Activity
From 01/15/2012 to 02/13/2012
02/11/2012
- 04:56 PM Revision 7011 (metacat): restore "test" target that I nuked when adding runoneclass. (thanks, Chris)
- 11:36 AM Revision 7010 (metacat): ObjectFormatCache.getFormat(String formatStr) has been deprecated, and now only takes a formatId instance to get a format from the cache. It also throws Service Failure and NotImplemented, so here just set the format to application/octet-stream in any case.
- 11:25 AM Revision 7009 (metacat): Update D1NodeService to reflect new ObjectFormatCache signature.
- 10:08 AM Revision 7008 (metacat): Adding the new d1 [common|libclient] RC2 jars from the D1_COMMON_JAVA_v1.0.1-RC2 and D1_LIBCLIENT_JAVA_v1.0.1-RC2 tags in the repository.
02/09/2012
- 04:11 PM Revision 7007 (metacat): only run ORE generation for EML docs -- no need to run this for _all_ documents (yikes!)
- 03:48 PM Revision 7006 (metacat): use IdMan method to find docids that do not already have system metadata records -- this lets us re-run without re computing system metadata for every entry (in case the process is interrupted). I haven' been using this option because I wanted to continually regenerate all SM for everything in my test DBs, but we are so close to release that I want to get this in there.
- 02:39 PM Revision 7005 (metacat): for testing: limit and randomize the docs to generate metadata for
- 08:39 AM Revision 7004 (metacat): FOR TESTING ONLY: limit number of records to 100 so that we can get an estimate
02/08/2012
- 03:46 PM Revision 7003 (metacat): update the memberNodeId in existing system metadata only after the register/update is successful with the CN -- we can avoid unneeded SM updates in cases when the register/update fails because we gave the CN bad info that it rejects.
- https://redmine.dataone.org/issues/2308
- 03:12 PM Revision 7002 (metacat): include member node id text field now that the CN is not assigning random Ids.
- https://redmine.dataone.org/issues/2308
- 01:20 PM Revision 7001 (metacat): 1. lookup and use the guid when processing obsoletes/obsoletedBy entries -- had previously been assuming localId==guid but now that we have introduced DOIs as part of the Metacat upgrade process, we may have DOIs for the guid that map to localIds.
- 2. base ORE guids on the localid of the data package they are describing and not on their DOI -- otherwise we might m...
- 11:23 AM Revision 7000 (metacat): use updated authorization policies as discussed in:
- https://redmine.dataone.org/issues/2277
and
http://epad.dataone.org/20120131-authn-authz-questions - 10:58 AM Revision 6999 (metacat): refactor D1-specific upgrade utilities into their own package
- 10:53 AM Revision 6998 (metacat): remove createAndInsertSystemMetadat() method that acts on a single localId -- incorporated this into the localId-list-based method.
- 10:50 AM Revision 6997 (metacat): refactor IdentityManager.createSystemMetadata(sm) to be insertSystemMetadata(sm) so that it is clear that this method inserts the SM object into the backing store. This differentiates it from the "generation" methods we use when we need to create SM about pre-existing objects or objects we get from non-D1 api calls.
- 10:44 AM Revision 6996 (metacat): generate SystemMetadata during D1 registration (not 2.0.0 upgrade). This process runs in a thread and updates a metacat.properties value when it is complete.
02/07/2012
- 09:54 PM Revision 6995 (metacat): getMultipartParameters() outside of debug block -- thanks Mark Reyes @ CDL for catching this.
- 04:53 PM Revision 6994 (metacat): dataone configuration and registration enhancements:
- -include flag to disable D1 services, currently only the MN side enforces this
-do not allow multiple registration at... - 03:18 PM Revision 6993 (metacat): use correct Collections import
- 11:08 AM Revision 6992 (metacat): Show "Update" button if this MemberNodeId is already registered with DataONE, otherwise use the "Register" label
- 09:54 AM Revision 6991 (metacat): match changes to MN service methods (return type as boolean)
- 09:31 AM Revision 6990 (metacat): updated d1 jars with latest libclient changes and objectformatcache use
- 03:12 AM Revision 6989 (metacat): Updated configuration documentation in admin guide for Metacat DataONE section. Changed links in configuration utility to point at the Admin guide.
- 12:02 AM Revision 6988 (metacat): Added new methods to generate a default replication policy based on properties from the metacat configuration. This is called during system metadata creation for objects that lack any system metadata.
- 12:00 AM Revision 6987 (metacat): Modify admin configuration to include default replication policy. Extensively revised the DataONE configuration page, including new wording for intro, improved tooltips throughout, new arrangement of sections, and other cosmetic changes.
