Revision 6068
Added by rnahf over 13 years ago
| src/edu/ucsb/nceas/metacat/dataone/CrudService.java | ||
|---|---|---|
| 255 | 255 |
* @param token an authtoken with appropriate permissions to read all |
| 256 | 256 |
* documents in the object store. To work correctly, this should probably |
| 257 | 257 |
* be an adminstrative credential. |
| 258 |
* @throws SQLException |
|
| 259 |
* @throws AccessionNumberException |
|
| 260 |
* @throws NoSuchAlgorithmException |
|
| 261 |
* @throws InvalidRequest |
|
| 262 |
* @throws NotImplemented |
|
| 263 |
* @throws NotFound |
|
| 264 |
* @throws NotAuthorized |
|
| 265 |
* @throws InvalidToken |
|
| 266 |
* @throws PropertyNotFoundException |
|
| 267 |
* @throws McdbDocNotFoundException |
|
| 268 |
* @throws ServiceFailure |
|
| 258 | 269 |
*/ |
| 259 |
public void generateMissingSystemMetadata(AuthToken token) {
|
|
| 270 |
public void generateMissingSystemMetadata(AuthToken token) |
|
| 271 |
throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized, |
|
| 272 |
NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException |
|
| 273 |
{
|
|
| 260 | 274 |
IdentifierManager im = IdentifierManager.getInstance(); |
| 261 | 275 |
//get the list of ids with no SM |
| 262 | 276 |
List<String> idList = im.getLocalIdsWithNoSystemMetadata(); |
| ... | ... | |
| 276 | 290 |
* documents in the object store. To work correctly, this should |
| 277 | 291 |
* be an adminstrative credential. |
| 278 | 292 |
* @param localId the identifier of the object to be processed |
| 293 |
* @throws ServiceFailure |
|
| 294 |
* @throws SQLException |
|
| 295 |
* @throws AccessionNumberException |
|
| 296 |
* @throws NoSuchAlgorithmException |
|
| 297 |
* @throws InvalidRequest |
|
| 298 |
* @throws NotImplemented |
|
| 299 |
* @throws NotFound |
|
| 300 |
* @throws NotAuthorized |
|
| 301 |
* @throws InvalidToken |
|
| 302 |
* @throws PropertyNotFoundException |
|
| 303 |
* @throws McdbDocNotFoundException |
|
| 279 | 304 |
*/ |
| 280 |
public void generateMissingSystemMetadata(AuthToken token, String localId) {
|
|
| 281 |
|
|
| 282 |
logCrud.debug("CrudService.generateMissingSystemMetadata() called.");
|
|
| 283 |
|
|
| 305 |
public void generateMissingSystemMetadata(AuthToken token, String localId) |
|
| 306 |
throws ServiceFailure, McdbDocNotFoundException, PropertyNotFoundException, InvalidToken, NotAuthorized, |
|
| 307 |
NotFound, NotImplemented, InvalidRequest, NoSuchAlgorithmException, AccessionNumberException, SQLException |
|
| 308 |
{
|
|
| 309 |
logCrud.debug("CrudService.generateMissingSystemMetadata() called.");
|
|
| 284 | 310 |
logCrud.debug("Creating SystemMetadata for localId " + localId);
|
| 311 |
SystemMetadata sm = null; |
|
| 312 |
|
|
| 313 |
//generate required system metadata fields from the document |
|
| 285 | 314 |
try {
|
| 286 |
//generate required system metadata fields from the document |
|
| 287 |
SystemMetadata sm = createSystemMetadata(localId, token); |
|
| 288 |
|
|
| 289 |
//insert the systemmetadata object |
|
| 290 |
SessionData sessionData = getSessionData(token); |
|
| 291 |
String smlocalid = insertSystemMetadata(sm, sessionData); |
|
| 292 |
