Metacat

11/01/2013

12:31 PM Bug #6193 (In Progress): obsoleted versions of objects show up in KNB theme

Tested on dev2 and it works as expected:
original:
http://dev2.nceas.ucsb.edu/metacat/d1/mn/v1/meta/knb.438.1
pu... ben leinfelder

12:05 PM Bug #6193: obsoleted versions of objects show up in KNB theme

Corrected my comments (was reading too fast this morning) - yes, the MN.update() call should be updating the obsolete... ben leinfelder

10:33 AM Bug #6193: obsoleted versions of objects show up in KNB theme

That's not what I am seeing. Did you change something manually?
The sysmeta for the new DOI: https://knb.ecoinfor... Matt Jones

07:29 AM Bug #6193: obsoleted versions of objects show up in KNB theme

This is not a UI issue, the SM.obsoletedBy field is null for 'solson.11.6'. This was supposed to be fixed by https://... ben leinfelder

08:23 AM Bug #4690 (Closed): register-dataset.cgi should have its permissions set

Now using runtime exec to do a chmod +x on the *.cgi files during the main configuration. ben leinfelder

07:57 AM Bug #4690: register-dataset.cgi should have its permissions set

Can do this on *nix deployments. ben leinfelder

07:34 AM Feature #6196 (Rejected): ORE documents should be generated for new EML records from the Metacat API

This behavior was added in v2.2.0. https://projects.ecoinformatics.org/ecoinfo/issues/6061 ben leinfelder

12:16 AM Feature #6196 (Rejected): ORE documents should be generated for new EML records from the Metacat API

Currently, if a metadata document is uploaded via the Metacat API (action=insert or action=update), it does not conta... Matt Jones

10/31/2013

11:59 PM Bug #6194 (Closed): publish service does not create an ORE document

When the 'publish' service is called from the GUI in MetacatUI, it should generate an OAI-ORE package so that the lin... Matt Jones

11:53 PM Bug #6193 (Closed): obsoleted versions of objects show up in KNB theme

From the MetacatUI page for solson.11.6, I logged in and used the Publish button to generate the DOI doi:10.5063/F1QN... Matt Jones

04:48 PM Bug #6191 (Closed): Wrap ldapweb.cgi links from register-data.cgi metacatui template in div

ben leinfelder

01:46 PM Bug #6183: CNodeService API calls don't honor authoritative MN certificates

This method will be applied to both the CN and MN methods. Jing Tao

09:41 AM Feature #6099 (Closed): Remove temporary LDAP accounts after X amount of time has passed

Now removing expired user accounts in the dc=tmp subtree. This is done whenever someone tries to register an account ... ben leinfelder

10/30/2013

05:22 PM Bug #6185 (New): Chinese characters are sorted before alphanumeric characters

Not sure if this is a MetacatUI or Metacat bug?
It may be technically correct, but it is not very user friendly to... Lauren Walker

03:25 PM Bug #6183 (Resolved): CNodeService API calls don't honor authoritative MN certificates

In working with Mark Reyes on calling CN.archive() and CN.setObsoletedBy() calls for the Merritt repository, he repor... Chris Jones

10:50 AM Bug #3218 (Closed): nceas skin front page has font size differences

Matt Jones

10:45 AM Bug #213 (New): transaction support for packages

Need to decide if this transaction feature is useful or not, and if not then delete this request. We have operated f... Matt Jones

10:44 AM Feature #6109 (Closed): Keep the SOLR index for obsoleted objects

Now, the solr index has the same behavior of the cn: remove the index for archived objects; keep the index for obsol... Jing Tao

10:42 AM Bug #1366 (Rejected): Changes in review entry page

Rejecting this bug report because it is no longer relevant bcse we aren;t supporting review entry any longer, plus it... Matt Jones

10:39 AM Bug #433 (Closed): browse interface to metacat

Closing as no longer relevant with the new MetacatUI theme work. Matt Jones

10:22 AM Feature #6099 (In Progress): Remove temporary LDAP accounts after X amount of time has passed

Trying a dry-run of this on dev2. Using 36 hour expiration for now - configurable in metacat.properties on a per-orga... ben leinfelder

08:49 AM Story #6114 (Closed): Include updated D1 indexing library

I believe this is complete. ben leinfelder

10/29/2013

07:38 AM Feature #6109 (Rejected): Keep the SOLR index for obsoleted objects

I believe we decided to keep this as is: removing archived objects from the index, but keeping the entries that have ... ben leinfelder

