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  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121

# Date Author Comment
6913 01/17/2012 01:57 PM ben leinfelder

use final tag for building with ecogrid
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6912 01/17/2012 12:06 PM ben leinfelder

-generate system meta for all docids, even those not originating on the server (replicas from the past)
-generate ORE docs and download remote data only for those documents that originated on this server being upgraded.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

6911 01/17/2012 11:43 AM ben leinfelder

refactor generate system meta loop to the factory class -- to be reused in sysmeta and ORE generation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

6910 01/17/2012 11:34 AM Chris Jones

When managing obsoletes/obsoletedBy system metadata fields, set the archived flag to false initially, and set it to true on system metadata for objects that a revision obsoletes.

6909 01/13/2012 04:57 PM ben leinfelder

do NOT generate ORE maps or download data when we do the initial System Metadata generation -- this is deferred until D1 registration.

6908 01/13/2012 02:25 PM ben leinfelder

make more generic so that a custom list of IDs can be passed in.

6907 01/13/2012 02:01 PM ben leinfelder

check that the resourceMap (based on Id only) does not currently exist in the local metacat when generating OREs

6906 01/13/2012 01:31 PM ben leinfelder

insert OR update system metadata -- no need to do an update right after initial insert...

6905 01/13/2012 01:05 PM ben leinfelder

call the System Metadata generator during upgrade to 2.0.0

6904 01/13/2012 11:17 AM Chris Jones

In IdentifierManager.updateSystemMetadata(), add a check for invalid system metadata (fields that throw a NullPointerException on access) to ensure that system metadata is populated correctly. Updated calling classes to handle the exception.

6903 01/13/2012 01:41 AM Matt Jones

Fixed formatting to make fixed-width line much shorter so boxes fit on the page.

6902 01/13/2012 01:19 AM Matt Jones

Removing obsoleted Admin Guide -- this guide is now maintained using Sphinx in docs/user/metacat -- the word document and PDF file are now obsolete.

6901 01/13/2012 01:14 AM Matt Jones

Properly initialize the servlet context when starting alternate servlets, which makes sure that the configuration files have been loaded and config properties are available.

6900 01/13/2012 01:00 AM Matt Jones

Removed link to obsolete PDF file.

6899 01/12/2012 10:34 PM Matt Jones

Modifications to make the build more readily find locally installed versions of
sphinx-build, and to remove the unneccary 'html' directory; output of
admindoc is now written directly into build/docs.

6898 01/12/2012 06:52 PM Matt Jones

Modified build to include documentation in the war file that is generated as
part of the build, if the 'documentation' target has been run before the
war target. This is not done automatically because its not clear if all
people will have the proper sphinx environment set up to build the...

6897 01/12/2012 06:03 PM Matt Jones

Adapted the build to be able to generate the Sphinx Admin Guide, and to
better handle the copyright for Javadoc generation.

6896 01/12/2012 06:01 PM Matt Jones

Added links to Javadoc. Tuned the layout a bit.

6895 01/12/2012 04:13 PM Matt Jones

Completed first draft of Admin guide chapter on DataONE.

6894 01/12/2012 01:56 PM Chris Jones

Handle SQLExceptions when trying to save system metadata locally.

6893 01/12/2012 01:56 PM Chris Jones

Convert SQLExceptions to RuntimeExceptions for Hazelcast MapStore operations.

6892 01/12/2012 01:54 PM Chris Jones

In IdentifierManager, throw SQLExceptions rather than just logging them, and let them be handled higher up in the stack.

6891 01/12/2012 01:32 PM ben leinfelder

use new endpoint/method:
http://mule1.dataone.org/ArchitectureDocs-current/apis/CN_APIs.html#CNReplication.deleteReplicationMetadata

6890 01/12/2012 12:18 PM ben leinfelder

use PUT /obsoletedBy/{pid} for CNCore.setObsoletedBy per our discussion today

6889 01/12/2012 07:53 AM Chris Jones

Keep the hzIdentifiers set in sync with the Metacat systemmetadata table. If entries are added/updated in the hzSystemMetadata map, make sure the identifier is in the set. If (for some administrative reason) the entry is removed, remove the identifier from the set. This usually doesn't happen.

6888 01/12/2012 07:47 AM Chris Jones

When loading all keys from Metacat into the hzSystemMetadata map, also load identifiers into the hzIdentifiers set if they are not already there. Although entries may be evicted from the map, the list of identifiers will remain. The list will have a fairly small memory footprint since it's just identifiers.

6887 01/12/2012 07:44 AM Chris Jones

Add support for the distributed Set of unique identifiers in the storage cluster called 'hzIdentifiers'. This set is a persistent total list of all identifiers (even when entries in the hzSystemMetadata map are evicted). It reflects the state of the identifiers in the postgresql systemmetadata table, but is distributed across the cluster. Add the getIdentifiers() method, which returns the ISet of identifiers.

