Activity
From 10/07/2013 to 11/05/2013
11/05/2013
- 04:27 PM Revision 8369 (metacat): always return the metacat logout form when calling the perl registry logout action, even when there is no perl session to invalidate -- needed for metacatui.
- 04:25 PM Revision 8368 (metacat): use "Username" in header
- 03:27 PM Revision 8366 (metacat): include update statement for marking newer revisions
- 02:31 PM Revision 8365 (metacat): use UI RC3 tag
- 01:04 PM Revision 8364 (metacat): use RC2 metacatui tag
11/04/2013
- 04:27 PM Bug #6183 (Resolved): CNodeService API calls don't honor authoritative MN certificates
- Implemented the D1NodeService.isAuthoritativeNodeAdmin() method and put them into the appropriate place. The both MN ...
- 02:35 PM Revision 8363 (metacat): use RC1 metacatUI tag
- 01:57 PM Bug #6194 (In Progress): publish service does not create an ORE document
- Will deploy and test this on dev2.
- 01:56 PM Revision 8362 (metacat): generate ORE object when publishing even if there was not an ORE for the original package. https://projects.ecoinformatics.org/ecoinfo/issues/6194
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... - 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...
- 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... - 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://...
- 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.
- 07:57 AM Bug #4690: register-dataset.cgi should have its permissions set
- Can do this on *nix deployments.
- 08:22 AM Revision 8361 (metacat): set registry permissions when configuring the exploded war on *nix systems. https://projects.ecoinformatics.org/ecoinfo/issues/4690
- 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
- 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...
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...
- 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...
- 04:48 PM Bug #6191 (Closed): Wrap ldapweb.cgi links from register-data.cgi metacatui template in div
- 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.
- 01:07 PM Revision 8360 (metacat): Add the methond named isAuthoritativeMNodeAdmin method. It applies to both CN and MN methods.
- 09:57 AM Revision 8359 (metacat): include href on the captcha link so that it shows as a pointer -- but doesn't navigate anywhere.
- 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 ...
- 09:34 AM Revision 8358 (metacat): include perl DateTime module in registry install instructions. https://projects.ecoinformatics.org/ecoinfo/issues/6099
- 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
- 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
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... - 03:37 PM Revision 8355 (metacat): On calls to archive(), log the correct call (not delete()).
- 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...
- 12:23 PM Revision 8354 (metacat): correct some syntax errors, date filter formatting. https://projects.ecoinformatics.org/ecoinfo/issues/6099
- 10:50 AM Bug #3218 (Closed): nceas skin front page has font size differences
- 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...
- 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...
- 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...
- 10:39 AM Bug #433 (Closed): browse interface to metacat
- Closing as no longer relevant with the new MetacatUI theme work.
- 10:37 AM Revision 8353 (metacat): Renamed the test class.
- 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...
- 10:19 AM Revision 8352 (metacat): Rename the IndexGenerator to IndexGeneratorTimerTask.
- 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
- 08:49 AM Story #6114 (Closed): Include updated D1 indexing library
- I believe this is complete.
- 08:47 AM Revision 8350 (metacat): change method name from copy and paste.
- 07:02 AM Revision 8349 (metacat): add more details about 2.3.0 features in the README
10/29/2013
- 03:48 PM Revision 8348 (metacat): do not include default organization for the metacatui "skin"
- 11:51 AM Revision 8347 (metacat): do not include admin moderator for registry entries by default.
- 11:14 AM Revision 8346 (metacat): show the Organization input field now that we will use keywords for the working group.
- 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 ...
10/28/2013
- 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.
- 05:49 PM Revision 8344 (metacat): made the delete method synchronized.
- 04:54 PM Revision 8343 (metacat): If an object was archived, the solr index will be removed for it.
- 11:01 AM Feature #6109: Keep the SOLR index for obsoleted objects
- Note: we only removed the solr index for the archived objects.
- 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...
10/25/2013
10/24/2013
10/21/2013
- 02:01 PM Revision 8340 (metacat): Adding theme configuration screenshot to docs
- 01:56 PM Revision 8339 (metacat): use 2.3.0 for this next release of metacat.
- 12:56 PM Revision 8337 (metacat): correct rst formatting.
- 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.
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 ...
- 12:14 PM Bug #6161 (Closed): Add access_log indexes to support DataONE log retrieval
- 12:16 PM Revision 8335 (metacat): add 2 indexes to speed up dataONE log retrieval. https://projects.ecoinformatics.org/ecoinfo/issues/6161
- 09:38 AM Revision 8334 (metacat): Added Lauren to contributors list in the metacat guide, and made the two lists match in sort order.
