Metacat

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

reformatting logs for robert

fixed update bug I introduced yesterday while fixing replication

still working on getting guid problems fixed with replication

fixed yet another null sessionData bug

fixed more access control problems. also fixed extraneous white space that was getting put into the listobject output stream

fixed problems with access control on sysmeta

fix for set access bug

added functionality to set access permissions to system metadata the same as the document that it describes

hopefully fixed get bug where session was null

fixing another null auth token bug

changing d1 log format

added code to make sure the localId and guid get added to get and create d1 logs

removing println

fixed more NPE problems with sessionData. hopefully got them all this time

fix for null session bug

updated for date format that supports time zones correctly.

changed date comparison to compare to gmt only

fixed NPE with sessionData

fixed bug in access control where the sessionid was not correctly passed along so changes of privileges were not being made

fixing date formatting and timezone issues

fixed bug with log processing

fixed some bugs in time handling for listObjects and getLogRecords

bug fix to handle nulls

fixed bug in getLogRecords where the wrong id was getting set as the identifier

added new exception handling to serialize number format exceptions for rest calls

fixed listObject bugs, added params to the listObjects rest interface, consolidated the date format passed in params

fixed query for listObjects so that paging works as advertised.

fixed error with listObjects and get.

still looking for listObjects problem

more debug for another instance

adding some debug info