Revision 6337
Added by ben leinfelder over 13 years ago
| test/edu/ucsb/nceas/metacat/dataone/MNodeServiceTest.java | ||
|---|---|---|
| 59 | 59 |
import org.dataone.service.types.Node; |
| 60 | 60 |
import org.dataone.service.types.NodeReference; |
| 61 | 61 |
import org.dataone.service.types.ObjectFormat; |
| 62 |
import org.dataone.service.types.ObjectFormatIdentifier; |
|
| 62 | 63 |
import org.dataone.service.types.ObjectList; |
| 63 | 64 |
import org.dataone.service.types.Permission; |
| 64 | 65 |
import org.dataone.service.types.Session; |
| ... | ... | |
| 618 | 619 |
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
|
| 619 | 620 |
Date startTime = sdf.parse("2010-01-01");
|
| 620 | 621 |
Date endTime = new Date(); |
| 621 |
ObjectFormat objectFormat = null;
|
|
| 622 |
ObjectFormatIdentifier objectFormatId = null;
|
|
| 622 | 623 |
boolean replicaStatus = false; |
| 623 | 624 |
int start = 0; |
| 624 | 625 |
int count = 1; |
| ... | ... | |
| 628 | 629 |
// now check that we have at least one |
| 629 | 630 |
ObjectList objectList = |
| 630 | 631 |
MNodeService.getInstance().listObjects(session, startTime, endTime, |
| 631 |
objectFormat, replicaStatus, start, count);
|
|
| 632 |
objectFormatId, replicaStatus, start, count);
|
|
| 632 | 633 |
assertNotNull(objectList); |
| 633 | 634 |
assertTrue(objectList.getCount() == count); |
| 634 | 635 |
assertTrue(objectList.getStart() == 0); |
| src/xmltables-oracle.sql | ||
|---|---|---|
| 404 | 404 |
*/ |
| 405 | 405 |
CREATE TABLE systemMetadata ( |
| 406 | 406 |
guid VARCHAR2(2000), -- the globally unique string identifier |
| 407 |
provisional boolean, -- for reserving IDs |
|
| 408 | 407 |
date_uploaded DATE, -- the date/time the document was first submitted |
| 409 | 408 |
rights_holder VARCHAR2(250), --the user who has rights to the document, usually the first persons to upload it |
| 410 | 409 |
checksum VARCHAR2(512), --the checksum of the doc using the given algorithm (see below) |
| src/xmltables-postgres.sql | ||
|---|---|---|
| 296 | 296 |
*/ |
| 297 | 297 |
CREATE TABLE systemMetadata ( |
| 298 | 298 |
guid text, -- the globally unique string identifier of the object that the system metadata describes |
| 299 |
provisional boolean, -- for reserved identifiers |
|
| 300 | 299 |
date_uploaded TIMESTAMP, -- the date/time the document was first submitted |
| 301 | 300 |
rights_holder VARCHAR(250), --the user who has rights to the document, usually the first persons to upload it |
| 302 | 301 |
checksum VARCHAR(512), --the checksum of the doc using the given algorithm (see below) |
| ... | ... | |
| 317 | 316 |
* ALTER TABLE systemMetadata DROP COLUMN rev; |
| 318 | 317 |
* ALTER TABLE systemMetadata ADD COLUMN replication_allowed boolean; |
| 319 | 318 |
* ALTER TABLE systemMetadata ADD COLUMN number_replicas INT8; |
| 320 |
* ALTER TABLE systemMetadata ADD COLUMN provisional boolean; |
|
| 321 | 319 |
*/ |
| 322 | 320 |
|
| 323 | 321 |
/* |
| src/edu/ucsb/nceas/metacat/restservice/MNResourceHandler.java | ||
|---|---|---|
| 759 | 759 |
|
| 760 | 760 |
ObjectList ol = |
| 761 | 761 |
MNodeService.getInstance().listObjects(session, startTime, endTime, |
| 762 |
objectFormat, replicaStatus, start, count); |
|
| 762 |
objectFormat.getFmtid(), replicaStatus, start, count);
|
|
| 763 | 763 |
|
| 764 | 764 |
out = response.getOutputStream(); |
| 765 | 765 |
response.setStatus(200); |
| src/edu/ucsb/nceas/metacat/restservice/ResourceHandler.java | ||
|---|---|---|
| 1354 | 1354 |
" start: " + start + " count: " + count); |
