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From 12/07/2011 to 01/05/2012

01/06/2012

06:32 PM Revision 6858 (metacat): After reviewing CNodeService and D1NodeService prompted by Robert comparing the Hazelcast locking with the d1_synchronization locking, I've made a number of changes that will prevent locking problems:
1) Multiple methods contained try/catch blocks that would:
try
lock();
catch
throw();
try
put();
catch
throw();
f...
Chris Jones
06:02 PM Revision 6857 (metacat): Converted the metacat-properties chapter to RST format. Still need to merge in
newer changes from the trunk, as I was accidentally working from the 1.9.4
branch for this whole conversion process.
Matt Jones

01/05/2012

02:49 PM Revision 6856 (metacat): only delete replicated data files (server_location != 1)
ben leinfelder
01:37 PM Revision 6855 (metacat): use inherited access control from EML for the data file we download from a remote source
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522 ben leinfelder
01:06 PM Revision 6854 (metacat): Removing unused screenshots that are duplicates of the others in the admin doc.
Matt Jones
12:53 PM Revision 6853 (metacat): Converted Harvester chapter to RST.
Matt Jones
12:06 PM Revision 6852 (metacat): download remote data and save locally when it is referenced by an EML package, then include it in the ORE map.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522 ben leinfelder
12:05 PM Revision 6851 (metacat): remove systemmetadata replication option -- it is no longer a separate document in metacat
ben leinfelder
11:31 PM Revision 6850 (metacat): Added stub documents for chapters on DataONE and OAI-PMH (to be converted from
Duane's Word doc). Matt Jones
11:23 PM Revision 6849 (metacat): Small word choice change.
Matt Jones
11:18 PM Revision 6848 (metacat): Improved formatting for index.
Matt Jones
11:14 PM Revision 6847 (metacat): Added AuthInterface chapter, and a License chapter.
Matt Jones
10:53 PM Revision 6846 (metacat): Converted Event Logging and Sitemaps chapters to RST.
Matt Jones
10:41 PM Revision 6845 (metacat): Fixed table layout on geoserver and submission chapters. Converted Replication
chapter to RST. Matt Jones
09:57 PM Revision 6844 (metacat): Completed 'Submission' page conversion, and also converted GeoServer docs to
RST format. Matt Jones
04:07 PM Revision 6843 (metacat): Partial conversion of the accessing and submitting metadata section to RST.
More coming later. Matt Jones

01/04/2012

02:48 PM Revision 6842 (metacat): include the EML and data tests in the suite
ben leinfelder
02:38 PM Revision 6841 (metacat): debugging data locking test
ben leinfelder
02:06 PM Revision 6840 (metacat): cannot check for deleted data since it is forever available (archived)
ben leinfelder
01:22 PM Revision 6839 (metacat): Updated the configuration section, converted word doc to RST.
Matt Jones
08:02 PM Revision 6838 (metacat): Updated the Installation chapter, coverted to RST.
Matt Jones
07:32 PM Revision 6837 (metacat): When the requested count in a call to listObjects() is 0, return an empty object list, not a full one. Fixes https://redmine.dataone.org/issues/2122
Chris Jones
07:30 PM Revision 6836 (metacat): Minor formatting for querySystemMetadata().
Chris Jones
04:50 PM Revision 6835 (metacat): Updated contributors.
Matt Jones
04:48 PM Revision 6834 (metacat): Modified index to fix typo.
Matt Jones
04:46 PM Revision 6833 (metacat): Edited introduction to Metacat admin guide, inserted figure.
Matt Jones
04:07 PM Revision 6832 (metacat): Screenshots from the Metacat admin guide.
Matt Jones

01/03/2012

03:57 PM Revision 6831 (metacat): Updating Sphinx doc structure in prep for moving metacat admin guide to Sphinx.
Matt Jones
03:56 PM Revision 6830 (metacat): exapnd permissions on the _exisiting_ access rule not on the permission being checked. (hierarchical permissions)
ben leinfelder
03:38 PM Revision 6829 (metacat): defer to super class member variables
ben leinfelder
11:33 AM Revision 6828 (metacat): Upgrade to Hazelcast-1.9.4.5 to try to solve CLIENT_CONNECTION_LOST problems seen on the Coordinating Node.
Chris Jones
11:10 AM Revision 6827 (metacat): mark client/servlet API and EarthGrid API as deprecated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5517 ben leinfelder
10:56 AM Revision 6826 (metacat): upgrade routine to purge empty replicated data files so that they can be re-replicated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536 ben leinfelder

