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From 06/10/2013 to 07/09/2013

07/09/2013

04:46 PM Revision 7873 (metacat): Stubs for 'metacatui' rendering. Initial target is to support Perl registry styling, but also general structured html views on metadata. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:46 PM Revision 7872 (metacat): Stubs for 'metacatui' rendering. Initial target is to support Perl registry styling, but also general structured html views on metadata. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:46 PM Revision 7871 (metacat): Stubs for 'metacatui' rendering. Initial target is to support Perl registry styling, but also general structured html views on metadata. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:46 PM Revision 7870 (metacat): Stubs for 'metacatui' rendering. Initial target is to support Perl registry styling, but also general structured html views on metadata. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:45 PM Revision 7869 (metacat): Stubs for 'metacatui' rendering. Initial target is to support Perl registry styling, but also general structured html views on metadata. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:12 PM Revision 7868 (metacat): Include the 'metacatui' portion of the path to .js file. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
04:10 PM Revision 7867 (metacat): Initial copy of original Perl templates - before making any changes. https://projects.ecoinformatics.org/ecoinfo/issues/5951
ben leinfelder
03:41 PM Task #6004: Figure out why there are only 422 documents indexed in mn-demo-4.test.dataone.org
After we modified the SystemMetadataEventListener class to listen to a dedicated map for indexing, I indexed the meta... Jing Tao
02:55 PM Task #5921 (Closed): Design and implement Metacat-Index module
Jing Tao
02:54 PM Task #5921: Design and implement Metacat-Index module
All sub-tasks were done. Close the feature. Jing Tao
02:52 PM Task #5923 (Closed): Discover missed documents and queue them for indexing
We create a HazelcastEventLog class.
When a timed indexing finishes, it will set a property in a file. The file co...
Jing Tao
12:41 PM Task #5923 (In Progress): Discover missed documents and queue them for indexing
This is well-underway, mostly just testing (I believe). ben leinfelder
02:50 PM Bug #5812: Rework default skin[s] to use SOLR query
TBD: actually do the same thing we did for the NCEAS skin (qformat=nceas) for the standard Metacat default skin (qfor... ben leinfelder
02:48 PM Story #5811 (Closed): Redesign KNB look and feel
See the entire MetacatUI project for details. https://projects.ecoinformatics.org/ecoinfo/projects/metacatui ben leinfelder
02:46 PM Task #6005 (Closed): Incomplete solr index for the data objects if the resourcemap was indexed first
When Metacat-index indexes a resource map document, it will check if all data objects of the resource map have been i... Jing Tao
02:45 PM Story #5940 (Closed): Support session-based Metacat authentication (for D1 services)
ben leinfelder
01:43 PM Story #5940 (In Progress): Support session-based Metacat authentication (for D1 services)
ben leinfelder
02:38 PM Task #5941 (Rejected): Add login/logout methods to DataONE MN service
These methods don't really fit with our current model. I think it's fine to allow the "back door" (i.e., Metacat serv... ben leinfelder
02:37 PM Revision 7866 (metacat): Use schedule method to start the index.
Jing Tao
02:32 PM Feature #6034 (New): Simplify configuration for certificate delegation
So we don't loose this in the shuffle - we could probably fill out some of the MyProxy configuration values based on ... ben leinfelder
02:28 PM Feature #5936 (Closed): Include certificate delegation inside Metacat
ben leinfelder
01:41 PM Feature #5936 (In Progress): Include certificate delegation inside Metacat
Aside from making the myProxy configuration easier, this is done. It does require a bit of administration from regist... ben leinfelder
