Metacat

/**

 *  Name: SrbJavaGlue.java

 *  Institution: National Center for Ecological Analysis and Synthesis

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

 *         National Center for Ecological Analysis and Synthesis,

 *         University of California, Santa Barbara 2000.

 *         All rights reserved.

 *

 *  Authors: Dan Higgins, John Moreland

 *

 *     Version: '$Id: SrbJavaGlue.java 299 2000-07-27 17:14:36Z higgins $'

 */

 /* Note: Based on Java code originally produced at SDSC

 * Copyright   1999   The Regents of the University of California

 * All Rights Reserved

 */

/**

 * SrbJavaGlue

 *

 * Implementation of RMI Interface

 *

 * @version 1.1 6/8/00

 * @author Dan Higgins - NCEAS

 */

 import java.rmi.*;

 import java.rmi.server.*;

 import java.io.*;   //DFH 6/8/00

public class SrbJavaGlue extends UnicastRemoteObject implements SrbJavaGlueInterface

{

 byte[] ByteData;

 String FileName;

 boolean previouslyConnected = false;

	// JNI (Java Native Interface) Glue Routines for the SRB client library.

public SrbJavaGlue() throws RemoteException {

                  super();

              }

	public synchronized native int clConnectJ( String host, String port, String auth );

	public synchronized int rmiConnectJ(String host, String port, String auth, String user ) {

	    if (previouslyConnected) {

	        return -1;

	    }

	    else {

	        writeMdasEnv(user);

	        int res = clConnectJ(host, port, auth );

	        if (res>0) {previouslyConnected = true;}

	        return res;

	    }

	}

	public synchronized native int srbListCollectJ( int conn, int catType,

		String collectionName, String flag, int types[] );

	public synchronized native String getFileListItem( int index );

	public synchronized native int clFinishJ( int conn );

	public synchronized int rmiFinishJ(int conn) {

	    Reset();

	    return clFinishJ(conn);

	}

	public synchronized native int srbObjCopyNewJ( String srcDir, String srcFile,

		String dstDir, String dstFile, String dstRes );

	public synchronized native int srbListResourceJ( int bs );

	public synchronized native String getResListItem( int index );

	public synchronized native String getDefCollection();

	public synchronized native String getDefResource();

	public synchronized native String getUser();

	public synchronized native String getDomain();

	public synchronized native String getLocalCacheDir();

	public synchronized native int srbObjReplicateJ(int conn, int catType,

	  String objID, String replNum, String collection, String resource);

	public synchronized native int srbCollReplicateJ(int conn, int catType,

	  String collection, String resource);

	public synchronized native int queryDataInCollJ (int conn, int catType, 

	  String parColl);

	public synchronized native int queryDataJ (int conn, int catType, String objID,

	  String parColl);

	public synchronized native int querySubCollInCollJ (int conn, int catType, 

	  String parColl);

	public synchronized native String getDataResultJ( int metaIndex, int rowIndex );

	public synchronized native String getCollResultJ( int metaIndex, int rowIndex );

	public synchronized native String getGenQueResultJ( int metaIndex, int rowIndex );

	public synchronized native int getNCollAttriJ ();

	public synchronized native int getNDataAttriJ ();

	public synchronized native int srbObjUnlinkJ (int conn,  int catType, 

	  String objID, String replNum, String parColl);

	public synchronized native int srbCreateCollectJ (int conn,  int catType, 

	  String parColl, String newColl);

	public synchronized native int srbModifyDatasetMetaDJ (int conn,  int catType,

	  String objID, String collection, 

	   String newValue1, String newValue2, int retractionType);

	public synchronized native int srbModifyCollectMetaDJ (int conn,  int catType,

	  String collection, String newValue1, String newValue2, 

	   String newValue3, int retractionType);

	public synchronized native int importToOldObjJ (int conn,  int catType, 

	  String objID, String replNum, String parColl, String resource,

	   String localFile, String container);

	public synchronized native int importToNewObjJ (int conn,  int catType, 

	 String objID, String parColl, String resource, String localFile,

	  String container);

	public synchronized native int importDirJ (int conn,  int catType, 

	  String parColl, String resource, String localDir, String container);

	public synchronized native int srbRmCollJ (int conn, int catType, String parColl);

	public synchronized native int srbUnregCollJ (int conn, int catType, String parColl);

	public synchronized native int copyToOldObjJ (int conn,  int catType, 

	 String objID, String replNum, String srcColl, String targObj, 

	  String targReplNum, String targColl, String targResource, 

	   String container);

	public synchronized native int copyDataToCollJ (int conn,  int catType, 

	 String objID, String replNum, String srcColl,

	  String dataType, String size, String targColl, String targResource,

	   String container);

	public synchronized native int copyCollToCollJ (int conn, int catType, 

	 String srcColl, String targColl, String targResource, 

	  String container);

	public synchronized native int exportToFileJ(int conn, int catType,

	 String objID, String replNum, String srcColl,

	  String targFile, int forceFlag);

	public synchronized native int exportToDirJ(int conn, int catType,

	 String objID, String replNum, String srcColl,

	  String targDir);

	public synchronized native int exportCollToDirJ(int conn, int catType,

	 String srcColl, String targDir);

