Revision 6367
Added by ben leinfelder almost 13 years ago
| src/edu/ucsb/nceas/metacat/restservice/MNResourceHandler.java | ||
|---|---|---|
| 28 | 28 |
import java.io.IOException; |
| 29 | 29 |
import java.io.InputStream; |
| 30 | 30 |
import java.io.OutputStream; |
| 31 |
import java.io.UnsupportedEncodingException; |
|
| 32 | 31 |
import java.text.DateFormat; |
| 33 | 32 |
import java.text.ParseException; |
| 34 | 33 |
import java.text.SimpleDateFormat; |
| ... | ... | |
| 73 | 72 |
import org.dataone.service.types.v1.Permission; |
| 74 | 73 |
import org.dataone.service.types.v1.Subject; |
| 75 | 74 |
import org.dataone.service.types.v1.SystemMetadata; |
| 75 |
import org.dataone.service.util.TypeMarshaller; |
|
| 76 | 76 |
import org.jibx.runtime.JiBXException; |
| 77 | 77 |
|
| 78 | 78 |
import edu.ucsb.nceas.metacat.dataone.MNodeService; |
| ... | ... | |
| 307 | 307 |
* @throws ServiceFailure |
| 308 | 308 |
* @throws NotAuthorized |
| 309 | 309 |
* @throws InvalidRequest |
| 310 |
* @throws UnsupportedEncodingException |
|
| 311 | 310 |
* @throws JiBXException |
| 311 |
* @throws IllegalAccessException |
|
| 312 |
* @throws InstantiationException |
|
| 313 |
* @throws IOException |
|
| 312 | 314 |
*/ |
| 313 |
private void syncError() throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest, UnsupportedEncodingException, JiBXException {
|
|
| 315 |
private void syncError() throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest, JiBXException, IOException, InstantiationException, IllegalAccessException {
|
|
| 314 | 316 |
SynchronizationFailed syncFailed = null; |
| 315 | 317 |
if (params.containsKey("message")) {
|
| 316 | 318 |
String message = params.get("message")[0];
|
| 317 |
syncFailed = (SynchronizationFailed) deserializeServiceType(SynchronizationFailed.class, new ByteArrayInputStream(message.getBytes("UTF-8")));
|
|
| 319 |
syncFailed = TypeMarshaller.unmarshalTypeFromStream(SynchronizationFailed.class, new ByteArrayInputStream(message.getBytes("UTF-8")));
|
|
| 318 | 320 |
} |
| 319 | 321 |
MNodeService.getInstance().synchronizationFailed(session, syncFailed); |
| 320 | 322 |
} |
| ... | ... | |
| 415 | 417 |
response.setStatus(200); |
| 416 | 418 |
response.setContentType("text/xml");
|
| 417 | 419 |
|
| 418 |
serializeServiceType(MonitorList.class, monitorList, out);
|
|
| 420 |
TypeMarshaller.marshalTypeToOutputStream(monitorList, out);
|
|
| 419 | 421 |
|
| 420 | 422 |
return true; |
| 421 | 423 |
|
| ... | ... | |
| 484 | 486 |
logMetacat.debug("got checksum " + c.getValue());
|
| 485 | 487 |
response.setStatus(200); |
| 486 | 488 |
logMetacat.debug("serializing response");
|
| 487 |
serializeServiceType(Checksum.class, c, response.getOutputStream());
|
|
| 489 |
TypeMarshaller.marshalTypeToOutputStream(c, response.getOutputStream());
|
|
| 488 | 490 |
logMetacat.debug("done serializing response.");
|
| 489 | 491 |
|
| 490 | 492 |
} |
| ... | ... | |
| 500 | 502 |
* @throws InsufficientResources |
| 501 | 503 |
* @throws NotAuthorized |
| 502 | 504 |
* @throws NotImplemented |
| 505 |
* @throws IllegalAccessException |
|
| 506 |
* @throws InstantiationException |
|
| 503 | 507 |
*/ |
| 504 |
private void replicate() throws ServiceFailure, InvalidRequest, IOException, FileUploadException, JiBXException, NotImplemented, NotAuthorized, InsufficientResources, UnsupportedType {
|
|
| 508 |
private void replicate() throws ServiceFailure, InvalidRequest, IOException, FileUploadException, JiBXException, NotImplemented, NotAuthorized, InsufficientResources, UnsupportedType, InstantiationException, IllegalAccessException {
|
|
| 505 | 509 |
|
| 506 | 510 |
logMetacat.debug("in POST replicate()");
|
| 507 | 511 |
|
| ... | ... | |
| 510 | 514 |
|
| 511 | 515 |
String sn = multipartparams.get("sourceNode").get(0);
|
| 512 | 516 |
logMetacat.debug("sourceNode: " + sn);
|
| 513 |
NodeReference sourceNode = (NodeReference) deserializeServiceType(NodeReference.class, new ByteArrayInputStream(sn.getBytes("UTF-8")));
|
|
| 517 |
NodeReference sourceNode = TypeMarshaller.unmarshalTypeFromStream(NodeReference.class, new ByteArrayInputStream(sn.getBytes("UTF-8")));
|
|
| 514 | 518 |
|
| 515 | 519 |
MNodeService.getInstance().replicate(session, sysmeta, sourceNode); |
| 516 | 520 |
|
| ... | ... | |
| 538 | 542 |
|
| 539 | 543 |
