From 10/23/2011 to 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
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 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 --
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 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


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
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


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


03:44 PM Revision 6675 (metacat): give the Metacat admin users FULL permissions on all data/docs 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 ben leinfelder
02:47 PM Revision 6672 (metacat): replication control panel now fully implemented as an admin configuration screen 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 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


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


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


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


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


11:18 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 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. ben leinfelder


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
ben leinfelder
04:26 PM Revision 6628 (metacat): get server param only when it is expected
ben leinfelder


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:
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


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:
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


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


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 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


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
10:10 PM Revision 6598 (metacat): correctly set the prepared statement parameters for start and end date
ben leinfelder
10:09 PM Revision 6597 (metacat): check object format id values since they are not Comparable objects
ben leinfelder
09:58 PM Revision 6596 (metacat): make MNodeServiceTest pass JUnit testing
ben leinfelder
08:40 PM Revision 6595 (metacat):
ben leinfelder
08:08 PM Revision 6594 (metacat): Update CNodeService test to include serialVersion in it's calls as appropriate.
Chris Jones
08:04 PM Revision 6593 (metacat): Update CNodeService to use the serialVersion parameter and compare it to the current serialVersion of the system metadata found in the hzSystemMetadata map. Throw an InvalidRequest exception if they are not equal. This affects updateReplicationMetadata(), setReplicationStatus(), setReplicationPolicy(), setAccessPolicy(), and setOwner().
Chris Jones
08:00 PM Revision 6592 (metacat): Handle calls to CNReplication REST services. Modify handle() to field calls to /replicaPolicies, /replicaMetadata, /replicaAuthorizations, and /replicaNotifications. Add the isNodeAuthorized(), setReplicationPolicy(), setReplicationStatus(), and updateReplicationMetadata() methods to parse and pass multipart form data and params on to the CNodeService implementing class.
The CNreplication additions also include support for the serialVersion parameter that was added to some of the API ca... Chris Jones
07:50 PM Revision 6591 (metacat): Add new d1_common jar with the API changes that add serialVersion parameters to CNAuthorization and CNReplication methods.
Chris Jones
07:46 PM Revision 6590 (metacat): Add support for the various CNReplication calls. Add collectReplicationPolicy() to parse the policy out of the multipart form, and collectReplicaMetadata() to parse out the replica to be updated.
Chris Jones
05:32 PM Revision 6589 (metacat): restore -- apparently this was used with reflection in a test...
ben leinfelder


09:20 AM Revision 6588 (metacat): change to 2.0.0 release ben leinfelder
07:35 PM Revision 6587 (metacat): skip verification -- remaining TODO
ben leinfelder
07:08 PM Revision 6586 (metacat): verify certificate
ben leinfelder
06:41 PM Revision 6585 (metacat): inspect keystore entries for matching client certificate
ben leinfelder
05:27 PM Revision 6584 (metacat): lookup the correct property for keystore file
ben leinfelder


