Metacat

When the requested count in a call to listObjects() is 0, return an empty object list, not a full one. Fixes https://redmine.dataone.org/issues/2122

Minor formatting for querySystemMetadata().

Updated contributors.

Modified index to fix typo.

Edited introduction to Metacat admin guide, inserted figure.

Screenshots from the Metacat admin guide.

Updating Sphinx doc structure in prep for moving metacat admin guide to Sphinx.

exapnd permissions on the exisiting access rule not on the permission being checked. (hierarchical permissions)

defer to super class member variables

Upgrade to Hazelcast-1.9.4.5 to try to solve CLIENT_CONNECTION_LOST problems seen on the Coordinating Node.

mark client/servlet API and EarthGrid API as deprecated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5517

upgrade routine to purge empty replicated data files so that they can be re-replicated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536

format the execution time to be a date.

Use "post" to replace "get" to fix caching issue on IE.

Make the display of the schedule table fit the IE browser.

Make sure the local id isn't null when we try to get the object from the local instance.

Simplify the error handling, and throw the exception once the CN is updated with the new status.

Set the replica status to failed (not invalidated) when we get exceptions trying to read the object bytes. Not much of a difference, but only the CN, in theory, is supposed to be able to set the invalidated status.

Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.

Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).

Get the object inputstream from the local metacat instance using MetacatHandler.get() rather than MN.getReplica() so we don't throw an InvalidToken exception when passing in a null Session. The D1Client object is never used for this local call.

interpret permissions as hierarchical
https://redmine.dataone.org/issues/2150

Use submitLoginFormIntoDivAndReload to replace submitLoginFormIntoDiv js function.

remove flag for independent system metadata replication -- these entries are replicated along with the data/metadata objects or via hazelcast when the actual object is not on the server.

update documentation to reflect changes to replication (client certificate)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

include SSL settings for client certificate-based replication

do not include the "v1" in the base url for the target MN

New D1 jars with a minor CNode.setReplicationStatus() bugfix.

The kar id will have version number.

process the current revision, not the latest!
use direct object/system metadata insertion for ORE maps.

allow other Metacat process (system metadata and ORE generation) to directly insert objects and system metadata without having to go through the MN/CN methods.

sort the docids so that "old" revisions are processed before newer ones

only attempt to unlock a lock if it was created (in the finally block)

update tests to comply with these chenages:
new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().

new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().

refresh the SystemMetadata entry for EML and referenced data files when parsing EML access rules -- this ensures our in-memory system metadata map is up to date WRT the DB entries.

Using a branch name for the utilities project. This branch is a copy of the trunk and it uses the BSD license.
We will move this branch to a tag soon.

add revision history to the generated ORE objects -- we use the revision history of the EML package as a basis because the each ORE revision mirrors the revision of the EML package.
Add a placeholder for checking if an equivalent ORE map exists in the DataONE infrastructure - this will be a call to CN.search() that looks at the solr index for OREs based on the EML package ID.

Update the parameter names expected for listObjects() to reflect the MN API changes in the architecture docs.

Change the query semantics such that we implement the MN.listObjects() where the lower datetime bound is inclusive (greater than or equal to" and the upper datetime bound in exclusive (less than). This allows easier paging in client applications.

for test to compile, provide BaseException param for setReplicationStatus. I used a NotAuthorized instance.

adjust after refactoring tests that use EML queries

In the call to MNReplication.replicate(), call back to CNReplication.setReplicationStatus() and set the status to failed when we get local exceptions, exceptions from the source MN when calling getReplica(). Send back an exception with a description when setting the status. Add a private setReplicationStatus() method to refactor these calls out.

Modify CNresourceHandler.setReplicationStatus() to use the new API signature, including the failure BaseException that is parsed out of the MMP as a file section. Log the exception message. Since this is an asynchronous call, ReplicationManager won't see a failed status, but the MNAuditTask eventually will.