logCrud.debug("setting access on SM doc with localid " + smlocalid);
|
|
| 293 |
handler.setAccess(metacatUrl, sessionData.getUserName(), smlocalid, "public", "4", "allow", "allowFirst"); |
|
| 315 |
sm = createSystemMetadata(localId, token); |
|
| 316 |
} catch (IOException e1) {
|
|
| 317 |
e1.printStackTrace(); |
|
| 318 |
ServiceFailure sf = new ServiceFailure("00","IOException in generateMissingSystemMetadata: " +
|
|
| 319 |
e1.getMessage()); |
|
| 320 |
sf.setStackTrace(e1.getStackTrace()); |
|
| 321 |
throw sf; |
|
| 322 |
} |
|
| 323 |
|
|
| 324 |
//insert the systemmetadata object |
|
| 325 |
SessionData sessionData = getSessionData(token); |
|
| 326 |
String smlocalid = insertSystemMetadata(sm, sessionData); |
|
| 327 |
logCrud.debug("setting access on SM doc with localid " + smlocalid);
|
|
| 328 |
try {
|
|
| 329 |
handler.setAccess(metacatUrl, sessionData.getUserName(), smlocalid, "public", "4", "allow", "allowFirst"); |
|
| 330 |
} catch (Exception e) {
|
|
| 331 |
logCrud.debug("Unspecified exception thrown by MetacatHandler.setAccess(): " + e.getMessage());
|
|
| 332 |
logMetacat.error("Could not generate missing systemMetadata: " + e.getMessage());
|
|
| 333 |
logMetacat.error(e.getStackTrace()); |
|
| 334 |
ServiceFailure sf = new ServiceFailure("0","Unspecified exception thrown by MetacatHandler.setAccess(): " + e.getMessage());
|
|
| 335 |
sf.setStackTrace(e.getStackTrace()); |
|
| 336 |
throw sf; |
|
| 337 |
} |
|
| 294 | 338 |
|
| 295 |
String username = "public"; |
|
| 296 |
if (sessionData != null) {
|
|
| 297 |
username = sessionData.getUserName(); |
|
| 298 |
} |
|
| 299 |
EventLog.getInstance().log(metacatUrl, username, localId, "generateMissingSystemMetadata"); |
|
| 300 |
} catch (Exception e) { // TODO: Please don't catch Exception -- it masks bad things
|
|
| 301 |
e.printStackTrace(); |
|
| 302 |
logCrud.debug("Exception generating missing system metadata: " + e.getMessage());
|
|
| 303 |
logMetacat.error("Could not generate missing system metadata: " + e.getMessage());
|
|
| 339 |
String username = "public"; |
|
| 340 |
if (sessionData != null) {
|
|
| 341 |
username = sessionData.getUserName(); |
|
| 304 | 342 |
} |
| 343 |
EventLog.getInstance().log(metacatUrl, username, localId, "generateMissingSystemMetadata"); |
|
| 344 |
|
|
| 345 |
// catch (Exception e) { // TODO: Please don't catch Exception -- it masks bad things
|
|
| 346 |
// e.printStackTrace(); |
|
| 347 |
// logCrud.debug("Exception generating missing system metadata: " + e.getMessage());
|
|
| 348 |
// logMetacat.error("Could not generate missing system metadata: " + e.getMessage());
|
|
| 349 |
// } |
|
| 305 | 350 |
logCrud.info("generateMissingSystemMetadata(token, localId)");
|
| 306 | 351 |
} |
| 307 | 352 |
|
| ... | ... | |
| 426 | 471 |
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique, |
| 427 | 472 |
UnsupportedType, InsufficientResources, NotFound, InvalidSystemMetadata, |
| 428 | 473 |
NotImplemented {
|
| 429 |
try
|
|
| 430 |
{
|
|
| 431 |
SessionData sessionData = getSessionData(token);
|
|
| 474 |
try
|
|
| 475 |
{
|
|
| 476 |
SessionData sessionData = getSessionData(token);
|
|
