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# Date Author Comment
5340 05/10/2010 01:15 PM berkley

refactored XMLSchemaService to not have static methods. made the CrudServiceTest more robust.

5339 05/07/2010 04:30 PM berkley

removed system.outs

5338 05/07/2010 04:28 PM berkley

fixed schema location bug. the dataone schemas are now correclty found

5337 05/07/2010 03:15 PM berkley

removed CrudService dependency on servlet params. CrudService is now a singleton. I'm getting an error from metacat saying it can't find teh systemmetadata schema, even though it is, in fact, registered with metacat. need to identify why this is happening.

5334 05/03/2010 03:28 PM berkley

refactoring to remove duplicate code

5333 05/03/2010 03:05 PM berkley

adding a system to track system metadata documents for dataone

5332 04/29/2010 09:14 AM Matt Jones

Added initial implementation of getSystemMetadata and its associated REST service. Current implementation is returning a hardcoded system metadata document -- need to look up the real document for each guid and return that.

5331 04/29/2010 01:28 AM Matt Jones

Completed main parts of CrudService.create(). Now the method writes both data and metadata objects along with their system metadata, and handles the mapping between global identifiers and local identifiers. Access control and logging still need to be dealt with to properly authenticate and then log activities.

5329 04/28/2010 07:04 PM Matt Jones

Modify CrudService to write SystemMetadata to disk with an autogenerated localId and an autogenerated GUID. Validation depends on the DataONE schemas being setup in xml_catalog properly, so still need to check upgrade scripts to be sure these new schemas are added. Still need to handle the metadata document insert, but should be same as system metadata insert.

5327 04/28/2010 06:55 PM Matt Jones

Added comment about MIME form processing.

5326 04/28/2010 06:54 PM Matt Jones

Refactored schema service to call doRefresh() in constructor to eliminate code duplication.

5325 04/28/2010 06:52 PM Matt Jones

Added note on TODO for access bug.

5324 04/26/2010 04:11 PM berkley

replication of guids now works. tested this for both forced replication and update/insert/delete triggered replication

5323 04/26/2010 02:25 PM berkley

fixed bug where guid end tag wasn't getting printed

5322 04/26/2010 12:29 PM berkley

added a method in IdentifierManager to get a guid from a docid and rev. added fields in the documentinfo replication document to pass the guid. now need to handle the guid and insert it into the table if its found

5320 04/19/2010 10:14 PM Matt Jones

Refactored metacat to use dataone-service-api-0.3.0 jar file, with the new JIBX generated types and serialization. Included JIBX runtime jar in metacat to handle serialization and deserialization of SystemMetadata objects. Removed the old API jar file.

5319 04/19/2010 04:51 PM Matt Jones

Modifications to support the DataONE service API version 0.1.0. For DataONE, the get() and
create() services are partially complete. Several more functions and checks need to be added to
create() before it is viable. This DataONE support is not complete, and the current support breaks the MetacatRestClientTest for the time being (this client will eventually be removed).

5311 04/14/2010 11:31 AM daigle

Merge 1.9.2 changes back into the trunk

5301 04/06/2010 05:58 PM Matt Jones

Modified ResourceHandler to return error codes in XML format for the get() method.

5299 04/02/2010 06:54 PM Matt Jones

Modifications to metacat rest service to use the new DataONE CrudService for
get() operation. Minor issue with permissions errors propagating up the
stack, but otherwise this is the first implementation of a full DataONE
method.

5298 04/02/2010 11:29 AM Matt Jones

Modified readFromMetacat() to pass most exceptions up the call stack, which
allows creation of new entry points for calling reads. Still need to
continue factoring out the HTTPServletResponse that is passed in in order to
make entrypoints that are not servlet based possible. Problem now is in...

5293 03/23/2010 01:13 PM ben leinfelder

when looking up group membership, skip referrals that have errors
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900

5292 03/23/2010 12:56 PM ben leinfelder

skip referrals that have errors (connection timeout, host down, etc)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4900

5291 03/22/2010 08:55 PM Matt Jones

Refactored putObject method to separate the create() and update() portions in order to match the method signatures needed for DataONE.

5287 03/18/2010 04:02 AM Matt Jones

Modified ResourceHandler.deleteObject() to take a globally unique id (guid)
as input rather than a metacat-conformant docid. The guid is translated
into a metacat docid which is then used in the handleDelete() call. So now
Metacat supports use of arbitrary identifiers for delete operations, but...

5286 03/18/2010 03:11 AM Matt Jones

Added support to ResourceHandler to allow the putObject method to use
arbitrary guid strings as input. These strings are examined, and if they
match the Metacat docid format (scope.id.rev), they are used directly. If
the id is a string in another format, a new localId is generated based on...