Add collectReplicationStatus() to CNResourcHandler to return the BaseException or it's subclass, if any, provided in the the call to setReplicationStatus. The exception will be reported on the CN.

Change setReplicationStatus() to drop serialVersion and report the failure exception message in the CN log.

Add new D1 jars with update CNreplication API changes to SetReplicationStatus().

query for deleted metadata when testing that replication communicated the deletion. to check data, we try to update the data object on the target node (which should fail)

add test for data locking

delete data and eml on the home Metacat and check that the change propagates to the target

set SystemMetadata.archived=true on MN.delete
There is ongoing discussion on what the exact behavior should be here, but this mimics Metacat's delete-as-archive action.
http://redmine.dataone.org/issues/882

In MNodeService.replicate(), check to see if we have a replica (via an out of band channel) before we call sourceMN.getReplica().

actually include the test in the suite
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

EML replication test with insert, update and set access
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

only create guid->docid mapping during metadata replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

do not treat access change as an update -- it should not attempt to retrieve the contents of the object
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

Change the ecogrid tag to 1.2.2.RC5.

only create guid->docid mapping during data replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

remove xml_acccess.docid reference (oops)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

test update and set access during replication from A->B
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

updated D1 API -- removed Permission.REPLICATE and associated parameters

a minute for replication?

process system metadata before access rules (access control is now driven by GUID so the mapping needs to be there)

Change the key of query result cache. The key now has the real search value.

include SerialVersion in describe response
https://redmine.dataone.org/issues/2135
NOTE: d1 jars should be replaced once all schema changes are finalized and the generate d1_common code is committed to svn

comment out B->A test
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

use correct URLs for replication/Metacat client

simple tests for 2-way data replication
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520

ROLLBACK: check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi

check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi

redirect to the registry form following successful login - but allow an override in case we only want to render the success and stay there (ajax call from main sanparks page).

include 'archived' system metadata element in backing DB store

include the logging level with configuring logger (with file appender) for replication and dataone
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5534

add ; to end of update command

add ; to end of update command

only update accessfileid for our new guid-based records

move latest postgres access upgrade statements to oracle script
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

include revision clause when updating the accessfileid on the xml_acccess table

remove docid column in favor of guid
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

include "esa" context in the data registry URL.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5114

If a member node cannot be found in the node list matching the targetNodeSubject given in isNodeAuthorized(), throw a ServiceFailure exception.

Minor reformatting for readability.

fix tests:
-insert default objectFormatList from d1_common (includes schemaLocation now)
-calculate checksum for the system metadata using the ChecksumUtil in d1_common

update with latest d1_common/d1_lib (includes latest schema changes)

prepared statement toString() does not include quotes (') around the inserted values -- now the test reflects this.

only handle 100 (consecutive!) docId generations per millisecond, otherwise the generated docid part is bigger than Long.MAX_VALUE and Metacat cannot fully handle that.

Metacat now keeps track of permissions on a per-version basis -- the test reflects this change in behavior.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

check previous revision when attempting to update access control with EML 2.0.x docs
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

remove old access rules for a data object when they are being updated by rules contained in an EML document. Now the OnlineDataAccessTest EML 2.1.0 tests pass.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

construct the proper previousDocId when checking for update permission

for now, look up SystemMetadata directly from the table otherwise we won't have the latest access information. Need to refresh the in-memory copy everytime we edit the access policy via Metacat (includes EML parser)

check previous revision for permissions to update (includes data described by EML)

use correct "rev" column in xml_revisions table

refactor Metacat access handling to be on a per-revision basis so that it more closely aligns with the DataONE approach
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

To avoid id generation conflicts happening at the same millisecond, append a 5 character random string to the end of the docid.

Remove header2, footer2 and left-nav2 files.

change the default scheduler and workflow run engine urls.

retry: add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561

update test to reflect newer change:
handle queries with predicates correctly.
when docids are used in the return field look up, we need to make sure they are included in the values in the correct order for their corresponding parameter place holders (?)

add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561