10/28/2013

11:01 AM Feature #6109: Keep the SOLR index for obsoleted objects

Note: we only removed the solr index for the archived objects. Jing Tao

10:56 AM Feature #6109 (In Progress): Keep the SOLR index for obsoleted objects

Currently, the solr index will keep both obsoleted and archived objects. The cn only keeps obsoleted objects but remo... Jing Tao

10/18/2013

04:01 PM Bug #6161 (Closed): Add access_log indexes to support DataONE log retrieval

These are in the trunk now. For large repositories, it may be necessary to increase postgres configuration values so ... ben leinfelder

12:14 PM Bug #6161 (Closed): Add access_log indexes to support DataONE log retrieval

ben leinfelder

10/17/2013

04:04 PM Bug #6123: Rework on the IndexGenerator class in the metacat-index module

I am thinking of the issues about moving the class to Metacat:
This class is a backup plan. If we move it to Metac... Jing Tao

01:43 PM Bug #6157 (Resolved): Couldn't control the log level in solr

It turned out that the solr-core.jar and other solr jar files are using the slf4j logging mechanism. It comes with tw... Jing Tao

01:36 PM Bug #6157 (Resolved): Couldn't control the log level in solr

Our current log control didn't work with the log from solr. It has the default value - INFO. The log message was very... Jing Tao

10/16/2013

05:24 PM Bug #6154 (Resolved): The metacat configuration showed that it was done even though the dataONE configuration hadn't been touched

Add a new class DataONEConfigUtil. It has a method to determine if the configuration for DataONE is done or not.
Thi... Jing Tao

05:23 PM Bug #6154 (Resolved): The metacat configuration showed that it was done even though the dataONE configuration hadn't been touched

It seems the configuration ignore the dataONE part. Jing Tao

10/15/2013

10:34 AM Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch

ben leinfelder

10:31 AM Bug #6141 (In Progress): Permission denied to update/publish metadata for group member on Gulfwatch

In the branch - being included in 2.2.1 patch for MN and CNs ben leinfelder

08:36 AM Bug #6141: Permission denied to update/publish metadata for group member on Gulfwatch

Yes, she was logged in fully. I was tailing the logs and watched her log in, and could see the entry scroll by. Als... Matt Jones

06:47 AM Bug #6141: Permission denied to update/publish metadata for group member on Gulfwatch

My first guess is that there is something not quite right with the login/session since the error message only mention... ben leinfelder

10:34 AM Bug #6136 (Closed): files left open causes too many file descriptors on OS

ben leinfelder

10:33 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context

This is in the 2.2 branch. ben leinfelder

06:47 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context

This should be included in the upcoming patch release. ben leinfelder

10:31 AM Bug #6138 (Closed): Metacat-index assumes default "knb" context

ben leinfelder

10/11/2013

05:39 PM Bug #6142 (Resolved): Metacat.property guid.ezid.unitemplate.metadata includes context

This has been changed to just be the hostname only.
The metacat.properties file on the Gulfwatch server is also ... Lauren Walker

05:36 PM Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch

Sarah Clark was unable to publish metadata on Gulfwatch even though she is a member of the evos group which has permi... Lauren Walker

10/10/2013

12:43 PM Bug #6136: files left open causes too many file descriptors on OS

A brief overview of how I was inspecting memory, threads, file descriptors, etc. while stress testing Metacat. This ... Matt Jones

12:12 PM Bug #6138 (Closed): Metacat-index assumes default "knb" context

ben leinfelder

09:39 AM Task #6040: Metacat-index does not handle <references>

Even with a SAX parser, the implementation could keep track of all elements with "id" attributes and anytime a "refer... ben leinfelder

09:36 AM Task #6040: Metacat-index does not handle <references>

Skye said that the sax parser is used to parse those information. This change may require to use DOM parser. It is a... Jing Tao

09:37 AM Bug #6137 (Resolved): Add a new action reindexall to reindex all the solr index

Just leave as it is. Jing Tao

09:33 AM Task #6110 (Resolved): Use a new schema of dataone solr index so that the author last name can be sortable

Skype released a "buildout" component DATAONE-CN-INDEX_v1.2.1. It only has the schema change. Now our schema is using... Jing Tao

10/09/2013

11:57 PM Bug #6136: files left open causes too many file descriptors on OS

Checked all instances of FileInputReader and ensured that close() was being called properly. See commit r8304.
Matt Jones

03:05 PM Bug #6136: files left open causes too many file descriptors on OS

After looking into this, its not just file handles that are left open, but many InputStream and OutputStream instance... Matt Jones

