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metacat / src / edu / ucsb / nceas / metacat / dataone @ 7515

# Date Author Comment
7515 03/13/2013 03:13 PM Chris Jones

Set the session to null so that the call uses the CN certificate when calling MN.systemMetadataChanged();

7514 03/13/2013 07:26 AM Chris Jones

To keep all nodes up to date with regard to system metadata changes, add the broadcastSystemMetadataChange() method that finds replica MNs in the node list and calls systemMetadataChanged(). Modify setReplicationStatus() and updateReplicationMetadata() to fire this off when a replica status changes to completed. We may decide to inform MNs at other times too, but this is a conservative amount of calls going to the MNs for now.

7512 03/12/2013 04:44 PM ben leinfelder

refactor DOI registration into separate class. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7511 03/12/2013 04:26 PM ben leinfelder

refactor using ezid-client changes that split field names and values into separate enums. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7510 03/12/2013 03:20 PM ben leinfelder

Correctly mint and register DOIs in teh MN API implementation. Add tests to exercise minting and creating. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7507 03/11/2013 04:48 PM ben leinfelder

register DOIs with minimal DataCite metadata. still need to determine which details to include and when, but the plumbing is in place as we refine those rules. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

7503 02/26/2013 10:27 AM ben leinfelder

disable EZID/DOI minting by default since we do not yet have a means of tracking minted DOIs and augmenting metadata for them when we actually receive the object in a subsequent create() or update() call. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5753

7489 01/31/2013 04:02 PM ben leinfelder

generate ID from UUID. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5840

7486 01/18/2013 02:12 PM ben leinfelder

make sure serial version is included or set on MN.update().
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5793

7467 12/07/2012 10:39 AM ben leinfelder

make sure to call lock() on the SM when updating rightsholder (like every other method that gets a lock object from HZ).

7464 12/07/2012 10:25 AM ben leinfelder

CN.search() id not implemented by metacat -- making that explicit and also testing for it.

7448 12/02/2012 08:58 AM ben leinfelder

first pass at DOI minting using the EZID service in mn.generateIdentifier()
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

7443 11/30/2012 12:17 PM ben leinfelder

for MN.update() we needed to pass the original pid, not the new pid

7442 11/30/2012 10:49 AM ben leinfelder

do not reject any schemes -- all handled the same at the moment.

7441 11/30/2012 10:23 AM ben leinfelder

simple autogen-based implementation of MN.generateIdentifier(). does not support DOIs, ARKs, etc. It does support including a fragment, returning an identifier like "<fragment>.2012113010215298206"

7439 11/29/2012 04:52 PM ben leinfelder

limit /log and /object calls to configurable maximum count for paging. defaults to existing Metacat value of 7000

7430 11/23/2012 10:02 AM ben leinfelder

no need to mark SM as archived now that DocumentImpl.delete() does it.
https://redmine.dataone.org/issues/3406

7421 11/10/2012 03:34 PM Chris Jones

In migrating to Hazelcast 2.4.x, replace deprecated methods. Use Hazelcast.newHazelcastInstance() rather than Hazelcast.init(). For other deprecated static methods, use the HazelcastInstance equivalent calls.

7420 11/09/2012 10:57 AM Chris Jones

In CNodeService.updateReplicationMetadata(), we are setting the replicaVerifiedDate() when we update or wholesale add a new replica. However, in setReplicationStatus(), we only do so when there's a new entry. Change setReplicationStatus() to also update the replicaVerifiedDate on updates of existing entries to be more consistent with other changes. This affects node prioritization based on this date timestamp. Thanks to Skye for pointing this out.

7419 11/09/2012 08:56 AM Chris Jones

To attempt to address performance and stability WRT Hazelcast communication, we're upgrading to the 2.x series of Hazelcast. remove the 1.9.x jar files, and add the 2.4.1-SNAPSHOT jars. Modify HazelcastService to handle the minor change in the ItemListener interface (now passes ItemEvent<Identifier> as an argument)....

7418 11/07/2012 04:27 PM ben leinfelder

implement query description for pathquery -- only tells callers about the pre-indexed paths we have in Metacat since there are an infinite number of "fields" when storing arbitrary XML, but we really don't want people using non-indexed paths for performance reasons anyway. I've typed all the fields as String, even though some are not just strings and can be used for numeric or data comparisons.

