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From 11/27/2011 to 12/26/2011

12/22/2011

11:51 AM Revision 6822 (metacat): Make sure the local id isn't null when we try to get the object from the local instance.
Chris Jones
11:16 AM Revision 6821 (metacat): Simplify the error handling, and throw the exception once the CN is updated with the new status.
Chris Jones
11:13 AM Revision 6820 (metacat): Set the replica status to failed (not invalidated) when we get exceptions trying to read the object bytes. Not much of a difference, but only the CN, in theory, is supposed to be able to set the invalidated status.
Chris Jones
11:07 AM Revision 6819 (metacat): Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.
Chris Jones
10:51 AM Revision 6818 (metacat): Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).
Chris Jones
10:40 AM Revision 6817 (metacat): Get the object inputstream from the local metacat instance using MetacatHandler.get() rather than MN.getReplica() so we don't throw an InvalidToken exception when passing in a null Session. The D1Client object is never used for this local call.
Chris Jones
09:24 AM Revision 6816 (metacat): interpret permissions as hierarchical
https://redmine.dataone.org/issues/2150 ben leinfelder

12/21/2011

02:08 PM Bug #5569: The sanparks skin doesn't show welcome message when user login again (after doing logout)
It turns out, the html page showing after logout used a wrong js function for login.
After modifying the sanparksLog...
Jing Tao
01:41 PM Bug #5569 (Resolved): The sanparks skin doesn't show welcome message when user login again (after doing logout)
When user first time logins, the sanpark skin will show a welcome message, upload data link and search form.
Howev...
Jing Tao
01:53 PM Bug #5523: setting authoritative MN and rightsHolder for KNB data on conversion
We decided to generate system metadata for every object housed in the KNB and use the KNB nodeId as the authoritative... ben leinfelder
01:50 PM Revision 6815 (metacat): Use submitLoginFormIntoDivAndReload to replace submitLoginFormIntoDiv js function.
Jing Tao
01:00 PM Revision 6814 (metacat): remove flag for independent system metadata replication -- these entries are replicated along with the data/metadata objects or via hazelcast when the actual object is not on the server.
ben leinfelder
12:33 PM Revision 6813 (metacat): update documentation to reflect changes to replication (client certificate)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516 ben leinfelder
10:52 AM Revision 6812 (metacat): include SSL settings for client certificate-based replication
ben leinfelder

12/20/2011

05:13 PM Revision 6811 (metacat): do not include the "v1" in the base url for the target MN
ben leinfelder
12:19 PM Revision 6810 (metacat): New D1 jars with a minor CNode.setReplicationStatus() bugfix.
Chris Jones
11:57 AM Bug #5567: Click the schedule button on sankparks skin got an blank page
In scheduleWorkflowRun.jsp file, it has code like:
String karId = LSIDUtil.getDocId(karLsid, false);
PermissionContro...
Jing Tao
11:52 AM Bug #5568 (Resolved): Get an exception during startup metacat
I got an exception when i started metacat. However, it seems that metacat still can work.
SEVERE: /127.0.0.1:570...
Jing Tao
11:29 AM Revision 6809 (metacat): The kar id will have version number.
Jing Tao
11:25 AM Revision 6808 (metacat): process the _current_ revision, not the latest!
use direct object/system metadata insertion for ORE maps. ben leinfelder
11:21 AM Revision 6807 (metacat): allow other Metacat process (system metadata and ORE generation) to directly insert objects and system metadata without having to go through the MN/CN methods.
ben leinfelder
11:19 AM Revision 6806 (metacat): sort the docids so that "old" revisions are processed before newer ones
ben leinfelder

12/19/2011

01:07 PM Revision 6805 (metacat): only attempt to unlock a lock if it was created (in the finally block)
ben leinfelder
12:56 PM Revision 6804 (metacat): update tests to comply with these chenages:
new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPo... ben leinfelder

