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metacat @ 7489

  • svn:ignore: build
  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121
# Date Author Comment
7489 01/31/2013 04:02 PM ben leinfelder

generate ID from UUID. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5840

7486 01/18/2013 02:12 PM ben leinfelder

make sure serial version is included or set on MN.update().
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5793

7481 01/07/2013 04:39 PM ben leinfelder

remove duplicate cgi-bin part in path to create account

7480 01/07/2013 04:23 PM Brendan Hahn

Quick fix for bad handling of non-default data/backup directories.

7479 12/20/2012 03:54 PM Chris Jones

Also add the 2.4.1 hazelcast jars to the trunk.

7477 12/18/2012 05:33 PM ben leinfelder

remove indexing task from the queue when we are updating the document

7476 12/12/2012 02:38 PM ben leinfelder

move DocInfo parsing into utilities project so that it can be used by Morpho as well as Metacat.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5737

7475 12/12/2012 02:38 PM ben leinfelder

move DocInfo parsing into utilities project so that it can be used by Morpho as well as Metacat.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5737

7474 12/12/2012 02:32 PM ben leinfelder

use utilities tag to build (remember to 'fullclean' after this update!)

7471 12/10/2012 09:07 AM ben leinfelder

use default count = 1000 for CN.listObjects rather than -1 (because now -1 will cause an SQL error)

7469 12/08/2012 06:41 PM ben leinfelder

default replicaStatus to true for the CN.listObject call

7467 12/07/2012 10:39 AM ben leinfelder

make sure to call lock() on the SM when updating rightsholder (like every other method that gets a lock object from HZ).

7466 12/07/2012 10:35 AM ben leinfelder

return from test when we encounter the NotImplemented exception for CN.search()

7465 12/07/2012 10:30 AM ben leinfelder

include identifier.guid in the test SQL clause.

7464 12/07/2012 10:25 AM ben leinfelder

CN.search() id not implemented by metacat -- making that explicit and also testing for it.

7462 12/05/2012 11:04 AM ben leinfelder

default replicaStatus (aka "show replicas in results") to true rather than false

7461 12/05/2012 10:29 AM ben leinfelder

add debug statements for listObject slice debugging

7459 12/04/2012 07:23 PM Chris Jones

Add the non-snapshot jars for the D1 libraries.

7458 12/04/2012 02:32 PM ben leinfelder

use utilities and eml RC tags for building Metacat.

7457 12/04/2012 02:18 PM ben leinfelder

include dataone.contactSubject in backup properties so it will be "remembered" during upgrades.

7456 12/04/2012 02:13 PM ben leinfelder

update release date to December

7455 12/04/2012 01:57 PM ben leinfelder

additional db indexes for pathquery performance
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

7454 12/03/2012 02:25 PM Brendan Hahn

Do not set headers until response is ready to send (5756)

7453 12/03/2012 12:43 PM ben leinfelder

use jar generated from the git repo source (just in case it was different from svn). http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

7452 12/03/2012 12:30 PM ben leinfelder

use dual query for query slicing - one for count, another for the actual records when requested.
https://redmine.dataone.org/issues/3065

7451 12/03/2012 11:32 AM ben leinfelder

get total (or subtotal when non-slicing params are present) count as a separate query from the field selection query.

7450 12/03/2012 10:16 AM ben leinfelder

include Skye's suggestions about correctly limiting by D1 Event types

7449 12/02/2012 11:53 AM ben leinfelder

use test doi shoulder as the default for local server, at least during testing phase. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

7448 12/02/2012 08:58 AM ben leinfelder

first pass at DOI minting using the EZID service in mn.generateIdentifier()
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5755

7447 11/30/2012 05:19 PM Chris Jones

Fix a minor bug in listObjects() where total was set incorrectly when total was set incorrectly when count=0. The definition of total in the D1 architecture docs says 'The total number of entries in the source list from which the slice was extracted.' With count=0, we assume the total is the total count from the entire object store. Needs testing.

7446 11/30/2012 03:23 PM ben leinfelder

remove empty package

7445 11/30/2012 02:53 PM ben leinfelder

rollback the delete() when there is an error performing part of it -- don't want to end up with partial delete.

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)