7417 11/07/2012 02:53 PM ben leinfelder

Implement MNQuery for "pathquery" engine. Optionally include guid in the pathquery results (https://redmine.dataone.org/issues/3083)

7411 10/26/2012 09:08 AM ben leinfelder

add count for the total processed pids (from ISet iterator)

7401 10/15/2012 02:38 PM Chris Jones

Update d1_common_java and d1_libclient_java to the newest jar files. Add methods to CNodeService to throw NotImplemented exceptions for query(), listQueryEngines(), and getQueryEngineDescription() since these API calls are handled outside of metacat.

7400 10/12/2012 01:35 PM ben leinfelder

do not allow updates to orphan another branch of revision history. https://redmine.dataone.org/issues/3338

7398 10/08/2012 11:09 AM ben leinfelder

include the subjects we are testing for authentication.
https://redmine.dataone.org/issues/2778

7355 08/15/2012 03:46 PM ben leinfelder

make sure data objects correctly use force replicate with action "insert"
https://redmine.dataone.org/issues/3138

7346 08/03/2012 02:27 PM ben leinfelder

allow SM resynch to be executed any time, not just during start up.
https://redmine.dataone.org/issues/3116

7345 08/03/2012 01:01 PM ben leinfelder

change to debug log level when processing shared/local pids)

7344 08/03/2012 10:41 AM ben leinfelder

only lock the missing pid event if we know we have it locally to contribute.
https://redmine.dataone.org/issues/3117

7343 08/03/2012 09:26 AM Chris Jones

Add locking to the itemAdded() method so ideally only one CN will respond to the request for a 'wanted' pid from the cluster. The lock is on a string, not the pid, and so won't conflict with system metadata locking. The string is based on the pid, with "missing-" as a prefix.

7342 08/03/2012 08:53 AM ben leinfelder

only publish to the missing pid "wanted list" when resynching system metadata. we were seeing redundant entry added/updated events when looking up the shared systemmetadata first.

7341 08/02/2012 10:18 PM ben leinfelder

print the missing pid count, not the total shared pid count so we know how many will be processed.

7340 08/02/2012 05:50 PM ben leinfelder

change the system metadata resynch approach: nodes will publish PIDs that they are missing after inspecting the shared identifier set. other nodes will be listening for the "wanted" pids and will put their local copy of SystemMetadata on the shared SM map. This should dramatically decrease the hazelcast chatter during a resynch and targets only the pids that are missing from any of the various nodes.

7339 08/01/2012 10:40 PM ben leinfelder

logging for processing identifier set on restart.

7330 07/26/2012 12:08 PM ben leinfelder

check if the caller is the Node admin (the member node calling itself) as well as the existing check for the CN calling the service. Both of those callers should be given full admin rights.

7326 07/23/2012 11:55 AM ben leinfelder

use local Set processing to determine which pids (if any) should be contributed to the shared set by this node during the resync. Should save time rather than checking each and every pid against the shared set.

7325 07/20/2012 03:44 PM ben leinfelder

move the hzIdentifiers initialization into the resync thread so that it does not affect start up time. cleaned up unused methods and superfluous code.

7323 07/20/2012 10:51 AM ben leinfelder

only load local pids into hzIdentifiers if t hey do not already exist in the shared set. increase logging severity and detail of messages emitted during this process to get a better sense of what is taking so long.

7322 07/19/2012 02:38 PM ben leinfelder

utility methods to update/reserialize existing ORE maps that were generated with older foresite (and included bad dateTime strings).
https://redmine.dataone.org/issues/3046

7319 07/17/2012 03:57 PM Chris Jones

On the coordinating Nodes, we often get McdbDocNotFoundExceptions for data (doctype == 'BIN') documents because they are not synchronized to the CNs. Change the logging to only print the stack trace during load() and loadAll() when log debug is enabled.

7318 07/17/2012 01:34 PM ben leinfelder

check for invalid (!) pids. thanks, M. Reyes for catching this
https://redmine.dataone.org/issues/3047

7315 07/17/2012 11:09 AM ben leinfelder

check for whitespace in identifiers during create() and update()
https://redmine.dataone.org/issues/3047

7297 07/10/2012 10:20 AM ben leinfelder

set date SM modified when we are setting obsoletes/obsoletedBy/archived values. This way the CN can actualy pick up the changes in revision history.

7295 07/09/2012 04:23 PM ben leinfelder

log error when looking up non-existent local SM rather than completely bombing out of the resynch thread.

7286 07/02/2012 03:35 PM ben leinfelder

use secure Metacat context URL for D1 registration
https://redmine.dataone.org/issues/3030

7285 07/02/2012 12:06 PM ben leinfelder

first pass: DataONE-specific log retrieval to avoid java-based post-processing.

