Metacat

/**

 *  '$RCSfile$'

 *    Purpose: A Class for upgrading the database to version 1.5

 *  Copyright: 2000 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    Authors: Saurabh Garg

 *

 *   '$Author$'

 *     '$Date$'

 * '$Revision$'

 *

 * This program is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 2 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU General Public License for more details.

 *

 * You should have received a copy of the GNU General Public License

 * along with this program; if not, write to the Free Software

 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat.dataone;

import java.io.IOException;

import java.io.InputStream;

import java.math.BigInteger;

import java.sql.SQLException;

import java.util.Map;

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.xpath.XPathExpressionException;

import org.apache.commons.io.IOUtils;

import org.dataone.service.exceptions.InvalidSystemMetadata;

import org.dataone.service.exceptions.InvalidToken;

import org.dataone.service.exceptions.NotAuthorized;

import org.dataone.service.exceptions.ServiceFailure;

import org.dataone.service.types.v1.Identifier;

import org.dataone.service.types.v1.NodeReference;

import org.dataone.service.types.v1.ObjectFormatIdentifier;

import org.dataone.service.types.v1.SystemMetadata;

import org.dataone.service.types.v1.util.ChecksumUtil;

import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface;

import org.ecoinformatics.datamanager.parser.DataPackage;

import org.jibx.runtime.JiBXException;

import org.xml.sax.SAXException;

import edu.ucsb.nceas.metacat.AccessionNumber;

import edu.ucsb.nceas.metacat.AccessionNumberException;

import edu.ucsb.nceas.metacat.McdbDocNotFoundException;

import edu.ucsb.nceas.metacat.McdbException;

import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;

import edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory;

import edu.ucsb.nceas.metacat.properties.PropertyService;

import edu.ucsb.nceas.utilities.ParseLSIDException;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

public class SystemMetadataFactory {

	 *

	 * @param localId

	 *            The local document identifier

	 * @param user

	 *            The user submitting the system metadata document

	 * @param groups

	 *            The groups the user belongs to

	 *

	 * @return sysMeta The system metadata object created

	 * @throws HandlerException

	 * @throws AccessControlException

			IOException, AccessionNumberException, ClassNotFoundException,

			InsufficientKarmaException, ParseLSIDException,

			PropertyNotFoundException, BaseException, NoSuchAlgorithmException,

		logMetacat.debug("provided localId: " + localId);

		SystemMetadata sysMeta = new SystemMetadata();

		sysMeta.setSerialVersion(BigInteger.valueOf(1));

		InputStream inputStream;

		try {

			inputStream = MetacatHandler.read(localId);

		} catch (ParseLSIDException ple) {

			logMetacat.debug("There was a problem parsing the LSID from "

					+ localId + ". The error message was: " + ple.getMessage());

			throw ple;

			logMetacat.debug("There was a problem finding a property. "

					+ "The error message was: " + pnfe.getMessage());

			throw pnfe;

		} catch (McdbException me) {

			logMetacat.debug("There was a Metacat problem. "

					+ "The error message was: " + me.getMessage());

			throw me;

		} catch (SQLException sqle) {

			logMetacat.debug("There was a SQL problem. "

					+ "The error message was: " + sqle.getMessage());

			throw sqle;

		} catch (ClassNotFoundException cnfe) {

			logMetacat.debug("There was a problem finding a class. "

					+ "The error message was: " + cnfe.getMessage());

			throw cnfe;

		} catch (IOException ioe) {

			logMetacat.debug("There was an I/O exception. "

					+ "The error message was: " + ioe.getMessage());

			throw ioe;

		// get/make the guid

		String guid = null;

		try {

			// get the guid if it exists

			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);

		} catch (McdbDocNotFoundException dnfe) {

			// otherwise create the mapping

			logMetacat.debug("There was a problem getting the guid from "

							+ "the given localId (docid and revision). The error message was: "

							+ dnfe.getMessage());

			logMetacat.debug("No guid in the identifier table.  adding it for " + localId);

			IdentifierManager.getInstance().createMapping(localId, localId);

			logMetacat.debug("Mapping created for " + localId);

			logMetacat.debug("accessionNumber: " + accNum);

