Revision 5466
Added by berkley over 14 years ago
| src/edu/ucsb/nceas/metacat/dataone/CrudService.java | ||
|---|---|---|
| 188 | 188 |
public AuthToken authenticate(String username, String password) |
| 189 | 189 |
throws ServiceFailure |
| 190 | 190 |
{
|
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/* TODO: |
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* This method is not in the original D1 crud spec. It is highly |
|
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* metacat centric. Higher level decisions need to be made on authentication |
|
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* interfaces for D1 nodes. |
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*/ |
|
| 191 | 196 |
try |
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{
|
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MetacatRestClient restClient = new MetacatRestClient(getContextUrl()); |
| ... | ... | |
| 283 | 288 |
|
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if (username == null || username.equals("public"))
|
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{
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//TODO: many of the thrown exceptions do not use the correct error codes |
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//check these against the docs and correct them |
|
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throw new NotAuthorized("1000", "User " + username + " is not authorized to create content." +
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" If you are not logged in, please do so and retry the request."); |
| 288 | 295 |
} |
| ... | ... | |
| 305 | 312 |
// Check if we are handling metadata or data |
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boolean isScienceMetadata = isScienceMetadata(sysmeta); |
| 307 | 314 |
|
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/* TODO: |
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* For EML documents, the data url field needs to be checked here |
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* and the describes and describedBy fields of the system metadata |
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* need to be set with the appropriate uri. Older EML documents |
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* maybe have ecogrid:// uri's embedded in them. See bug 618 |
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* (https://trac.dataone.org/ticket/618) for more info on this. |
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*/ |
|
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if (isScienceMetadata) {
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// CASE METADATA: |
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try {
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System.out.println("CrudService: inserting document with guid " + guid.getValue());
|
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//System.out.println("CrudService: inserting document with guid " + guid.getValue());
|
|
| 312 | 326 |
this.insertDocument(object, guid, sessionData); |
| 313 | 327 |
localId = im.getLocalId(guid.getValue()); |
| 314 | 328 |
} catch (IOException e) {
|
| ... | ... | |
| 332 | 346 |
// For Metadata and Data, insert the system metadata into the object store too |
| 333 | 347 |
String sysMetaLocalId = insertSystemMetadata(sysmeta, sessionData); |
| 334 | 348 |
//get the document info. add any access params for the sysmeta too |
| 335 |
System.out.println("looking for access records to add for system " +
|
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"metadata who's parent doc's local id is " + localId); |
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//System.out.println("looking for access records to add for system " +
|
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// "metadata who's parent doc's local id is " + localId);
|
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| 337 | 351 |
try |
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{
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Hashtable<String, Object> h = im.getDocumentInfo(localId.substring(0, localId.lastIndexOf(".")));
|
| ... | ... | |
| 346 | 360 |
String permissionType = (String)ah.get("permission_type");
|
| 347 | 361 |
String permissionOrder = (String)ah.get("permission_order");
|
| 348 | 362 |
int perm = new Integer(permission).intValue(); |
| 349 |
System.out.println("found access record for principal " + principal);
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System.out.println("permission: " + perm + " perm_type: " + permissionType +
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" perm_order: " + permissionOrder); |
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//System.out.println("found access record for principal " + principal);
|
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//System.out.println("permission: " + perm + " perm_type: " + permissionType +
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// " perm_order: " + permissionOrder);
