Metacat

Fixed a bug that the eml object wasn't changed checksum but its content was modified in the publish method.

Add the code to remove the pid from the identifier table if the update method failed.

Add the checksum as a parameter to the method handleInsertOrUpdate.

Removed the duplicated code to check the checksum in the replicate method since the method D1Node.create, which is called by the replicate method, has the mechanism.

Add some debug information.

Make sure it is same as branch 2.8 except the mdq stuff

Still use syncFailed.getPid to get identifier in the syncFailed method.

Fixed typos in the vairable name.

In the synchronizationFailed method, use syncExcpetion.getIdentifier method to try before the obsoleted method getPid.

Trigger MDQ when inserting or updating metadata documents. https://projects.ecoinformatics.org/ecoinfo/issues/7171 and https://github.com/NCEAS/mdqengine/issues/73

Change the calling code when the method insertOrUpdateDocument signature is changed.

Add some performace debug information.

Don't share the same executor in the two classes.

Call the cn.synchronize method asynchronously in the mn.updateSystemmetadata method.

Add some information about pid on the log statement.

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

Use the method getContextURL rather than getSecureContextURL in the getCapacities method.
So if the server doesn't support sll, the getCapacities will return a baseURL with http.

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 changes from the 2.6.0 branch in MNodeService.allowUpdating() so it honors the localhost MN certificate.

refs https://projects.ecoinformatics.org/ecoinfo/issues/7018

Reformat the create and update method.

Close the input stream on the create/update method when the code aborts.

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.

Close the input stream object on the MN.replicate method.

use SM.fileName if we have it. https://projects.ecoinformatics.org/ecoinfo/issues/6970

ensure there is a file extension included for the data files in a package download. https://projects.ecoinformatics.org/ecoinfo/issues/6970

Add code to print the the stack trace on the getPackage method in order to help us to identity some tmp file issues.

Put a detal code on the InvalidRequest exception in the getPackage method.

If the pid it is a package id in the getPackage method, the method will throw an InvalidRequest exception.

set authoritative MN to origin MN if the client did not set it on mn.create. https://projects.ecoinformatics.org/ecoinfo/issues/6938

Use the ServiceFailure to replace the InvalidRequest when it is the read-only mode (CN throws the exception).

In the replicate method, the checking of the read-only mode was moved from MNodeService class to the MNResourceHandler class since it is asynchronized.

The systemmetadataChanged method is asynchronized, so we put the read-only checking on the ResourceHandler class.

Add the code to check if the mn is on the read-only mode.

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

The archived field can't be reset to false if it is true in the systemMetadataChanged method.

In the systemMetadataChanged method, we will update system metadata when the local serial version is less than or equals the comming one.

refs #7453: modified the metacatLog message from mn.synchronizationFailed to include the syncFailed.message field. Also increased the log level to WARN.

Remove the method editScienceMetadata from the update method. This method will add a packageId attribute into the eml document. Lauren will add the method to the publish method.

In the systemMetadataChanged method, the object will be archived if the new archive value is true and old value is false.
The log event is recorded in the systemMetadataChanged method as well.

Make the isAuthoritativeNode throw exception if some value is null.

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.

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

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 some incorrect exceptions in the getReplica method.

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

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

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.

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

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

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

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

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

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

Created the updateSystemMetadata method.

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

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

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 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.

Enforce the sid requirement in the update method.

Enforce the mn.getChecksum only to handle an PID.

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

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

add support for v2 DataONE API.

Include PDF version of the metadata in the package download. https://projects.ecoinformatics.org/ecoinfo/issues/6053

take advantage of the ezidclient for multi-threaded/asynchronous DOI registration. This will be most useful for doing large batch updates and not so much for the one-at-a-time publish actions but works in either context. https://projects.ecoinformatics.org/ecoinfo/issues/6440

correct the ORE lookup query syntax and add junit assertion to check that it continues to function as expected. https://projects.ecoinformatics.org/ecoinfo/issues/6529

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

add comment (and commented out code) for possibly inspecting the /dirtySysMeta call for archive=true flag. https://projects.ecoinformatics.org/ecoinfo/issues/6417

make all objects in a package publicly readable when published. https://projects.ecoinformatics.org/ecoinfo/issues/6415

make all package contents publicly readable when publishing with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6415

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

retrieve the given file names (entityName) of the data files from the EML and use those for our file names in the BagIt content.

Change the BagIt file names to the pid+resource type. Create new Files instead of createTempFile to avoid the randomly generated numbers in the name.

Add the code to set the replication status when some exceptions happen.

generate ORE object when publishing even if there was not an ORE for the original package. https://projects.ecoinformatics.org/ecoinfo/issues/6194

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

do not modify existing SystemMetadata on MN.update() if something goes wrong during content insertion. https://projects.ecoinformatics.org/ecoinfo/issues/6101

require authenticated session when minting a DOI/other identifier. https://projects.ecoinformatics.org/ecoinfo/issues/6086

only attempt to generate OREs for objects that we know not to have them already. https://projects.ecoinformatics.org/ecoinfo/issues/6061

better checking for ORE maps when publishing DOIs (need to update the packages that contain sci meta). https://projects.ecoinformatics.org/ecoinfo/issues/6061

Add code to throw an exception if the pathquery is not enabled.
We also need to disable building index if the pathquery is disabled.

use consistent file names and zip content names. Opted for "-" separator so that the zip writer does not remove the unique part of the filename. https://projects.ecoinformatics.org/ecoinfo/issues/6054

copy the original systemMetadata when publishing a revision in order to avoid overwriting the original values - the shared map is listening! https://projects.ecoinformatics.org/ecoinfo/issues/6014