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# Date Author Comment
5543 09/07/2010 04:30 PM ben leinfelder

separate the class and the ontology from the the URI for easier reading. putting them in a table also helps

5542 09/07/2010 03:49 PM ben leinfelder

include links from annotation to the data package metadata

5541 09/07/2010 03:06 PM ben leinfelder

include stylesheet to display annotation document on it's own (in addition to within a resultset)

5540 09/07/2010 02:40 PM ben leinfelder

include the column name that the measurement is mapped to

5539 09/07/2010 11:39 AM ben leinfelder

list the currently registered ontologies (in case someone wants to unregister them?)

5538 09/07/2010 10:06 AM ben leinfelder

rearrange the ontology registration page - bioportal-hosted ontologies come first

5537 09/06/2010 04:50 PM ben leinfelder

include dropdown of all bioportal ontologies - you can choose to register or unregister them with metacat for annotation-based searching. perhaps not the most elegant workflow, but better than having to manually collect the URIs and URLs.

5536 09/03/2010 04:53 PM ben leinfelder

include annotation display in the search results - NOTE using XPath 2.0 function for accessing the ontology URIs that are included as namespaces in the annotation. adding Saxon jar for this.

5535 09/01/2010 02:19 PM ben leinfelder

include a page for [un]registering ontologies with the ontology manager in the semtools plugin

5534 08/31/2010 02:29 PM ben leinfelder

minor upgrade to commons-logging (1.0.3->1.0.4)

5533 08/30/2010 04:34 PM ben leinfelder

basic query can be issued and includes:
-match any/all
-from same observation
-for Entity, Characteristic, Standard, Protocol, Measurement

5532 08/27/2010 09:21 PM ben leinfelder

use same xercesImpl as geoserver (2.4)

5531 08/27/2010 07:28 PM ben leinfelder

upgrade to xalan 2.7 from 2.5.1 (geoserver was using 2.7 already)

5530 08/27/2010 02:59 PM ben leinfelder

upgrade commons-collections (3.2) and commons-lang (2.5) - avoid conflicts with semtools plugin that requires these newer jars.

5529 08/27/2010 02:29 PM ben leinfelder

upgrade the log4j jar - reduces the duplicate jars to wade though in the build process

5528 08/27/2010 02:24 PM ben leinfelder

don't include the semtools plugin in the default config

5527 08/27/2010 02:20 PM ben leinfelder

remove chad's local changes (server, db, etc) - but preserve the D1 config values that were added

5526 08/27/2010 12:27 PM berkley

new values for mets namespace

5525 08/27/2010 11:27 AM berkley

added METS schemas to db scripts

5524 08/27/2010 11:20 AM berkley

added METS schema to the catalog

5523 08/27/2010 11:09 AM berkley

moved the dataone types to the metacat.properties file

5522 08/27/2010 08:27 AM berkley

updated for new dataone jars

5521 08/27/2010 08:25 AM berkley

changes to work with new dataone jars

5520 08/27/2010 08:25 AM berkley

removing old service api jar

5519 08/27/2010 08:24 AM berkley

new dataone jars

5518 08/26/2010 05:10 PM ben leinfelder

include MetacatHandlerPlugin interface so that other projects [semtools] can extend the actions handled by Metcat without editing the codebase directly. The SemtoolsPlugin is the prototype for this and can be registered using the Metacat admin interface. Note that the plugin implementation class and supporting jars must be included in the webapp in order for the request to be handled correctly (the semtools build is injecting these as part of it's build process).

5517 08/26/2010 02:43 PM ben leinfelder

include 1.9.3 upgrade script in trunk

5516 08/26/2010 12:55 PM berkley

updated folder name for schemas

5515 08/26/2010 10:40 AM berkley

added explicit 200 codes to ResourceHandler

5514 08/25/2010 02:43 PM ben leinfelder

use localhost as defaults for the properties

5513 08/25/2010 02:39 PM ben leinfelder

print the workflow server name

5512 08/25/2010 11:33 AM berkley

added better logging and http code setting

5511 08/24/2010 12:07 PM berkley

changed metacat to get the new version of the d1 schemas

5510 08/23/2010 02:41 PM berkley

fixed bug where the query cache was not getting reset by a REST insert/query combo.

