Metacat

Move the checking if the checksum exists into the create method.

Add code to check the check sum by the DigestOutputStream.

In the expandRightHolder method, we don't use the parameter count=-1 to query the cn. Now we use count=200 and will use the page query to query again if it is necessary.

In the archive method, add a new mechanism to check if the local id is in the xml_revision table if it is not in the xml_documents table.

Change the param from the class field to a local variable.

Change the condition that remove identifier from the identifier table in the method removeSystemMetaAndIdentifier.

Add the pid in a debug statement.

Add the code to check if the object does exist in the create method. If it doesn't, the system metadata and identifier will be removed.

Add methods to check if there are circular obsoletes/obsoletedBy chains in the mn.updateSystemmetadata method.

Change an exception to more appropriate exception.

Add more debug statement for deleting.

Add some information about pid on the log statement.

Clear the code for the method handleInsertOrUpdate.

Add the code to expand the rights holder if it is a group.

correct two minor differences from 2.6 merge: formatId parameter for MetacatHandler and using AuthUtils for gathering group membership information.

Merge in changes from the 2.6.0 release.

merge from 2.6 branch: use AuthUtils to gather user group subjects

merge from 2.6 branch: use AuthUtils to get group and equivalent identities rather than manually try to extract groups from subject info (can include incorrect groups for given primary subject). https://github.nceas.ucsb.edu/KNB/arctic-data/issues/163

merge from 2.6 branch: use group subject (not name) when translating Session.subjectInfo into group list for Metacat's DocumentImpl. https://github.nceas.ucsb.edu/KNB/arctic-data/issues/163

Close the the input stream from the method parameter in the create method.

If a format id in the system metadata is registered in the xml_catalog table, we will use the schema location for the format id to validate the xml instance;
otherwise, we will use our previous way.

In the isScienceMetacata method, the ServiceFailure exception shouldn't be caught anymore, since the code doesn't throw it.

include check for d1 rightsholder when checking permissions in original metacat code base. https://redmine.dataone.org/issues/7560

Move the editScienceMetadata method to the MNodeService class - only update packageId in EML on publish()

Fixed a bug in the condition check for the archive field in the updateSystemMetadata method.

Doesn't allow to reset the archived field to be false if the field is true in the updateSystemMetadata method.

In the updateSystemMetadata method, we avoid to log the event twice for archive=true.

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.

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

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

Add more debug messages for the isCNAdmin method.

Add more debug statement for the updateSystemMetadata method.

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.

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

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.

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.

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

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

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

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

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.

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.

Make the REST api work for views.

Add the code to support CNView interface in CNodeService. Both CNodeService and MNodeService share the same code base.

Add the rules to check the if a sid is valid in the updateSystemMetadata method.

Implemented the feature to support the identifier(both sid and pid) feature in the objectLists method.

The MN.listobjects and CN.listobjects methods will call the one in the D1NodeService class.

Moved the rules for the SID from D1NodeService.create to MNodeService.create.
Also moved the code to check the validation of an pid from D1NodeService.create to MNodeService.create, MNodeService.replicate and CNodeService.create.

Add the code to handle SID in the getLogRecords method.

Add the code to support the sereis id on isAuthorized and systemMetadataChanged method.

Add the code to handle the sid in the delete and archive method.

Add a check that the sid shouldn't equals the pid in the update and create method.

Add the enforcement for the sid in the create method.

Add the code to handle the deleted identifier in the checking v1 system metadata existing method.

Implement the series id in the getSystemMetadata method.

Looking for sid for the method describe.

Refactor the code to check a pid exists in the v1 api.

Modified the get method to handle the sid in the v2 api.

Fixed a bug that the method getLocalId swallowed an exception incorrectly in the IdentifierManager.

Fixed a bug that some service failure exceptions were handled as the NotFound exception.

1. In the identifierExists method, the code to check if the identifier exist on the serial-id fields of the system metadata table.
2. Fixed a bug on the identifierExists - it considered an identifier didn't exist when the determining process threw an exception.

Add delete log for data objects on CNs.

Write the input stream into the file system without alteration in dataone create and update methods.

Added the code to inform users the pid was deleted in the NotFound exception.

Added the code to check if a not-found object was deleted in the isAuthorized method.

update to use v2 types for indexing

add support for v2 DataONE API.

recursively submit obsoleted objects for indexing when instructed. https://projects.ecoinformatics.org/ecoinfo/issues/6424

Unify solr indexing with an IndexTask that is added to the queue -- allows us to send more than just the systemMetadata to the indexer. Initially this is for READ event counts for each document. https://projects.ecoinformatics.org/ecoinfo/issues/6346

Add the methond named isAuthoritativeMNodeAdmin method. It applies to both CN and MN methods.

Fixed a bug that the group information couldn't be retrived from the session.

comment out the index queue call when archive() is called - I think it is causing the duplicate events for the listener. https://projects.ecoinformatics.org/ecoinfo/issues/6030

correct regex for whitespace in D1 identifier.

use an independent ISet<SystemMetadata> structure to communicate objects that should be indexed by metacat-index. https://projects.ecoinformatics.org/ecoinfo/issues/5943

limit /log and /object calls to configurable maximum count for paging. defaults to existing Metacat value of 7000

no need to mark SM as archived now that DocumentImpl.delete() does it.
https://redmine.dataone.org/issues/3406

Implement MNQuery for "pathquery" engine. Optionally include guid in the pathquery results (https://redmine.dataone.org/issues/3083)

include the subjects we are testing for authentication.
https://redmine.dataone.org/issues/2778

make sure data objects correctly use force replicate with action "insert"
https://redmine.dataone.org/issues/3138

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.

check for invalid (!) pids. thanks, M. Reyes for catching this
https://redmine.dataone.org/issues/3047

check for whitespace in identifiers during create() and update()
https://redmine.dataone.org/issues/3047

first pass: DataONE-specific log retrieval to avoid java-based post-processing.

Add debug logging to delete() to understand why we're getting InsufficientKarmaException.

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.

restrict getLogRecrods (both MN and CN) to be called only by admin users (the CN)
https://redmine.dataone.org/issues/2855

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

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.

add Session-less archive() method

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