7278 06/18/2012 03:43 PM ben leinfelder

set archived flag (true) when we set the obsoletedBy value in the ORE system metadata

7273 06/18/2012 12:13 PM ben leinfelder

use the localId for obsoletes/obsoletedBy ORE system metadata (https://redmine.dataone.org/issues/2964)

7252 06/06/2012 03:14 PM Chris Jones

Oops, previous commit suffered from a happy trigger finger. During deleteReplicationMetadata(), don't delete the replica on the replica Member Node. Call CN.delete() for that functionality. This call just updates sytem metadata (according to the API description).

7251 06/06/2012 03:10 PM Chris Jones
7245 06/06/2012 10:23 AM Chris Jones

Minor logging change.

7244 06/06/2012 10:01 AM Chris Jones

Add debug logging to delete() to understand why we're getting InsufficientKarmaException.

7236 06/05/2012 02:07 PM Chris Jones

Since we already have determined access via isAuthorized() and isAdminAuthorized(), act as the Metacat administrator during calls to DocumentImpl.delete() in archive(), passing in null username and group.

7234 06/04/2012 08:49 PM ben leinfelder

restrict getLogRecrods (both MN and CN) to be called only by admin users (the CN)
https://redmine.dataone.org/issues/2855

7231 06/02/2012 05:46 AM Chris Jones

In setReplicationStatus() and UpdateReplicationMetadata(), don't allow a status state change from COMPLETED to anything other than INVALIDATED. This prevents the completed status from being overwritten due to race conditions.

7222 05/31/2012 09:04 PM ben leinfelder

use metacat.properties to specify the default checksum algorithm to use -- this way it will be easy for us to switch to whatever DataONE decrees.
https://redmine.dataone.org/issues/2834

7221 05/31/2012 06:16 PM ben leinfelder

put(sm) for every pid we have a SM value for so that all members receive the entry event and can save locally.

7218 05/31/2012 10:56 AM Chris Jones

Throw an exception when NOT allowed, not when allowed =).

7217 05/31/2012 10:53 AM ben leinfelder

ignore partition owner -- always attempt to look up form local store if we were unable to get the SM from the shared map.

7216 05/31/2012 10:13 AM ben leinfelder

do not check if this CN has a "perfect" copy of the SM identifiers -- we need any CN coming online to contribute the records that they have locally so that in the event that all three CNs have a partial view of things they all eventually share each others' SM entries.

7215 05/31/2012 10:10 AM Chris Jones

Also get the list size, which may throw an NPE.

7214 05/31/2012 09:53 AM Chris Jones

Only add an AccessPolicy to SystemMetadata during generation when the AccessPolicy is not empty. We've had some scenarios where IdentifierManager.getaccessPolicy() is returning an empty policy because of an empty permission list coming from the db. This was causing InvalidSystemMetadata exceptions during MN to MN replication.

7213 05/31/2012 09:19 AM ben leinfelder

push SystemMetadata entries from the CN that has them all to the shared map where other nodes may not have all entries. The CN with the complete copy only pushes SM entries that it does not own and that return as null because those are the ones that are missing on the other, non-complete CNs....

7212 05/30/2012 10:00 PM ben leinfelder

trace level log for looping over EVERY pid in the system.

7211 05/30/2012 09:47 PM ben leinfelder

meant to log the guids (source) not the pids (target)

7210 05/30/2012 08:51 PM ben leinfelder

trace level log for looping over EVERY pid in the system.

7209 05/30/2012 08:18 PM ben leinfelder

logging for each step of shared identifiers loading.

7208 05/30/2012 08:07 PM ben leinfelder

remove pause/resume - seemed to make metacat just hang on SM retrieval. Add more logging when returned SM is null -- want to make sure it is becuase the local node "owns" the pid key even though there is no value for it.

7207 05/30/2012 06:12 PM ben leinfelder

due to hudson build issue, did not actually end up testing pause/resume -- trying that again

7206 05/30/2012 05:53 PM ben leinfelder

pause/resume was not enough. trying shutdown/restart

7205 05/30/2012 05:02 PM ben leinfelder

experiment with lifecycle pause/resume. hopefully it prevents our node from taking ownership of any keys before we are sure we have them all.

7204 05/30/2012 08:29 AM ben leinfelder

increase logging and add back in the call to saveLocally() in case the SM object has already been loaded into the shared map but before this node came back online.

7203 05/29/2012 11:21 PM ben leinfelder

no need to call saveLocally explicitly since loading from the shared store triggers that behavior locally because of the configured listeners.
use an iterator over the shared identifiers in case this set is constantly changing.