			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);

		}

		Identifier identifier = new Identifier();

		identifier.setValue(guid);

		sysMeta.setIdentifier(identifier);

		// set the object format, fall back to defaults

		try {

			try {

				// format is not registered, use default

				if (doctype.trim().equals("BIN")) {

					fmtid = ObjectFormatCache.getInstance().getFormat(

							"application/octet-stream").getFormatId();

				} else {

					fmtid = ObjectFormatCache.getInstance().getFormat(

							"text/plain").getFormatId();

				}

			} catch (NotFound nf) {

								+ nf.getMessage());

				throw nf;

			}

		}

		sysMeta.setFormatId(fmtid);

		inputStream = MetacatHandler.read(localId);

		String algorithm = "MD5";

		Checksum checksum = ChecksumUtil.checksum(inputStream, algorithm);

		sysMeta.setChecksum(checksum);

		// set the size

		inputStream = MetacatHandler.read(localId);

		String sizeStr = new Long(sizeOfStream(inputStream)).toString();

		sysMeta.setSize(new BigInteger(sizeStr));

		// submitter

		Subject submitter = new Subject();

		submitter.setValue(docInfo.get("user_updated"));

		sysMeta.setSubmitter(submitter);

		// rights holder

		Subject owner = new Subject();

		owner.setValue(docInfo.get("user_owner"));

		sysMeta.setRightsHolder(owner);

		// dates

		String createdDateString = docInfo.get("date_created");

		String updatedDateString = docInfo.get("date_updated");

		Date createdDate = DateTimeMarshaller.deserializeDateToUTC(createdDateString);

		Date updatedDate = DateTimeMarshaller.deserializeDateToUTC(updatedDateString);

		sysMeta.setDateUploaded(createdDate);

		sysMeta.setDateSysMetadataModified(updatedDate);

		// set the revision history

		String docidWithoutRev = accNum.getDocid();

		Identifier obsoletedBy = null;

		Identifier obsoletes = null;

		Vector<Integer> revisions = DBUtil.getRevListFromRevisionTable(docidWithoutRev);

		Collections.sort(revisions);

			// use the docid+rev as the guid

			String existingPid = docidWithoutRev + "." + existingRev;

			if (existingRev < rev) {

				// it's the old docid, until it's not

				obsoletes = new Identifier();

				obsoletes.setValue(existingPid);

			}

			if (existingRev > rev) {

				// it's the newer docid

				obsoletedBy = new Identifier();

				obsoletedBy.setValue(existingPid);

				// only want the version just after it

				break;

			}

		}

		sysMeta.setObsoletes(obsoletes);

		if (obsoletedBy != null) {

			SystemMetadata obsoletedBySysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletedBy.getValue());

				obsoletedBySysMeta.setObsoletes(identifier);

				HazelcastService.getInstance().getSystemMetadataMap().put(obsoletedBy, obsoletedBySysMeta);

			}

		}

		if (obsoletes != null) {

			SystemMetadata obsoletesSysMeta = IdentifierManager.getInstance().getSystemMetadata(obsoletes.getValue());

				obsoletesSysMeta.setObsoletedBy(identifier);

				HazelcastService.getInstance().getSystemMetadataMap().put(obsoletes, obsoletesSysMeta);

		}

		AccessPolicy accessPolicy = IdentifierManager.getInstance().getAccessPolicy(guid);

		// authoritative node

		NodeReference nr = new NodeReference();

		nr.setValue(PropertyService.getProperty("dataone.memberNodeId"));

		sysMeta.setOriginMemberNode(nr);

		sysMeta.setAuthoritativeMemberNode(nr);

		// describes and describedBy information

		if (fmtid == ObjectFormatCache.getInstance().getFormat(

				"eml://ecoinformatics.org/eml-2.0.0").getFormatId()

				|| fmtid == ObjectFormatCache.getInstance().getFormat(

						"eml://ecoinformatics.org/eml-2.0.1").getFormatId()

				|| fmtid == ObjectFormatCache.getInstance().getFormat(

						"eml://ecoinformatics.org/eml-2.1.0").getFormatId()

				|| fmtid == ObjectFormatCache.getInstance().getFormat(

						"eml://ecoinformatics.org/eml-2.1.1").getFormatId()) {

			try {

					MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();