02/06/2012
- 11:56 PM Revision 6986 (metacat): Clean up warnings in class.
- 01:06 PM Revision 6985 (metacat): Remove ability to edit NodeID from D1 configuration page. Fix update of contactSubject and dataone.ore.generated property name.
- 01:05 PM Revision 6984 (metacat): Remove ability to edit NodeID from D1 configuration page. Fix update of contactSubject and dataone.ore.generated property name.
- 12:52 PM Revision 6983 (metacat): include flag indicating that system metadata generation has completed (useful for independent long-running thread)
- 12:38 PM Revision 6982 (metacat): handle "BIN" objects so as to avoid repeated calls to lookup the non-existent ObjectFormat
- 11:40 AM Revision 6981 (metacat): do not wait for SM generation to complete during the upgrade -- this way the web UI wont hang for days. the process sets a metacat property when it is complete.
- 11:38 AM Revision 6980 (metacat)
- 11:02 AM Revision 6979 (metacat): Fixed a bug the a hyper-link included the username/password input fields.
- 09:46 AM Revision 6978 (metacat): use RC-2 DataONE jars -- these are built from trunk still, but include the next tag naming convention
02/03/2012
- 10:43 AM Bug #5572: Couldn't upload a kar file from kepler to metacat
- Tried a fresh metacat, the error has gone.
So my local changes may cause the issue. I am going to close the bug. - 08:17 AM Bug #5572: Couldn't upload a kar file from kepler to metacat
- Ben,
Did you make the kar file public readable?
02/02/2012
- 09:25 PM Bug #5572: Couldn't upload a kar file from kepler to metacat
- Running Kepler 2.3 (just installed from installer) and saving to localhost repository (Metacat trunk) works for me. I...
- 03:51 PM Bug #5572 (Resolved): Couldn't upload a kar file from kepler to metacat
- I used "ant clean install" a metacat. Then I went through the web pages to configure the metacat with a fresh db.
... - 05:15 PM Revision 6977 (metacat): do not shutdown hazelcast -- it needs to be running after the upgrade process so that Metacat actually works.
- I think the newer version of HZ makes it so the threads are all released as needed.
http://bugzilla.ecoinformatics.or... - 03:17 PM Revision 6976 (metacat): Commenting out the parts of the upgrade script that started to refer to EXID. At this point, the registration of EZID identifiers will be done out-of-band with respect to the upgrade.
- 02:17 PM Revision 6975 (metacat): use plain String parameter for {pid} instead of XML serialization of it.
- 11:23 AM Revision 6974 (metacat): remove {pid} from POST URL on CN.registerSystemMetadata()
- https://redmine.dataone.org/issues/2284
- 11:15 AM Revision 6973 (metacat): remove {pid} from POST URL on CN.create()
- https://redmine.dataone.org/issues/2284
- 11:10 AM Revision 6972 (metacat): remove {pid} from POST URL on MN.create()
- https://redmine.dataone.org/issues/2284
02/01/2012
- 04:09 PM Revision 6971 (metacat): catch cases where the previous/next revision of objects have not had system metadata generated yet
- 03:52 PM Revision 6970 (metacat): create system metadata object if it wasn't found in HZ
- 03:02 PM Revision 6969 (metacat): adjust the width of the label suffix.
- 09:44 AM Revision 6968 (metacat): process systemMetadata from the docInfo string _before_ writing to the database so that we guarantee guid-docid mapping exists before attempting to look it up.
01/31/2012
01/30/2012
- 02:49 PM Revision 6966 (metacat): upgrade to hazelcast 1.9.4.6 so that threadpools are released when not needed (http://code.google.com/p/hazelcast/issues/detail?id=765).
- include ant target to run a specific main class (mostly for debugging)
- 02:44 PM Revision 6965 (metacat): use File.deleteOnExit() not a half hour timer thread to do it.
01/27/2012
- 05:15 PM Revision 6964 (metacat): multithreaded implementation for processing docids for system metadata generation.
- need to investigate ant/junit running that deadlocks hazelcast (config?)
- 05:12 PM Revision 6963 (metacat): additional logging of the config file being used - seem to have thread locking on the xmlConfig use when running under ant/junit
- 10:53 AM Revision 6962 (metacat): calculate object size using the size on the file system rather than re-reading as an input stream.
