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metacat / src / edu / ucsb / nceas / metacat / dataone @ 8210

# Date Author Comment
8210 09/16/2013 04:33 PM ben leinfelder

require authenticated session when minting a DOI/other identifier. https://projects.ecoinformatics.org/ecoinfo/issues/6086

8202 09/16/2013 12:00 PM ben leinfelder

use optional template for registering DOIs at a given target. https://projects.ecoinformatics.org/ecoinfo/issues/6092

8200 09/13/2013 03:53 PM ben leinfelder

only attempt to generate OREs for objects that we know not to have them already. https://projects.ecoinformatics.org/ecoinfo/issues/6061

8190 09/12/2013 04:50 PM ben leinfelder

better checking for ORE maps when publishing DOIs (need to update the packages that contain sci meta). https://projects.ecoinformatics.org/ecoinfo/issues/6061

8189 09/12/2013 01:45 PM ben leinfelder

implement ORE check method to actually query the MN for OREs that reference the given pid.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

8162 08/23/2013 04:01 PM Jing Tao

Add code to throw an exception if the pathquery is not enabled.
We also need to disable building index if the pathquery is disabled.

8160 08/22/2013 04:04 PM ben leinfelder

use consistent file names and zip content names. Opted for "-" separator so that the zip writer does not remove the unique part of the filename. https://projects.ecoinformatics.org/ecoinfo/issues/6054

8141 08/13/2013 12:57 PM ben leinfelder

copy the original systemMetadata when publishing a revision in order to avoid overwriting the original values - the shared map is listening! https://projects.ecoinformatics.org/ecoinfo/issues/6014

8028 07/18/2013 10:53 AM ben leinfelder

type the doctype="metadata" objects as "FGDC-STD-001-1998" formatId for rendering XSLT and for DataONE SystemMetadata.

8026 07/18/2013 08:13 AM ben leinfelder

use custom FileInputStream subclass to delete the temporary bagit zip when the inputstream is closed (after someone has downloaded the zip).

8025 07/18/2013 08:02 AM ben leinfelder

use ObjectFormatCache instead of ObjectFormatService because we are not calling it as a CN.

8014 07/16/2013 04:21 PM ben leinfelder

include the localid when rendering the view (used in stylesheets)

8013 07/16/2013 04:05 PM ben leinfelder

use ObjectFormatCache.getInstance().getFormat() instead of the CN service (the MN does not typically act as a CN!)

7864 07/09/2013 10:40 AM ben leinfelder

include mn.publish() REST endpoint handling. https://projects.ecoinformatics.org/ecoinfo/issues/6024

7862 07/08/2013 06:19 PM ben leinfelder

comment out the index queue call when archive() is called - I think it is causing the duplicate events for the listener. https://projects.ecoinformatics.org/ecoinfo/issues/6030

7861 07/08/2013 06:10 PM ben leinfelder

implement the view service (uses existing skin-based dbtransform) - and include the REST endpoint. https://projects.ecoinformatics.org/ecoinfo/issues/6028

7860 07/08/2013 05:51 PM ben leinfelder

use StreamSource instead of StringReader for method signature -- can be used with different sources this way. https://projects.ecoinformatics.org/ecoinfo/issues/6019

7855 07/08/2013 12:14 PM ben leinfelder

include GET /package/{pid} endpoint in MN service. https://projects.ecoinformatics.org/ecoinfo/issues/6027

7853 07/05/2013 06:33 PM ben leinfelder

MN.getPackage() - test with ORE that includes 2 data files and a "metadata" file (still should be using EML for that test). https://projects.ecoinformatics.org/ecoinfo/issues/6026

7850 07/04/2013 12:33 PM ben leinfelder

First pass at MN.getPackage() implementation using Bagit library from LOC. https://projects.ecoinformatics.org/ecoinfo/issues/6026

7849 07/03/2013 09:58 PM ben leinfelder

add method for publishing existing object (usually assumed to be scimeta) with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6014

7842 07/03/2013 12:28 AM ben leinfelder

only use MapStore/MapLoader for saving/loading IndexEvent objects. No need to use a listener since there is only the single node -- all entries are persisted to DB using the hazelcast.xml config we have for the map. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7841 07/03/2013 12:03 AM ben leinfelder

add MapStore/Loader test for the IndexEvents -- adding and removing events in the DB table through hazelcast. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7829 06/25/2013 01:23 PM ben leinfelder

stub for storing IndexEvent objects in Metacat (from metacat-index processing). https://projects.ecoinformatics.org/ecoinfo/issues/5944

7827 06/25/2013 01:17 PM ben leinfelder

do not force a get() during refresh (causing EML-defined data access rules to be lost when inserting EML docs about data files). note that this reverses a change that was meant to trigger indexing, but now we are using a new queue to share index events with metacat-index and so should not be necessary.

7816 06/21/2013 11:11 AM ben leinfelder

correct regex for whitespace in D1 identifier.

7812 06/20/2013 04:49 PM ben leinfelder

use an independent ISet<SystemMetadata> structure to communicate objects that should be indexed by metacat-index. https://projects.ecoinformatics.org/ecoinfo/issues/5943

7781 05/28/2013 01:20 PM Jing Tao

Solr will be enabled if it is in the db.enabledEngines.

7772 05/23/2013 06:39 PM Jing Tao

Use some contants from the EnabledQueryEngines.

7757 05/23/2013 10:20 AM ben leinfelder

use ContentTypeInputStream interface (and ByteArray implementation) to specify the desired content-type of the InputStream returned by MN.query().

7755 05/22/2013 04:44 PM ben leinfelder

load the evicted SM back into the map on a "Refresh" so that listeners hear the update. (metacat-index, for example)

7680 05/09/2013 10:04 AM Jing Tao

Use the set of subjects to replace the user and groups for the solr query.

7662 05/02/2013 12:47 PM Jing Tao

Use a new class to handle the solr query engine description request.

7648 05/01/2013 02:38 PM Jing Tao

Add the access query filter.

7634 04/29/2013 04:59 PM Jing Tao

Add code to handle the solr index information. we still need to figure out how to get the information.

7625 04/25/2013 05:09 PM Jing Tao

Add the solr engine to the engine list.

7622 04/24/2013 07:34 PM ben leinfelder

use maven to manage most jar dependencies in Metacat.
Exceptions include: LSID, Datamamager (EML),

7620 04/24/2013 05:00 PM Jing Tao

Add code to handle solr query.

7600 04/20/2013 06:19 PM Chris Jones

Merging the METACAT_2_0_6_BRANCH changes for [M|C]NodeService into the trunk.

7534 04/05/2013 12:38 PM ben leinfelder

allow verification date to be updated for replicas (patch from Skye). https://redmine.dataone.org/issues/3699

7517 03/14/2013 09:56 AM ben leinfelder

include size and format datcite elements (optional) and use more general resourceType without formatId in them (Dataset/metadata and Dataset/data). http://schema.datacite.org/meta/kernel-2.2/doc/DataCite-MetadataKernel_v2.2.pdf

7516 03/13/2013 05:11 PM ben leinfelder

lookup the title for EML files when registering DOIs.
lookup the creator from DataONE CN (if available).
add EML-based test. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

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.