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From 11/03/2011 to 12/02/2011

12/03/2011

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
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

12/02/2011

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
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
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

12/01/2011

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
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

11/30/2011

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
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

11/29/2011

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
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
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
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
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
04:09 PM Revision 6701 (metacat): simplify SystemMetadata generation -- will be done during Metacat upgrade for D1 features/support.
ben leinfelder

11/28/2011

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
02:36 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
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

11/23/2011

02:55 PM Bug #5553 (New): setaccess action may have deleting access rule functionality
Currently, setaccess action can only add access rules to the metacat. There is a limitation.
Sometimes, we want to...
Jing Tao
02:48 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
Also i noticed after set the access, the delete, update and set access button disappeared. Only download button can b... Jing Tao
02:36 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
Since "setaccess" action can add access rules, this will cause problem.
Since the documents' allow rules for public r...
Jing Tao
02:23 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
To a none-public readable document, if we click the set access button with the checked public read check box, the doc... Jing Tao
01:59 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).
The kepler_kepler_21 is a FGDC document with the public readable access rule. Here is the record on xml_access:
keple...
Jing Tao
11:09 AM Bug #5551 (Resolved): Set public access button on the FGDC document display page doesn't work (on sanparks skin).
When I tried to grant a public readable access to a nonpublic readable document, i got an error:
User public does n...
Jing Tao
01:07 PM Bug #5537: Move replication control panel to /admin servlet
There is now a separate /admin screen for replication configuration. Now /replication can require SSL client certific... ben leinfelder
12:49 PM Revision 6694 (metacat): remove the D1 configuration group (header)
ben leinfelder
12:10 PM Revision 6693 (metacat): verify checksum when retrieving replica from another member node.
https://redmine.dataone.org/issues/1794 ben leinfelder
11:59 AM Revision 6692 (metacat): make sure to get/put system metadata to the HZ map instead of using IdentifierManager directly
verified changes for: https://redmine.dataone.org/issues/1999 ben leinfelder
11:37 AM Revision 6691 (metacat): match documentation for the MN.describe() header
https://redmine.dataone.org/issues/1904 ben leinfelder
11:31 AM Revision 6690 (metacat): configure synch schedule in the admin screen
https://redmine.dataone.org/issues/1933 ben leinfelder
11:03 AM Revision 6689 (metacat): look-up sych schedule from metacat properties instead of hardcoding them
https://redmine.dataone.org/issues/1933 ben leinfelder
11:00 AM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package
Ben:
Okay. This is the current behavior. I am going to close the bug.
Jing Tao
10:44 AM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package
I think the checkbox should reflect the current state of the document. If it is unchecked, that indicates that it is ... ben leinfelder
05:10 PM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package
If fgdc-root.xsl, it has the control to display the buttons or not. The control is the parameter "enableFGDCediting".... Jing Tao
10:19 AM Revision 6688 (metacat): when comparing D1 Subject objects, use the equals() method not direct string comparison
https://redmine.dataone.org/issues/2050 ben leinfelder
10:07 AM Revision 6687 (metacat): access nodeList list correctly
https://redmine.dataone.org/issues/2049 ben leinfelder
04:10 PM Revision 6686 (metacat): When read a FGDC document, Metacat will add a new parameter enableFGDCediting params for the xml transforming.
Jing Tao

11/21/2011

02:23 PM Revision 6685 (metacat): New d1 common jar. Fixing my overwritten jar.
Chris Jones
02:22 PM Bug #5548 (New): Replace COS Mime multipart library
Here is a comment from Matt in bug 5543:
The COS Mime multipart library is incredibly old, and we should
seriousl...
Jing Tao
02:20 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin
Ben committed a new version of cos.jar file and modified the MetacatClient.java to handle the file size being -1. In ... Jing Tao
11:33 AM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin
We may not even have to require a known size -- Metacat isn't storing that information. Sure, the new DataONE apis us... ben leinfelder
02:16 PM Revision 6684 (metacat): set the uploade file size -1.
Jing Tao
02:11 PM Revision 6683 (metacat): New d1 jars with changes to SubjectBase in the types classes.
Chris Jones
12:10 PM Revision 6682 (metacat): remove D1 configuration -- it has its own admin screen now
ben leinfelder
12:09 PM Revision 6681 (metacat): updated cos.jar -- cos-26Dec2008.zip
File upload improvements:
Added support for Servlets 2.4 and Java 5.
Added an ExceededSizeException type to make cat...
ben leinfelder
11:21 AM Revision 6680 (metacat): allow unknown content sizes
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5543 ben leinfelder
10:17 AM Bug #5547 (New): Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin
When you click "Register Data" tab on Sanparks skin, it will show a login form if you haven't login. However, it will... Jing Tao