| 1355 | 1355 |
|
| 1356 | 1356 |
ObjectList ol = MNodeService.getInstance().listObjects(session, startTime, endTime, |
| 1357 |
objectFormat, replicaStatus, start, count); |
|
| 1357 |
objectFormat.getFmtid(), replicaStatus, start, count);
|
|
| 1358 | 1358 |
|
| 1359 | 1359 |
StringReader sr = new StringReader(ol.toString()); |
| 1360 | 1360 |
out = response.getOutputStream(); |
| src/edu/ucsb/nceas/metacat/dataone/MNodeService.java | ||
|---|---|---|
| 597 | 597 |
*/ |
| 598 | 598 |
@Override |
| 599 | 599 |
public ObjectList listObjects(Session session, Date startTime, Date endTime, |
| 600 |
ObjectFormat objectFormat, Boolean replicaStatus, Integer start, Integer count)
|
|
| 600 |
ObjectFormatIdentifier objectFormatId, Boolean replicaStatus, Integer start, Integer count)
|
|
| 601 | 601 |
throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, |
| 602 | 602 |
InvalidToken {
|
| 603 | 603 |
|
| ... | ... | |
| 605 | 605 |
|
| 606 | 606 |
try {
|
| 607 | 607 |
objectList = IdentifierManager.getInstance().querySystemMetadata(startTime, endTime, |
| 608 |
objectFormat, replicaStatus, start, count); |
|
| 608 |
objectFormatId, replicaStatus, start, count);
|
|
| 609 | 609 |
} catch (Exception e) {
|
| 610 | 610 |
throw new ServiceFailure("1580", "Error querying system metadata: " + e.getMessage());
|
| 611 | 611 |
} |
| src/edu/ucsb/nceas/metacat/dataone/CNodeService.java | ||
|---|---|---|
| 541 | 541 |
logMetacat.debug("Checking if identifier exists...");
|
| 542 | 542 |
// Check that the identifier does not already exist |
| 543 | 543 |
if (IdentifierManager.getInstance().identifierExists(guid.getValue())) {
|
| 544 |
// check if we reserved the id |
|
| 545 |
boolean reserved = IdentifierManager.getInstance().hasReservation(guid, session); |
|
| 546 |
// throw an exception if not |
|
| 547 |
if (!reserved) {
|
|
| 548 | 544 |
throw new InvalidRequest("4863",
|
| 549 | 545 |
"GUID is already in use by an existing object."); |
| 550 |
} |
|
| 546 |
|
|
| 551 | 547 |
} |
| 552 | 548 |
|
| 553 | 549 |
// insert the system metadata into the object store |
| ... | ... | |
| 600 | 596 |
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique, |
| 601 | 597 |
NotImplemented, InvalidRequest {
|
| 602 | 598 |
|
| 603 |
// generate a pid if not provided |
|
| 604 |
if (pid == null) {
|
|
| 605 |
pid = new Identifier(); |
|
| 606 |
// TODO: go to EZID |
|
| 607 |
StringBuffer sb = new StringBuffer(); |
|
| 608 |
if (scope != null) {
|
|
| 609 |
sb.append(scope); |
|
| 610 |
sb.append(".");
|
|
| 611 |
} |
|
| 612 |
sb.append(System.currentTimeMillis()); |
|
| 613 |
pid.setValue(sb.toString()); |
|
| 614 |
} |
|
| 615 |
// does this identifier exist? |
|
| 616 |
if (IdentifierManager.getInstance().identifierExists(pid.getValue())) {
|
|
| 617 |
// check if it was reserved already |
|
| 618 |
if (IdentifierManager.getInstance().hasReservation(pid, session)) {
|
|
| 619 |
throw new IdentifierNotUnique("4210", "Identifier already reserved: " + pid.getValue());
|
|
| 620 |
} |
|
| 621 |
throw new IdentifierNotUnique("4210", "Identifier already exists: " + pid.getValue());
|
|
| 622 |
} |
|
| 623 |
|
|
| 624 |
// if we got this far, save it |
|
| 625 |
SystemMetadata provisoinalSystemMetadata = new SystemMetadata(); |
|
| 626 |
provisoinalSystemMetadata.setIdentifier(pid); |
|
| 627 |
provisoinalSystemMetadata.setRightsHolder(session.getSubject()); |
|
| 628 |
provisoinalSystemMetadata.setSubmitter(session.getSubject()); |
|
| 629 |
provisoinalSystemMetadata.setDateSysMetadataModified(new Date()); |
