Metacat

Add contrains for the v1/v2.registerSystemMetadata method. See https://redmine.dataone.org/issues/7380

For the v1/v2 setObsoletedBy and setRightsHolder method, they only apply the objects whose authoriative member node is v1.

Add the constrains that v1/v2.archive only applies the object whose authoritative node is a v1 node.

Add the case the mn.updateSystemMetadata and cn.updateSystemMetadata will call the archive method internally.

Refactory the mn.archive and cn.archive method so the mn.update and cn.update can reuse them.

Update the packageId attribute in EML documents on update. Never display the local docid in the rendered EML.

In the archive method, add the lock.

check for auth before doing asynch call to MN dirtySysMeta implementation

Only applies the setAccessPolicy method to objects whose authoritative mn is v1.

Add a comment to specify that the setReplicationPolicy only applys to v1.

The setReplicationPolicy method only apply to the pids whose authoritative member node has v2 MNStorage.

Add the code to check if the serialVersion object is null before it is saved to the db.

Add a flag on the systemMetadataChanged method. If it is true, the authoritative member node will only accepts the serial version and replica list; the replica node accepts everything. If it is false, it will accept everything.

Add a note for the updateSystemMetadata method.

CN.updateSystemMetadata will ignore the serial version and replica list in the comming system metadata from the mn.

Add the code to check the date of system metadata modification match in MN.updateSystemMetadata only. CN.updateSystemMetadata doesn't check.

use request query string first when handling MN.query() method. https://redmine.dataone.org/issues/7384

Commented out the code to check serial version on the updateSystemMetadata method.

Add more debug messages for the isCNAdmin method.

Put a the systemMetadataChanged method into a queue, so it will not hold the block.

Change updateReplicationMetadata() and setReplicationStatus() to no longer set the dateSysmetaModified date per our discussion on 9/16/15.

Add more debug statement for the updateSystemMetadata method.

In the getLog method, if the event is null, we will set it unknown.

If the event string is null, we will skip this log in the getLog method.

Add the code to check if we can't get the current system metadata from the node in the mn.systemMetadataChanged method.
If we can't find it, an InvalidRequest will be thrown.

Fixed a bug that a client can set the original member node to be null.

Change some exceptions from the InvalidSystem to the InvalidRequest in the updateSystemMetadata method.

rollback: set session.subject so libclient can look up certificate. Seems like the default behavior may have changed?

set session.subject so libclient can look up certificate. Seems like the default behavior may have changed?

use the TypeFactory to convert the Log and ObjectFormatList objects from the v2 to v1.

In the setReplicaStatus method, if the coming status is the same one of the existing one, the system metadata will not be updated.

Fixed some incorrect exceptions in the getReplica method.

In the isAdminAuthorized method, the faiure of the isNodeAdmin method will not interrupt the next check - if it is a cn.

Fixed a bug that when the count is 0, the total is incorrect in the querySystemMetadata method.

Fixed a bug the total was not correct in the querySystemMetadata method.

Use the application/bagit-097 to replace application/bagit.

Use the TypeFactory to replace the TypeMarshaller according to the change in the d1_common_java.

Use the key word "packages" to replace the "package".

Decode the string of the uri after we break the uri into parts base on the "/".

Decode the string of the uri after we break the uri into parts base on the "/".

Decode the string of the uri after we break the uri into parts base on the "/".

Decode the string of the uri after we break the uri into parts base on the "/".

Use the D1NodeVersionChecker to determine the mn's version rather than using ping.

When the cn.notifyReplicaNodes method, if the target MN source code is a v2 mn, we will use v2 api; if it is a v1 node, we will use v1 api.

A new class is used to get the version of service for a given node.

Only support the application/bagit format in the getPackage method.

Use the status of mn.ping to guess the version of the source node in the replicate method.

In the replicate method, it will use the v1.getReplica method if the source node only supports v1 replication service.

The code was added to compare the serial version in the updateSystemMetadata method. If the serial version in the new system metadata is less than or equals previous version, an exception will be thrown.

Increase the version number after updating the existing object's system metadata in the update method.

Fixed a possible null exception in the updateSystemmetadata method.

In the MN.updateSystemMetadata method, when we set the obsoletedBy and obsoletes method, we will check if those values already exist in other chains.