12/16/2011

04:24 PM Revision 6803 (metacat): new jars with many changes -- including new CN methods: ping, describe, listChecksumAlgorithm. Removed MN.setAccessPolicy. Refactored CN.setOwner() to CN.setRightsHolder().
ben leinfelder
02:48 PM Bug #5560: Upgrade access control rules in Metacat DB
I'm now also forcing the shared System Metadata map to reload into memory all the system metadata for data objects th... ben leinfelder
12:21 PM Revision 6802 (metacat): refresh the SystemMetadata entry for EML and referenced data files when parsing EML access rules -- this ensures our in-memory system metadata map is up to date WRT the DB entries.
ben leinfelder
11:37 AM Revision 6801 (metacat): Using a branch name for the utilities project. This branch is a copy of the trunk and it uses the BSD license.
We will move this branch to a tag soon. Jing Tao
11:00 AM Revision 6800 (metacat): add revision history to the generated ORE objects -- we use the revision history of the EML package as a basis because the each ORE revision mirrors the revision of the EML package.
Add a placeholder for checking if an equivalent ORE map exists in the DataONE infrastructure - this will be a call to... ben leinfelder
10:03 AM Bug #5522: download linked KNB data and convert links in EML to ORE packages
From discussion yesterday:
Converting a node from KNB to D1
--------------------------------------------------
0. Ge...
ben leinfelder
09:56 AM Revision 6799 (metacat): Update the parameter names expected for listObjects() to reflect the MN API changes in the architecture docs.
Chris Jones
09:44 AM Revision 6798 (metacat): Change the query semantics such that we implement the MN.listObjects() where the lower datetime bound is inclusive (greater than or equal to" and the upper datetime bound in exclusive (less than). This allows easier paging in client applications.
Chris Jones
09:42 AM Revision 6797 (metacat): for test to compile, provide BaseException param for setReplicationStatus. I used a NotAuthorized instance.
ben leinfelder
09:37 AM Revision 6796 (metacat): adjust after refactoring tests that use EML queries
ben leinfelder
07:42 AM Revision 6795 (metacat): In the call to MNReplication.replicate(), call back to CNReplication.setReplicationStatus() and set the status to failed when we get local exceptions, exceptions from the source MN when calling getReplica(). Send back an exception with a description when setting the status. Add a private setReplicationStatus() method to refactor these calls out.
Chris Jones
07:36 AM Revision 6794 (metacat): Modify CNresourceHandler.setReplicationStatus() to use the new API signature, including the failure BaseException that is parsed out of the MMP as a file section. Log the exception message. Since this is an asynchronous call, ReplicationManager won't see a failed status, but the MNAuditTask eventually will.
Chris Jones
07:32 AM Revision 6793 (metacat): Add collectReplicationStatus() to CNResourcHandler to return the BaseException or it's subclass, if any, provided in the the call to setReplicationStatus. The exception will be reported on the CN.
Chris Jones
07:29 AM Revision 6792 (metacat): Change setReplicationStatus() to drop serialVersion and report the failure exception message in the CN log.
Chris Jones
07:13 AM Revision 6791 (metacat): Add new D1 jars with update CNreplication API changes to SetReplicationStatus().
Chris Jones

12/15/2011

05:32 PM Revision 6790 (metacat): query for deleted metadata when testing that replication communicated the deletion. to check data, we try to update the data object on the target node (which should fail)
ben leinfelder
05:11 PM Revision 6789 (metacat): add test for data locking
ben leinfelder
01:59 PM Revision 6788 (metacat): delete data and eml on the home Metacat and check that the change propagates to the target
ben leinfelder
01:29 PM Revision 6787 (metacat): set SystemMetadata.archived=true on MN.delete
There is ongoing discussion on what the exact behavior should be here, but this mimics Metacat's delete-as-archive ac... ben leinfelder
12:22 PM Bug #5536: Restore replicated data files that are 0 bytes
Current proposal for upgrade script solution:
-find all data files in the configured data directory for Metacat
-dele...
ben leinfelder
10:40 AM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
Jing says it's fixed! ben leinfelder
10:31 AM Bug #5567 (Resolved): Click the schedule button on sankparks skin got an blank page
Click TPC worklfow link on the sanparks skin, user will get a list of workflows. Every workflow has three associated ... Jing Tao

12/14/2011

08:48 AM Revision 6786 (metacat): In MNodeService.replicate(), check to see if we have a replica (via an out of band channel) before we call sourceMN.getReplica().
Chris Jones