|
| 630 |
provisoinalSystemMetadata.setDateUploaded(new Date()); |
|
| 631 |
provisoinalSystemMetadata.setSize(0); |
|
| 632 |
try {
|
|
| 633 |
IdentifierManager.getInstance().createSystemMetadata(provisoinalSystemMetadata); |
|
| 634 |
IdentifierManager.getInstance().setProvisional(pid.getValue(), true); |
|
| 635 |
} catch (McdbDocNotFoundException e) {
|
|
| 636 |
throw new ServiceFailure("4210", e.getMessage());
|
|
| 637 |
} |
|
| 638 |
|
|
| 639 |
return pid; |
|
| 599 |
throw new NotImplemented("4191", "reserveIdentifier not implemented on this node");
|
|
| 640 | 600 |
} |
| 641 | 601 |
|
| 642 | 602 |
/** |
| src/edu/ucsb/nceas/metacat/dataone/D1NodeService.java | ||
|---|---|---|
| 173 | 173 |
logMetacat.debug("Checking if identifier exists...");
|
| 174 | 174 |
// Check that the identifier does not already exist |
| 175 | 175 |
if (IdentifierManager.getInstance().identifierExists(pid.getValue())) {
|
| 176 |
// check if we reserved the id |
|
| 177 |
boolean reserved = IdentifierManager.getInstance().hasReservation(pid, session); |
|
| 178 |
// throw an exception if not |
|
| 179 |
if (!reserved) {
|
|
| 180 | 176 |
throw new IdentifierNotUnique("1120",
|
| 181 | 177 |
"The requested identifier " + pid.getValue() + |
| 182 | 178 |
" is already used by another object and" + |
| 183 | 179 |
"therefore can not be used for this object. Clients should choose" + |
| 184 | 180 |
"a new identifier that is unique and retry the operation or " + |
| 185 | 181 |
"use CN_crud.reserveIdentifier() to reserve one."); |
| 186 |
} |
|
| 182 |
|
|
| 187 | 183 |
} |
| 188 | 184 |
|
| 189 | 185 |
// check for permission |
| src/edu/ucsb/nceas/metacat/dataone/CrudService.java | ||
|---|---|---|
| 535 | 535 |
ObjectList objectList = null; |
| 536 | 536 |
try {
|
| 537 | 537 |
objectList = IdentifierManager.getInstance().querySystemMetadata(startTime, endTime, |
| 538 |
objectFormat, replicaStatus, start, count); |
|
| 538 |
objectFormat.getFmtid(), replicaStatus, start, count);
|
|
| 539 | 539 |
} catch (Exception e) {
|
| 540 | 540 |
throw new ServiceFailure("1580", "Error querying system metadata: " + e.getMessage());
|
| 541 | 541 |
} |
| src/edu/ucsb/nceas/metacat/IdentifierManager.java | ||
|---|---|---|
| 782 | 782 |
} catch (McdbDocNotFoundException e) {
|
| 783 | 783 |
// try system metadata only |
| 784 | 784 |
try {
|
| 785 |
boolean provisional = false; |
|
| 786 |
idExists = systemMetadataExisits(guid, provisional); |
|
| 785 |
idExists = systemMetadataExisits(guid); |
|
| 787 | 786 |
} catch (McdbDocNotFoundException e2) {
|
| 788 | 787 |
idExists = false; |
| 789 | 788 |
} |
| ... | ... | |
| 791 | 790 |
return idExists; |
| 792 | 791 |
} |
| 793 | 792 |
|
| 794 |
public boolean hasReservation(Identifier pid, Session session) {
|
|
| 795 |
// check if it was reserved |
|
| 796 |
boolean reserved = false; |
|
| 797 |
try {
|
|
| 798 |
// check that we reserved it |
|
| 799 |
if (IdentifierManager.getInstance().systemMetadataExisits(pid.getValue(), true)) {
|
|
| 800 |
SystemMetadata provisionalMetadata = IdentifierManager.getInstance().getSystemMetadata(pid.getValue()); |
|
| 801 |
Subject rightsHolder = provisionalMetadata.getRightsHolder(); |
|
| 802 |
// TODO: check groups? |
|
| 803 |
if (session.getSubject().equals(rightsHolder)) {
|
|
| 804 |
reserved = true; |
|
| 805 |
} |
|
| 806 |
} |
|
| 807 |
} catch (McdbDocNotFoundException e) {
|
|
| 808 |
reserved = false; |
|
| 809 |
} |
|
| 810 |
return reserved; |
|
| 811 |
} |
|
| 812 |
