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Revision 8948

Added by Jing Tao over 9 years ago

Write the input stream into the file system without alteration in dataone create and update methods.

View differences:

src/edu/ucsb/nceas/metacat/MetaCatServlet.java
931 931
				PrintWriter out = response.getWriter();
932 932
				if ((userName != null) && !userName.equals("public")) {
933 933
					handler.handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), response, out, params, userName,
934
							groupNames, true, true);
934
							groupNames, true, true, null);
935 935
				} else {
936 936
					response.setContentType("text/xml");
937 937
					out.println("<?xml version=\"1.0\"?>");
src/edu/ucsb/nceas/metacat/DocumentImpl.java
1498 1498
	 * @param accNumber
1499 1499
	 *            the document id which is used to name the output file
1500 1500
	 */
1501
    private static void writeToFileSystem(String xml, String accNumber, String encoding) throws McdbException {
1501
    private static void writeToFileSystem(byte[] xml, String accNumber) throws McdbException {
1502 1502

  
1503 1503
		// write the document to disk
1504 1504
		String documentDir = null;
......
1528 1528
			    FileOutputStream fos = null;
1529 1529
                try {
1530 1530
                    fos = new FileOutputStream(documentPath);
1531
                    IOUtils.write(xml.getBytes(encoding), fos);
1531
                    IOUtils.write(xml, fos);
1532 1532

  
1533 1533
                    fos.flush();
1534 1534
                    fos.close();
......
2657 2657

  
2658 2658
    public static String write(DBConnection conn, String xmlString, String pub,
2659 2659
            Reader dtd, String action, String docid, String user,
2660
            String[] groups, String ruleBase, boolean needValidation, boolean writeAccessRules)
2660
            String[] groups, String ruleBase, boolean needValidation, boolean writeAccessRules, byte[] xmlBytes)
2661 2661
            throws Exception
2662 2662
    {
2663 2663
        //this method will be called in handleUpdateOrInsert method
......
2665 2665
        // get server location for this doc
2666 2666
        int serverLocation = getServerLocationNumber(docid);
2667 2667
        return write(conn, xmlString, pub, dtd, action, docid, user, groups,
2668
                serverLocation, false, ruleBase, needValidation, writeAccessRules);
2668
                serverLocation, false, ruleBase, needValidation, writeAccessRules, xmlBytes);
2669 2669
    }
2670 2670

  
2671 2671
    /**
......
2702 2702
    public static String write(DBConnection conn, String xmlString, String pub,
2703 2703
            Reader dtd, String action, String accnum, String user,
2704 2704
            String[] groups, int serverCode, boolean override, String ruleBase,
2705
            boolean needValidation, boolean writeAccessRules) throws Exception
2705
            boolean needValidation, boolean writeAccessRules, byte[] xmlBytes) throws Exception
2706 2706
    {
2707 2707
        // NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT
2708 2708
    	
2709 2709
    	// Get the xml as a string so we can write to file later
2710 2710
    	StringReader xmlReader = new StringReader(xmlString);
2711
    	// detect encoding
2712
        XmlStreamReader xsr = null;
2713
        if(xmlBytes == null || xmlBytes.length == 0 ) {
2714
            xsr = new XmlStreamReader(new ByteArrayInputStream(xmlString.getBytes()));
2715
        } else {
2716
            xsr = new XmlStreamReader(new ByteArrayInputStream(xmlBytes));
2717
        }         
2718
        String encoding = xsr.getEncoding();
2719
        //get the byte array from xmlString if the xmlbyte is null (this comes from metacat api)
2720
        if(xmlBytes == null || xmlBytes.length == 0) {
2721
            xmlBytes = xmlString.getBytes(encoding);
2722
        }
2711 2723

  
2712 2724
        logMetacat.debug("DocumentImpl.write - conn usage count before writing: "
2713 2725
                + conn.getUsageCount());
......
2767 2779
                	logReplication.info("lock granted for " + accnum
2768 2780
                            + " from " + server);
2769 2781
                	
2770
                	// detect encoding
2771
                    XmlStreamReader xsr = new XmlStreamReader(new ByteArrayInputStream(xmlString.getBytes()));
2772
			        String encoding = xsr.getEncoding();
2782
                	