04:53 PM Revision 6583 (metacat): drop old identifier when upgrading from 1.9.5 to 2.0.0
ben leinfelder
03:23 PM Revision 6582 (metacat): use HttpClient to set up SSL connection when doing replication calls -- this will use the server's configured certificate as the client certificate on the request. The server it is calling can then inspect that certificate and decide whether or not it trusts the caller.
ben leinfelder
02:10 PM Bug #5499: citation format odd for metacat data sets
added to EML project and updated the Metacat build to pull from that tagged style update. ben leinfelder
01:57 PM Bug #5499: citation format odd for metacat data sets
Close. All that needs to change is delete #3 -- if BOTH are provided, only list the individualName and omit the orga... Matt Jones
12:43 PM Bug #5499: citation format odd for metacat data sets
After looking more closely at the code, I think we already have what you propose -- it just depends on the content of... ben leinfelder
02:09 PM Revision 6581 (metacat): use EML style tag for: only show organization when the individual is omitted ben leinfelder
01:34 PM Revision 6580 (metacat): newer d1 jar (for good measure)
ben leinfelder
01:33 PM Revision 6579 (metacat): check client-provided certificate when servicing ReplicationServlet requests.
ben leinfelder
11:54 AM Revision 6578 (metacat): Add updateReplicationMetadata() to the CN service implementation. This was missing from the API, and likely never called. It fully replaces the given replica item in the list of replicas in system metadata.
Chris Jones
09:10 AM Revision 6577 (metacat): MN.setAccessPolicy() is deprecated, commenting out the test.
Chris Jones
08:59 AM Revision 6576 (metacat): getReplica() should log replication events as DataONE Types.Event.replicate (vs 'getreplica')
Chris Jones
08:54 AM Revision 6575 (metacat): Minor indentation cleanup.
Chris Jones
06:48 AM Revision 6574 (metacat): Modify isAuthorized() to get the most up to date system metadata from the hzSystemMetadata map.
Chris Jones
06:40 AM Revision 6573 (metacat): Add a placeholder setAccessPolicy() method in MNodeService that throws NotImplemented since this method is being deprecated. Note: need to confirm that this shouldn't be calling D1Client.getCN().setAccessPolicy().
Chris Jones
06:37 AM Revision 6572 (metacat): Update getSystemMetadata() to lock(); get(); unlock() to ensure we have the latest version of system metadata from the hzSystemMetadata map. Remove the setAccessPolicy() method since it is being deprecated in the MNAuthorization API.
change insertSystemMetadata() to use a finer grained Date object on insertion. Locking of the pid happens in the sub... Chris Jones
06:33 AM Revision 6571 (metacat): Add setAccessPolicy() to CNodeService since the CN should only make changes to access policies for objects registered with the D1 system. Increment the serial version after locling and getting the most up to fdate system metadata.
Note: CCIT meeting decision says the serial version of the system metadata (during the change) should equal the curre... Chris Jones
05:21 PM Bug #2495: Charset bug: Internationalization
Moving this to 2.0.0.
Also, I think relying on the XML-declared encoding is a much safer (easier) bet than inspectin...
ben leinfelder
05:13 PM Bug #5519: Replicated data files are 0 bytes
After installing Metacat 1.9.5 on I was able to see the failure point. It was something that I fixe... ben leinfelder


04:37 PM Revision 6570 (metacat): In CNodeService, separate the CN.create() functionality from the MN.create() functionality while still using the superclass to call create(). Deal with Hazelcast locks and setting serial versions only in the CN implementation.
Chris Jones
02:27 PM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package
also see: ben leinfelder
02:21 PM Bug #5530 (Resolved): Sanparks skin shows update and delete action when user public reads a FGDC package
Here is an email from Judith:
Hi Jing
I have successfully uploaded a number of GIS layers What concerns me is
Jing Tao
02:27 PM Bug #5394: FGDC interface does not correctly show controls and permission settings
consolidating into one bug ben leinfelder
02:18 PM Bug #5519: Replicated data files are 0 bytes
There's no difference between 1.9.5 tag and trunk for the ReplicationService.handleGetDataFileRequest() method -- may... ben leinfelder
02:06 PM Bug #5519: Replicated data files are 0 bytes
Now with BOTH servers using Apache certificate/SSL mechanisms the replication is still successful.
ben leinfelder
01:25 PM Bug #5519: Replicated data files are 0 bytes
Switching to use Apache for the SSL handling still left the data replication working as expecte... ben leinfelder
12:34 PM Bug #5519: Replicated data files are 0 bytes
I set up one-way replication from -->
Using the Tomcat-only certificate gene...
ben leinfelder
01:13 PM Revision 6569 (metacat): Change updateSystemMetadata() to evaluate the incoming system metadata serial version against that found in the hzSystemMetadata map. If they are the same, do the update. If not, throw an InvalidRequest explaining that they need the most current version.
Chris Jones
08:40 AM Bug #5499: citation format odd for metacat data sets
No, I don't think that's quite right. If a Creator contains an individualName, use that and not the organization. If ... Matt Jones