|
|
| 813 | 793 |
/** |
| 814 | 794 |
* |
| 815 | 795 |
* @param guid |
| ... | ... | |
| 918 | 898 |
return guid; |
| 919 | 899 |
} |
| 920 | 900 |
|
| 921 |
public boolean systemMetadataExisits(String guid, boolean provisional)
|
|
| 901 |
public boolean systemMetadataExisits(String guid) |
|
| 922 | 902 |
throws McdbDocNotFoundException {
|
| 923 | 903 |
logMetacat.debug("looking up system metadata for guid " + guid);
|
| 924 | 904 |
boolean exists = false; |
| 925 |
String query = "select guid from systemmetadata where guid = ? and provisional = ?";
|
|
| 905 |
String query = "select guid from systemmetadata where guid = ?"; |
|
| 926 | 906 |
|
| 927 | 907 |
DBConnection dbConn = null; |
| 928 | 908 |
int serialNumber = -1; |
| ... | ... | |
| 934 | 914 |
// Execute the insert statement |
| 935 | 915 |
PreparedStatement stmt = dbConn.prepareStatement(query); |
| 936 | 916 |
stmt.setString(1, guid); |
| 937 |
stmt.setBoolean(2, provisional); |
|
| 938 | 917 |
ResultSet rs = stmt.executeQuery(); |
| 939 | 918 |
if (rs.next()) {
|
| 940 | 919 |
exists = true; |
| ... | ... | |
| 965 | 944 |
public void createSystemMetadata(SystemMetadata sysmeta) throws McdbDocNotFoundException |
| 966 | 945 |
{
|
| 967 | 946 |
String guid = sysmeta.getIdentifier().getValue(); |
| 968 |
// remove any provisional records -- it is the responsibility of the caller to check this |
|
| 969 |
try {
|
|
| 970 |
if (systemMetadataExisits(guid, true)) {
|
|
| 971 |
deleteSystemMetadata(guid); |
|
| 972 |
} |
|
| 973 |
} catch (McdbDocNotFoundException e) {
|
|
| 974 |
// ignore |
|
| 975 |
} |
|
| 976 |
// insert the true record |
|
| 977 |
insertSystemMetadata(guid, false); |
|
| 947 |
// insert the record |
|
| 948 |
insertSystemMetadata(guid); |
|
| 949 |
// update with the values |
|
| 978 | 950 |
updateSystemMetadata(sysmeta); |
| 979 | 951 |
} |
| 980 | 952 |
|
| ... | ... | |
| 1089 | 1061 |
} |
| 1090 | 1062 |
} |
| 1091 | 1063 |
|
| 1092 |
public void setProvisional(String guid, boolean provisional) {
|
|
| 1093 |
DBConnection dbConn = null; |
|
| 1094 |
int serialNumber = -1; |
|
| 1095 |
|
|
| 1096 |
try {
|
|
| 1097 |
// Get a database connection from the pool |
|
| 1098 |
dbConn = |
|
| 1099 |
DBConnectionPool.getDBConnection("IdentifierManager.setProvisional");
|
|
| 1100 |
serialNumber = dbConn.getCheckOutSerialNumber(); |
|
| 1101 |
|
|
| 1102 |
// Execute the insert statement |
|
| 1103 |
String query = "update " + TYPE_SYSTEM_METADATA + |
|
| 1104 |
" set provisional = ? where guid = ?"; |
|
| 1105 |
PreparedStatement stmt = dbConn.prepareStatement(query); |
|
| 1106 |
|
|
| 1107 |
//data values |
|
| 1108 |
stmt.setBoolean(1, provisional); |
|
| 1109 |
//where clause |
|
| 1110 |
stmt.setString(2, guid); |
|
| 1111 |
logMetacat.debug("stmt: " + stmt.toString());
|
|
| 1112 |
//execute |
|
| 1113 |
int rows = stmt.executeUpdate(); |
|
| 1114 |
|
|
| 1115 |
stmt.close(); |
|
| 1116 |
} catch (SQLException e) {
|
|
| 1117 |
e.printStackTrace(); |
|
| 1118 |
logMetacat.error("setProvisional: SQL error while creating a mapping to the system metadata identifier: "
|
|
| 1119 |
+ e.getMessage()); |
|
| 1120 |
} finally {
|
|
| 1121 |
// Return database connection to the pool |
|
| 1122 |
DBConnectionPool.returnDBConnection(dbConn, serialNumber); |
|
| 1123 |
} |
|
| 1124 |
} |
|
| 1125 |
|
|
| 1126 | 1064 |
private void insertSystemMetadataProvenance(String guid, String relationship, List<String> targetGuids) |
| 1127 | 1065 |
{
|
| 1128 | 1066 |
DBConnection dbConn = null; |