response.setContentType("text/xml");
|
| 540 | 544 |
response.setStatus(200); |
| 541 |
serializeServiceType(NodeList.class, nl, response.getOutputStream());
|
|
| 545 |
TypeMarshaller.marshalTypeToOutputStream(nl, response.getOutputStream());
|
|
| 542 | 546 |
|
| 543 | 547 |
} |
| 544 | 548 |
|
| ... | ... | |
| 565 | 569 |
DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss.SZ");
|
| 566 | 570 |
response.addHeader("pid", pid);
|
| 567 | 571 |
response.addHeader("checksum", dr.getDataONE_Checksum().getValue());
|
| 568 |
response.addHeader("checksum_algorithm", dr.getDataONE_Checksum().getAlgorithm().name());
|
|
| 572 |
response.addHeader("checksum_algorithm", dr.getDataONE_Checksum().getAlgorithm().xmlValue());
|
|
| 569 | 573 |
response.addHeader("content_length", dr.getContent_Length() + "");
|
| 570 | 574 |
response.addHeader("last_modified", dateFormat.format(dr.getLast_Modified()));
|
| 571 | 575 |
response.addHeader("format", dr.getDataONE_ObjectFormat().toString());
|
| ... | ... | |
| 633 | 637 |
response.setStatus(200); |
| 634 | 638 |
response.setContentType("text/xml");
|
| 635 | 639 |
|
| 636 |
serializeServiceType(Log.class, log, out);
|
|
| 640 |
TypeMarshaller.marshalTypeToOutputStream(log, out);
|
|
| 637 | 641 |
|
| 638 | 642 |
} |
| 639 | 643 |
|
| ... | ... | |
| 771 | 775 |
response.setStatus(200); |
| 772 | 776 |
response.setContentType("text/xml");
|
| 773 | 777 |
// Serialize and write it to the output stream |
| 774 |
serializeServiceType(ObjectList.class, ol, out);
|
|
| 778 |
TypeMarshaller.marshalTypeToOutputStream(ol, out);
|
|
| 775 | 779 |
|
| 776 | 780 |
} |
| 777 | 781 |
|
| ... | ... | |
| 801 | 805 |
OutputStream out = response.getOutputStream(); |
| 802 | 806 |
|
| 803 | 807 |
// Serialize and write it to the output stream |
| 804 |
serializeServiceType(SystemMetadata.class, sysmeta, out);
|
|
| 808 |
TypeMarshaller.marshalTypeToOutputStream(sysmeta, out);
|
|
| 805 | 809 |
} |
| 806 | 810 |
|
| 807 | 811 |
|
| ... | ... | |
| 822 | 826 |
* @throws InvalidToken |
| 823 | 827 |
* @throws NotFound |
| 824 | 828 |
* @throws IOException |
| 829 |
* @throws IllegalAccessException |
|
| 830 |
* @throws InstantiationException |
|
| 825 | 831 |
*/ |
| 826 |
protected void putObject(String pid, String action) throws ServiceFailure, InvalidRequest, JiBXException, InvalidToken, NotAuthorized, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, NotFound, IOException {
|
|
| 832 |
protected void putObject(String pid, String action) throws ServiceFailure, InvalidRequest, JiBXException, InvalidToken, NotAuthorized, IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, NotFound, IOException, InstantiationException, IllegalAccessException {
|
|
| 827 | 833 |
logMetacat.debug("putObject with pid " + pid);
|
| 828 | 834 |
logMetacat.debug("Entering putObject: " + pid + "/" + action);
|
| 829 | 835 |
|
| ... | ... | |
| 844 | 850 |
if (action.equals(FUNCTION_NAME_INSERT)) {
|
| 845 | 851 |
// handle inserts |
| 846 | 852 |
logMetacat.debug("Commence creation...");
|
| 847 |
SystemMetadata smd = (SystemMetadata) deserializeServiceType(SystemMetadata.class, sysmeta);
|
|
| 853 |
SystemMetadata smd = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, sysmeta);
|
|
| 848 | 854 |
|
| 849 | 855 |
Identifier id = new Identifier(); |
| 850 | 856 |
id.setValue(pid); |
| 851 | 857 |
logMetacat.debug("creating object with pid " + pid);
|
| 852 | 858 |
Identifier rId = MNodeService.getInstance().create(session, id, object, smd); |
| 853 |
serializeServiceType(Identifier.class, rId, out);
|
|
| 859 |
TypeMarshaller.marshalTypeToOutputStream(rId, out);
|
|
| 854 | 860 |
|
| 855 | 861 |
} else if (action.equals(FUNCTION_NAME_UPDATE)) {
|
| 856 | 862 |
// handle updates |
| ... | ... | |
| 870 | 876 |
logMetacat.debug("Commence update...");
|
| 871 | 877 |
|
| 872 | 878 |
// get the systemmetadata object |
| 873 |
SystemMetadata smd = (SystemMetadata) deserializeServiceType(SystemMetadata.class, sysmeta);
|
|
| 879 |
SystemMetadata smd = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, sysmeta);
|
|
| 874 | 880 |
|
| 875 | 881 |
Identifier rId = MNodeService.getInstance().update(session, newPid, object, obsoletedPid, smd); |
| 876 |
serializeServiceType(Identifier.class, rId, out);
|
|
| 882 |
TypeMarshaller.marshalTypeToOutputStream(rId, out);