07:21 PM Revision 6568 (metacat): Modify CNodeService's registerSystemMetadata() with support for SystemMetadata's serialVersion field. Also, use the hzSystemMetadata map for all system metadata reads using a lock on the pid in order to get the very latest version. This affected isNodeAuthorized(), getChecksum(), and assertRelation(). Since we're using Hazelcast, exceptions are masked as RuntimeException, so throw a ServiceFailure with the underlying message.
Chris Jones


09:46 PM Revision 6567 (metacat): Modify CNodeService's updateSystemMetadata(), setReplicationStatus(), setReplicationPolicy(), and setOwner() with support for SystemMetadata's serialVersion field. Other methods still pending an update. Use the hzSystemMetadata map for all system metadata reads using a lock on the pid in order to get the very latest version.
Chris Jones
08:42 PM Revision 6566 (metacat): removing non-junit file from the test area
ben leinfelder
08:39 PM Revision 6565 (metacat): load hazelcast test files from the classpath rather than from rob's personal directory.
ben leinfelder


04:25 PM Bug #5499: citation format odd for metacat data sets
Does there need to be an XSLT parameter that allows different skins to specify whether they want organizations treate... ben leinfelder
04:21 PM Bug #5499: citation format odd for metacat data sets
Okay, what's the final decision here?
We have givenName, surName and an organizationName. It sounds like the citatio...
ben leinfelder
04:05 PM Revision 6564 (metacat): SystemMetadataManager's functionality is handled by IdentifierManager. Removing it and it's test.
Chris Jones
04:01 PM Revision 6563 (metacat): MetadataTypeRegister is now replaced by ObjectFormatService. Removing it and it's test.
Chris Jones
02:48 PM Bug #5526 (Resolved): final test issue
One final test, sorry for the spam. Matt Jones
02:46 PM Bug #5525: test issue again
Test bug. Matt Jones
02:36 PM Bug #5525 (Resolved): test issue again
Another test to be ignored. Matt Jones
02:36 PM Bug #5524: test issue
Test bug. Closing. Matt Jones
02:34 PM Bug #5524 (Resolved): test issue
Please ignore -- this is a test issue. Matt Jones
02:23 PM Bug #5522: download linked KNB data and convert links in EML to ORE packages
Creation of SystemMetadata when no SystemMetadata is provided (i.e. any object creation not through the DataONE API) ... Chris Jones
02:06 PM Bug #5522 (New): download linked KNB data and convert links in EML to ORE packages
The KNB data sets, and EML data in general, represent linkages to data as online/url linkages in EML documents. When... Matt Jones
02:16 PM Bug #5523 (Resolved): setting authoritative MN and rightsHolder for KNB data on conversion
When EML and data in the NCEAS and LTER metacat is converted to use in the new KNB MN, we need to generate system me... Matt Jones
01:28 PM Bug #5515: change version to 2.0.0 in prep for release
db version scripts and properties are updated to 2.0.0 ben leinfelder
01:23 PM Bug #3815: Ampersand character not correctly encoded
I only see delNormalize() being called from the deleteData() function in register-dataset.cgi -- but perhaps similar ... ben leinfelder
01:11 PM Bug #3815: Ampersand character not correctly encoded
The specific example looks to have its origins in delNormalize (sic) within register-dataset.cgi -- the first regex o... Shaun Walbridge
10:23 PM Bug #3815: Ampersand character not correctly encoded
Using the Java MetacatClient API to insert a document with &amp; also worked fine (no additional encoding of the & sy... ben leinfelder
08:23 PM Bug #3815: Ampersand character not correctly encoded
Using the dev skin to load an XML document with an ampersand encoded as: &amp; kept the character intact. To me, this... ben leinfelder
01:17 PM Bug #4907: Replication error stops insert/update of valid EML document
Added clearer error handling when replication lock requests cannot be gotten ben leinfelder
01:16 PM Revision 6562 (metacat): include clearer error message when UPDATE action is requested on a replicated document and we fail to successfully get a lock from the source Metacat server ben leinfelder
01:01 PM Bug #4083: Metacat doesn't declare XML document encoding
For incoming XML files, Metacat will inspect the encoding specified in the prolog and use that if found; defaulting t... ben leinfelder
12:48 PM Bug #2236: metacat parser allows eml with missing content
I tried inserting this document as is: it was fine because it validates against the 2.0.1 schema.
I tries modifying i...
ben leinfelder
07:41 PM Bug #5054: Unable to insert large EML documents and no error status returned
On first inspection, it appears that the request is coming into Metacat with no parameters set when I use the dev ski... ben leinfelder
07:00 PM Bug #5273: docs with inline-data allow invalid xml into metacat
I tried this with the attached inline.xml file that has an invalid unescaped ampersand in the inline section -- Metac... ben leinfelder
06:58 PM Bug #5273: docs with inline-data allow invalid xml into metacat
This file uses unescaped ampersand (&) in the inline data section. ben leinfelder
05:51 PM Revision 6561 (metacat): move the DataONE 1.0.0-SNAPSHOT
ben leinfelder


