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# Date Author Comment
8307 10/10/2013 01:01 PM ben leinfelder

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

8306 10/10/2013 12:27 PM ben leinfelder

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

8304 10/09/2013 11:52 PM Matt Jones

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.

8303 10/09/2013 08:53 PM Jing Tao

Sparate the action reindex and reindexall.

8301 10/09/2013 02:42 PM Matt Jones

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.

8300 10/09/2013 01:52 PM Matt Jones

Adding build files to ignore.

8299 10/09/2013 01:47 PM Matt Jones

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

8298 10/09/2013 01:26 PM Matt Jones

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

8297 10/09/2013 12:44 PM Matt Jones

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

8289 10/08/2013 12:04 PM ben leinfelder

add sample SSLCertificateChainFile directive to DataONE section.

8268 09/27/2013 04:44 PM Jing Tao

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

8267 09/24/2013 04:21 PM ben leinfelder

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

8265 09/23/2013 03:54 PM ben leinfelder

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

8264 09/23/2013 01:20 PM ben leinfelder

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

8262 09/20/2013 04:36 PM Jing Tao

Remove an extra print content type statement.

8261 09/20/2013 03:26 PM Jing Tao

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

8259 09/20/2013 02:42 PM ben leinfelder

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

8258 09/20/2013 01:17 PM Jing Tao

Comment out some extral "contet type".

8254 09/20/2013 12:20 PM ben leinfelder

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

8253 09/20/2013 11:46 AM ben leinfelder

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

8250 09/20/2013 07:48 AM ben leinfelder

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

8248 09/19/2013 05:03 PM Jing Tao

Remove an extra space in the email message.

8239 09/18/2013 03:15 PM ben leinfelder

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

8234 09/18/2013 01:23 PM Jing Tao

Remove the knb information in the emails.

8229 09/17/2013 05:02 PM Jing Tao

Add code to handle the looking up names.

8223 09/17/2013 04:32 PM ben leinfelder

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

8221 09/17/2013 03:22 PM Jing Tao

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

8220 09/17/2013 10:36 AM Jing Tao

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

8217 09/16/2013 09:58 PM Jing Tao

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

8216 09/16/2013 09:45 PM Jing Tao

Use the specific template for the verification.

8211 09/16/2013 05:00 PM Jing Tao

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

8210 09/16/2013 04:33 PM ben leinfelder

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

8208 09/16/2013 03:47 PM ben leinfelder

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

8207 09/16/2013 03:16 PM Jing Tao

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

8206 09/16/2013 02:31 PM Jing Tao

Pass a organization list to the template.

8202 09/16/2013 12:00 PM ben leinfelder

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

8201 09/16/2013 10:32 AM Jing Tao

Add code to get organization information from the ldapconfig.

8200 09/13/2013 03:53 PM ben leinfelder

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

8197 09/13/2013 03:01 PM Jing Tao

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

8194 09/13/2013 01:25 PM Jing Tao

Reword a message for the failed verification.

8193 09/13/2013 11:12 AM ben leinfelder

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

8191 09/12/2013 05:12 PM Jing Tao

Add code to handle the failure of the email server.

8190 09/12/2013 04:50 PM ben leinfelder

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

8189 09/12/2013 01:45 PM ben leinfelder

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

8186 09/11/2013 09:57 PM Jing Tao

Add code to check if password match in the registeration.

8185 09/11/2013 09:36 PM Jing Tao

Add the new feature for the email verification.

8184 09/11/2013 10:59 AM ben leinfelder

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

8182 09/11/2013 09:28 AM Jing Tao

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

8181 09/10/2013 11:03 PM Jing Tao

Send the verification email.

8180 09/10/2013 05:58 PM Jing Tao

Add code to add a user to the tmp subtree.

8178 09/10/2013 03:17 PM ben leinfelder

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

8177 09/10/2013 12:18 PM Jing Tao

Fixed a bug in creating a subtree.

8176 09/10/2013 07:52 AM Jing Tao

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

8175 09/09/2013 05:55 PM Jing Tao

add a new subroutine to create a temporary account.