6886 01/12/2012 07:38 AM Chris Jones

Add the dataone.hazelcast.storageCluster.identifiersSet property that defines the name of the distributed set of unique DataONE identifiers (called 'hzIdentifiers'). This ISet can't be configured in the hazelcast.xml file (only maps and queues can).

6885 01/11/2012 07:25 PM Matt Jones

Continued authoring the description of DataONE in Metacat. More to come.

6884 01/11/2012 04:42 PM ben leinfelder

include new methods needed for replication (in new d1 jars)
https://redmine.dataone.org/issues/2203

6883 01/11/2012 01:25 PM ben leinfelder

add method: setObsoletedBy (https://redmine.dataone.org/issues/2185)
augement new method: deleteReplicationMetadata

6882 01/11/2012 11:31 AM ben leinfelder

remove method: assertRelation
https://redmine.dataone.org/issues/2158

6881 01/11/2012 11:24 AM ben leinfelder

add method: deleteReplicationMetadata
remove method: assertRelation
update the D1 jars
https://redmine.dataone.org/issues/2187
https://redmine.dataone.org/issues/2158

6880 01/11/2012 10:41 AM ben leinfelder

serialize the Identifier for the systemMetadata being registered
https://redmine.dataone.org/issues/2204

6879 01/11/2012 09:39 AM Chris Jones

Use a Date with resolution to milliseconds.

6878 01/10/2012 07:57 PM Matt Jones

Initial outline for DataONE chapter.

6877 01/10/2012 07:02 PM Matt Jones

Added OAI-PMH chapter that was contributed by Duane Costa from LTER.

6876 01/10/2012 05:04 PM Chris Jones

Simplify setReplicationStatus() to not call updateReplicationMetadata() if a replica doesn't exist. Just create it and update the system metadata, which we already have a lock for.

6875 01/10/2012 05:03 PM Chris Jones

Minor null checks to avoid NPEs when calling replicate()

6874 01/10/2012 05:01 PM Chris Jones

Don't throw a NotAuthorized exception in isAdminAuthorized() - just return false.

6873 01/10/2012 12:12 PM ben leinfelder

do not download and save remote data resources which are HTML but are not expected to be such (login or info/splash pages before data content).
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

6872 01/10/2012 01:06 AM Matt Jones

Fixed formatting.

6871 01/10/2012 01:00 AM Matt Jones

Moving Metacat Sphinx RST documentation from docs/dev to docs/user directory.

6870 01/10/2012 12:42 AM Matt Jones

Merged most recent changes from trunk into the RST converted version of the Administrator's Guide. Now the Sphinx/RST version is up to date rlative to the most recent word document, and is now the active copy. The MS Word document will be deprecated and removed. All future changes should be made to the RST version.

6869 01/09/2012 05:08 PM Chris Jones

Update the CN methods to throw a VersionMismatch where the API changed (where serialVersion is a required parameter). These were previously throwing an InvalidRequest exception.
Change the exception handling for calls to Hazelcast to catch a RuntimeException (not Exception) so we don't catch exceptions that we purposefully throw....

6868 01/09/2012 04:59 PM Chris Jones

Use a Logger instead of System.out for SystemMetadataMap.

6867 01/07/2012 06:01 PM Chris Jones

Don't lock() on the map.get() in isNodeAuthorized() (this assumes that the CN has queued the task already). Add more lock/unlock debug statements, and fix setReplicationStatus() - I missed a finally statement to unlock the pid.

6866 01/07/2012 12:39 PM Chris Jones

Modify CNReplication methods setReplicationStatus(), updateReplicationMetadata() and setReplicationPolicy() to allow administrative access from a Coordinating Node by calling isAdminAuthorized().

6865 01/07/2012 12:34 PM Chris Jones

Add isAdminAuthorized() to D1NodeService to check if the operation is being requested from a CN. Consult the NodeList from the CN and test the NodeType of the given node and the X509 certificate Subject. Perhaps we should expand this to also check for service-level access in the future.

6864 01/06/2012 01:51 PM ben leinfelder

store D1 configuration properties in the main backup so that they persist between upgrades.

6863 01/06/2012 12:51 PM Chris Jones

In registerSystemMetadata(), lock the pid prior to calling map.containsKey(pid) since a put to the map could occur between the check and the subsequent put().

6862 01/06/2012 10:45 AM ben leinfelder

update authoritative member node id when we change it (reconfiguration) and when we initially register as a MN with the CN.

6861 01/06/2012 09:42 AM ben leinfelder

add description about what becoming a Member Node entails

6860 01/06/2012 07:40 AM Chris Jones

Correctly deserialize the BaseException subclass in handling calls to setReplicationStatus()

6859 01/06/2012 07:23 AM Chris Jones

Use Lock instead of ILock to be consistent across classes.