04:33 PM Revision 6560 (metacat): correctly check for missing config values during geoserver configuration
ben leinfelder
04:05 PM Bug #5515: change version to 2.0.0 in prep for release
updated docs and the source tree to use tomcat6 rather than tomcat5.5 ben leinfelder
04:05 PM Revision 6559 (metacat): call the web.xml tomcat6 not tomcat5
ben leinfelder
04:01 PM Revision 6558 (metacat): remove reference to tomcat5.5 in favor of tomcat6. including the "custom" start up script that used the sun jdk -- this can be configured rather than coded into the script.
ben leinfelder
03:59 PM Revision 6557 (metacat): correctly check for missing config values during geoserver configuration
ben leinfelder
03:45 PM Revision 6556 (metacat): remove reference to the "custom" /etc/init.d/tomcat6 script -- this should not be used since there are now better ways to customize the tomcat start up
ben leinfelder
03:27 PM Revision 6555 (metacat): use 2.0.0
ben leinfelder
03:21 PM Revision 6554 (metacat): -use 2.0.0 version
-use tomcat6
-use /var/lib/tomcat6 as the example tomcat home directory
ben leinfelder
02:22 PM Revision 6553 (metacat): use 2.0.0 -- stub out the release notes
ben leinfelder
02:13 PM Revision 6552 (metacat): Configure and use CertificateManager in order to act as the MN when performing replicate() and getReplica() mthods.
ben leinfelder
01:30 PM Bug #3811: Spatial caches should be backed up and restored
If someone wants to put the spatial cache in /var/metacat they will have to do it manually, then configure metacat (w... ben leinfelder
01:01 PM Bug #2084: Pathquery support for temporal search on date fields
Will exercise this during testing for release. ben leinfelder
01:00 PM Revision 6551 (metacat): use logging, not system.out
ben leinfelder
12:40 PM Revision 6550 (metacat): change upgrade scripts/routines to use 2.0.0 version number instead of 1.10.0
ben leinfelder
11:35 AM Revision 6549 (metacat): make sure we close the prepared statement always
ben leinfelder
11:17 AM Revision 6548 (metacat): The incoming source node param is just a string, not XML, so don't attempt to deserialize it. Rather, just make a new NodeReference object and set it's value to the value of the incoming param.
Chris Jones
08:58 AM Revision 6547 (metacat): include CILogon link and more explanation about what is going on with the mapping.
ben leinfelder
08:49 AM Revision 6546 (metacat): Change the version from 1.9.4 to 1.9.5.
Jing Tao
06:59 PM Bug #5520 (Resolved): Create replication integration test suite
Replication integration tests should include:
-force replication between two servers -- A, B (write, update, delete)...
ben leinfelder
06:31 PM Bug #5519 (Resolved): Replicated data files are 0 bytes
We set up 2-way replication between PPBio and PELD (Brazilian Metacat instances) and have since seen that the replica... ben leinfelder