| 432 | 477 |
|
| 433 | 478 |
//find the old systemmetadata (sm.old) document id (the one linked to obsoletedGuid) |
| 434 | 479 |
SystemMetadata sm = getSystemMetadata(token, obsoletedGuid); |
| ... | ... | |
| 469 | 514 |
":D1SYSMETADATA:"+ sysMetaLocalId + ":"); |
| 470 | 515 |
return guid; |
| 471 | 516 |
} |
| 472 |
catch(Exception e) |
|
| 473 |
{
|
|
| 517 |
|
|
| 518 |
catch(IOException e) {
|
|
| 474 | 519 |
throw new ServiceFailure("1310", "Error updating document in CrudService: " + e.getMessage());
|
| 475 | 520 |
} |
| 521 |
catch( McdbDocNotFoundException e) {
|
|
| 522 |
throw new ServiceFailure("1310", "Error updating document in CrudService: " + e.getMessage());
|
|
| 523 |
} |
|
| 524 |
catch( InvalidRequest e) {
|
|
| 525 |
throw new ServiceFailure("1310", "Error updating document in CrudService: " + e.getMessage());
|
|
| 526 |
} |
|
| 476 | 527 |
} |
| 477 | 528 |
|
| 478 | 529 |
/** |
| ... | ... | |
| 1650 | 1701 |
} |
| 1651 | 1702 |
catch(Exception e) |
| 1652 | 1703 |
{
|
| 1653 |
throw new ServiceFailure("1030", "Error updating system metadata: " + e.getMessage());
|
|
| 1704 |
throw new ServiceFailure("1030", "Error updating system metadata: " + e.getClass() + ": " + e.getMessage());
|
|
| 1654 | 1705 |
} |
| 1655 | 1706 |
} |
| 1656 | 1707 |
|
| ... | ... | |
| 1976 | 2027 |
* @throws IOException |
| 1977 | 2028 |
* @throws NoSuchAlgorithmException |
| 1978 | 2029 |
* @throws PropertyNotFoundException |
| 2030 |
* @throws NotImplemented |
|
| 2031 |
* @throws NotFound |
|
| 2032 |
* @throws NotAuthorized |
|
| 2033 |
* @throws InvalidToken |
|
| 2034 |
* @throws InvalidRequest |
|
| 2035 |
* @throws NoSuchAlgorithmException |
|
| 1979 | 2036 |
*/ |
| 1980 | 2037 |
private SystemMetadata createSystemMetadata(String localId, AuthToken token) |
| 1981 |
throws McdbDocNotFoundException, NumberFormatException, AccessionNumberException, |
|
| 1982 |
SQLException, NoSuchAlgorithmException, IOException, PropertyNotFoundException, BaseException {
|
|
| 1983 |
|
|
| 1984 |
logCrud.debug("CrudService.createSystemMetadata() called.");
|
|
| 1985 |
|
|
| 1986 |
IdentifierManager im = IdentifierManager.getInstance(); |
|
| 1987 |
Hashtable<String, Object> docInfo = im.getDocumentInfo(localId); |
|
| 2038 |
throws McdbDocNotFoundException, PropertyNotFoundException, AccessionNumberException, SQLException, |
|
| 2039 |
ServiceFailure, InvalidToken, NotAuthorized, NotFound, NotImplemented, InvalidRequest, |
|
| 2040 |
IOException, NoSuchAlgorithmException |
|
| 2041 |
{
|
|
| 2042 |
logCrud.debug("CrudService.createSystemMetadata() called.");
|
|
| 1988 | 2043 |
|
| 1989 |
//get the document text |
|
| 1990 |
int rev = im.getLatestRevForLocalId(localId); |
|
| 1991 |
Identifier identifier = new Identifier(); |
|
| 1992 |
try {
|
|
| 1993 |
identifier.setValue(im.getGUID(localId, rev)); |
|
| 1994 |
|
|
| 1995 |
} catch (McdbDocNotFoundException mcdbe) {
|
|
| 1996 |
//we're creating a new SM doc for a doc that is not in the identifier table |
|
| 1997 |
//so we need to add it to |
|
| 1998 |
logCrud.debug("No guid in the identifier table. adding it for " + localId);
|
|
| 1999 |
