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  • svn:mergeinfo: /branches/D1_0_6_2_BRANCH:6107-6121

# Date Author Comment
6967 01/31/2012 03:43 PM Jing Tao

Adjust the column width of the search result.

6966 01/30/2012 02:49 PM ben leinfelder

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)

6965 01/30/2012 02:44 PM ben leinfelder

use File.deleteOnExit() not a half hour timer thread to do it.

6964 01/27/2012 05:15 PM ben leinfelder

multithreaded implementation for processing docids for system metadata generation.
need to investigate ant/junit running that deadlocks hazelcast (config?)

6963 01/27/2012 05:12 PM ben leinfelder

additional logging of the config file being used - seem to have thread locking on the xmlConfig use when running under ant/junit

6962 01/27/2012 10:53 AM ben leinfelder

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

6961 01/26/2012 11:14 PM ben leinfelder

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

6960 01/26/2012 09:35 PM ben leinfelder

remove DML for parsing -- the D1 EML parser still uses DOM, so this may not be too big of a perfromance improvement

6959 01/26/2012 09:34 PM ben leinfelder

test harness for running system metadata generation outside of the upgrade process

6958 01/26/2012 02:20 PM ben leinfelder

include comment about KNB estimated time to run during upgrade:
Total time: 20 minutes 58 seconds

6957 01/26/2012 12:48 PM ben leinfelder

only attempt to update date-like nodedata values.

6956 01/26/2012 10:49 AM ben leinfelder

use "test" to exercise upgrade code on staging DB.

6955 01/26/2012 10:03 AM ben leinfelder

include generate system metadata upgrade in the success flag

6954 01/26/2012 10:02 AM ben leinfelder

more clean up - reuse prepared statement for data update

6953 01/26/2012 08:40 AM ben leinfelder

look up nodedata values first, then update each one - trying to avoid out of memory exception.

6952 01/25/2012 03:50 PM ben leinfelder

eliminate the cross product that occurred when updating xml_access with a join

6951 01/25/2012 07:41 AM ben leinfelder

rollback processing Error change -- creates a loop on error. ugh

6950 01/24/2012 10:55 PM ben leinfelder

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.

6949 01/24/2012 10:47 PM ben leinfelder

semicolons!

6948 01/24/2012 04:32 PM Chris Jones

fix a bug in MNodeService.replicate() where the checksum value was being compared to the computed checksum object, not its value.

6947 01/24/2012 04:22 PM ben leinfelder

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....

6946 01/24/2012 12:20 PM ben leinfelder

do not insert duplicate GUID entries when adding rows from the xml_revisions table

6945 01/24/2012 11:57 AM ben leinfelder

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)

6944 01/24/2012 10:35 AM ben leinfelder

use UTC serialization for log entries so that the timestamp, not just the date, is preserved
https://redmine.dataone.org/issues/2257

6943 01/23/2012 03:52 PM ben leinfelder

edited the configuration docs, swapped in new fully-configured screen shot
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

6942 01/23/2012 03:36 PM Chris Jones

Update the MNodeServiceTest to test the validity of the node document returned by getCapabilities() by parsing it with the TypeMarshaller.

6941 01/23/2012 03:09 PM Chris Jones

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.

6940 01/23/2012 02:48 PM ben leinfelder

marked the properties that are only editable manually in metacat.properties
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

6939 01/23/2012 02:44 PM Chris Jones

Add the dataone.contactSubject property to be used when getCapabilities() returns the MN node instance.

6938 01/23/2012 02:43 PM Chris Jones

In MN.getCapabilities(), the required contact subject was not being added to the node instance from the dataone properties. Add it in.

6937 01/23/2012 02:37 PM ben leinfelder

format xml/eml table -- added missing row delimiter
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

6936 01/23/2012 02:33 PM ben leinfelder

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

6935 01/23/2012 12:53 PM ben leinfelder

generate ORE maps only once -- and persist the flag to the main backup properties so that subsequent Metacat upgrades remember this value.

6934 01/23/2012 11:08 AM ben leinfelder

use RC-1 Dataone jars

6933 01/20/2012 10:46 PM Matt Jones

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.

6932 01/20/2012 10:38 PM Matt Jones

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.

6931 01/20/2012 03:45 PM ben leinfelder

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)

6930 01/20/2012 02:35 PM ben leinfelder

add note to enable ssl mod

6929 01/20/2012 12:59 PM ben leinfelder

-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!)

6928 01/20/2012 11:08 AM ben leinfelder

include instructions for installing Sun's Java6 JDK since it is no longer in apt-get repos

6927 01/20/2012 10:14 AM Chris Jones

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.

