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From 10/09/2011 to 11/07/2011

11/08/2011

05:16 PM Revision 6618 (metacat): New D1 libraries, fix for MNode.isNodeAuthorized() and other exception handling.
Chris Jones
05:03 PM Revision 6617 (metacat): MockCNode.getSystemMetadata() no longer throws InvalidRequest.
Chris Jones

11/07/2011

03:53 PM Revision 6616 (metacat): add note about alternative methods for getting cert/key
ben leinfelder
03:50 PM Revision 6615 (metacat): use prepared statement place holder (?)
ben leinfelder
02:31 PM Revision 6614 (metacat): use DateTimeMarshaller for all replication date transfers
ben leinfelder
12:31 PM Revision 6613 (metacat): print the stacktrace when there is an error -- debuggin!
ben leinfelder
11:50 AM Revision 6612 (metacat): remove catch blocks for unthrown exceptions
ben leinfelder
10:55 AM Revision 6611 (metacat): use SSL to get content from stream
ben leinfelder
10:52 AM Revision 6610 (metacat): Update methods in MNodeService to reflect they modifications of the MN API with regard to exceptions being raised. Largely removed InvalidRequest from a number of methods, and instead threw an appropriate NotFound or ServiceFailure instead.
Chris Jones
10:01 AM Revision 6609 (metacat): D1NodeService get(), getSystemMetadata(), and isAuthorized() no longer throw InvalidRequest.
Chris Jones

11/04/2011

03:17 PM Revision 6608 (metacat): Add new D1 jars with 1.0.0 API additions (MNStorage.systemMetadataChanged()) and libclient fixes.
Chris Jones
03:04 PM Revision 6607 (metacat): newer seek tag
ben leinfelder
02:45 PM Revision 6606 (metacat): uses prepared statement instead of plain old statement.
deprecated the DBConnection.createStatement() method to discourage direct parameter value use in favor of parameter b... ben leinfelder
02:35 PM Revision 6605 (metacat): Add a test for systemMetadataChanged. This should be fleshed out more so that the test uses a CN certificate.
Chris Jones
02:21 PM Revision 6604 (metacat): Fix getReplica() handling code for getReplica() and systemMetadataChanged(). Calls to getReplica() in MNode were calling get(), so the lack of resource handling was being missed.
Chris Jones
02:19 PM Revision 6603 (metacat): Handle multipart params where the libclient methods are using them.
Chris Jones
12:32 PM Revision 6602 (metacat): uses prepared statement parameter binding for queries
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527 ben leinfelder

11/03/2011

12:59 PM Revision 6601 (metacat): Add new D1 jars with the new MNStorage.systemMetadataChanged() additions.
Chris Jones
12:55 PM Revision 6600 (metacat): Add in the systemMetadataChanged() method in MNodeService to respond to notifications. Only allow subjects from CNs listed in the node list to make the call. Update the local copy of the system metadata document for the given pid.
Chris Jones
10:36 AM Revision 6599 (metacat): Include the serialVersion in the call to CN.setReplicationStatus() after replicating data.
Chris Jones
10:10 PM Revision 6598 (metacat): correctly set the prepared statement parameters for start and end date
ben leinfelder
10:09 PM Revision 6597 (metacat): check object format id values since they are not Comparable objects
ben leinfelder
09:58 PM Revision 6596 (metacat): make MNodeServiceTest pass JUnit testing
ben leinfelder
08:40 PM Revision 6595 (metacat): http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527
ben leinfelder
08:08 PM Revision 6594 (metacat): Update CNodeService test to include serialVersion in it's calls as appropriate.
Chris Jones
08:04 PM Revision 6593 (metacat): Update CNodeService to use the serialVersion parameter and compare it to the current serialVersion of the system metadata found in the hzSystemMetadata map. Throw an InvalidRequest exception if they are not equal. This affects updateReplicationMetadata(), setReplicationStatus(), setReplicationPolicy(), setAccessPolicy(), and setOwner().
Chris Jones
08:00 PM Revision 6592 (metacat): Handle calls to CNReplication REST services. Modify handle() to field calls to /replicaPolicies, /replicaMetadata, /replicaAuthorizations, and /replicaNotifications. Add the isNodeAuthorized(), setReplicationPolicy(), setReplicationStatus(), and updateReplicationMetadata() methods to parse and pass multipart form data and params on to the CNodeService implementing class.
The CNreplication additions also include support for the serialVersion parameter that was added to some of the API ca... Chris Jones
07:50 PM Revision 6591 (metacat): Add new d1_common jar with the API changes that add serialVersion parameters to CNAuthorization and CNReplication methods.
Chris Jones
07:46 PM Revision 6590 (metacat): Add support for the various CNReplication calls. Add collectReplicationPolicy() to parse the policy out of the multipart form, and collectReplicaMetadata() to parse out the replica to be updated.
Chris Jones
05:32 PM Revision 6589 (metacat): restore -- apparently this was used with reflection in a test...
ben leinfelder

