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From 09/12/2013 to 10/11/2013

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

10/02/2013

11:41 AM Story #6062 (Closed): Deprecate skin configuration
ben leinfelder
11:40 AM Task #6067 (Closed): Update documentation to reflect the new metacatui theme mechanism
ben leinfelder
11:36 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
move it to 2.2.1 Jing Tao
10:58 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
I agree to add guidelines for users. Jing Tao
10:55 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
While we do allow someone to create an account with special characters as the password, I am unable to login using th... ben leinfelder
11:12 AM Story #6063 (Closed): ldapweb.cgi enhancements
ben leinfelder
10:50 AM Task #6113 (Resolved): Getting "Bad header" error when similar accounts are present
the new installation fixed the issue. Jing Tao
10:24 AM Task #6115 (Resolved): ldapweb.cgi - default configuration should use o=unaffiliated
I change the configuration in the metacat.properties and nceas.properties. The default value now is unaffiliated. Jing Tao
09:48 AM Task #6115 (Resolved): ldapweb.cgi - default configuration should use o=unaffiliated
We are not yet ready to use ou=Account by default in our ldapweb skin configurations. ben leinfelder
09:46 AM Bug #6086 (Closed): publish service call fails to authenticate properly
ben leinfelder
09:23 AM Story #6114 (Closed): Include updated D1 indexing library
ben leinfelder

10/01/2013

05:59 PM Task #6113: Getting "Bad header" error when similar accounts are present
i installed a new metacat with the trunk code. The ldap server points to ldap-dev. It works great with similar accou... Jing Tao
05:08 PM Task #6113 (Resolved): Getting "Bad header" error when similar accounts are present
WHen I try to register with an account that has similar info as an existing one (email, last name etc) on dev2.nceas.... ben leinfelder
04:59 PM Task #6096 (Closed): Add reCaptcha library instructions to admin docs
Added to the registry installation section. ben leinfelder
04:22 PM Task #6110 (Resolved): Use a new schema of dataone solr index so that the author last name can be sortable
Ben said skye developed a new schema of the dataone solr index so that the author last name can be sortable. We need ... Jing Tao
04:09 PM Feature #6109 (Closed): Keep the SOLR index for obsoleted objects
Currently, metacat only keeps the solr index for the current objects. The solr index for the obsoleted objects are re... Jing Tao
01:27 PM Feature #6107 (Rejected): Make publication year in search results less prominent
Should have put this in MetacatUI project Lauren Walker

09/30/2013

02:25 PM Feature #6107 (Rejected): Make publication year in search results less prominent
Move to the end of the citation line and preface with "Published:" Lauren Walker

09/24/2013

04:34 PM Bug #6101 (Closed): MN.update() fails but modifies revision chain
Moved the call "existingSysMeta.setObsoletedBy(newPid);" to after the insert/update in Metacat is called.
ben leinfelder
04:09 PM Bug #6101 (Closed): MN.update() fails but modifies revision chain
Hello Ben, Chris,

I was trying to update two data and metadata files for some old subtidal data today and ran int...
ben leinfelder

09/23/2013

04:36 PM Story #6082 (Closed): Rename knb.war to ???.war
Using metacat.war now. ben leinfelder
04:35 PM Task #6087 (Closed): Change all default configurations to use new context
ben leinfelder
04:34 PM Task #6088 (Closed): Update documentation to use new context name
ben leinfelder
01:21 PM Bug #6100 (Closed): Metacat search does not work for Chinese characters
Now forcing UTF-8 if the request does not specify and encoding. ben leinfelder
10:33 AM Bug #6100 (Closed): Metacat search does not work for Chinese characters
Hi Ben,
We found there is a searching problem on Metacat Home page. We can search Chinese characters correctly on ...
ben leinfelder
12:03 PM Task #6067 (Feedback): Update documentation to reflect the new metacatui theme mechanism
Lauren Walker
11:51 AM Feature #6080 (Closed): Update Metacat admin screen using cues from the new default look and feel
Went through a review and it looks complete. Lauren Walker
11:50 AM Bug #6094 (Closed): Replace all screenshot images in the documentation with screenshots of the new documentation style
Added new screenshot images. Lauren Walker
10:30 AM Task #6066 (Closed): Add email verification for new accounts
I made the activation link accessible via a configured #external url in the metacatui.properties file. This let's us ... ben leinfelder