02:25 PM Bug #5395: Get unexpected result if a search was done before metacat finishes its indexing during the inserting process.
Deferring - though we don't really have a solution for this. Only affects a deprecated mechanism (pathquery), however. ben leinfelder
02:17 PM Feature #5910 (In Progress): Build index from scratch
ben leinfelder
02:16 PM Bug #2792 (Rejected): KNB home link needed on the Map Page
The entire KNB site is being redone, I don't even know if we will have a full map page! ben leinfelder
01:59 PM Task #5930 (Closed): Add a configuration property to turn on/off the indexing processes (SOLR indexing)
ben leinfelder
01:58 PM Feature #6033 (Closed): Add configuration to disable 'pathquery'
As we move toward SOLR-based query support, pathquery will play less of a role in Metacat. We should be able to disab... ben leinfelder
01:56 PM Feature #5913 (In Progress): Handle indexing errors
Remains to be seen how quickly this queue gets populated. We dont currently have any qualifiers on the kind of error ... ben leinfelder
01:53 PM Feature #5914 (Closed): Reconcile SOLR server/client versions
Both client and server are using v3.x now. Eventually DataONE plans to update the SOLR version, so we can consider t... ben leinfelder
01:46 PM Feature #5911 (In Progress): Repair index after outage
This may even be a duplicate of related task #5923 ben leinfelder
01:44 PM Feature #5912 (Closed): Force indexing on individual object[s]
There is now a Metacat servlet API action for this:... ben leinfelder
12:43 PM Revision 7865 (metacat): use tagged/released version of d1-portal project. https://projects.ecoinformatics.org/ecoinfo/issues/5936
ben leinfelder
12:38 PM Task #5945 (Closed): Implement reindex action for individual PID
ben leinfelder
12:38 PM Task #5944 (Closed): Metacat-index need an IndexEvent and IndexEventLog mechanism
Main development on this is complete - enhancements to this can be added in other tasks. ben leinfelder
10:40 AM Revision 7864 (metacat): include mn.publish() REST endpoint handling. https://projects.ecoinformatics.org/ecoinfo/issues/6024
ben leinfelder
10:16 AM Revision 7863 (metacat): Add the code to write the error message to the log in the itemRemvoed method.
Jing Tao
09:55 AM Bug #6030 (Closed): Deleting a document causes the method itemAdded(ItemEvent<SystemMetadata> entryEvent) in the SysteMetadataEventListener class being called twice
I used the morpho to test it and it seems that the issue was fixed. Jing Tao
06:20 PM Bug #6030 (In Progress): Deleting a document causes the method itemAdded(ItemEvent<SystemMetadata> entryEvent) in the SysteMetadataEventListener class being called twice
There were two calls to this - one in the D1 service implementation and another in the Metacat implementation that th... ben leinfelder
05:23 PM Bug #6030 (Closed): Deleting a document causes the method itemAdded(ItemEvent<SystemMetadata> entryEvent) in the SysteMetadataEventListener class being called twice
When we delete a document from the Metacat, the method itemAdded in the in the SysteMetadataEventListener class (Meta... Jing Tao
09:45 PM Feature #6031 (Rejected): Add rendered metadata to Bagit package contents
ben leinfelder
06:19 PM Revision 7862 (metacat): 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
ben leinfelder
06:10 PM Revision 7861 (metacat): implement the view service (uses existing skin-based dbtransform) - and include the REST endpoint. https://projects.ecoinformatics.org/ecoinfo/issues/6028
ben leinfelder
05:51 PM Revision 7860 (metacat): use StreamSource instead of StringReader for method signature -- can be used with different sources this way. https://projects.ecoinformatics.org/ecoinfo/issues/6019
ben leinfelder
05:10 PM Revision 7859 (metacat): clean up DBTransform in preparation for "view" service. https://projects.ecoinformatics.org/ecoinfo/issues/6019
ben leinfelder

