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metacat @ 7300

  • svn:ignore: build
  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121
# Date Author Comment
7300 07/10/2012 04:26 PM ben leinfelder

prep for 2.0.2 release by updating the version numbers.

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.

7298 07/10/2012 12:29 PM ben leinfelder

updated foresite (snapshot) to include dateTime serialization fix.
https://redmine.dataone.org/issues/3035

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.

7296 07/09/2012 04:58 PM ben leinfelder

update creator and publisher using LDAP dump. unfortunately LDAP has shifted over the years and not all identities are still active in LDAP...but we did get quite a few creator names updated!
https://redmine.dataone.org/issues/2815

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.

7294 07/09/2012 10:46 AM ben leinfelder

include parameter for deleting system metadata records (or not). Intending to also use this for https://redmine.dataone.org/issues/3055

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

7292 07/07/2012 12:02 PM ben leinfelder

function/procedure for removing all content related to a PID from the DB.
https://redmine.dataone.org/issues/3037

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...

7290 07/05/2012 04:13 PM ben leinfelder

save point - adding more columns for access, data packaging, revision history
https://redmine.dataone.org/issues/2815

7289 07/03/2012 03:53 PM ben leinfelder

script to find and update missing SystemMetadata revision history. https://redmine.dataone.org/issues/2938

7288 07/03/2012 03:45 PM ben leinfelder

update the table to indicate which DOI account we are targeting
https://redmine.dataone.org/issues/2815

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.

7284 06/22/2012 08:55 AM ben leinfelder

use production cn url for the resolve url

7283 06/20/2012 01:46 PM ben leinfelder

remove the non-doi identifiers before updating the LTER - should save time on the update.
https://redmine.dataone.org/issues/2858

7281 06/18/2012 11:57 PM ben leinfelder

use eml stylesheet tag (1.0.3)

7280 06/18/2012 11:57 PM ben leinfelder

use 1.0.2 d1_libclient jar (built by hudson)

7278 06/18/2012 03:43 PM ben leinfelder

set archived flag (true) when we set the obsoletedBy value in the ORE system metadata

7276 06/18/2012 02:27 PM ben leinfelder

update for 2.0.1 upgrade -- scripts, docs, readme

7275 06/18/2012 02:24 PM ben leinfelder

remove saxon jar (XSLT 2.0 support) with plans to re-add when we understand how to make it more lenient WRT to invalid character content in source XML

7274 06/18/2012 12:43 PM ben leinfelder

move to 1.0.2 d1_libclient jar for ORE generation change (URI for aggregation)

7273 06/18/2012 12:13 PM ben leinfelder

use the localId for obsoletes/obsoletedBy ORE system metadata (https://redmine.dataone.org/issues/2964)

7272 06/18/2012 12:12 PM ben leinfelder

use correct esa email list

7271 06/11/2012 08:41 PM ben leinfelder

include xml-apis*.jar when building the LSID authority.war -- without this file the authority webapp has a fatal error (no class def found) on init.

7270 06/07/2012 05:16 PM ben leinfelder

correct block formatting for tomcat config changes

7269 06/07/2012 05:01 PM ben leinfelder

add tomcat config options for DataONE identifiers with slashes

7267 06/07/2012 12:55 PM Jing Tao

excluded the HzObjectPathMapTest$1 and HzObjectPathMapTest$2 classes which are not test classes in the test taraget.

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

Print the stack trace when the MMP cannot be resolved.

7264 06/07/2012 10:45 AM Jing Tao

Use a final static string to replace the hard code.
Search document title rather than id in testReplicateEML_AtoB method.

7263 06/07/2012 09:19 AM ben leinfelder

use 1.0.2 tag for EML stylesheets

7262 06/07/2012 09:04 AM ben leinfelder

update MN registration screen shot and amend instructions that say a nodeId will be assigned during registration.
add section about generating SM for a new Member Node that has existing Metacat data.

7261 06/07/2012 08:23 AM ben leinfelder

use CN session when testing getLogRecords() and getOperationStatistics() becuase they are now protecting "sensitive" information

7259 06/07/2012 12:43 AM ben leinfelder

use RC for EML stylesheets before going to yet another minor revision number.