2773 2783
			        Vector<String>guidsToSync = new Vector<String>();
2774 2784

  
2775 2785
                    /*
......
2794 2804
                    
2795 2805
                    //write the file to disk
2796 2806
                    logMetacat.debug("DocumentImpl.write - Writing xml to file system");                    
2797
                	writeToFileSystem(xmlString, accnum, encoding);
2807
                	writeToFileSystem(xmlBytes, accnum);
2798 2808

  
2799 2809
                    // write to xml_node complete. start the indexing thread.
2800 2810
                    addDocidToIndexingQueue(docid, rev);
......
2878 2888
        }
2879 2889
        XMLReader parser = null;
2880 2890
        try {
2881
            // detect encoding
2882
        	XmlStreamReader xsr = new XmlStreamReader(new ByteArrayInputStream(xmlString.getBytes()));
2883
	        String encoding = xsr.getEncoding();
2891
            
2892
	        
2884 2893
	        Vector<String>guidsToSync = new Vector<String>();
2885 2894

  
2886 2895
            parser = initializeParser(conn, action, docid, xmlReader, rev, user, groups,
......
2900 2909
            updateNodeValues(conn, docid);
2901 2910
            
2902 2911
            //write the file to disk
2903
        	writeToFileSystem(xmlString, accnum, encoding);
2912
        	writeToFileSystem(xmlBytes, accnum);
2904 2913

  
2905 2914
            addDocidToIndexingQueue(docid, rev);
2906 2915
    		if (guidsToSync.size() > 0) {
......
3103 3112
            conn.setAutoCommit(true);
3104 3113
            
3105 3114
            // Write the file to disk
3106
        	writeToFileSystem(xmlString, accnum, encoding);
3115
            byte[] bytes = xmlString.getBytes(encoding);
3116
        	writeToFileSystem(bytes, accnum);
3107 3117
            
3108 3118
            // write to xml_node complete. start the indexing thread.
3109 3119
            // this only for xml_documents
src/edu/ucsb/nceas/metacat/DocumentImplWrapper.java
59 59
	}//Constructor
60 60

  
61 61
	public String write(DBConnection conn, String xml, String pub, Reader dtd,
62
			String action, String docid, String user, String[] groups) throws Exception {
62
			String action, String docid, String user, String[] groups, byte[]xmlBytes) throws Exception {
63 63
		return DocumentImpl.write(conn, xml, pub, dtd, action, docid, user, groups,
64
				ruleBase, needValidation, writeAccessRules);
64
				ruleBase, needValidation, writeAccessRules, xmlBytes);
65 65
	}
66 66

  
67 67
	public String writeReplication(DBConnection conn, String xml, String pub, Reader dtd,
src/edu/ucsb/nceas/metacat/MetacatHandler.java
1628 1628
     */
1629 1629
    public String handleInsertOrUpdateAction(String ipAddress, String userAgent,
1630 1630
            HttpServletResponse response, PrintWriter out, Hashtable<String, String[]> params,
1631
            String user, String[] groups, boolean generateSystemMetadata, boolean writeAccessRules) {
1631
            String user, String[] groups, boolean generateSystemMetadata, boolean writeAccessRules, byte[] xmlBytes) {
1632 1632
        Logger logMetacat = Logger.getLogger(MetacatHandler.class);
1633 1633
        DBConnection dbConn = null;
1634 1634
        int serialNumber = -1;
......
1805 1805
              
1806 1806
              } else {*/
1807 1807
              newdocid = documentWrapper.write(dbConn, doctext[0], pub, dtd,
1808
                          doAction, accNumber, user, groups);
1808
                          doAction, accNumber, user, groups, xmlBytes);
1809 1809
            
1810 1810
              EventLog.getInstance().log(ipAddress, userAgent, user, accNumber, action[0]);
1811 1811
              
