From 10/05/2011 to 11/03/2011
- 12:59 PM Revision 6601 (metacat): Add new D1 jars with the new MNStorage.systemMetadataChanged() additions.
- 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.
- 10:36 AM Revision 6599 (metacat): Include the serialVersion in the call to CN.setReplicationStatus() after replicating data.
- 10:10 PM Revision 6598 (metacat): correctly set the prepared statement parameters for start and end date
- 10:09 PM Revision 6597 (metacat): check object format id values since they are not Comparable objects
- 09:58 PM Revision 6596 (metacat): make MNodeServiceTest pass JUnit testing
- 08:40 PM Revision 6595 (metacat): http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5527
- 08:08 PM Revision 6594 (metacat): Update CNodeService test to include serialVersion in it's calls as appropriate.
- 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().
- 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...
- 07:50 PM Revision 6591 (metacat): Add new d1_common jar with the API changes that add serialVersion parameters to CNAuthorization and CNReplication methods.
- 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.
- 05:32 PM Revision 6589 (metacat): restore -- apparently this was used with reflection in a test...
- 09:20 AM Revision 6588 (metacat): change to 2.0.0 release
- 07:35 PM Revision 6587 (metacat): skip verification -- remaining TODO
- 07:08 PM Revision 6586 (metacat): verify certificate
- 06:41 PM Revision 6585 (metacat): inspect keystore entries for matching client certificate
- 05:27 PM Revision 6584 (metacat): lookup the correct property for keystore file
- 04:53 PM Revision 6583 (metacat): drop old identifier when upgrading from 1.9.5 to 2.0.0
- 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.
- 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.
- 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...
- 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...
- 02:09 PM Revision 6581 (metacat): use EML style tag for: only show organization when the individual is omitted
- 01:34 PM Revision 6580 (metacat): newer d1 jar (for good measure)
- 01:33 PM Revision 6579 (metacat): check client-provided certificate when servicing ReplicationServlet requests.
- 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.
- 09:10 AM Revision 6577 (metacat): MN.setAccessPolicy() is deprecated, commenting out the test.
- 08:59 AM Revision 6576 (metacat): getReplica() should log replication events as DataONE Types.Event.replicate (vs 'getreplica')
- 08:54 AM Revision 6575 (metacat): Minor indentation cleanup.
- 06:48 AM Revision 6574 (metacat): Modify isAuthorized() to get the most up to date system metadata from the hzSystemMetadata map.
- 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().
- 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...
- 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...
- 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...
- 05:13 PM Bug #5519: Replicated data files are 0 bytes
- After installing Metacat 1.9.5 on fred.msi.ucsb.edu I was able to see the failure point. It was something that I fixe...
- 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...
- 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.
- 01:25 PM Bug #5519: Replicated data files are 0 bytes
- Switching bespin.nceas.ucsb.edu to use Apache for the SSL handling still left the data replication working as expecte...
- 12:34 PM Bug #5519: Replicated data files are 0 bytes
- I set up one-way replication from bespin.nceas.ucsb.edu --> fred.msi.ucsb.edu.
Using the Tomcat-only certificate gene...
- 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.
- 02:27 PM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package
- also see: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5394
- 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:
I have successfully uploaded a number of GIS layers What concerns me is
- 02:27 PM Bug #5394: FGDC interface does not correctly show controls and permission settings
- consolidating into one bug
- 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.
- 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 ...
- 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.
- 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.
- 08:42 PM Revision 6566 (metacat): removing non-junit file from the test area
- 08:39 PM Revision 6565 (metacat): load hazelcast test files from the classpath rather than from rob's personal directory.
- 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...
- 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...
- 04:05 PM Revision 6564 (metacat): SystemMetadataManager's functionality is handled by IdentifierManager. Removing it and it's test.
- 04:01 PM Revision 6563 (metacat): MetadataTypeRegister is now replaced by ObjectFormatService. Removing it and it's test.
- 02:48 PM Bug #5526 (Resolved): final test issue
- One final test, sorry for the spam.
- 02:46 PM Bug #5525: test issue again
- Test bug.
- 02:36 PM Bug #5525 (Resolved): test issue again
- Another test to be ignored.
- 02:36 PM Bug #5524: test issue
- Test bug. Closing.
- 02:34 PM Bug #5524 (Resolved): test issue
- Please ignore -- this is a test issue.
- 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) ...
- 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...
- 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...
- 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
- 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 ...
- 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...
- 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
- 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
- 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...
- 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...
- 10:23 PM Bug #3815: Ampersand character not correctly encoded
- Using the Java MetacatClient API to insert a document with & also worked fine (no additional encoding of the & sy...
- 08:23 PM Bug #3815: Ampersand character not correctly encoded
- Using the dev skin to load an XML document with an ampersand encoded as: & kept the character intact. To me, this...
- 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...
