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metacat / src / edu / ucsb / nceas / metacat @ 6613

# Date Author Comment
6613 11/07/2011 12:31 PM ben leinfelder

print the stacktrace when there is an error -- debuggin!

6611 11/07/2011 10:55 AM ben leinfelder

use SSL to get content from stream

6610 11/07/2011 10:52 AM Chris Jones

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.

6609 11/07/2011 10:01 AM Chris Jones

D1NodeService get(), getSystemMetadata(), and isAuthorized() no longer throw InvalidRequest.

6606 11/04/2011 02:45 PM ben leinfelder

uses prepared statement instead of plain old statement.
deprecated the DBConnection.createStatement() method to discourage direct parameter value use in favor of parameter binding.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527

6604 11/04/2011 02:21 PM Chris Jones

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.

6603 11/04/2011 02:19 PM Chris Jones

Handle multipart params where the libclient methods are using them.

6602 11/04/2011 12:32 PM ben leinfelder

uses prepared statement parameter binding for queries
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527

6600 11/03/2011 12:55 PM Chris Jones

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.

6599 11/03/2011 10:36 AM Chris Jones

Include the serialVersion in the call to CN.setReplicationStatus() after replicating data.

6598 11/02/2011 10:10 PM ben leinfelder

correctly set the prepared statement parameters for start and end date

6596 11/02/2011 09:58 PM ben leinfelder

make MNodeServiceTest pass JUnit testing

6595 11/02/2011 08:40 PM ben leinfelder

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527

6593 11/02/2011 08:04 PM Chris Jones

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().

6592 11/02/2011 08:00 PM Chris Jones

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....

6590 11/02/2011 07:46 PM Chris Jones

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.

6587 11/01/2011 07:35 PM ben leinfelder

skip verification -- remaining TODO

6586 11/01/2011 07:08 PM ben leinfelder

verify certificate

6585 11/01/2011 06:41 PM ben leinfelder

inspect keystore entries for matching client certificate

6584 11/01/2011 05:27 PM ben leinfelder

lookup the correct property for keystore file

6582 11/01/2011 03:23 PM ben leinfelder

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.

6579 11/01/2011 01:33 PM ben leinfelder

check client-provided certificate when servicing ReplicationServlet requests.

6578 11/01/2011 11:54 AM Chris Jones

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.

6576 11/01/2011 08:59 AM Chris Jones

getReplica() should log replication events as DataONE Types.Event.replicate (vs 'getreplica')

6575 11/01/2011 08:54 AM Chris Jones

Minor indentation cleanup.

6574 11/01/2011 06:48 AM Chris Jones

Modify isAuthorized() to get the most up to date system metadata from the hzSystemMetadata map.

6573 11/01/2011 06:40 AM Chris Jones

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().

6572 11/01/2011 06:37 AM Chris Jones

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 subclass prior to the insert.

6571 11/01/2011 06:33 AM Chris Jones

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 current serial version, but setAccessPolicy() does not pass in the entire system metadata object, so there's no way to check. For now, increment the latest system metadata from the hzSystemMetadata map.

6570 10/31/2011 04:37 PM Chris Jones

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.

6569 10/31/2011 01:13 PM Chris Jones

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.

6568 10/29/2011 07:21 PM Chris Jones

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.

6567 10/28/2011 09:46 PM Chris Jones

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.

6564 10/28/2011 04:05 PM Chris Jones

SystemMetadataManager's functionality is handled by IdentifierManager. Removing it and it's test.

6563 10/28/2011 04:01 PM Chris Jones

MetadataTypeRegister is now replaced by ObjectFormatService. Removing it and it's test.

6562 10/28/2011 01:16 PM ben leinfelder

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

6561 10/27/2011 05:51 PM ben leinfelder

move the DataONE 1.0.0-SNAPSHOT

6560 10/27/2011 04:33 PM ben leinfelder

correctly check for missing config values during geoserver configuration

6557 10/27/2011 03:59 PM ben leinfelder

correctly check for missing config values during geoserver configuration

6552 10/27/2011 02:13 PM ben leinfelder

Configure and use CertificateManager in order to act as the MN when performing replicate() and getReplica() mthods.

