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# Date Author Comment
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.

7191 05/25/2012 04:23 PM ben leinfelder

include revisions table in the initial temp table population.
use the "first" creator listed in the EML (either org or person).
use other reasonable default values as needed to fully populate the spreadsheet columns
https://redmine.dataone.org/issues/2815

7190 05/25/2012 02:30 PM ben leinfelder

add columns: publisher and pub_date. include default values for all columns - even data files should have title.
still a few todos but closer.
https://redmine.dataone.org/issues/2815

7189 05/25/2012 12:07 PM ben leinfelder

script to generate DOI registration spreadsheet
https://redmine.dataone.org/issues/2815

7188 05/23/2012 04:41 PM ben leinfelder

share the same dbConnection when inserting and then updating SystemMetadata objects in the backing store.
any errors encountered during the update will rollback the entire transaction and the SM record will not exist, even in part.

7187 05/23/2012 03:28 PM ben leinfelder

Do not loadAllKeys() for SystemMetadataMap when Metacat first starts up. hzIdentifiers will be populated with a simple SQL statement rather than the serial loading of every single SystemMetadata object. It will remain in synch using the usual entryXXX() methods as before....

7186 05/23/2012 02:22 PM ben leinfelder

use LRU eviction policy and a small (1000) map size limit to avoid running out of memory because of a large number of system metadata objects

7185 05/23/2012 02:17 PM Chris Jones

Set the default maximum number of database connections back to 200. After discussion, we've decided it will be better to increase the PostgreSQL limit to 300 and keep Metacat's pool size pretty big.

7184 05/23/2012 09:57 AM ben leinfelder

include pidFilter handling - only matches the complete pid. Issues a warning in the Metacat logs when pidFilter cannot be applied but allows the call to getLogs() to return as though there was no pidFilter given.
https://redmine.dataone.org/issues/2798

7183 05/23/2012 09:33 AM ben leinfelder

use at least one thread on single-processor machines.
https://redmine.dataone.org/issues/2800

7182 05/22/2012 05:46 PM Chris Jones

Change the database.maximumConnections property to 100. PostgreSQL's docs says it can handle "a few hundred", and would need to be increased from the default 100 max_connections. For DataONE optimization, we increase max_connections, however there are more processes making connections other than metacat, so I'll reduce metacat's default share.

7181 05/22/2012 04:47 PM ben leinfelder

script for re-applying missing FK constraints on KNB production DB.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5608

7180 05/21/2012 03:04 PM ben leinfelder

include TRACE level debugging for specific classes we want to have performance metrics for.

7179 05/21/2012 02:31 PM Chris Jones

Add a few logging statemnts for round trip replication metrics.

7178 05/21/2012 02:12 PM ben leinfelder

add trace statements for measuring time to complete SM generation.

7177 05/21/2012 11:25 AM ben leinfelder

new D1 jars:
prevent NPEs from the object format cache when formatId.value is null. This came up during PISCO testing

7176 05/18/2012 03:05 PM ben leinfelder

default replication policy set to 0.

7175 05/18/2012 12:09 PM ben leinfelder

instead of generating SM and ORE maps during dataone configuration/MN registration, moved this all to the replication admin screen where we can target generation for specific nodes. That way it's more controlled as to when and where we generate DataONE required content....

7174 05/18/2012 12:00 PM ben leinfelder

include all EML versions (had been only eml 2.1 for testing)

7173 05/18/2012 11:59 AM ben leinfelder

new d1 jars for: remove exception from method decl - was not matching the interface def and not compiling.

7172 05/17/2012 05:43 PM Jing Tao

Append more information such as user name and group to the validating session response.

7171 05/17/2012 12:46 PM ben leinfelder

remove exception from method decl - was not matching the interface def and not compiling.