- Now only EML document bytes will be read twice: once for the checksum and again for parsing out datapackage details
01/26/2012
- 11:14 PM Revision 6961 (metacat): system metadata generation optionally skips entries that have already been generated (data size, checksum) but allows the latest EML that describes them to have the last word on object format
- 09:35 PM Revision 6960 (metacat): remove DML for parsing -- the D1 EML parser still uses DOM, so this may not be too big of a perfromance improvement
- 09:34 PM Revision 6959 (metacat): test harness for running system metadata generation outside of the upgrade process
- 02:20 PM Revision 6958 (metacat): include comment about KNB estimated time to run during upgrade:
- Total time: 20 minutes 58 seconds
- 12:48 PM Revision 6957 (metacat): only attempt to update date-like nodedata values.
- 10:49 AM Revision 6956 (metacat): use "test" to exercise upgrade code on staging DB.
- 10:03 AM Revision 6955 (metacat): include generate system metadata upgrade in the success flag
- 10:02 AM Revision 6954 (metacat): more clean up - reuse prepared statement for data update
- 08:40 AM Revision 6953 (metacat): look up nodedata values first, then update each one - trying to avoid out of memory exception.
01/25/2012
- 03:50 PM Revision 6952 (metacat): eliminate the cross product that occurred when updating xml_access with a join
- 07:41 AM Revision 6951 (metacat): rollback processing Error change -- creates a loop on error. ugh
01/24/2012
- 10:55 PM Revision 6950 (metacat): report processing errors _after_ exceptions have been caught and recorded, otherwise the web UI is blank and there is no clue what happened unless you look in the logs.
- 10:47 PM Revision 6949 (metacat): semicolons!
- 04:32 PM Revision 6948 (metacat): fix a bug in MNodeService.replicate() where the checksum value was being compared to the computed checksum object, not its value.
- 04:22 PM Revision 6947 (metacat): use a temporary table to calculate the maximum revision for a given docid and use that when setting the accessfileid during upgrade. the query plan for the all-in-one statement must be brutal as it's been running for 4 hours at this point....
- 12:20 PM Revision 6946 (metacat): do not insert duplicate GUID entries when adding rows from the xml_revisions table
- 11:57 AM Revision 6945 (metacat): add "IF EXISTS" clause to identifier table drop in case it does not exist on the given deployment (as is the case on the KNB)
- 10:35 AM Revision 6944 (metacat): use UTC serialization for log entries so that the timestamp, not just the date, is preserved
- https://redmine.dataone.org/issues/2257
01/23/2012
- 03:52 PM Revision 6943 (metacat): edited the configuration docs, swapped in new fully-configured screen shot
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
- 03:36 PM Revision 6942 (metacat): Update the MNodeServiceTest to test the validity of the node document returned by getCapabilities() by parsing it with the TypeMarshaller.
- 03:09 PM Revision 6941 (metacat): Update the D1Admin class to set the dataone.contactSubject property. I've added the property to the http request to be added to the JSP form, but for now am setting the property using the dataone.subject field value. Not sure if we want to expose the contact subject in the form yet or not.
- 02:48 PM Revision 6940 (metacat): marked the properties that are only editable manually in metacat.properties
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
- 02:44 PM Revision 6939 (metacat): Add the dataone.contactSubject property to be used when getCapabilities() returns the MN node instance.
- 02:43 PM Revision 6938 (metacat): In MN.getCapabilities(), the required contact subject was not being added to the node instance from the dataone properties. Add it in.
- 02:37 PM Revision 6937 (metacat): format xml/eml table -- added missing row delimiter
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
- 02:33 PM Revision 6936 (metacat): some minimal editing on replication configuration -- bulk of it had been done in the Word doc before rst conversion
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
- 01:05 PM Bug #5518: Track down the performance issue of metacat query.
- With all production data transfered to our new staging server (http://knb-mn-stage-1.dataone.org/knb) a search for "w...
- 12:53 PM Revision 6935 (metacat): generate ORE maps only once -- and persist the flag to the main backup properties so that subsequent Metacat upgrades remember this value.
- 11:08 AM Revision 6934 (metacat): use RC-1 Dataone jars
01/20/2012
- 10:46 PM Revision 6933 (metacat): Added DOI generation to the 2.0.0 upgrade process. To succeed, this script must be run on a fresh 2.0.0 database, or on a 1.9.5 version database, as those are the only ways to get the needed foreign keys to be marked as deferrable. The identifier conversion must be turned on by setting correct properties in metacat.properties. See the comments in GenerateGlobalIdentifiers for details. By default, conversion is set to false in the properties file. If you want to convert an instance to use DOIs, be sure to set metacat.properties up BEFORE running through the Metacat configuration and database upgrade.
- 10:38 PM Revision 6932 (metacat): Refactoring classes that throw generic Exception class to throw their more specific subclasses so that new exceptions are not hidden behind generic messages. Makes debugging easier.