12/13/2011

05:28 PM Revision 6785 (metacat): actually include the test in the suite
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
05:17 PM Revision 6784 (metacat): EML replication test with insert, update and set access
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
05:06 PM Revision 6783 (metacat): only create guid->docid mapping during metadata replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
04:50 PM Revision 6782 (metacat): do not treat access change as an update -- it should not attempt to retrieve the contents of the object
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
04:43 PM Bug #5563: Kepler can't get search result from metacat 2.0.0
It turned out that the ecogrid tag (1.2.2.rc4) which the trunk used has wrong version of ecogridToPathquery.xsl. The ... Jing Tao
04:36 PM Revision 6781 (metacat): Change the ecogrid tag to 1.2.2.RC5.
Jing Tao
04:18 PM Revision 6780 (metacat): only create guid->docid mapping during data replication if it does not already exist
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
03:49 PM Bug #5534: Replication log somehow doesn't work.
As configured, all INFO level (and above) messages for ReplicationLogging will go to the replication log file and not... ben leinfelder
03:30 PM Revision 6779 (metacat): remove xml_acccess.docid reference (oops)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
03:15 PM Revision 6778 (metacat): test update and set access during replication from A->B
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
03:09 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
there is an Ecogrid change needed ben leinfelder
02:58 PM Bug #5516: continue updating user documentation
Also add in the OAI-PMH documentation contributed by Duane Costa. Matt Jones
12:22 PM Revision 6777 (metacat): updated D1 API -- removed Permission.REPLICATE and associated parameters
ben leinfelder
11:51 AM Revision 6776 (metacat): a minute for replication?
ben leinfelder
11:34 AM Revision 6775 (metacat): process system metadata before access rules (access control is now driven by GUID so the mapping needs to be there)
ben leinfelder
11:07 AM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
Now the cache key is using populated string with parameter values rather than just "?". It is working. Jing Tao
10:19 AM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
Yeah.
this is the way i am doing :)
Jing Tao
10:18 AM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
Good catch!
We can use the query string _after_ the parameter values are bound to the prepared statement.
Would look...
ben leinfelder
11:06 AM Revision 6774 (metacat): Change the key of query result cache. The key now has the real search value.
Jing Tao
10:58 AM Revision 6773 (metacat): include SerialVersion in describe response
https://redmine.dataone.org/issues/2135
NOTE: d1 jars should be replaced once all schema changes are finalized and th...
ben leinfelder
10:21 AM Bug #5547: Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
I played around with that, but it basically means the Perl code would have to act as a proxy for the browser session ... ben leinfelder
09:17 AM Revision 6772 (metacat): comment out B->A test
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder

12/12/2011

04:48 PM Bug #5547: Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
I like main page still keeping to use Java login. So user can do uploading data, schedule workflow et al without inst... Jing Tao
12:22 PM Bug #5547: Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
I've fixed the first issue where after logging in from the "Register Data" you are now redirected to the registry for... ben leinfelder
11:00 AM Bug #5547: Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
And the login/logout action on the home page seems not affect the login status on the "Register Data" at all. Jing Tao
04:33 PM Revision 6771 (metacat): use correct URLs for replication/Metacat client
ben leinfelder
02:57 PM Revision 6770 (metacat): simple tests for 2-way data replication
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5520 ben leinfelder
01:51 PM Bug #5560: Upgrade access control rules in Metacat DB
Access control JUnit tests are all passing. I would like to test this from a 1.9.5 Metacat installation being upgrade... ben leinfelder
01:49 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
okay, that's simple enough to have agreed on! ben leinfelder
01:49 PM Bug #5523: setting authoritative MN and rightsHolder for KNB data on conversion
More musing on the authoritative MN/replica policy for upgrading Metacat deployments:
-If we only generate SystemMeta...
ben leinfelder
01:22 PM Revision 6769 (metacat): ROLLBACK: check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi ben leinfelder
12:41 PM Revision 6768 (metacat): check for non-public session in Metacat before showing the registry form
http://bugzilla.ecoinformatics.org/process_bug.cgi ben leinfelder
11:26 AM Revision 6767 (metacat): redirect to the registry form following successful login - but allow an override in case we only want to render the success and stay there (ajax call from main sanparks page).
ben leinfelder
10:50 AM Revision 6766 (metacat): include 'archived' system metadata element in backing DB store
ben leinfelder