7170 05/14/2012 02:36 PM ben leinfelder

add "Generate System Metadata" button to the replication server list display. When clicked, we generate SM for records belonging to that source server. This is only enabled when DataONE has been configured.
https://redmine.dataone.org/issues/2762

7169 05/09/2012 03:45 PM ben leinfelder

expose serverLocation parameter to run GenerateSystemMetadata for different replication parters as needed.
https://redmine.dataone.org/issues/2740

7168 05/08/2012 04:30 PM ben leinfelder

only generate system metadata for original objects.
https://redmine.dataone.org/issues/2721

7167 05/04/2012 02:50 PM ben leinfelder

test for running concurrent Metacat queries to mimic Kepler data search.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5518

7166 05/02/2012 04:21 PM ben leinfelder

check if person's equivalentIdentity list is null before processing recursively
https://redmine.dataone.org/issues/2689

7165 05/02/2012 03:59 PM ben leinfelder

D1 common lib AuthUtils update

7164 05/02/2012 09:11 AM ben leinfelder

include testSynchronizationFailed() and call as the CN subject so that it is authorized.

7163 05/02/2012 09:06 AM ben leinfelder

use MN (self) as the Session.subject so that the MN.delete() call is successful.

7162 05/02/2012 08:58 AM ben leinfelder

handle authorization for delete() differently for CN vs MN.
On the CN, only the CN (or tbd admin user) can call it.
On the MN, both the CN (or admin user) and the same MN can call it.

7161 05/01/2012 02:55 PM ben leinfelder

comment out testDelete because it requires acting as the MN
comment out testSynchronizationFailed because it requires acting as the CN

7160 05/01/2012 02:49 PM ben leinfelder

uncomment the MN tests (I bet this was an oversight during local testing)

7159 05/01/2012 02:48 PM ben leinfelder

add Session-less archive() method

7158 05/01/2012 11:59 AM ben leinfelder

jars with CN/MN.archive() libclient implementations

7157 05/01/2012 11:14 AM ben leinfelder

only admin users can call MN/CN.delete(). This is limited to any CN and only the MN that is calling itself

7156 05/01/2012 10:47 AM ben leinfelder

update the sysmeta data modified when setting archived=true
https://redmine.dataone.org/issues/882

7155 05/01/2012 10:26 AM ben leinfelder

handle CN.archive() rest call: PUT /archive/{pid}
https://redmine.dataone.org/issues/2678

7154 05/01/2012 10:25 AM ben leinfelder

correct log about 'archive' being called

7153 05/01/2012 10:15 AM ben leinfelder

handle 'archive' rest calls
https://redmine.dataone.org/issues/2678

7152 05/01/2012 10:15 AM ben leinfelder

updated d1 jars

7151 05/01/2012 09:18 AM ben leinfelder

[optionally] do not archive the xml_documents and xml_nodes to *_revisions when 'deleting' a document. This will effectively guarantee that the document/data cannot be retrieved after delete.
NOTE: D1 system metadata will persist (for now) so that the ID cannot be reused with the DataONE API but Metacat calls may allow the ID to be reused -- may need to reconsider this behavior....

7150 04/30/2012 04:03 PM ben leinfelder

optionally remove the document/data file from the filesystem completely when 'deleting' it.
https://redmine.dataone.org/issues/2677

7149 04/30/2012 03:42 PM ben leinfelder

newer d1 jars that include shared AuthUtilsmethod for isAuthorized() consistency
https://redmine.dataone.org/issues/2661

7148 04/30/2012 03:35 PM ben leinfelder

implement MN and CN.archive() method -- really just the existing delete() methods.
https://redmine.dataone.org/issues/2674
https://redmine.dataone.org/issues/2675

7147 04/30/2012 03:05 PM ben leinfelder

call MN.delete() for each replica when CN.delete() is called
https://redmine.dataone.org/issues/2676

7146 04/30/2012 02:20 PM ben leinfelder

defer to AuthUtils for flattening out the equivIdent subject list.
https://redmine.dataone.org/issues/2661

7145 04/27/2012 10:24 AM ben leinfelder

check normal access control rules for getSystemMetadata before deferring to MN replica information that may grant MNs additional access to the SM.
https://redmine.dataone.org/issues/2656

7144 04/25/2012 03:33 PM ben leinfelder

include Session-less interface methods and updated jars that define them.

7143 04/24/2012 10:42 AM ben leinfelder

use a shared ExecutorService for replicate() calls.
https://redmine.dataone.org/issues/2623

7142 04/19/2012 02:04 PM ben leinfelder

remove extraneous pid and permission parameters from isAdminAuthorized() method and make public so that it can be called in other locations - namely before our asynchronous replicate() implementation on the MN.

