Revision 10292
Added by Jing Tao almost 7 years ago
| src/edu/ucsb/nceas/metacat/DocumentImpl.java | ||
|---|---|---|
| 42 | 42 |
import java.io.Writer; |
| 43 | 43 |
import java.math.BigInteger; |
| 44 | 44 |
import java.net.URL; |
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import java.security.DigestOutputStream; |
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| 46 |
import java.security.MessageDigest; |
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import java.security.NoSuchAlgorithmException; |
|
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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 org.apache.commons.io.IOUtils; |
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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.dataone.service.exceptions.InvalidSystemMetadata; |
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import org.dataone.service.types.v1.Checksum; |
|
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import org.dataone.service.types.v1.Identifier; |
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import org.dataone.service.types.v2.SystemMetadata; |
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import org.xml.sax.ContentHandler; |
| ... | ... | |
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* @param accNumber |
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* the document id which is used to name the output file |
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*/ |
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private static void writeToFileSystem(byte[] xml, String accNumber) throws McdbException {
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private static void writeToFileSystem(byte[] xml, String accNumber, Checksum checksum) throws McdbException, InvalidSystemMetadata {
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|
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|
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// write the document to disk |
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String documentDir = null; |
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String documentPath = null; |
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boolean needCalculateChecksum = false; |
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String checksumValue = null; |
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MessageDigest md = null; |
|
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|
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try {
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documentDir = PropertyService.getProperty("application.documentfilepath");
|
| ... | ... | |
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if (accNumber != null |
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&& (FileUtil.getFileStatus(documentPath) == FileUtil.DOES_NOT_EXIST |
| 1528 | 1536 |
|| FileUtil.getFileSize(documentPath) == 0)) {
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if(checksum != null) {
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needCalculateChecksum = true; |
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checksumValue = checksum.getValue(); |
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logMetacat.info("DocumentImple.writeToFileSystem - the checksum from the system metadata is "+checksumValue);
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if(checksumValue == null || checksumValue.trim().equals("")) {
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logMetacat.error("DocumentImple.writeToFileSystem - the checksum value from the system metadata shouldn't be null or blank");
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throw new InvalidSystemMetadata("1180", "The checksum value from the system metadata shouldn't be null or blank.");
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} |
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String algorithm = checksum.getAlgorithm(); |
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logMetacat.info("DocumentImple.writeToFileSystem - the algorithm to calculate the checksum from the system metadata is "+algorithm);
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if(algorithm == null || algorithm.trim().equals("")) {
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logMetacat.error("DocumentImple.writeToFileSystem - the algorithm to calculate the checksum from the system metadata shouldn't be null or blank");
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throw new InvalidSystemMetadata("1180", "The algorithm to calculate the checksum from the system metadata shouldn't be null or blank.");
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} |
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try {
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md = MessageDigest.getInstance(algorithm); |
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} catch (NoSuchAlgorithmException ee) {
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logMetacat.error("DocumentImple.writeToFileSystem - we don't support the algorithm "+algorithm+" to calculate the checksum.", ee);
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throw new InvalidSystemMetadata("1180", "The algorithm "+algorithm+" to calculate the checksum is not supported: "+ee.getMessage());
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} |
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} |
|
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FileOutputStream fos = null;
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OutputStream fos = null; |
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try {
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fos = new FileOutputStream(documentPath); |
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if(needCalculateChecksum) {
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logMetacat.info("DocumentImple.writeToFileSystem - we need to compute the checksum since it is from DataONE API");
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fos = new DigestOutputStream(new FileOutputStream(documentPath), md); |
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} else {
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logMetacat.info("DocumentImple.writeToFileSystem - we don't need to compute the checksum since it is from Metacat API");
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fos = new FileOutputStream(documentPath); |
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} |
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IOUtils.write(xml, fos); |
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fos.flush(); |
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fos.close(); |
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if(needCalculateChecksum) {
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String localChecksum = DatatypeConverter.printHexBinary(md.digest()); |