6551 10/27/2011 01:00 PM ben leinfelder

use logging, not system.out

6550 10/27/2011 12:40 PM ben leinfelder

change upgrade scripts/routines to use 2.0.0 version number instead of 1.10.0

6549 10/27/2011 11:35 AM ben leinfelder

make sure we close the prepared statement always

6548 10/27/2011 11:17 AM Chris Jones

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.

6542 10/20/2011 02:03 PM ben leinfelder

add User-Agent logging to support D1 requirements

6541 10/20/2011 12:40 PM ben leinfelder

remove old RestServlet handler -- not used now

6540 10/16/2011 10:47 AM Chris Jones

Add debugging output to MNodeService.

6539 10/14/2011 05:49 PM ben leinfelder

use default fmtid if we can't find the user-supplied data mime type in our list

6538 10/14/2011 05:13 PM ben leinfelder

including newer d1 libclient that uses Foresite (and Jena) to construct/parse ORE resource maps for DataONE

6536 10/14/2011 02:57 PM ben leinfelder

delete the xml access rules by either docid or guid to make sure we have the most up to date information

6535 10/14/2011 10:45 AM Chris Jones

Fix a data-typing issue when pulling replicationAllowed from postgres. Use getBoolean(), not getString().

6534 10/13/2011 05:13 PM ben leinfelder

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 one for more official use). I was only able to get the former certificate type to work with our existing MN servers

6533 10/12/2011 07:19 PM Chris Jones

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.

6532 10/12/2011 11:17 AM ben leinfelder

update D1 jars to include recent SubjectList -> SubjectInfo refactoring and the SUBJECT_PUBLIC constant

6531 10/12/2011 11:08 AM ben leinfelder

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)

6530 10/12/2011 10:00 AM ben leinfelder

throw InvalidToken when the Session parameter is null for create()
https://redmine.dataone.org/issues/1850

6528 10/09/2011 02:50 PM Chris Jones

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.

6527 09/29/2011 11:43 PM Matt Jones

Bug fix for access control rules coming in from the dataone system metadata. Previously, the code used getLocalId() to get the docid to insert into the XML access table, but that docid included the revision number (e.g., foo.1.1), which it shouldn't. Now use the AccessionNumber class to strip off the rev to get a real docid for insertion into the table.

6526 09/28/2011 07:28 PM ben leinfelder

allow the XML namespace to be given in both double and single quotes. The regex pattern was only looking for xmlns values that were in double quotes. This was brought to light by LTER:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5497

6525 09/26/2011 10:59 PM ben leinfelder

set date uploaded and date system metadata updated date to current time when calling MN.create() and MN.update()

6522 09/26/2011 12:07 PM ben leinfelder

do not allow system metadata to have obsoletes or obsoletedBy fields when calling the create() method -- these are only allowed for updates so that we do not subvert object versioning by [un]knowingly submitting system metadata that directs one id to another.

6521 09/26/2011 11:59 AM ben leinfelder

set the originating member node on update()

6520 09/26/2011 11:53 AM ben leinfelder

set the originating member node on create()

6519 09/26/2011 11:52 AM ben leinfelder

-use whatever object format id is stored in the DB
-only set originating node and authoritative node if we have non-null values for them

6518 09/26/2011 11:10 AM ben leinfelder

set sysmeta submitter based on the subject given in the certificate

6516 09/26/2011 09:42 AM ben leinfelder

skip Objects that have null format ids are invalid checksums

6515 09/23/2011 10:18 PM ben leinfelder

MN.setAccess() is a PUT

6514 09/23/2011 09:54 PM ben leinfelder

correctly handle incoming "accessPolicy" parameters for the setAccess() method

6513 09/23/2011 08:46 PM ben leinfelder

swap the parameters for update: existing pid should be first, and then newPid

6512 09/23/2011 02:59 PM Matt Jones

Modified cron schedule to fix the incorrect crontab entry.