|
|
| 877 | 883 |
} else {
|
| 878 | 884 |
throw new InvalidRequest("1000", "Operation must be create or update.");
|
| 879 | 885 |
} |
| ... | ... | |
| 905 | 911 |
|
| 906 | 912 |
logMetacat.debug("Calling delete");
|
| 907 | 913 |
MNodeService.getInstance().delete(session, id); |
| 908 |
serializeServiceType(Identifier.class, id, out);
|
|
| 914 |
TypeMarshaller.marshalTypeToOutputStream(id, out);
|
|
| 909 | 915 |
|
| 910 | 916 |
} |
| 911 | 917 |
|
| 912 | 918 |
/** |
| 913 | 919 |
* set the access perms on a document |
| 914 | 920 |
* @throws JiBXException |
| 915 |
* @throws UnsupportedEncodingException |
|
| 916 | 921 |
* @throws InvalidRequest |
| 917 | 922 |
* @throws NotImplemented |
| 918 | 923 |
* @throws NotAuthorized |
| 919 | 924 |
* @throws NotFound |
| 920 | 925 |
* @throws ServiceFailure |
| 921 | 926 |
* @throws InvalidToken |
| 927 |
* @throws IllegalAccessException |
|
| 928 |
* @throws InstantiationException |
|
| 929 |
* @throws IOException |
|
| 922 | 930 |
*/ |
| 923 |
protected void setAccess() throws UnsupportedEncodingException, JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest
|
|
| 931 |
protected void setAccess() throws JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest, IOException, InstantiationException, IllegalAccessException
|
|
| 924 | 932 |
{
|
| 925 | 933 |
|
| 926 | 934 |
String pid = params.get("pid")[0];
|
| 927 | 935 |
Identifier id = new Identifier(); |
| 928 | 936 |
id.setValue(pid); |
| 929 | 937 |
String accesspolicy = params.get("accesspolicy")[0];
|
| 930 |
AccessPolicy accessPolicy = (AccessPolicy) deserializeServiceType(AccessPolicy.class, new ByteArrayInputStream(accesspolicy.getBytes("UTF-8")));
|
|
| 938 |
AccessPolicy accessPolicy = TypeMarshaller.unmarshalTypeFromStream(AccessPolicy.class, new ByteArrayInputStream(accesspolicy.getBytes("UTF-8")));
|
|
| 931 | 939 |
MNodeService.getInstance().setAccessPolicy(session, id, accessPolicy); |
| 932 | 940 |
|
| 933 | 941 |
|
| src/edu/ucsb/nceas/metacat/restservice/ResourceHandler.java | ||
|---|---|---|
| 50 | 50 |
|
| 51 | 51 |
import org.apache.commons.io.IOUtils; |
| 52 | 52 |
import org.apache.log4j.Logger; |
| 53 |
import org.apache.maven.artifact.ant.shaded.IOUtil; |
|
| 54 | 53 |
import org.dataone.client.MNode; |
| 55 | 54 |
import org.dataone.client.ObjectFormatCache; |
| 56 | 55 |
import org.dataone.client.auth.CertificateManager; |
| ... | ... | |
| 87 | 86 |
import org.dataone.service.types.v1.Session; |
| 88 | 87 |
import org.dataone.service.types.v1.SystemMetadata; |
| 89 | 88 |
import org.dataone.service.types.v1.util.ChecksumUtil; |
| 90 |
import org.dataone.service.types.util.ServiceTypeUtil;
|
|
| 89 |
import org.dataone.service.util.TypeMarshaller;
|
|
| 91 | 90 |
import org.jibx.runtime.BindingDirectory; |
| 92 | 91 |
import org.jibx.runtime.IBindingFactory; |
| 93 | 92 |
import org.jibx.runtime.IUnmarshallingContext; |
| ... | ... | |
| 825 | 824 |
DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss.SZ");
|
| 826 | 825 |
response.addHeader("guid", guid);
|
| 827 | 826 |
response.addHeader("checksum", dr.getDataONE_Checksum().getValue());
|
| 828 |
response.addHeader("checksum_algorithm", dr.getDataONE_Checksum().getAlgorithm().name());
|
|
| 827 |
response.addHeader("checksum_algorithm", dr.getDataONE_Checksum().getAlgorithm().xmlValue());
|
|
| 829 | 828 |
response.addHeader("content_length", dr.getContent_Length() + "");
|
| 830 | 829 |
response.addHeader("last_modified", dateFormat.format(dr.getLast_Modified()));
|
| 831 | 830 |
response.addHeader("format", dr.getDataONE_ObjectFormat().toString());
|
| ... | ... | |
| 1361 | 1360 |
* @param object the object to serialize |
| 1362 | 1361 |
* @param out the stream to serialize it to |
| 1363 | 1362 |
* @throws JiBXException |
| 1363 |
* @throws IOException |
|
| 1364 | 1364 |
*/ |
| 1365 | 1365 |
protected void serializeServiceType(Class type, Object object, OutputStream out) |
| 1366 |
throws JiBXException |
|
| 1366 |
throws JiBXException, IOException
|
|
| 1367 | 1367 |
{
|
| 1368 |
ServiceTypeUtil.serializeServiceType(type, object, out);
|
|
| 1368 |
TypeMarshaller.marshalTypeToOutputStream(object, out);
|
|
| 1369 | 1369 |
} |
| 1370 | 1370 |
|
| 1371 | 1371 |
/** |
| ... | ... | |
| 1373 | 1373 |
