Metacat

use Data Manager Library to parse EML when needed in DataONE classes.
(augmented DML to parse data format elements in EML to estimate MIME type)
https://redmine.dataone.org/issues/1634

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

transfer full System Metadata (as XML) during document and data replication

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....

zero padded date string in DocumentUtil.generateDocumentId() for readability

Add in correct node references in system metadata.

remove httpclient 3.1 and custom-built httpclient.jar
rework MetacatClient (and other classes) to use httpclient 4
updated build to not create httpclient.jar
encoding tests now pass.

some new code for debugging mmp

updated the populator

always re-write web.xml in case geoserver has been redeployed
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4307

Modified MetacatPopulator to deal with change in D1Client static methods.

rework geoserver configuration:
-geoserver context is set to 'geoserver' by default, but can be reconfigured
-data directory is set in the geoserver web.xml file (we have a template, set the value accordingly, then overwrite the deployed version in the geoserver webapp)...

fixed bug with http/https port

use detected document encoding or Metacat's default encoding (UTF-8)

fixed bug 818

updated the metacatpopulator to use the d1 eml parser to create system metadata in a smarter fashion.

changed improper use of getFS() to a /. getFS() should never be used with a URL since it will return \ on windows which is not a valid separator in a URL.

updated for new dataone jars

fixed identifier manager problem with getting guid for systememtadaa doc

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

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

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

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

Merge 1.9.2 changes back into the trunk

Added support to ResourceHandler to allow the putObject method to use
arbitrary guid strings as input. These strings are examined, and if they
match the Metacat docid format (scope.id.rev), they are used directly. If
the id is a string in another format, a new localId is generated based on...

Move the chunking of large test element data to centralized location in DBSAXNode.writeChildNodeToDB(). Beff up logging

Pass the doc xml as a string to docImpl.write and writeRepication. This is so a reader can be create for the parsing and for the write to disk. Also created a db access class for xml query result deletion.

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

Add authorization functionality

Add user name to SessionData object

change pw.println to print to remove newline at end of url

Change location of PropertyService to properties directory

Change MetaCatVersion to MetacatVersion

Move document specific utilities to DocumentUtil from MetacatUtil. This makes it easier to define a layer between the core metacat services and the rest of the code.

Create database and shared directories for database management code and shared code respectively.

Add the ability to delete a scheduled workflow (move status to deleted in database)

Created new AuthStub class to always authenticate.

Workflow scheduler and archiving fixes for TPC workflow engine

Added generic scheduler and workflow scheduling functionality.

Add scheduler and workflow schedule functionality

Add scheduler and workflow schedule functionality

Beef up exception handling from file utilities. Move UtilException to MetacatUtilException to eliminate conflict with similar exception in utility package.

Format indexPaths in metacat.properties. Remove from build.properties and build.xml. Move indexPath list getter from MetacatUtil to SystemUtil.

Separate the concept of a backup file location and a metacat external directory location. These can be totally different.

Allow for backup properties to be written to context based subdirectory of the external configuration directory. This allow multiple instances of metacat to be run side by side.

Change name of writeTempFile to writeTempUploadFile since this instance deals with the temporary upload dir specifically

writeTempFile was trying to write the same file as the registry. Changed to write the file to an "upload" subdirectory. Also throws IOException so errors get reported back to api.

Handle sessions with null ids gracefully.

Get the organization list from org.name.<orgname>= property. Add these values back into metacat.properties.

Try to create the backup directories before creating th ebackup files.

Add external (backup) directory discovery methods.

Renamed MetaCatUtil to MetacatUtil

Add method to save transforming message into files.

Use a while loop to replace if.

Add code to go through eml201 document list to transform them to eml210.

Add a new class which will transform eml201 and eml 200 to eml210.

Discover the external (backup) directory based on OS

Catch login errors and report the details via an exception.

Added code to populate moderators from metacat.properties

Add release info property to provide a brief description of the release (release candidate info mostly)

Rename LDAPUtil to AuthUtil

Add some generic typing

Fix the deploy directory autodiscovery code so that it works regardless of where the metacat application directory is.

Add some generics typing

include context for replication server

use secure server for replication - note that this is WITHOUT "https://" prepended

adding document "cart" feature to metacat. will not be highly published as a feature until well-vetted.

Replace usage of temp-dir with proper application.tempDir property

Move the DBAdaptor accessor into a DatabaseService class

remove skin.configs directory.
migrate those properties to the style/skins/* properties files
do not load them during Metacat init.

Added methods to get session data, parameters and cookies from request

change session attribute reference from "groups" to "groupname"

Continue to qualify property names

Intial addition of geoserver utility file

Remove commented lines

Add a post method

Remove the organization configuration stuff for the moment. Add geoserver configuration.

use context url to get cgi url

Change discoverTomcatDir to discoverDeployDir

Add support for separate LDAP and organization level configurations

Add functionality to allow developer to bypass configuration utility

FIx comments for getContextDir to reflect that we no long append webapps to the path

Differentiate between tomcat directory and deployment directory.

Move references to sql scripts into the WEB-INF directory.

Add method to return a map of db script suffixes from metacat.properties

Merge 1.9 changes into Head