01:53 PM Bug #6136: files left open causes too many file descriptors on OS

Switched to using IOUtils.closeQuietly() which handles nulls and already closed file handles in r8299. Matt Jones

01:28 PM Bug #6136: files left open causes too many file descriptors on OS

Also added a close() to the finally block in DocumentImpl.readFromFileSystem() in r8298. This is probably not causin... Matt Jones

01:05 PM Bug #6136: files left open causes too many file descriptors on OS

Closed file handles in DocumentImpl and ReplicationService in commit r8297. Matt Jones

01:03 PM Bug #6136 (Closed): files left open causes too many file descriptors on OS

Metacat writes temp files to disk, and in the process has been failing to close file handles. Over time, especially ... Matt Jones

10:03 PM Bug #6137: Add a new action reindexall to reindex all the solr index

I read this message after i committed the change :)
I still think we should give an expensive process a dedicated ... Jing Tao

04:52 PM Bug #6137: Add a new action reindexall to reindex all the solr index

I think this would be redundant and it would be better to just leave it as is, and have administrators use care. The... Matt Jones

04:14 PM Bug #6137 (Resolved): Add a new action reindexall to reindex all the solr index

Currently we have an action named reindex. If the action has a parameter pid, it will reindex the solr index of the s... Jing Tao

04:02 PM Story #6114: Include updated D1 indexing library

After changing the version depency on the metacat-index pom.xml and some code change, the new version works.
Ther... Jing Tao

03:27 PM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable

Won't this be included in the next (1.2.1) release of the library as well? Could just wait for that if it is coming u... ben leinfelder

03:23 PM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable

After adopting the d1_cn_index_processor 1.2.0, the authorSurNameSort field is sortable. But it doesn't work very wel... Jing Tao

03:20 PM Feature #6109 (Resolved): Keep the SOLR index for obsoleted objects

Removed the code which excluded the obsoleted objects from indexing. Next release, we need to notice the metacat owne... Jing Tao

03:17 PM Bug #6122 (Resolved): Metacat-index can't index taxon information

Adopted d1_cn_index_processor 1.2.0 into metacat. The new version processor can index taxon information. Jing Tao

10/07/2013

04:09 PM Story #6128 (Closed): Wait for MetacatUI 1.1.0 release

Using MetacatUI 1.1.0 tag.
https://github.com/NCEAS/metacatui/tree/METACATUI_1_1_0 ben leinfelder

10/04/2013

05:32 PM Story #6128 (Closed): Wait for MetacatUI 1.1.0 release

ben leinfelder

11:39 AM Bug #6123 (Rejected): Rework on the IndexGenerator class in the metacat-index module

The IndexGenerator class has two purpose - first, to create the solr index for all data objects for a Metacat which i... Jing Tao

11:20 AM Bug #6122: Metacat-index can't index taxon information

This will be fixed by adopting d1_cn_index_processor 1.2 in the 2.2.1 release. Jing Tao

10/03/2013

09:54 PM Bug #6117 (Resolved): Reindexing (action=reindex) only works once

I installed a metacat from the 2.2.0 branch. It works very well for the reindex action.
I also deleted the solr in... Jing Tao

12:46 PM Bug #6117 (In Progress): Reindexing (action=reindex) only works once

Added code to remove from the queue when responding to the add event. Testing now. ben leinfelder

12:39 PM Bug #6117 (Resolved): Reindexing (action=reindex) only works once

ben leinfelder

05:47 PM Bug #6122: Metacat-index can't index taxon information

I committed those files to the trunk and it works. I haven't committed to the 2.2.0 branch. Jing Tao

05:46 PM Bug #6122 (Resolved): Metacat-index can't index taxon information

With the help of Skye, we patched 5 files: application-context-eml-base.xml, application-context-eml201.xml, applicat... Jing Tao

12:17 PM Task #6040: Metacat-index does not handle <references>

Spaces aren't really sufficient as a solution, and there are a lot of references fields in EML. We probably need to ... Matt Jones

12:01 PM Task #6040: Metacat-index does not handle <references>

This is included in the 1.2.0 d1 index release. It will not include || but instead will use blanks. Not a very great ... ben leinfelder

11:07 AM Task #6040: Metacat-index does not handle <references>

Apparently this is fixed in cn-index-processor v1.2.0 -- so we will need to pull in this newer dependency in metacat-... ben leinfelder

11:59 AM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable

This is included in the v1.2.0 release of d1 indexing -- called "authorSurNameSort"
Schema:
https://repository.da... ben leinfelder

11:47 AM Feature #6031 (Rejected): Add rendered metadata to Bagit package contents

Duplicate of 6053 ben leinfelder