- 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...
- 06:58 PM Bug #5273: docs with inline-data allow invalid xml into metacat
- This file uses unescaped ampersand (&) in the inline data section.
- 05:51 PM Revision 6561 (metacat): move the DataONE 1.0.0-SNAPSHOT
- 04:33 PM Revision 6560 (metacat): correctly check for missing config values during geoserver configuration
- 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
- 04:05 PM Revision 6559 (metacat): call the web.xml tomcat6 not tomcat5
- 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.
- 03:59 PM Revision 6557 (metacat): correctly check for missing config values during geoserver configuration
- 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
- 03:27 PM Revision 6555 (metacat): use 2.0.0
- 03:21 PM Revision 6554 (metacat): -use 2.0.0 version
- -use tomcat6
-use /var/lib/tomcat6 as the example tomcat home directory
- 02:22 PM Revision 6553 (metacat): use 2.0.0 -- stub out the release notes
- 02:13 PM Revision 6552 (metacat): Configure and use CertificateManager in order to act as the MN when performing replicate() and getReplica() mthods.
- 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...
- 01:01 PM Bug #2084: Pathquery support for temporal search on date fields
- Will exercise this during testing for release.
- 01:00 PM Revision 6551 (metacat): use logging, not system.out
- 12:40 PM Revision 6550 (metacat): change upgrade scripts/routines to use 2.0.0 version number instead of 1.10.0
- 11:35 AM Revision 6549 (metacat): make sure we close the prepared statement always
- 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.
- 08:58 AM Revision 6547 (metacat): include CILogon link and more explanation about what is going on with the mapping.
- 08:49 AM Revision 6546 (metacat): Change the version from 1.9.4 to 1.9.5.
- 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)...
- 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...
- 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 -- ...
- 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....
- 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.
- 03:54 PM Bug #4651: data packages losing data tables (and then finding them again)
- Unable to replicate. Please reopen if more details emerge.
- 03:48 PM Bug #4442: Spatial indexing should not run and block metacat
- Related to bug #3811.
- 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.
- 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.
- 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...
- 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.
- 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 ...
- 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...
- 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.
- 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?
- 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...
- 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...
- 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...
- 12:17 PM Bug #5514: implement DataONE service API
- Duplicate bug to #5011.
- 12:15 PM Bug #5514 (Resolved): implement DataONE service API
- Support the new DataONE service API for interoperable data repositories:
- 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:
- 11:08 AM Revision 6545 (metacat): correctly check that user is logged into metacat before proceeding
- 11:07 AM Revision 6544 (metacat): use null session for now
- 02:03 PM Revision 6542 (metacat): add User-Agent logging to support D1 requirements
- 12:40 PM Revision 6541 (metacat): remove old RestServlet handler -- not used now
- 05:49 PM Revision 6539 (metacat): use default fmtid if we can't find the user-supplied data mime type in our list
- 05:13 PM Revision 6538 (metacat): including newer d1 libclient that uses Foresite (and Jena) to construct/parse ORE resource maps for DataONE
- 02:57 PM Revision 6536 (metacat): delete the xml access rules by either docid or guid to make sure we have the most up to date information
- 10:45 AM Revision 6535 (metacat): Fix a data-typing issue when pulling replicationAllowed from postgres. Use getBoolean(), not getString().
- 05:13 PM Revision 6534 (metacat): cleaned up to use for populating a DataONE MN using the D1 api. Retrieves packages from a Metacat and generates system metadata for them before calling MN.create() for both data and metadata.
- NOTE: you need a client certificate that the target server accepts (either DataONE-generated for testing or a CILogon...
- 07:19 PM Revision 6533 (metacat): IdentifierManager.getSystemMetadata() was missing the number_replicas and replication_allowed fields when building a ReplicationPolicy section of a SystemMetadata document being returned. Add in these two attributes.
- 11:17 AM Revision 6532 (metacat): update D1 jars to include recent SubjectList -> SubjectInfo refactoring and the SUBJECT_PUBLIC constant
- 11:08 AM Revision 6531 (metacat): include SystemMetadata when replicating data and metadata documents -- this allows us to establish the guid-to-docid mapping that is crucial for being able to read the replicated document by guid (d1 api)
- 10:00 AM Revision 6530 (metacat): throw InvalidToken when the Session parameter is null for create()
- 08:37 PM Revision 6529 (metacat): Fix service versioning in metacat.properties so that when Metacat nodes are registered they report the correct service version for use in resolve() -- i.e., use "v1" instead of "0.6.4" in resolve urls.
- 02:50 PM Revision 6528 (metacat): Once a CN calls replicate() on an MN, the MN needs to call getReplica() on the source MN (not get()). Once the bytes are retrieved, the MN must then call back to the CN with setReplicationStatus() to indicate that the replication status is complete. Modify MNodeService to do so.
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