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# Date Author Comment
7190 05/25/2012 02:30 PM ben leinfelder

add columns: publisher and pub_date. include default values for all columns - even data files should have title.
still a few todos but closer.
https://redmine.dataone.org/issues/2815

7189 05/25/2012 12:07 PM ben leinfelder

script to generate DOI registration spreadsheet
https://redmine.dataone.org/issues/2815

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

7183 05/23/2012 09:33 AM ben leinfelder

use at least one thread on single-processor machines.
https://redmine.dataone.org/issues/2800

7181 05/22/2012 04:47 PM ben leinfelder

script for re-applying missing FK constraints on KNB production DB.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5608

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.

7175 05/18/2012 12:09 PM ben leinfelder

instead of generating SM and ORE maps during dataone configuration/MN registration, moved this all to the replication admin screen where we can target generation for specific nodes. That way it's more controlled as to when and where we generate DataONE required content....

7174 05/18/2012 12:00 PM ben leinfelder

include all EML versions (had been only eml 2.1 for testing)

7172 05/17/2012 05:43 PM Jing Tao

Append more information such as user name and group to the validating session response.

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

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

7170 05/14/2012 02:36 PM ben leinfelder

add "Generate System Metadata" button to the replication server list display. When clicked, we generate SM for records belonging to that source server. This is only enabled when DataONE has been configured.
https://redmine.dataone.org/issues/2762

7169 05/09/2012 03:45 PM ben leinfelder

expose serverLocation parameter to run GenerateSystemMetadata for different replication parters as needed.
https://redmine.dataone.org/issues/2740

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

7155 05/01/2012 10:26 AM ben leinfelder

handle CN.archive() rest call: PUT /archive/{pid}
https://redmine.dataone.org/issues/2678

7154 05/01/2012 10:25 AM ben leinfelder

correct log about 'archive' being called

7153 05/01/2012 10:15 AM ben leinfelder

handle 'archive' rest calls
https://redmine.dataone.org/issues/2678

7151 05/01/2012 09:18 AM ben leinfelder

[optionally] do not archive the xml_documents and xml_nodes to *_revisions when 'deleting' a document. This will effectively guarantee that the document/data cannot be retrieved after delete.
NOTE: D1 system metadata will persist (for now) so that the ID cannot be reused with the DataONE API but Metacat calls may allow the ID to be reused -- may need to reconsider this behavior....

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.

7143 04/24/2012 10:42 AM ben leinfelder

use a shared ExecutorService for replicate() calls.
https://redmine.dataone.org/issues/2623

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)

7137 04/17/2012 03:15 PM ben leinfelder

no not record EML access rules that use the "denyFirst" permOrder.
https://redmine.dataone.org/issues/2614

7136 04/17/2012 09:20 AM ben leinfelder

needed to initialize the nodeList that stores matching nodes (by subject) -- this was the source of a NPE when we had a matching node subject.

7135 04/16/2012 05:38 PM ben leinfelder

do not create docid-guid mapping unless we are supposed to write access rules for the data to the dbase
https://redmine.dataone.org/issues/2572

7134 04/13/2012 04:40 PM Chris Jones

As Ben suggested, don't compare to the node list if there are no replicas listed. This reduces the number of calls to listNodes() on the CN.

7133 04/13/2012 04:32 PM Chris Jones

Minor logging change in throwing ServiceFailure when Hazelcast throws a RuntimeException.

7132 04/13/2012 04:07 PM Chris Jones

Modify getSystemMetadata() to allow nodes that are listed as replicas to access the system metadata. Use the Session.Subject to find a list of nodes from the CN that match the subject, and compare those node ids to the listed replica node ids. Add listNodesBySubject() helper method to do so.

7129 04/10/2012 10:42 AM ben leinfelder

save backup properties before attempting node registration/update so that we don't "forget" the user input

7128 04/09/2012 03:18 PM ben leinfelder

add a parameter for optionally writing EML-embedded access control rules to the Metacat DB.
https://redmine.dataone.org/issues/2584
https://redmine.dataone.org/issues/2583

7127 04/06/2012 04:22 PM ben leinfelder

added comments and logging about https://redmine.dataone.org/issues/2572

7126 04/06/2012 03:01 PM ben leinfelder

generalize the exception handling because our actions are the same no matter what the specific error is during create - we just notify the CN that the replicate call failed

7125 04/06/2012 02:58 PM ben leinfelder

catch general Exception that may be thrown during MN.replicate() when creating the object locally. There are a few records that keep slipping off our radar with no explanation as to why they remain in "REQUESTED" status.