09/20/2013

11:20 AM Task #6066 (In Progress): Add email verification for new accounts
This working great - only issue is that using the metacatui cfg we get an un-styled "Activation Successful!" page. Th... ben leinfelder
11:06 AM Task #6065 (Closed): Add reCaptcha widget to initial registration page
ben leinfelder
10:59 AM Task #6098 (Closed): Make reCaptcha work with AJAX include
Works as expected now. ben leinfelder
08:33 AM Task #6098: Make reCaptcha work with AJAX include
This is now rendering on dev2. I did not know the private key for our recaptcha config, so it needs to be tested when... ben leinfelder
07:50 AM Task #6098: Make reCaptcha work with AJAX include
I included the ajax-style of recaptcha, but need to verify that it works. Jing - do you foresee any issues with using... ben leinfelder
07:45 AM Task #6098 (Closed): Make reCaptcha work with AJAX include
Instead of having the perl code generate the catcha content, the template can include the ajax-style of constructing ... ben leinfelder
10:47 AM Feature #6099 (Closed): Remove temporary LDAP accounts after X amount of time has passed
Users are added to a temporary LDAP tree until they activate their account via email. We should remove these accounts... ben leinfelder
10:44 AM Task #3306 (Closed): NCEAS skin account creation needs more thought
We've now made the text more generic so that the LDAP account creation feature can be used in multiple contexts and i... ben leinfelder
10:40 AM Task #2635 (Closed): Look up for forgotten KNB account names
This is working nicely. ben leinfelder

09/19/2013

12:38 PM Task #6096 (Closed): Add reCaptcha library instructions to admin docs
THis is a new dependency and should be documented in the registry install docs. ben leinfelder
11:39 AM Story #6082: Rename knb.war to ???.war
[11:34am] matt: ben: the more I think about it, I still think we should go with metacat.war, despite the duplicate pa... ben leinfelder

09/18/2013

03:50 PM Task #6095 (Closed): Pull metacatui from specific tag
added to build, but still pointing to 'master' for the time being. ben leinfelder
03:17 PM Task #6095 (Closed): Pull metacatui from specific tag
Right now it is pulling the HEAD for the build. Should pull a specific tag. ben leinfelder
09:04 AM Bug #6094 (Closed): Replace all screenshot images in the documentation with screenshots of the new documentation style
Lauren Walker

09/17/2013

04:19 PM Feature #6080 (Feedback): Update Metacat admin screen using cues from the new default look and feel
"wow" factor has been upped. :)
Pulled in more styling from the metacatUI default theme so the config pages have a...
Lauren Walker
10:40 AM Feature #6080 (In Progress): Update Metacat admin screen using cues from the new default look and feel
Via Ben, I'm upping the 'wow' factor Lauren Walker
09:35 AM Feature #6092 (Closed): Science Metadata DOIs should point to "view" landing page
Added two optional entries in metacat.properties for including a template for the view landing page:... ben leinfelder

09/16/2013

04:34 PM Bug #6086 (Feedback): publish service call fails to authenticate properly
Now requiring authentication (session) to generate an identifier. Not reserving it with the CN at this point. ben leinfelder
03:49 PM Bug #6086: publish service call fails to authenticate properly
Added the dataone.subject to the list of metacat admins. This identity will enjoy the perks of being an admin when ac... ben leinfelder
02:34 PM Bug #6086: publish service call fails to authenticate properly
Part of the issue was not running under SSL. Fixing that, the correct update() command would be:... Matt Jones
01:42 PM Feature #6080 (Closed): Update Metacat admin screen using cues from the new default look and feel
Configuration pages have new CSS and the HTML was updated a bit so it now fits in with the default metacatUI theme. Lauren Walker
11:14 AM Feature #6092 (Closed): Science Metadata DOIs should point to "view" landing page
We'll use a configurable template for the URI in metacat.properties that will allow us flexibility in determining wha... ben leinfelder

09/13/2013

03:58 PM Bug #6061 (Closed): Ensure that all packages from metacat API have resource map
Now generating OREs when Metacat API is used to insert science metadata.
Also added a better check for existing OR...
ben leinfelder

09/12/2013

11:25 AM Feature #6075 (Closed): Modify Metacat admin documentation so that it uses the chosen theme in the browser
It won't be possible to view the docs in a theme before configuration, so I created a new Sphinx theme to mirror the ... Lauren Walker
10:48 AM Feature #6089 (Closed): Remove index_event record when reindex is successful
Now calling the event log remove() method for all successful reindex attempts. ben leinfelder
10:43 AM Feature #6089 (In Progress): Remove index_event record when reindex is successful
I think this will be useful, especially for cases like what Mike Frenock is experiencing - manually reindexing items ... ben leinfelder
 

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