Metacat

changes for schema update (d1_common)

Update tests to use the DataONE 0.6.4 schema and types.

latest D1 jars - changes include:
updateSystemMetadata() impl for CN
new identifier methods (generate is its own method)
removal of the resourceMap pointer from system metadata

refactor Constants

refactor Constants and ServiceTypeUtil

use new "v1" types from DataONE

remove CrudService -- replaced by MNodeService and CNodeService

remove CrudServiceTest reference in main Metacat test (about to remove from svn)

reset object input stream (testGet)
check for reserveIdentifier NotImplemented (expected)

merge changes from 1.9.5 branch that read site docs from SVN not a defunct LTER server

Return the new pid (not the obsoleted pid) on update(), and set the correct system metadata.

include Mock version of looking up the base url for our own node - for testReplicate().
still expecting a failure during MN.replicate() since we are trying to add the replica to the same MN from which it came.

allow alternative CNode implementations (subclasses) to be returned when D1Client.getCN() is called. The alternative is given in the Settings configuration via the D1Client.cnClassName property.
MockCNode in Metacat is an example of such an alternative and is used when Metacat requires methods of a CN be present for unit testing.

Test that the obsoletes and derivedFrom system metadata fields were set correctly.

use objectFormatIdentifier for listObjects()
remove provisional system metadata indicator - Metacat will not implement reserveIdentifier()

add test for synchronization failed -- TODO: verify that the log record made it in the logs

provisional replicate() implementation -- does not check if the session's subject is "allowed" to do this.
the test also requires 2 servers -- right now it attempts to replicate with itself which will fail because of duplicate IDs

provisional version of getOperationStatistics() -- not clear if we are meant to aggregate by hour or by day

include test for replicate() method -- still fails as not implemented

allow null objects (use default checksum)

wire-up the getCapabilities() and getOperationStatistics() methods for when they are actually implemented (tests fail now)

test listObjects()

include MNAuthorization tests

refactor to use common superclass D1NodeServiceTest for shared methods

test for getLogRecords -- with some semi-reasonable expectations on the return that is expected

tests for isAuthorized and setAccessPolicy

include getLogRecords() test, though it is commented out at the moment

test for CN.getSystemMetadata()

test CN.get()

Uncommented MNStorage tests.

Send the correct Date format in testGetLogRecords(). I've commented out certain tests in the suite until isAuthorized() functionality is working. It is returning a NotFound exception even though the object is clearly in Metacat.

Add MNodeServiceTest tests for MNCore, MNRead, MNStorage, MNAuthorization implementations. MNReplication remains to be tested, as does MNCore.getCapabilities() and getOperationStatistics().

add the d1_common formats if they do not exist on the server

remove resolve() test -- not implemented in Metacat

add methods for testing CNodeService impl. Still some failing tests, but whittling them down

refactor to test the entire CN service impl

do not use pisco for referral testing (merge from 1.9.5)

merge 1.9.5 changes to trunk (delete now preserves access rules and docs can be read after deletion)

CNCoreImpl is replaced by CNodeService

Get username and password from a property file.

Updated tests to use ObjectFormatCache.getInstance(), and added tests for CNCoreImpl.listFormats and getFormat().

When calling SystemMetadata.getObjectFormat(), return the string value of the ObjectFormatIdentifier rather than ObjectFormat.toString() (which no longer returns the fmtid string).

organize imports so that it is clearer what dependencies exist on the D1 jars

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

include GUID column for xml_access and related methods for storing/retrieving access rules

handle timed replication of system metadata. there are still a few outstanding issues:
-track server location of system metadata-only entries
-replication policy flag for system metadata-only entries?
-locking for replicated entries?
-forced replication of entries

-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.

Commenting out these MetacatRestClient tests because the Metacat RestService is no longer registered as a servlet and needs to be removed, along with the associated MetacatRestClient and tests.

Fixed MetaCatServletTest test failures by removing the hardcoded username/passwords used in the tests and replacing those with data from metacat.properties.

Fix AuthLdapTest to use accounts that are more reliable when searching for existing accounts in the getPrincipals output.

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.

updating CrudServiceTest with better exception handling (more specific) to match refactored CrudService.java class

removed newline addition to test doc now that the newline problem is fixed in utilities project. Small adjustments to comments and debug statements to aid in debugging. Reordered tests to remove possible insertion between read and getLastDocid test.

Make this class be the subclass of the MCTestCase. The super class will initialize the property service for it.

commenting out the pisco user tests, since they only work in production.

put in more explanatory exception methods in the private helper functions that throw exceptions, and some debug statements in the onlineData201CasesTest_1 test.

Due to changes in MetacatHandler that creates system metadata from uploaded EML documents, OnlineDataAccessTest was failing certain tests because of errors in how the test documents were originally uploaded. MetacatHandler.createSystemMetadata() was throwing exceptions because of these errors, specifically when a data document is uploaded with a docid that is difeerent than the docid statement in the EML distribution URL. Most errors involved stated docids with .2 versions, and the metadata had .1 versions....

Cleaned up imports.

Updated D1 libraries to head to eliminate problems with date parsing -- added
Joda jar to support date parsing. Removed hardcoded DN from test file. Now
CrudServiceTest is passing again.

Remove hardcoded LDAP usernames from testing so that MetaCatServletNetTest will work even using alternate
LDAP servers.

Fixed the testNCEASLogin() password that I mistakenly changed.

Now that MetacatHandler creates GUID identifier mappings and system metadata, many of the tests in IdentifierManagerTest were failing that were manually creating id mappings and system metadata.
Modified testCreateMapping() and testCreateSystemMetadataMapping() to use docids that haven't been inserted to just exercise the methods....

Added a new test method testDeleteDocumentByGUID() to ensure MetacatHandler can delete based on GUID, but fall back to docid if the GUID isn't present. Modified CrudServiceTest and made some private methods public to leverage the D1 REST calls in that library (i.e. create() a doc with a GUID).

Add a method to test download a schema with included schemas.

Add a test file for XMLSchemaServcieTest.

Add a junit test file for testing the XMLSchemaParser class.

removed comments from crudservicetest

fixed bugs in listObjects

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.

Fix the MetadataTypeRegisterTest because it had the wrong URI for METS.

added code to do database query for listObjects

remove the empty dir.

This is redundant to the WorkflowSchedulerCleintTest in wsfscheduler svn module.

use more unique scope (document id prefix) so that getlastdocid runs successfully. use superclass generateDocumentId() method

adding fields for additional system metadata info

new paths for metacat populator

updated the populator

fixed compile errors

uncommented tests

fixes for creating SM for legacy docs

uncommenting tests

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

include shared method in superclass

create another test for various i18n features including eml 2.1.1
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2495

uncomment the other test cases and make sure we do the clean up when the tests are complete (delete the uploaded documents)

use detected XML encoding when reading/writing files
use UTF-8 as default when performing queries in the DB (assume DB is using UTF-8)
remove as many PrintWriters (uses system default character encoding only) as possible and construct OutputStreamWriters where explicit encoding can be given....

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

correct the prolog

changed test to use actual semi-colons instead of colons

add XmlStreamReader test for determining encoding

added semi-colon id test

found a failure when using an InputStreamReader without an encoding

a test to explore character encoding with utf8 chars

support EML 2.1.1

include anonymous parameter when getting report

add support for EML 2.1.1

organized code for inputstream handling

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

changes for new d1 schemas