Metacat

The deleteSystemmetadata method will delete the records on xml_access as well.

Merge changes from the 2.6.0 release.

Fixed a bug to use an identifier object to get a value in a vector.

Check the chain end if obsoleted by another object.
See ticket https://redmine.dataone.org/issues/7624

Use sql command to get some information rather than hazelcast.

Use a hashmap to replace a sql query to improve performance in the getHeadPID method.

In the getHeadPID method, we got the field obsoletedBy from the systemmetadata table rather than the hazelcast service.

Use the "order by" to preserve the nodes order in the replication policy.

Close the sql statements on the four methods - getGUID, getHeadPID, systemMetadataSIDExist and systemMetadataPIDExist.

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

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

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.

Throw an exception if the saving system metadata fails.

Use the log to the replace system.out.print.

Add the code to get the head version.

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

Add the series id to the system metadata.

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

Change a method name to use pid rather than guid.

Add the code to get the most recent version of a sid which all pids are obsoleted.

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

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 a method to check if a serial id exists.

Add a method to get the pid of the head version of a sid.

Make the deleteSystemmetadata method really roll-backable.

add support for v2 DataONE API.

Allow null SM.submitter (per schema). There were null values in cn-dev (and probably elsewhere since it is technically allowed in the schema. But with a null value, we need to have a null Subject for the SM.submitter field, not a Subject with a null getValue() return. Encountered this when testing for: https://projects.ecoinformatics.org/ecoinfo/issues/5929.

move DocInfo parsing into utilities project so that it can be used by Morpho as well as Metacat.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5737

default replicaStatus (aka "show replicas in results") to true rather than false

add debug statements for listObject slice debugging

use dual query for query slicing - one for count, another for the actual records when requested.
https://redmine.dataone.org/issues/3065

Fix a minor bug in listObjects() where total was set incorrectly when total was set incorrectly when count=0. The definition of total in the D1 architecture docs says 'The total number of entries in the source list from which the slice was extracted.' With count=0, we assume the total is the total count from the entire object store. Needs testing.

use RDBMS-specific features to limit the resultset for paging the object list -- postgres and oracle have implementations. we don''t really support mssql so I skipped that one.

look up the archived value when retrieving SystemMetadata record.
https://redmine.dataone.org/issues/3405

handle /object?count=0 queries using simpler (quicker) sql
https://redmine.dataone.org/issues/3065

Change the set and get methods for the replication verified date to use java.sql.Timestamp rather than java.util.Date via setTimestamp(), not setDate(). The hh:mm:ss.sss was previously getting truncated.

shorten the systemmetadata* table names for Oracle's 30 character limit. move version to 2.0.5. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

order the listObjects() results by identifier to mitigate random paged results
https://redmine.dataone.org/issues/3065

share the same dbConnection when inserting and then updating SystemMetadata objects in the backing store.
any errors encountered during the update will rollback the entire transaction and the SM record will not exist, even in part.

Do not loadAllKeys() for SystemMetadataMap when Metacat first starts up. hzIdentifiers will be populated with a simple SQL statement rather than the serial loading of every single SystemMetadata object. It will remain in synch using the usual entryXXX() methods as before....

only generate system metadata for original objects.
https://redmine.dataone.org/issues/2721

include debug statements for systemMetadataReplicationStatus and systemMetadataReplicationPolicy SQL

handle case where EML access rule "permission" is not in our constrained list (EML 2.0.0 doc showed this with a "none" permission for public principal). we now omit this invalid access rule when interpreting it in system metadata -- effectively dropping that invalid access rule. "none" had been stored as a 0 in the DB xml_access table and would not have given or denied access for the document so I think it can safely be omitted for good. for example, see knb-lter-gce.101.2 with this rule:...

do not allow "Metacat-conforming" identifiers to be used. "test.1.001" is interpreted as "test.1.1" which renders "test.1.002" unusable unless a traditional Metacat "update" is used for that id/revision which contradicts the DataONE use of Identifiers that have no lexical requirements for revisions.

use Timestamp object from results, not a new Date object from that Timestamp object

check whether mapping (

Globally change the property 'dataone.memberNodeId' to 'dataone.nodeId'. This is more useful for both MNs and CNs implemented in Metacat. Also, change D1NodeService.getLogRecords() to return log entries with the actual node id rather than the IP address (looks like a cut/paste error)....

do not "lookup" object format when retrieving system metadata -- just return what we have stored as the formatId and don't [erroneously] default it to binary when there's a problem with the lookup (cache or service or otherwise).
https://redmine.dataone.org/issues/2365

actually, let's set the serialVersion during the MN.create() call so that the HZ map and the backing store have the same information immediately. Also, this is how the docs specify it.
http://mule1.dataone.org/ArchitectureDocs-current/design/SystemMetadata.html

if serialVersion is null, use defualt value of 0

remove ID mapping when a create()/"insert" call fails so that subsequent calls do not return an IdentifierNotUnique error. In this case it was due to invalid XML.
https://redmine.dataone.org/issues/2341