im.createMapping(localId, localId); |
|
| 2000 |
logCrud.debug("Mapping created for " + localId);
|
|
| 2001 |
AccessionNumber accNum = new AccessionNumber(localId, "NONE"); |
|
| 2002 |
identifier.setValue(im.getGUID(accNum.getDocid(), rev)); |
|
| 2003 |
} |
|
| 2044 |
IdentifierManager im = IdentifierManager.getInstance(); |
|
| 2045 |
Hashtable<String, Object> docInfo = im.getDocumentInfo(localId); |
|
| 2004 | 2046 |
|
| 2005 |
logCrud.debug("Creating system metadata for guid " + identifier.getValue());
|
|
| 2006 |
InputStream is = this.get(token, identifier); |
|
| 2007 |
SystemMetadata sm = new SystemMetadata(); |
|
| 2008 |
|
|
| 2009 |
//set the id |
|
| 2010 |
sm.setIdentifier(identifier); |
|
| 2047 |
//get the document text |
|
| 2048 |
int rev = im.getLatestRevForLocalId(localId); |
|
| 2049 |
Identifier identifier = new Identifier(); |
|
| 2050 |
try {
|
|
| 2051 |
identifier.setValue(im.getGUID(localId, rev)); |
|
| 2011 | 2052 |
|
| 2012 |
//set the default object format |
|
| 2013 |
String doctype = (String) docInfo.get("doctype");
|
|
| 2014 |
ObjectFormat format = ObjectFormat.convert(doctype); |
|
| 2015 |
if (format == null) {
|
|
| 2016 |
if (doctype.trim().equals("BIN")) {
|
|
| 2017 |
format = ObjectFormat.OCTET_STREAM; |
|
| 2018 |
} else {
|
|
| 2019 |
format = ObjectFormat.convert("text/plain");
|
|
| 2020 |
} |
|
| 2021 |
} |
|
| 2022 |
sm.setObjectFormat(format); |
|
| 2023 |
logCrud.debug("The ObjectFormat for " + localId + " is " + format.toString());
|
|
| 2024 |
|
|
| 2025 |
// further parse EML documents to get data object format, |
|
| 2026 |
// describes and describedBy information |
|
| 2027 |
if ( format == ObjectFormat.EML_2_0_0 || |
|
| 2028 |
format == ObjectFormat.EML_2_0_1 || |
|
| 2029 |
format == ObjectFormat.EML_2_1_0 ) {
|
|
| 2030 |
|
|
| 2031 |
try {
|
|
| 2032 |
DataoneEMLParser emlParser = DataoneEMLParser.getInstance(); |
|
| 2033 |
EMLDocument emlDocument = emlParser.parseDocument(is); |
|
| 2034 |
|
|
| 2035 |
// iterate through the data objects in the EML doc and add sysmeta |
|
| 2036 |
logCrud.debug("The number of data entities is: " +
|
|
| 2037 |
emlDocument.distributionMetadata.size()); |
|
| 2038 |
|
|
| 2039 |
for( int j = 0; j < emlDocument.distributionMetadata.size(); j++ ) {
|
|
| 2040 |
|
|
| 2041 |
DistributionMetadata distMetadata = |
|
| 2042 |
emlDocument.distributionMetadata.elementAt(j); |
|
| 2043 |
String dataDocUrl = distMetadata.url; |
|
| 2044 |
String dataDocMimeType = distMetadata.mimeType; |
|
| 2045 |
String dataDocLocalId = ""; |
|
| 2046 |
logCrud.debug("\tData local ID: " + dataDocLocalId);
|
|
| 2047 |
logCrud.debug("\tData URL: " + dataDocUrl);
|
|
| 2048 |
logCrud.debug("\tData mime: " + dataDocMimeType);
|
|
| 2049 |
|
|
| 2050 |
//we only handle ecogrid urls right now |
|
| 2051 |
if ( dataDocUrl.trim().startsWith("ecogrid://knb/") ) {
|
|
| 2052 |
dataDocLocalId = |
|
| 2053 |
dataDocUrl.substring(dataDocUrl.indexOf("ecogrid://knb/") +
|
|
| 2054 |
"ecogrid://knb/".length(), dataDocUrl.length()); |
|
| 2055 |
|
|
| 2056 |
//set the id |
|
| 2057 |
Identifier dataDocId = new Identifier(); |
|
| 2058 |
dataDocId.setValue(dataDocLocalId); |