6511 09/23/2011 01:44 PM ben leinfelder

do not require ID reservation before create() or update()

6510 09/23/2011 01:39 PM ben leinfelder

use "action" parameter instead of "permission"

6509 09/23/2011 01:38 PM ben leinfelder

use "action" parameter instead of "permission"

6508 09/22/2011 03:57 PM ben leinfelder

catch datapackage parsing errors as before

6507 09/22/2011 03:30 PM ben leinfelder

include checksum algorithm when setting describe
https://redmine.dataone.org/issues/1799

6506 09/22/2011 03:30 PM ben leinfelder

check for null session before logging sync failed
https://redmine.dataone.org/issues/1798

6503 09/22/2011 02:02 PM ben leinfelder

use Settings augmentation to customize the D1Client.CN_URL when used in a Metacat deployment.

6502 09/22/2011 02:01 PM ben leinfelder

correctly implement MN.describe
https://redmine.dataone.org/issues/1799

6501 09/22/2011 01:40 PM ben leinfelder

return Node not NodeList for getCapabilities
https://redmine.dataone.org/issues/1800

6500 09/22/2011 01:32 PM Matt Jones

Use setProperty() instead of addProperty() to properly override the Settings property.

6499 09/22/2011 01:19 PM Matt Jones

Modify to set the CN URL before getting a CN instance.

6497 09/22/2011 10:55 AM Matt Jones

Pull the certificate path for dataone certificates from the metacat properties file.

6496 09/22/2011 10:12 AM ben leinfelder

return null instead of throwing an exception when pid is not found in store

6495 09/22/2011 10:12 AM ben leinfelder

log errors on create() and registerSM

6494 09/22/2011 10:11 AM ben leinfelder

more stringent NP checking when saving replication policy

6493 09/22/2011 12:05 AM Matt Jones

Register as a MN on the DataONE network as part of the properties setup. This is currently done always, but it needs to be conditional rather than automatically triggered.

6492 09/22/2011 12:03 AM Matt Jones

Added subject field to getCapabilities() call.

6490 09/21/2011 05:45 PM ben leinfelder

comment out resynch() method until errors are resolved

6489 09/21/2011 05:25 PM ben leinfelder

use default hazelcast config when not configured to use an external one

6484 09/21/2011 04:58 PM Chris Jones

Don't use the hzNodes map yet (as a hazelcast client). Use D1Client instead to get the node list in isNodeAuthorized().

6483 09/21/2011 04:51 PM Chris Jones

For now, remove the hzClient code connecting to the DataONE process cluster to get the hzNodes map. This will be moved into the storage cluster, but use D1Client to get the node list for now.

6481 09/21/2011 10:54 AM rnahf

going back to using IDentifier as the key for the ObjectPAthMap.

6476 09/20/2011 10:20 PM Matt Jones

Fix getCapabilities to properly throw ServiceFailure when properties can not be read, rather than failing with a log message. Fix properties in the Node object to reflect their correct values. Set the sync schedule properly to default to 5 minute intervals. Improve documentation.

6475 09/20/2011 08:52 PM Matt Jones

Reformatted to correct indentation to make class readable.

6474 09/20/2011 02:32 PM ben leinfelder

newer d1 jars -- contains CN.isNodeAuthorized() method

6472 09/20/2011 02:11 PM ben leinfelder

collect "message" param from multipart request for MN.synchronizationFailed method

6471 09/20/2011 02:08 PM Matt Jones

Reverting previous @Overrides chanrge from r6470, as that is the desired
behavior under Java 1.6 -- previous versions of Java (e.g., 1.5) will not
comile with this usage of the @Overrides annotation, but the currently
supported version will. So reverting to the 1.6 convention.

6470 09/20/2011 01:36 PM Matt Jones

Removing incorrect @Override annotations that were preventing compilation. The methods marked did not actually override a method in the superclass, so they were not compiling. I think @Overrides was being mistaken for methods that implement an interface but aren't actually in the superclass.

6469 09/20/2011 11:55 AM ben leinfelder

use d1_common_java's date serialization utility for parsing parameters

6468 09/20/2011 10:48 AM ben leinfelder

catch runtime exceptions that arise from hazelcast storage errors in the system metadata map