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

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

7257 06/06/2012 09:57 PM ben leinfelder

add 'fulldist' target to combine building of src and bin distributions

7256 06/06/2012 09:56 PM ben leinfelder

include gastil's changes re: pathquery and 'delete'
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

7254 06/06/2012 07:39 PM ben leinfelder

Add details for configuring Apache to use client certificate authentication.

7253 06/06/2012 03:33 PM ben leinfelder

use production CN url as the default (instead of cn-dev)

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
7250 06/06/2012 01:13 PM ben leinfelder

remove distribution tar.gz and zip files on fullclean.

7249 06/06/2012 12:55 PM ben leinfelder

use iframe id for the login anchor since the anchor inside the iframe does not work.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5619

7248 06/06/2012 12:50 PM ben leinfelder

get utilities source from the correct checkout location

7247 06/06/2012 12:50 PM ben leinfelder

clarify release notes for 2.0.0 (minor)

7246 06/06/2012 11:01 AM ben leinfelder

correct Javadoc link http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

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.

7243 06/05/2012 09:42 PM ben leinfelder

apply Gastil's edits. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

7242 06/05/2012 09:20 PM ben leinfelder

add section about configuring the metacat.properties with the paths to the server certificate and key

7241 06/05/2012 07:02 PM ben leinfelder

remove unused replication properties (all certificate file based now)

7240 06/05/2012 04:46 PM ben leinfelder

use 1.0.1 DataONE jars

7239 06/05/2012 04:44 PM ben leinfelder

use KNB identifier table (post DOI generation) to update LTER identifier table.
https://redmine.dataone.org/issues/2857

7238 06/05/2012 03:34 PM Jing Tao

exclude the MockObjectPathMap class from the test target since it is not a junit test.

7237 06/05/2012 03:22 PM Jing Tao

exclude QueryRunner in test target. This is not a junit test file.

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

7233 06/04/2012 08:15 PM ben leinfelder

use updated tag for EML stylesheet-only changes
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5597

7232 06/04/2012 08:04 PM ben leinfelder

use updated tag for EML stylesheet-only changes
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5597

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.

7229 06/01/2012 12:47 PM ben leinfelder

do not include releaseCandidate property - does not seem to be used except for debian? packaging which was never fully implemented.

7228 06/01/2012 12:39 PM ben leinfelder

use non-snapshot D1 jars in prep for tagging/release. Still RCs

7227 06/01/2012 10:45 AM ben leinfelder

script to aid in converting denyFirst rules to allowFirst
https://redmine.dataone.org/issues/2613

7226 06/01/2012 10:40 AM ben leinfelder

use kepler account as default

7225 06/01/2012 10:39 AM ben leinfelder

use current default tomcat6 deploy directory

7224 06/01/2012 09:35 AM ben leinfelder

include test shoulder defaults for KNB, PISCO and LTER

7223 05/31/2012 09:25 PM Matt Jones

Fixed formatting problem in a documentation file.

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.

7220 05/31/2012 02:11 PM ben leinfelder

add section about importing self-signed certificates into the Java keystore (now that we use strict verification on the java client side when calling replication endpoints).

7219 05/31/2012 02:01 PM ben leinfelder

a few additional notes about Metacat replication configuration.

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.

7200 05/29/2012 04:19 PM ben leinfelder

use 'allowFirst' for access rules. We have deprecated 'denyFirst' and deny rules in Metacat as of 2.0.0

7199 05/29/2012 03:02 PM ben leinfelder

handle https-only server configuration -- must pull resources from https not http for the skins etc.

7198 05/29/2012 02:53 PM ben leinfelder

handle https-only server configuration -- must pull resources from https not http for the skins etc.

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.

7194 05/28/2012 01:25 PM ben leinfelder

include eml2.0.0beta4 DTD during Metacat build so that we can continue to accept (and validate) beta4 documents.
This arose when testing Metacat as DataONE Coordinating Node where legacy documents are being housed in the CN.

7193 05/27/2012 09:03 AM ben leinfelder

encode '/' and ':' in the DOI used for the resolve URL

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.