7124 04/06/2012 01:53 PM ben leinfelder

do not download data at this point

7123 04/06/2012 01:53 PM ben leinfelder

catch errors for each localid we are processing so that they do do prevent other ids from having ORE content generated

7122 04/06/2012 01:52 PM ben leinfelder

additional debug logging for tracking down MN replication errors

7121 04/06/2012 01:35 PM ben leinfelder

only 2.1.0 EML docs for ORE generation right now...

7120 04/05/2012 04:28 PM ben leinfelder

band-aid for CN-CN replication permOrder issue when access control is embedded in EML and the system metadata is replicated before the EML. we just log the inconsistency and allow the insert to succeed
https://redmine.dataone.org/issues/2583

7117 04/04/2012 04:55 PM ben leinfelder

add comment about returning early when no system metadata can be found.
removed extraneous check on the content type of the SM -- was unused.
formatted indenting

7116 04/04/2012 04:49 PM ben leinfelder

for SystemMetadata events we first check the event for the SM value. If it returns null, we look it up from the shared map. It seems as if we don't always get a value with our events.

7115 04/04/2012 03:35 PM ben leinfelder

comment out: synchronize local system metadata on cn restart

7114 04/03/2012 01:31 PM ben leinfelder

synchronize local system metadata on cn restart

7113 04/03/2012 11:58 AM ben leinfelder

additional logging in MN.replicate()

7112 04/03/2012 11:32 AM ben leinfelder

double check "ecogrid" data urls for valid docid.rev - namely integer rev numbers - when parsing EML and also generating system metadata when necessary. Log the errors as warnings.

7111 04/02/2012 04:11 PM ben leinfelder

log calls to store() system metadata to the backing store

7109 04/02/2012 11:50 AM ben leinfelder

register stmml-1.1 schema (distributed as part of EML 2.1.0) in an effort to avoid unnecessary network traffic or the failed retrieval of the stale XSD sitting on unofficial servers

7108 03/30/2012 05:24 PM ben leinfelder

Add the listener for LifecycleEvent state changes

7107 03/30/2012 05:23 PM ben leinfelder

synchronizeLocalStore() when the cluster has a LifecycleEvent state change to RESUMED.

7106 03/29/2012 02:48 PM ben leinfelder

refactor memberAdded code to separate method - synchronizeLocalStore for possible reuse

7105 03/29/2012 11:19 AM ben leinfelder

handle last group of ids (oops)

7104 03/29/2012 10:33 AM ben leinfelder

use range of the list for test system metadata

7103 03/29/2012 08:48 AM ben leinfelder

use non-random list for generating system metadata in test mode

7102 03/28/2012 03:19 PM ben leinfelder

include debug statements for systemMetadataReplicationStatus and systemMetadataReplicationPolicy SQL

7101 03/28/2012 11:08 AM ben leinfelder

change ordering of getLogRecords() parameter -- pidFilter is in the middle now

7100 03/28/2012 10:21 AM ben leinfelder

use 'formatId' for listObjects() parameter
https://redmine.dataone.org/issues/2550

7099 03/27/2012 04:35 PM ben leinfelder

upgrade to latest RC in libclient and common jars -- includes updated getLogRecords and new mn.generateIdentifier method

7098 03/27/2012 02:25 PM ben leinfelder

-use MembershipListener to keep new members' backing store for system metadata synchronized with the shared system metadata map.
-remove the unused InstanceListener interface

7097 03/27/2012 09:22 AM Chris Jones

Modify deleteReplica() to use parameters parsed from the mime multipart entity rather than the request params. Need to check that the unit test uses MMP params. This partially addresses https://redmine.dataone.org/issues/2526.

7096 03/27/2012 09:11 AM Chris Jones

Modify CN.setObsoletedBy() to use parameters parsed from the mime multipart entity rather than the request params. Need to check that the unit test uses MMP params. This partially addresses https://redmine.dataone.org/issues/2526.

7095 03/27/2012 08:53 AM Chris Jones

Modify reserveIdentifier() to use parameters parsed from the mime multipart entity rather than the request params. Need to check that the unit test uses MMP params. This partially addresses https://redmine.dataone.org/issues/2526.

7094 03/27/2012 08:29 AM Chris Jones

Don't throw a JibXException, but rather convert it to a ServiceFailure.

7093 03/27/2012 08:27 AM Chris Jones

Modify owner() to set the rights holder from parameters parsed from the mime multipart entity rather than the request params. Need to check that the unit test uses MMp params. This partially addresses https://redmine.dataone.org/issues/2526.

