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metacat / src / edu @ 7428

# Date Author Comment
7428 11/21/2012 04:35 PM ben leinfelder

look up the archived value when retrieving SystemMetadata record.
https://redmine.dataone.org/issues/3405

7427 11/19/2012 04:03 PM ben leinfelder

surround returned query in CDATA to prevent parsing of xml within xml

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)

7412 10/26/2012 09:11 AM ben leinfelder

use ObjectFormatInfo libclient utility to look up mimeType and filename extension during get() calls. Configurable mapping file is deployed by default to /var/metacat/dataone where it can then be augmented as needed. This location is controlled in the metacat.properties file (which is injected into the DataONE Settings values during weapp intitialization)....

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

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

7410 10/22/2012 01:38 PM ben leinfelder

handle /object?count=0 queries using simpler (quicker) sql
https://redmine.dataone.org/issues/3065

7409 10/19/2012 10:20 AM ben leinfelder

allow getlog action to use docid parameters that do not include revision. In these cases, the latest revision will be used.

7408 10/19/2012 10:05 AM ben leinfelder

handle case where we do not have a pathexpr to check
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

7407 10/18/2012 03:14 PM ben leinfelder

simplify the xml_access query, and instead use guid to check for permission. Now the docid/rev join (to get most recent version for search results) happens "higher up" in the query.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

7404 10/18/2012 11:10 AM ben leinfelder

pass parameters to the getLog action for rendering in xslt

7403 10/16/2012 01:50 PM ben leinfelder

remove morpho.jar -- moved needed classes into shared utilities project. (currently building form utilities trunk -- be sure to 'ant fullclean' to get the latest utilities.jar built)

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

7399 10/12/2012 08:27 AM Chris Jones

Change the set and get methods for the replication verified date to use java.sql.Timestamp rather than java.util.Date via setTimestamp(), not setDate(). The hh:mm:ss.sss was previously getting truncated.

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

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

7397 09/28/2012 09:06 AM ben leinfelder

remove the max(rev) clause in favor of a more straight-forward join to xml_documents (that will have the max rev). http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

7395 09/25/2012 09:49 AM ben leinfelder

include inverted sendParameters() method that uses the keys as values, and the values as keys so that multiple docid parameters can be specified for the zip download. This was a regression when moving to standard httpclient rather than the roll-your-own version we had been using. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5718

7392 09/24/2012 01:09 PM ben leinfelder

shorten the systemmetadata* table names for Oracle's 30 character limit. move version to 2.0.5. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

7382 09/14/2012 02:01 PM ben leinfelder

use correct docid format when checking for existing mappings.

7379 09/12/2012 02:22 PM ben leinfelder

use CDATA for docname field in docInfo so that XML parser ignores the content that can contain characters like "&

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.