|
| 2059 |
|
|
| 2060 |
// add describes into EML system metadata |
|
| 2061 |
sm.addDescribe(dataDocId); |
|
| 2062 |
|
|
| 2063 |
SystemMetadata dataSysMeta = new SystemMetadata(); |
|
| 2064 |
// check if data system metadata exists |
|
| 2065 |
try {
|
|
| 2066 |
logCrud.debug("Checking for existing system metadata for " + dataDocId.getValue());
|
|
| 2067 |
dataSysMeta = this.getSystemMetadata(token, dataDocId); |
|
| 2068 |
// add describedBy sysmeta |
|
| 2069 |
logCrud.debug("Setting describedBy for " + dataDocId.getValue() +
|
|
| 2070 |
" to " + identifier.getValue()); |
|
| 2071 |
dataSysMeta.addDescribedBy(identifier); |
|
| 2072 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType)); |
|
| 2073 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
|
| 2074 |
|
|
| 2075 |
} catch ( NotFound nf ) {
|
|
| 2076 |
// System metadata for data doesn't exist |
|
| 2077 |
logCrud.debug("There was not an existing system metadata " + "document for " + dataDocId.getValue());
|
|
| 2078 |
try {
|
|
| 2079 |
logCrud.debug("Creating a system metadata " + "document for " + dataDocId.getValue());
|
|
| 2080 |
dataSysMeta = this.createSystemMetadata(dataDocLocalId, token); |
|
| 2081 |
|
|
| 2082 |
logCrud.debug("Setting describedBy for " + dataDocId.getValue() + " to " + identifier.getValue());
|
|
| 2083 |
dataSysMeta.addDescribedBy(identifier); |
|
| 2084 |
|
|
| 2085 |
logCrud.debug("Setting mimeType for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
|
| 2086 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType)); |
|
| 2087 |
|
|
| 2088 |
logCrud.debug("Updating system metadata for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
|
| 2089 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
|
| 2090 |
|
|
| 2091 |
} catch ( McdbDocNotFoundException mdnf) {
|
|
| 2092 |
mdnf.printStackTrace(); |
|
| 2093 |
throw mdnf; |
|
| 2094 |
} catch ( NumberFormatException nfe) {
|
|
| 2095 |
nfe.printStackTrace(); |
|
| 2096 |
throw nfe; |
|
| 2097 |
} catch ( AccessionNumberException ane) {
|
|
| 2098 |
ane.printStackTrace(); |
|
| 2099 |
throw ane; |
|
| 2100 |
} catch ( SQLException sqle) {
|
|
| 2101 |
sqle.printStackTrace(); |
|
| 2102 |
throw sqle; |
|
| 2103 |
} catch ( NoSuchAlgorithmException nsae) {
|
|
| 2104 |
nsae.printStackTrace(); |
|
| 2105 |
throw nsae; |
|
| 2106 |
} catch ( IOException ioe) {
|
|
| 2107 |
ioe.printStackTrace(); |
|
| 2108 |
throw ioe; |
|
| 2109 |
} catch ( PropertyNotFoundException pnfe) {
|
|
| 2110 |
pnfe.printStackTrace(); |
|
| 2111 |
throw pnfe; |
|
| 2112 |
} catch ( BaseException be) {
|
|
| 2113 |
be.printStackTrace(); |
|
| 2114 |
throw be; |
|
| 2115 |
|
|
| 2116 |
} |
|
| 2117 |
|
|
| 2118 |
} |
|
| 2119 |
|
|
| 2120 |
} // end if() |
|
| 2121 |
|
|
| 2122 |
} // end for() |
|
| 2123 |
|
|
| 2124 |
} catch ( ParserConfigurationException pce ) {
|
|
| 2125 |
logCrud.debug("There was a problem parsing the EML document. " +
|
|
| 2126 |
"The error message was: " + pce.getMessage()); |
|
| 2127 |
|
|
| 2128 |
} catch ( SAXException saxe ) {
|
|
| 2129 |
logCrud.debug("There was a problem traversing the EML document. " +
|
|
| 2130 |