12/09/2011

04:40 PM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
in the cache system, we use the combination of the selection and extended query as the key to store the cache result.... Jing Tao
04:05 PM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
After restarting tomcat, i ran the two queries on the dev skin. The second one is from cache. This is wrong since the... Jing Tao
04:29 PM Bug #5534: Replication log somehow doesn't work.
Ben: after you change the debug level, the replication log will go to catalina.out or the metacatreplication.log file... Jing Tao
04:25 PM Bug #5534: Replication log somehow doesn't work.
had to add the log level when defining the replication logger:
log4j.logger.ReplicationLogging=INFO, replication
ben leinfelder
04:25 PM Revision 6765 (metacat): include the logging level with configuring logger (with file appender) for replication and dataone
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5534 ben leinfelder
03:28 PM Revision 6764 (metacat): add ; to end of update command
ben leinfelder
03:11 PM Revision 6763 (metacat): add ; to end of update command
ben leinfelder
02:56 PM Bug #5560: Upgrade access control rules in Metacat DB
Metacat now tracks permissions for each revision of a document/data object.
The upgrade goes like this:
1. Generate ...
ben leinfelder
02:54 PM Revision 6762 (metacat): only update accessfileid for our new guid-based records
ben leinfelder
02:42 PM Revision 6761 (metacat): move latest postgres access upgrade statements to oracle script
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
02:35 PM Revision 6760 (metacat): include revision clause when updating the accessfileid on the xml_acccess table
ben leinfelder
12:12 PM Revision 6759 (metacat): remove docid column in favor of guid
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
10:21 AM Bug #5114: ESA registry: Bad link in 'register dataset' instructions
Added "esa" context to the URL so now it points to the correct page.
http://data.esa.org/esa/cgi-bin/register-dataset...
ben leinfelder
10:20 AM Revision 6758 (metacat): include "esa" context in the data registry URL.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5114 ben leinfelder
09:05 AM Revision 6757 (metacat): If a member node cannot be found in the node list matching the targetNodeSubject given in isNodeAuthorized(), throw a ServiceFailure exception.
Chris Jones
08:04 AM Revision 6756 (metacat): Minor reformatting for readability.
Chris Jones

12/08/2011

04:15 PM Bug #5523: setting authoritative MN and rightsHolder for KNB data on conversion
On further reflection, I think we might only want to be generating SystemMetadata for objects that were added directl... ben leinfelder
03:13 PM Bug #5523: setting authoritative MN and rightsHolder for KNB data on conversion
We can certainly find out our local KNB MN Id since it will be configured, but I'm not sure how we would go about def... ben leinfelder
04:10 PM Bug #5244: ldapweb.cgi shouldn't report ou=Account accounts since they're unusable
Used Jing's test server to verify that ou=Account entries were not shown.
http://chico1.dyndns.org/knb/cgi-bin/ldapwe...
ben leinfelder
03:52 PM Bug #5522: download linked KNB data and convert links in EML to ORE packages
Items I am suspicious about:
2(c)(i) -- Generating new objects from external data (URLs) that metadata points to. The...
ben leinfelder
02:44 PM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
No, it is not. I haven't update your code yet.
I figured it out somehow the search result was cached even the querie...
Jing Tao
02:17 PM Bug #5566: Click View Run link get 0 result if user doesn't login on the sanparks skin
Do you think this is because of the new permission handling in Metacat?
The change I just made to trunk means that e...
ben leinfelder
02:06 PM Revision 6755 (metacat): fix tests:
-insert default objectFormatList from d1_common (includes schemaLocation now)
-calculate checksum for the system meta...
ben leinfelder
01:51 PM Revision 6754 (metacat): update with latest d1_common/d1_lib (includes latest schema changes)
ben leinfelder
01:15 PM Revision 6753 (metacat): prepared statement toString() does not include quotes (') around the inserted values -- now the test reflects this.
ben leinfelder
01:12 PM Revision 6752 (metacat): only handle 100 (consecutive!) docId generations per millisecond, otherwise the generated docid part is bigger than Long.MAX_VALUE and Metacat cannot fully handle that.
ben leinfelder
11:27 AM Revision 6751 (metacat): Metacat now keeps track of permissions on a per-version basis -- the test reflects this change in behavior.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
11:22 AM Revision 6750 (metacat): check previous revision when attempting to update access control with EML 2.0.x docs
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
10:17 AM Revision 6749 (metacat): remove old access rules for a data object when they are being updated by rules contained in an EML document. Now the OnlineDataAccessTest EML 2.1.0 tests pass.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder

