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From 11/17/2011 to 12/16/2011

12/16/2011

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
12:21 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

12/15/2011

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
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

12/13/2011

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
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

12/12/2011

04:33 PM Revision 6771 (metacat): use correct URLs for replication/Metacat client
ben leinfelder
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

12/09/2011

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
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

12/07/2011

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
12:18 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

12/06/2011

04:31 PM Revision 6741 (metacat): change the default scheduler and workflow run engine urls.
Jing Tao
03:03 PM Revision 6740 (metacat): retry: add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561 ben leinfelder
02:51 PM Revision 6739 (metacat): update test to reflect newer change:
handle queries with predicates correctly.
when docids are used in the return field look up, we need to make sure they...
ben leinfelder
02:50 PM Revision 6738 (metacat): add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561 ben leinfelder

12/05/2011

06:04 PM Revision 6737 (metacat): Use the absolute path for the change permission jsp page.
Jing Tao
05:43 PM Revision 6736 (metacat): Add header style to distiguish header and normal row.
Jing Tao
11:58 AM Revision 6735 (metacat): Make TPC link to use the same mechanism to open header and left panel.
Jing Tao

12/02/2011

05:32 PM Revision 6734 (metacat): handle queries with predicates correctly.
when docids are used in the return field look up, we need to make sure they are included in the values in the correct... ben leinfelder
04:40 PM Revision 6733 (metacat): widen the third column.
Jing Tao
11:27 AM Revision 6732 (metacat): close prepared statement only if not null
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5562 ben leinfelder
10:54 AM Revision 6731 (metacat): fixed a bug that using a wrong table name - acces_log.
Jing Tao
10:53 AM Revision 6730 (metacat): fixed a bug that using acces_log table name.
Jing Tao
07:37 AM Revision 6729 (metacat): Upgrade the hazelcast libraries to 1.9.4.4 from 1.9.3.4.
Chris Jones

12/01/2011

03:38 PM Revision 6728 (metacat): Use accessblock in setaccess method. So user can grant/revoke public readable access.
Jing Tao
01:30 PM Revision 6727 (metacat): ensure that the revision list is ordered ascending in case someone changes the sql query without realizing that it matters...
ben leinfelder
01:21 PM Revision 6726 (metacat): set the byte size of the ORE map before adding it
ben leinfelder
01:12 PM Revision 6725 (metacat): set/update the obsoletes/obsoletedBy fields in system metadata so that we always have a complete revision history for each object.
Note: ORE maps do not have revision history...yet(?) ben leinfelder
01:10 PM Revision 6724 (metacat): order the revision list, ascending.
ben leinfelder
11:57 AM Revision 6723 (metacat): removing unused class -- can't find a reference to it and it's causing compilation errors for me.
ben leinfelder
11:53 AM Revision 6722 (metacat): for "all" permission, return a list of READ, WRITE, CHANGE_PERMISSION
ben leinfelder

11/30/2011

05:31 PM Revision 6721 (metacat): generating ORE maps and creating/updating system metadata now. There are some Permission conversion issues to be worked out yet
ben leinfelder
05:25 PM Revision 6720 (metacat): look up access policy by guid or local id
TODO: resolve the Metacat/EML "all" permission as it relates to DataONE (there is only READ, WRITE, CHANGE_PERMISSION... ben leinfelder
05:23 PM Revision 6719 (metacat): make exception/error reporting clearer -- was getting lock messages when perhaps that was not the correct exception.
ben leinfelder
05:22 PM Revision 6718 (metacat): look up all docids is now a static method (ORE/SystemMetadata generation)
ben leinfelder
02:22 PM Revision 6717 (metacat): Add log statements for each call to ILock.unlock() for debugging.
Chris Jones

11/29/2011

04:21 PM Revision 6716 (metacat): Add new test method to test getAccessControl.
Jing Tao
04:20 PM Revision 6715 (metacat): Add eml test file which contains access part.
Jing Tao
03:43 PM Revision 6714 (metacat): evict the HazelCast SystemMetadata entry if we update the access control rules via Metacat's legacy API, otherwise stale SystemMetadata stays in memory instead of being looked up from the backing table store.
ben leinfelder
03:41 PM Revision 6713 (metacat): optionally include ORE generation/insertion into Metacat when generating SystemMetadata
https://redmine.dataone.org/issues/2056 ben leinfelder
02:15 PM Revision 6712 (metacat): optionally include ORE generation/insertion into Metacat when generating SystemMetadata
https://redmine.dataone.org/issues/2056 ben leinfelder
01:44 PM Revision 6711 (metacat): Set a default HazelcastInstance after init() is called, and use this instance in getLock() to acquire a lock in the cluster.
Chris Jones
01:41 PM Revision 6710 (metacat): no need to cast docInfo entries to String -- they are all strings
ben leinfelder
01:39 PM Revision 6709 (metacat): set revision history, the create/update dates and the owner/submitter (correctly)
ben leinfelder
01:05 PM Revision 6708 (metacat): use shared method for looking up "docInfo" map -- both in Metacat replication and in D1 system metadata generation
ben leinfelder
12:38 PM Revision 6707 (metacat): make default formatting a little bit easier to read
ben leinfelder
12:33 PM Revision 6706 (metacat): reformat code -- no changes
ben leinfelder
12:31 PM Revision 6705 (metacat): refactor SystemMetadata creation into separate class from the MetacatHandler -- this will be shared by upgrade code and normal metacat api.
ben leinfelder
11:00 AM Revision 6704 (metacat): include all document revisions when generating "missing" system metadata
TODO: revision graph captured in obsoletes/obsoletedBy ben leinfelder
10:10 AM Revision 6703 (metacat): When using ILock.lock(), get a lock on the string value of the Identifier, not the Identifier object itself. Hazelcast locking won't work otherwise.
Chris Jones
08:55 AM Revision 6702 (metacat): Use the Hazelcast ILock mechanism to lock the system metadata identifier rather than using IMap.lock(pid).
Chris Jones

