Revision 6105
Added by ben leinfelder over 13 years ago
| src/edu/ucsb/nceas/metacat/MetacatHandler.java | ||
|---|---|---|
| 1852 | 1852 |
// calls to handleInsertOrUpdateAction() |
| 1853 | 1853 |
if ( !(ipAddress.contains("/d1")) ) {
|
| 1854 | 1854 |
|
| 1855 |
SystemMetadata sysMeta = new SystemMetadata(); |
|
| 1856 |
IdentifierManager im = IdentifierManager.getInstance(); |
|
| 1857 |
Hashtable<String, Object> docInfo = |
|
| 1858 |
im.getDocumentInfo(newdocid); |
|
| 1859 |
int rev = im.getLatestRevForLocalId(newdocid); |
|
| 1860 |
Identifier identifier = new Identifier(); |
|
| 1861 |
String sysMetaLocalId = ""; |
|
| 1862 |
|
|
| 1863 |
// it's possible that system metadata exists although |
|
| 1855 |
SystemMetadata sysMeta = null; |
|
| 1856 |
// it's possible that system metadata exists although |
|
| 1864 | 1857 |
// older clients don't support it. Try updates first. |
| 1865 | 1858 |
try {
|
| 1866 |
// handle updates |
|
| 1867 |
identifier.setValue(im.getGUID(newdocid, rev)); |
|
| 1868 |
sysMeta = getSystemMetadata(identifier); |
|
| 1869 |
IdentifierManager.getInstance().updateSystemMetadata(sysMeta); |
|
| 1859 |
// get the docid parts |
|
| 1860 |
String docidWithoutRev = DocumentUtil.getSmartDocId(newdocid); |
|
| 1861 |
int rev = IdentifierManager.getInstance().getLatestRevForLocalId(newdocid); |
|
| 1862 |
String guid = IdentifierManager.getInstance().getGUID(docidWithoutRev, rev); |
|
| 1863 |
sysMeta = IdentifierManager.getInstance().getSystemMetadata(guid); |
|
| 1864 |
// TODO: need to update? we just looked it up |
|
| 1865 |
//IdentifierManager.getInstance().updateSystemMetadata(sysMeta); |
|
| 1870 | 1866 |
|
| 1871 | 1867 |
} catch ( McdbDocNotFoundException mnfe) {
|
| 1872 | 1868 |
|
| 1873 | 1869 |
// handle inserts |
| 1874 | 1870 |
try {
|
| 1875 | 1871 |
sysMeta = createSystemMetadata(newdocid, user, groups); |
| 1872 |
IdentifierManager.getInstance().createSystemMetadata(sysMeta); |
|
| 1876 | 1873 |
IdentifierManager.getInstance().updateSystemMetadata(sysMeta); |
| 1877 | 1874 |
|
| 1878 | 1875 |
} catch ( McdbDocNotFoundException dnfe ) {
|
| ... | ... | |
| 3528 | 3525 |
logMetacat.debug("provided username: " + username);
|
| 3529 | 3526 |
|
| 3530 | 3527 |
// create system metadata for the document |
| 3531 |
IdentifierManager im = IdentifierManager.getInstance(); |
|
| 3532 |
Hashtable<String, Object> docInfo; |
|
| 3533 |
docInfo = im.getDocumentInfo(localId); |
|
| 3534 | 3528 |
SystemMetadata sysMeta = new SystemMetadata(); |
| 3535 |
InputStream inputStream; |
|
| 3536 |
int rev = im.getLatestRevForLocalId(localId); |
|
| 3529 |
int rev = IdentifierManager.getInstance().getLatestRevForLocalId(localId); |
|
| 3537 | 3530 |
AccessionNumber accNum = new AccessionNumber(localId, "NONE"); |
| 3538 |
Identifier identifier = new Identifier(); |
|
| 3539 |
|
|
| 3531 |
String guid = null; |
|
| 3540 | 3532 |
try {
|
| 3541 |
// get the identifier if it exists |
|
| 3542 |
identifier.setValue(im.getGUID(accNum.getDocid(), rev)); |
|
| 3543 |
|
|
| 3533 |
// get the guid if it exists |
|
| 3534 |
guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev); |
|
| 3544 | 3535 |
} catch ( McdbDocNotFoundException dnfe ) {
|
| 3545 | 3536 |
// otherwise create the mapping |
| 3546 | 3537 |