- 03:45 PM Revision 6931 (metacat): try to read the local document before making the localid->guid mapping (in cases where we fail to read the data locally like if it is referenced in an EML file but does not exist on this Metacat instance)
- 02:35 PM Revision 6930 (metacat): add note to enable ssl mod
- 12:59 PM Revision 6929 (metacat): -include instructions about enabling AJP connector in Tomcat config
- -use postgres 8.4
-include hint to disable default Apache site (otherwise the knb config never gets used!) - 11:08 AM Revision 6928 (metacat): include instructions for installing Sun's Java6 JDK since it is no longer in apt-get repos
- 10:14 AM Revision 6927 (metacat): Ensure we have the object and sysmeta params for MN.create(). We were getting a fatal SAX parsing error encapsulated in a ServiceFailure when a science metadata object param was null. Cut it off at the pass after parsing the MMP entity.
01/19/2012
- 04:02 PM Revision 6926 (metacat): An example python script that uses the python client to loop through a list of
- files, read them from disk, and insert them into metacat.
- 03:32 PM Revision 6925 (metacat): make it clear that the Apache config files are samples and may need to be modified for different servers
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516
- 03:16 PM Revision 6924 (metacat): update system requirements to be more reasonable
- 12:26 PM Bug #5518: Track down the performance issue of metacat query.
- Hi -
I routinely get a timeout (or equivalent?) when querying the LNO or KNB production metacats, on indexed fields....
01/18/2012
- 04:18 PM Revision 6923 (metacat): use larger ("text") db field for guid in the xml_access.accessfileid column
- 12:01 PM Bug #5518: Track down the performance issue of metacat query.
- Running the same simple search ("water") on http://dev2.nceas.ucsb.edu/knb returns in a reasonable (tens of seconds) ...
- 11:48 AM Bug #5518: Track down the performance issue of metacat query.
- the indexPaths are all present in metacat.properties.
These are what the main KNB page are searching with:
-organizat... - 11:06 AM Bug #5532: Use strict build tag strategy for 2.0.0 release
- I've updated all the tags that Metacat uses during its build process.
- 11:05 AM Revision 6922 (metacat): use EML 2.1.1 tag as final tag for the schema
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532
- 10:40 AM Revision 6921 (metacat): use RELEASE_EML_UTILS_1_0_0 for EML style sheets
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532
01/17/2012
- 04:31 PM Revision 6920 (metacat): comment our the Demis world map layer -- it was prompting for username/password to use the WMS
- 04:21 PM Revision 6919 (metacat): Use the Collections class from java.util.
- 03:20 PM Revision 6918 (metacat): Remove null field tests in the IdentifierManager class. Schema-level required fields are checked on serialization/deserialization using JibX during the REST resource handler classes. Other required fields are checked in MNodeService and CNodeService, higher in the stack.
- 03:17 PM Revision 6917 (metacat): For MNs that haven't set the archived flag to false on create(), set it here. Also, ensure that the CN sync code sets the authoritative and origin member node fields.
- 03:15 PM Revision 6916 (metacat): On MN.create(), set the archived flag to be false. This field isn't required in the schema, but is needed by the DataONE indexer once objects are sync'd.
- 02:57 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
- Utilities is now pulling from the final tag.
EML has a schema and a style tag -- those are still at RC level. - 01:49 PM Bug #5532: Use strict build tag strategy for 2.0.0 release
- I've merged the Ecogrid RC5 changes to trunk and now am using RC6 that was made from trunk (make sense?).
Should be f... - 02:28 PM Revision 6915 (metacat): use EML 2.1.1 RC4 tag before final tag (schema)
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532
- 02:21 PM Revision 6914 (metacat): use final tag for building with utilities (tags/UTILITIES_1_1_0)
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532
- 01:57 PM Revision 6913 (metacat): use final tag for building with ecogrid
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532
- 12:06 PM Revision 6912 (metacat): -generate system meta for all docids, even those not originating on the server (replicas from the past)
- -generate ORE docs and download remote data only for those documents that originated on this server being upgraded.
h... - 11:43 AM Revision 6911 (metacat): refactor generate system meta loop to the factory class -- to be reused in sysmeta and ORE generation
- http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522
- 11:34 AM Revision 6910 (metacat): When managing obsoletes/obsoletedBy system metadata fields, set the archived flag to false initially, and set it to true on system metadata for objects that a revision obsoletes.
- 09:28 AM Bug #5520: Create replication integration test suite
- Decent foundation for replication testing is in place. We can build on this as needed. Closing ticket.
01/16/2012
- 06:52 PM Bug #5513: add support for DOI identifiers from EZID
- Decisions from our (M Jones, Leinfleder, C Jones) recent discussion about incorporation of DOI identifier services in...
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