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metacat / src @ 7370

# Date Author Comment
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.

7305 07/11/2012 04:38 PM ben leinfelder

make sure we only get the publisher text content (not attribute value)

7303 07/11/2012 03:05 PM ben leinfelder

DOI registration:
-include more revision history based on the identifier table not just the generated SM metadata
-include ecogrid data urls for revisions (long query in xml_nodes_revisions table)

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.

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

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

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

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

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

Print the stack trace when the MMP cannot be resolved.

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

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

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
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.

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

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

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.

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

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.

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.