Add the identifier in the message of the exception when a client tries to reset the obsoletes or obsoletedBy fields.

Check the obosoletedBy and Obsoletes only can be set once.

The method of setReplicationstatus can be called by CNs and MNs.

merge from V2 impl: check for optional "failure" param instead of throwing exception when it is missing (often is). https://redmine.dataone.org/issues/7283

check for optional "failure" param instead of throwing exception when it is missing (often is). https://redmine.dataone.org/issues/7283

Fixed a possible null pointer exception bug. https://redmine.dataone.org/issues/7280

Only CNs can call those methods:
CNCore.registerSystemMetadata()
CNCore,updateSystemMetadata()
CNReplication.setReplicationStatus()
CNReplication.updateReplicationMetadata()
CNReplication.deleteReplicationMetadata()

On mn.update and mn.updateSystemMetadata, those clients are allowed:
1. CNs.
2. Clients with appropriate permission calling the method on the authoritative nodes.

When compare the dateUploaded, now we use sysmetadata.getDateUploaded().getTime(). It used systemmetadata.getDateUploaded() (Date objects) to compare.

Add code to catch the BaseException in the updateSystemMetadata method.

Add the code to handle if the cn is null.

Handle multiple versions (v1 and v2) of a service in getCapacity method.

Use the NodeReference object to replace the replicaStatus to restrict the listObjects method.

[re]register DOI when system metadata is updated (typically access policy). https://projects.ecoinformatics.org/ecoinfo/issues/6796

Change the signature of listObject method - remove replicaStatus and add nodeId.

Add the code to call cn.synchroinize at the method of updateSystemMetadata.

Throw an exception if the request doesn't specify the name of the theme in the view method.

use objectFormat.extension in cases where we need to construct a filename for download. https://redmine.dataone.org/issues/3312

use v1 and v2 xsl as appropriate for rendering d1 types (object format list, mostly)

use MediaType from v2.SystemMetadata and v2.ObjectFormat to better determine mime-type, charset and filename for the get() method. https://redmine.dataone.org/issues/3309

Fixed a bug that two columns were missing in the sql command.

Add the code to read/write the new system metadata fields - file name, media type and media type properties into the db tables.

Add code to update smmediatypeproperties table.

Throw an exception if the saving system metadata fails.

Add the code to roll back the saved system metadata if the object can't be saved.

Don't use ssClient as a class field. Now it is a local variable. This fixed an issue that two statements using the client caused the exception - java.net.SocketTimeoutException: Read timed out.

refs: #7092. found another unclosed inputStream, this time in ReplicationService.handleForceReplicationDataFileRequest(...).

fixes #7092: added finally clause to ReplicationHandler.update method to unconditionally close the inputStreams it keeps in a Vector. Needs testing.

Add the code to check if the client is trying to update an archived object. If it is, reject it.

Add a new method -updateSystemMetadata. It only can be called by CNs.

Refactory the authorize methods on D1NodeService.
Add the check for whom can call mn.updatesystemMetadata.

Committed the change which Andreit did.
1. Add the code for synchronize(not implemented)
2. Add the code for addForm.

remove portal servlet and configuration - no need for this if we are supporting auth tokens from authentication service.

defer to D1 PortalCertificateManager to pull authentication credentials from the request before defering to old Metacat cookie session

Add the code to check the authorization of the client which is reindexing a pid.

Created the updateSystemMetadata method.

Add the code to check if the current node is the authoritative node for the the given pid.

Add the check of permission to update the system metadata.

add whoami endpoint to make debugging authn/authz easier as we use additional mechanisms for proving identity.

Remove the code to check sid on create and registerSystemMetadata.

Fixed a bug that put the detail code in a wrong position.

Add the code to check if a user tries to modify an immutable field on system metadata.

If an Event object is null in the v1 log entry, we won't add it to the log.

use singleton for getting JWT token - refactor in d1_portal project

use secure context url for loading XSLTs in db transform

ReplicationServices.getUrlStream(url) callers were not closing the inputstream properly, as was revealed when switching to libclient v2 (a pooling connection manager in HttpClient) and encountering reasource leaks.

remove classes annotator classes that have moved to a different project under dataone's github.

bullet-proofed exception handling in ReplicationService.getURLStream, to make sure client communication exceptions are handled and logged.