testIndexAnnotations")); |
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return suite; |
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} |
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public void testStandaloneAnnotation() throws Exception { |
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// insert the test document to sem-index |
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Identifier metadataPid = new Identifier(); |
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metadataPid.setValue("testAnnotation.eml." + System.currentTimeMillis()); |
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Session session = getTestSession(); |
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try { |
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InputStream object = new ByteArrayInputStream(this.getTestDocFromFile(ANNOTATION_TEST_DOC).getBytes("UTF-8")); |
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SystemMetadata sysmeta = createSystemMetadata(metadataPid, session.getSubject(), object); |
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier(); |
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formatId.setValue("eml://ecoinformatics.org/eml-2.0.0"); |
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sysmeta.setFormatId(formatId); |
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Identifier pid = MNodeService.getInstance(request).create(session, metadataPid, object, sysmeta); |
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assertEquals(metadataPid.getValue(), pid.getValue()); |
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} catch (Exception e) { |
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e.printStackTrace(); |
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fail("Could not add metadata test file: " + e.getMessage()); |
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} |
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// index it |
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DatapackageSummarizer ds = new DatapackageSummarizer(); |
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ds.indexEphemeralAnnotation(metadataPid); |
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// check it |
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} |
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/** |
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* Generate a single annotation based exclusively on the metadata |
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* @throws Exception |
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*/ |
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public void testGenerateAnnotation() throws Exception { |
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Identifier metadataPid = new Identifier(); |
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metadataPid.setValue("testAnnotation.eml." + System.currentTimeMillis()); |
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Session session = getTestSession(); |
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try { |
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InputStream object = new ByteArrayInputStream(this.getTestDocFromFile(ANNOTATION_TEST_DOC).getBytes("UTF-8")); |
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SystemMetadata sysmeta = createSystemMetadata(metadataPid, session.getSubject(), object); |
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier(); |
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formatId.setValue("eml://ecoinformatics.org/eml-2.0.0"); |
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sysmeta.setFormatId(formatId); |
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Identifier pid = MNodeService.getInstance(request).create(session, metadataPid, object, sysmeta); |
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assertEquals(metadataPid.getValue(), pid.getValue()); |
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} catch (Exception e) { |
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e.printStackTrace(); |
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fail("Could not add metadata test file: " + e.getMessage()); |
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} |
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// generate the annotation for the metadata |
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DatapackageSummarizer ds = new DatapackageSummarizer(); |
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String rdfContent = ds.generateAnnotation(metadataPid); |
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// save the annotation |
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Identifier annotationPid = new Identifier(); |
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annotationPid.setValue("http://annotation/" + metadataPid.getValue()); |
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try { |
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InputStream object = new ByteArrayInputStream(rdfContent.getBytes("UTF-8")); |
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SystemMetadata sysmeta = createSystemMetadata(annotationPid, session.getSubject(), object); |
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier(); |
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formatId.setValue("http://www.w3.org/TR/rdf-syntax-grammar"); |
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sysmeta.setFormatId(formatId); |
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Identifier pid = MNodeService.getInstance(request).create(session, annotationPid, object, sysmeta); |
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assertEquals(annotationPid.getValue(), pid.getValue()); |
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} catch (Exception e) { |
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e.printStackTrace(); |
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fail("Could not add annotation test file: " + e.getMessage()); |
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} |
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// check that it was parsed? |
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} |
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public void testIndexAnnotations() throws Exception { |
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testGenerateAnnotations(true); |
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} |
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public void testGenerateAnnotations() throws Exception { |
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testGenerateAnnotations(false); |
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} |
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private void testGenerateAnnotations(boolean indexOnly) throws Exception { |
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// summarize the packages |
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DatapackageSummarizer ds = new DatapackageSummarizer(); |
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List<Identifier> identifiers = new ArrayList<Identifier>(); |
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Map<Integer, String> serverCodes = ReplicationService.getServerCodes(); |
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// select the metadata ids we want to summarize |
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boolean includeReplicas = false; |
