Metacat

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

changes for dataone .5 schema updates

updated all exception codes to match spec

fixed task 729

fixed a bunch of small errors, did some reformatting, and fixed a bug that I thought was fixed last week

changed log labels per trac 843

fixed bug 818

better log message

more debugging for objectInfo problem

checking for a null objectformat

checking for a null objectformat

checking for a null objectformat

backtracking

add some error output

add some error output

added a check for bad data into listObjects

commented out a println

updated DB scripts for D1 schemas

moved the dataone types to the metacat.properties file

changes to work with new dataone jars

fixed bug where the query cache was not getting reset by a REST insert/query combo.

new todos from code review with roger

added TODOs and cleaned up the code a bit

fixed mime multipart problems so that roger can try to use the d1client

fixed error where insert/update errors were not getting caught as exceptions

fixed bug with logger where localid didn't get appended when inserting a data file