| ... | ... | |
| 1525 | 1463 |
* @throws PropertyNotFoundException |
| 1526 | 1464 |
*/ |
| 1527 | 1465 |
public ObjectList querySystemMetadata(Date startTime, Date endTime, |
| 1528 |
ObjectFormat objectFormat, boolean replicaStatus, int start, int count) throws SQLException, PropertyNotFoundException, ServiceException
|
|
| 1466 |
ObjectFormatIdentifier objectFormatId, boolean replicaStatus, int start, int count) throws SQLException, PropertyNotFoundException, ServiceException
|
|
| 1529 | 1467 |
{
|
| 1530 | 1468 |
ObjectList ol = new ObjectList(); |
| 1531 | 1469 |
int total = 0; |
| ... | ... | |
| 1556 | 1494 |
f2 = true; |
| 1557 | 1495 |
} |
| 1558 | 1496 |
|
| 1559 |
if (objectFormat != null) {
|
|
| 1497 |
if (objectFormatId != null) {
|
|
| 1560 | 1498 |
if (!f1 && !f2) {
|
| 1561 | 1499 |
sql += " where object_format = ?"; |
| 1562 | 1500 |
} |
| ... | ... | |
| 1583 | 1521 |
if (f1 && f2 && f3) {
|
| 1584 | 1522 |
stmt.setTimestamp(1, new Timestamp(startTime.getTime())); |
| 1585 | 1523 |
stmt.setTimestamp(2, new Timestamp(endTime.getTime())); |
| 1586 |
stmt.setString(3, objectFormat.getFmtid().getValue());
|
|
| 1524 |
stmt.setString(3, objectFormatId.getValue());
|
|
| 1587 | 1525 |
} |
| 1588 | 1526 |
else if (f1 && f2 && !f3) {
|
| 1589 | 1527 |
stmt.setTimestamp(1, new Timestamp(startTime.getTime())); |
| ... | ... | |
| 1591 | 1529 |
} |
| 1592 | 1530 |
else if (f1 && !f2 && f3) {
|
| 1593 | 1531 |
stmt.setTimestamp(1, new Timestamp(startTime.getTime())); |
| 1594 |
stmt.setString(2, objectFormat.getFmtid().getValue());
|
|
| 1532 |
stmt.setString(2, objectFormatId.getValue());
|
|
| 1595 | 1533 |
} |
| 1596 | 1534 |
else if (f1 && !f2 && !f3) {
|
| 1597 | 1535 |
stmt.setTimestamp(1, new Timestamp(startTime.getTime())); |
| 1598 | 1536 |
} |
| 1599 | 1537 |
else if (!f1 && f2 && f3) {
|
| 1600 | 1538 |
stmt.setTimestamp(1, new Timestamp(endTime.getTime())); |
| 1601 |
stmt.setString(2, objectFormat.getFmtid().getValue());
|
|
| 1539 |
stmt.setString(2, objectFormatId.getValue());
|
|
| 1602 | 1540 |
} |
| 1603 | 1541 |
else if (!f1 && !f2 && f3) {
|
| 1604 |
stmt.setString(1, objectFormat.getFmtid().getValue());
|
|
| 1542 |
stmt.setString(1, objectFormatId.getValue());
|
|
| 1605 | 1543 |
} |
| 1606 | 1544 |
else if (!f1 && f2 && !f3) {
|
| 1607 | 1545 |
stmt.setTimestamp(1, new Timestamp(endTime.getTime())); |
| ... | ... | |
| 1753 | 1691 |
* create the systemmetadata record |
| 1754 | 1692 |
* @param guid |
| 1755 | 1693 |
*/ |
| 1756 |
private void insertSystemMetadata(String guid, boolean provisional)
|
|
| 1694 |
private void insertSystemMetadata(String guid) |
|
| 1757 | 1695 |
{
|
| 1758 | 1696 |
|
| 1759 | 1697 |
int serialNumber = -1; |
| ... | ... | |
| 1765 | 1703 |
serialNumber = dbConn.getCheckOutSerialNumber(); |
| 1766 | 1704 |
|
| 1767 | 1705 |
// Execute the insert statement |
| 1768 |
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid, provisional) values (?, ?)";
|
|
| 1706 |
String query = "insert into " + TYPE_SYSTEM_METADATA + " (guid) values (?)";
|
|
| 1769 | 1707 |
PreparedStatement stmt = dbConn.prepareStatement(query); |
| 1770 | 1708 |
stmt.setString(1, guid); |
| 1771 |
stmt.setBoolean(2, provisional); |
|
| 1772 | 1709 |
logMetacat.debug("system metadata query: " + stmt.toString());
|
| 1773 | 1710 |
int rows = stmt.executeUpdate(); |
| 1774 | 1711 |
|
Also available in: Unified diff
use objectFormatIdentifier for listObjects()
remove provisional system metadata indicator - Metacat will not implement reserveIdentifier()