do not allow updates to orphan another branch of revision history. https://redmine.dataone.org/issues/3338
include the subjects we are testing for authentication.https://redmine.dataone.org/issues/2778
make sure data objects correctly use force replicate with action "insert" https://redmine.dataone.org/issues/3138
allow SM resynch to be executed any time, not just during start up.https://redmine.dataone.org/issues/3116
change to debug log level when processing shared/local pids)
only lock the missing pid event if we know we have it locally to contribute.https://redmine.dataone.org/issues/3117
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.
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.
print the missing pid count, not the total shared pid count so we know how many will be processed.
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.
logging for processing identifier set on restart.
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.
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.
move the hzIdentifiers initialization into the resync thread so that it does not affect start up time. cleaned up unused methods and superfluous code.
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.
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
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.
check for invalid (!) pids. thanks, M. Reyes for catching thishttps://redmine.dataone.org/issues/3047
check for whitespace in identifiers during create() and update()https://redmine.dataone.org/issues/3047
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.
log error when looking up non-existent local SM rather than completely bombing out of the resynch thread.
use secure Metacat context URL for D1 registrationhttps://redmine.dataone.org/issues/3030
first pass: DataONE-specific log retrieval to avoid java-based post-processing.
set archived flag (true) when we set the obsoletedBy value in the ORE system metadata
use the localId for obsoletes/obsoletedBy ORE system metadata (https://redmine.dataone.org/issues/2964)
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).
Minor logging change.
Add debug logging to delete() to understand why we're getting InsufficientKarmaException.
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.
restrict getLogRecrods (both MN and CN) to be called only by admin users (the CN)https://redmine.dataone.org/issues/2855
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.
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
put(sm) for every pid we have a SM value for so that all members receive the entry event and can save locally.
Throw an exception when NOT allowed, not when allowed =).
ignore partition owner -- always attempt to look up form local store if we were unable to get the SM from the shared map.
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.
Also get the list size, which may throw an NPE.
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.
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....
trace level log for looping over EVERY pid in the system.
meant to log the guids (source) not the pids (target)
logging for each step of shared identifiers loading.
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.
due to hudson build issue, did not actually end up testing pause/resume -- trying that again
pause/resume was not enough. trying shutdown/restart
experiment with lifecycle pause/resume. hopefully it prevents our node from taking ownership of any keys before we are sure we have them all.
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.
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.
make only one DB call to look up local pids - no need to do a pstmt for every single shared pid.
on init (start up) launch a synchronization thread that ensures all shared identifier entries have a corresponding local System Metadata entry.
fix NPE (logMetacat object was not initialized) that was occurring during store()
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.
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.
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....
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
Add a few logging statemnts for round trip replication metrics.
add trace statements for measuring time to complete SM generation.
remove exception from method decl - was not matching the interface def and not compiling.
only generate system metadata for original objects.https://redmine.dataone.org/issues/2721
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.
add Session-less archive() method
only admin users can call MN/CN.delete(). This is limited to any CN and only the MN that is calling itself
update the sysmeta data modified when setting archived=truehttps://redmine.dataone.org/issues/882
optionally remove the document/data file from the filesystem completely when 'deleting' it.https://redmine.dataone.org/issues/2677
newer d1 jars that include shared AuthUtilsmethod for isAuthorized() consistencyhttps://redmine.dataone.org/issues/2661
implement MN and CN.archive() method -- really just the existing delete() methods.https://redmine.dataone.org/issues/2674https://redmine.dataone.org/issues/2675
call MN.delete() for each replica when CN.delete() is calledhttps://redmine.dataone.org/issues/2676
defer to AuthUtils for flattening out the equivIdent subject list.https://redmine.dataone.org/issues/2661
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
include Session-less interface methods and updated jars that define them.
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.
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)
just use the e.getMessage() as e.getCause() may be null (seeing NPE when testing via the MN IT tester)
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.
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.
Minor logging change in throwing ServiceFailure when Hazelcast throws a RuntimeException.
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.
add a parameter for optionally writing EML-embedded access control rules to the Metacat DB.https://redmine.dataone.org/issues/2584https://redmine.dataone.org/issues/2583
added comments and logging about https://redmine.dataone.org/issues/2572
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
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.
catch errors for each localid we are processing so that they do do prevent other ids from having ORE content generated
additional debug logging for tracking down MN replication errors
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
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.
comment out: synchronize local system metadata on cn restart
synchronize local system metadata on cn restart
additional logging in MN.replicate()
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.
log calls to store() system metadata to the backing store
Add the listener for LifecycleEvent state changes
synchronizeLocalStore() when the cluster has a LifecycleEvent state change to RESUMED.
refactor memberAdded code to separate method - synchronizeLocalStore for possible reuse
change ordering of getLogRecords() parameter -- pidFilter is in the middle now
upgrade to latest RC in libclient and common jars -- includes updated getLogRecords and new mn.generateIdentifier method
-use MembershipListener to keep new members' backing store for system metadata synchronized with the shared system metadata map.-remove the unused InstanceListener interface
add logging statements when there is a problem calling setReplicationStatus