12/07/2011

05:31 PM Revision 6748 (metacat): construct the proper previousDocId when checking for update permission
ben leinfelder
05:05 PM Revision 6747 (metacat): for now, look up SystemMetadata directly from the table otherwise we won't have the latest access information. Need to refresh the in-memory copy everytime we edit the access policy via Metacat (includes EML parser)
ben leinfelder
05:04 PM Revision 6746 (metacat): check previous revision for permissions to update (includes data described by EML)
ben leinfelder
05:02 PM Revision 6745 (metacat): use correct "rev" column in xml_revisions table
ben leinfelder
02:42 PM Bug #5566 (Resolved): Click View Run link get 0 result if user doesn't login on the sanparks skin
On the sanparks skin, if you click the TPC workflows link, you will get a list of workflows. There are three actions ... Jing Tao
01:12 PM Bug #5544: the footer of the output page after clicking TPC status/workflow can't be read on Sanparks skin
It turns out that the TPC workflow/status use another set of css and jsp files. I use the the way of home page to rep... Jing Tao
12:18 PM Revision 6744 (metacat): refactor Metacat access handling to be on a per-revision basis so that it more closely aligns with the DataONE approach
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560 ben leinfelder
12:16 PM Revision 6743 (metacat): To avoid id generation conflicts happening at the same millisecond, append a 5 character random string to the end of the docid.
Chris Jones
11:54 AM Revision 6742 (metacat): Remove header2, footer2 and left-nav2 files.
Jing Tao

12/06/2011

04:31 PM Revision 6741 (metacat): change the default scheduler and workflow run engine urls.
Jing Tao
03:48 PM Bug #5563 (Resolved): Kepler can't get search result from metacat 2.0.0
I used kepler 2.3 to do a % query against a metacat which was built from the trunk. It didn't show any result. Actual... Jing Tao
03:03 PM Revision 6740 (metacat): retry: add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561 ben leinfelder
02:51 PM Revision 6739 (metacat): update test to reflect newer change:
handle queries with predicates correctly.
when docids are used in the return field look up, we need to make sure they...
ben leinfelder
02:50 PM Revision 6738 (metacat): add node name in the correct order for predicate navigation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5561 ben leinfelder

12/05/2011

06:04 PM Revision 6737 (metacat): Use the absolute path for the change permission jsp page.
Jing Tao
05:43 PM Revision 6736 (metacat): Add header style to distiguish header and normal row.
Jing Tao
11:58 AM Revision 6735 (metacat): Make TPC link to use the same mechanism to open header and left panel.
Jing Tao
09:02 AM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
Hi, Ben:
I just tried and the sql error has gone. Thanks!
However, it seems that all worklfow and run kar files are...
Jing Tao