	public synchronized native int srbGenQuery (int conn, int catType,

	 String[] qval, int qvalInx[], int selVal[]);

        public synchronized native int srbRegisterDatasetJ(int conn, int catType,

         String objID, String dataType, String resource, String collection,

	  String pathName, int dataSize);

	public synchronized native int srbUnregisterDatasetJ (int conn, int catType,

	 String objID, String replNum, String collection);

        public synchronized native int srbRegisterDirJ (int conn, int catType,

	 String srcDirPath, String targColl, String resource);

        public synchronized native int getMoreDataRowsJ (int conn, int catType);

        public synchronized native int getMoreCollRowsJ (int conn, int catType);

        public synchronized native int getMoreGenQueRowsJ (int conn, int catType);

	public synchronized native int chmodInCollJ (int conn, int catType, 

	 String collection, String user, String domain, String mode);

	public synchronized native int ingestUserJ (int conn, int catType, 

	 String userName, String passwd, String domain, 

	  String userType, String userAddr, String userPhone, String userEmail,

	   String parentColl);

	public synchronized native int ingestGroupJ (int conn, int catType, 

	 String groupName, String passwd,

	  String groupAddr, String groupPhone, String groupEMail);

	public synchronized native int ingestLocJ (int conn, int catType, 

	 String locName, String fullAddr, String parentLoc); 

        public synchronized native int ingestResourceJ (int conn, int catType,

         String rescName, String rescType, String location, String phyPath);

        public synchronized native int ingestLogRescJ (int conn, int catType,

         String logRescName, String phyResc, String phyPath);

        public synchronized native int addLogRescJ (int conn, int catType,

         String logResc, String phyResc, String phyPath);

        public synchronized native int modifyUserJ (int conn, int catType,

         int modOpr, String userName, String domain, String modValue);

	public synchronized native int containerCreateJ (int conn, int catType,

	 String contName, String dataType, String logResc, int size);

	public synchronized native int containerDeleteJ (int conn, int catType,

	 String contName, int forceFlag);

        public native int containerSyncJ (int conn, int catType,

         String contName, int purgeFlag);

 //DFH 6/8/00

 public synchronized byte[] getByteData(String name) {

    File tmp = new File("./tmp/");

    if (!tmp.exists()) { tmp.mkdir();}

    File temp = new File("./tmp/"+name);    // looks for file in tmp dir under current directory

    if (temp.exists()) {

        ByteData = new byte[(int)temp.length()];

        try{

            FileInputStream fis = new FileInputStream(temp);

            fis.read(ByteData);

            fis.close();

        }

        catch (Exception e) {;}

        temp.delete();

    }

    else {

        ByteData = new byte[0];   

    }

    return ByteData;

 } 

 public synchronized void setByteData(String name, byte[] in) {

    ByteData = in;

    FileName = name;

    File tmp = new File("./tmp/");

    if (!tmp.exists()) { tmp.mkdir();}

    File temp = new File("./tmp/"+name);

        try{

            FileOutputStream fos = new FileOutputStream(temp);

            fos.write(ByteData);

            fos.close();

        }

        catch (Exception e) {;}

 }

 public synchronized void clearTmpFiles() {

    File temp = new File("./tmp/"+FileName);

    if (temp.exists()) { temp.delete(); }

 }

 public synchronized void Reset() {

      try{

        String[] cmdarray = {"java", "-Djava.security.policy=mypolicy", "SrbJavaGlue"};

	    Runtime.getRuntime().exec(cmdarray);

        Runtime.getRuntime().exit(0);

      }

      catch (Exception e) {System.out.println("Could not run exec and exit"); }

 }

 public synchronized void writeMdasEnv(String username) {

	   try{

	    String userhome = System.getProperty("user.home");

	    File file = new File(userhome+"/.srb/.MdasEnv");

		FileWriter fw = new FileWriter(file);

		StringBuffer env = new StringBuffer();

		env.append("mdasCollectionHome '/home/higgins.bioinfo'\n");

		env.append("mdasDomainHome 'bioinfo'\n");

		env.append("srbUser '"+username+"'\n");

		env.append("srbHost 'penelope.nceas.ucsb.edu'\n");

		env.append("defaultResource 'test-unix-nceas'\n");

		env.append("SEA_OPT '0'");

		StringReader sr = new StringReader(env.toString());

		int c;

		while ((c = sr.read()) != -1)

                 {    

                    fw.write(c);

                 }

		fw.close();

		sr.close();

	   }

	   catch (Exception e) {}  

 }

 // --

	static

	{

		System.loadLibrary( "SrbJavaGlue" );

	}

	    public static void main(String[] args) {

                  if (System.getSecurityManager() == null) {

                      System.setSecurityManager(new RMISecurityManager());

                  }

                  String name = "//localhost/SrbJavaGlue";

                  if (args.length==1) name = "//localhost" + ":"+args[0]+"/SrbJavaGlue";

                  try {

                      SrbJavaGlue engine = new SrbJavaGlue();

                      Naming.rebind(name, engine);

                      System.out.println("SrbJavaGlue bound");

                  } catch (Exception e) {

                      System.err.println("SrbJavaGlue exception: " + 

                                         e.getMessage());

                      e.printStackTrace();

                  }

              }

}