5283 03/17/2010 11:22 PM Matt Jones

Fixed bug in getNextRevision() where "error" documents were not being
detected properly before searching for the next identifier.

5282 03/17/2010 06:54 PM Matt Jones

Added initial support for arbitrary string identifiers in metacat (referred to as a guid). The new identifier table is used to map arbitrary string identifiers to Metacat's current docid format (referred to as the localId). Added a new IdentifierManager class to manage this table, adding new mappings as objects are added to the system. Modified the MetacatTest service to utilize this mapping table to look up a localId from a guid. IdentiferManagerTest is working with these guids now, as is the MetacatTest service get() method, but other parts of the system are unaware of them (e.g., create, update, delete operations are unaware, and no mapping is created when new documents are created). As a consequence, the MetacatRestClientTest is not working (although it also had lots of hardcoded dependencies that need to be fixed as well).

5277 03/16/2010 02:12 AM Matt Jones

Added copyright, license, and class documentation.

5224 02/11/2010 08:48 AM Matt Jones

Modified ResourceHandler to change the GET url from /objects to /object to
match the DataONE method name.

5211 02/03/2010 06:58 PM Matt Jones

Merging in REST interface implementation that was created by Serhan Akin. Main change is
a refactored MetaCatServlet.java class, in which all of the handle* methods were moved
into a separate MetacatHandler.java class. This allows both the standard MetaCatServlet...

5210 02/03/2010 05:03 PM Matt Jones

Adding missing brackets in else clause. Need to verify with Daigle that this is what he meant.

5208 02/03/2010 01:29 PM daigle

Move the chunking of large test element data to centralized location in DBSAXNode.writeChildNodeToDB(). Beff up logging

5207 02/03/2010 01:16 PM daigle

Beef up log messages

5205 02/03/2010 01:11 PM daigle

Add debug log statements

5204 01/28/2010 12:35 PM daigle

make sure querygroup is not null before trying to print it.

5201 01/26/2010 03:50 PM daigle

Get the latest revision from metacat when a modify call docid does not have a revision number.

5200 01/25/2010 03:02 PM daigle

Send appropriate message when trying to update a docid that was previously deleted.

5199 01/22/2010 10:06 AM daigle

Reformat file. No code change.

5198 01/21/2010 03:02 PM daigle

do a quick retry if building path index fails with a SQL error

5197 01/20/2010 02:55 PM daigle

Make sure buildIndex throws an exception if it has a sqlexception. That way the indexing object will be added to the indexing queue and reprocessed.

5195 01/19/2010 10:25 AM daigle

Pass the doc xml as a string to docImpl.write and writeRepication. This is so a reader can be create for the parsing and for the write to disk. Also created a db access class for xml query result deletion.

5189 01/11/2010 08:54 AM daigle

Add comments

5188 01/11/2010 08:54 AM daigle

make constants final

5186 01/06/2010 04:18 PM Jing Tao

Fix the bug of http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4645. handleGetRevisionAndDocTypeAction will search both xml_documents and xml_revisions table.
It also changed some constrain in AccessionNumber when user update a document, of which all previous versions are in xml_revisions table.

5177 01/05/2010 02:08 PM daigle

Add a sleep statement between getting the dtd from source and checking for it via url. Add method names to log output.

5175 01/04/2010 09:01 AM daigle

Log doc and rev query counts and times. Fix mis-spellings.

5174 01/04/2010 09:00 AM daigle

Log doc and rev query counts and times. Fix mis-spellings.

5172 12/30/2009 09:22 AM daigle

remove call to print busy db connections

5170 12/30/2009 09:20 AM daigle

Add debug to show sql

5169 12/21/2009 12:10 PM Duane Costa

Fix for Bug #4637 - Metacat Harvester fails to catch some insert and update failures. As per comments in the bug entry, the Metacat Harvester logic has been modified to examine the Metacat client return string to confirm that it contains the substring "<success>" following an insert or update operation. It no longer considers just the absence of an exception as indicative of a successful operation.

5168 12/18/2009 01:39 PM daigle

log connection warnings only when thresholds are exceeded. Add method names to log output

5167 12/18/2009 01:37 PM daigle

add method name to log statements

5166 12/18/2009 01:36 PM daigle

fix spelling of word additional

5165 12/18/2009 01:26 PM daigle

add method name to log messages and create configured thresholds for warning messages

5162 12/09/2009 11:54 AM daigle

Change log levels where appropriate and add class/method name to output.