......
3189 3189
                boolean writeAccessRules = true;
3190 3190
                //call the insert routine
3191 3191
                handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), response, out, 
3192
                          params, username, groupnames, true, writeAccessRules);
3192
                          params, username, groupnames, true, writeAccessRules, null);
3193 3193
              }
3194 3194
              catch(Exception e)
3195 3195
              {
src/edu/ucsb/nceas/metacat/util/EMLVersionsTransformer.java
165 165
                 .getDBConnection("EMLVersionsTransformer.handleSingleEML200Document");
166 166
                  serialNumber = dbconn.getCheckOutSerialNumber();
167 167
                  documentWrapper.write(dbconn, eml210Content, pub, dtd,
168
                          doAction, newId, owner, groups);
168
                          doAction, newId, owner, groups, null);
169 169
                  logMetacat.warn("Doc "+docidWithRev+" was transformed to eml210 with new id "+newId);
170 170
                  transformLog("Doc "+docidWithRev+" was transformed to eml210 with new id "+newId);
171 171
             }
src/edu/ucsb/nceas/metacat/dataone/MNodeService.java
359 359
                // update the science metadata XML document
360 360
                // TODO: handle non-XML metadata/data documents (like netCDF)
361 361
                // TODO: don't put objects into memory using stream to string
362
                String objectAsXML = "";
362
                //String objectAsXML = "";
363 363
                try {
364
                    objectAsXML = IOUtils.toString(object, "UTF-8");
364
                    //objectAsXML = IOUtils.toString(object, "UTF-8");
365 365
                    // give the old pid so we can calculate the new local id 
366
                    localId = insertOrUpdateDocument(objectAsXML, pid, session, "update");
366
                    localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update");
367 367
                    // register the newPid and the generated localId
368 368
                    if (newPid != null) {
369 369
                        IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);
src/edu/ucsb/nceas/metacat/dataone/D1NodeService.java
402 402
      if ( isScienceMetadata(sysmeta) ) {
403 403
        
404 404
        // CASE METADATA:
405
      	String objectAsXML = "";
405
      	//String objectAsXML = "";
406 406
        try {
407
	        objectAsXML = IOUtils.toString(object, "UTF-8");
408
	        localId = insertOrUpdateDocument(objectAsXML, pid, session, "insert");
407
	        //objectAsXML = IOUtils.toString(object, "UTF-8");
408
	        localId = insertOrUpdateDocument(object,"UTF-8", pid, session, "insert");
409 409
	        //localId = im.getLocalId(pid.getValue());
410 410

  
411 411
        } catch (IOException e) {
......
1148 1148
   * @return localId - the resulting docid of the document created or updated
1149 1149
   * 
1150 1150
   */
1151
  public String insertOrUpdateDocument(String xml, Identifier pid, 
1151
  public String insertOrUpdateDocument(InputStream xml, String encoding,  Identifier pid, 
1152 1152
    Session session, String insertOrUpdate) 
1153
    throws ServiceFailure {
1153
    throws ServiceFailure, IOException {
1154 1154
    
1155 1155
  	logMetacat.debug("Starting to insert xml document...");
1156 1156
    IdentifierManager im = IdentifierManager.getInstance();
1157 1157

  
1158 1158
    // generate pid/localId pair for sysmeta
1159 1159
    String localId = null;
1160
    
1160
    byte[] xmlBytes  = IOUtils.toByteArray(xml);
1161
    String xmlStr = new String(xmlBytes, encoding);
1161 1162
    if(insertOrUpdate.equals("insert")) {
1162 1163
      localId = im.generateLocalId(pid.getValue(), 1);
1163 1164
      
......
1197 1198
    docid[0] = localId;
1198 1199
    params.put("docid", docid);
1199 1200
    String[] doctext = new String[1];
1200
    doctext[0] = xml;
1201
    doctext[0] = xmlStr;
1201 1202
    params.put("doctext", doctext);
1202 1203
    
1203 1204
    String username = Constants.SUBJECT_PUBLIC;
......
1218 1219
    // do the insert or update action
1219 1220
    handler = new MetacatHandler(new Timer());
1220 1221
    String result = handler.handleInsertOrUpdateAction(request.getRemoteAddr(), request.getHeader("User-Agent"), null, 
1221
                        null, params, username, groupnames, false, false);
1222
                        null, params, username, groupnames, false, false, xmlBytes);
1222 1223
    
1223 1224
    if(result.indexOf("<error>") != -1) {
1224 1225
    	String detailCode = "";

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