Metacat

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.

Update DataONE jar files to 0.6.4. Updated classes to follow.

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

updated jars after recent schema changes (no real change for us here)

use correct enum method

refactor Constants

refactor Constants

refactor Constants and ServiceTypeUtil

use NodelistUtil

use correct enum method

remove ServiceTypeUtil - replace with TypeMarshaller

use new "v1" types from DataONE

exclude non-test cases (d1)

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

remove CrudServiceTest reference in main Metacat test (about to remove from svn)

-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

reset object input stream (testGet)
check for reserveIdentifier NotImplemented (expected)

merge changes from 1.9.5 branch that read site docs from SVN not a defunct LTER server

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.

Use CamelCaps for properties for better readability.

include Mock version of looking up the base url for our own node - for testReplicate().
still expecting a failure during MN.replicate() since we are trying to add the replica to the same MN from which it came.

allow alternative CNode implementations (subclasses) to be returned when D1Client.getCN() is called. The alternative is given in the Settings configuration via the D1Client.cnClassName property.
MockCNode in Metacat is an example of such an alternative and is used when Metacat requires methods of a CN be present for unit testing.

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

Added node synchronization and replication properties.

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

Added service availability properties for each of the MN services.

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

Added service version properties for each of the MN services.

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)

Test that the obsoletes and derivedFrom system metadata fields were set correctly.

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

newer jars with better certificate exception handling as well as additional libclient implementations

use correct log name for the class

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

add test for synchronization failed -- TODO: verify that the log record made it in the logs

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.

include test for replicate() method -- still fails as not implemented

allow null objects (use default checksum)

wire-up the getCapabilities() and getOperationStatistics() methods for when they are actually implemented (tests fail now)

test listObjects()

include MNAuthorization tests

refactor to use common superclass D1NodeServiceTest for shared methods

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

test for getLogRecords -- with some semi-reasonable expectations on the return that is expected

implement d1 paging for the log record results

tests for isAuthorized and setAccessPolicy

include getLogRecords() test, though it is commented out at the moment

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

test for CN.getSystemMetadata()

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.

test CN.get()

Uncommented MNStorage tests.

save systemmetadata when create() is called

Send the correct Date format in testGetLogRecords(). I've commented out certain tests in the suite until isAuthorized() functionality is working. It is returning a NotFound exception even though the object is clearly in Metacat.

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

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

Add MNodeServiceTest tests for MNCore, MNRead, MNStorage, MNAuthorization implementations. MNReplication remains to be tested, as does MNCore.getCapabilities() and getOperationStatistics().

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

add the d1_common formats if they do not exist on the server

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

newer d1_common jar with updated MNCore interface

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.

add methods for testing CNodeService impl. Still some failing tests, but whittling them down

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

add "public" user subject

make the left panle look exactly the same as the left panel of index.jsp.

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.

refactor to test the entire CN service impl

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