Revision 9387
Added by Lauren Walker about 9 years ago
| src/edu/ucsb/nceas/metacat/dataone/D1NodeService.java | ||
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package edu.ucsb.nceas.metacat.dataone; |
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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.FileNotFoundException; |
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import java.io.InputStream; |
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import java.io.OutputStream; |
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import java.io.OutputStreamWriter; |
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import java.io.StringReader; |
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import java.io.UnsupportedEncodingException; |
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import java.io.Writer; |
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import java.math.BigInteger; |
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import java.nio.charset.Charset; |
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import java.sql.PreparedStatement; |
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import java.sql.ResultSet; |
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import java.sql.SQLException; |
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import java.util.Vector; |
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import java.util.concurrent.locks.Lock; |
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import javax.xml.transform.Result; |
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import javax.xml.transform.Source; |
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import javax.xml.transform.TransformerException; |
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import javax.xml.transform.TransformerFactory; |
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import javax.xml.transform.dom.DOMSource; |
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import javax.xml.transform.stream.StreamResult; |
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import javax.servlet.http.HttpServletRequest; |
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import org.apache.commons.io.IOUtils; |
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import org.dataone.service.types.v1.util.AuthUtils; |
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import org.dataone.service.types.v1.util.ChecksumUtil; |
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import org.dataone.service.util.Constants; |
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import org.w3c.dom.Document; |
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import edu.ucsb.nceas.metacat.AccessionNumber; |
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import edu.ucsb.nceas.metacat.AccessionNumberException; |
| ... | ... | |
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler; |
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import edu.ucsb.nceas.metacat.util.SkinUtil; |
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import edu.ucsb.nceas.utilities.PropertyNotFoundException; |
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import edu.ucsb.nceas.utilities.XMLUtilities; |
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public abstract class D1NodeService {
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public static final String DELETEDMESSAGE = "The object with the PID has been deleted from the node."; |
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private static String XPATH_EML_ID = "/eml:eml/@packageId"; |
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private static Logger logMetacat = Logger.getLogger(D1NodeService.class); |
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/** For logging the operations */ |
| ... | ... | |
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return objectList; |
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} |
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|
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/** |
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* Update a science metadata document with its new Identifier |
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* |
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* @param session - the Session object containing the credentials for the Subject |
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* @param object - the InputStream for the XML object to be edited |
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* @param pid - the Identifier of the XML object to be updated |
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* @param newPid = the new Identifier to give to the modified XML doc |
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* |
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* @return newObject - The InputStream for the modified XML object |
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* |
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* @throws ServiceFailure |
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* @throws IOException |
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* @throws UnsupportedEncodingException |
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* @throws InvalidToken |
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* @throws NotAuthorized |
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* @throws NotFound |
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* @throws NotImplemented |
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*/ |
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public InputStream editScienceMetadata(Session session, InputStream object, Identifier pid, Identifier newPid) |
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throws ServiceFailure, IOException, UnsupportedEncodingException, InvalidToken, NotAuthorized, NotFound, NotImplemented {
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logMetacat.debug("D1NodeService.editScienceMetadata() called.");
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InputStream newObject = null; |
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try{
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//Get the root node of the XML document |
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byte[] xmlBytes = IOUtils.toByteArray(object); |
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String xmlStr = new String(xmlBytes, "UTF-8"); |
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Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new StringReader(xmlStr)); |
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org.w3c.dom.Node docNode = doc.getDocumentElement(); |
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//Get the system metadata for this object |
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SystemMetadata sysMeta = null; |
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try{
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sysMeta = getSystemMetadata(session, pid); |
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} catch(NotAuthorized e){
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throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
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"This session is not authorized to access the system metadata for " + |
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pid.getValue() + " : " + e.getMessage()); |
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} catch(NotFound e){
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throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
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"Could not find the system metadata for " + |
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pid.getValue() + " : " + e.getMessage()); |
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} |
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//Get the formatId |
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ObjectFormatIdentifier objFormatId = sysMeta.getFormatId(); |
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String formatId = objFormatId.getValue(); |
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//For all EML formats |
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if(formatId.indexOf("eml") == 0){
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//Update or add the id attribute |
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XMLUtilities.addAttributeNodeToDOMTree(docNode, XPATH_EML_ID, newPid.getValue()); |
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} |
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//The modified object InputStream |
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ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); |
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Source xmlSource = new DOMSource(docNode); |
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Result outputTarget = new StreamResult(outputStream); |
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TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget); |
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newObject = new ByteArrayInputStream(outputStream.toByteArray()); |
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} catch(TransformerException e) {
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throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
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"Could not update the ID in the XML document for " + |
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"pid " + pid.getValue() +" : " + e.getMessage()); |
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} |
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return newObject; |
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} |
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/** |
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* Update a systemMetadata document |
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* |
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throw new InvalidRequest("4869", "Can't find the pid "+pid.getValue()+" for archive.");
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} |
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} |
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} else if((currentSysmeta.getArchived() != null && currentSysmeta.getArchived() == true) && (sysmeta.getArchived() == null || sysmeta.getArchived() == false)) {
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throw new InvalidRequest("4869", "The pid "+pid.getValue()+" has been archived and it can't be set archive false again.");
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} else {
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logMetacat.debug("D1Node.update - regularly update the system metadata of the pid "+pid.getValue());
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updateSystemMetadataWithoutLock(sysmeta, needUpdateModificationDate); |
| src/edu/ucsb/nceas/metacat/dataone/MNodeService.java | ||
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import java.io.InputStream; |
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import java.io.InputStreamReader; |
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import java.io.OutputStreamWriter; |
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import java.io.StringReader; |
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import java.io.UnsupportedEncodingException; |
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import java.io.Writer; |
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import java.math.BigInteger; |
| ... | ... | |
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import java.util.Vector; |
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|
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import javax.servlet.http.HttpServletRequest; |
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import javax.xml.transform.Result; |
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import javax.xml.transform.Source; |