|
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| 352 | 366 |
this.setAccess(token, guid, principal, perm, permissionType, permissionOrder, true); |
| 353 | 367 |
} |
| 354 | 368 |
} |
| ... | ... | |
| 356 | 370 |
{
|
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logMetacat.error("Error setting permissions on System Metadata object " +
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| 358 | 372 |
" with id " + sysMetaLocalId + ": " + e.getMessage()); |
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//TODO: decide if this error should cancel the entire create or |
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//if it should continue with just a logged error. |
|
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} |
| 360 | 376 |
|
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|
| ... | ... | |
| 445 | 461 |
{
|
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perm = "write"; |
| 447 | 463 |
} |
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System.out.println("perm in setAccess: " + perm);
|
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System.out.println("permission in setAccess: " + permission);
|
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//System.out.println("perm in setAccess: " + perm);
|
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//System.out.println("permission in setAccess: " + permission);
|
|
| 450 | 466 |
setAccess(token, id, principal, perm, permissionType, permissionOrder, |
| 451 | 467 |
setSystemMetadata); |
| 452 | 468 |
|
| ... | ... | |
| 465 | 481 |
String permissionType, String permissionOrder, boolean setSystemMetadata) |
| 466 | 482 |
throws ServiceFailure |
| 467 | 483 |
{
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/* TODO: |
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* This is also not part of the D1 Crud spec. This method is needed for |
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* systems such as metacat where access to objects is controlled by |
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* and ACL. Higher level decisions need to be made about how this |
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* should work within D1. |
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*/ |
|
| 468 | 490 |
try |
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{
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final SessionData sessionData = getSessionData(token); |
| ... | ... | |
| 551 | 573 |
int totalAfterQuery = 0; |
| 552 | 574 |
try |
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{
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//TODO: Milliseconds need to be added to the dateFormat |
|
| 554 | 577 |
System.out.println("=========== Listing Objects =============");
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| 555 | 578 |
System.out.println("Current server time is: " + new Date());
|
| 556 | 579 |
if(startTime != null) |
| ... | ... | |
| 562 | 585 |
System.out.println("query end time is " + endTime);
|
| 563 | 586 |
} |
| 564 | 587 |
params.clear(); |
| 588 |
/* TODO: |
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* These metacat queries should not be hard coded here. They |
|
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* should be accessed from within a .properties file |
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*/ |
|
| 565 | 592 |
params.put("returndoctype", new String[] {"http://dataone.org/service/types/SystemMetadata/0.1"});
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| 566 | 593 |
params.put("qformat", new String[] {"xml"});
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| 567 | 594 |
params.put("returnfield", new String[] {"size", "originMemberNode",
|
| ... | ... | |
| 592 | 619 |
Vector<Document> docCopy = new Vector<Document>(); |
| 593 | 620 |
|
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//preparse the list to remove any that don't match the query params |
| 622 |
/* TODO: this type of query/subquery processing is probably not scalable |
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* to larger object stores. This code should be revisited. The metacat |
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* query handler should probably be altered to handle the type of query |
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* done here. |
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*/ |
|
| 595 | 627 |
for(int i=0; i<docs.size(); i++) |
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{
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Document d = (Document)docs.get(i); |
| ... | ... | |
| 617 | 649 |
//dateSysMetadataModified = parseDate(dateSMM); |
| 618 | 650 |
if(dateSMM.indexOf(".") != -1)
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| 619 | 651 |
{ //strip the milliseconds
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//TODO: don't do this. we need milliseconds now. |
|
| 620 | 653 |
