Adapted the build to be able to generate the Sphinx Admin Guide, and tobetter handle the copyright for Javadoc generation.
Added links to Javadoc. Tuned the layout a bit.
Completed first draft of Admin guide chapter on DataONE.
Handle SQLExceptions when trying to save system metadata locally.
Convert SQLExceptions to RuntimeExceptions for Hazelcast MapStore operations.
In IdentifierManager, throw SQLExceptions rather than just logging them, and let them be handled higher up in the stack.
use new endpoint/method:http://mule1.dataone.org/ArchitectureDocs-current/apis/CN_APIs.html#CNReplication.deleteReplicationMetadata
use PUT /obsoletedBy/{pid} for CNCore.setObsoletedBy per our discussion today
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.
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.
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.
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).
Continued authoring the description of DataONE in Metacat. More to come.
include new methods needed for replication (in new d1 jars)https://redmine.dataone.org/issues/2203
add method: setObsoletedBy (https://redmine.dataone.org/issues/2185)augement new method: deleteReplicationMetadata
remove method: assertRelationhttps://redmine.dataone.org/issues/2158
add method: deleteReplicationMetadataremove method: assertRelationupdate the D1 jarshttps://redmine.dataone.org/issues/2187https://redmine.dataone.org/issues/2158
serialize the Identifier for the systemMetadata being registeredhttps://redmine.dataone.org/issues/2204
Use a Date with resolution to milliseconds.
Initial outline for DataONE chapter.
Added OAI-PMH chapter that was contributed by Duane Costa from LTER.
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.
Minor null checks to avoid NPEs when calling replicate()
Don't throw a NotAuthorized exception in isAdminAuthorized() - just return false.
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
Fixed formatting.
Moving Metacat Sphinx RST documentation from docs/dev to docs/user directory.
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.
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....
Use a Logger instead of System.out for SystemMetadataMap.
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.
Modify CNReplication methods setReplicationStatus(), updateReplicationMetadata() and setReplicationPolicy() to allow administrative access from a Coordinating Node by calling isAdminAuthorized().
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.
store D1 configuration properties in the main backup so that they persist between upgrades.
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().
update authoritative member node id when we change it (reconfiguration) and when we initially register as a MN with the CN.
add description about what becoming a Member Node entails
Correctly deserialize the BaseException subclass in handling calls to setReplicationStatus()
Use Lock instead of ILock to be consistent across classes.
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:...
Converted the metacat-properties chapter to RST format. Still need to merge innewer changes from the trunk, as I was accidentally working from the 1.9.4branch for this whole conversion process.
only delete replicated data files (server_location != 1)
use inherited access control from EML for the data file we download from a remote sourcehttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522
Removing unused screenshots that are duplicates of the others in the admin doc.
Converted Harvester chapter to RST.
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
remove systemmetadata replication option -- it is no longer a separate document in metacat
Added stub documents for chapters on DataONE and OAI-PMH (to be converted fromDuane's Word doc).
Small word choice change.
Improved formatting for index.
Added AuthInterface chapter, and a License chapter.
Converted Event Logging and Sitemaps chapters to RST.
Fixed table layout on geoserver and submission chapters. Converted Replicationchapter to RST.
Completed 'Submission' page conversion, and also converted GeoServer docs toRST format.
Partial conversion of the accessing and submitting metadata section to RST.More coming later.
include the EML and data tests in the suite
debugging data locking test
cannot check for deleted data since it is forever available (archived)
Updated the configuration section, converted word doc to RST.
Updated the Installation chapter, coverted to RST.
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
Minor formatting for querySystemMetadata().
Updated contributors.
Modified index to fix typo.
Edited introduction to Metacat admin guide, inserted figure.
Screenshots from the Metacat admin guide.
Updating Sphinx doc structure in prep for moving metacat admin guide to Sphinx.
exapnd permissions on the exisiting access rule not on the permission being checked. (hierarchical permissions)
defer to super class member variables
Upgrade to Hazelcast-1.9.4.5 to try to solve CLIENT_CONNECTION_LOST problems seen on the Coordinating Node.
mark client/servlet API and EarthGrid API as deprecatedhttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=5517
upgrade routine to purge empty replicated data files so that they can be re-replicatedhttp://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536
format the execution time to be a date.
Use "post" to replace "get" to fix caching issue on IE.
Make the display of the schedule table fit the IE browser.
Make sure the local id isn't null when we try to get the object from the local instance.
Simplify the error handling, and throw the exception once the CN is updated with the new status.
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.
Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.
Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).
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.
interpret permissions as hierarchicalhttps://redmine.dataone.org/issues/2150
Use submitLoginFormIntoDivAndReload to replace submitLoginFormIntoDiv js function.
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.
update documentation to reflect changes to replication (client certificate)http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
include SSL settings for client certificate-based replication
do not include the "v1" in the base url for the target MN
New D1 jars with a minor CNode.setReplicationStatus() bugfix.
The kar id will have version number.
process the current revision, not the latest!use direct object/system metadata insertion for ORE maps.
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.
sort the docids so that "old" revisions are processed before newer ones
only attempt to unlock a lock if it was created (in the finally block)
update tests to comply with these chenages:new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().
new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().
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.
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.
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 CN.search() that looks at the solr index for OREs based on the EML package ID.
Update the parameter names expected for listObjects() to reflect the MN API changes in the architecture docs.
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.