12/30/2011

06:22 PM Revision 6825 (metacat): format the execution time to be a date.
Jing Tao

12/28/2011

03:56 PM Revision 6824 (metacat): Use "post" to replace "get" to fix caching issue on IE.
Jing Tao
03:34 PM Revision 6823 (metacat): Make the display of the schedule table fit the IE browser.
Jing Tao

12/22/2011

11:51 AM Revision 6822 (metacat): Make sure the local id isn't null when we try to get the object from the local instance.
Chris Jones
11:16 AM Revision 6821 (metacat): Simplify the error handling, and throw the exception once the CN is updated with the new status.
Chris Jones
11:13 AM Revision 6820 (metacat): Set the replica status to failed (not invalidated) when we get exceptions trying to read the object bytes. Not much of a difference, but only the CN, in theory, is supposed to be able to set the invalidated status.
Chris Jones
11:07 AM Revision 6819 (metacat): Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.
Chris Jones
10:51 AM Revision 6818 (metacat): Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).
Chris Jones
10:40 AM Revision 6817 (metacat): Get the object inputstream from the local metacat instance using MetacatHandler.get() rather than MN.getReplica() so we don't throw an InvalidToken exception when passing in a null Session. The D1Client object is never used for this local call.
Chris Jones
09:24 AM Revision 6816 (metacat): interpret permissions as hierarchical
https://redmine.dataone.org/issues/2150 ben leinfelder

12/21/2011

01:50 PM Revision 6815 (metacat): Use submitLoginFormIntoDivAndReload to replace submitLoginFormIntoDiv js function.
Jing Tao
01:00 PM Revision 6814 (metacat): remove flag for independent system metadata replication -- these entries are replicated along with the data/metadata objects or via hazelcast when the actual object is not on the server.
ben leinfelder
12:33 PM Revision 6813 (metacat): update documentation to reflect changes to replication (client certificate)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516 ben leinfelder
10:52 AM Revision 6812 (metacat): include SSL settings for client certificate-based replication
ben leinfelder
05:13 PM Revision 6811 (metacat): do not include the "v1" in the base url for the target MN
ben leinfelder

12/20/2011

12:19 PM Revision 6810 (metacat): New D1 jars with a minor CNode.setReplicationStatus() bugfix.
Chris Jones
11:29 AM Revision 6809 (metacat): The kar id will have version number.
Jing Tao
11:25 AM Revision 6808 (metacat): process the _current_ revision, not the latest!
use direct object/system metadata insertion for ORE maps. ben leinfelder
11:21 AM Revision 6807 (metacat): allow other Metacat process (system metadata and ORE generation) to directly insert objects and system metadata without having to go through the MN/CN methods.
ben leinfelder
11:19 AM Revision 6806 (metacat): sort the docids so that "old" revisions are processed before newer ones
ben leinfelder

12/19/2011

01:07 PM Revision 6805 (metacat): only attempt to unlock a lock if it was created (in the finally block)
ben leinfelder
12:56 PM Revision 6804 (metacat): update tests to comply with these chenages:
new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPo... ben leinfelder

12/17/2011

04:24 PM Revision 6803 (metacat): new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().
ben leinfelder

