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Revision 6130

organize imports so that it is clearer what dependencies exist on the D1 jars

View differences:

test/edu/ucsb/nceas/metacat/dataone/MetadataTypeRegisterTest.java
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package edu.ucsb.nceas.metacat.dataone;
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import edu.ucsb.nceas.MCTestCase;
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import junit.framework.Test;
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import junit.framework.TestSuite;
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import org.dataone.client.ObjectFormatCache;
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import org.dataone.service.exceptions.NotFound;
33
import org.dataone.service.types.*;
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import org.dataone.service.types.ObjectFormat;
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import edu.ucsb.nceas.MCTestCase;
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/**
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 * A JUnit test for testing the dataone MetadataTypeRegister class
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 */
test/edu/ucsb/nceas/metacat/dataone/CNCoreTest.java
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import org.dataone.service.types.ChecksumAlgorithm;
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import org.dataone.service.types.Identifier;
37 37
import org.dataone.service.types.NodeReference;
38
import org.dataone.service.types.ObjectFormat;
39 38
import org.dataone.service.types.Session;
40 39
import org.dataone.service.types.Subject;
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import org.dataone.service.types.SystemMetadata;
src/edu/ucsb/nceas/metacat/restservice/ResourceHandler.java
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 */
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package edu.ucsb.nceas.metacat.restservice;
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import java.io.*;
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import java.io.ByteArrayInputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.io.PrintWriter;
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import java.io.StringReader;
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import java.net.URL;
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import java.util.*;
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.Enumeration;
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import java.util.Hashtable;
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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.TimeZone;
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import java.util.Timer;
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29
import javax.mail.BodyPart;
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import javax.mail.MessagingException;
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import javax.mail.internet.MimeMultipart;
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import javax.servlet.ServletContext;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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36
import java.security.NoSuchAlgorithmException;
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import java.sql.SQLException;
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.ParsePosition;
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import java.text.SimpleDateFormat;
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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.apache.maven.artifact.ant.shaded.IOUtil;
......
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.exceptions.UnsupportedType;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.types.*;
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import org.dataone.service.types.AuthToken;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.DescribeResponse;
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import org.dataone.service.types.Event;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.Log;
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import org.dataone.service.types.Node;
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import org.dataone.service.types.NodeList;
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import org.dataone.service.types.NodeReference;
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import org.dataone.service.types.NodeType;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.ObjectList;
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import org.dataone.service.types.Service;
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import org.dataone.service.types.ServiceMethod;
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import org.dataone.service.types.Services;
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import org.dataone.service.types.Session;
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import org.dataone.service.types.SystemMetadata;
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import org.dataone.service.types.util.ServiceTypeUtil;
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import org.jibx.runtime.BindingDirectory;
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import org.jibx.runtime.IBindingFactory;
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import org.jibx.runtime.IMarshallingContext;
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import org.jibx.runtime.IUnmarshallingContext;
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import org.jibx.runtime.JiBXException;
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import edu.ucsb.nceas.metacat.AccessionNumberException;
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import edu.ucsb.nceas.metacat.DBUtil;
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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.MetaCatServlet;
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import edu.ucsb.nceas.metacat.MetacatHandler;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.dataone.CNCoreImpl;
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import edu.ucsb.nceas.metacat.dataone.CrudService;
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import edu.ucsb.nceas.metacat.dataone.HealthService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.util.RequestUtil;
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import edu.ucsb.nceas.metacat.util.SessionData;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.metacat.util.SessionData;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import org.dataone.service.streaming.util.StreamUtil;
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import com.gc.iotools.stream.is.InputStreamFromOutputStream;
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import com.oreilly.servlet.multipart.FilePart;
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import com.oreilly.servlet.multipart.MultipartParser;
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import com.oreilly.servlet.multipart.ParamPart;
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import com.oreilly.servlet.multipart.Part;
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/**
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 * 
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 * Implements Earthgrid REST API to Metacat <br/><br/> 
src/edu/ucsb/nceas/metacat/MetacatHandler.java
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package edu.ucsb.nceas.metacat;
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import au.com.bytecode.opencsv.CSVWriter;
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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.IdentifierManager;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlInterface;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;
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import edu.ucsb.nceas.metacat.cart.CartManager;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.dataquery.DataQuery;
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import edu.ucsb.nceas.metacat.event.MetacatDocumentEvent;
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import edu.ucsb.nceas.metacat.event.MetacatEventService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.service.XMLSchemaService;