				DataManager dataManager =

					DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());

				DataPackage dataPackage = dataManager.parseMetadata(inputStream);

								+ dataPackage.getEntityNumber());

	            Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>();

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

					for (int j = 0; j < dataPackage.getEntityList().length; j++) {

						String dataDocUrl = dataPackage.getEntityList()[j].getURL();

						String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();

						// default to binary

						if (dataDocMimeType == null) {

							dataDocMimeType = ObjectFormatCache.getInstance()

									.getFormat("application/octet-stream")

									.getFormatId().getValue();

						// process the data

						Identifier dataGuid = new Identifier();

						// handle ecogrid, or downloadable data

						String ecogridPrefix = "ecogrid://knb/";

						if (dataDocUrl.trim().startsWith(ecogridPrefix)) {

							dataDocLocalId = dataDocUrl.substring(dataDocUrl.indexOf(ecogridPrefix) + ecogridPrefix.length());

						} else {

							// should we try downloading the remote data?

							if (downloadData) {

								InputStream dataObject = null;

								try {

									// download the data from the URL

									URL dataURL = new URL(dataDocUrl);

									// default is to download the data

									dataObject = dataConnection.getInputStream();

									String detectedContentType = dataConnection.getContentType();

									logMetacat.info("Detected content type: " + detectedContentType);

									if (detectedContentType != null) {

										// seems to be HTML from the remote location

										if (detectedContentType.contains("html")) {

											// if we are not expecting it, we skip it

											if (!dataDocMimeType.contains("html")) {

												// set to null so we don't download it

												dataObject = null;

												logMetacat.warn("Skipping remote resource, unexpected HTML content type at: " + dataDocUrl);

											}

										}

										// TODO: any other special processing (csv, images, etc)?

									} else {

										// if we don't know what it is, should we skip it?

										dataObject = null;

										logMetacat.warn("Skipping remote resource, unknown content type at: " + dataDocUrl);

									}

									// error with the download

									logMetacat.warn("Error downloading remote data. " + e.getMessage());

								}

								if (dataObject != null) {

									// create the local version of it

									dataDocLocalId = DocumentUtil.generateDocumentId(1);

									IdentifierManager.getInstance().createMapping(dataDocLocalId, dataDocLocalId);

									dataGuid.setValue(dataDocLocalId);

									// save it locally

									Session session = new Session();

									session.setSubject(submitter);

									MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);

									MNodeService.getInstance(request).insertDataObject(dataObject, dataGuid, session);

									remoteData = true;

							}

						}

						logMetacat.debug("Data URL     : " + dataDocUrl);

						logMetacat.debug("Data mime    : " + dataDocMimeType);

						// now we have a local id for the data

						if (dataDocLocalId != null) {

							String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);

							int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);

							// check if data system metadata exists already

							SystemMetadata dataSysMeta = null;

							String dataGuidString = null;

								} catch (Exception e) {

									// probably not in the system

									dataSysMeta = null;

							} catch (McdbDocNotFoundException nf) {

								// we didn't find it

								dataSysMeta = null;

							}

							if (dataSysMeta == null) {

								// System metadata for data doesn't exist yet, so create it

								logMetacat.debug("There was not an existing system metadata document for " + dataDocLocalId);

								try {

									logMetacat.debug("Creating a system metadata " + "document for " + dataDocLocalId);

									// now look it up again

									dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);

									// set the guid

									dataGuid.setValue(dataGuidString);

									// set object format

									logMetacat.debug("Updating system metadata for "

													+ dataGuid.getValue() + " to "

													+ dataDocMimeType);

									try {

										ObjectFormatIdentifier fmt =

											ObjectFormatCache.getInstance().getFormat(dataDocMimeType).getFormatId();

										dataSysMeta.setFormatId(fmt);

									} catch (NotFound nfe) {

										logMetacat.debug("Couldn't find format identifier for: "

