Metacat

add space to error message

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

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)

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

Add placeholder NotImplemented exceptions for getOperationsStatistics() and getCapabilities() in MNodeService.

Implement MNCore.ping() by testing for a successful database connection.

Minor housekeeping - tabs to spaces.

Implement update() in MNodeService. Handle both XML science metadata updates and data object updates. Keep system metadata up to date, and log the update event.

Make isScienceMetadata() protected for access from subclasses.

Add insertSystemMetadata() to D1NodeService, wrap the exception handling from calls to IdentifierManager.

Add updateSystemMetadata() to D1NodeService as a helper method to wrap the exception handling from calls to IdentifierManager.

At Ben's suggestion, add metacatUrl to D1NodeService and make it available to subclasses. Set the metacatUrl in the constructor using SystemUtil rather than all roll your own PropertyService calls. More concise. Also, log the delete event in MNodeService.delete().

throw NotAllowed in MNodeService.delete() when isAuthorized() returns false.

Implement the MNStorage.delete() MNodeService. There is debate about what permissions are needed to 'delete' an object (archive it in metacat terms): D1 'WRITE' (metacat 'write') or D1 CHANGE_PERMISSION (metacat 'all'). For now we are using CHANGE_PERMISSION until it is ironed out.

isAuthorized: check for nulls in Session subjects, catch any unexpected errors and deny access when in doubt

Remove setParamsFromRequest() from D1NodeService. This was called (previously as CrudService) from ResourceHandler, but will be deprecated in favor of manually creating a param map for each method that needs to pass params on to MetacatHandler.

Implement [MN|CN]Storage.create() in D1NodeService. Since MetacatHandler requires an IP for event logging, we pass in the metacat URL (hold over from CrudService). To do this in the abstract D1NodeService, change the constructors to take metacatUrl as a parameter and get the URL from the metacat properties file in getInstance() of the subclasses. Needs testing.

include URL in resolve() method as well as placeholder for preference

Metacat does not implement CNRegister

Implement CNRead.synchronizationFailed() in MNodeService. Note: The CN URL is not yet available in the SynchronizationFailed exception, but will be once the d1_common_java exception is updated. See https://redmine.dataone.org/issues/1656. Once updated, change this method to explicitly state the CN URL making the call.

Change Metacathandler.read() to be public since it's internal to Metacat, and use read() in D1NodeService after isAuthorized() for the calling Subject from the Session object.

Implement MNRead.listObjects() in MNodeService.

Implement MNRead.describe() in MNodeService.

Implement MNRead.getChecksum() in MNodeService.

Minor formatting changes - tabs to spaces, indents, etc.

Implement [MN|CN]Read.get() in D1NodeService. Added setParamsFromRequest() to pass through parameters from the request object. Since the D1 Authorization API doesn't specify which authentication system a subject belongs to, we don't know if the subject listed is a KNB LDAP DN. isAuthorized() may return true for a mapped identity, but we don't know the DN of the KNB identity per se. This needs to be tested.

-use every Subject in the session (alt Ids and Group membership)
-consolidate to single isAuthorized method

throw exception for unimplemented methods

implement resolve() method

implement assertRelation

implement CNReplication.setReplicationStatus() but with a note about selecting which replica's status should be set (right now it is all)

implement CNReplication.setReplicationPolicy

correction: implementation is CN-specific

implement getChecksum() in the superclass

implement getChecksum (retrieves from system metadata)

use shared get() method from superclass

use shared getLogRecords method

Remove isAuthorized(), setAccessPolicy(), and getLogRecords() methods since they're implemented in the superclass.

use Permission, not Event for isAuthorized() methods

CNCoreImpl is replaced by CNodeService

implement CNAuthorization

Metacat does not implement CNIdentity - it is a stand-alone service

implement registerSystemMetadata

implement object format methods - using a separate class to do the actual metacat lookup/caching so that teh CN implementation looks cleaner

implement getLogRecords

include latest D1 common/lib changes

Initial check in of the MNodeService stub methods that implement the D1 MN* interfaces. CrudService methods will be transitioned into this class. The methods follow the D1 0.6.2 API thus far.

Also changed CNodeService to reflect minor changes to the D1NodeService class.

Add a static getInstance() method to CNodeService and make CNodeService a singleton.

Initial check in of the CNodeService stub methods that implement the D1 CN* interfaces. CNCoreImpl methods will be transitioned into this class. The methods follow the D1 0.6.2 API thus far.

