Metacat

small code cleanup - removed unused instantiations of DBUtils.

fixed logic wrt localID and docid. Implemented new method in IdentifierManager to getAllGUIDs from identifier table for implementation of loadAllKeys in ObjectPathMapLoader.

further development of ObjectPathMapLoader.

new class for refreshing the hazelcast map with metacat. Initial commit.

check session != null before checking authorization

Add stub methods in CNodeService that implement the Hazelcast EntryListener interface: entryAdded(), entryRemoved(), entryUpdated(), and entryEvicted(). Add a listener to the hzSystemMetadata map so the CNodeService can respond to those events and create appropriate CNReplicationTask objects for distributed execution across the CN cluster. Again, stubs only so far.

Minor cleanup - tabs to spaces.

Enable CNodeService to access 1) the hzNodes map defined in the DataONE process cluster by becoming a Hazelcast client (hzClient) to that cluster and 2) the hzSystemMetadata map defined in the DataONE storage cluster by becoming a member to that cluster (using direct Hazelcast calls). Added fields for maintaining the DataONE cluster properties.

Add in the Hazelcast Id generation namespace and an IdGenerator instance for task ids. Hazelcast will produce cluster-wide unique ids for the "task-ids" namespace, to be used when creating CNreplicationTask objects.

Add a CNReplicationTask class that will be submitted to the CN storage cluster when there are changes to the object store involving system metadata, science metadata, and resource maps. When a new entry is added to the hzSystemMetadata map, a new data, science metadata, or resource map was added to the VO, and all CN cluster members need to be updated with the object and it's system metadata. This task is executed on each CN to replicate the information. If the event is an update to an existing system metadata entry, it may only involve a change to system metadata, or may involve a change to science metadata as well. The task will return with the PID of the object replicated, be it a sysmeta, scimeta, or resource object. Locking of the PID will be handled by the task.

Catch D1nodeService up to the DataONE 0.6.4 schema where there is no ObjectFormat.isScienceMetadata() method, but rather ObjectFormat.getFormatType() where type is currently one of 'DATA, 'METADATA', or 'RESOURCE'.

Modify HazelcastService to read configuration information from an on-disk file (not from a jar file). Added init() to start up the service (was calling doRefresh() before. We still need to decide if this is a refreshable service.

move HazelcastService to D1 package

Adding a HazelcastService for Metacat to enable Metacat as a Hazelcast cluster member in DataONE. This will require the hazelcast.xml configuration file used for the DataONE cluster to be on the Metacat classpath.

changes for schema update (d1_common)

do not parse from last slash ("/") to the end when processing the request uri - otherwise things like format ids (text/csv) will be handled incorrectly.
https://redmine.dataone.org/issues/1773

added HazelCast MapStore and MapLoader implementation for SystemMetadata

use InvalidRequest when the PID is not found. https://redmine.dataone.org/issues/1768

use Permission.REPLICATE not EXECUTE

check with the CN if replication is allowed for the object in question for getReplica()

add getReplica() implementation. same as get() but with different logging. seems silly, but maybe I missed something important that distinguishes this method.

Update MetacatPopulator to use the DataONE 0.6.4 schema and types.

Update classes to use the DataONE 0.6.4 schema and types. Major changes involve using BigInteger vs long in SystemMetadata.size, and using ObjectFormatIdentifier rather than Object format.

Insert system metadata after the data object is inserted.

Fix bug in updateSystemMetadataFields() where guid is set from the wrong parameter in the prepared SQL statement.

latest D1 jars - changes include:
updateSystemMetadata() impl for CN
new identifier methods (generate is its own method)
removal of the resourceMap pointer from system metadata

remove ORE mapping from system metadata

Update the d1 common java jar to include the changes to BaseException, and update MNodeService.synchronizationFailed() to use the BaseException.getNodeId() method to report which node the exception came from.

include obsoletes and obsoletedBy for system metadata
repurpose the "provenance" table as the ORE mapping table for system metadata

use correct enum method

refactor Constants

use NodelistUtil

use correct enum method

remove ServiceTypeUtil - replace with TypeMarshaller

use new "v1" types from DataONE

remove CrudService -- replaced by MNodeService and CNodeService

handle more than "contains" searchmode when using the path index for queries
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5443

-handle NotFound object format when generating system metadata
-improve EML DML for null entity/attribute elements

use the ObjectFormat Id (not toString()) to check against the configured science metadata formats

Return the new pid (not the obsoleted pid) on update(), and set the correct system metadata.

In D1NodeService.getLogRecords(), don't pass in null start and count params - set them to the defaults (0 and 1000).

MNResourceHandler.getObject() was making a call to ObjectFormat.getFmtid() when an object format was null. Check that it is not null before trying getFmtid().