logMetacat.debug("There was a problem getting the guid from " +
|
| 3547 | 3538 |
"the given localId (docid and revision). The error message was: " + dnfe.getMessage()); |
| 3548 | 3539 |
logMetacat.debug("No guid in the identifier table. adding it for " + localId);
|
| 3549 |
im.createMapping(localId, localId);
|
|
| 3540 |
IdentifierManager.getInstance().createMapping(localId, localId);
|
|
| 3550 | 3541 |
logMetacat.debug("Mapping created for " + localId);
|
| 3551 | 3542 |
logMetacat.debug("accessionNumber: " + accNum);
|
| 3552 |
identifier.setValue(im.getGUID(accNum.getDocid(), rev)); |
|
| 3553 |
|
|
| 3543 |
guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev); |
|
| 3554 | 3544 |
} |
| 3545 |
Identifier identifier = new Identifier(); |
|
| 3546 |
identifier.setValue(guid); |
|
| 3555 | 3547 |
|
| 3548 |
//set the id |
|
| 3549 |
sysMeta.setIdentifier(identifier); |
|
| 3550 |
|
|
| 3556 | 3551 |
// get the data or metadata object |
| 3552 |
InputStream inputStream; |
|
| 3557 | 3553 |
try {
|
| 3558 | 3554 |
inputStream = this.read(localId); |
| 3559 |
|
|
| 3560 | 3555 |
} catch ( ParseLSIDException ple ) {
|
| 3561 | 3556 |
logMetacat.debug("There was a problem parsing the LSID from " +
|
| 3562 | 3557 |
localId + ". The error message was: " + ple.getMessage()); |
| ... | ... | |
| 3588 | 3583 |
throw ioe; |
| 3589 | 3584 |
|
| 3590 | 3585 |
} // end try() |
| 3591 |
|
|
| 3592 |
//set the id |
|
| 3593 |
sysMeta.setIdentifier(identifier); |
|
| 3594 | 3586 |
|
| 3587 |
// get additional docinfo |
|
| 3588 |
Hashtable<String, Object> docInfo = IdentifierManager.getInstance().getDocumentInfo(localId); |
|
| 3595 | 3589 |
//set the default object format |
| 3596 | 3590 |
String doctype = (String) docInfo.get("doctype");
|
| 3597 | 3591 |
ObjectFormat format = ObjectFormat.convert(doctype); |
| ... | ... | |
| 3603 | 3597 |
} |
| 3604 | 3598 |
} |
| 3605 | 3599 |
sysMeta.setObjectFormat(format); |
| 3606 |
logMetacat.debug("The ObjectFormat for " + localId +
|
|
| 3607 |
" is " + format.toString()); |
|
| 3600 |
logMetacat.debug("The ObjectFormat for " + localId + " is " + format.toString());
|
|
| 3608 | 3601 |
|
| 3609 | 3602 |
// further parse EML documents to get data object format, |
| 3610 | 3603 |
// describes and describedBy information |
| 3611 | 3604 |
if ( format == ObjectFormat.EML_2_0_0 || |
| 3612 | 3605 |
format == ObjectFormat.EML_2_0_1 || |
| 3613 |
format == ObjectFormat.EML_2_1_0 ) {
|
|
| 3606 |
format == ObjectFormat.EML_2_1_0 || |
|
| 3607 |
format == ObjectFormat.EML_2_1_1 ) {
|
|
| 3614 | 3608 |
|
| 3615 | 3609 |
try {
|
| 3616 | 3610 |
DataoneEMLParser emlParser = DataoneEMLParser.getInstance(); |
| ... | ... | |
| 3633 | 3627 |
dataDocMimeType = distMetadata.mimeType; |
| 3634 | 3628 |
} |
| 3635 | 3629 |
String dataDocLocalId = ""; |
| 3636 |
String dataSysMetaId = ""; |
|
| 3637 | 3630 |
logMetacat.debug("Data local ID: " + dataDocLocalId);
|
| 3638 | 3631 |
logMetacat.debug("Data URL : " + dataDocUrl);
|
| 3639 | 3632 |
logMetacat.debug("Data mime : " + dataDocMimeType);
|
| 3640 | 3633 |
|
| 3641 | 3634 |
//we only handle ecogrid urls right now |
| 3642 |
if ( dataDocUrl.trim().startsWith("ecogrid://knb/") ) {
|
|
| 3635 |
String ecogridPrefix = "ecogrid://knb/"; |
|
| 3636 |
