Metacat

[merged from 1.9.3 branch] security fix: never unregister the "public" user session

re-added some code inadvertently removed

merged with version from 1.9.3 branch to fix bug with character encodings

added a todo

new todos from code review with roger

added TODOs and cleaned up the code a bit

do not read from the inputstream before passing it off to the SAXParser

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

added another logging statement

added replicate log statements with the guid and localId

fixed update bug I introduced yesterday while fixing replication

hopefully fixed bug with systemmetadata replication

debug statements in dbsaxhandler

still working on getting guid problems fixed with replication

fixed identifier manager problem with getting guid for systememtadaa doc

fixing problems with replication and systemmetadata

set the content type to text/xml for the rest interface

fixed yet another null sessionData bug

Fixed spelling error.

Set content type on listObjects to be XML so that it is recognized by clients.
Reformatted method to use original file conventions.

Reformatted code to fix indenting.

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

fixes for the access control setting for sysmeta

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

fixed major bug in replication where the document info was being truncated due to a poorly implemented sax parser

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

hudson tests are now running. needed date conversions. still more work to do with systemmetadata date format.

updated for date format that supports time zones correctly.

changed date comparison to compare to gmt only

fixed NPE with sessionData

added some new error handling to work around this issue https://trac.dataone.org/ticket/706

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

fixed bug where null session data was not treated properly.

Correct log warning message - not "Account" but "Accession" number

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.

formatting

fixed error with listObjects and get.

got the crud test to pass on knb-mn, now need to figure out why the rest service still isn't working

still looking for listObjects problem

more debug for another instance

adding some debug info

fixed bug with upper case comparison

changed getSessionData so that it will respond property to public tokens

Added SQL lines for registering D1 schemas in the upgrade process.

Removing drop statements from upgrade scripts because the systemmetadata table
does not exist in 1.9.2, so these objects can't be dropped on upgrade.

MetacatPopulator is now working. It allows you to do a query from one metacat instance, then insert any returned docs into another metacat instance

cleanup of 'fixed' ResourceHandler

tracked down streaming bug. now need to figure out a better way to fix it.

added getValue() to the guid so that it prints the guid and not an object id

added a DataOneLogger for event notifications on the CN. The logger is called DataOneLogger and can be managed in the log4j.properties file

finished getLogRecords. Fixed some date bugs in metacat.

adding getlogrecords to the rest interface.

changed getLogRecords to use new classes for log events

fixed bug in metacat that allowed attribute data to be appended to element data in returnfields

fixed bugs associated with crud access control changes.

implementing getLogRecords

added EventLog statements to all public methods in CrudService in preparation for addin the getLogRecords() method

added better debugging error messages for CN dev errors

added generateMissingSystemMetadata to the ResourceHandler so it is now available via a REST call.

made the test functional so that it checks that missing system metadata will be created.

mostly done with generating systemmetadata from legacy knb docs. need to write a better test and enable this through the ResourceHandler then it will be done.

working on getting systemmetadata creation working for legacy knb objects

working on a function to create dataone system metadata docs for legacy metacat objects that do not have SM.

moved authentication checking out of ResourceHandler and into CrudService

refactored the sessionService to use a correct singleton initialization scheme. Added true authentication to ResourceHandler.

new class to handle system metadata tasks in metacat

added systemMetadata table to the upgrade scripts

listObjects is now working for rest calls as well as crud calls

added some params to the loop that segments the listObjects resultset

allow any nonquote characters in the schemaLocation attribute, otherwise the whole line is matched and this prevents schemaLocation from appearing anywhere but at the end of the line.

finished the crud part of listObjects. need to implement it in the rest interface now.

implementing getObjects in CrudService.

implementing getObjects in CrudService.

implementing getObjects in CrudService.

listObjects is almost working. need to get the result set parsed when returned to CrudService.

setting up the framework for the listObjects api call

changed the detailCode for DataOne exceptions to a string

added getSystemMetadata to ResourceHandler and changed the url format to be meta/guid. added a new servlet reponse handler in the web.xml file to handle the new urls and send them to the RestServlet.

implemented update in ResourceHandler and fixed a bug in CrudService where data files were not handled correctly on update

removed system.outs

amost have update working. still need to get unit test squared away.

added exception testing to the crud test