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import javax.xml.transform.TransformerException; |
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import javax.xml.transform.TransformerFactory; |
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import javax.xml.transform.dom.DOMSource; |
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import javax.xml.transform.stream.StreamResult; |
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import org.apache.commons.io.IOUtils; |
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import org.apache.log4j.Logger; |
| ... | ... | |
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import org.ecoinformatics.datamanager.parser.Entity; |
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import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface; |
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import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser; |
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import org.w3c.dom.Document; |
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import edu.ucsb.nceas.ezid.EZIDException; |
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import edu.ucsb.nceas.metacat.DBQuery; |
| ... | ... | |
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public static final String UUID_SCHEME = "UUID"; |
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public static final String DOI_SCHEME = "DOI"; |
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private static final String UUID_PREFIX = "urn:uuid:"; |
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private static String XPATH_EML_ID = "/eml:eml/@packageId"; |
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/* the logger instance */ |
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private Logger logMetacat = null; |
| ... | ... | |
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try {
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//objectAsXML = IOUtils.toString(object, "UTF-8"); |
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//InputStream editedObject = editScienceMetadata(session, object, pid, newPid); |
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//localId = insertOrUpdateDocument(editedObject, "UTF-8", pid, session, "update"); |
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localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update"); |
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// register the newPid and the generated localId |
| ... | ... | |
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* @throws UnsupportedType |
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* @throws IdentifierNotUnique |
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*/ |
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public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata {
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public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken, |
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ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique, |
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UnsupportedType, InsufficientResources, InvalidSystemMetadata, IOException {
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String serviceFailureCode = "1030"; |
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Identifier sid = getPIDForSID(originalIdentifier, serviceFailureCode); |
| ... | ... | |
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// ensure it is publicly readable |
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sysmeta = makePublicIfNot(sysmeta, originalIdentifier); |
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// get the bytes |
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InputStream inputStream = this.get(session, originalIdentifier); |
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//Get the bytes |
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InputStream inputStream = null; |
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boolean isScienceMetadata = isScienceMetadata(sysmeta); |
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//If it's a science metadata doc, we want to update the packageId first |
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if(isScienceMetadata){
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InputStream originalObject = this.get(session, originalIdentifier); |
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//Edit the science metadata with the new package Id (EML) |
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inputStream = editScienceMetadata(session, originalObject, originalIdentifier, newIdentifier); |
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} |
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else{
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inputStream = this.get(session, originalIdentifier); |
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} |
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// update the object |
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this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta); |
| ... | ... | |
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} |
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|
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/** |
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* Update a science metadata document with its new Identifier |
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* |
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* @param session - the Session object containing the credentials for the Subject |
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* @param object - the InputStream for the XML object to be edited |
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* @param pid - the Identifier of the XML object to be updated |
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* @param newPid = the new Identifier to give to the modified XML doc |
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* |
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* @return newObject - The InputStream for the modified XML object |
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* |
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* @throws ServiceFailure |
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* @throws IOException |
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* @throws UnsupportedEncodingException |
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* @throws InvalidToken |
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* @throws NotAuthorized |
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* @throws NotFound |
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* @throws NotImplemented |
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*/ |
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public InputStream editScienceMetadata(Session session, InputStream object, Identifier pid, Identifier newPid) |
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throws ServiceFailure, IOException, UnsupportedEncodingException, InvalidToken, NotAuthorized, NotFound, NotImplemented {
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logMetacat.debug("D1NodeService.editScienceMetadata() called.");
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InputStream newObject = null; |
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try{
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//Get the root node of the XML document |
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byte[] xmlBytes = IOUtils.toByteArray(object); |
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String xmlStr = new String(xmlBytes, "UTF-8"); |
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Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new StringReader(xmlStr)); |
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org.w3c.dom.Node docNode = doc.getDocumentElement(); |
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//Get the system metadata for this object |
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SystemMetadata sysMeta = null; |
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try{
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sysMeta = getSystemMetadata(session, pid); |
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} catch(NotAuthorized e){
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throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
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"This session is not authorized to access the system metadata for " + |
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pid.getValue() + " : " + e.getMessage()); |
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} catch(NotFound e){
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throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
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"Could not find the system metadata for " + |
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pid.getValue() + " : " + e.getMessage()); |
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} |
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|
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//Get the formatId |
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ObjectFormatIdentifier objFormatId = sysMeta.getFormatId(); |
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String formatId = objFormatId.getValue(); |
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//For all EML formats |
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if(formatId.indexOf("eml") == 0){
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//Update or add the id attribute |
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XMLUtilities.addAttributeNodeToDOMTree(docNode, XPATH_EML_ID, newPid.getValue()); |
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} |
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//The modified object InputStream |
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ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); |
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Source xmlSource = new DOMSource(docNode); |
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Result outputTarget = new StreamResult(outputStream); |
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TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget); |
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newObject = new ByteArrayInputStream(outputStream.toByteArray()); |
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} catch(TransformerException e) {
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throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
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"Could not update the ID in the XML document for " + |
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"pid " + pid.getValue() +" : " + e.getMessage()); |
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} catch(IOException e){
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throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
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"Could not update the ID in the XML document for " + |
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"pid " + pid.getValue() +" : " + e.getMessage()); |
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} |
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return newObject; |
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} |
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/** |
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* Determines if we already have registered an ORE map for this package |
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* NOTE: uses a solr query to locate OREs for the object |
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* @param guid of the EML/packaging object |
Also available in: Unified diff
Move the editScienceMetadata method to the MNodeService class - only update packageId in EML on publish()