Metacat

import java.util.HashMap;

import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;

import org.ecoinformatics.datamanager.parser.DataPackage;

import org.ecoinformatics.datamanager.parser.Entity;

import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;

import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;

import edu.ucsb.nceas.metacat.DocumentImpl;

import edu.ucsb.nceas.metacat.McdbException;

			//Create a map of dataone ids and file names

			Map<Identifier, String> fileNames = new HashMap<Identifier, String>();

				//Get the resource map as a map of Identifiers

				//Loop through each object in this resource map

					//Loop through each metadata object in this entry

					Set<Identifier> metadataIdentifiers = entries.keySet();

					for(Identifier metadataID: metadataIdentifiers){

						try{

							//Get the system metadata for this metadata object

							SystemMetadata metadataSysMeta = this.getSystemMetadata(session, metadataID);

							//If this is in eml format, extract the filename and GUID from each entity in its package

							if (metadataSysMeta.getFormatId().getValue().startsWith("eml://")) {

								//Get the package

								DataPackageParserInterface parser = new Eml200DataPackageParser();

								InputStream emlStream = this.get(session, metadataID);

								parser.parse(emlStream);

								DataPackage dataPackage = parser.getDataPackage();

								//Get all the entities in this package and loop through each to extract its ID and file name

								Entity[] entities = dataPackage.getEntityList();

								for(Entity entity: entities){

									try{

										//Get the file name from the metadata

										String fileNameFromMetadata = entity.getName();

										//Get the ecogrid URL from the metadata

										String ecogridIdentifier = entity.getEntityIdentifier();

										//Parse the ecogrid URL to get the local id

										String idFromMetadata = DocumentUtil.getAccessionNumberFromEcogridIdentifier(ecogridIdentifier);

										//Get the docid and rev pair

										String docid = DocumentUtil.getDocIdFromString(idFromMetadata);

										String rev = DocumentUtil.getRevisionStringFromString(idFromMetadata);

										//Get the GUID

										String guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(rev));

										Identifier dataIdentifier = new Identifier();

										dataIdentifier.setValue(guid);

										//Add the GUID to our GUID & file name map

										fileNames.put(dataIdentifier, fileNameFromMetadata);

									}

									catch(Exception e){

										//Prevent just one entity error

										e.printStackTrace();

										logMetacat.debug(e.getMessage(), e);

									}

								}

							}

						}

						catch(Exception e){

							//Catch errors that would prevent package download

							logMetacat.debug(e.toString());

						}

					}

			//Create a temp file, then delete it and make a directory with that name

			File tempDir = File.createTempFile("temp", Long.toString(System.nanoTime()));

			tempDir.delete();

			tempDir = new File(tempDir.getPath() + "_dir");

			tempDir.mkdir();			

				SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);					

				String fileName = null;

				//TODO: Be more specific of what characters to replace. Make sure periods arent replaced for the filename from metadata

				//Our default file name is just the ID + format type (e.g. walker.1.1-DATA)

				fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + objectFormatType;

				if(fileNames.containsKey(entryPid)){

					//Let's use the file name and extension from the metadata is we have it

					fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + fileNames.get(entryPid).replaceAll("[^a-zA-Z0-9\\-\\.]", "_");

				}

				else{

					//If we couldn't find a given file name, use the system metadata extension

					String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());

					fileName += extension;

				}

				File tempFile = new File(tempDir, fileName);

			//Use the pid as the file name prefix, replacing all non-word characters

			String zipName = pid.getValue().replaceAll("\\W", "_");