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# Date Author Comment
7068 03/14/2012 12:02 PM Chris Jones

Remove individual calls to isAdminAuthorized() in favor of the centralized isAuthorized() call that handles it now.

7067 03/14/2012 11:57 AM Chris Jones

Incorporate isAdminAuthorized() into isAuthorized() for blanket CN access to objects.

7066 03/13/2012 04:00 PM ben leinfelder

check for null Session before continuing with setReplicationStatus()
https://redmine.dataone.org/issues/2476#note-3

7065 03/13/2012 03:09 PM ben leinfelder

do not attempt to parse empty file for the failure (BaseException serialization). There are cases when this is not given (failure="") when there is not a failure.
https://redmine.dataone.org/issues/2476

7064 03/13/2012 03:05 PM ben leinfelder

check for null session (public) calls to MN.replicate() before passing it to the asynchronous implementation

7063 03/13/2012 02:58 PM ben leinfelder

do not replicate if session is null

7062 03/13/2012 02:19 PM ben leinfelder

throw not authorized when attempting to getReplica as an invalid/non-existent node

7061 03/13/2012 12:19 PM ben leinfelder

transitive properties for mapped subjects:
-group membership
-verified flag
https://redmine.dataone.org/issues/2430
https://redmine.dataone.org/issues/2432

7060 03/13/2012 11:24 AM ben leinfelder

check group membership defined at group level (in addition to membership defined as part of of the Person level)
https://redmine.dataone.org/issues/2429

7059 03/13/2012 10:43 AM ben leinfelder

logging for permission checks - trying to nail down details of MN checking

7058 03/13/2012 10:08 AM ben leinfelder

use Event.CREATE.xmlValue() when converting "insert" to "create"
http://redmine.dataone.org/issues/2471

7057 03/12/2012 08:20 PM ben leinfelder

log records should be inclusive of fromDate parameter (>=)
https://redmine.dataone.org/issues/2471

7056 03/12/2012 04:38 PM ben leinfelder

use Timestamp object from results, not a new Date object from that Timestamp object

7055 03/12/2012 12:12 PM ben leinfelder

add an alternative method for loading system metadata identifiers but leave it commented out. We may find that using the ObjectList method is too much overhead, but it will always be consistent with what metacat reports for listObjects().

7054 03/12/2012 12:09 PM ben leinfelder

add note about long-running load for shared system metadata map

7051 03/08/2012 04:16 PM Chris Jones

If PID is not part of the multipart params, we end up with a NullPointerException. Throw an InvalidRequest in this case rather than ServiceFailure resulting from the NPE.

7049 03/08/2012 02:21 PM ben leinfelder

translate "insert" events in Metacat as Event.CREATE events ("create") for DataONE
https://redmine.dataone.org/issues/2461

7048 03/08/2012 11:18 AM ben leinfelder

for good measure, use the D1 encoding util for url decoding the parameters for listObjects
https://redmine.dataone.org/issues/2460

7047 03/08/2012 10:42 AM ben leinfelder

log record paging:
-use start and count parameters
-if start+count exceeds the total number of records, then only return from start to the end of the list
-if start exceeds total record count, start at the end of the list (will be empty list)
https://redmine.dataone.org/issues/2458

7046 03/07/2012 02:49 PM Chris Jones

Use 'fromDate' and 'toDate' as listObject param filters to comply with the API documentation. We had changed this in MNResourceHandler, but somehow missed it in CNResourceHandler.

7045 03/07/2012 02:30 PM ben leinfelder

check whether mapping (

7044 03/06/2012 08:26 PM ben leinfelder

catch additional NotFound exception for: "do not include log entries for documents that the caller is not allowed to read." https://redmine.dataone.org/issues/2444

7043 03/06/2012 02:03 PM ben leinfelder

serialize exception in header for describe response when there is a BaseException
https://redmine.dataone.org/issues/2440

7042 03/06/2012 01:41 PM ben leinfelder

do not include log entries for documents that the caller is not allowed to read. https://redmine.dataone.org/issues/2444

7041 03/06/2012 01:35 PM ben leinfelder

use revision provided in the docid when looking up guid. had been using latest revision which I think incorrectly reports on the log history.
noticed this when looking at: https://redmine.dataone.org/issues/2444

7039 03/05/2012 06:30 PM Chris Jones

A minor change to isAuthorized() - compare each Person in the SubjectInfo (not just the primary Subject) since each person could have an equivalent identity mapped to the primary Subject. Add debug logging for the comparison.