07/08/2013

03:09 PM Revision 7858 (metacat): In determining the time arrange, the equality was removed.
Jing Tao
03:05 PM Revision 7857 (metacat): Add code to handle failed ids.
Jing Tao
02:00 PM Revision 7856 (metacat): Remove the EventLog write.
Jing Tao
12:14 PM Revision 7855 (metacat): include GET /package/{pid} endpoint in MN service. https://projects.ecoinformatics.org/ecoinfo/issues/6027
ben leinfelder
12:09 PM Revision 7854 (metacat): Add the EventLog code.
Jing Tao

07/06/2013

06:33 PM Revision 7853 (metacat): 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
ben leinfelder
05:14 PM Revision 7852 (metacat): It will throw an exception if the subprocessor can't handle the document.
Jing Tao

07/05/2013

04:59 PM Revision 7851 (metacat): Check if the all components of a resource map have been processed before processing the resource map.
Jing Tao

07/04/2013

12:33 PM Revision 7850 (metacat): First pass at MN.getPackage() implementation using Bagit library from LOC. https://projects.ecoinformatics.org/ecoinfo/issues/6026
ben leinfelder
09:58 PM Revision 7849 (metacat): add method for publishing existing object (usually assumed to be scimeta) with a DOI. https://projects.ecoinformatics.org/ecoinfo/issues/6014
ben leinfelder

07/03/2013

04:34 PM Revision 7848 (metacat): Fixed a bug that the event log can't save the real lastest process date.
Jing Tao
03:56 PM Revision 7847 (metacat): Change the date format.
Remove the replication part of log4j. Jing Tao
10:28 AM Revision 7846 (metacat): Use a new date format.
Jing Tao
10:25 AM Revision 7845 (metacat): Add a log4j properties file.
Jing Tao
10:24 AM Revision 7844 (metacat): Add a file to specify the log4j as the logger.
Jing Tao
10:15 AM Task #5945 (In Progress): Implement reindex action for individual PID
This is in trunk now. You must be logged in as admin of Metacat in order to invoke it which makes a JUnit test diffic... ben leinfelder
10:13 AM Revision 7843 (metacat): 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
ben leinfelder
09:02 AM Task #5944 (In Progress): Metacat-index need an IndexEvent and IndexEventLog mechanism
I have the hzIndexEventMap set up and persisting IndexEvent objects to postgres db now (using Metacat's connection). ... ben leinfelder
12:28 AM Revision 7842 (metacat): 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
ben leinfelder
12:03 AM Revision 7841 (metacat): add MapStore/Loader test for the IndexEvents -- adding and removing events in the DB table through hazelcast. https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder

07/02/2013

04:47 PM Revision 7840 (metacat): 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").
ben leinfelder
04:41 PM Revision 7839 (metacat): add simple test for the IndexEventDAO class -- adding, removing, listing events in the DB table. https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder
03:21 PM Revision 7838 (metacat): Add the code that only the ids with the correct system metadata modification time will be added to the index queue.
Jing Tao
12:38 PM Task #6004: Figure out why there are only 422 documents indexed in mn-demo-4.test.dataone.org
I queried the database and got the following result. There are 4998 in the xml_documents and 0 in the xml_revisions.
...
Jing Tao
12:18 PM Task #5924 (Closed): Add the configuration page for the Solr server in the Metacat configuration utility
Matt Jones
12:18 PM Task #5924: Add the configuration page for the Solr server in the Metacat configuration utility
Done. Ben added to main property page. Matt Jones
11:25 AM Task #5945: Implement reindex action for individual PID
Proposal is:
-create Metacat action "reindex" that takes an identifier.
-Metacat places the SystemMetadata for that...
ben leinfelder

07/01/2013

03:09 PM Revision 7837 (metacat): Use the hazelcast event log.
Jing Tao
01:59 PM Revision 7836 (metacat): Add code to get and set the last process date.
Jing Tao

06/26/2013

04:43 PM Revision 7834 (metacat): merging upgrade scripts from 2.0 branch to trunk. https://redmine.dataone.org/issues/3847
ben leinfelder
04:42 PM Revision 7833 (metacat): scripts for 2.1.0 upgrade
ben leinfelder