8173 09/06/2013 02:22 PM ben leinfelder

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

8169 09/06/2013 07:53 AM Jing Tao

Read the recaptcha key from the metacat.properties.

8166 09/05/2013 04:58 PM Jing Tao

Add the recaptcha protection.

8164 08/26/2013 04:30 PM Jing Tao

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

8163 08/26/2013 11:50 AM Jing Tao

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

8162 08/23/2013 04:01 PM Jing Tao

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

8160 08/22/2013 04:04 PM ben leinfelder

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

8146 08/13/2013 04:16 PM ben leinfelder

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

8141 08/13/2013 12:57 PM ben leinfelder

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

8075 07/25/2013 01:16 PM ben leinfelder

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

8074 07/24/2013 06:12 PM Jing Tao

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

8034 07/18/2013 02:49 PM ben leinfelder

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.

8028 07/18/2013 10:53 AM ben leinfelder

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

8026 07/18/2013 08:13 AM ben leinfelder

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

8025 07/18/2013 08:02 AM ben leinfelder

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

8018 07/17/2013 11:35 AM ben leinfelder

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

8014 07/16/2013 04:21 PM ben leinfelder

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

8013 07/16/2013 04:05 PM ben leinfelder

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

7984 07/15/2013 10:56 AM ben leinfelder

add slash for harvesterRegistration redirect.

7864 07/09/2013 10:40 AM ben leinfelder

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

7862 07/08/2013 06:19 PM ben leinfelder

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

7861 07/08/2013 06:10 PM ben leinfelder

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

7860 07/08/2013 05:51 PM ben leinfelder

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

7859 07/08/2013 05:10 PM ben leinfelder

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

7855 07/08/2013 12:14 PM ben leinfelder

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

7853 07/05/2013 06:33 PM ben leinfelder

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

7850 07/04/2013 12:33 PM ben leinfelder

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

7849 07/03/2013 09:58 PM ben leinfelder

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

7843 07/03/2013 10:13 AM ben leinfelder

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

7842 07/03/2013 12:28 AM ben leinfelder

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

7841 07/03/2013 12:03 AM ben leinfelder

add MapStore/Loader test for the IndexEvents -- adding and removing events in the DB table through hazelcast. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7840 07/02/2013 04:47 PM ben leinfelder

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").

7839 07/02/2013 04:41 PM ben leinfelder

add simple test for the IndexEventDAO class -- adding, removing, listing events in the DB table. https://projects.ecoinformatics.org/ecoinfo/issues/5944

7834 06/26/2013 04:43 PM ben leinfelder

merging upgrade scripts from 2.0 branch to trunk. https://redmine.dataone.org/issues/3847

7833 06/26/2013 04:42 PM ben leinfelder

scripts for 2.1.0 upgrade

7830 06/25/2013 04:42 PM ben leinfelder

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

7829 06/25/2013 01:23 PM ben leinfelder

stub for storing IndexEvent objects in Metacat (from metacat-index processing). https://projects.ecoinformatics.org/ecoinfo/issues/5944

7827 06/25/2013 01:17 PM ben leinfelder

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.

7824 06/24/2013 12:05 PM ben leinfelder

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

7823 06/21/2013 09:44 PM ben leinfelder

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

7822 06/21/2013 04:15 PM ben leinfelder

correctly delete data file when we are done with it. https://projects.ecoinformatics.org/ecoinfo/issues/6007

7821 06/21/2013 04:06 PM ben leinfelder

include filename in the filepart part. https://projects.ecoinformatics.org/ecoinfo/issues/6007

7820 06/21/2013 03:18 PM ben leinfelder

send the original filename in the upload() method since that is supported by the Metacat API. https://projects.ecoinformatics.org/ecoinfo/issues/6007

7819 06/21/2013 03:10 PM ben leinfelder

remove the unique string when generating data file metadata. https://projects.ecoinformatics.org/ecoinfo/issues/6007

7818 06/21/2013 02:48 PM ben leinfelder

debugging. https://projects.ecoinformatics.org/ecoinfo/issues/6007

7817 06/21/2013 01:44 PM ben leinfelder

use File::Temp to write data files in registry. https://projects.ecoinformatics.org/ecoinfo/issues/6007