"The error message was: " + saxe.getMessage()); |
|
| 2131 |
|
|
| 2132 |
} catch ( XPathExpressionException xpee ) {
|
|
| 2133 |
logCrud.debug("There was a problem searching the EML document. " +
|
|
| 2134 |
"The error message was: " + xpee.getMessage()); |
|
| 2135 |
} // end try |
|
| 2136 |
|
|
| 2137 |
} // end if() |
|
| 2138 |
|
|
| 2139 |
//create the checksum |
|
| 2140 |
is = this.get(token, identifier); |
|
| 2141 |
String checksumS = checksum(is); |
|
| 2142 |
ChecksumAlgorithm ca = ChecksumAlgorithm.convert("MD5");
|
|
| 2143 |
Checksum checksum = new Checksum(); |
|
| 2144 |
checksum.setValue(checksumS); |
|
| 2145 |
checksum.setAlgorithm(ca); |
|
| 2146 |
sm.setChecksum(checksum); |
|
| 2053 |
} catch (McdbDocNotFoundException mcdbe) {
|
|
| 2054 |
//we're creating a new SM doc for a doc that is not in the identifier table |
|
| 2055 |
//so we need to add it to |
|
| 2056 |
logCrud.debug("No guid in the identifier table. adding it for " + localId);
|
|
| 2057 |
im.createMapping(localId, localId); |
|
| 2058 |
logCrud.debug("Mapping created for " + localId);
|
|
| 2059 |
AccessionNumber accNum = new AccessionNumber(localId, "NONE"); |
|
| 2060 |
identifier.setValue(im.getGUID(accNum.getDocid(), rev)); |
|
| 2061 |
} |
|
| 2147 | 2062 |
|
| 2148 |
//set the size
|
|
| 2149 |
is = this.get(token, identifier);
|
|
| 2150 |
sm.setSize(sizeOfStream(is));
|
|
| 2063 |
logCrud.debug("Creating system metadata for guid " + identifier.getValue());
|
|
| 2064 |
InputStream is = this.get(token, identifier);
|
|
| 2065 |
SystemMetadata sm = new SystemMetadata();
|
|
| 2151 | 2066 |
|
| 2152 |
//submitter |
|
| 2153 |
Principal p = new Principal(); |
|
| 2154 |
p.setValue((String) docInfo.get("user_owner"));
|
|
| 2155 |
sm.setSubmitter(p); |
|
| 2156 |
sm.setRightsHolder(p); |
|
| 2157 |
try {
|
|
| 2158 |
Date dateCreated = parseMetacatDate((String) docInfo.get("date_created"));
|
|
| 2159 |
sm.setDateUploaded(dateCreated); |
|
| 2160 |
Date dateUpdated = parseMetacatDate((String) docInfo.get("date_updated"));
|
|
| 2161 |
sm.setDateSysMetadataModified(dateUpdated); |
|
| 2162 |
} catch (Exception e) {
|
|
| 2163 |
logCrud.debug("POSSIBLE ERROR: couldn't parse a date: " + e.getMessage());
|
|
| 2164 |
Date dateCreated = new Date(); |
|
| 2165 |
sm.setDateUploaded(dateCreated); |
|
| 2166 |
Date dateUpdated = new Date(); |
|
| 2167 |
sm.setDateSysMetadataModified(dateUpdated); |
|
| 2168 |
} |
|
| 2169 |
NodeReference nr = new NodeReference(); |
|
| 2170 |
nr.setValue(PropertyService.getProperty("dataone.memberNodeId"));
|
|
| 2171 |
sm.setOriginMemberNode(nr); |
|
| 2172 |
sm.setAuthoritativeMemberNode(nr); |
|
| 2173 |
|
|
| 2174 |
// TODO: Need to set describes/describedBy |
|
| 2175 |
|
|
| 2176 |
return sm; |
|
| 2067 |
//set the id |
|
| 2068 |
sm.setIdentifier(identifier); |
|
| 2069 |
|
|
| 2070 |
//set the default object format |
|
| 2071 |
String doctype = (String) docInfo.get("doctype");
|
|
| 2072 |
ObjectFormat format = ObjectFormat.convert(doctype); |
|
| 2073 |
if (format == null) {
|
|
| 2074 |
if (doctype.trim().equals("BIN")) {
|
|
| 2075 |
format = ObjectFormat.OCTET_STREAM; |
|
| 2076 |
} else {
|
|
