Activity
From 01/23/2012 to 02/21/2012
02/21/2012
- 01:11 PM Revision 7022 (metacat): Get ReplicationPolicy correctly generated:
- -tweak the regular expression for getting the pref/blocked node list for default replication policy.
-set blocked lis... - 10:55 AM Revision 7021 (metacat): actually, let's set the serialVersion during the MN.create() call so that the HZ map and the backing store have the same information immediately. Also, this is how the docs specify it.
- http://mule1.dataone.org/ArchitectureDocs-current/design/SystemMetadata.html
- 10:08 AM Revision 7020 (metacat): if serialVersion is null, use defualt value of 0
02/20/2012
- 03:39 PM Revision 7019 (metacat): handle both listing and getting checksums using the GET endpoint -- depends whether or not a pid is included in the URL
- https://redmine.dataone.org/issues/2089
- 03:01 PM Revision 7018 (metacat): include systemmetadata and ore generation flags as "remembered" configuration values for the admin UI.
- 12:38 PM Revision 7017 (metacat): remove ID mapping when a create()/"insert" call fails so that subsequent calls do not return an IdentifierNotUnique error. In this case it was due to invalid XML.
- https://redmine.dataone.org/issues/2341
- 12:20 PM Revision 7016 (metacat): use RC-3 DataONE jars and fix compilation error that arose. https://redmine.dataone.org/issues/2351
02/17/2012
- 04:54 PM Revision 7015 (metacat): overload getAllDocidsByType() method for backward semtools compatibility
02/16/2012
- 07:05 PM Revision 7014 (metacat): Use 'a2dissite' to disable the default site (not 'a2ensite').
- 02:47 PM Revision 7013 (metacat): do not subset the list for MS generation testing -- at least not as the default in svn!
02/15/2012
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
02/02/2012
- 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
- 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
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