* @param type the class of the object to serialize (i.e. SystemMetadata.class) |
| 1374 | 1374 |
* @param is the stream to deserialize from |
| 1375 | 1375 |
* @throws JiBXException |
| 1376 |
* @throws IllegalAccessException |
|
| 1377 |
* @throws InstantiationException |
|
| 1378 |
* @throws IOException |
|
| 1376 | 1379 |
*/ |
| 1377 | 1380 |
protected Object deserializeServiceType(Class type, InputStream is) |
| 1378 |
throws JiBXException |
|
| 1381 |
throws JiBXException, IOException, InstantiationException, IllegalAccessException
|
|
| 1379 | 1382 |
{
|
| 1380 |
return ServiceTypeUtil.deserializeServiceType(type, is);
|
|
| 1383 |
return TypeMarshaller.unmarshalTypeFromStream(type, is);
|
|
| 1381 | 1384 |
} |
| 1382 | 1385 |
|
| 1383 | 1386 |
/** |
| ... | ... | |
| 1546 | 1549 |
* |
| 1547 | 1550 |
* @param guid - ID of data object to be inserted or updated. If action is update, the pid |
| 1548 | 1551 |
* is the existing pid. If insert, the pid is the new one |
| 1549 |
* @throws IOException |
|
| 1552 |
* @throws IOException
|
|
| 1550 | 1553 |
*/ |
| 1551 |
protected void putObject(String pid, String action) {
|
|
| 1554 |
protected void putObject(String pid, String action) throws IOException {
|
|
| 1552 | 1555 |
System.out.println("ResourceHandler: putObject with pid " + pid);
|
| 1553 | 1556 |
logMetacat.debug("Entering putObject: " + pid + "/" + action);
|
| 1554 | 1557 |
OutputStream out = null; |
| ... | ... | |
| 1952 | 1955 |
response.setStatus(200); |
| 1953 | 1956 |
serializeException(e, out); |
| 1954 | 1957 |
|
| 1955 |
} catch (JiBXException jibxe) {
|
|
| 1958 |
} catch (Exception e) {
|
|
| 1956 | 1959 |
response.setStatus(501); |
| 1957 |
ServiceFailure e = |
|
| 1960 |
ServiceFailure se =
|
|
| 1958 | 1961 |
new ServiceFailure("4841", "Unexpected exception from the service - " +
|
| 1959 |
jibxe.getClass() + ": " + jibxe.getMessage());
|
|
| 1960 |
serializeException(e, out); |
|
| 1962 |
e.getClass() + ": " + e.getMessage());
|
|
| 1963 |
serializeException(se, out);
|
|
| 1961 | 1964 |
|
| 1962 | 1965 |
} |
| 1963 | 1966 |
|
| ... | ... | |
| 2012 | 2015 |
response.setStatus(200); |
| 2013 | 2016 |
serializeException(e, out); |
| 2014 | 2017 |
|
| 2015 |
} catch (JiBXException jibxe) {
|
|
| 2016 |
ServiceFailure e = |
|
| 2018 |
} catch (Exception e) {
|
|
| 2019 |
ServiceFailure se =
|
|
| 2017 | 2020 |
new ServiceFailure("4841", "Unexpected exception from the service - " +
|
| 2018 |
jibxe.getClass() + ": " + jibxe.getMessage());
|
|
| 2019 |
serializeException(e, out); |
|
| 2021 |
e.getClass() + ": " + e.getMessage());
|
|
| 2022 |
serializeException(se, out);
|
|
| 2020 | 2023 |
|
| 2021 | 2024 |
} |
| 2022 | 2025 |
|
| ... | ... | |
| 2137 | 2140 |
+ guid.getValue()); |
| 2138 | 2141 |
boolean result = CNodeService.getInstance().registerSystemMetadata( |
| 2139 | 2142 |
session, guid, systemMetadata); |
| 2140 |
serializeServiceType(Boolean.class, result, out);
|
|
| 2143 |
TypeMarshaller.marshalTypeToOutputStream(result, out);
|
|
| 2141 | 2144 |
|
| 2142 | 2145 |
} catch (NotAuthorized e) {
|
| 2143 | 2146 |
response.setStatus(500); |
| ... | ... | |
| 2154 | 2157 |
} catch (InvalidRequest e) {
|
| 2155 | 2158 |
response.setStatus(500); |
| 2156 | 2159 |
serializeException(e, out); |
| 2157 |
} catch (JiBXException e) {
|
|
| 2160 |
} catch (InvalidSystemMetadata e) {
|
|
| 2161 |
serializeException(e, out); |
|
| 2162 |
} catch (Exception e) {
|
|
| 2158 | 2163 |
response.setStatus(500); |
| 2159 | 2164 |
e.printStackTrace(System.out); |
| 2160 | 2165 |
InvalidSystemMetadata ism = new InvalidSystemMetadata("1080", e
|
| 2161 | 2166 |
.getMessage()); |
| 2162 | 2167 |
serializeException(ism, out); |
| 2163 |
} catch (InvalidSystemMetadata e) {
|
|
| 2164 |
serializeException(e, out); |
|
| 2165 |
} |
|
| 2168 |
} |
|
| 2166 | 2169 |
} |
| 2167 | 2170 |
|
| 2168 | 2171 |
} |
| src/edu/ucsb/nceas/metacat/restservice/CNResourceHandler.java | ||
|---|---|---|
| 28 | 28 |
import java.io.IOException; |
| 29 | 29 |
import java.io.InputStream; |
| 30 | 30 |
import java.io.OutputStream; |
| 31 |
import java.io.UnsupportedEncodingException; |
|
| 32 | 31 |
import java.util.Date; |
| 33 | 32 |
import java.util.Map; |
| 34 | 33 |
|
| ... | ... | |
| 64 | 63 |
import org.dataone.service.types.v1.QueryType; |
| 65 | 64 |
import org.dataone.service.types.v1.Subject; |
