Metacat

Add the timestamp for the printing out the start and end of hazelcast synchronization.

Call the method lock.lock() immediately after getting the lock. Otherwise, if an exception happened between the two calls (in another word, lock.lock() was called), lock.unlock() can cause an issue:
Current thread is not owner of lock!
See https://redmine.dataone.org/issues/6836.

Add a cap to only write 512 characters of the user-agent to db.

Modify v1 and v2 calls to MultipartRequestResolver to use MAX_UPLOAD_SIZE from configuration.

The constrcutor of EventLogData missed the user-agent field. So the user-agent wasn't recorded.
The bug was fixed.

organize imports. move exception-throwing method call into try block.

use HttpMultipartRestClient since the DefaultHttpMultipartRestClient was removed from d1_libclient_java

Updated D1ResourceHandler to not hardcode a file size limit. This will allow
large, multi-gigabyte files to be uploaded, but still needs testing. The limit
is now drawn from the metacat.properties file. An alternative would be to inspect
the Content-Length header of the request and set the max to a value greater than the...

The setReplicationStatus method only supports sid and the setRightsHolder method supports both PID and SID.

Add the code transform a sid to a pid in publish, getPackage and view method. Fefer dataONE #6734.

Fixed a bug that it should use getReplica rather than get method.

Add the option -h for tar command in order to follow the link.

The CN.setReplicationPolicy method now only support PIDs. Refer to https://redmine.dataone.org/issues/6734.

Went through the v2 ObjectFormatList and convert every v2 ObjectFormat to v1 ObjectFormat and put them into a v1 objectFormatList.

Add the log messages to indicate the hazelcast synchronization starting and ending.

Add the code to handle sid in the publish method.

Add the code to exclude the sid in the view and getPackage.

Add a converter to convert the V2 Log object to the V1 Log object.

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.

Add the code to check if the pid is an SID in the registerSystemMetadata method.

Add code to check if the sid equals pid for the method checkSidInRegisterSystemMetadata.

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 check if a sid is legitimate in the method create and registerSystemMetadata.

The the code to handle sids on the v2 api - setReplicationPolicy, setReplicationStatus, setAccessPolicy and setObsoletedBy.

Add the code to handle if a identifier is a sid in setAccessPolicy, setReplicationPolicy, setObsoletedBy and setRreplicationStatus.

Comment out a print of an error message. It will show up for every public request.

Add the code to handle SID in the getLogRecords method.

In the getLogRecords method, the pidFilter is checked if it exists.

In the getLogRecords method, the pidFilter is checked if it exists.

Fixed a bug that the getLogRecords can't handle the case that the event is null.

Fixed a bug that the getLogRecords can't handle the case that the event is null.

Add the code to check the if the new series id is legitimate in the systemMetadataChanged 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.

Fixed a bug in comparing two identifiers in the update method.

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

Add the code the check if the format of the sid is valid in the system metadata.

Add the enforcement for the sid in the create method.

Enforce the sid requirement in the update method.

Check if the identifier is a sid for the v1 update.

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

Enforce the mn.getChecksum only to handle an PID.

Add the series id to the system metadata.

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.

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.

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 a method to check if a serial id exists.

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

add Annotator Store implementation -- pass through to D1 API for the AnnotatorJS API

use 2.5.0 for current DB version

Don't remove postgresql 8.4 and 9.1
Don't remove data directory of postgresql 8.4

include person's full name in the JWT returned from /token

Merge changes in the 2.4 branch into the trunk for the ORNL Mercury schema support. References https://projects.ecoinformatics.org/ecoinfo/issues/6619.

This schema is maintained by Jim Green (jgreen@iiaweb.com) and Ranjeet Devarakonda (devarakondar@ornl.gov). The schema uses a subset of the FGDC 1998 CSDGM elements, along with custom elements specific to the Mercury Metadata web application. Support is included in Metacat for Coordinating Node operations in the DataONE network.

Fixed a bug that the reindex of data objects may index an archived data object.

Fixed a bug that the solr index of data files doesn't reflect the change of access control.

[merge from 2.4 branch] use solr schema upgrader for 2.4.2 release -- need to replace the solr schema to include geohash fields

add 2.4.2 upgrade scripts so they are available in the 2.5.0 release as well

remove AnnotatorService completely - was moved to cn-index-processor

let metacat-index lookup annotations for indexing rather than the metacat "reindex" action.

Add delete log for data objects on CNs.

only index non-empty comment text

index both tags and text from annotateit.org

query by consumerKey until the pid search facets are fully supported on annotateit.org

add JkOptions directive and encoded slash options for dataone and solr query support in the URLs that metacat can get (they were in the -ssl version of this file already)

During the replication, the remote content will be saved without alteration.

allow per-document reindexing to be initiated by any user (to support third-party annotations)

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

look up annotations when reindexing a given pid. still very much a prototype in that we are looking up annotations from an external annotator-store. TODO: add pid filtering to query when annotateit.org supports it (pending upgrade on their site).

add the code to install xmlstarlet.

Find files of which type is link.

Keep /var/lib/postgresql/8.4/main directory.

Add the code to stop tomcat and apache.

Add the "-y" option to force removing the old postgresql without prompting a y/n question.

Restore the database for a gzipped sql file.

Added the code to gzip the output file in the dumpall command. This will save disk space.

Modified the redirect rules which didn't work.

Add the code to add the attribute useHttpOnly='false' to the Context element in the context.xml file.

Fixed a bug the code can get the argument from the command line.

Added the code to change the permission of the backup file so the postgres user can read it.

Added the code to check if the metacat backup file exists.
Added the code "exist 0" at the end of the scripts.

Added the .conf to those site files since the new apache server only loads the sites with the extension.

Add the code to vacuum the db.

Add the code to enable the 8009 port for ajp connection in the server.xml of tomcat7.

Added the code to modify the geo data directory in the metacat.properties file.

Fixed some bugs to restore postgresql data.

Add the code install some components for installing tomcat7

Use a variable to replace the hard code.

Use the version directly.

Fixed a typo.

put the date to an output file.

A script for vacuum the db.

Add a script to move the db from 8.3 to 9.1 base on a dumped file.