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Iterator<Integer> codeIter = Arrays.asList(new Integer[] {1}).iterator(); |
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if (includeReplicas ) { |
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codeIter = serverCodes.keySet().iterator(); |
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} |
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Vector<String> idList = new Vector<String>(); |
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while (codeIter.hasNext()) { |
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int serverLocation = codeIter.next(); |
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Vector<String> idList0 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_0NAMESPACE, false, serverLocation); |
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idList.addAll(idList0); |
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Vector<String> idList1 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_1NAMESPACE, false, serverLocation); |
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idList.addAll(idList1); |
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Vector<String> idList2 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_0NAMESPACE, false, serverLocation); |
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idList.addAll(idList2); |
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Vector<String> idList3 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_1NAMESPACE, false, serverLocation); |
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idList.addAll(idList3); |
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} |
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// go through all the identifiers now |
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for (String localId : idList) { |
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try { |
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String guid = IdentifierManager.getInstance().getGUID( |
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DocumentUtil.getDocIdFromAccessionNumber(localId), |
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DocumentUtil.getRevisionFromAccessionNumber(localId)); |
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Identifier pid = new Identifier(); |
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pid.setValue(guid); |
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identifiers.add(pid); |
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// just index the annotation, don't save it |
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if (indexOnly) { |
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ds.indexEphemeralAnnotation(pid); |
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continue; |
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} |
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String annotation = ds.generateAnnotation(pid); |
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Identifier annotationPid = new Identifier(); |
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annotationPid.setValue("http://annotation/" + guid); |
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Session session = getTestSession(); |
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SystemMetadata sysmeta = null; |
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// look for the latest version of the annotation, if there is one |
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do { |
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try { |
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sysmeta = MNodeService.getInstance(request).getSystemMetadata(null, annotationPid); |
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if (sysmeta.getObsoletedBy() != null) { |
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annotationPid.setValue(sysmeta.getObsoletedBy().getValue()); |
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} |
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} catch (NotFound nf) { |
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break; |
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} |
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} while (sysmeta != null && sysmeta.getObsoletedBy() != null); |
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boolean exists = (sysmeta != null); |
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InputStream object = null; |
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object = IOUtils.toInputStream(annotation, "UTF-8"); |
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sysmeta = createSystemMetadata(annotationPid, session.getSubject(), object); |
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ObjectFormatIdentifier formatId = new ObjectFormatIdentifier(); |
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formatId.setValue("http://www.w3.org/TR/rdf-syntax-grammar"); |
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sysmeta.setFormatId(formatId); |
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sysmeta.setSize(BigInteger.valueOf(annotation.getBytes("UTF-8").length)); |
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// get the stream fresh for inserting/updating |
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object = IOUtils.toInputStream(annotation, "UTF-8"); |
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if (!exists) { |
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MNodeService.getInstance(request).create(session, annotationPid, object, sysmeta); |
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} else { |
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Identifier newAnnotationPid = new Identifier(); |
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// use an old-style revision scheme for updating the annotation identifier |
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String value = annotationPid.getValue(); |
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int rev = DocumentUtil.getRevisionFromAccessionNumber(value); |
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String partialId = DocumentUtil.getSmartDocId(value); |
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rev++; |
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newAnnotationPid.setValue(partialId + "." + rev); |
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sysmeta.setIdentifier(newAnnotationPid); |
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sysmeta.setObsoletes(annotationPid); |
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MNodeService.getInstance(request).update(session, annotationPid, object, newAnnotationPid, sysmeta); |
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} |
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System.out.println("Generated annotation for pid: " + guid); |
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} catch (McdbDocNotFoundException nfe) { |
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// just skip it |
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continue; |
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} |
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} |
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//System.exit(0); |
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} |
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} |
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Also available in: Unified diff
Deleted a unnecessary test class.