| 66 | 65 |
import org.dataone.service.types.v1.SystemMetadata; |
| 66 |
import org.dataone.service.util.TypeMarshaller; |
|
| 67 | 67 |
import org.jibx.runtime.JiBXException; |
| 68 | 68 |
|
| 69 | 69 |
import edu.ucsb.nceas.metacat.dataone.CNodeService; |
| ... | ... | |
| 316 | 316 |
logMetacat.debug("got checksum " + c.getValue());
|
| 317 | 317 |
response.setStatus(200); |
| 318 | 318 |
logMetacat.debug("serializing response");
|
| 319 |
serializeServiceType(Checksum.class, c, response.getOutputStream());
|
|
| 319 |
TypeMarshaller.marshalTypeToOutputStream(c, response.getOutputStream());
|
|
| 320 | 320 |
logMetacat.debug("done serializing response.");
|
| 321 | 321 |
|
| 322 | 322 |
} |
| ... | ... | |
| 383 | 383 |
response.setStatus(200); |
| 384 | 384 |
response.setContentType("text/xml");
|
| 385 | 385 |
|
| 386 |
serializeServiceType(Log.class, log, out);
|
|
| 386 |
TypeMarshaller.marshalTypeToOutputStream(log, out);
|
|
| 387 | 387 |
|
| 388 | 388 |
} |
| 389 | 389 |
|
| ... | ... | |
| 461 | 461 |
OutputStream out = response.getOutputStream(); |
| 462 | 462 |
|
| 463 | 463 |
// Serialize and write it to the output stream |
| 464 |
serializeServiceType(SystemMetadata.class, sysmeta, out);
|
|
| 464 |
TypeMarshaller.marshalTypeToOutputStream(sysmeta, out);
|
|
| 465 | 465 |
} |
| 466 | 466 |
|
| 467 | 467 |
/** |
| ... | ... | |
| 480 | 480 |
* @throws NotAuthorized |
| 481 | 481 |
* @throws InvalidToken |
| 482 | 482 |
* @throws IOException |
| 483 |
* @throws IllegalAccessException |
|
| 484 |
* @throws InstantiationException |
|
| 483 | 485 |
*/ |
| 484 |
protected void putObject(String pid, String action) throws ServiceFailure, InvalidRequest, IdentifierNotUnique, JiBXException, InvalidToken, NotAuthorized, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, IOException {
|
|
| 486 |
protected void putObject(String pid, String action) throws ServiceFailure, InvalidRequest, IdentifierNotUnique, JiBXException, InvalidToken, NotAuthorized, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, IOException, InstantiationException, IllegalAccessException {
|
|
| 485 | 487 |
logMetacat.debug("Entering putObject: " + pid + "/" + action);
|
| 486 | 488 |
|
| 487 | 489 |
// Read the incoming data from its Mime Multipart encoding |
| ... | ... | |
| 497 | 499 |
if (action.equals(FUNCTION_NAME_INSERT)) { //handle inserts
|
| 498 | 500 |
|
| 499 | 501 |
logMetacat.debug("Commence creation...");
|
| 500 |
SystemMetadata smd = (SystemMetadata) deserializeServiceType(SystemMetadata.class, sysmeta);
|
|
| 502 |
SystemMetadata smd = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, sysmeta);
|
|
| 501 | 503 |
|
| 502 | 504 |
Identifier id = new Identifier(); |
| 503 | 505 |
id.setValue(pid); |
| ... | ... | |
| 508 | 510 |
response.setStatus(200); |
| 509 | 511 |
response.setContentType("text/xml");
|
| 510 | 512 |
|
| 511 |
serializeServiceType(Identifier.class, rId, out);
|
|
| 513 |
TypeMarshaller.marshalTypeToOutputStream(rId, out);
|
|
| 512 | 514 |
|
| 513 | 515 |
} else {
|
| 514 | 516 |
throw new InvalidRequest("1000", "Operation must be create.");
|
| ... | ... | |
| 534 | 536 |
response.setStatus(200); |
| 535 | 537 |
response.setContentType("text/xml");
|
| 536 | 538 |
|
| 537 |
serializeServiceType(ObjectFormatList.class, objectFormatList, out);
|
|
| 539 |
TypeMarshaller.marshalTypeToOutputStream(objectFormatList, out);
|
|
| 538 | 540 |
|
| 539 | 541 |
} |
| 540 | 542 |
|
| ... | ... | |
| 563 | 565 |
response.setStatus(200); |
| 564 | 566 |
response.setContentType("text/xml");
|
| 565 | 567 |
|
| 566 |
serializeServiceType(ObjectFormat.class, objectFormat, out);
|
|
| 568 |
TypeMarshaller.marshalTypeToOutputStream(objectFormat, out);
|
|
| 567 | 569 |
|
| 568 | 570 |
} |
| 569 | 571 |
|
| ... | ... | |
| 605 | 607 |
OutputStream out = response.getOutputStream(); |
| 606 | 608 |
response.setStatus(200); |
| 607 | 609 |
response.setContentType("text/xml");
|
| 608 |
serializeServiceType(Identifier.class, retPid, out);
|
|
| 610 |
TypeMarshaller.marshalTypeToOutputStream(retPid, out);
|
|
| 609 | 611 |
|
| 610 | 612 |
} |
| 611 | 613 |
|
| ... | ... | |
| 628 | 630 |
OutputStream out = response.getOutputStream(); |
| 629 | 631 |
response.setStatus(200); |
| 630 | 632 |
response.setContentType("text/xml");
|
| 631 |