6926 01/19/2012 04:02 PM Matt Jones

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.

6925 01/19/2012 03:32 PM ben leinfelder

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

6924 01/19/2012 03:16 PM ben leinfelder

update system requirements to be more reasonable

6923 01/18/2012 04:18 PM ben leinfelder

use larger ("text") db field for guid in the xml_access.accessfileid column

6922 01/18/2012 11:05 AM ben leinfelder

use EML 2.1.1 tag as final tag for the schema
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6921 01/18/2012 10:40 AM ben leinfelder

use RELEASE_EML_UTILS_1_0_0 for EML style sheets
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6920 01/17/2012 04:31 PM ben leinfelder

comment our the Demis world map layer -- it was prompting for username/password to use the WMS

6919 01/17/2012 04:21 PM Chris Jones

Use the Collections class from java.util.

6918 01/17/2012 03:20 PM Chris Jones

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.

6917 01/17/2012 03:17 PM Chris Jones

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.

6916 01/17/2012 03:15 PM Chris Jones

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.

6915 01/17/2012 02:28 PM ben leinfelder

use EML 2.1.1 RC4 tag before final tag (schema)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6914 01/17/2012 02:21 PM ben leinfelder

use final tag for building with utilities (tags/UTILITIES_1_1_0)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6913 01/17/2012 01:57 PM ben leinfelder

use final tag for building with ecogrid
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5532

6912 01/17/2012 12:06 PM ben leinfelder

-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.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

6911 01/17/2012 11:43 AM ben leinfelder

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

6910 01/17/2012 11:34 AM Chris Jones

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.

6909 01/13/2012 04:57 PM ben leinfelder

do NOT generate ORE maps or download data when we do the initial System Metadata generation -- this is deferred until D1 registration.

6908 01/13/2012 02:25 PM ben leinfelder

make more generic so that a custom list of IDs can be passed in.

6907 01/13/2012 02:01 PM ben leinfelder

check that the resourceMap (based on Id only) does not currently exist in the local metacat when generating OREs

6906 01/13/2012 01:31 PM ben leinfelder

insert OR update system metadata -- no need to do an update right after initial insert...

6905 01/13/2012 01:05 PM ben leinfelder

call the System Metadata generator during upgrade to 2.0.0

6904 01/13/2012 11:17 AM Chris Jones

In IdentifierManager.updateSystemMetadata(), add a check for invalid system metadata (fields that throw a NullPointerException on access) to ensure that system metadata is populated correctly. Updated calling classes to handle the exception.

6903 01/13/2012 01:41 AM Matt Jones

Fixed formatting to make fixed-width line much shorter so boxes fit on the page.

6902 01/13/2012 01:19 AM Matt Jones

Removing obsoleted Admin Guide -- this guide is now maintained using Sphinx in docs/user/metacat -- the word document and PDF file are now obsolete.

6901 01/13/2012 01:14 AM Matt Jones

Properly initialize the servlet context when starting alternate servlets, which makes sure that the configuration files have been loaded and config properties are available.

6900 01/13/2012 01:00 AM Matt Jones

Removed link to obsolete PDF file.

6899 01/12/2012 10:34 PM Matt Jones

Modifications to make the build more readily find locally installed versions of
sphinx-build, and to remove the unneccary 'html' directory; output of
admindoc is now written directly into build/docs.

6898 01/12/2012 06:52 PM Matt Jones

Modified build to include documentation in the war file that is generated as
part of the build, if the 'documentation' target has been run before the
war target. This is not done automatically because its not clear if all
people will have the proper sphinx environment set up to build the...

6897 01/12/2012 06:03 PM Matt Jones

Adapted the build to be able to generate the Sphinx Admin Guide, and to
better handle the copyright for Javadoc generation.

6896 01/12/2012 06:01 PM Matt Jones

Added links to Javadoc. Tuned the layout a bit.

6895 01/12/2012 04:13 PM Matt Jones

Completed first draft of Admin guide chapter on DataONE.

6894 01/12/2012 01:56 PM Chris Jones

Handle SQLExceptions when trying to save system metadata locally.

6893 01/12/2012 01:56 PM Chris Jones

Convert SQLExceptions to RuntimeExceptions for Hazelcast MapStore operations.

6892 01/12/2012 01:54 PM Chris Jones

In IdentifierManager, throw SQLExceptions rather than just logging them, and let them be handled higher up in the stack.