														+ dataDocMimeType

														+ ". Setting it to application/octet-stream.");

										ObjectFormatIdentifier newFmtid = new ObjectFormatIdentifier();

										newFmtid.setValue("application/octet-stream");

									}

									// inherit access rules from metadata, if we don't have our own

									if (remoteData) {

										dataSysMeta.setAccessPolicy(sysMeta.getAccessPolicy());

										// TODO: use access rules defined in EML, per data file

									}

									HazelcastService.getInstance().getSystemMetadataMap().put(dataSysMeta.getIdentifier(), dataSysMeta);

								} catch (McdbDocNotFoundException mdnf) {

									mdnf.printStackTrace();

									throw mdnf;

								} catch (NumberFormatException nfe) {

									nfe.printStackTrace();

									throw nfe;

								} catch (AccessionNumberException ane) {

									ane.printStackTrace();

									throw ane;

								} catch (SQLException sqle) {

									sqle.printStackTrace();

									throw sqle;

								} catch (NoSuchAlgorithmException nsae) {

									nsae.printStackTrace();

									throw nsae;

								} catch (IOException ioe) {

									ioe.printStackTrace();

									throw ioe;

								} catch (PropertyNotFoundException pnfe) {

									pnfe.printStackTrace();

									throw pnfe;

								} catch (BaseException be) {

									be.printStackTrace();

									throw be;

								}

							}

							dataIds.add(dataGuid);

						} // end if (EML package)

					} // end for (data entities)

	            } // data entities not null

			        	if (!oreExistsFor(sysMeta.getIdentifier())) {

				            // generate the ORE map for this datapackage

				            Identifier resourceMapId = new Identifier();

				            // want to be able to run this over and over again for now

				            resourceMapId.setValue(resourceMapPrefix + sysMeta.getIdentifier().getValue());

				            idMap.put(sysMeta.getIdentifier(), dataIds);

				            ResourceMap rm = ResourceMapFactory.getInstance().createResourceMap(resourceMapId, idMap);

				            String resourceMapXML = ResourceMapFactory.getInstance().serializeResourceMap(rm);

				            // copy most of the same system metadata as the packaging metadata

				            SystemMetadata resourceMapSysMeta = new SystemMetadata();

				            BeanUtils.copyProperties(resourceMapSysMeta, sysMeta);

				            resourceMapSysMeta.setIdentifier(resourceMapId);

				            Checksum oreChecksum = ChecksumUtil.checksum(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), "MD5");

							resourceMapSysMeta.setChecksum(oreChecksum);

				            ObjectFormatIdentifier formatId = ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId();

							resourceMapSysMeta.setFormatId(formatId);

							resourceMapSysMeta.setSize(BigInteger.valueOf(sizeOfStream(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING))));

							// set the revision graph

							resourceMapSysMeta.setObsoletes(null);

							resourceMapSysMeta.setObsoletedBy(null);

							// look up the resource map that this one obsoletes

							if (sysMeta.getObsoletes() != null) {

								Identifier resourceMapObsoletes = new Identifier();

								resourceMapObsoletes.setValue(resourceMapPrefix + sysMeta.getObsoletes().getValue());

								resourceMapSysMeta.setObsoletes(resourceMapObsoletes);

								SystemMetadata resourceMapObsoletesSystemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(resourceMapObsoletes);

								if (resourceMapObsoletesSystemMetadata != null) {

									resourceMapObsoletesSystemMetadata.setObsoletedBy(resourceMapId);

									HazelcastService.getInstance().getSystemMetadataMap().put(resourceMapObsoletes, resourceMapObsoletesSystemMetadata);

								}

							}

							// look up the resource map that this one is obsoletedBy

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

								Identifier resourceMapObsoletedBy = new Identifier();

								resourceMapObsoletedBy.setValue(resourceMapPrefix + sysMeta.getObsoletedBy().getValue());

								resourceMapSysMeta.setObsoletedBy(resourceMapObsoletedBy);