serializeServiceType(ObjectLocationList.class, locationList, out);
|
|
| 633 |
TypeMarshaller.marshalTypeToOutputStream(locationList, out);
|
|
| 632 | 634 |
|
| 633 | 635 |
} |
| 634 | 636 |
|
| ... | ... | |
| 676 | 678 |
* @throws NotImplemented |
| 677 | 679 |
* @throws InvalidRequest |
| 678 | 680 |
* @throws IOException |
| 681 |
* @throws IllegalAccessException |
|
| 682 |
* @throws InstantiationException |
|
| 679 | 683 |
*/ |
| 680 |
private void owner(String id) throws JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest, IOException {
|
|
| 684 |
private void owner(String id) throws JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest, IOException, InstantiationException, IllegalAccessException {
|
|
| 681 | 685 |
Identifier pid = new Identifier(); |
| 682 | 686 |
pid.setValue(id); |
| 683 | 687 |
String subjectStr = params.get("subject")[0];
|
| 684 |
Subject subject = (Subject) deserializeServiceType(Subject.class, new ByteArrayInputStream(subjectStr.getBytes("UTF-8")));
|
|
| 688 |
Subject subject = TypeMarshaller.unmarshalTypeFromStream(Subject.class, new ByteArrayInputStream(subjectStr.getBytes("UTF-8")));
|
|
| 685 | 689 |
Identifier retPid = CNodeService.getInstance().setOwner(session, pid, subject); |
| 686 | 690 |
OutputStream out = response.getOutputStream(); |
| 687 | 691 |
response.setStatus(200); |
| 688 | 692 |
response.setContentType("text/xml");
|
| 689 |
serializeServiceType(Identifier.class, retPid, out);
|
|
| 693 |
TypeMarshaller.marshalTypeToOutputStream(retPid, out);
|
|
| 690 | 694 |
} |
| 691 | 695 |
|
| 692 | 696 |
/** |
| ... | ... | |
| 721 | 725 |
* @throws InvalidSystemMetadata |
| 722 | 726 |
* @throws NotAuthorized |
| 723 | 727 |
* @throws NotImplemented |
| 728 |
* @throws IllegalAccessException |
|
| 729 |
* @throws InstantiationException |
|
| 724 | 730 |
*/ |
| 725 |
protected boolean registerSystemMetadata(String pid) throws ServiceFailure, InvalidRequest, IOException, FileUploadException, JiBXException, NotImplemented, NotAuthorized, InvalidSystemMetadata {
|
|
| 731 |
protected boolean registerSystemMetadata(String pid) throws ServiceFailure, InvalidRequest, IOException, FileUploadException, JiBXException, NotImplemented, NotAuthorized, InvalidSystemMetadata, InstantiationException, IllegalAccessException {
|
|
| 726 | 732 |
logMetacat.debug("Entering registerSystemMetadata: " + pid);
|
| 727 | 733 |
|
| 728 | 734 |
// get the system metadata from the request |
| ... | ... | |
| 742 | 748 |
/** |
| 743 | 749 |
* set the access perms on a document |
| 744 | 750 |
* @throws JiBXException |
| 745 |
* @throws UnsupportedEncodingException |
|
| 746 | 751 |
* @throws InvalidRequest |
| 747 | 752 |
* @throws NotImplemented |
| 748 | 753 |
* @throws NotAuthorized |
| 749 | 754 |
* @throws NotFound |
| 750 | 755 |
* @throws ServiceFailure |
| 751 | 756 |
* @throws InvalidToken |
| 757 |
* @throws IllegalAccessException |
|
| 758 |
* @throws InstantiationException |
|
| 759 |
* @throws IOException |
|
| 752 | 760 |
*/ |
| 753 |
protected void setAccess() throws UnsupportedEncodingException, JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest {
|
|
| 761 |
protected void setAccess() throws JiBXException, InvalidToken, ServiceFailure, NotFound, NotAuthorized, NotImplemented, InvalidRequest, IOException, InstantiationException, IllegalAccessException {
|
|
| 754 | 762 |
|
| 755 | 763 |
String guid = params.get("guid")[0];
|
| 756 | 764 |
Identifier id = new Identifier(); |
| 757 | 765 |
id.setValue(guid); |
| 758 | 766 |
String accesspolicy = params.get("accesspolicy")[0];
|
| 759 |
AccessPolicy accessPolicy = (AccessPolicy) deserializeServiceType(AccessPolicy.class, new ByteArrayInputStream(accesspolicy.getBytes("UTF-8")));
|
|
| 767 |
AccessPolicy accessPolicy = TypeMarshaller.unmarshalTypeFromStream(AccessPolicy.class, new ByteArrayInputStream(accesspolicy.getBytes("UTF-8")));
|
|
| 760 | 768 |
CNodeService.getInstance().setAccessPolicy(session, id, accessPolicy); |
| 761 | 769 |
|
| 762 | 770 |
} |
| src/edu/ucsb/nceas/metacat/restservice/D1ResourceHandler.java | ||
|---|---|---|
| 56 | 56 |
import org.dataone.service.exceptions.ServiceFailure; |
| 57 | 57 |
import org.dataone.service.types.v1.Session; |
| 58 | 58 |
import org.dataone.service.types.v1.SystemMetadata; |
| 59 |