12/16/2011

12:21 PM Revision 6802 (metacat): refresh the SystemMetadata entry for EML and referenced data files when parsing EML access rules -- this ensures our in-memory system metadata map is up to date WRT the DB entries.
ben leinfelder
11:37 AM Revision 6801 (metacat): Using a branch name for the utilities project. This branch is a copy of the trunk and it uses the BSD license.
We will move this branch to a tag soon. Jing Tao
11:00 AM Revision 6800 (metacat): add revision history to the generated ORE objects -- we use the revision history of the EML package as a basis because the each ORE revision mirrors the revision of the EML package.
Add a placeholder for checking if an equivalent ORE map exists in the DataONE infrastructure - this will be a call to... ben leinfelder
09:56 AM Revision 6799 (metacat): Update the parameter names expected for listObjects() to reflect the MN API changes in the architecture docs.
Chris Jones
09:44 AM Revision 6798 (metacat): Change the query semantics such that we implement the MN.listObjects() where the lower datetime bound is inclusive (greater than or equal to" and the upper datetime bound in exclusive (less than). This allows easier paging in client applications.
Chris Jones
09:42 AM Revision 6797 (metacat): for test to compile, provide BaseException param for setReplicationStatus. I used a NotAuthorized instance.
ben leinfelder
09:37 AM Revision 6796 (metacat): adjust after refactoring tests that use EML queries
ben leinfelder
07:42 AM Revision 6795 (metacat): In the call to MNReplication.replicate(), call back to CNReplication.setReplicationStatus() and set the status to failed when we get local exceptions, exceptions from the source MN when calling getReplica(). Send back an exception with a description when setting the status. Add a private setReplicationStatus() method to refactor these calls out.
Chris Jones
07:36 AM Revision 6794 (metacat): Modify CNresourceHandler.setReplicationStatus() to use the new API signature, including the failure BaseException that is parsed out of the MMP as a file section. Log the exception message. Since this is an asynchronous call, ReplicationManager won't see a failed status, but the MNAuditTask eventually will.
Chris Jones
07:32 AM Revision 6793 (metacat): Add collectReplicationStatus() to CNResourcHandler to return the BaseException or it's subclass, if any, provided in the the call to setReplicationStatus. The exception will be reported on the CN.
Chris Jones
07:29 AM Revision 6792 (metacat): Change setReplicationStatus() to drop serialVersion and report the failure exception message in the CN log.
Chris Jones
07:13 AM Revision 6791 (metacat): Add new D1 jars with update CNreplication API changes to SetReplicationStatus().
Chris Jones
05:32 PM Revision 6790 (metacat): query for deleted metadata when testing that replication communicated the deletion. to check data, we try to update the data object on the target node (which should fail)
ben leinfelder
05:11 PM Revision 6789 (metacat): add test for data locking
ben leinfelder

12/15/2011

01:59 PM Revision 6788 (metacat): delete data and eml on the home Metacat and check that the change propagates to the target
ben leinfelder
01:29 PM Revision 6787 (metacat): set SystemMetadata.archived=true on MN.delete
There is ongoing discussion on what the exact behavior should be here, but this mimics Metacat's delete-as-archive ac... ben leinfelder

12/14/2011

08:48 AM Revision 6786 (metacat): In MNodeService.replicate(), check to see if we have a replica (via an out of band channel) before we call sourceMN.getReplica().
Chris Jones
05:28 PM Revision 6785 (metacat): actually include the test in the suite
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
05:17 PM Revision 6784 (metacat): EML replication test with insert, update and set access
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
05:06 PM Revision 6783 (metacat): only create guid->docid mapping during metadata replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
04:50 PM Revision 6782 (metacat): do not treat access change as an update -- it should not attempt to retrieve the contents of the object
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
04:36 PM Revision 6781 (metacat): Change the ecogrid tag to 1.2.2.RC5.
Jing Tao
04:18 PM Revision 6780 (metacat): only create guid->docid mapping during data replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder

12/13/2011

03:30 PM Revision 6779 (metacat): remove xml_acccess.docid reference (oops)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
03:15 PM Revision 6778 (metacat): test update and set access during replication from A->B
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
12:22 PM Revision 6777 (metacat): updated D1 API -- removed Permission.REPLICATE and associated parameters
ben leinfelder
11:51 AM Revision 6776 (metacat): a minute for replication?
ben leinfelder
11:34 AM Revision 6775 (metacat): process system metadata before access rules (access control is now driven by GUID so the mapping needs to be there)
ben leinfelder
11:06 AM Revision 6774 (metacat): Change the key of query result cache. The key now has the real search value.
Jing Tao
10:58 AM Revision 6773 (metacat): include SerialVersion in describe response
https://redmine.dataone.org/issues/2135
NOTE: d1 jars should be replaced once all schema changes are finalized and th...
ben leinfelder
09:17 AM Revision 6772 (metacat): comment out B->A test
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
04:33 PM Revision 6771 (metacat): use correct URLs for replication/Metacat client
ben leinfelder