if ( dataDocUrl.trim().startsWith(ecogridPrefix) ) {
|
|
| 3643 | 3637 |
dataDocLocalId = |
| 3644 |
dataDocUrl.substring(dataDocUrl.indexOf("ecogrid://knb/") +
|
|
| 3645 |
"ecogrid://knb/".length(), dataDocUrl.length()); |
|
| 3638 |
dataDocUrl.substring(dataDocUrl.indexOf(ecogridPrefix) + ecogridPrefix.length()); |
|
| 3646 | 3639 |
|
| 3647 |
//set the id
|
|
| 3648 |
Identifier dataDocId = new Identifier();
|
|
| 3649 |
dataDocId.setValue(dataDocLocalId);
|
|
| 3640 |
// look up the guid for the data
|
|
| 3641 |
String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);
|
|
| 3642 |
int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);
|
|
| 3650 | 3643 |
|
| 3651 |
// add describes into EML system metadata |
|
| 3652 |
sysMeta.addDescribe(dataDocId); |
|
| 3653 |
|
|
| 3654 |
SystemMetadata dataSysMeta = new SystemMetadata(); |
|
| 3644 |
SystemMetadata dataSysMeta = null; |
|
| 3655 | 3645 |
// check if data system metadata exists |
| 3646 |
String dataGuidString = null; |
|
| 3656 | 3647 |
try {
|
| 3657 |
logMetacat.debug("Checking for existing system metadata for " +
|
|
| 3658 |
dataDocId.getValue()); |
|
| 3659 |
dataSysMeta = this.getSystemMetadata(dataDocId); |
|
| 3660 |
// add describedBy sysmeta |
|
| 3661 |
logMetacat.debug("Setting describedBy for " + dataDocId.getValue() +
|
|
| 3662 |
" to " + identifier.getValue()); |
|
| 3663 |
dataSysMeta.addDescribedBy(identifier); |
|
| 3664 |
ObjectFormat f = ObjectFormat.convert(dataDocMimeType); |
|
| 3665 |
if (f == null) {
|
|
| 3666 |
f = ObjectFormat.OCTET_STREAM; |
|
| 3667 |
} |
|
| 3668 |
dataSysMeta.setObjectFormat(f); |
|
| 3669 |
IdentifierManager.getInstance().updateSystemMetadata(dataSysMeta); |
|
| 3670 |
|
|
| 3648 |
dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev); |
|
| 3649 |
dataSysMeta = IdentifierManager.getInstance().getSystemMetadata(dataGuidString); |
|
| 3671 | 3650 |
} catch ( McdbDocNotFoundException nf ) {
|
| 3672 |
// System metadata for data doesn't exist |
|
| 3673 |
logMetacat.debug("There was not an existing system metadata " +
|
|
| 3674 |
"document for " + dataDocId.getValue()); |
|
| 3675 |
try {
|
|
| 3676 |
logMetacat.debug("Creating a system metadata " +
|
|
| 3677 |
"document for " + dataDocId.getValue()); |
|
| 3678 |
dataSysMeta = |
|
| 3679 |
this.createSystemMetadata(dataDocLocalId, username, groups); |
|
| 3651 |
// System metadata for data doesn't exist yet, so create it |
|
| 3652 |
logMetacat.debug("There was not an existing system metadata " + "document for " + dataDocLocalId);
|
|
| 3653 |
try {
|
|
| 3654 |
logMetacat.debug("Creating a system metadata " + "document for " + dataDocLocalId);
|
|
| 3655 |
dataSysMeta = this.createSystemMetadata(dataDocLocalId, username, groups); |
|
| 3656 |
|
|
| 3657 |
// now look it up again |
|
| 3658 |
dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev); |
|
| 3659 |
|
|
| 3660 |
//set the guid |
|
| 3661 |
Identifier dataGuid = new Identifier(); |
|
| 3662 |
dataGuid.setValue(dataGuidString); |
|
| 3663 |
|
|
| 3664 |
// add describes into EML system metadata |
|
| 3665 |
sysMeta.addDescribe(dataGuid); |
|
| 3666 |
|
|
| 3667 |
// add describedBy sysmeta |
|
| 3668 |
logMetacat.debug("Setting describedBy for " + dataGuid.getValue() + " to " + identifier.getValue());
|
|