import org.dataone.service.types.util.ServiceTypeUtil;
|
|
| 59 |
import org.dataone.service.util.TypeMarshaller;
|
|
| 60 | 60 |
import org.jibx.runtime.JiBXException; |
| 61 | 61 |
|
| 62 | 62 |
import edu.ucsb.nceas.metacat.MetacatHandler; |
| ... | ... | |
| 150 | 150 |
} |
| 151 | 151 |
} |
| 152 | 152 |
|
| 153 |
protected SystemMetadata collectSystemMetadata() throws IOException, FileUploadException, ServiceFailure, InvalidRequest, JiBXException {
|
|
| 153 |
protected SystemMetadata collectSystemMetadata() throws IOException, FileUploadException, ServiceFailure, InvalidRequest, JiBXException, InstantiationException, IllegalAccessException {
|
|
| 154 | 154 |
|
| 155 | 155 |
// Read the incoming data from its Mime Multipart encoding |
| 156 | 156 |
logMetacat.debug("Disassembling MIME multipart form");
|
| ... | ... | |
| 221 | 221 |
sysmeta = new FileInputStream(smFile); |
| 222 | 222 |
|
| 223 | 223 |
logMetacat.debug("Commence creation...");
|
| 224 |
SystemMetadata systemMetadata = (SystemMetadata) deserializeServiceType(SystemMetadata.class, sysmeta);
|
|
| 224 |
SystemMetadata systemMetadata = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, sysmeta);
|
|
| 225 | 225 |
return systemMetadata; |
| 226 | 226 |
} |
| 227 | 227 |
|
| ... | ... | |
| 335 | 335 |
} |
| 336 | 336 |
} |
| 337 | 337 |
|
| 338 |
/** |
|
| 339 |
* serialize an object of type to out |
|
| 340 |
* @param type the class of the object to serialize (i.e. SystemMetadata.class) |
|
| 341 |
* @param object the object to serialize |
|
| 342 |
* @param out the stream to serialize it to |
|
| 343 |
* @throws JiBXException |
|
| 344 |
*/ |
|
| 345 |
protected void serializeServiceType(Class type, Object object, OutputStream out) |
|
| 346 |
throws JiBXException {
|
|
| 347 |
ServiceTypeUtil.serializeServiceType(type, object, out); |
|
| 348 |
} |
|
| 349 |
|
|
| 350 |
/** |
|
| 351 |
* deserialize an object of type from is |
|
| 352 |
* @param type the class of the object to serialize (i.e. SystemMetadata.class) |
|
| 353 |
* @param is the stream to deserialize from |
|
| 354 |
* @throws JiBXException |
|
| 355 |
*/ |
|
| 356 |
protected Object deserializeServiceType(Class type, InputStream is) |
|
| 357 |
throws JiBXException {
|
|
| 358 |
return ServiceTypeUtil.deserializeServiceType(type, is); |
|
| 359 |
} |
|
| 360 | 338 |
|
| 361 | 339 |
/** |
| 362 | 340 |
* locate the boundary marker for an MMP |
| src/edu/ucsb/nceas/metacat/MetacatHandler.java | ||
|---|---|---|
| 84 | 84 |
import org.dataone.service.types.v1.Subject; |
| 85 | 85 |
import org.dataone.service.types.v1.SystemMetadata; |
| 86 | 86 |
import org.dataone.service.types.v1.util.ChecksumUtil; |
| 87 |
import org.dataone.service.types.util.ServiceTypeUtil; |
|
| 88 | 87 |
import org.ecoinformatics.datamanager.DataManager; |
| 89 | 88 |
import org.ecoinformatics.datamanager.database.DatabaseConnectionPoolInterface; |
| 90 | 89 |
import org.ecoinformatics.datamanager.parser.DataPackage; |
| 91 |
import org.ecoinformatics.datamanager.parser.TextComplexDataFormat; |
|
| 92 | 90 |
import org.ecoinformatics.eml.EMLParser; |
| 93 | 91 |
import org.jibx.runtime.JiBXException; |
| 94 | 92 |
import org.xml.sax.SAXException; |
| src/edu/ucsb/nceas/metacat/dataone/MNodeService.java | ||
|---|---|---|
| 81 | 81 |
import org.dataone.service.types.v1.Synchronization; |
| 82 | 82 |
import org.dataone.service.types.v1.SystemMetadata; |
| 83 | 83 |
import org.dataone.service.types.v1.util.ChecksumUtil; |
| 84 |
import org.dataone.service.types.util.ServiceTypeUtil; |
|
| 85 | 84 |
|
| 86 | 85 |
import edu.ucsb.nceas.metacat.DocumentImpl; |
| 87 | 86 |
import edu.ucsb.nceas.metacat.EventLog; |
| src/edu/ucsb/nceas/metacat/replication/ReplicationHandler.java | ||
|---|---|---|
| 55 | 55 |
|
| 56 | 56 |
import org.apache.log4j.Logger; |
| 57 | 57 |
import org.dataone.service.types.v1.SystemMetadata; |
| 58 |
import org.dataone.service.types.util.ServiceTypeUtil;
|
|
| 58 |
import org.dataone.service.util.TypeMarshaller;
|
|
| 59 | 59 |
import org.xml.sax.ContentHandler; |
| 60 | 60 |
import org.xml.sax.ErrorHandler; |
| 61 | 61 |
import org.xml.sax.InputSource; |
| ... | ... | |
| 442 | 442 |
// process system metadata |
| 443 | 443 |
if (systemMetadataXML != null) {
|
| 444 | 444 |
SystemMetadata sysMeta = |
| 445 |