11/02/2011

09:20 AM Revision 6588 (metacat): change to 2.0.0 release
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5515 ben leinfelder
07:35 PM Revision 6587 (metacat): skip verification -- remaining TODO
ben leinfelder
07:08 PM Revision 6586 (metacat): verify certificate
ben leinfelder
06:41 PM Revision 6585 (metacat): inspect keystore entries for matching client certificate
ben leinfelder
05:27 PM Revision 6584 (metacat): lookup the correct property for keystore file
ben leinfelder

11/01/2011

04:53 PM Revision 6583 (metacat): drop old identifier when upgrading from 1.9.5 to 2.0.0
ben leinfelder
03:23 PM Revision 6582 (metacat): use HttpClient to set up SSL connection when doing replication calls -- this will use the server's configured certificate as the client certificate on the request. The server it is calling can then inspect that certificate and decide whether or not it trusts the caller.
ben leinfelder
02:09 PM Revision 6581 (metacat): use EML style tag for: only show organization when the individual is omitted
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5499 ben leinfelder
01:34 PM Revision 6580 (metacat): newer d1 jar (for good measure)
ben leinfelder
01:33 PM Revision 6579 (metacat): check client-provided certificate when servicing ReplicationServlet requests.
ben leinfelder
11:54 AM Revision 6578 (metacat): Add updateReplicationMetadata() to the CN service implementation. This was missing from the API, and likely never called. It fully replaces the given replica item in the list of replicas in system metadata.
Chris Jones
09:10 AM Revision 6577 (metacat): MN.setAccessPolicy() is deprecated, commenting out the test.
Chris Jones
08:59 AM Revision 6576 (metacat): getReplica() should log replication events as DataONE Types.Event.replicate (vs 'getreplica')
Chris Jones
08:54 AM Revision 6575 (metacat): Minor indentation cleanup.
Chris Jones
06:48 AM Revision 6574 (metacat): Modify isAuthorized() to get the most up to date system metadata from the hzSystemMetadata map.
Chris Jones
06:40 AM Revision 6573 (metacat): Add a placeholder setAccessPolicy() method in MNodeService that throws NotImplemented since this method is being deprecated. Note: need to confirm that this shouldn't be calling D1Client.getCN().setAccessPolicy().
Chris Jones
06:37 AM Revision 6572 (metacat): Update getSystemMetadata() to lock(); get(); unlock() to ensure we have the latest version of system metadata from the hzSystemMetadata map. Remove the setAccessPolicy() method since it is being deprecated in the MNAuthorization API.
change insertSystemMetadata() to use a finer grained Date object on insertion. Locking of the pid happens in the sub... Chris Jones
06:33 AM Revision 6571 (metacat): Add setAccessPolicy() to CNodeService since the CN should only make changes to access policies for objects registered with the D1 system. Increment the serial version after locling and getting the most up to fdate system metadata.
Note: CCIT meeting decision says the serial version of the system metadata (during the change) should equal the curre... Chris Jones

10/31/2011

04:37 PM Revision 6570 (metacat): In CNodeService, separate the CN.create() functionality from the MN.create() functionality while still using the superclass to call create(). Deal with Hazelcast locks and setting serial versions only in the CN implementation.
Chris Jones
01:13 PM Revision 6569 (metacat): Change updateSystemMetadata() to evaluate the incoming system metadata serial version against that found in the hzSystemMetadata map. If they are the same, do the update. If not, throw an InvalidRequest explaining that they need the most current version.
Chris Jones

10/30/2011

07:21 PM Revision 6568 (metacat): Modify CNodeService's registerSystemMetadata() with support for SystemMetadata's serialVersion field. Also, use the hzSystemMetadata map for all system metadata reads using a lock on the pid in order to get the very latest version. This affected isNodeAuthorized(), getChecksum(), and assertRelation(). Since we're using Hazelcast, exceptions are masked as RuntimeException, so throw a ServiceFailure with the underlying message.
Chris Jones

10/29/2011

09:46 PM Revision 6567 (metacat): Modify CNodeService's updateSystemMetadata(), setReplicationStatus(), setReplicationPolicy(), and setOwner() with support for SystemMetadata's serialVersion field. Other methods still pending an update. Use the hzSystemMetadata map for all system metadata reads using a lock on the pid in order to get the very latest version.
Chris Jones
08:42 PM Revision 6566 (metacat): removing non-junit file from the test area
ben leinfelder
08:39 PM Revision 6565 (metacat): load hazelcast test files from the classpath rather than from rob's personal directory.
ben leinfelder

10/28/2011

04:05 PM Revision 6564 (metacat): SystemMetadataManager's functionality is handled by IdentifierManager. Removing it and it's test.
Chris Jones
04:01 PM Revision 6563 (metacat): MetadataTypeRegister is now replaced by ObjectFormatService. Removing it and it's test.
Chris Jones
01:16 PM Revision 6562 (metacat): include clearer error message when UPDATE action is requested on a replicated document and we fail to successfully get a lock from the source Metacat server
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4907 ben leinfelder
05:51 PM Revision 6561 (metacat): move the DataONE 1.0.0-SNAPSHOT
ben leinfelder