11/19/2011

07:51 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin
Jing --
I'm not sure what the right solution is here, but here are some thoughts. First, trying to get the length o...
Matt Jones
05:58 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin
After dug around the code, i figured out the problem is at the CoientViewHelper.java.
In handlePackageUpload method,...
Jing Tao
05:00 PM Revision 6679 (metacat): run replicate() in a separate thread so that we don't wait for potentially large data objects to be moved around the system.
ben leinfelder

11/18/2011

12:13 PM Revision 6678 (metacat): Call replicate() asynchronously.
Chris Jones
09:13 AM Revision 6677 (metacat): Use status.toLowerCase() to deal with ReplicationStatus conversion issues. This needs to be reviewed.
Chris Jones
09:10 AM Revision 6676 (metacat): Use Subject.equals() when comparing DNs rather than CertificateManager.equalsDN(). Don't lock the pid in isNodeAuthorized() to debug for timeout issues. Minor debugging changes.
Chris Jones
04:04 PM Bug #4728: grant document management privileges to admin user
Admin user[s] now have complete control of the Metacata data and metadata. The list of items here (1-6) are covered n... ben leinfelder

11/17/2011

03:44 PM Revision 6675 (metacat): give the Metacat admin users FULL permissions on all data/docs
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4728 ben leinfelder
03:20 PM Revision 6674 (metacat): correct path for question mark icon -- though the documentation link is broken
ben leinfelder
02:49 PM Revision 6673 (metacat): remove replication control panel from dev skin -- now in admin interface
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
02:47 PM Revision 6672 (metacat): replication control panel now fully implemented as an admin configuration screen
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
02:40 PM Bug #5544 (Resolved): the footer of the output page after clicking TPC status/workflow can't be read on Sanparks skin
The text of the footer of the output page is black and can be read when a user click TPC workflow/status menu. Jing Tao
02:31 PM Bug #5542: Data Package Upload form in SANParks skin missing the description text
In footer, set some text to be regwhitetext. So everything looks fine. Jing Tao
02:30 PM Bug #5542: Data Package Upload form in SANParks skin missing the description text
The text was not missing, but its color was white and couldn't be read.
The regtext class in sanparks.css was set:
....
Jing Tao
02:23 PM Revision 6671 (metacat): change the footer to be regwhitetext style.
Jing Tao
02:22 PM Revision 6670 (metacat): make regtext style black and add new style regwhitetext.
Jing Tao
12:19 PM Revision 6669 (metacat): move replication configuration actions to the admin servlet and out of the replication servlet
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5528 ben leinfelder
12:03 PM Bug #5533: Sanpark skin main page has login issue
For the first issue that a user could not log in on IE, the reason is IE invalid the login form after a div, which co... Jing Tao
11:42 AM Revision 6668 (metacat): Using the method sending form parameters rather than form object.
The reason is IE will invalidate the form object after putting a login message on the div which contains the form. Jing Tao
11:38 AM Revision 6667 (metacat): Add methods to send form parameters to the server.
Jing Tao
11:19 AM Revision 6666 (metacat): save SystemMetadata when replicating data and metadata -- this way if/when the node decides to be a DataONE MN it already has the information needed for each object
ben leinfelder
06:15 PM Revision 6665 (metacat): Minor logging for isNodeAuthorized(), and compare subjects properly. Change this to Subject.compareTo() when it is vetted.
Chris Jones
04:09 PM Revision 6664 (metacat): check for authenticated and verified user permissions
ben leinfelder

