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From 10/02/2013 to 10/31/2013

11/01/2013

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

10/31/2013

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
01:07 PM Revision 8360 (metacat): Add the methond named isAuthoritativeMNodeAdmin method. It applies to both CN and MN methods.
Jing Tao
09:57 AM Revision 8359 (metacat): include href on the captcha link so that it shows as a pointer -- but doesn't navigate anywhere.
ben leinfelder
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
09:34 AM Revision 8358 (metacat): include perl DateTime module in registry install instructions. https://projects.ecoinformatics.org/ecoinfo/issues/6099
ben leinfelder
09:31 AM Revision 8357 (metacat): actually remove the entry if it is expired (uncomment the function call). https://projects.ecoinformatics.org/ecoinfo/issues/6099
ben leinfelder
08:02 AM Revision 8356 (metacat): 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
ben leinfelder
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

10/30/2013

03:37 PM Revision 8355 (metacat): On calls to archive(), log the correct call (not delete()).
Chris Jones
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
12:23 PM Revision 8354 (metacat): correct some syntax errors, date filter formatting. https://projects.ecoinformatics.org/ecoinfo/issues/6099
ben leinfelder
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
10:37 AM Revision 8353 (metacat): Renamed the test class.
Jing Tao
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
10:19 AM Revision 8352 (metacat): Rename the IndexGenerator to IndexGeneratorTimerTask.
Jing Tao
10:16 AM Revision 8351 (metacat): clear temporary accounts that have not been activated after a configurable number of hours. https://projects.ecoinformatics.org/ecoinfo/issues/6099
ben leinfelder
08:49 AM Story #6114 (Closed): Include updated D1 indexing library
I believe this is complete. ben leinfelder
08:47 AM Revision 8350 (metacat): change method name from copy and paste.
ben leinfelder
07:02 AM Revision 8349 (metacat): add more details about 2.3.0 features in the README
ben leinfelder

10/29/2013

03:48 PM Revision 8348 (metacat): do not include default organization for the metacatui "skin"
ben leinfelder
11:51 AM Revision 8347 (metacat): do not include admin moderator for registry entries by default.
ben leinfelder
11:14 AM Revision 8346 (metacat): show the Organization input field now that we will use keywords for the working group.
ben leinfelder
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
08:21 PM Revision 8345 (metacat): Fixed a bug that when a data file was archived, the solr index for the metadata object still kept the "documents" element.
Jing Tao
05:49 PM Revision 8344 (metacat): made the delete method synchronized.
Jing Tao

10/28/2013

04:54 PM Revision 8343 (metacat): If an object was archived, the solr index will be removed for it.
Jing Tao
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

10/26/2013

05:22 PM Revision 8342 (metacat): Create a utility target to generate a war file which manage ldap accounts - register, password set.
Jing Tao

10/24/2013

02:03 PM Revision 8341 (metacat): Make UI include the Organization (called "site" in the form params) instead of the registry code. https://projects.ecoinformatics.org/ecoinfo/issues/6162
ben leinfelder

10/21/2013

02:01 PM Revision 8340 (metacat): Adding theme configuration screenshot to docs
Lauren Walker
01:56 PM Revision 8339 (metacat): use 2.3.0 for this next release of metacat.
ben leinfelder
12:56 PM Revision 8337 (metacat): correct rst formatting.
ben leinfelder
12:44 PM Revision 8336 (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.
ben leinfelder

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
12:16 PM Revision 8335 (metacat): add 2 indexes to speed up dataONE log retrieval. https://projects.ecoinformatics.org/ecoinfo/issues/6161
ben leinfelder
09:38 AM Revision 8334 (metacat): Added Lauren to contributors list in the metacat guide, and made the two lists match in sort order.
Matt Jones

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
01:33 PM Revision 8333 (metacat): 1.Remved the dependency on solr-core since the metacat-common alreay has the dependency.
2.Excluded the slf4j-log jar files since we are using slf4j-log4j jar file. Jing Tao
12:26 PM Revision 8332 (metacat): Use the slf4j-log4j jar to replace slf4j-jdk one.
Jing Tao
05:27 PM Revision 8328 (metacat): Change the version to 2.2.2
Jing Tao
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
05:19 PM Revision 8327 (metacat): Fixed a bug that the configuration page shows complete even though the DataONE configuration hadn't done yet.
Jing Tao
05:18 PM Revision 8326 (metacat): Add a util class for dataone configuration.
Jing Tao
05:17 PM Revision 8325 (metacat): Change the button from Cancel to Bypass. So it is consistent with the Geoserver configuration page.
Jing Tao