| 2077 |
format = ObjectFormat.convert("text/plain");
|
|
| 2078 |
} |
|
| 2079 |
} |
|
| 2080 |
sm.setObjectFormat(format); |
|
| 2081 |
logCrud.debug("The ObjectFormat for " + localId + " is " + format.toString());
|
|
| 2082 |
|
|
| 2083 |
// further parse EML documents to get data object format, |
|
| 2084 |
// describes and describedBy information |
|
| 2085 |
if ( format == ObjectFormat.EML_2_0_0 || |
|
| 2086 |
format == ObjectFormat.EML_2_0_1 || |
|
| 2087 |
format == ObjectFormat.EML_2_1_0 ) {
|
|
| 2088 |
|
|
| 2089 |
try {
|
|
| 2090 |
DataoneEMLParser emlParser = DataoneEMLParser.getInstance(); |
|
| 2091 |
EMLDocument emlDocument = emlParser.parseDocument(is); |
|
| 2092 |
|
|
| 2093 |
// iterate through the data objects in the EML doc and add sysmeta |
|
| 2094 |
logCrud.debug("The number of data entities is: " +
|
|
| 2095 |
emlDocument.distributionMetadata.size()); |
|
| 2096 |
|
|
| 2097 |
for( int j = 0; j < emlDocument.distributionMetadata.size(); j++ ) {
|
|
| 2098 |
|
|
| 2099 |
DistributionMetadata distMetadata = |
|
| 2100 |
emlDocument.distributionMetadata.elementAt(j); |
|
| 2101 |
String dataDocUrl = distMetadata.url; |
|
| 2102 |
String dataDocMimeType = distMetadata.mimeType; |
|
| 2103 |
String dataDocLocalId = ""; |
|
| 2104 |
logCrud.debug("\tData local ID: " + dataDocLocalId);
|
|
| 2105 |
logCrud.debug("\tData URL: " + dataDocUrl);
|
|
| 2106 |
logCrud.debug("\tData mime: " + dataDocMimeType);
|
|
| 2107 |
|
|
| 2108 |
//we only handle ecogrid urls right now |
|
| 2109 |
if ( dataDocUrl.trim().startsWith("ecogrid://knb/") ) {
|
|
| 2110 |
dataDocLocalId = |
|
| 2111 |
dataDocUrl.substring(dataDocUrl.indexOf("ecogrid://knb/") +
|
|
| 2112 |
"ecogrid://knb/".length(), dataDocUrl.length()); |
|
| 2113 |
|
|
| 2114 |
//set the id |
|
| 2115 |
Identifier dataDocId = new Identifier(); |
|
| 2116 |
dataDocId.setValue(dataDocLocalId); |
|
| 2117 |
|
|
| 2118 |
// add describes into EML system metadata |
|
| 2119 |
sm.addDescribe(dataDocId); |
|
| 2120 |
|
|
| 2121 |
SystemMetadata dataSysMeta = new SystemMetadata(); |
|
| 2122 |
// check if data system metadata exists |
|
| 2123 |
try {
|
|
| 2124 |
logCrud.debug("Checking for existing system metadata for " + dataDocId.getValue());
|
|
| 2125 |
dataSysMeta = this.getSystemMetadata(token, dataDocId); |
|
| 2126 |
// add describedBy sysmeta |
|
| 2127 |
logCrud.debug("Setting describedBy for " + dataDocId.getValue() +
|
|
| 2128 |
" to " + identifier.getValue()); |
|
| 2129 |
dataSysMeta.addDescribedBy(identifier); |
|
| 2130 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType)); |
|
| 2131 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
|
| 2132 |
|
|
| 2133 |
} catch ( NotFound nf ) {
|
|
| 2134 |
// System metadata for data doesn't exist |
|
| 2135 |
logCrud.debug("There was not an existing system metadata " + "document for " + dataDocId.getValue());
|
|
| 2136 |
logCrud.debug("Creating a system metadata " + "document for " + dataDocId.getValue());
|
|
| 2137 |
dataSysMeta = this.createSystemMetadata(dataDocLocalId, token); |
|
| 2138 |
|
|
| 2139 |
logCrud.debug("Setting describedBy for " + dataDocId.getValue() + " to " + identifier.getValue());
