Metacat

import java.math.BigInteger;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Vector;

import org.apache.commons.io.IOUtils;

import org.dataone.service.exceptions.NotFound;

import edu.ucsb.nceas.metacat.DBUtil;

import edu.ucsb.nceas.metacat.DocumentImpl;

import edu.ucsb.nceas.metacat.IdentifierManager;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.replication.ReplicationService;

import edu.ucsb.nceas.metacat.util.DocumentUtil;

		suite.addTest(new DatapackageSummarizerTest("testGenerateAnnotations"));

//		suite.addTest(new DatapackageSummarizerTest("testGenerateAnnotation"));

	public void testGenerateAnnotations() throws Exception {

		// summarize the packages

		DatapackageSummarizer ds = new DatapackageSummarizer();

		List<Identifier> identifiers = new ArrayList<Identifier>();

		Map<Integer, String> serverCodes = ReplicationService.getServerCodes();

		// select the metadata ids we want to summarize

		boolean includeReplicas = false;

		Iterator<Integer> codeIter = Arrays.asList(new Integer[] {1}).iterator();

		if (includeReplicas ) {

			codeIter = serverCodes.keySet().iterator();

		}

		Vector<String> idList = new Vector<String>();

		while (codeIter.hasNext()) {

			int serverLocation = codeIter.next();

			Vector<String> idList0 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_0NAMESPACE, false, serverLocation);

			idList.addAll(idList0);

			Vector<String> idList1 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_0_1NAMESPACE, false, serverLocation);

			idList.addAll(idList1);

			Vector<String> idList2 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_0NAMESPACE, false, serverLocation);

			idList.addAll(idList2);

			Vector<String> idList3 = DBUtil.getAllDocidsByType(DocumentImpl.EML2_1_1NAMESPACE, false, serverLocation);

			idList.addAll(idList3);

		}

		// go through all the identifiers now

		for (String localId : idList) {

			try {

				String guid = IdentifierManager.getInstance().getGUID(

						DocumentUtil.getDocIdFromAccessionNumber(localId), 

						DocumentUtil.getRevisionFromAccessionNumber(localId));

				Identifier pid = new Identifier();

				pid.setValue(guid);

				identifiers.add(pid);

				String annotation = ds.generateAnnotation(pid);

				Identifier annotationPid = new Identifier();

				annotationPid.setValue("http://annotation/" + guid);

				Session session = getTestSession();

				SystemMetadata sysmeta = null;

				// look for the latest version of the annotation, if there is one

				do {

					try {

						sysmeta = MNodeService.getInstance(request).getSystemMetadata(annotationPid);

						if (sysmeta.getObsoletedBy() != null) {

							annotationPid.setValue(sysmeta.getObsoletedBy().getValue());

						}

					} catch (NotFound nf) {

						break;

					}

				} while (sysmeta != null && sysmeta.getObsoletedBy() != null);

				boolean exists = (sysmeta != null);

				InputStream object = null;

				object = IOUtils.toInputStream(annotation, "UTF-8");

				sysmeta = createSystemMetadata(annotationPid, session.getSubject(), object);

				ObjectFormatIdentifier formatId = new ObjectFormatIdentifier();

				formatId.setValue("http://www.w3.org/TR/rdf-syntax-grammar");

				sysmeta.setFormatId(formatId);

				sysmeta.setSize(BigInteger.valueOf(annotation.getBytes("UTF-8").length));

				// get the stream fresh for inserting/updating

				object = IOUtils.toInputStream(annotation, "UTF-8");

				if (!exists) {

					MNodeService.getInstance(request).create(session, annotationPid, object, sysmeta);

				} else {

					Identifier newAnnotationPid = new Identifier();

					// use an old-style revision scheme for updating the annotation identifier

					String value = annotationPid.getValue();

					int rev = DocumentUtil.getRevisionFromAccessionNumber(value);

					String partialId = DocumentUtil.getSmartDocId(value);

					rev++;

					newAnnotationPid.setValue(partialId + "." + rev);

					sysmeta.setIdentifier(newAnnotationPid);

					sysmeta.setObsoletes(annotationPid);

					MNodeService.getInstance(request).update(session, annotationPid, object, newAnnotationPid, sysmeta);

				}

				System.out.println("Generated annotation for pid: " + guid);

			} catch (McdbDocNotFoundException nfe) {

				// just skip it

				continue;

			}

		}

		//System.exit(0);

	}