04:30 PM Bug #2084: Pathquery support for temporal search on date fields
This should be in 2.0.0 since it is already in the trunk. The upgrade script is the only thing I am worried about -- ... ben leinfelder
04:11 PM Bug #5262: EML document owner can't read the document
Probably solution is to use Java's canonicalization routines to normalize the DN, as Ben has done on the DataONE DNs.... Matt Jones
03:59 PM Bug #5244: ldapweb.cgi shouldn't report ou=Account accounts since they're unusable
Need to check with Shaun if this is actually fixed. Matt Jones
03:54 PM Bug #4651: data packages losing data tables (and then finding them again)
Unable to replicate. Please reopen if more details emerge. Matt Jones
03:48 PM Bug #4442: Spatial indexing should not run and block metacat
Related to bug #3811. Matt Jones
03:47 PM Bug #5518 (In Progress): Track down the performance issue of metacat query.
Matt queried knb with the word "water". It took one minute and half. We need to figured out why it so slow. Jing Tao
03:46 PM Bug #3811: Spatial caches should be backed up and restored
Decided that its best to move these files to /var/metacat by default. Matt Jones
03:44 PM Bug #5234: Replication -- user does not have permission to update access rule for data file
In v1.9.5 we use a null replication user to perform replication (rather than the user_owner from the xml_documents ta... ben leinfelder
03:17 PM Bug #4900: LDAP referral connection timeout
Decided that #3 is not feasible since accounts may be in groups defined on various LDAP servers. ben leinfelder
01:20 PM Bug #5517 (Resolved): mark EcoGrid and Servlet APIs as deprecated
EcoGrid and Servlet APIs in metacat are being replaced (gradally) by the DataONE services. Mark these older APIs as ... Matt Jones
01:19 PM Bug #5516 (Resolved): continue updating user documentation
Documentation needs editing to describe new 2.0.0 features, including support for new DataONE APIs, deprecation of ol... Matt Jones
01:15 PM Bug #5515 (Resolved): change version to 2.0.0 in prep for release
To prepare for the release, change te version number to 2.0.0 for all documentation, including README, Sphinx docs, etc. Matt Jones
01:01 PM Bug #5288: Metacat got "java.lang.OutOfMemoryError: PermGen space" after new geoserver update
Not sure if there is an action here. Maybe add this information to the Metacat documentation/faq? Matt Jones
12:47 PM Bug #4083: Metacat doesn't declare XML document encoding
I think these encoding issues have been fixed by Ben in trunk, but we need to discuss it to see if anything further n... Matt Jones
12:38 PM Bug #1601: Metacat will add default value for optional parameter into eml 2 document
Marking as complete, because the read problem is fixed based on now reading original from disk. The insert problem i... Matt Jones
12:34 PM Bug #4275: Earthgrid REST API Implementation
Task now being handled via #5011 DataONE service API implementation. This original work on interfaces has been obsol... Matt Jones
12:17 PM Bug #5514: implement DataONE service API
Duplicate bug to #5011. Matt Jones
12:15 PM Bug #5514 (Resolved): implement DataONE service API
Support the new DataONE service API for interoperable data repositories:
Matt Jones
12:10 PM Bug #5513 (Resolved): add support for DOI identifiers from EZID
DOI identifiers can be created through the EZID service run by the California Digital Library. See:
Matt Jones
11:08 AM Revision 6545 (metacat): correctly check that user is logged into metacat before proceeding
ben leinfelder
11:07 AM Revision 6544 (metacat): use null session for now
ben leinfelder
05:54 PM Revision 6543 (metacat): draft of legacy-to-d1 account mapping interface
ben leinfelder

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