|
|
| 2140 |
dataSysMeta.addDescribedBy(identifier); |
|
| 2141 |
|
|
| 2142 |
logCrud.debug("Setting mimeType for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
|
| 2143 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType)); |
|
| 2144 |
|
|
| 2145 |
logCrud.debug("Updating system metadata for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
|
| 2146 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
|
| 2147 |
} |
|
| 2148 |
} // end if() |
|
| 2149 |
} // end for() |
|
| 2150 |
|
|
| 2151 |
} catch ( ParserConfigurationException pce ) {
|
|
| 2152 |
logCrud.debug("There was a problem parsing the EML document. " +
|
|
| 2153 |
"The error message was: " + pce.getMessage()); |
|
| 2154 |
|
|
| 2155 |
} catch ( SAXException saxe ) {
|
|
| 2156 |
logCrud.debug("There was a problem traversing the EML document. " +
|
|
| 2157 |
"The error message was: " + saxe.getMessage()); |
|
| 2158 |
|
|
| 2159 |
} catch ( XPathExpressionException xpee ) {
|
|
| 2160 |
logCrud.debug("There was a problem searching the EML document. " +
|
|
| 2161 |
"The error message was: " + xpee.getMessage()); |
|
| 2162 |
} // end try |
|
| 2163 |
|
|
| 2164 |
} // end if() |
|
| 2165 |
|
|
| 2166 |
//create the checksum |
|
| 2167 |
is = this.get(token, identifier); |
|
| 2168 |
String checksumS = checksum(is); |
|
| 2169 |
ChecksumAlgorithm ca = ChecksumAlgorithm.convert("MD5");
|
|
| 2170 |
Checksum checksum = new Checksum(); |
|
| 2171 |
checksum.setValue(checksumS); |
|
| 2172 |
checksum.setAlgorithm(ca); |
|
| 2173 |
sm.setChecksum(checksum); |
|
| 2174 |
|
|
| 2175 |
//set the size |
|
| 2176 |
is = this.get(token, identifier); |
|
| 2177 |
sm.setSize(sizeOfStream(is)); |
|
| 2178 |
|
|
| 2179 |
//submitter |
|
| 2180 |
Principal p = new Principal(); |
|
| 2181 |
p.setValue((String) docInfo.get("user_owner"));
|
|
| 2182 |
sm.setSubmitter(p); |
|
| 2183 |
sm.setRightsHolder(p); |
|
| 2184 |
try {
|
|
| 2185 |
Date dateCreated = parseMetacatDate((String) docInfo.get("date_created"));
|
|
| 2186 |
sm.setDateUploaded(dateCreated); |
|
| 2187 |
Date dateUpdated = parseMetacatDate((String) docInfo.get("date_updated"));
|
|
| 2188 |
sm.setDateSysMetadataModified(dateUpdated); |
|
| 2189 |
} catch (Exception e) {
|
|
| 2190 |
logCrud.debug("POSSIBLE ERROR: couldn't parse a date: " + e.getMessage());
|
|
| 2191 |
Date dateCreated = new Date(); |
|
| 2192 |
sm.setDateUploaded(dateCreated); |
|
| 2193 |
Date dateUpdated = new Date(); |
|
| 2194 |
sm.setDateSysMetadataModified(dateUpdated); |
|
| 2195 |
} |
|
| 2196 |
NodeReference nr = new NodeReference(); |
|
| 2197 |
nr.setValue(PropertyService.getProperty("dataone.memberNodeId"));
|
|
| 2198 |
sm.setOriginMemberNode(nr); |
|
| 2199 |
sm.setAuthoritativeMemberNode(nr); |
|
| 2200 |
|
|
| 2201 |
// TODO: Need to set describes/describedBy |
|
| 2202 |
|
|
| 2203 |
return sm; |
|
| 2177 | 2204 |
} |
| 2178 | 2205 |
|
| 2179 | 2206 |
/** |
Also available in: Unified diff
generateMissingSystemMetadata was swallowing Exceptions instead of throwing. Refactored so that specific exceptions are thrown, affecting [create/update]SystemMetadata methods, too.