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

# Date Author Comment
7002 02/08/2012 03:12 PM ben leinfelder

include member node id text field now that the CN is not assigning random Ids.
https://redmine.dataone.org/issues/2308

7001 02/08/2012 01:20 PM ben leinfelder

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 mash up the DOI prefix (or other id scheme that we are unaware of). By using resourceMapPreix + localId we are sure to have a valid localid and guid for the ORE map we create and add to the system

7000 02/08/2012 11:23 AM ben leinfelder

use updated authorization policies as discussed in:
https://redmine.dataone.org/issues/2277
and
http://epad.dataone.org/20120131-authn-authz-questions

6999 02/08/2012 10:58 AM ben leinfelder

refactor D1-specific upgrade utilities into their own package

6998 02/08/2012 10:53 AM ben leinfelder

remove createAndInsertSystemMetadat() method that acts on a single localId -- incorporated this into the localId-list-based method.

6997 02/08/2012 10:50 AM ben leinfelder

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.

6996 02/08/2012 10:44 AM ben leinfelder

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.

6995 02/07/2012 09:54 PM ben leinfelder

getMultipartParameters() outside of debug block -- thanks Mark Reyes @ CDL for catching this.

6994 02/07/2012 04:53 PM ben leinfelder

dataone configuration and registration enhancements:
-include flag to disable D1 services, currently only the MN side enforces this
-do not allow multiple registration attempts if we have just submitted and are awaiting Node verification by the CN.
-do not allow configuration "bypass" if D1 settings have been configured previously....

6993 02/07/2012 03:18 PM ben leinfelder

use correct Collections import

6992 02/07/2012 11:08 AM ben leinfelder

Show "Update" button if this MemberNodeId is already registered with DataONE, otherwise use the "Register" label

6991 02/07/2012 09:54 AM ben leinfelder

match changes to MN service methods (return type as boolean)

6990 02/07/2012 09:31 AM ben leinfelder

updated d1 jars with latest libclient changes and objectformatcache use

6989 02/07/2012 03:12 AM Matt Jones

Updated configuration documentation in admin guide for Metacat DataONE section. Changed links in configuration utility to point at the Admin guide.

6988 02/07/2012 12:02 AM Matt Jones

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.

6987 02/07/2012 12:00 AM Matt Jones

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.

6986 02/06/2012 11:56 PM Matt Jones

Clean up warnings in class.

6985 02/06/2012 01:06 PM Matt Jones

Remove ability to edit NodeID from D1 configuration page. Fix update of contactSubject and dataone.ore.generated property name.

6984 02/06/2012 01:05 PM Matt Jones

Remove ability to edit NodeID from D1 configuration page. Fix update of contactSubject and dataone.ore.generated property name.

6983 02/06/2012 12:52 PM ben leinfelder

include flag indicating that system metadata generation has completed (useful for independent long-running thread)

6982 02/06/2012 12:38 PM ben leinfelder

handle "BIN" objects so as to avoid repeated calls to lookup the non-existent ObjectFormat

6981 02/06/2012 11:40 AM ben leinfelder

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.

6980 02/06/2012 11:38 AM ben leinfelder
6979 02/06/2012 11:02 AM Jing Tao

Fixed a bug the a hyper-link included the username/password input fields.

6978 02/06/2012 09:46 AM ben leinfelder

use RC-2 DataONE jars -- these are built from trunk still, but include the next tag naming convention

6977 02/02/2012 05:15 PM ben leinfelder

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.org/show_bug.cgi?id=5572

6976 02/02/2012 03:17 PM Matt Jones

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.

6975 02/02/2012 02:17 PM ben leinfelder

use plain String parameter for {pid} instead of XML serialization of it.

6974 02/02/2012 11:23 AM ben leinfelder

remove {pid} from POST URL on CN.registerSystemMetadata()
https://redmine.dataone.org/issues/2284

6973 02/02/2012 11:15 AM ben leinfelder

remove {pid} from POST URL on CN.create()
https://redmine.dataone.org/issues/2284

6972 02/02/2012 11:10 AM ben leinfelder

remove {pid} from POST URL on MN.create()
https://redmine.dataone.org/issues/2284

6971 02/01/2012 04:09 PM ben leinfelder

catch cases where the previous/next revision of objects have not had system metadata generated yet

6970 02/01/2012 03:52 PM ben leinfelder

create system metadata object if it wasn't found in HZ

6969 02/01/2012 03:02 PM Jing Tao

adjust the width of the label suffix.

6968 02/01/2012 09:44 AM ben leinfelder

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.

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.