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
add Metacat servlet action to force the reindexing of one or more or all pids in the system. https://projects.ecoinformatics.org/ecoinfo/issues/5945
only use MapStore/MapLoader for saving/loading IndexEvent objects. No need to use a listener since there is only the single node -- all entries are persisted to DB using the hazelcast.xml config we have for the map. https://projects.ecoinformatics.org/ecoinfo/issues/5944
add MapStore/Loader test for the IndexEvents -- adding and removing events in the DB table through hazelcast. https://projects.ecoinformatics.org/ecoinfo/issues/5944
support a "force replication delete all action" during replication. This is used when we want Metacat to remove the content from the other target replicas because the DataONE delete() action was called (more powerful than just "archive").
add simple test for the IndexEventDAO class -- adding, removing, listing events in the DB table. https://projects.ecoinformatics.org/ecoinfo/issues/5944
merging upgrade scripts from 2.0 branch to trunk. https://redmine.dataone.org/issues/3847
scripts for 2.1.0 upgrade
upgrade to Metacat 2.1.0 on the trunk. This includes a new index_event table for storing indexing events that need to be reprocessed. https://projects.ecoinformatics.org/ecoinfo/issues/5944
stub for storing IndexEvent objects in Metacat (from metacat-index processing). https://projects.ecoinformatics.org/ecoinfo/issues/5944
do not force a get() during refresh (causing EML-defined data access rules to be lost when inserting EML docs about data files). note that this reverses a change that was meant to trigger indexing, but now we are using a new queue to share index events with metacat-index and so should not be necessary.
do not use tmp file to return an inputstream on read() operations - just read from the file we already have. https://projects.ecoinformatics.org/ecoinfo/issues/6009
use standard File.createTempFile() method for uploaded data files and delete them when we are done with them. https://projects.ecoinformatics.org/ecoinfo/issues/6008
correctly delete data file when we are done with it. https://projects.ecoinformatics.org/ecoinfo/issues/6007
include filename in the filepart part. https://projects.ecoinformatics.org/ecoinfo/issues/6007
send the original filename in the upload() method since that is supported by the Metacat API. https://projects.ecoinformatics.org/ecoinfo/issues/6007
remove the unique string when generating data file metadata. https://projects.ecoinformatics.org/ecoinfo/issues/6007