12/02/2011

05:36 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
One problem was that the predicate expression was incorrectly escaping the predicate quotes -- now that they are prep... ben leinfelder
04:23 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
The parameterValues is:
[karEntry/karEntryAttributes/tpcStatus, mainAttributes/lsid, karEntry/karEntryAttributes/Name...
Jing Tao
04:22 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
The sql statement is:
select xml_nodes.docid, xml_index.path, xml_nodes.nodedata, xml_nodes.parentnodeid, xml_nodes....
Jing Tao
04:21 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
The pathquery doesn't work:
<pathquery version='1.2'><returndoctype>http://www.kepler-project.org/kar-2.0.0</returndo...
Jing Tao
04:19 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
Okay. It turned out the query on comment 2 does work. Jing Tao
03:39 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
i added a printStatckTrace statement and it gave me this:
at org.postgresql.core.v3.SimpleParameterList.bind(SimplePa...
Jing Tao
03:36 PM Bug #5561: Got a SQL error when click TPC workflows or TPC link on sanparks skin
actually, it is not only for the sanpark skin. This query will cause same issue:
<?xml version="1.0"?>
<pathquery ver...
Jing Tao
10:31 AM Bug #5561 (Resolved): Got a SQL error when click TPC workflows or TPC link on sanparks skin
Clicked TPC status, I saw:
knb 20111202-10:30:51: [ERROR]: DBQuery.createResultDocument - SQL Error: The column in...
Jing Tao
05:32 PM Revision 6734 (metacat): handle queries with predicates correctly.
when docids are used in the return field look up, we need to make sure they are included in the values in the correct... ben leinfelder
04:40 PM Revision 6733 (metacat): widen the third column.
Jing Tao
11:28 AM Bug #5562: Got an NPE when upgrade db from 1.9.5 to 2.0.0
it was possible to have a null prepared statement if there were no data values to convert to dates -- now checking fo... ben leinfelder
11:23 AM Bug #5562 (Resolved): Got an NPE when upgrade db from 1.9.5 to 2.0.0
knb 20111202-11:20:14: [ERROR]: SkinsAdmin.configureSkins - Could not find properties for skin: semtools [edu.ucsb.nc... Jing Tao
11:27 AM Revision 6732 (metacat): close prepared statement only if not null
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5562 ben leinfelder
11:25 AM Bug #5560: Upgrade access control rules in Metacat DB
By removing the 'docid' column from the 'xml_access' table, we introduce a huge amount of refactoring -- the custom E... ben leinfelder
09:02 AM Bug #5560 (Resolved): Upgrade access control rules in Metacat DB
Metacat handles a single access control policy for ALL revisions of an object whereas DataONE allows different access... ben leinfelder
10:54 AM Revision 6731 (metacat): fixed a bug that using a wrong table name - acces_log.
Jing Tao
10:53 AM Revision 6730 (metacat): fixed a bug that using acces_log table name.
Jing Tao
07:37 AM Revision 6729 (metacat): Upgrade the hazelcast libraries to 1.9.4.4 from 1.9.3.4.
Chris Jones

12/01/2011

04:34 PM Bug #5547: Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
If you login on the sanparks home page, you will get the login form when you click Register Data link. It seems that ... Jing Tao
03:43 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
Use accessBlock parameter on setaccess action to replace the original access rules by the new access rules. The new a... Jing Tao
03:38 PM Revision 6728 (metacat): Use accessblock in setaccess method. So user can grant/revoke public readable access.
Jing Tao
01:30 PM Revision 6727 (metacat): ensure that the revision list is ordered ascending in case someone changes the sql query without realizing that it matters...
ben leinfelder
01:21 PM Revision 6726 (metacat): set the byte size of the ORE map before adding it
ben leinfelder
01:12 PM Revision 6725 (metacat): set/update the obsoletes/obsoletedBy fields in system metadata so that we always have a complete revision history for each object.
Note: ORE maps do not have revision history...yet(?) ben leinfelder
01:10 PM Revision 6724 (metacat): order the revision list, ascending.
ben leinfelder
12:29 PM Bug #5522: download linked KNB data and convert links in EML to ORE packages
Disregard the Xerces panic -- I had an old XercesImpl.jar hanging out in my classpath. ben leinfelder
11:57 AM Revision 6723 (metacat): removing unused class -- can't find a reference to it and it's causing compilation errors for me.
ben leinfelder
11:53 AM Revision 6722 (metacat): for "all" permission, return a list of READ, WRITE, CHANGE_PERMISSION
ben leinfelder

11/30/2011

05:31 PM Revision 6721 (metacat): generating ORE maps and creating/updating system metadata now. There are some Permission conversion issues to be worked out yet
ben leinfelder
05:25 PM Revision 6720 (metacat): look up access policy by guid or local id
TODO: resolve the Metacat/EML "all" permission as it relates to DataONE (there is only READ, WRITE, CHANGE_PERMISSION... ben leinfelder
05:23 PM Revision 6719 (metacat): make exception/error reporting clearer -- was getting lock messages when perhaps that was not the correct exception.
ben leinfelder
05:22 PM Revision 6718 (metacat): look up all docids is now a static method (ORE/SystemMetadata generation)
ben leinfelder
02:22 PM Revision 6717 (metacat): Add log statements for each call to ILock.unlock() for debugging.
Chris Jones
01:06 PM Bug #5522: download linked KNB data and convert links in EML to ORE packages
Using the Foresite library in Metacat to build the ORE maps fails because of jar dependencies. The dependencies are a... ben leinfelder