7092 03/27/2012 07:42 AM Chris Jones

Add a collectMultipartParams() convenience method to D1ResourceHandler to parse multipart parameters from the entity when the entity contains no file parts.

7091 03/26/2012 04:25 PM ben leinfelder

add logging statements when there is a problem calling setReplicationStatus

7090 03/26/2012 03:11 PM Chris Jones

Get the serialVersion param from the MMP params map rather than the request object params map in setAccess().

7089 03/26/2012 02:10 PM Chris Jones

Add a few more debugging statements to HazelcastService for troubleshooting hazelcast map concurrency.

7088 03/23/2012 05:22 PM ben leinfelder

handle case where EML access rule "permission" is not in our constrained list (EML 2.0.0 doc showed this with a "none" permission for public principal). we now omit this invalid access rule when interpreting it in system metadata -- effectively dropping that invalid access rule. "none" had been stored as a 0 in the DB xml_access table and would not have given or denied access for the document so I think it can safely be omitted for good. for example, see knb-lter-gce.101.2 with this rule:...

7087 03/22/2012 09:31 PM Chris Jones

Use Jjava.util.Calendar rather than com.ibm ...

7086 03/22/2012 03:14 PM Chris Jones

Also allow MNs to set the FAILED status in setReplicationStatus(). this was an oversight on my part, trying to keep MNs that truly did succeed from overriding the COMPLETED status with FAILED.

7085 03/22/2012 12:13 PM ben leinfelder

use Java-based temp file creation instead of Date (ms) timestamp to ensure uniqueness of the file and avoid re-use by two concurrent threads.

7084 03/21/2012 11:26 AM ben leinfelder

use current datetime (at system metadata generation) as the date last modified

7083 03/19/2012 06:14 PM Chris Jones

Don't check for populated obsoletes and obsoletedBy fields during CN.create(), only MN.create(). The CN should expect that the MN has populated this field because of existing revision information, and should trust the MN information. Addresses https://redmine.dataone.org/issues/2507.

7082 03/19/2012 06:08 PM Chris Jones

Some minor logging changes.

7081 03/19/2012 12:40 PM ben leinfelder

use scope prefix (knb-lter-%) for random test doc population

7079 03/19/2012 10:12 AM ben leinfelder

use isAdminAuthorized() to check access to CN.create(). Note this method takes a pid and permission parameter and neither is used. Also removed the NotFound exception because it would never come up.

7078 03/19/2012 10:01 AM ben leinfelder

check that caller is CN/admin for CN.delete()
https://redmine.dataone.org/issues/2506

7077 03/19/2012 09:52 AM ben leinfelder

include CN.delete()
https://redmine.dataone.org/issues/2506

7076 03/16/2012 04:07 PM Chris Jones

Notify each replica MN when critical portions of system metadata change so the MN can pull the latest copy into its store. AccessPolicy and RightsHolder changes are the most critical for the MN to keep updated on.

7075 03/16/2012 11:40 AM Chris Jones

Only allow CNs to call MN.synchronizationFailed() by calling isAdminAuthorized(). The pid must also be valid.

7074 03/15/2012 07:50 PM Chris Jones

Modify CNodeService.setReplicationStatus() slightly to restrict MN-based calls to only set the status to COMPLETED. The CNs should be setting failures or invalidations, or the status can remain at QUEUED or REQUESTED, and the MNAuditTask can revisit those replicas as needed.

7073 03/15/2012 07:14 PM Chris Jones

Add a notifyReplicaNodes() method that calls MNStorage.systemMetadataChanged() on MN replica nodes for a given object identifier. This will be called when there are changes to AccessPolicy and rights holder since these are critical access metadata for an MN, but they can only be changed on the CN.

7072 03/15/2012 12:10 PM Chris Jones

Add some debugging statements in isAuthorized().

7071 03/15/2012 12:08 PM Chris Jones

In setReplicationStatus(), first check for a replica target MN subject match with the session subject. If this fails, look to see if CN admin access is allowed. Otherwise throw NotAuthorized. Addresses https://redmine.dataone.org/issues/2494

7070 03/15/2012 11:46 AM ben leinfelder

do not allow "Metacat-conforming" identifiers to be used. "test.1.001" is interpreted as "test.1.1" which renders "test.1.002" unusable unless a traditional Metacat "update" is used for that id/revision which contradicts the DataONE use of Identifiers that have no lexical requirements for revisions.

7069 03/15/2012 08:08 AM ben leinfelder

check for session when checking administrative authorization

7068 03/14/2012 12:02 PM Chris Jones

Remove individual calls to isAdminAuthorized() in favor of the centralized isAuthorized() call that handles it now.