CNAuthorization.isAuthorized() and MNAuthorization.isAuthorized() differ. Removed it from the base class.

getChecksum() is intentionally different on the CN vs MN, so I'm removing it as a common method.

Initial check in of the D1NodeService class that provides methods common to both CNodeService and MNodeService implementation classes. The common API methods are:

Methods common to CNCore and MNCore APIs
getLogRecords()

Methods common to CNRead and MNRead APIs...

take getLogRecords impl form CrudService and use in CNCoreImpl

Updated CNCoreImpl to implement listFormats() and getFormat(), and changed calls to ObjectFormatCache in IdentifierManager, MetacatHandler to call getInstance(). Removed the ObjectFormatService registration from MetaCatServlet since it is replaced by CNCoreImpl.

include create() and reserveIdentifier() methods

include override annotation for register method

use Date not joda's DateTime

force replication for newly-registered system metadata

Merged in the D1_0_6_2_BRANCH changes that include the transition from ObjectFormat calls to ObjectFormatCache calls.

implement the old interface for now (until 0.6.2)

include CNCore implementation - only registerSystemMetadata is implemented at the moment. also - updated d1 jar (0.6.2) should be used since that is where the method is defined.
would like to consider making ResourceHandler more modular - seems like it does A LOT of different things

read and write D1 access policy rules from metacat xml_access table.
still TBD: which mechanism takes precedence when there are systemMetadata access rules and EML access rules and other access rules?

-remove system metadata guid -> local id mapping (there is no document for system metadata now)
-include system metadata elements when replicating data objects (TODO: transfer all system metadata structures with the docinfo request).
TODO: remove docid+rev from the systemMetadata table definition

do not use XML files for storing SystemMetadata - use DB tables only.

Modified Metacat to build against the D1_SCHEMA_0_6_1 branch of the dataone schemas by incorporating the 0.6.1-SNAPSHOT version of d1_common and d1_libclient libraries, and refactoring Metacat code references to the d1 schema changed types.

In order to sync up with DataONE 0.6.1 changes, I'm backing out ObjectFormatService changes temporarily in Metacat. Most functionality will be rolled back in using the DataONE 0.6.2 tag, but some methods in ObjectFormatService (such as getListFromDisk()) will be moved into d1_libclient_java.

Changes in the DataONE ObjectFormat class deprecate the convert() method, and we're now using Metacat's ObjectFormatService to look up object format attributes. The following changes replace ObjectFormat.convert() with ObjectFormatService.getFormat() in several classes....

generateMissingSystemMetadata was swallowing Exceptions instead of throwing. Refactored so that specific exceptions are thrown, affecting [create/update]SystemMetadata methods, too.

DocumentImpl.delete() now throws finer grained exceptions (not a general exception). Consequently, the classes that call it have been updated to handle the thrown exceptions, including CrudService, ReplicationHandler, and ReplicationService.

fixed bug where the wrong checksum alg got written to the db

To support the generatemissingsystemmetadata REST call, modified CrudService.createSystemMetadata() to use DataoneEMLParser and further determine object formats from EML metadata. Formats currently supported are text/plain, text/csv, image/[jpg|jp2|bmp|tiff|png], and only for EML documents with 'ecogrid://' defined entity urls....

Cleaned up warnings, removed dead code.

Updated to most recent DataONE libraries. Updated CrudService to set the correct origin MN and auth MN in system metadata. Refactored exception passing. More work to come in generating SystemMetadata.

added code to do database query for listObjects

Cleaned up unused imports.

adding fields for additional system metadata info

added code to run an squery for listObjects instead of an anyfield query

refactor checksum and some other stuff

replicate works on metacat now. just waiting for roberts changes to the mmp clients

removing code I just added

adding default url to test against

fixes for creating SM for legacy docs

fixing generateSystemMetadata

implemented health api

new class

implemented ping

fix for paths with semi-colons or other 'reserved' characters in them for D1 rest services

added semi-colon id test

allow public access to log information when docid is given. IP and principal are not returned unless an administrator makes the request.

organized code for inputstream handling

fixed date problem

add a timer to delete the temp file

removed dependency on InputStreamToOutputStream so that exceptions will be passed correctly.

got getChecksum working. working on delete now. all tests in d1clienttest now pass

implemented crud.delete

changed date format a bit to get the parser to like it

implemented crud.describe

adding getChecksum method

added milliseconds back onto date format

fixed a couple bugs with dates and fixed a major bug where metacat was reading the entire document from the database everytime a DocumentImpl instance was created even though it didn't need to