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metacat @ 7444

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  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121
# 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.

7436 11/28/2012 01:53 PM Chris Jones

Add the latest SNAPSHOT build of the hazelcast jars built by robert at:

http://dev-testing.dataone.org/maven/com/hazelcast/hazelcast/2.4.1-SNAPSHOT/hazelcast-2.4.1-SNAPSHOT.jar
http://dev-testing.dataone.org/maven/com/hazelcast/hazelcast-client/2.4.1-SNAPSHOT/hazelcast-client-2.4.1-SNAPSHOT.jar...

7435 11/26/2012 02:54 PM Chris Jones

Update the hazelcast libraries based on the most recent build from the hazelcast trunk using patches that robert submitted via git pull requests.

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

7431 11/23/2012 10:14 AM ben leinfelder

additional release notes about archive/delete behavior and HZ upgrade

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

7426 11/13/2012 10:35 AM Chris Jones

Update the two hazelcast jars to 2.4.1-SNAPSHOT versions that Robert generated after fixing certain hazelcast build problems.

7425 11/12/2012 01:25 PM ben leinfelder

correct the metacat.properties help anchors.

7424 11/12/2012 11:57 AM ben leinfelder

use sleeker "?" icon for the admin help links

7423 11/12/2012 11:28 AM ben leinfelder

correct the "?" links in the admin pages to the docs pages that are deployed as part of metacat.

7422 11/10/2012 03:35 PM Chris Jones

In migrating to Hazelcast 2.4.x, replace deprecated methods.

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.

7413 10/26/2012 11:04 AM ben leinfelder

include note about pathquery performance fix (when using indexed fields)

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

7406 10/18/2012 11:18 AM ben leinfelder

include log stats for total 'read' events when rendering a package.

7405 10/18/2012 11:11 AM ben leinfelder

rework simple log stats so that there is no saxon requirement (xslt 2)

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)

7402 10/15/2012 04:41 PM ben leinfelder

remove use of HttpMessage (in morpho.jar) in favor of standard httpclient methods for calling the servlet in tests

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

7396 09/25/2012 09:51 AM ben leinfelder

add note about sanparks/saeon spatial file download: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5718

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

7394 09/24/2012 03:41 PM ben leinfelder

integrate ecoinformatics login with the CIlogon identity mapping flow so that a user is directed through the process with no manual navigation needed (at least in the url bar). https://redmine.dataone.org/issues/1480

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

7391 09/24/2012 10:07 AM ben leinfelder

ajax-ify the call to perform identity mapping (including errors)

7390 09/21/2012 02:02 PM ben leinfelder

look up CN url for portal servlet instead of hardcoding it.

7389 09/21/2012 01:46 PM ben leinfelder

look up CN url for portal servlet instead of hardcoding it.

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

7384 09/14/2012 02:43 PM ben leinfelder

use correct release date (September 2012)

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

use correct docid format when checking for existing mappings.

7380 09/12/2012 03:23 PM ben leinfelder

include sessionid when constructing the EML download link. pull from RELEASE_EML_UTILS_1_0_5 eml tag.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5709

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 "&

7377 09/12/2012 08:33 AM ben leinfelder

include sessionid when constructing the EML download link. pull from RELEASE_EML_UTILS_1_0_5_RC1 eml tag.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5709

7376 09/10/2012 11:42 AM ben leinfelder

use RELEASE_EML_UTILS_1_0_4 for EML stylesheets

7374 09/07/2012 09:21 AM ben leinfelder

use RELEASE_EML_UTILS_1_0_4_RC1 for EML stylesheets

7373 09/06/2012 10:24 PM ben leinfelder

include qformat parameter in docs for squery
remove mention of 'username' for getLastDocid -- should only use scope param

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

7352 08/07/2012 12:10 PM ben leinfelder

sleep before updating and deleting test documents - otherwise their index entries may not be fully written and this causes errors (update and delete first attempt to remove index references, but if they are not in the DB yet then they are not removed but then they do get added and the FK constraints make the delete fail). Since we know indexing occurs in a separate thread with a configured delay, we just use this same delay in our testing.

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