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logMetacat.info("DocumentImple.writeToFileSystem - the check sum calculated from the saved local file is "+localChecksum);
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if(localChecksum == null || localChecksum.trim().equals("") || !localChecksum.equalsIgnoreCase(checksumValue)) {
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logMetacat.error("DocumentImple.writeToFileSystem - the check sum calculated from the saved local file is "+localChecksum+ ". But it doesn't match the value from the system metadata "+checksumValue);
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File newFile = new File(documentPath); |
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boolean success = newFile.delete(); |
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logMetacat.info("Delete the file "+newFile.getAbsolutePath()+" sucessfully? "+success);
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throw new InvalidSystemMetadata("1180", "The checksum calculated from the saved local file is "+localChecksum+ ". But it doesn't match the value from the system metadata "+checksumValue+".");
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} |
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} |
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} catch (IOException ioe) {
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throw new McdbException("Could not write file: " + documentPath + " : " + ioe.getMessage());
|
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} finally {
|
| ... | ... | |
| 2659 | 2705 |
|
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public static String write(DBConnection conn, String xmlString, String pub, |
| 2661 | 2707 |
Reader dtd, String action, String docid, String user, |
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String[] groups, String ruleBase, boolean needValidation, boolean writeAccessRules, byte[] xmlBytes, String schemaLocation) |
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String[] groups, String ruleBase, boolean needValidation, boolean writeAccessRules, byte[] xmlBytes, String schemaLocation, Checksum checksum)
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throws Exception |
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{
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//this method will be called in handleUpdateOrInsert method |
| ... | ... | |
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// get server location for this doc |
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int serverLocation = getServerLocationNumber(docid); |
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return write(conn, xmlString, pub, dtd, action, docid, user, groups, |
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serverLocation, false, ruleBase, needValidation, writeAccessRules, xmlBytes, schemaLocation); |
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serverLocation, false, ruleBase, needValidation, writeAccessRules, xmlBytes, schemaLocation, checksum);
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|
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} |
| 2672 | 2718 |
|
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/** |
| ... | ... | |
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public static String write(DBConnection conn, String xmlString, String pub, |
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Reader dtd, String action, String accnum, String user, |
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String[] groups, int serverCode, boolean override, String ruleBase, |
| 2707 |
boolean needValidation, boolean writeAccessRules, byte[] xmlBytes, String schemaLocation) throws Exception |
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boolean needValidation, boolean writeAccessRules, byte[] xmlBytes, String schemaLocation, Checksum checksum) throws Exception
|
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{
|
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// NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT |
| 2710 | 2756 |
|
| ... | ... | |
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conn.setAutoCommit(false); |
| 2799 | 2845 |
logMetacat.debug("DocumentImpl.write - parsing xml");
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parser.parse(new InputSource(xmlReader)); |
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conn.commit(); |
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conn.setAutoCommit(true); |
|
| 2803 | 2847 |
|
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// update the node data to include numeric and date values |
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updateNodeValues(conn, docid); |
| 2806 | 2850 |
|
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//write the file to disk |
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logMetacat.debug("DocumentImpl.write - Writing xml to file system");
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| 2809 |
writeToFileSystem(xmlBytes, accnum); |
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writeToFileSystem(xmlBytes, accnum, checksum); |
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| 2854 |
|
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conn.commit(); |
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| 2856 |
conn.setAutoCommit(true); |
|
| 2810 | 2857 |
|
| 2811 | 2858 |
// write to xml_node complete. start the indexing thread. |
| 2812 | 2859 |
addDocidToIndexingQueue(docid, rev); |
| ... | ... | |
| 2904 | 2951 |
//logMetacat.debug("DocumentImpl.write - XML to be parsed: " + xmlString);
|
| 2905 | 2952 |
parser.parse(new InputSource(xmlReader)); |
| 2906 | 2953 |
|
| 2907 |
conn.commit(); |
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conn.setAutoCommit(true); |
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| 2909 |
|
|
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//update nodes |
| 2911 | 2955 |
updateNodeValues(conn, docid); |
| 2912 | 2956 |
|
| 2913 | 2957 |
//write the file to disk |
| 2914 |
writeToFileSystem(xmlBytes, accnum); |
|
| 2958 |
writeToFileSystem(xmlBytes, accnum, checksum); |
|
| 2959 |
|
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| 2960 |
conn.commit(); |
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| 2961 |
conn.setAutoCommit(true); |
|
| 2915 | 2962 |
|
| 2916 | 2963 |
addDocidToIndexingQueue(docid, rev); |
| 2917 | 2964 |
if (guidsToSync.size() > 0) {
|
| ... | ... | |
| 3116 | 3163 |
|
| 3117 | 3164 |
// Write the file to disk |
| 3118 | 3165 |
//byte[] bytes = xmlString.getBytes(encoding); |
| 3119 |
writeToFileSystem(xmlBytes, accnum); |
|
| 3166 |
Checksum checksum = null; |
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| 3167 |
writeToFileSystem(xmlBytes, accnum, checksum); |
|
| 3120 | 3168 |
|
| 3121 | 3169 |
// write to xml_node complete. start the indexing thread. |
| 3122 | 3170 |
// this only for xml_documents |
Also available in: Unified diff
Add the code to computer the checksum.