(SystemMetadata) ServiceTypeUtil.deserializeServiceType(
|
|
| 445 |
TypeMarshaller.unmarshalTypeFromStream(
|
|
| 446 | 446 |
SystemMetadata.class, |
| 447 | 447 |
new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
|
| 448 | 448 |
String guid = sysMeta.getIdentifier().getValue(); |
| ... | ... | |
| 601 | 601 |
// process system metadata |
| 602 | 602 |
if (systemMetadataXML != null) {
|
| 603 | 603 |
SystemMetadata sysMeta = |
| 604 |
(SystemMetadata) ServiceTypeUtil.deserializeServiceType(
|
|
| 604 |
TypeMarshaller.unmarshalTypeFromStream(
|
|
| 605 | 605 |
SystemMetadata.class, |
| 606 | 606 |
new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
|
| 607 | 607 |
String guid = sysMeta.getIdentifier().getValue(); |
| ... | ... | |
| 837 | 837 |
|
| 838 | 838 |
// process system metadata |
| 839 | 839 |
if (systemMetadataXML != null) {
|
| 840 |
SystemMetadata sysMeta = (SystemMetadata) ServiceTypeUtil |
|
| 841 |
.deserializeServiceType(SystemMetadata.class, |
|
| 840 |
SystemMetadata sysMeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, |
|
| 842 | 841 |
new ByteArrayInputStream(systemMetadataXML |
| 843 | 842 |
.getBytes("UTF-8")));
|
| 844 | 843 |
// String guid = sysMeta.getIdentifier().getValue(); |
| src/edu/ucsb/nceas/metacat/replication/ReplicationService.java | ||
|---|---|---|
| 58 | 58 |
|
| 59 | 59 |
import org.apache.log4j.Logger; |
| 60 | 60 |
import org.dataone.service.types.v1.SystemMetadata; |
| 61 |
import org.dataone.service.types.util.ServiceTypeUtil;
|
|
| 61 |
import org.dataone.service.util.TypeMarshaller;
|
|
| 62 | 62 |
import org.xml.sax.InputSource; |
| 63 | 63 |
import org.xml.sax.SAXException; |
| 64 | 64 |
import org.xml.sax.XMLReader; |
| ... | ... | |
| 586 | 586 |
// process system metadata |
| 587 | 587 |
if (systemMetadataXML != null) {
|
| 588 | 588 |
SystemMetadata sysMeta = |
| 589 |
(SystemMetadata) ServiceTypeUtil.deserializeServiceType(
|
|
| 589 |
TypeMarshaller.unmarshalTypeFromStream(
|
|
| 590 | 590 |
SystemMetadata.class, |
| 591 | 591 |
new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
|
| 592 | 592 |
String guid = sysMeta.getIdentifier().getValue(); |
| ... | ... | |
| 867 | 867 |
// process system metadata |
| 868 | 868 |
if (systemMetadataXML != null) {
|
| 869 | 869 |
SystemMetadata sysMeta = |
| 870 |
(SystemMetadata) ServiceTypeUtil.deserializeServiceType(
|
|
| 870 |
TypeMarshaller.unmarshalTypeFromStream(
|
|
| 871 | 871 |
SystemMetadata.class, |
| 872 | 872 |
new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
|
| 873 | 873 |
String guid = sysMeta.getIdentifier().getValue(); |
| ... | ... | |
| 977 | 977 |
String guid = IdentifierManager.getInstance().getGUID(doc.getDocID(), doc.getRev()); |
| 978 | 978 |
SystemMetadata systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid); |
| 979 | 979 |
ByteArrayOutputStream baos = new ByteArrayOutputStream(); |
| 980 |
ServiceTypeUtil.serializeServiceType(SystemMetadata.class, systemMetadata, baos);
|
|
| 980 |
TypeMarshaller.marshalTypeToOutputStream(systemMetadata, baos);
|
|
| 981 | 981 |
String systemMetadataXML = baos.toString("UTF-8");
|
| 982 | 982 |
sb.append("<systemMetadata>");
|
| 983 | 983 |
sb.append(systemMetadataXML); |
| ... | ... | |
| 1038 | 1038 |
// serialize the System Metadata as XML |
| 1039 | 1039 |
SystemMetadata systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid); |
| 1040 | 1040 |
ByteArrayOutputStream baos = new ByteArrayOutputStream(); |
| 1041 |
ServiceTypeUtil.serializeServiceType(SystemMetadata.class, systemMetadata, baos);
|
|
| 1041 |
TypeMarshaller.marshalTypeToOutputStream(systemMetadata, baos);
|
|
| 1042 | 1042 |
systemMetadataXML = baos.toString("UTF-8");
|
| 1043 | 1043 |
|
| 1044 | 1044 |
// get a writer for sending back to response |
| ... | ... | |
| 1078 | 1078 |
// process system metadata |
| 1079 | 1079 |
if (systemMetadataXML != null) {
|
| 1080 | 1080 |
SystemMetadata sysMeta = |
| 1081 |
(SystemMetadata) ServiceTypeUtil.deserializeServiceType(
|
|
| 1081 |
TypeMarshaller.unmarshalTypeFromStream(
|
|
| 1082 | 1082 |
SystemMetadata.class, |
| 1083 | 1083 |
new ByteArrayInputStream(systemMetadataXML.getBytes("UTF-8")));
|
| 1084 | 1084 |
if (!IdentifierManager.getInstance().identifierExists(guid)) {
|
Also available in: Unified diff
remove ServiceTypeUtil - replace with TypeMarshaller