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metacat / src @ 7444

# Date Author Comment
7444 11/30/2012 02:27 PM ben leinfelder

use Identifier object not String when retrieving SM from the HZ map to set archived during delete()

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"

7440 11/29/2012 04:54 PM ben leinfelder

add link for reference on how to do record limits in oracle

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

7438 11/29/2012 04:33 PM ben leinfelder

use RDBMS-specific features to limit the resultset for paging the object list -- postgres and oracle have implementations. we don''t really support mssql so I skipped that one.

7437 11/29/2012 04:12 PM ben leinfelder

use RDBMS-specific features to limit the resultset for paging -- postgres and oracle have implementations. we don''t really support mssql so I skipped that one.

7434 11/26/2012 02:28 PM ben leinfelder

include debug msg about removing docid from index queue. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

7433 11/26/2012 02:25 PM ben leinfelder

remove document from the indexing queue when delete is called. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

7432 11/26/2012 01:50 PM ben leinfelder

clean up index queue code before tackling index/delete race condition. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5750

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

7429 11/23/2012 10:00 AM ben leinfelder

mark documents as archived=true when they are deleted using the Metacat API.
https://redmine.dataone.org/issues/3406

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)

7416 11/05/2012 09:15 AM ben leinfelder

update pub_date when the length of that field is != 4 (use date_created in this scenario). There were 2 entries that had "193" as the pub_date.

7415 11/01/2012 09:03 AM ben leinfelder

replace new lines in creator with spaces. set blank " " titles and creators to "unknown". use "Baltimore Ecosystem Study LTER" for publisher on all BES objects.

7414 10/26/2012 06:50 PM ben leinfelder

include John Kunze's latest suggestions for improved metadata -- a lot of clean-up, especially on characters in the file. Note UTF-8 encoding of the script.

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

7393 09/24/2012 01:12 PM ben leinfelder

use version 2.0.5

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

7388 09/21/2012 01:30 PM ben leinfelder

use alternative syntax for xml_access table update since oracle does not use joins in a update statement that same way as postgres. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

7387 09/21/2012 01:18 PM ben leinfelder

correct Oracle syntax
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

7386 09/21/2012 01:14 PM ben leinfelder

use correct column (guid) for temporary index

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 "&

7372 09/05/2012 02:13 PM ben leinfelder

include missing identifier mappings during 2.0.4 upgrade (mappings may be missing due to previous replication between servers that do not house SystemMetadata)

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.

7369 09/03/2012 09:05 PM ben leinfelder

prep for 2.0.4 release

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.

7365 08/23/2012 10:41 PM ben leinfelder

use resourceMapLocation (resolve url for the ore map) as the datacite_relatedIdentifier_isPartOf property

7364 08/23/2012 10:38 PM ben leinfelder

use lowercase 'metadata' and 'data' for the resourceType

7363 08/23/2012 10:36 PM ben leinfelder

set publisher to the source system when publisher == creator (we want them to be different, even if just for appearances)

7362 08/23/2012 10:25 PM ben leinfelder

only include public (readable) DOIs in the final output

7361 08/23/2012 10:24 PM ben leinfelder

use "lastname, firstname" convention throughout

7360 08/23/2012 10:18 PM ben leinfelder

include more descriptive data file name for title of data records

7359 08/23/2012 10:04 PM ben leinfelder

include publisher given name correctly

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.

7357 08/23/2012 03:03 PM ben leinfelder

include certificate export SSL options as an example (used heavily for DataONE and Metacat Replication)

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

7353 08/08/2012 03:39 PM ben leinfelder

correct the update statement for setting archived flag on SM where document revision does not exist in the xml_documents table

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"

7347 08/06/2012 10:40 AM ben leinfelder

prep for 2.0.3 release

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.

7336 07/31/2012 07:12 AM ben leinfelder

use correct EZID account names for the three different nodes.
https://redmine.dataone.org/issues/2815

7335 07/30/2012 10:12 PM ben leinfelder

align the final column headers with the datacite schema, as applicable.
https://redmine.dataone.org/issues/2815

7334 07/30/2012 06:34 PM ben leinfelder

add block for finding and updating records that should be marked as archived.
https://redmine.dataone.org/issues/3109

7333 07/30/2012 01:46 PM ben leinfelder

use DataCite isNewVersionOf/isPreviousVersionOf for revision history

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.

7328 07/23/2012 05:13 PM ben leinfelder

not every EML file has an ORE datapackage descriptor -- join only to those when setting the resourceMapId

7327 07/23/2012 04:29 PM ben leinfelder

correctly use document revision for object format and resource map joins.

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.

7324 07/20/2012 02:28 PM ben leinfelder

use correct children of 'publisher' element

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

7321 07/18/2012 10:11 AM ben leinfelder

include the resourceMapId for the metadata objects, not just the data files.

7320 07/18/2012 08:56 AM ben leinfelder

updated LDAP dump and corrected missing entries that had been removed from LDAP.

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

7306 07/11/2012 05:05 PM ben leinfelder

handle null givenNames from the LDAP dump.