In MNodeService.getCapabilities(), update the properties to match those in metacat.properties. Flesh out the NodeHealth object, adding NodeState, Ping, and Status information. Flesh out the Synchronization object information, but for now, use mock values. TODO: This should be determined from configuration and on-the-fly information.

In MNodeService.getCapabilities(), set the synchronization and replication properties of the node.

In MNodeService.getCapabilities(), set the serviceAvailable for each service supported.

In MNodeService.getCapabilities(), set the serviceVersion for each service supported.

check reservation before create/update

Use D1 properties to set node values, and add the 'WAR VERSION' back into the node name for deployments.

add hasReservation() method (NotImplemented, however)

use objectFormatIdentifier for listObjects()
remove provisional system metadata indicator - Metacat will not implement reserveIdentifier()

use correct log name for the class

consistently construct username/groups for MetacatHandler calls - also consistently call isAuthorized

provisional replicate() implementation -- does not check if the session's subject is "allowed" to do this.
the test also requires 2 servers -- right now it attempts to replicate with itself which will fail because of duplicate IDs

provisional version of getOperationStatistics() -- not clear if we are meant to aggregate by hour or by day

provisional getCapabilities() implementation. Much of the synchronization information and node health is omitted.

simplify the get() method -- no need to use temp files for this operation

implement d1 paging for the log record results

Reverting the resultset order in querySystemMetadata(). Thanks Ben.

Because of the new 'provisional' column, the resultset field order in querySystemMetadata() was out of order. Changed the order to reflect the new table column order.

save systemmetadata when create() is called

allow very minimal system metadata for provisional entries (CN.reserveIdentifier)

Fix a NullPointerException issue when the SubjectList in a Session is null.

Add the missing URL delimiter when building the D1 base service URL.

allow the test to read the OFL docid

check for null docid from access table -- using guid for many system meta rows

use docImpl getBytes() to preserve encoding
no need to catch an exception only to throw it (those I was playing around with looking up the fmt from the d1_common lib if it was not found on the server...but this is redundant with other client code)

remove resolve() test -- not implemented in Metacat

handle data objects (not sci meta) and also set the resulting pid so that create() can succeed

catch exceptions from system meta data query and throw service failure rather than swallowing them with an error msg

handle null values from DB better when querying system metadata

Update getOperationStatistics() to reflect the change in the signature, using ObjectFormatIdentifier instead of ObjectFormat.

Modify monitor() to accept new parameters for getOperationStatisics() (fromDate, toDate) instead of 'period'. Added getDateAsUTC() to parse incoming fromDate and toDate parameter strings.

Fixed problems in IdentifierManager asSystemMetadata(), getSystemMetadata(), and querySystemMetadata() that were using ObjectFormat.toString() rather than ObjectFormat.getFmtid().getValue(). Metacat was storing the string memory pointer rather than the actual format string in the systemmetadata table.

use super class' create() method
use string comparison for assertRelation method

beef up isAuthorized method to check for "public" access rules and also for the rights holder

do not delete if the sysmeta doesn't exist

Use 'synchronization_failed' for the event string in synchronizationFailed(), and add a TODO to use the event enum when the 0.6.3 types are updated.

return all public objects for the search() method [for now]

Changed 'guid' to 'pid' to be in line with the D1 API.

simplify the MN rest servlet mapping to match CN mappings - also streamlined the handler code to share extra path info parsing

add space to error message

route all /d1/cn/* traffic through the CNRestServlet/Handler -- inspect the pathInfo when deciding what action to take and also strip off any extra parts (like pid).
include query() method pass-through to CNodeService

add the old ecogrid query code (still commented out) from the old Rest handler

allow service implementation method to throw exception when guid parameter is null

allow parameters to be omitted in reserveIdentifier handling

implement reserveIdentifier() and check whether the id is reserved when creating records (only allow the create when the Subject creating matches the Subject who reserved it -- currently stored in rightsHolder)

allow for provisional SystemMetadata records (provisional=true)

remove extraneous update() call when create() does the call for us

use monitor() return value when processing response

throw exceptions up the call stack and handle exception reporting/serialization centrally in the handle() method

use logging, not system.out

consolidate session management and parameter preparation in the superclass

throw exceptions up the call stack rather than catching and handling them differently for each possible rest path

consolidate multi part handling in the super class - subclasses need only call the appropriate helper to get access to the needed resources. superclass does some validation to make sure the files are in place in the request

cleaning up the handlers -- removing superclass methods.

refactor to use D1RestServlet and D1ResourceHandler for the D1 rest interface

deprecate the old rest servlet in favor of the new D1-specific (CN/MN) versions

MN rest servlet, handler and mappings

share getSystemMetadata (before refactoring the superclass)

share getSystemMetadata (before refactoring this superclass)