11/16/2011

03:34 PM Revision 6663 (metacat): throw NotAuthorized when there is no session
ben leinfelder
02:55 PM Bug #5543 (Resolved): Can't upload a FGDC metadata file with a data file in SANParks skin
I tried to use the data package upload form to upload a FGDC file, it succeeded. However, if i uploaded a FGDC file w... Jing Tao
02:45 PM Bug #5542 (Resolved): Data Package Upload form in SANParks skin missing the description text
It misses the text like:
Enter the Meta Data File (*.xml)
Enter Data File 1 (*.shp)
Enter Data File 2 (*.dbf)
....
Jing Tao
02:27 PM Revision 6662 (metacat): Catch RuntimeExceptions thrown by Hazelcast as opposed to general Exceptions to we don't catch exceptions we're trying to throw.
Chris Jones
01:51 PM Revision 6661 (metacat): include Subject comparator changes
ben leinfelder
12:58 PM Revision 6660 (metacat): get params from multipart params for systemMetadataChanged call
ben leinfelder
10:45 AM Revision 6659 (metacat): generalize exception handling -- add cause detail
ben leinfelder
10:38 AM Revision 6658 (metacat): remove DataONE schema reference in xml_catalog
ben leinfelder
10:34 AM Revision 6657 (metacat): Changes to setReplicationStatus and isNodeAuthorized(), working out minor bugs in replication.
Chris Jones
09:50 AM Revision 6656 (metacat): include exception cause when throwing new exception (combine RuntimeException in Exception handling -- they are almst identical)
ben leinfelder
04:01 PM Revision 6655 (metacat): use /cn/xslt/ for the standard cn deployment
ben leinfelder

11/15/2011

03:55 PM Revision 6654 (metacat): new jars with (at least) xslt updates for the D1 CN
ben leinfelder
10:48 AM Revision 6653 (metacat): throw InvalidToken when session is null
ben leinfelder
10:47 AM Revision 6652 (metacat): correct typo
ben leinfelder
09:37 AM Revision 6651 (metacat): Send the correct node id (the target node) when calling setReplicationStatus()
Chris Jones
01:30 AM Bug #5513: add support for DOI identifiers from EZID
I created a new library called 'ezid' in its own project that can be used to access the EZID REST services from withi... Matt Jones
04:00 PM Revision 6650 (metacat): get pid from normal params, not the URL -- the client should include them in the params -- and not as a serialized "object" since it is just a string value
ben leinfelder

11/14/2011

03:49 PM Revision 6649 (metacat): check obsoletes and obsoletedBy PIDs when updating objects
ben leinfelder
03:34 PM Revision 6648 (metacat): delete system metadata when MN.delete() is called.
ben leinfelder
03:31 PM Revision 6647 (metacat): Using the method which reloads the page after sending login. This will fix an issue that the search function couldn't get the session id after login.
Jing Tao
03:29 PM Revision 6646 (metacat): Add a new method which will reload the page after submitting a form.
Jing Tao
02:59 PM Revision 6645 (metacat): throw InvalidToken when there is no session (certificate) provided in update() and delete() methods.
ben leinfelder
05:47 PM Revision 6644 (metacat): Calls to setReplicationStatus() can only be made by a CN or the MN that is the target replica node. Implement this service restriction in CNodeService using CertificateManager's equalsDN() method.
Chris Jones
04:47 PM Revision 6643 (metacat): The ReplicationStatus parameter is 'status', not 'replicationStatus', in the architecture documentation.
Chris Jones

11/13/2011

03:50 PM Revision 6642 (metacat): Although parameters for setReplicationStatus() are expected as multipart/form-data fields, they seem to be added to the HttpServletRequest as URL parameters during the proxy forwarding in d1_cn_rest_proxy. Test for their existence as multipart fields, but fall back to request params, otherwise, throw an InvalidRequest exception.
Chris Jones

11/11/2011

11:18 AM Revision 6641 (metacat): updated d1_libclient jar from trunk
ben leinfelder
11:17 AM Revision 6640 (metacat): updated d1_common jar from trunk
ben leinfelder
09:54 AM Revision 6639 (metacat): lookup stylesheet from metacat.properties for CN list objects and list formats. This is used in conjunction with the CN rest service deployment where the xslt is actually kept.
ben leinfelder
09:12 AM Revision 6638 (metacat): actually persist the MN id value to the properties file
ben leinfelder
09:10 AM Bug #5537 (Resolved): Move replication control panel to /admin servlet
Instead of using the SSL client certificate secured /replication servlet to administer replication settings via the w... ben leinfelder
09:06 AM Revision 6637 (metacat): set the newly assigned MN id after we call CN.register().
ben leinfelder
09:00 AM Bug #5531: Remove/make optional the DataONE MN registration that occurs during Metacat configuration
There is now a separate admin configuration screen for dataone:
-you can bypass it in the same way you can bypass geo...
ben leinfelder
08:58 AM Revision 6636 (metacat): Added stack trace debugging for CNodeService.isNodeAuthorized() for tracking down replication issues.
Chris Jones
11:36 PM Revision 6635 (metacat): DataONE MN registration/configuration is now its own configuration page in the admin interface.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5531 ben leinfelder