7202 05/29/2012 10:10 PM ben leinfelder

make only one DB call to look up local pids - no need to do a pstmt for every single shared pid.

7201 05/29/2012 09:05 PM ben leinfelder

on init (start up) launch a synchronization thread that ensures all shared identifier entries have a corresponding local System Metadata entry.

7197 05/29/2012 10:31 AM ben leinfelder

fix NPE (logMetacat object was not initialized) that was occurring during store()

7192 05/25/2012 06:20 PM Chris Jones

Don't set the replication status to failed for an object when it is called by a public user. Just throw the NotAuthorized exception. This prevents this node from being de-prioritized because of public calls to the method.

7188 05/23/2012 04:41 PM ben leinfelder

share the same dbConnection when inserting and then updating SystemMetadata objects in the backing store.
any errors encountered during the update will rollback the entire transaction and the SM record will not exist, even in part.

7187 05/23/2012 03:28 PM ben leinfelder

Do not loadAllKeys() for SystemMetadataMap when Metacat first starts up. hzIdentifiers will be populated with a simple SQL statement rather than the serial loading of every single SystemMetadata object. It will remain in synch using the usual entryXXX() methods as before....

7184 05/23/2012 09:57 AM ben leinfelder

include pidFilter handling - only matches the complete pid. Issues a warning in the Metacat logs when pidFilter cannot be applied but allows the call to getLogs() to return as though there was no pidFilter given.
https://redmine.dataone.org/issues/2798

7179 05/21/2012 02:31 PM Chris Jones

Add a few logging statemnts for round trip replication metrics.

7178 05/21/2012 02:12 PM ben leinfelder

add trace statements for measuring time to complete SM generation.

7171 05/17/2012 12:46 PM ben leinfelder

remove exception from method decl - was not matching the interface def and not compiling.

7168 05/08/2012 04:30 PM ben leinfelder

only generate system metadata for original objects.
https://redmine.dataone.org/issues/2721

7162 05/02/2012 08:58 AM ben leinfelder

handle authorization for delete() differently for CN vs MN.
On the CN, only the CN (or tbd admin user) can call it.
On the MN, both the CN (or admin user) and the same MN can call it.

7159 05/01/2012 02:48 PM ben leinfelder

add Session-less archive() method

7157 05/01/2012 11:14 AM ben leinfelder

only admin users can call MN/CN.delete(). This is limited to any CN and only the MN that is calling itself

7156 05/01/2012 10:47 AM ben leinfelder

update the sysmeta data modified when setting archived=true
https://redmine.dataone.org/issues/882

7150 04/30/2012 04:03 PM ben leinfelder

optionally remove the document/data file from the filesystem completely when 'deleting' it.
https://redmine.dataone.org/issues/2677

7149 04/30/2012 03:42 PM ben leinfelder

newer d1 jars that include shared AuthUtilsmethod for isAuthorized() consistency
https://redmine.dataone.org/issues/2661

7148 04/30/2012 03:35 PM ben leinfelder

implement MN and CN.archive() method -- really just the existing delete() methods.
https://redmine.dataone.org/issues/2674
https://redmine.dataone.org/issues/2675

7147 04/30/2012 03:05 PM ben leinfelder

call MN.delete() for each replica when CN.delete() is called
https://redmine.dataone.org/issues/2676

7146 04/30/2012 02:20 PM ben leinfelder

defer to AuthUtils for flattening out the equivIdent subject list.
https://redmine.dataone.org/issues/2661

7145 04/27/2012 10:24 AM ben leinfelder

check normal access control rules for getSystemMetadata before deferring to MN replica information that may grant MNs additional access to the SM.
https://redmine.dataone.org/issues/2656

7144 04/25/2012 03:33 PM ben leinfelder

include Session-less interface methods and updated jars that define them.

7142 04/19/2012 02:04 PM ben leinfelder

remove extraneous pid and permission parameters from isAdminAuthorized() method and make public so that it can be called in other locations - namely before our asynchronous replicate() implementation on the MN.

7141 04/19/2012 01:50 PM ben leinfelder

check for empty null (missing) node.subjectList. This should probably be a required element in the D1 schema, but it appears not. (ORNL entry was missing subjects in cn-dev environment)

7140 04/19/2012 11:57 AM ben leinfelder

just use the e.getMessage() as e.getCause() may be null (seeing NPE when testing via the MN IT tester)

7139 04/18/2012 04:04 PM ben leinfelder

check for empty null (missing) node.subjectList. This should probably be a required element in the D1 schema, but it appears not. (ORNL entry was missing subjects in cn-dev environment)