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import edu.ucsb.nceas.metacat.shared.HandlerException;
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;
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import edu.ucsb.nceas.metacat.spatial.SpatialQuery;
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import edu.ucsb.nceas.metacat.util.AuthUtil;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.metacat.util.MetacatUtil;
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import edu.ucsb.nceas.metacat.util.RequestUtil;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.utilities.FileUtil;
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import edu.ucsb.nceas.utilities.LSIDUtil;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import java.io.BufferedInputStream;
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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.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
......
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import java.io.PrintWriter;
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import java.io.Reader;
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import java.io.StringReader;
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import java.io.ByteArrayOutputStream;
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import java.io.UnsupportedEncodingException;
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import java.io.Writer;
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import java.net.MalformedURLException;
......
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import java.util.Hashtable;
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import java.util.Iterator;
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import java.util.Map;
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import java.util.TimeZone;
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import java.util.Timer;
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import java.util.TimerTask;
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import java.util.TimeZone;
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import java.util.Vector;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipOutputStream;
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import javax.activation.MimetypesFileTypeMap;
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import javax.servlet.ServletOutputStream;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import javax.servlet.http.HttpSession;
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import javax.activation.MimetypesFileTypeMap;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPathExpressionException;
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import org.apache.commons.io.input.XmlStreamReader;
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import org.apache.log4j.Logger;
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import org.ecoinformatics.eml.EMLParser;
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import org.dataone.client.ObjectFormatCache;
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import org.dataone.eml.DataoneEMLParser;
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import org.dataone.eml.EMLDocument;
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import org.dataone.eml.EMLDocument.DistributionMetadata;
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import org.dataone.service.exceptions.BaseException;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.ChecksumAlgorithm;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.NodeReference;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.Subject;
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import org.dataone.service.types.SystemMetadata;
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import org.dataone.service.types.util.ServiceTypeUtil;
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import org.jibx.runtime.BindingDirectory;
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import org.jibx.runtime.IBindingFactory;
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import org.jibx.runtime.IMarshallingContext;
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import org.ecoinformatics.eml.EMLParser;
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import org.jibx.runtime.JiBXException;
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import org.xml.sax.SAXException;
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import au.com.bytecode.opencsv.CSVWriter;
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import com.oreilly.servlet.multipart.FilePart;
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import com.oreilly.servlet.multipart.MultipartParser;
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import com.oreilly.servlet.multipart.ParamPart;
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import com.oreilly.servlet.multipart.Part;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.ChecksumAlgorithm;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.Subject;
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import org.dataone.service.types.SystemMetadata;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlException;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlInterface;
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import edu.ucsb.nceas.metacat.accesscontrol.AccessControlList;
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import edu.ucsb.nceas.metacat.cart.CartManager;
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import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
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import edu.ucsb.nceas.metacat.database.DBConnection;
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import edu.ucsb.nceas.metacat.database.DBConnectionPool;
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import edu.ucsb.nceas.metacat.dataquery.DataQuery;
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import edu.ucsb.nceas.metacat.event.MetacatDocumentEvent;
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import edu.ucsb.nceas.metacat.event.MetacatEventService;
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import edu.ucsb.nceas.metacat.properties.PropertyService;
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import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
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import edu.ucsb.nceas.metacat.service.SessionService;
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import edu.ucsb.nceas.metacat.service.XMLSchemaService;
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import edu.ucsb.nceas.metacat.shared.HandlerException;
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import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
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import edu.ucsb.nceas.metacat.shared.ServiceException;
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import edu.ucsb.nceas.metacat.spatial.SpatialHarvester;
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import edu.ucsb.nceas.metacat.spatial.SpatialQuery;
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import edu.ucsb.nceas.metacat.util.AuthUtil;
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import edu.ucsb.nceas.metacat.util.DocumentUtil;
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import edu.ucsb.nceas.metacat.util.MetacatUtil;
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import edu.ucsb.nceas.metacat.util.RequestUtil;
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import edu.ucsb.nceas.metacat.util.SystemUtil;
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import edu.ucsb.nceas.utilities.FileUtil;
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import edu.ucsb.nceas.utilities.LSIDUtil;
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import edu.ucsb.nceas.utilities.ParseLSIDException;
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import edu.ucsb.nceas.utilities.PropertyNotFoundException;
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import org.dataone.service.exceptions.BaseException;
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/**
146 132
 * General entry point for the Metacat server which is called from various 
147 133
 * mechanisms such as the standard MetacatServlet class and the various web
src/edu/ucsb/nceas/metacat/service/ObjectFormatService.java
27 27
package edu.ucsb.nceas.metacat.service;
28 28