5161 12/09/2009 11:01 AM daigle

Change warn messages to info

5160 12/08/2009 11:40 AM daigle

beef up error log messages

5159 12/08/2009 11:39 AM daigle

Make sure session data exists before extracting information

5158 12/08/2009 11:39 AM daigle

Separate code to do tls and non-tls authentication. Introduce AuthTLSException to make error handling easier.

5157 12/08/2009 10:20 AM daigle

Beefed up the logging

5151 12/02/2009 04:00 PM daigle

Change add sql to use a prepared statement. Only try to download a cert if a url was provided.

5150 12/02/2009 03:59 PM daigle

change unregister error message to be an info message

5139 11/24/2009 12:28 PM daigle

Fix errors in workflow scheduler unit test

5137 11/24/2009 12:25 PM daigle

Do not register the session service

5122 11/19/2009 08:19 AM ben leinfelder

special handling for RDF namespace documents (semtools project)

5120 11/10/2009 03:13 PM daigle

add connection serial number where it was missing.

5116 11/09/2009 10:37 AM daigle

Add ability to schedule daily, weekly and monthly jobs.

5115 11/09/2009 10:07 AM daigle

Format and add comments.

5112 11/06/2009 02:47 PM daigle

add getaccesscontrol and setaccess api calls

5109 11/06/2009 02:44 PM daigle

Handle the case of trying to insert a conflicting permission order for a document

5108 11/06/2009 02:43 PM daigle

move dbconnection object out of base class and create it for each db access so it can be released

5107 11/06/2009 02:41 PM daigle

Add success message to metacat response for setaccess action

5104 11/05/2009 10:32 AM ben leinfelder

handle multiple <principal> elements in the allow/deny blocks

5103 11/04/2009 03:05 PM daigle

Verify we are in the permission and principal sections before setting values on dao object.

5100 11/03/2009 11:52 AM daigle

Use OR to add permissions, not AND

5099 11/03/2009 10:31 AM daigle

Change access section in getaccesscontrol and getdocumentinfo apis to be more eml 2.1.0 compliant. Add a block access option to setaccess api.

5098 10/30/2009 03:39 PM daigle

change AccessControlForSingleFile to only be instantiated for one file. move ACL methods to AccessControlForSingleFile. Change format of access sections returned to EML 2.1.0.

5096 10/30/2009 03:34 PM daigle

Removed some old commented out code

5095 10/30/2009 03:31 PM daigle

Remove unneeded references to Timer

5094 10/27/2009 03:42 PM ben leinfelder

SMS-related addition: retrieve docids for a given doctype

5093 10/26/2009 10:20 AM Chris Jones

QueryTerm.java will produce an incorrect SQL statement when there is an attribute in the XPath being used to search on. Regardless of the presence of the attribute, the clause:

(SELECT nodeid FROM xml_index WHERE path LIKE " + "'" + path + "') "

would be added to the query....

5091 10/16/2009 11:12 AM daigle

Create access dao and centralized db access classes. Update create access code to combine access records for principal/doc/accesstype when multiple exist.

5090 10/16/2009 11:10 AM daigle

Move access control source to it's own directory.

5089 10/16/2009 11:10 AM daigle

Move access control source to it's own directory.

5082 10/13/2009 03:01 PM daigle

Add ability for doc owner to add user access to workflows.

5079 10/06/2009 10:58 AM daigle

Add authorization check before scheduling a job in the workflow scheduler

5078 10/06/2009 10:57 AM daigle

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

5076 10/06/2009 10:55 AM daigle

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

5072 10/02/2009 01:11 PM daigle

Add authorization functionality

5071 10/02/2009 01:07 PM daigle

Change sanparks skin to log in with browser session instead of metacat client session so session can be validated on other pages.

5070 10/02/2009 12:59 PM daigle

Add user name to SessionData object

5069 10/01/2009 03:20 PM ben leinfelder

use arguments for the main() method - hardcoded URLs and test docids are poor form

5066 10/01/2009 12:12 PM ben leinfelder

return InputStream instead of Reader in the MetacatClient read() and readInlineData() methods. Can now handle binary data
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4432

5057 09/04/2009 03:12 PM daigle

Add session validation to metacat tpc and workflow scheduler. Fix sanparks skin session management so it always uses the logged in session id.

5056 09/04/2009 03:08 PM daigle

Make some error messages more understandable

5053 09/03/2009 01:47 PM ben leinfelder

add performance debugging statements for dataquery action

5048 08/27/2009 12:07 PM daigle

remove web directory

5047 08/27/2009 12:06 PM daigle

Remove the recently created metacat web servlet

5045 08/27/2009 12:04 PM daigle

change name of workflowjobid parameter to be workflowjobname which is more accurate