11/28/2011

04:09 PM Revision 6701 (metacat): simplify SystemMetadata generation -- will be done during Metacat upgrade for D1 features/support.
ben leinfelder
03:53 PM Revision 6700 (metacat): clean up populator; use IOUtils library to do string<->stream conversions
ben leinfelder
03:37 PM Revision 6699 (metacat): utilities jar should not be committed to Metacat otherwise we will not retrieve the tagged version during Metacat build process.
ben leinfelder
03:04 PM Revision 6698 (metacat): catch all possible exceptions
ben leinfelder
02:44 PM Revision 6697 (metacat): act as a registered CN when calling CN methods -- create(), for example, is restricted to only be callable by a node of type CN.
ben leinfelder
02:22 PM Revision 6696 (metacat): Set sessionid for clientVeiwBean when it handle a request.
Always set the order type to "allowFirst". Jing Tao
12:34 PM Revision 6695 (metacat): use IOUtils for testing read/write of XML strings. This goes along with the utilities project change to use the same apache commons IO library. Be sure to clean the utilities checkout in order to catch the right utilities svn tag when building!
ben leinfelder

11/23/2011

12:49 PM Revision 6694 (metacat): remove the D1 configuration group (header)
ben leinfelder
12:10 PM Revision 6693 (metacat): verify checksum when retrieving replica from another member node.
https://redmine.dataone.org/issues/1794 ben leinfelder
11:59 AM Revision 6692 (metacat): make sure to get/put system metadata to the HZ map instead of using IdentifierManager directly
verified changes for: https://redmine.dataone.org/issues/1999 ben leinfelder
11:37 AM Revision 6691 (metacat): match documentation for the MN.describe() header
https://redmine.dataone.org/issues/1904 ben leinfelder
11:31 AM Revision 6690 (metacat): configure synch schedule in the admin screen
https://redmine.dataone.org/issues/1933 ben leinfelder
11:03 AM Revision 6689 (metacat): look-up sych schedule from metacat properties instead of hardcoding them
https://redmine.dataone.org/issues/1933 ben leinfelder
10:19 AM Revision 6688 (metacat): when comparing D1 Subject objects, use the equals() method not direct string comparison
https://redmine.dataone.org/issues/2050 ben leinfelder
10:07 AM Revision 6687 (metacat): access nodeList list correctly
https://redmine.dataone.org/issues/2049 ben leinfelder

11/22/2011

04:10 PM Revision 6686 (metacat): When read a FGDC document, Metacat will add a new parameter enableFGDCediting params for the xml transforming.
Jing Tao

11/21/2011

02:23 PM Revision 6685 (metacat): New d1 common jar. Fixing my overwritten jar.
Chris Jones
02:16 PM Revision 6684 (metacat): set the uploade file size -1.
Jing Tao
02:11 PM Revision 6683 (metacat): New d1 jars with changes to SubjectBase in the types classes.
Chris Jones
12:10 PM Revision 6682 (metacat): remove D1 configuration -- it has its own admin screen now
ben leinfelder
12:09 PM Revision 6681 (metacat): updated cos.jar -- cos-26Dec2008.zip
File upload improvements:
Added support for Servlets 2.4 and Java 5.
Added an ExceededSizeException type to make cat...
ben leinfelder
11:21 AM Revision 6680 (metacat): allow unknown content sizes
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5543 ben leinfelder

11/18/2011

05:00 PM Revision 6679 (metacat): run replicate() in a separate thread so that we don't wait for potentially large data objects to be moved around the system.
ben leinfelder
12:13 PM Revision 6678 (metacat): Call replicate() asynchronously.
Chris Jones
09:13 AM Revision 6677 (metacat): Use status.toLowerCase() to deal with ReplicationStatus conversion issues. This needs to be reviewed.
Chris Jones
09:10 AM Revision 6676 (metacat): Use Subject.equals() when comparing DNs rather than CertificateManager.equalsDN(). Don't lock the pid in isNodeAuthorized() to debug for timeout issues. Minor debugging changes.
Chris Jones

11/17/2011

03:44 PM Revision 6675 (metacat): give the Metacat admin users FULL permissions on all data/docs
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4728 ben leinfelder
03:20 PM Revision 6674 (metacat): correct path for question mark icon -- though the documentation link is broken
ben leinfelder
02:49 PM Revision 6673 (metacat): remove replication control panel from dev skin -- now in admin interface
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
02:47 PM Revision 6672 (metacat): replication control panel now fully implemented as an admin configuration screen
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
02:23 PM Revision 6671 (metacat): change the footer to be regwhitetext style.
Jing Tao
02:22 PM Revision 6670 (metacat): make regtext style black and add new style regwhitetext.
Jing Tao
12:19 PM Revision 6669 (metacat): move replication configuration actions to the admin servlet and out of the replication servlet
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
11:42 AM Revision 6668 (metacat): Using the method sending form parameters rather than form object.
The reason is IE will invalidate the form object after putting a login message on the div which contains the form. Jing Tao
11:38 AM Revision 6667 (metacat): Add methods to send form parameters to the server.
Jing Tao
11:19 AM Revision 6666 (metacat): save SystemMetadata when replicating data and metadata -- this way if/when the node decides to be a DataONE MN it already has the information needed for each object
ben leinfelder
 

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