								SystemMetadata resourceMapObsoletedBySystemMetadata = HazelcastService.getInstance().getSystemMetadataMap().get(resourceMapObsoletedBy);

								if (resourceMapObsoletedBySystemMetadata != null) {

									resourceMapObsoletedBySystemMetadata.setObsoletes(resourceMapId);

									HazelcastService.getInstance().getSystemMetadataMap().put(resourceMapObsoletedBy, resourceMapObsoletedBySystemMetadata);

								}

							}

							if (!IdentifierManager.getInstance().identifierExists(resourceMapId.getValue())) {

								Session session = new Session();

								session.setSubject(submitter);

								MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);

								MNodeService.getInstance(request).insertDataObject(IOUtils.toInputStream(resourceMapXML, MetaCatServlet.DEFAULT_ENCODING), resourceMapId, session);

								MNodeService.getInstance(request).insertSystemMetadata(resourceMapSysMeta);

								logMetacat.info("Inserted ORE package: " + resourceMapId.getValue());

							}

				}

			} catch (ParserConfigurationException pce) {

			} catch (SAXException saxe) {

			} catch (XPathExpressionException xpee) {

			} catch (Exception e) {

		} // end if()

		return sysMeta;

	}

	/**

     * not already have it.  SystemMetadata documents themselves, are, of course,

     * exempt.  This is a utility method for migration of existing object

     * stores to DataONE where SystemMetadata is required for all objects.

     * @param idList

     * @param includeOre

     * @param downloadData

     * @throws ServiceFailure

     * @throws McdbDocNotFoundException

     * @throws PropertyNotFoundException

     * @throws InvalidToken

     * @throws NotAuthorized

     * @throws NotFound

     * @throws NotImplemented

     * @throws InvalidRequest

     * @throws NoSuchAlgorithmException

     * @throws AccessionNumberException

     * @throws SQLException

     */

    public static void generateSystemMetadata(List<String> idList, boolean includeOre, boolean downloadData)

    throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,

    NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException

    {

        for (String localId : idList) {

            //for each id, add a system metadata doc

        	try {

        		logMetacat.debug("generating system metadata for " + localId);

        		generateSystemMetadata(localId, includeOre, downloadData);

        	} catch (Exception e) {

        		logMetacat.error("Error generating system metadata for: " + localId, e);

			}

        }

        logMetacat.info("done generating system metadata");

    }

    /**

     * Generate SystemMetadata for a particular object with identifier localId.

     * This is a utility method for migration of existing objects

     * to DataONE where SystemMetadata is required for all objects.

     * @param localId

     * @param includeOre

     * @param downloadData

     * @throws ServiceFailure

     * @throws McdbDocNotFoundException

     * @throws PropertyNotFoundException

     * @throws InvalidToken

     * @throws NotAuthorized

     * @throws NotFound

     * @throws NotImplemented

     * @throws InvalidRequest

     * @throws NoSuchAlgorithmException

     * @throws AccessionNumberException

     * @throws SQLException

     * @throws InvalidSystemMetadata

     */

    protected static void generateSystemMetadata(String localId, boolean includeOre, boolean downloadData)

    throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized,

    NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException, InvalidSystemMetadata

    {

    	logMetacat.debug("generateSystemMetadata() called.");

    	logMetacat.debug("Creating SystemMetadata for localId " + localId);

        SystemMetadata sm = null;

        //generate required system metadata fields from the document

        try {

        	sm = SystemMetadataFactory.createSystemMetadata(localId, includeOre, downloadData);

        } catch (Exception e1) {

        	e1.printStackTrace();

        	ServiceFailure sf = new ServiceFailure("00","Exception in generateSystemMetadata: " +

        			e1.getMessage());

        	sf.setStackTrace(e1.getStackTrace());

        	throw sf;

        }

        //insert the systemmetadata object or just update it as needed

        boolean exists = IdentifierManager.getInstance().systemMetadataExists(sm.getIdentifier().getValue());

        if (!exists) {

        	IdentifierManager.getInstance().createSystemMetadata(sm);

        	logMetacat.info("Generated SystemMetadata for " + localId);

        } else {

        	IdentifierManager.getInstance().updateSystemMetadata(sm);