06/25/2013

04:42 PM Revision 7830 (metacat): 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
ben leinfelder
02:51 PM Task #5915 (Closed): Use MN.query(solr) in NCEAS skin
ben leinfelder
02:50 PM Task #5918 (Closed): Separate unit tests from integration tests
ben leinfelder
02:43 PM Bug #6007 (Resolved): Registry uses filename from upload form to save in temporary directory
I deployed this in KNB today (June 25th, 2013). This was not part of an official release but is in the code for 2.1.x... ben leinfelder
01:23 PM Revision 7829 (metacat): stub for storing IndexEvent objects in Metacat (from metacat-index processing). https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder
01:23 PM Revision 7828 (metacat): move IndexEvent into metacat-common. Perparation for Metacat responding to events and writing them to a persistent store. https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder
01:17 PM Revision 7827 (metacat): 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.
ben leinfelder
09:10 AM Bug #6009 (Closed): Metacat uses "metacat.output" temp files for all read() operations
This is in trunk now. ben leinfelder

06/24/2013

12:07 PM Bug #6009 (In Progress): Metacat uses "metacat.output" temp files for all read() operations
now reading directly from the filesystem, or in the case of EML with inline-data, the partial file contents. ben leinfelder
12:05 PM Revision 7824 (metacat): 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
ben leinfelder

06/22/2013

09:47 PM Bug #6008 (Closed): Metacat servlet API upload() method uses user-supplied filename for temp upload
Now using File.createTempFile() and deleting the data files when done. ben leinfelder
05:32 PM Bug #6008 (Closed): Metacat servlet API upload() method uses user-supplied filename for temp upload
This can be problematic if users simultaneously attempt to upload a data file with the same name. ben leinfelder
09:44 PM Revision 7823 (metacat): 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
ben leinfelder
05:35 PM Bug #6009 (Closed): Metacat uses "metacat.output" temp files for all read() operations
The KNB has 1.3 GB of these that have accumulated since ?.
There should be two scenarios:
-stream the contents fr...
ben leinfelder
05:02 PM Bug #6007: Registry uses filename from upload form to save in temporary directory
I deployed the changes on dev2.nceas for testing. Feel pretty good about them - using File::Temp to manager unique up... ben leinfelder

06/21/2013

04:15 PM Revision 7822 (metacat): correctly delete data file when we are done with it. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
04:06 PM Revision 7821 (metacat): include filename in the filepart part. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
03:18 PM Revision 7820 (metacat): send the original filename in the upload() method since that is supported by the Metacat API. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
03:10 PM Revision 7819 (metacat): remove the unique string when generating data file metadata. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
02:48 PM Revision 7818 (metacat): debugging. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
01:44 PM Revision 7817 (metacat): use File::Temp to write data files in registry. https://projects.ecoinformatics.org/ecoinfo/issues/6007
ben leinfelder
12:22 PM Bug #6007 (Resolved): Registry uses filename from upload form to save in temporary directory
This can cause collisions when a room of 22 people all submit a datapackage with the same data file name....
The r...
ben leinfelder
11:11 AM Revision 7816 (metacat): correct regex for whitespace in D1 identifier.
ben leinfelder
09:09 AM Revision 7815 (metacat): refactor IndexEventLog a bit to simplify type/action information. prep for serializing IndexEvent objects to Metacat. https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder
05:28 PM Revision 7814 (metacat): remove serial number from indexeventlog - it is not used elsewhere in the api. https://projects.ecoinformatics.org/ecoinfo/issues/5944
ben leinfelder
05:28 PM Bug #6006 (Closed): Metacat admin screen requires metacat-index directories
Now skipping the template creation if metacat-index war is not deployed along with metacat. ben leinfelder
05:21 PM Revision 7813 (metacat): correct spelling for index.eventlog.classname property
ben leinfelder