10/16/2013

04:31 PM Revision 8324 (metacat): Add a jsp file to display the schema modification exception.
Jing Tao
04:29 PM Revision 8323 (metacat): Add code the display the SchemaModification exception.
Jing Tao
08:46 PM Revision 8321 (metacat): Fixed a catch clause syntax which is only compatible with java 1.7.
Jing Tao

10/15/2013

03:39 PM Revision 8320 (metacat): Add code the overwrite the schema.xml in the solr-home/conf.
Jing Tao
03:37 PM Revision 8319 (metacat): Add two scripts to update the db to 2.2.2
Jing Tao
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

10/14/2013

03:22 PM Revision 8314 (metacat): Fixed a bug that the group information couldn't be retrived from the session.
Jing Tao

10/12/2013

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

10/11/2013

04:35 PM Revision 8313 (metacat): Change the guid.ezid.uritemplate.metadata property value to the hostname only, with no context
Lauren Walker
02:57 PM Revision 8312 (metacat): Add properties to keep the hash values for the schema.xml of the solr.
Jing Tao
02:42 PM Revision 8311 (metacat): Fixed compile error that an ioexception should be caught.
Jing Tao
11:07 AM Revision 8310 (metacat): Use the setting from the metacat-common component.
Jing Tao
11:06 AM Revision 8309 (metacat): Some settings will be shared between metacat and metacat-index components.
Jing Tao

10/10/2013

01:01 PM Revision 8307 (metacat): prep project for 2.2.1 patch release -- will also merge to the 2.2.x branch.
ben leinfelder
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
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
12:27 PM Revision 8306 (metacat): correctly configure metacat-index to use metacat context/deployment location. https://projects.ecoinformatics.org/ecoinfo/issues/6138
ben leinfelder
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
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
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
09:20 AM Revision 8305 (metacat): Change the svn location of the schema.xml file to d1_cn_index_processor 1.2.1. The 1.2.1 release is a "buildout" release. There was no code change.
Skye change the attribute "stored" to be true for the authorSurNameSort and authorGivenNameSort. Otherwise the sortin... Jing Tao
11:52 PM Revision 8304 (metacat): 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.
Matt Jones
08:53 PM Revision 8303 (metacat): Sparate the action reindex and reindexall.
Jing Tao
05:49 PM Revision 8302 (metacat): The checked-out schema.xml will overwrite the one in src/main/resource/solr-home/conf.
Jing Tao

10/09/2013

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
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
02:42 PM Revision 8301 (metacat): 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.
Matt Jones
01:52 PM Revision 8300 (metacat): Adding build files to ignore.
Matt Jones
01:47 PM Revision 8299 (metacat): Refactor to use IOUtils.closeQuietly() which handles nulls and streams that are already closed.
Matt Jones
01:26 PM Revision 8298 (metacat): Added close() to finally block for readFromFileSystem() call.
Matt Jones
12:44 PM Revision 8297 (metacat): Closing FileOutputStream handles so that the OS limits on filehandles are not exceeded.
Matt Jones
12:10 PM Revision 8296 (metacat): Use the d1_cn_index_processor 1.2.0 version.
Jing Tao
12:09 PM Revision 8295 (metacat): Remove those files. They will be get from the d1_cn_index_processor 1.2.0 jar.
Jing Tao
12:07 PM Revision 8294 (metacat): Use the schema for the d1_cn_index_processor 1.2.0
Jing Tao
05:51 PM Revision 8293 (metacat): combine the index code for failed ids and other ids.
Jing Tao

10/08/2013

04:49 PM Revision 8292 (metacat): Clean up the code.
Jing Tao
02:22 PM Revision 8291 (metacat): The IndexGenerator will index the obsoleted data objects as well.
Jing Tao
12:05 PM Revision 8290 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
ben leinfelder
12:04 PM Revision 8289 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
ben leinfelder
11:33 AM Revision 8288 (metacat): Remove the obsoletes chain from the update method in the SolrIndex class.
Jing Tao
05:56 PM Revision 8287 (metacat): When an object is archvied, the solr index will not be removed.
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

10/05/2013

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

10/04/2013

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
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
09:26 AM Revision 8283 (metacat): merge from 2.2 branch: remove the index queue item when it is being processed. https://projects.ecoinformatics.org/ecoinfo/issues/6117
ben leinfelder
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
05:38 PM Revision 8282 (metacat): Add a patch for d1_cn_index_processor 1.1.2 version. So it can index taxon information.
Those files will overwrite the ones in the d1_cn_index_process-1.1.2.jar. Jing Tao

10/03/2013

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
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
05:55 PM Revision 8279 (metacat): Fixed a bug that the code copied the solr-home to the target directory before it checked out the schema from the dataone svn repository.
Jing Tao

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
11:40 AM Revision 8272 (metacat): minor edits to the UI theme section. https://projects.ecoinformatics.org/ecoinfo/issues/6067
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
 

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