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... - 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...
- 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...
- 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.
- 12:26 PM Revision 8332 (metacat): Use the slf4j-log4j jar to replace slf4j-jdk one.
10/16/2013
- 05:27 PM Revision 8328 (metacat): Change the version to 2.2.2
- 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... - 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.
- 05:19 PM Revision 8327 (metacat): Fixed a bug that the configuration page shows complete even though the DataONE configuration hadn't done yet.
- 05:18 PM Revision 8326 (metacat): Add a util class for dataone configuration.
- 05:17 PM Revision 8325 (metacat): Change the button from Cancel to Bypass. So it is consistent with the Geoserver configuration page.
- 04:31 PM Revision 8324 (metacat): Add a jsp file to display the schema modification exception.
- 04:29 PM Revision 8323 (metacat): Add code the display the SchemaModification exception.
10/15/2013
- 08:46 PM Revision 8321 (metacat): Fixed a catch clause syntax which is only compatible with java 1.7.
- 03:39 PM Revision 8320 (metacat): Add code the overwrite the schema.xml in the solr-home/conf.
- 03:37 PM Revision 8319 (metacat): Add two scripts to update the db to 2.2.2
- 10:34 AM Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch
- 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
- 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...
- 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...
- 10:34 AM Bug #6136 (Closed): files left open causes too many file descriptors on OS
- 10:33 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context
- This is in the 2.2 branch.
- 06:47 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context
- This should be included in the upcoming patch release.
- 10:31 AM Bug #6138 (Closed): Metacat-index assumes default "knb" context
10/14/2013
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 ...- 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...
- 04:35 PM Revision 8313 (metacat): Change the guid.ezid.uritemplate.metadata property value to the hostname only, with no context
- 02:57 PM Revision 8312 (metacat): Add properties to keep the hash values for the schema.xml of the solr.
- 02:42 PM Revision 8311 (metacat): Fixed compile error that an ioexception should be caught.
- 11:07 AM Revision 8310 (metacat): Use the setting from the metacat-common component.
- 11:06 AM Revision 8309 (metacat): Some settings will be shared between metacat and metacat-index components.
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.
- 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 ...
- 12:27 PM Revision 8306 (metacat): correctly configure metacat-index to use metacat context/deployment location. https://projects.ecoinformatics.org/ecoinfo/issues/6138
- 12:12 PM Bug #6138 (Closed): Metacat-index assumes default "knb" context
- 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...
- 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...
- 09:37 AM Bug #6137 (Resolved): Add a new action reindexall to reindex all the solr index
- Just leave as it is.
- 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...
- 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...
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.
- 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...
- 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.
- 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...
- 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.
- 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 ...
- 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.
- 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 ... - 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...
- 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...
- 08:53 PM Revision 8303 (metacat): Sparate the action reindex and reindexall.
- 05:49 PM Revision 8302 (metacat): The checked-out schema.xml will overwrite the one in src/main/resource/solr-home/conf.
- 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... - 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...
- 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...
- 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...
- 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.
- 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.
- 01:52 PM Revision 8300 (metacat): Adding build files to ignore.
- 01:47 PM Revision 8299 (metacat): Refactor to use IOUtils.closeQuietly() which handles nulls and streams that are already closed.
- 01:26 PM Revision 8298 (metacat): Added close() to finally block for readFromFileSystem() call.
- 12:44 PM Revision 8297 (metacat): Closing FileOutputStream handles so that the OS limits on filehandles are not exceeded.
- 12:10 PM Revision 8296 (metacat): Use the d1_cn_index_processor 1.2.0 version.
- 12:09 PM Revision 8295 (metacat): Remove those files. They will be get from the d1_cn_index_processor 1.2.0 jar.
- 12:07 PM Revision 8294 (metacat): Use the schema for the d1_cn_index_processor 1.2.0
10/08/2013
- 05:51 PM Revision 8293 (metacat): combine the index code for failed ids and other ids.
- 04:49 PM Revision 8292 (metacat): Clean up the code.
- 02:22 PM Revision 8291 (metacat): The IndexGenerator will index the obsoleted data objects as well.
- 12:05 PM Revision 8290 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
- 12:04 PM Revision 8289 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
- 11:33 AM Revision 8288 (metacat): Remove the obsoletes chain from the update method in the SolrIndex class.
10/07/2013
- 05:56 PM Revision 8287 (metacat): When an object is archvied, the solr index will not be removed.
- 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
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