11/10/2011

12:07 PM Revision 6634 (metacat): Since we're using a multipart form to encode parameters, extract the params out of the multipart form prior to doing a get() from the multipartparams map in setReplicationStatus(). Likewise, do the same in updateReplicationMetadata() and setReplicationPolicy().
Chris Jones
08:52 AM Revision 6633 (metacat): New libclient jar with changes to CNode.setReplicationStatus() (r5824).
Chris Jones
08:30 AM Revision 6632 (metacat): Use a session object that is set to null when calling CNode.setReplicationStatus()
Chris Jones
08:05 AM Revision 6631 (metacat): Add debugging code to MNodeService.getReplica().
Chris Jones
06:55 PM Revision 6630 (metacat): Set a new Session object to null, to be overwritten by the CertificateManager session information from the X.509 certificate.
Chris Jones
05:45 PM Revision 6629 (metacat): more changes for http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527
ben leinfelder
04:26 PM Revision 6628 (metacat): get server param only when it is expected
ben leinfelder

11/09/2011

03:34 PM Revision 6627 (metacat): check replication table (not keystore) for trusted server host name match
ben leinfelder
03:19 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.
Both Jing and I were unable to replicate this bug testing against a more recent Metacat trunk build ben leinfelder
02:56 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.
I tried this out with Kepler 2.1, writing sample EML 2.0.0 and EML 2.1.0 metadata (and data files). All worked out fi... ben leinfelder
12:14 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.
Is there a sample Kepler workflow we can use to debug this? ben leinfelder
02:28 PM Bug #3815: Ampersand character not correctly encoded
I just tried the registry on a test machine running most recent Metacat trunk and the ampersand was correctly encoded... ben leinfelder
12:51 PM Revision 6626 (metacat): Adding new D1 jars (r5818) with changes to libclient's CNode.setReplicationStatus(). It now sends multipart params rather than files since there's no XML structure to ReplicationStatus.
Chris Jones
12:47 PM Bug #5536: Restore replicated data files that are 0 bytes
Matt suggests an alternative approach: delete the files and the DB records for those files so that the next timed rep... ben leinfelder
12:23 PM Bug #5536 (Resolved): Restore replicated data files that are 0 bytes
Due to a replication bug, some data files were not replicated fully. These should be tracked down and restored. ben leinfelder
12:44 PM Bug #4405: PISCO, KNB and LTER have different query result for SBC datasets.
Running the query against the PISCO server returned the expected 14 records. ben leinfelder
12:33 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
Looks good to me. Matt Jones
12:31 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
Proposed tags. Please comment.
-eml schema 2.1.1 (tags/RELEASE_EML_2_1_1)
-eml style sheets (tags/RELEASE_EML_UTILS_1...
ben leinfelder
12:22 PM Bug #5519: Replicated data files are 0 bytes
This is fixed. We just need to figure out the files that have not replicated successfully. Any 0-length files on KNB ... ben leinfelder
12:20 PM Bug #3811: Spatial caches should be backed up and restored
The final step in the process should be to _NOT_ regenerate the spatial cache during 2.0 configuration. ben leinfelder
12:13 PM Revision 6625 (metacat): added note about PermGen space + Geoserver
ben leinfelder
12:13 PM Bug #5288: Metacat got "java.lang.OutOfMemoryError: PermGen space" after new geoserver update
added to word doc ben leinfelder
12:03 PM Bug #5513: add support for DOI identifiers from EZID
I've managed to get UCSB to agree to pay for an EZID account from CDL that we'll be able to use to programatically as... Matt Jones
10:31 AM Bug #5535 (New): The 611 CDR documents replicated to KNB need to be repaired by fixing their inline data.
This bug is the section 4 of the ongoing concerns:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3296
During...
Jing Tao
09:59 AM Bug #5534 (Resolved): Replication log somehow doesn't work.
Metacat logged the some important replication information into the metacatreplication.log file which stays in the dir... Jing Tao
09:41 AM Bug #3296: Replication: Many EML documents fail to replicate
Follow-up to the previous comment of 2008-06-05:
1. There are still 94 documents that fail to replicate. These are a...
Duane Costa
07:14 AM Revision 6624 (metacat): Fix cast to List<Node> in isNodeAuthorized().
Chris Jones
04:40 PM Revision 6623 (metacat): List the correct REST endpoints for replication in the documentation.
Chris Jones

