Metacat

actually remove the entry if it is expired (uncomment the function call). https://projects.ecoinformatics.org/ecoinfo/issues/6099

correct the createTimestamp filter and search base -- only remove inetOrgPerson entries, not any underlying structure that was added to store these temporary accounts. https://projects.ecoinformatics.org/ecoinfo/issues/6099

On calls to archive(), log the correct call (not delete()).

correct some syntax errors, date filter formatting. https://projects.ecoinformatics.org/ecoinfo/issues/6099

clear temporary accounts that have not been activated after a configurable number of hours. https://projects.ecoinformatics.org/ecoinfo/issues/6099

change method name from copy and paste.

do not include default organization for the metacatui "skin"

use 2.3.0 for this next release of metacat.

make sure all versions are using 2.2.2 of some sort -- thinking of making this release a 2.3.0 release because we will be branching/tagging from the trunk, not the 2.2.x branch.

add 2 indexes to speed up dataONE log retrieval. https://projects.ecoinformatics.org/ecoinfo/issues/6161

Fixed a bug that the configuration page shows complete even though the DataONE configuration hadn't done yet.

Add a util class for dataone configuration.

Add code the display the SchemaModification exception.

Fixed a catch clause syntax which is only compatible with java 1.7.

Add code the overwrite the schema.xml in the solr-home/conf.

Add two scripts to update the db to 2.2.2

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

Change the guid.ezid.uritemplate.metadata property value to the hostname only, with no context

prep project for 2.2.1 patch release -- will also merge to the 2.2.x branch.

correctly configure metacat-index to use metacat context/deployment location. https://projects.ecoinformatics.org/ecoinfo/issues/6138

Reviewed code for all uses of FileInputStream, checking to see if the method should be closing the stream, and if so, closing it in the method as well as in the finally clause to ensure we don't leak file descriptors.

Sparate the action reindex and reindexall.

Closing some more streams that were left open. This Bug #6136 seems to be pervasive and is going to require an extensive audit to find all of the places where streams are not closed properly.

Adding build files to ignore.

Refactor to use IOUtils.closeQuietly() which handles nulls and streams that are already closed.

Added close() to finally block for readFromFileSystem() call.

Closing FileOutputStream handles so that the OS limits on filehandles are not exceeded.

add sample SSLCertificateChainFile directive to DataONE section.

Add code to delete existing records for a id when we try to add the id to the index_event table.

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

Refer to metacat.war deployments since those are now the default. https://projects.ecoinformatics.org/ecoinfo/issues/6082

use UTF-8 if request encoding not given. https://projects.ecoinformatics.org/ecoinfo/issues/6100

Remove an extra print content type statement.

Add a print statment for "content type". Otherwise, the html can't show up.

do not email a specific account reset URL so that the emails can be used in multiple UI contexts. https://projects.ecoinformatics.org/ecoinfo/issues/6066

Comment out some extral "contet type".

ensure all emailed links make sense for the UI that initiated them. also format referrals using the same options as the primary accounts (recursive call needed the html parameter). https://projects.ecoinformatics.org/ecoinfo/issues/6066

include optional email.overrideURL property for the account management page to send an email link that will result in a styled response. https://projects.ecoinformatics.org/ecoinfo/issues/6066

use AJAX method of including the captcha. https://projects.ecoinformatics.org/ecoinfo/issues/6098

Remove an extra space in the email message.

Edit some of the instructions for activating an account. https://projects.ecoinformatics.org/ecoinfo/issues/6063

Remove the knb information in the emails.

Add code to handle the looking up names.

prep for 2.2.0 release. include configuration value for metacatui deployment context.

Add a method to lookup users'account for the people who forgot their user name.

Add code to generate dc=tmp. Clean up some code.

Remove a reistriction that it didn't show the similar accounts of "ou=Account" in the user registration.

Use the specific template for the verification.

Fixed a bug that email verificaton doesn't work well on "ou=Account".

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

include the dataone.subject (node admin) in the list of administrators. This allows full administrative access to objects when using certificates+d1 api. https://projects.ecoinformatics.org/ecoinfo/issues/6086

Fixed a bug to split the organization list from a property file.
Fixed a bug to use a wrong object class for the ou.

Pass a organization list to the template.

use optional template for registering DOIs at a given target. https://projects.ecoinformatics.org/ecoinfo/issues/6092

Add code to get organization information from the ldapconfig.

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

First get the email sender from the skin properties. If it is null, get it from the metacat.properties file.

Reword a message for the failed verification.

Generate an ORE when sci metadata is added via the Metacat API.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

Add code to handle the failure of the email server.

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

implement ORE check method to actually query the MN for OREs that reference the given pid.
https://projects.ecoinformatics.org/ecoinfo/issues/6061

Add code to check if password match in the registeration.

Add the new feature for the email verification.

change hazelcast group name to match the current context. https://projects.ecoinformatics.org/ecoinfo/issues/5624

Fixed a bug that the url link was not correct in the email.

Send the verification email.

Add code to add a user to the tmp subtree.

check both previous and current data revisions when updating packages. https://projects.ecoinformatics.org/ecoinfo/issues/5647

Fixed a bug in creating a subtree.

Add code to generate temporary subtree if it didn't exist.

add a new subroutine to create a temporary account.

avoid SQL errors when processing very old objects of type: "-//ecoinformatics.org//eml-access-2.0.0beta6//EN"

Read the recaptcha key from the metacat.properties.

Add the recaptcha protection.

If the pathquery engine is disabled, the xml path index queue will be disabled as well.

If the xpath query is disabled, the query, squery and spatial_query action will be disabled as well.

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

[merge from branch to keep trunk up to date with upgrade history] prep for Metacat 2.1.1 release

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

include user's fullName when validating a session. also, allow cookie session to be used if not passed in directly as a parameter

Add code to modify the web.xml in metacat-index context if the metacat's name is not knb.

include filename in the package download, though we can;t really use the PID because of all the potential characters in it that are not valid for filesystems.

type the doctype="metadata" objects as "FGDC-STD-001-1998" formatId for rendering XSLT and for DataONE SystemMetadata.

use custom FileInputStream subclass to delete the temporary bagit zip when the inputstream is closed (after someone has downloaded the zip).

use ObjectFormatCache instead of ObjectFormatService because we are not calling it as a CN.

allow running the Harvester client without a source code checkout. (D. Blankman comments)

include the localid when rendering the view (used in stylesheets)

use ObjectFormatCache.getInstance().getFormat() instead of the CN service (the MN does not typically act as a CN!)

add slash for harvesterRegistration redirect.

include mn.publish() REST endpoint handling. https://projects.ecoinformatics.org/ecoinfo/issues/6024

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

implement the view service (uses existing skin-based dbtransform) - and include the REST endpoint. https://projects.ecoinformatics.org/ecoinfo/issues/6028

use StreamSource instead of StringReader for method signature -- can be used with different sources this way. https://projects.ecoinformatics.org/ecoinfo/issues/6019

clean up DBTransform in preparation for "view" service. https://projects.ecoinformatics.org/ecoinfo/issues/6019

include GET /package/{pid} endpoint in MN service. https://projects.ecoinformatics.org/ecoinfo/issues/6027

MN.getPackage() - test with ORE that includes 2 data files and a "metadata" file (still should be using EML for that test). https://projects.ecoinformatics.org/ecoinfo/issues/6026

First pass at MN.getPackage() implementation using Bagit library from LOC. https://projects.ecoinformatics.org/ecoinfo/issues/6026

add method for publishing existing object (usually assumed to be scimeta) with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6014