6891 01/12/2012 01:32 PM ben leinfelder

use new endpoint/method:
http://mule1.dataone.org/ArchitectureDocs-current/apis/CN_APIs.html#CNReplication.deleteReplicationMetadata

6890 01/12/2012 12:18 PM ben leinfelder

use PUT /obsoletedBy/{pid} for CNCore.setObsoletedBy per our discussion today

6889 01/12/2012 07:53 AM Chris Jones

Keep the hzIdentifiers set in sync with the Metacat systemmetadata table. If entries are added/updated in the hzSystemMetadata map, make sure the identifier is in the set. If (for some administrative reason) the entry is removed, remove the identifier from the set. This usually doesn't happen.

6888 01/12/2012 07:47 AM Chris Jones

When loading all keys from Metacat into the hzSystemMetadata map, also load identifiers into the hzIdentifiers set if they are not already there. Although entries may be evicted from the map, the list of identifiers will remain. The list will have a fairly small memory footprint since it's just identifiers.

6887 01/12/2012 07:44 AM Chris Jones

Add support for the distributed Set of unique identifiers in the storage cluster called 'hzIdentifiers'. This set is a persistent total list of all identifiers (even when entries in the hzSystemMetadata map are evicted). It reflects the state of the identifiers in the postgresql systemmetadata table, but is distributed across the cluster. Add the getIdentifiers() method, which returns the ISet of identifiers.

6886 01/12/2012 07:38 AM Chris Jones

Add the dataone.hazelcast.storageCluster.identifiersSet property that defines the name of the distributed set of unique DataONE identifiers (called 'hzIdentifiers'). This ISet can't be configured in the hazelcast.xml file (only maps and queues can).

6885 01/11/2012 07:25 PM Matt Jones

Continued authoring the description of DataONE in Metacat. More to come.

6884 01/11/2012 04:42 PM ben leinfelder

include new methods needed for replication (in new d1 jars)
https://redmine.dataone.org/issues/2203

6883 01/11/2012 01:25 PM ben leinfelder

add method: setObsoletedBy (https://redmine.dataone.org/issues/2185)
augement new method: deleteReplicationMetadata

6882 01/11/2012 11:31 AM ben leinfelder

remove method: assertRelation
https://redmine.dataone.org/issues/2158

6881 01/11/2012 11:24 AM ben leinfelder

add method: deleteReplicationMetadata
remove method: assertRelation
update the D1 jars
https://redmine.dataone.org/issues/2187
https://redmine.dataone.org/issues/2158

6880 01/11/2012 10:41 AM ben leinfelder

serialize the Identifier for the systemMetadata being registered
https://redmine.dataone.org/issues/2204

6879 01/11/2012 09:39 AM Chris Jones

Use a Date with resolution to milliseconds.

6878 01/10/2012 07:57 PM Matt Jones

Initial outline for DataONE chapter.

6877 01/10/2012 07:02 PM Matt Jones

Added OAI-PMH chapter that was contributed by Duane Costa from LTER.

6876 01/10/2012 05:04 PM Chris Jones

Simplify setReplicationStatus() to not call updateReplicationMetadata() if a replica doesn't exist. Just create it and update the system metadata, which we already have a lock for.

6875 01/10/2012 05:03 PM Chris Jones

Minor null checks to avoid NPEs when calling replicate()

6874 01/10/2012 05:01 PM Chris Jones

Don't throw a NotAuthorized exception in isAdminAuthorized() - just return false.

6873 01/10/2012 12:12 PM ben leinfelder

do not download and save remote data resources which are HTML but are not expected to be such (login or info/splash pages before data content).
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

6872 01/10/2012 01:06 AM Matt Jones

Fixed formatting.

6871 01/10/2012 01:00 AM Matt Jones

Moving Metacat Sphinx RST documentation from docs/dev to docs/user directory.

6870 01/10/2012 12:42 AM Matt Jones

Merged most recent changes from trunk into the RST converted version of the Administrator's Guide. Now the Sphinx/RST version is up to date rlative to the most recent word document, and is now the active copy. The MS Word document will be deprecated and removed. All future changes should be made to the RST version.

6869 01/09/2012 05:08 PM Chris Jones

Update the CN methods to throw a VersionMismatch where the API changed (where serialVersion is a required parameter). These were previously throwing an InvalidRequest exception.
Change the exception handling for calls to Hazelcast to catch a RuntimeException (not Exception) so we don't catch exceptions that we purposefully throw....

6868 01/09/2012 04:59 PM Chris Jones

Use a Logger instead of System.out for SystemMetadataMap.