10/27/2011

04:33 PM Revision 6560 (metacat): correctly check for missing config values during geoserver configuration
ben leinfelder
04:05 PM Revision 6559 (metacat): call the web.xml tomcat6 not tomcat5
ben leinfelder
04:01 PM Revision 6558 (metacat): remove reference to tomcat5.5 in favor of tomcat6. including the "custom" start up script that used the sun jdk -- this can be configured rather than coded into the script.
ben leinfelder
03:59 PM Revision 6557 (metacat): correctly check for missing config values during geoserver configuration
ben leinfelder
03:45 PM Revision 6556 (metacat): remove reference to the "custom" /etc/init.d/tomcat6 script -- this should not be used since there are now better ways to customize the tomcat start up
ben leinfelder
03:27 PM Revision 6555 (metacat): use 2.0.0
ben leinfelder
03:21 PM Revision 6554 (metacat): -use 2.0.0 version
-use tomcat6
-use /var/lib/tomcat6 as the example tomcat home directory
ben leinfelder
02:22 PM Revision 6553 (metacat): use 2.0.0 -- stub out the release notes
ben leinfelder
02:13 PM Revision 6552 (metacat): Configure and use CertificateManager in order to act as the MN when performing replicate() and getReplica() mthods.
ben leinfelder
01:00 PM Revision 6551 (metacat): use logging, not system.out
ben leinfelder
12:40 PM Revision 6550 (metacat): change upgrade scripts/routines to use 2.0.0 version number instead of 1.10.0
ben leinfelder
11:35 AM Revision 6549 (metacat): make sure we close the prepared statement always
ben leinfelder
11:17 AM Revision 6548 (metacat): The incoming source node param is just a string, not XML, so don't attempt to deserialize it. Rather, just make a new NodeReference object and set it's value to the value of the incoming param.
Chris Jones
08:58 AM Revision 6547 (metacat): include CILogon link and more explanation about what is going on with the mapping.
ben leinfelder
08:49 AM Revision 6546 (metacat): Change the version from 1.9.4 to 1.9.5.
Jing Tao

10/26/2011

11:08 AM Revision 6545 (metacat): correctly check that user is logged into metacat before proceeding
ben leinfelder
11:07 AM Revision 6544 (metacat): use null session for now
ben leinfelder
05:54 PM Revision 6543 (metacat): draft of legacy-to-d1 account mapping interface
ben leinfelder

10/20/2011

02:03 PM Revision 6542 (metacat): add User-Agent logging to support D1 requirements
ben leinfelder
12:40 PM Revision 6541 (metacat): remove old RestServlet handler -- not used now
ben leinfelder

10/16/2011

10:47 AM Revision 6540 (metacat): Add debugging output to MNodeService.
Chris Jones

10/15/2011

05:49 PM Revision 6539 (metacat): use default fmtid if we can't find the user-supplied data mime type in our list
ben leinfelder
05:13 PM Revision 6538 (metacat): including newer d1 libclient that uses Foresite (and Jena) to construct/parse ORE resource maps for DataONE
ben leinfelder

10/14/2011

02:57 PM Revision 6536 (metacat): delete the xml access rules by either docid or guid to make sure we have the most up to date information
ben leinfelder
10:45 AM Revision 6535 (metacat): Fix a data-typing issue when pulling replicationAllowed from postgres. Use getBoolean(), not getString().
Chris Jones
05:13 PM Revision 6534 (metacat): cleaned up to use for populating a DataONE MN using the D1 api. Retrieves packages from a Metacat and generates system metadata for them before calling MN.create() for both data and metadata.
NOTE: you need a client certificate that the target server accepts (either DataONE-generated for testing or a CILogon... ben leinfelder

10/13/2011

07:19 PM Revision 6533 (metacat): IdentifierManager.getSystemMetadata() was missing the number_replicas and replication_allowed fields when building a ReplicationPolicy section of a SystemMetadata document being returned. Add in these two attributes.
Chris Jones

10/12/2011

11:17 AM Revision 6532 (metacat): update D1 jars to include recent SubjectList -> SubjectInfo refactoring and the SUBJECT_PUBLIC constant
ben leinfelder
11:08 AM Revision 6531 (metacat): include SystemMetadata when replicating data and metadata documents -- this allows us to establish the guid-to-docid mapping that is crucial for being able to read the replicated document by guid (d1 api)
ben leinfelder
10:00 AM Revision 6530 (metacat): throw InvalidToken when the Session parameter is null for create()
https://redmine.dataone.org/issues/1850 ben leinfelder
08:37 PM Revision 6529 (metacat): Fix service versioning in metacat.properties so that when Metacat nodes are registered they report the correct service version for use in resolve() -- i.e., use "v1" instead of "0.6.4" in resolve urls.
Matt Jones

10/09/2011

02:50 PM Revision 6528 (metacat): Once a CN calls replicate() on an MN, the MN needs to call getReplica() on the source MN (not get()). Once the bytes are retrieved, the MN must then call back to the CN with setReplicationStatus() to indicate that the replication status is complete. Modify MNodeService to do so.
Chris Jones
 

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