ObjectFormatCache.getFormat(String formatStr) has been deprecated, and now only takes a formatId instance to get a format from the cache. It also throws Service Failure and NotImplemented, so here just set the format to application/octet-stream in any case.

refactor IdentityManager.createSystemMetadata(sm) to be insertSystemMetadata(sm) so that it is clear that this method inserts the SM object into the backing store. This differentiates it from the "generation" methods we use when we need to create SM about pre-existing objects or objects we get from non-D1 api calls.

Remove null field tests in the IdentifierManager class. Schema-level required fields are checked on serialization/deserialization using JibX during the REST resource handler classes. Other required fields are checked in MNodeService and CNodeService, higher in the stack.

In IdentifierManager.updateSystemMetadata(), add a check for invalid system metadata (fields that throw a NullPointerException on access) to ensure that system metadata is populated correctly. Updated calling classes to handle the exception.

In IdentifierManager, throw SQLExceptions rather than just logging them, and let them be handled higher up in the stack.

update authoritative member node id when we change it (reconfiguration) and when we initially register as a MN with the CN.

When the requested count in a call to listObjects() is 0, return an empty object list, not a full one. Fixes https://redmine.dataone.org/issues/2122

Minor formatting for querySystemMetadata().

Change the query semantics such that we implement the MN.listObjects() where the lower datetime bound is inclusive (greater than or equal to" and the upper datetime bound in exclusive (less than). This allows easier paging in client applications.

include 'archived' system metadata element in backing DB store

use correct "rev" column in xml_revisions table

refactor Metacat access handling to be on a per-revision basis so that it more closely aligns with the DataONE approach
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

for "all" permission, return a list of READ, WRITE, CHANGE_PERMISSION

look up access policy by guid or local id
TODO: resolve the Metacat/EML "all" permission as it relates to DataONE (there is only READ, WRITE, CHANGE_PERMISSION). for now I am using CHANGE_PERMISSION when it is a Metacat "all"

optionally include ORE generation/insertion into Metacat when generating SystemMetadata
https://redmine.dataone.org/issues/2056

use shared method for looking up "docInfo" map -- both in Metacat replication and in D1 system metadata generation

include all document revisions when generating "missing" system metadata
TODO: revision graph captured in obsoletes/obsoletedBy

delete system metadata when MN.delete() is called.

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

move the DataONE 1.0.0-SNAPSHOT

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

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.

-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

skip Objects that have null format ids are invalid checksums

more stringent NP checking when saving replication policy

lookup latest system metadata update date for use in synchronizing CN-CN when an offline nodes comes back online

do not throw exception when checking for system metadata - boolean return is good.
use ReplicationStatus.valueOf() instead of convert()

treat access rules atomically - do not group them together otherwise the intent is subverted

check for null pointers when adding system metadata/creating records during cn.create()

do not add obsoletes and obsoletedBy elements if their values are null (jibx chokes on the emptiness)

fixed logic wrt localID and docid. Implemented new method in IdentifierManager to getAllGUIDs from identifier table for implementation of loadAllKeys in ObjectPathMapLoader.

changes for schema update (d1_common)

Update classes to use the DataONE 0.6.4 schema and types. Major changes involve using BigInteger vs long in SystemMetadata.size, and using ObjectFormatIdentifier rather than Object format.

Fix bug in updateSystemMetadataFields() where guid is set from the wrong parameter in the prepared SQL statement.

remove ORE mapping from system metadata

include obsoletes and obsoletedBy for system metadata
repurpose the "provenance" table as the ORE mapping table for system metadata

use correct enum method

use new "v1" types from DataONE

use objectFormatIdentifier for listObjects()
remove provisional system metadata indicator - Metacat will not implement reserveIdentifier()

Reverting the resultset order in querySystemMetadata(). Thanks Ben.

Because of the new 'provisional' column, the resultset field order in querySystemMetadata() was out of order. Changed the order to reflect the new table column order.

allow very minimal system metadata for provisional entries (CN.reserveIdentifier)

handle null values from DB better when querying system metadata

Fixed problems in IdentifierManager asSystemMetadata(), getSystemMetadata(), and querySystemMetadata() that were using ObjectFormat.toString() rather than ObjectFormat.getFmtid().getValue(). Metacat was storing the string memory pointer rather than the actual format string in the systemmetadata table.

do not delete if the sysmeta doesn't exist

allow for provisional SystemMetadata records (provisional=true)