  
29 29
import java.io.ByteArrayInputStream;
30
import java.io.FileInputStream;
31
import java.io.FileNotFoundException;
32 30
import java.io.InputStream;
33 31
import java.sql.SQLException;
34 32
import java.util.HashMap;
35
import java.util.List;
36 33

  
34
import org.apache.log4j.Logger;
35
import org.dataone.client.ObjectFormatCache;
36
import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.ObjectFormatList;
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import org.dataone.service.types.util.ServiceTypeUtil;
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import org.jibx.runtime.JiBXException;
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37 41
import edu.ucsb.nceas.metacat.DBUtil;
38 42
import edu.ucsb.nceas.metacat.DocumentImpl;
39 43
import edu.ucsb.nceas.metacat.McdbException;
40 44
import edu.ucsb.nceas.metacat.properties.PropertyService;
41
import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
42 45
import edu.ucsb.nceas.metacat.shared.BaseService;
43 46
import edu.ucsb.nceas.metacat.shared.ServiceException;
44
import edu.ucsb.nceas.metacat.util.SystemUtil;
45 47
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
46 48

  
47
import org.apache.log4j.Logger;
48

  
49
import org.dataone.client.CNode;
50
import org.dataone.client.D1Client;
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import org.dataone.client.ObjectFormatCache;
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import org.dataone.service.exceptions.InsufficientResources;
53
import org.dataone.service.exceptions.InvalidRequest;
54
import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.ObjectFormat;
59
import org.dataone.service.types.ObjectFormatList;
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//import org.dataone.service.types.ObjectFormatList;
61
import org.dataone.service.types.util.ServiceTypeUtil;
62
import org.jibx.runtime.JiBXException;
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64 49
/**
65 50
 *  The ObjectFormatService manages the list of object formats registered
66 51
 *  within Metacat.  This includes schema types, mime types, and other
......
100 85
  private String coordinatingNodeBaseURL = null;
101 86
  
102 87
  /* The D1 coordinating node reference object used for object format lookups */
103
  private CNode cn = null;
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  //private CNode cn = null;
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105 90
  /* The D1 node type for this instance of metacat */
106 91
  private String nodeType;
src/edu/ucsb/nceas/metacat/admin/upgrade/GenerateSystemMetadata.java
26 26
 */
27 27

  
28 28

  
29
import java.io.ByteArrayInputStream;
30
import java.io.IOException;
31
import java.io.InputStream;
32 29
import java.security.NoSuchAlgorithmException;
33 30
import java.sql.SQLException;
34
import java.util.Calendar;
35
import java.util.Date;
36
import java.util.Hashtable;
37 31
import java.util.List;
38
import java.util.TimeZone;
39 32
import java.util.Timer;
40 33

  
41
import javax.xml.parsers.ParserConfigurationException;
42
import javax.xml.xpath.XPathExpressionException;
43

  
44 34
import org.apache.commons.logging.Log;
45 35
import org.apache.commons.logging.LogFactory;
46
import org.dataone.eml.DataoneEMLParser;
47
import org.dataone.eml.EMLDocument;
48
import org.dataone.eml.EMLDocument.DistributionMetadata;
49 36
import org.dataone.service.exceptions.InvalidRequest;
50 37
import org.dataone.service.exceptions.InvalidToken;
51 38
import org.dataone.service.exceptions.NotAuthorized;
......
53 40
import org.dataone.service.exceptions.NotImplemented;
54 41
import org.dataone.service.exceptions.ServiceFailure;
55 42
import org.dataone.service.types.AuthToken;
56
import org.dataone.service.types.Checksum;
57
import org.dataone.service.types.ChecksumAlgorithm;
58
import org.dataone.service.types.Identifier;
59
import org.dataone.service.types.NodeReference;
60
import org.dataone.service.types.ObjectFormat;
61
import org.dataone.service.types.Subject;
62 43
import org.dataone.service.types.SystemMetadata;
63
import org.xml.sax.SAXException;
64 44

  
65
import edu.ucsb.nceas.metacat.AccessionNumber;
66 45
import edu.ucsb.nceas.metacat.AccessionNumberException;
67
import edu.ucsb.nceas.metacat.DocumentImpl;
68 46
import edu.ucsb.nceas.metacat.IdentifierManager;
69 47
import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
70
import edu.ucsb.nceas.metacat.McdbException;
71 48
import edu.ucsb.nceas.metacat.MetacatHandler;
72 49
import edu.ucsb.nceas.metacat.admin.AdminException;
73
import edu.ucsb.nceas.metacat.dataone.CrudService;
74 50
import edu.ucsb.nceas.metacat.properties.PropertyService;
75
import edu.ucsb.nceas.metacat.util.SessionData;
76 51
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
77 52
import edu.ucsb.nceas.utilities.SortedProperties;
78 53

  

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