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metacat / src / edu / ucsb @ 7370

# Date Author Comment
7370 09/04/2012 03:43 PM ben leinfelder

use SchemaLocationResolver to fetch remote entries for the xml_catalog -- we want to be able to fetch included xsd files as well as use any error handling it provides for checking the schemas.

7368 09/03/2012 01:50 PM ben leinfelder

when performing query, make sure we are using the access rules of the latest revision of a given docid, otherwise we may include documents that used to be public but have been made private in subsequent revisions.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

7367 08/31/2012 03:05 PM ben leinfelder

correct the number of prepared statement parameters when inserting to xml_revisions table.
Errors like the following were showing in the replication log file:
knb 20120831-19:42:38: [ERROR]: DocumentImpl.writeReplication - Failed to create access rule for package: john.15950.1 because The column index is out of range: 12, number of columns: 11. [ReplicationLogging]

7366 08/24/2012 08:24 AM ben leinfelder

include WHERE in the sql where clause - encountered by SAEON's node admin, Alex Niehaus.

7358 08/23/2012 09:45 PM ben leinfelder

create docid-guid mapping during replication if it does not exist. we were [incorrectly] assuming that there would be SM coming with the document info that would fill this information in, but for traditional non-MN Metacat deployments there is no SM to provide a mapping. In this case we use the docid as the guid.

7356 08/17/2012 12:42 PM ben leinfelder

stream the replication "update" response rather than building up a complete list in a stringbuffer. prompted by findings on t he CN: https://redmine.dataone.org/issues/3141

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

7350 08/06/2012 10:47 PM ben leinfelder

when updating a document on a remote server, we still need to use the previous docid to check that the user has permissions to do so (rather than the new id that is obsoleting the old id). This was discovered by M Servilla at LTER.

7348 08/06/2012 11:08 AM ben leinfelder

remove unused "dataonelogger"

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.

7338 08/01/2012 07:00 PM ben leinfelder

remove possibility for infinite loop in case data replication is not configured for the server and a data file is encountered (yikes!)

7337 08/01/2012 05:33 PM ben leinfelder

added logging debug statements to see where the replication timeout might be occurring.

7331 07/26/2012 04:26 PM ben leinfelder

check for null archived flag in ORE SM
https://redmine.dataone.org/issues/3046

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

7317 07/17/2012 12:06 PM ben leinfelder

only look up the client timeout property once, not every time we make a call
https://redmine.dataone.org/issues/3078

7316 07/17/2012 11:46 AM ben leinfelder

improve content type handling during the get() calls
https://redmine.dataone.org/issues/3070

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

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

7313 07/17/2012 10:19 AM ben leinfelder

configurable replication client timeout
https://redmine.dataone.org/issues/3078

7310 07/13/2012 07:57 AM ben leinfelder

order the listObjects() results by identifier to mitigate random paged results
https://redmine.dataone.org/issues/3065

7309 07/12/2012 04:04 PM ben leinfelder

correct the parameter/value setting in the prepared statements for retrieving log information.

7307 07/12/2012 12:21 PM ben leinfelder

use docid, not the guid when returning the accesscontrol block

7299 07/10/2012 02:12 PM ben leinfelder

include dataone.ore.downloaddata as a configurable property in case MNs (like LTER) want to have the process download externally-stored data files described in an EML data package.

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.

7293 07/08/2012 10:05 AM ben leinfelder

look up docid using mapped guid when checking permission on described data file
Addresses: http://support.nceas.ucsb.edu/rt/Ticket/Display.html?id=7490

7291 07/06/2012 05:29 PM ben leinfelder

use docid (not guid) when instantiating the PermissionController. Was getting an error with DOI-ified identifier and the metacat getaccesscontrol action:
https://knb.ecoinformatics.org/knb/metacat?action=getaccesscontrol&docid=Collinge.3.28
<error>
AccessControlForSingleFile.getACL() - MCDB error when getting ACL: No guid registered for docid doi:10.5063/AA/Collinge.3.28...

7287 07/02/2012 04:50 PM ben leinfelder

make sure we have non-null values where jibx serialization expects them for LogEntry

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)

7266 06/07/2012 12:03 PM Chris Jones

Print the stack trace when the MMP cannot be resolved.

7258 06/07/2012 12:25 AM ben leinfelder

report errors during XML->HTML transform
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5618

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()

7196 05/29/2012 09:33 AM ben leinfelder

stack trace the HZ put exception during CN-CN replication

7195 05/29/2012 07:37 AM ben leinfelder

additional debugging statements for CONCURRENT_MAP_PUT error during CN-CN replication.

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

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

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

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