7141 04/19/2012 01:50 PM ben leinfelder

check for empty null (missing) node.subjectList. This should probably be a required element in the D1 schema, but it appears not. (ORNL entry was missing subjects in cn-dev environment)

7140 04/19/2012 11:57 AM ben leinfelder

just use the e.getMessage() as e.getCause() may be null (seeing NPE when testing via the MN IT tester)

7139 04/18/2012 04:04 PM ben leinfelder

check for empty null (missing) node.subjectList. This should probably be a required element in the D1 schema, but it appears not. (ORNL entry was missing subjects in cn-dev environment)

7138 04/17/2012 04:02 PM ben leinfelder

added 2.0.0 targeted bugs to the release notes and fleshed out other major enhancements in the list

7137 04/17/2012 03:15 PM ben leinfelder

no not record EML access rules that use the "denyFirst" permOrder.
https://redmine.dataone.org/issues/2614

7136 04/17/2012 09:20 AM ben leinfelder

needed to initialize the nodeList that stores matching nodes (by subject) -- this was the source of a NPE when we had a matching node subject.

7135 04/16/2012 05:38 PM ben leinfelder

do not create docid-guid mapping unless we are supposed to write access rules for the data to the dbase
https://redmine.dataone.org/issues/2572

7134 04/13/2012 04:40 PM Chris Jones

As Ben suggested, don't compare to the node list if there are no replicas listed. This reduces the number of calls to listNodes() on the CN.

7133 04/13/2012 04:32 PM Chris Jones

Minor logging change in throwing ServiceFailure when Hazelcast throws a RuntimeException.

7132 04/13/2012 04:07 PM Chris Jones

Modify getSystemMetadata() to allow nodes that are listed as replicas to access the system metadata. Use the Session.Subject to find a list of nodes from the CN that match the subject, and compare those node ids to the listed replica node ids. Add listNodesBySubject() helper method to do so.

7131 04/13/2012 07:54 AM ben leinfelder

release notes for 2.0.0

7130 04/12/2012 04:28 PM ben leinfelder

correct typo for "dataone.mn.services.enabled" property on the admin screen checkbox

7129 04/10/2012 10:42 AM ben leinfelder

save backup properties before attempting node registration/update so that we don't "forget" the user input

7128 04/09/2012 03:18 PM ben leinfelder

add a parameter for optionally writing EML-embedded access control rules to the Metacat DB.
https://redmine.dataone.org/issues/2584
https://redmine.dataone.org/issues/2583

7127 04/06/2012 04:22 PM ben leinfelder

added comments and logging about https://redmine.dataone.org/issues/2572

7126 04/06/2012 03:01 PM ben leinfelder

generalize the exception handling because our actions are the same no matter what the specific error is during create - we just notify the CN that the replicate call failed

7125 04/06/2012 02:58 PM ben leinfelder

catch general Exception that may be thrown during MN.replicate() when creating the object locally. There are a few records that keep slipping off our radar with no explanation as to why they remain in "REQUESTED" status.

7124 04/06/2012 01:53 PM ben leinfelder

do not download data at this point

7123 04/06/2012 01:53 PM ben leinfelder

catch errors for each localid we are processing so that they do do prevent other ids from having ORE content generated

7122 04/06/2012 01:52 PM ben leinfelder

additional debug logging for tracking down MN replication errors

7121 04/06/2012 01:35 PM ben leinfelder

only 2.1.0 EML docs for ORE generation right now...

7120 04/05/2012 04:28 PM ben leinfelder

band-aid for CN-CN replication permOrder issue when access control is embedded in EML and the system metadata is replicated before the EML. we just log the inconsistency and allow the insert to succeed
https://redmine.dataone.org/issues/2583

7119 04/05/2012 03:05 PM Chris Jones

It looks like jk.conf and workers.properties were moved in the scripts dir: update the install docs accordingly.

7118 04/05/2012 02:56 PM Chris Jones

Fixed a minor typo in the tomcat config section.

7117 04/04/2012 04:55 PM ben leinfelder

add comment about returning early when no system metadata can be found.
removed extraneous check on the content type of the SM -- was unused.
formatted indenting