06/20/2013

04:59 PM Task #5943 (Resolved): Eliminate the unnecessary Systemmetadata event between the Metacat and Metacat-index modules.
Switched over to the new structure for communicating index events. Seems to be working as expected. ben leinfelder
04:49 PM Revision 7812 (metacat): use an independent ISet<SystemMetadata> structure to communicate objects that should be indexed by metacat-index. https://projects.ecoinformatics.org/ecoinfo/issues/5943
ben leinfelder
12:23 PM Revision 7811 (metacat): consolidate SystemMetadata map retrieval in preparation for using a different structure for objects to index.
ben leinfelder
10:22 AM Task #5944: Metacat-index need an IndexEvent and IndexEventLog mechanism
Added delete() method to remove entries that we do not need to reprocess again (because they were successful, finally... ben leinfelder
09:24 AM Revision 7810 (metacat): adding ability to remove event from the [error] queue.
ben leinfelder

06/18/2013

02:59 PM Revision 7809 (metacat): do not create solr-home if there is no template to compy into that directory (need to be able to create it later if/when someone decides to use and deploy metacat-index). https://projects.ecoinformatics.org/ecoinfo/issues/6006
ben leinfelder
02:54 PM Task #5943: Eliminate the unnecessary Systemmetadata event between the Metacat and Metacat-index modules.
Proposed solution is to use a different/independent structure for SystemMetadata events that should trigger a re-inde... ben leinfelder
01:54 PM Revision 7808 (metacat): do not attempt to copy solr-home template from metacat-index webapp if it does not exist. This would be in cases where metacat-index is not deployed. https://projects.ecoinformatics.org/ecoinfo/issues/6006
ben leinfelder
12:35 PM Bug #6006 (Closed): Metacat admin screen requires metacat-index directories
When configuring Metacat there is a dependency on metacat-index. This should be gracefully skipped if that webapp is ... ben leinfelder
10:19 AM Task #6005 (Closed): Incomplete solr index for the data objects if the resourcemap was indexed first
Currently the resource map should be indexed after the data objects in the resource map were indexed. If the resource... Jing Tao
05:07 PM Revision 7807 (metacat): Add code to implment set and get the last processed date.
Jing Tao

06/17/2013

04:28 PM Revision 7806 (metacat): It will make the index only for those objects which were modified after the marked time.
Jing Tao
01:50 PM Revision 7805 (metacat): Add set and get the lastprocessedDate in the IndexEventLog.
Remove the code to write the successful event. Jing Tao
10:31 AM Task #6004: Figure out why there are only 422 documents indexed in mn-demo-4.test.dataone.org
Attached a log file for the indexing process. Jing Tao
10:30 AM Task #6004 (Resolved): Figure out why there are only 422 documents indexed in mn-demo-4.test.dataone.org
There are more 4000 data objects in the mn-demo-4. But we only gets 422 documents indexed. Jing Tao

06/14/2013

05:39 PM Bug #6003 (Closed): The "war" target in the metacat will build the metacat-index.war
We added the target which build metacat-index.war as the dependency of the "war" target. Jing Tao
05:37 PM Bug #6003 (Closed): The "war" target in the metacat will build the metacat-index.war
The "war" target in the metacat doesn't build the metacat-index.war in the dist directory. It only builds knb.war and... Jing Tao
05:35 PM Task #5930: Add a configuration property to turn on/off the indexing processes (SOLR indexing)
If we removed the "solr" from the engine list, metacat-index will not build index anymore. And the solr query will be... Jing Tao
05:20 PM Revision 7804 (metacat): Add the dataone repository.
Jing Tao

06/13/2013

04:41 PM Revision 7803 (metacat): The "war" target will build the metacat-index.war as well.
Jing Tao

06/12/2013

02:36 PM Revision 7802 (metacat): Log the timed index jobs.
Jing Tao
02:08 PM Revision 7801 (metacat): Add the code to log the failed events.
Jing Tao
06:24 PM Revision 7800 (metacat): Add a temporary file log for debugging.
Jing Tao
06:23 PM Revision 7799 (metacat): Use commons-io 2.4
Jing Tao

06/11/2013

03:47 PM Revision 7798 (metacat): Add a new property for the index event log class name.
Jing Tao
 

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