dateSMM = dateSMM.substring(0, dateSMM.indexOf(".")) + 'Z';
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| 621 | 654 |
} |
| 622 | 655 |
//System.out.println("dateSMM: " + dateSMM);
|
| ... | ... | |
| 852 | 885 |
" dataSink: " + dataSink + " localId: " + localId + |
| 853 | 886 |
" username: " + username + " params: " + params.toString()); |
| 854 | 887 |
*/ |
| 888 |
/* TODO: |
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* This multithreaded approach to getting data without |
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* being memory bound causes problems with exception |
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* handling. The only exception the produce method |
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* will return is an IOException, rendering all of the |
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* catch blocks below mute. This should probably be changed |
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* to use a memory mapped solution instead so that we |
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* can properly pass exceptions to the client. |
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* see https://trac.dataone.org/ticket/706 |
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*/ |
|
| 855 | 898 |
handler.readFromMetacat(metacatUrl, null, |
| 856 | 899 |
dataSink, localId, "xml", |
| 857 | 900 |
username, |
| ... | ... | |
| 906 | 949 |
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, |
| 907 | 950 |
InvalidRequest, NotImplemented {
|
| 908 | 951 |
logCrud.info("getChecksum");
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//TODO: this could now easily be implemented |
|
| 909 | 953 |
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 910 | 954 |
} |
| 911 | 955 |
|
| ... | ... | |
| 916 | 960 |
String checksumAlgorithm) throws InvalidToken, ServiceFailure, |
| 917 | 961 |
NotAuthorized, NotFound, InvalidRequest, NotImplemented {
|
| 918 | 962 |
logCrud.info("getChecksum");
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//TODO: this could now easily be implemented |
|
| 919 | 964 |
throw new NotImplemented("1000", "This method not yet implemented.");
|
| 920 | 965 |
} |
| 921 | 966 |
|
| ... | ... | |
| 1153 | 1198 |
public Date parseDate(String s) |
| 1154 | 1199 |
throws Exception |
| 1155 | 1200 |
{
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/* TODO: |
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* This method should be replaced by a DateFormatter |
|
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*/ |
|
| 1156 | 1204 |
Date d = null; |
| 1157 | 1205 |
int tIndex = s.indexOf("T");
|
| 1158 | 1206 |
int zIndex = s.indexOf("Z");
|
| ... | ... | |
| 1242 | 1290 |
*/ |
| 1243 | 1291 |
private boolean isScienceMetadata(SystemMetadata sysmeta) {
|
| 1244 | 1292 |
boolean scimeta = false; |
| 1293 |
//TODO: this should be read from a .properties file instead of being hard coded |
|
| 1245 | 1294 |
switch (sysmeta.getObjectFormat()) {
|
| 1246 | 1295 |
case EML_2_1_0: scimeta = true; break; |
| 1247 | 1296 |
case EML_2_0_1: scimeta = true; break; |
| ... | ... | |
| 1378 | 1427 |
|
| 1379 | 1428 |
return newFile; |
| 1380 | 1429 |
} |
| 1381 |
|
|
| 1382 |
private static Date getDateInTimeZone(Date currentDate, String timeZoneId) |
|
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{
|
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TimeZone tz = TimeZone.getTimeZone(timeZoneId); |
|
| 1385 |
Calendar mbCal = new GregorianCalendar(TimeZone.getTimeZone(timeZoneId)); |
|
| 1386 |
mbCal.setTimeInMillis(currentDate.getTime()); |
|
| 1387 | 1430 |
|
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Calendar cal = Calendar.getInstance(); |
|
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cal.set(Calendar.YEAR, mbCal.get(Calendar.YEAR)); |
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cal.set(Calendar.MONTH, mbCal.get(Calendar.MONTH)); |
|
| 1391 |
cal.set(Calendar.DAY_OF_MONTH, mbCal.get(Calendar.DAY_OF_MONTH)); |
|
| 1392 |
cal.set(Calendar.HOUR_OF_DAY, mbCal.get(Calendar.HOUR_OF_DAY)); |
|
| 1393 |
cal.set(Calendar.MINUTE, mbCal.get(Calendar.MINUTE)); |
|
| 1394 |
cal.set(Calendar.SECOND, mbCal.get(Calendar.SECOND)); |
|
| 1395 |
cal.set(Calendar.MILLISECOND, mbCal.get(Calendar.MILLISECOND)); |
|
| 1396 |
|
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| 1397 |
return cal.getTime(); |
|
| 1398 |
} |
|
| 1399 |
|
|
| 1400 | 1431 |
/** |
| 1401 | 1432 |
* insert a systemMetadata doc, return the localId of the sysmeta |
| 1402 | 1433 |
*/ |
| ... | ... | |
| 1776 | 1807 |
sm.setDateSysMetadataModified(dateUpdated); |
| 1777 | 1808 |
} |
| 1778 | 1809 |
NodeReference nr = new NodeReference(); |
| 1810 |
//TODO: this should be set to be something more meaningful once the registry is up |
|
| 1779 | 1811 |
nr.setValue("metacat");
|
| 1780 | 1812 |
sm.setOriginMemberNode(nr); |
| 1781 | 1813 |
sm.setAuthoritativeMemberNode(nr); |
Also available in: Unified diff
added TODOs and cleaned up the code a bit