6858 01/05/2012 06:32 PM Chris Jones

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:...

6857 01/05/2012 06:02 PM Matt Jones

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.

6856 01/05/2012 02:49 PM ben leinfelder

only delete replicated data files (server_location != 1)

6855 01/05/2012 01:37 PM ben leinfelder

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

6854 01/05/2012 01:06 PM Matt Jones

Removing unused screenshots that are duplicates of the others in the admin doc.

6853 01/05/2012 12:53 PM Matt Jones

Converted Harvester chapter to RST.

6852 01/05/2012 12:06 PM ben leinfelder

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

6851 01/05/2012 12:05 PM ben leinfelder

remove systemmetadata replication option -- it is no longer a separate document in metacat

6850 01/04/2012 11:31 PM Matt Jones

Added stub documents for chapters on DataONE and OAI-PMH (to be converted from
Duane's Word doc).

6849 01/04/2012 11:23 PM Matt Jones

Small word choice change.

6848 01/04/2012 11:18 PM Matt Jones

Improved formatting for index.

6847 01/04/2012 11:14 PM Matt Jones

Added AuthInterface chapter, and a License chapter.

6846 01/04/2012 10:53 PM Matt Jones

Converted Event Logging and Sitemaps chapters to RST.

6845 01/04/2012 10:41 PM Matt Jones

Fixed table layout on geoserver and submission chapters. Converted Replication
chapter to RST.

6844 01/04/2012 09:57 PM Matt Jones

Completed 'Submission' page conversion, and also converted GeoServer docs to
RST format.

6843 01/04/2012 04:07 PM Matt Jones

Partial conversion of the accessing and submitting metadata section to RST.
More coming later.

6842 01/04/2012 02:48 PM ben leinfelder

include the EML and data tests in the suite

6841 01/04/2012 02:38 PM ben leinfelder

debugging data locking test

6840 01/04/2012 02:06 PM ben leinfelder

cannot check for deleted data since it is forever available (archived)

6839 01/04/2012 01:22 PM Matt Jones

Updated the configuration section, converted word doc to RST.

6838 01/03/2012 08:02 PM Matt Jones

Updated the Installation chapter, coverted to RST.

6837 01/03/2012 07:32 PM Chris Jones

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

6836 01/03/2012 07:30 PM Chris Jones

Minor formatting for querySystemMetadata().

6835 01/03/2012 04:50 PM Matt Jones

Updated contributors.

6834 01/03/2012 04:48 PM Matt Jones

Modified index to fix typo.

6833 01/03/2012 04:46 PM Matt Jones

Edited introduction to Metacat admin guide, inserted figure.

6832 01/03/2012 04:07 PM Matt Jones

Screenshots from the Metacat admin guide.

6831 01/03/2012 03:57 PM Matt Jones

Updating Sphinx doc structure in prep for moving metacat admin guide to Sphinx.

6830 01/03/2012 03:56 PM ben leinfelder

exapnd permissions on the exisiting access rule not on the permission being checked. (hierarchical permissions)

6829 01/03/2012 03:38 PM ben leinfelder

defer to super class member variables

6828 01/03/2012 11:33 AM Chris Jones

Upgrade to Hazelcast-1.9.4.5 to try to solve CLIENT_CONNECTION_LOST problems seen on the Coordinating Node.

6827 01/03/2012 11:10 AM ben leinfelder

mark client/servlet API and EarthGrid API as deprecated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5517

6826 01/03/2012 10:56 AM ben leinfelder

upgrade routine to purge empty replicated data files so that they can be re-replicated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536

6825 12/29/2011 06:22 PM Jing Tao

format the execution time to be a date.

6824 12/28/2011 03:56 PM Jing Tao

Use "post" to replace "get" to fix caching issue on IE.

6823 12/28/2011 03:34 PM Jing Tao

Make the display of the schedule table fit the IE browser.

6822 12/22/2011 11:51 AM Chris Jones

Make sure the local id isn't null when we try to get the object from the local instance.

6821 12/22/2011 11:16 AM Chris Jones

Simplify the error handling, and throw the exception once the CN is updated with the new status.

6820 12/22/2011 11:13 AM Chris Jones

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.

6819 12/22/2011 11:07 AM Chris Jones

Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.

6818 12/22/2011 10:51 AM Chris Jones

Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).

6817 12/22/2011 10:40 AM Chris Jones

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.

6816 12/22/2011 09:24 AM ben leinfelder

interpret permissions as hierarchical
https://redmine.dataone.org/issues/2150

6815 12/21/2011 01:50 PM Jing Tao

Use submitLoginFormIntoDivAndReload to replace submitLoginFormIntoDiv js function.

6814 12/21/2011 01:00 PM ben leinfelder

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.