11/29/2011

04:21 PM Revision 6716 (metacat): Add new test method to test getAccessControl.
Jing Tao
04:20 PM Revision 6715 (metacat): Add eml test file which contains access part.
Jing Tao
03:43 PM Revision 6714 (metacat): evict the HazelCast SystemMetadata entry if we update the access control rules via Metacat's legacy API, otherwise stale SystemMetadata stays in memory instead of being looked up from the backing table store.
ben leinfelder
03:41 PM Revision 6713 (metacat): optionally include ORE generation/insertion into Metacat when generating SystemMetadata
https://redmine.dataone.org/issues/2056 ben leinfelder
02:15 PM Revision 6712 (metacat): optionally include ORE generation/insertion into Metacat when generating SystemMetadata
https://redmine.dataone.org/issues/2056 ben leinfelder
01:44 PM Revision 6711 (metacat): Set a default HazelcastInstance after init() is called, and use this instance in getLock() to acquire a lock in the cluster.
Chris Jones
01:41 PM Revision 6710 (metacat): no need to cast docInfo entries to String -- they are all strings
ben leinfelder
01:39 PM Revision 6709 (metacat): set revision history, the create/update dates and the owner/submitter (correctly)
ben leinfelder
01:05 PM Revision 6708 (metacat): use shared method for looking up "docInfo" map -- both in Metacat replication and in D1 system metadata generation
ben leinfelder
12:38 PM Revision 6707 (metacat): make default formatting a little bit easier to read
ben leinfelder
12:33 PM Revision 6706 (metacat): reformat code -- no changes
ben leinfelder
12:31 PM Revision 6705 (metacat): refactor SystemMetadata creation into separate class from the MetacatHandler -- this will be shared by upgrade code and normal metacat api.
ben leinfelder
11:00 AM Revision 6704 (metacat): include all document revisions when generating "missing" system metadata
TODO: revision graph captured in obsoletes/obsoletedBy ben leinfelder
10:10 AM Revision 6703 (metacat): When using ILock.lock(), get a lock on the string value of the Identifier, not the Identifier object itself. Hazelcast locking won't work otherwise.
Chris Jones
09:46 AM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
reopen this bug since ben added a comment on bug 5553:
There is currently a method in Metacat's access API that allo...
Jing Tao
09:38 AM Bug #5553: setaccess action may have deleting access rule functionality
Sounds like we can use it. However, we have to parse the returned result of action=getaccesscontrol in order to prese... Jing Tao
09:16 AM Bug #5553: setaccess action may have deleting access rule functionality
There is currently a method in Metacat's access API that allows you to set the entire access block for a given docume... ben leinfelder
08:55 AM Revision 6702 (metacat): Use the Hazelcast ILock mechanism to lock the system metadata identifier rather than using IMap.lock(pid).
Chris Jones

11/28/2011

04:53 PM Bug #5553: setaccess action may have deleting access rule functionality
When this bug is fixed, we should reopen the bug 5551:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5551
Jing Tao
04:53 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
Now we had temporary solution for set/revoke public readable access:
user can grant public access to a document, then...
Jing Tao
02:36 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
For the issue on comment 4, I found the clientViewBean object wasn't set sesssion id in ClientViewHelper.java. After ... Jing Tao
04:09 PM Revision 6701 (metacat): simplify SystemMetadata generation -- will be done during Metacat upgrade for D1 features/support.
ben leinfelder
03:53 PM Revision 6700 (metacat): clean up populator; use IOUtils library to do string<->stream conversions
ben leinfelder
03:37 PM Revision 6699 (metacat): utilities jar should not be committed to Metacat otherwise we will not retrieve the tagged version during Metacat build process.
ben leinfelder
03:04 PM Revision 6698 (metacat): catch all possible exceptions
ben leinfelder
02:44 PM Revision 6697 (metacat): act as a registered CN when calling CN methods -- create(), for example, is restricted to only be callable by a node of type CN.
ben leinfelder
02:22 PM Revision 6696 (metacat): Set sessionid for clientVeiwBean when it handle a request.
Always set the order type to "allowFirst". Jing Tao
12:34 PM Revision 6695 (metacat): use IOUtils for testing read/write of XML strings. This goes along with the utilities project change to use the same apache commons IO library. Be sure to clean the utilities checkout in order to catch the right utilities svn tag when building!
ben leinfelder
 

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