11/08/2011

03:49 PM Revision 6622 (metacat): upgrade to 1.0.1-SNAPSHOT DataONE jars
ben leinfelder
01:59 PM Revision 6621 (metacat): check for blank key passwords
ben leinfelder
11:31 AM Revision 6620 (metacat): started replication unit test
ben leinfelder
10:36 AM Revision 6619 (metacat): Keep /dirtySystemMetadata as the REST endpoint for systemMetadataChanged() for now.
Chris Jones
08:19 AM Bug #5533: Sanpark skin main page has login issue
An additional message from judith:
Jing
I notice that when you login through the web page on firefox You get the me...
Jing Tao
05:43 PM Bug #4356: knb website query result shows old version of a document
Ben and I tested the updating and query on both forced replication and timed replication between two metacats. We cou... Jing Tao
04:07 PM Bug #4356: knb website query result shows old version of a document
I used a morpho to create a eml document and insert it to metacat. Then i did a search and records was added to xml_q... Jing Tao
05:16 PM Revision 6618 (metacat): New D1 libraries, fix for MNode.isNodeAuthorized() and other exception handling.
Chris Jones
05:03 PM Revision 6617 (metacat): MockCNode.getSystemMetadata() no longer throws InvalidRequest.
Chris Jones

11/07/2011

03:53 PM Revision 6616 (metacat): add note about alternative methods for getting cert/key
ben leinfelder
03:50 PM Revision 6615 (metacat): use prepared statement place holder (?)
ben leinfelder
02:31 PM Revision 6614 (metacat): use DateTimeMarshaller for all replication date transfers
ben leinfelder
12:31 PM Revision 6613 (metacat): print the stacktrace when there is an error -- debuggin!
ben leinfelder
11:50 AM Revision 6612 (metacat): remove catch blocks for unthrown exceptions
ben leinfelder
10:55 AM Revision 6611 (metacat): use SSL to get content from stream
ben leinfelder
10:52 AM Revision 6610 (metacat): Update methods in MNodeService to reflect they modifications of the MN API with regard to exceptions being raised. Largely removed InvalidRequest from a number of methods, and instead threw an appropriate NotFound or ServiceFailure instead.
Chris Jones
10:01 AM Revision 6609 (metacat): D1NodeService get(), getSystemMetadata(), and isAuthorized() no longer throw InvalidRequest.
Chris Jones

11/04/2011

04:33 PM Bug #5533 (Resolved): Sanpark skin main page has login issue
Hi Jing
Yes I see that it works on firefox the problem is that all our staff have to use IE So is there a way to f...
Jing Tao
03:18 PM Bug #5532 (Resolved): Use strict build tag strategy for 2.0.0 release
Currently Metacat relies on a number of external projects and repositories. We should take this opportunity to finali... ben leinfelder
03:17 PM Revision 6608 (metacat): Add new D1 jars with 1.0.0 API additions (MNStorage.systemMetadataChanged()) and libclient fixes.
Chris Jones
03:04 PM Revision 6607 (metacat): newer seek tag
ben leinfelder
02:45 PM Revision 6606 (metacat): uses prepared statement instead of plain old statement.
deprecated the DBConnection.createStatement() method to discourage direct parameter value use in favor of parameter b... ben leinfelder
02:35 PM Revision 6605 (metacat): Add a test for systemMetadataChanged. This should be fleshed out more so that the test uses a CN certificate.
Chris Jones
02:21 PM Revision 6604 (metacat): Fix getReplica() handling code for getReplica() and systemMetadataChanged(). Calls to getReplica() in MNode were calling get(), so the lack of resource handling was being missed.
Chris Jones
02:19 PM Revision 6603 (metacat): Handle multipart params where the libclient methods are using them.
Chris Jones
12:32 PM Revision 6602 (metacat): uses prepared statement parameter binding for queries
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527 ben leinfelder
10:26 AM Bug #5531 (Resolved): Remove/make optional the DataONE MN registration that occurs during Metacat configuration
Right now when I [re]configure Metacat I hit the DataONE CN in an attempt to register myself as a MN. This should be ... ben leinfelder

11/03/2011

12:59 PM Revision 6601 (metacat): Add new D1 jars with the new MNStorage.systemMetadataChanged() additions.
Chris Jones
12:55 PM Revision 6600 (metacat): Add in the systemMetadataChanged() method in MNodeService to respond to notifications. Only allow subjects from CNs listed in the node list to make the call. Update the local copy of the system metadata document for the given pid.
Chris Jones
10:36 AM Revision 6599 (metacat): Include the serialVersion in the call to CN.setReplicationStatus() after replicating data.
Chris Jones
 

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