Metacat

More bug tweaks to eml-text.xsl

- Fix use of non-existent HTML5 tag 'emphasis' and use 'em' instead as
intended
- Add target=_default to links

Merge changes from 2.8 branch - added a display of "Role" to the eml-party.xsl stylesheet for Associated Parties

Relax the EML text XSLs rendering of ulinks

This makes all content inside a ulink show up inside the <a> tag in
the output. Before this change, if CDATA was present inside a ulink
element, it would be ignored because the XSL was only extracting the
citetitle's CDATA

Overhaul EML Text XSLT to support everything in the entire module

Major touchup work in ISO XSL

- Fixes numerous bugs involving ISO's bizarre use of nilReasons
- Fixes numerous bugs involving differences between the ISO workbook
and the schema
- Adds support for Polygons

Fix a bug in the eml party xslt

Change the version of metacatui to 1.14.7.

Change back to use URLDecoder to decode the code.

Change the release note for 2.8.5.

Change the metacatui version to 1.14.6.

Change the mime type back to application/xml.

Change the mime type back to application/xml.

Change the mime type of those files.

Change the mime type.

Add the release note for 2.8.5 version.

add the script to upgrade the db to 2.8.5.

Add the script to upgrade the version to 2.8.5

Tidy up ISO stylesheets. This is an set of iterative tweaks both to the
in-file formatting as well as a bit of small tweaks to how things work.

Simplify keyword thesaurus display

Showing the whole thesaurus for every keyword set is way too much info
and is impossible to display with a naive implementation.

Fix bug in abstract handling in ISO XSLT

Before this change, a missing abstract would still show up but just as
an empty box with on content. This should be fixed now.

Add the code to submit index task in every methods which modified the system metadata.

Refactory the submit index methods.

Add the methods submitting the update and delete tasks.

Use the new manager class to get the messaging client.

Use a singleton class to get the messaging client.

Removed the code to initialize the index task client at the constructor.

Add the client code to submit the index task to the message broker. Now I only added the code for the create method.

Add the depency on the component d1_cn_index_common.

Move Additional Info in the EML stylesheet to after the keyword sets

Show the additionalInfo under Data Usage Rights to reflect the additional info collected in the Registry

Change isAuthorized() to prioritize user authz

Re-order the calls to userHasPermission(), isAdminAuthorized(), and isAuthoritativeMNodeAdmin() such that the user authorization comes first. This should drastically reduce the calls to CN.listNodes() and the resulting NodeList unmarsalling involved in comparing CN and MN Node Subjects to token or certificate Subjects. ...

Convert System.out.println() calls

We've had these calls printing to the log on every REST call. Change them to a logger debug() level so we can filter them out.

Use the EncodingUtilities method to decode a string.

Add the view service.

Add the code to handle query and view service.

Add the code to read the MNPackage configuration.

Add the MNPackage configuration.

Remove the duplicated alternate identifier section.

It seemed to have been caused by a branch code merge.

Add support for alternateIdentifier system in EML stylesheet

Fix a bug in the conditional for the EML XSLT for alternateIdentifiers

Add the release note for 2.8.4

Add the script to upgrade db to 2.8.4

Add the script to upgrade the db version to 2.8.4.

Use MetacatUI 1.14.2 release.

In the delete method, if we got not MdcDocNotFound exception, we will continue to delete the system metadata.

Add the code to add the ldap group information for the given user.

Add a new method to get all groups for a given user.

Make a debug statement clearer.

Display the dc:source field from dublin core metadata in the onedcx-common stylesheet

Modified the query to find the previous version of the ore document in the publish method.

Add a new bug was fixed in 2.8.3

Add the release node for 2.8.3

Change the test metacat deployment directory.

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

Make the checksum match during the create method.

Add the code to reget the object input stream after generating the system metadata. Otherwise, the checksum will be wrong.

Exclude the MockReplicationMNode class in the test method.

Add the script to update the version to 2.8.3

Add the script which update the db to 2.8.3.

Add the script to update db.

Add the db upgrade from 2.8.1 to 2.8.2

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

Add tests to test the miss-matched checkup in the update method.

Reget the object inputstream in order to calculate the correct checksum.

Add the checksum as the parameter to the method write.

Add the code to computer the checksum.

Add the checksum parameter to the write method.

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

Add the checksum parameter to the method DocumentImple.write.

Add a method to test the miss-matched checksum for creating a metadata object.

Add a new test method to test the miss-matched checksum for the data object.

Add the checksum as a parameter to the method handleInsertOrUpdate.

Add the checksum parameter to the handleInsertorUpdate method.

Add the checksum parameter to the handleInsertAndUpdate method.

Change the signature of the method handleInsertAndUpdate.

Add code to check the check sum by the DigestOutputStream.

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.

Revised the method for testing replication. It did nothing but does test the replication between the mock mn and the local host.

Add the replication source node into the node locator.

Add some methods to support the replicate.

Add a mock mn node as the source node during a replication operation.

Add a integration test.

Add two properties will be used in the dataone replication test.

Add some debug information.

Change MetacatHandler.generateOutputName() to use the SystemMetadata.fileName value when it is available. Needs testing.

refs https://projects.ecoinformatics.org/ecoinfo/issues/7187

Define location of the AWS binary so the tool works under CRON.

Modified backup script to improve efficiency.

Now, lists of metadata and data files that were last backed up is stored in the /var/metacat/metacat-backup folder, and
these are diffed with the current file lists to discover new files. These are then copied to AWS S3. The AWS...

Add the release note for the 2.8.2 version.

The metacatui version was changed to 1.14.1

Add the code to filter out the pids with white spaces in the query.

Add backup script to copy files to Amazon S3.

Call the method TripleStoreService.destroy to delete the dataset.

Disable indexing of 'prov_hasSources' field

Fix problem with prov_hasSources not being indexed

Add check in iindex unit test for 'prov_hasDerivations' field

Fix problem where 'prov_hasDerivations' field not being indexed (metacat issue 7176)

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.