| 3669 |
dataSysMeta.addDescribedBy(identifier); |
|
| 3670 |
|
|
| 3671 |
// set object format |
|
| 3672 |
logMetacat.debug("Updating system metadata for " + dataGuid.getValue() + " to " + dataDocMimeType);
|
|
| 3673 |
ObjectFormat f = ObjectFormat.convert(dataDocMimeType); |
|
| 3674 |
if (f == null) {
|
|
| 3675 |
f = ObjectFormat.OCTET_STREAM; |
|
| 3676 |
} |
|
| 3677 |
dataSysMeta.setObjectFormat(f); |
|
| 3680 | 3678 |
|
| 3681 |
logMetacat.debug("Setting describedBy for " +
|
|
| 3682 |
dataDocId.getValue() + " to " + identifier.getValue()); |
|
| 3683 |
dataSysMeta.addDescribedBy(identifier); |
|
| 3679 |
// update the values |
|
| 3680 |
IdentifierManager.getInstance().updateSystemMetadata(dataSysMeta); |
|
| 3684 | 3681 |
|
| 3685 |
logMetacat.debug("Setting mimeType for " +
|
|
| 3686 |
dataDocId.getValue() + " to " + dataDocMimeType); |
|
| 3687 |
ObjectFormat f = ObjectFormat.convert(dataDocMimeType); |
|
| 3688 |
if (f == null) {
|
|
| 3689 |
f = ObjectFormat.OCTET_STREAM; |
|
| 3690 |
} |
|
| 3691 |
dataSysMeta.setObjectFormat(f); |
|
| 3692 |
|
|
| 3693 |
logMetacat.debug("Updating system metadata for " +
|
|
| 3694 |
dataDocId.getValue() + " to " + dataDocMimeType); |
|
| 3695 |
IdentifierManager.getInstance().updateSystemMetadata(dataSysMeta); |
|
| 3696 |
|
|
| 3697 | 3682 |
} catch ( McdbDocNotFoundException mdnf) {
|
| 3698 | 3683 |
mdnf.printStackTrace(); |
| 3699 | 3684 |
throw mdnf; |
| ... | ... | |
| 3718 | 3703 |
} catch ( BaseException be) {
|
| 3719 | 3704 |
be.printStackTrace(); |
| 3720 | 3705 |
throw be; |
| 3721 |
|
|
| 3722 | 3706 |
} |
| 3723 |
|
|
| 3724 |
} catch ( McdbException me ) {
|
|
| 3725 |
logMetacat.debug("There was a Metacat problem. " +
|
|
| 3726 |
"The error message was: " + me.getMessage()); |
|
| 3727 |
throw me; |
|
| 3728 |
|
|
| 3729 |
} // end try() |
|
| 3707 |
} |
|
| 3730 | 3708 |
|
| 3731 | 3709 |
} // end if() |
| 3732 | 3710 |
|
| ... | ... | |
| 3789 | 3767 |
|
| 3790 | 3768 |
return sysMeta; |
| 3791 | 3769 |
} |
| 3792 |
|
|
| 3793 |
/** |
|
| 3794 |
* Get the system metadata for a document with a specified guid |
|
| 3795 |
* |
|
| 3796 |
* @param guid The identifier used to look up system metadata |
|
| 3797 |
* |
|
| 3798 |
* @return sysMeta The desired SystemMetadata object |
|
| 3799 |
*/ |
|
| 3800 |
private SystemMetadata getSystemMetadata(Identifier guid) |
|
| 3801 |
throws McdbDocNotFoundException {
|
|
| 3802 |
|
|
| 3803 |
logMetacat.debug("MetacatHandler.getSystemMetadata() called.");
|
|
| 3804 |
|
|
| 3805 |
SystemMetadata sysMeta = null; |
|
| 3806 |
|
|
| 3807 |
try {
|
|
| 3808 |
sysMeta = IdentifierManager.getInstance().getSystemMetadata(guid.getValue()); |
|
| 3809 |
} catch ( McdbDocNotFoundException dnfe ) {
|
|
| 3810 |
logMetacat.debug("There was a problem getting the system " +
|
|
| 3811 |
"metadata. The error was: " + dnfe.getMessage()); |
|
| 3812 |
throw dnfe; |
|
| 3813 |
} |
|
| 3814 |
return sysMeta; |
|
| 3815 |
|
|
| 3816 |
} |
|
| 3817 | 3770 |
|
| 3818 | 3771 |
/* |
| 3819 | 3772 |
* Find the size (in bytes) of a stream. Note: This needs to refactored out |
Also available in: Unified diff
rework SystemMetadata creation when inserting documents via the Metacat servlet api (in which case there was no client-supplued system metadata)