12/12/2011

02:57 PM Revision 6770 (metacat): simple tests for 2-way data replication
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
01:22 PM Revision 6769 (metacat): ROLLBACK: check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi ben leinfelder
12:41 PM Revision 6768 (metacat): check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi ben leinfelder
11:26 AM Revision 6767 (metacat): redirect to the registry form following successful login - but allow an override in case we only want to render the success and stay there (ajax call from main sanparks page).
ben leinfelder
10:50 AM Revision 6766 (metacat): include 'archived' system metadata element in backing DB store
ben leinfelder

12/10/2011

04:25 PM Revision 6765 (metacat): include the logging level with configuring logger (with file appender) for replication and dataone
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5534 ben leinfelder

12/09/2011

03:28 PM Revision 6764 (metacat): add ; to end of update command
ben leinfelder
03:11 PM Revision 6763 (metacat): add ; to end of update command
ben leinfelder
02:54 PM Revision 6762 (metacat): only update accessfileid for our new guid-based records
ben leinfelder
02:42 PM Revision 6761 (metacat): move latest postgres access upgrade statements to oracle script
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
02:35 PM Revision 6760 (metacat): include revision clause when updating the accessfileid on the xml_acccess table
ben leinfelder
12:12 PM Revision 6759 (metacat): remove docid column in favor of guid
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
10:20 AM Revision 6758 (metacat): include "esa" context in the data registry URL.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5114 ben leinfelder
09:05 AM Revision 6757 (metacat): If a member node cannot be found in the node list matching the targetNodeSubject given in isNodeAuthorized(), throw a ServiceFailure exception.
Chris Jones
08:04 AM Revision 6756 (metacat): Minor reformatting for readability.
Chris Jones

12/08/2011

02:06 PM Revision 6755 (metacat): fix tests:
-insert default objectFormatList from d1_common (includes schemaLocation now)
-calculate checksum for the system meta...
ben leinfelder
01:51 PM Revision 6754 (metacat): update with latest d1_common/d1_lib (includes latest schema changes)
ben leinfelder
01:15 PM Revision 6753 (metacat): prepared statement toString() does not include quotes (') around the inserted values -- now the test reflects this.
ben leinfelder
01:12 PM Revision 6752 (metacat): only handle 100 (consecutive!) docId generations per millisecond, otherwise the generated docid part is bigger than Long.MAX_VALUE and Metacat cannot fully handle that.
ben leinfelder
11:27 AM Revision 6751 (metacat): Metacat now keeps track of permissions on a per-version basis -- the test reflects this change in behavior.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
11:22 AM Revision 6750 (metacat): check previous revision when attempting to update access control with EML 2.0.x docs
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
10:17 AM Revision 6749 (metacat): remove old access rules for a data object when they are being updated by rules contained in an EML document. Now the OnlineDataAccessTest EML 2.1.0 tests pass.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
05:31 PM Revision 6748 (metacat): construct the proper previousDocId when checking for update permission
ben leinfelder
05:05 PM Revision 6747 (metacat): for now, look up SystemMetadata directly from the table otherwise we won't have the latest access information. Need to refresh the in-memory copy everytime we edit the access policy via Metacat (includes EML parser)
ben leinfelder
05:04 PM Revision 6746 (metacat): check previous revision for permissions to update (includes data described by EML)
ben leinfelder
05:02 PM Revision 6745 (metacat): use correct "rev" column in xml_revisions table
ben leinfelder

12/07/2011

12:18 PM Revision 6744 (metacat): refactor Metacat access handling to be on a per-revision basis so that it more closely aligns with the DataONE approach
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
12:16 PM Revision 6743 (metacat): To avoid id generation conflicts happening at the same millisecond, append a 5 character random string to the end of the docid.
Chris Jones
11:54 AM Revision 6742 (metacat): Remove header2, footer2 and left-nav2 files.
Jing Tao
 

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