7038 03/05/2012 04:36 PM ben leinfelder

added debug logging
https://redmine.dataone.org/issues/2429

7037 03/05/2012 04:27 PM ben leinfelder

check if verified flag is null before evaluating (NPE during MN Auth test)
https://redmine.dataone.org/issues/2429

7034 03/01/2012 02:20 PM ben leinfelder

do not include stylesheet for list of checksum algorithms -- there is no template for it and therefore looks blank in a browser

7030 02/24/2012 02:21 PM Chris Jones

Globally change the property 'dataone.memberNodeId' to 'dataone.nodeId'. This is more useful for both MNs and CNs implemented in Metacat. Also, change D1NodeService.getLogRecords() to return log entries with the actual node id rather than the IP address (looks like a cut/paste error)....

7029 02/24/2012 09:46 AM ben leinfelder

throw InvalidToken when an invalid Permission is passed in. THis requires that internal calls to the method also check for this exception.
https://redmine.dataone.org/issues/2388

7026 02/22/2012 02:53 PM ben leinfelder

call deleteReplica when we get that request (looks like an undetected copy and paste error)

7025 02/22/2012 02:31 PM ben leinfelder

do not allow blank node references to be used.
https://redmine.dataone.org/issues/2362

7024 02/22/2012 02:27 PM ben leinfelder

only generate system metadata when the call comes from the legacy Metacat API, not the D1 API.
https://redmine.dataone.org/issues/2362 (I think this was the culprit)

7023 02/22/2012 12:47 PM ben leinfelder

do not "lookup" object format when retrieving system metadata -- just return what we have stored as the formatId and don't [erroneously] default it to binary when there's a problem with the lookup (cache or service or otherwise).
https://redmine.dataone.org/issues/2365

7022 02/21/2012 01:11 PM ben leinfelder

Get ReplicationPolicy correctly generated:
-tweak the regular expression for getting the pref/blocked node list for default replication policy.
-set blocked list (had mistakenly been two calls to set pref list)

7021 02/21/2012 10:55 AM ben leinfelder

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

7020 02/21/2012 10:08 AM ben leinfelder

if serialVersion is null, use defualt value of 0

7019 02/20/2012 03:39 PM ben leinfelder

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

7017 02/20/2012 12:38 PM ben leinfelder

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

7016 02/20/2012 12:20 PM ben leinfelder

use RC-3 DataONE jars and fix compilation error that arose. https://redmine.dataone.org/issues/2351

7015 02/17/2012 04:54 PM ben leinfelder

overload getAllDocidsByType() method for backward semtools compatibility

7013 02/16/2012 02:47 PM ben leinfelder

do not subset the list for MS generation testing -- at least not as the default in svn!

7012 02/15/2012 09:35 AM Chris Jones

CNodeService.listChecksumAlgorithms() was returning null rather than the list. Fixed.

7010 02/11/2012 11:36 AM Chris Jones

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.

7009 02/11/2012 11:25 AM Chris Jones

Update D1NodeService to reflect new ObjectFormatCache signature.

7007 02/09/2012 04:11 PM ben leinfelder

only run ORE generation for EML docs -- no need to run this for all documents (yikes!)

7006 02/09/2012 03:48 PM ben leinfelder

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.

7005 02/09/2012 02:39 PM ben leinfelder

for testing: limit and randomize the docs to generate metadata for

7004 02/09/2012 08:39 AM ben leinfelder

FOR TESTING ONLY: limit number of records to 100 so that we can get an estimate

7003 02/08/2012 03:46 PM ben leinfelder

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

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)

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.

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.

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
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

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.

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

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

only attempt to update date-like nodedata values.

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.

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.

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.

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

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.

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.

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.