5509 08/23/2010 12:37 PM ben leinfelder

include bioportal widgets, at least for an example.
oboe-sbc and oboe are both registered as tests.

5508 08/20/2010 09:17 PM ben leinfelder

do not attempt to drop 'identifier_id_seq' - it does not seem to exist

5507 08/20/2010 02:22 PM ben leinfelder

add 1.9.3 upgrade scripts to trunk

5505 08/19/2010 05:03 PM ben leinfelder

[merged from 1.9.3 branch] security fix: never unregister the "public" user session

5504 08/19/2010 04:55 PM ben leinfelder

map the eml 2.1.0 documents to be rendered by the correct (existing) stylesheet.

5501 08/13/2010 01:50 PM Jing Tao

Merge 1.9.3 branch to the trunk.

5492 08/12/2010 11:31 AM ben leinfelder

merge 1.9.3 change to include karxml 2.1 documents in search/rendering

5491 08/11/2010 12:26 PM berkley

re-added some code inadvertently removed

5490 08/11/2010 12:23 PM berkley

merged with version from 1.9.3 branch to fix bug with character encodings

5484 08/09/2010 11:37 AM berkley

added a todo

5481 08/06/2010 01:11 PM berkley

new todos from code review with roger

5480 08/04/2010 02:47 PM berkley

merging changes from branch

5478 08/04/2010 02:45 PM berkley

merging test changes into the trunk

5476 08/04/2010 12:10 PM ben leinfelder

remove "indus" urls

5473 08/03/2010 03:47 PM berkley

fixed a bug where if you don't build from a directory called 'metacat' unintended files can be copied from another 'metacat' directory by the ecogrid build files

5466 08/02/2010 02:29 PM berkley

added TODOs and cleaned up the code a bit

5463 07/30/2010 04:11 PM ben leinfelder

do not read from the inputstream before passing it off to the SAXParser

5462 07/29/2010 12:22 PM berkley

fixed mime multipart problems so that roger can try to use the d1client

5461 07/28/2010 03:09 PM berkley

fixed error where insert/update errors were not getting caught as exceptions

5460 07/28/2010 10:53 AM berkley

fixed bug with logger where localid didn't get appended when inserting a data file

5459 07/28/2010 10:00 AM berkley

reformatting logs for robert

5458 07/27/2010 11:25 AM berkley

added another logging statement

5457 07/27/2010 11:04 AM berkley

added replicate log statements with the guid and localId

5456 07/27/2010 10:53 AM berkley

fixed update bug I introduced yesterday while fixing replication

5455 07/26/2010 08:21 PM berkley

hopefully fixed bug with systemmetadata replication

5454 07/26/2010 08:04 PM berkley

debug statements in dbsaxhandler

5453 07/26/2010 03:39 PM berkley

still working on getting guid problems fixed with replication

5452 07/26/2010 02:47 PM berkley

fixed identifier manager problem with getting guid for systememtadaa doc

5451 07/26/2010 02:05 PM berkley

fixing problems with replication and systemmetadata

5450 07/26/2010 10:44 AM berkley

set the content type to text/xml for the rest interface

5449 07/26/2010 10:33 AM berkley

fixed yet another null sessionData bug

5448 07/23/2010 04:35 PM Matt Jones

Fixed spelling error.

5447 07/23/2010 04:34 PM Matt Jones

Set content type on listObjects to be XML so that it is recognized by clients.
Reformatted method to use original file conventions.

5446 07/23/2010 03:54 PM Matt Jones

Reformatted code to fix indenting.

5445 07/23/2010 02:11 PM berkley

fixed more access control problems. also fixed extraneous white space that was getting put into the listobject output stream

5444 07/23/2010 01:30 PM berkley

fixed problems with access control on sysmeta

5443 07/23/2010 12:52 PM berkley

fix for set access bug

5442 07/23/2010 12:00 PM berkley

fixes for the access control setting for sysmeta

5441 07/22/2010 03:30 PM berkley

added functionality to set access permissions to system metadata the same as the document that it describes

5440 07/22/2010 12:32 PM berkley

fixed major bug in replication where the document info was being truncated due to a poorly implemented sax parser

5439 07/22/2010 08:58 AM berkley

hopefully fixed get bug where session was null

5438 07/20/2010 03:56 PM berkley

adding dataone to the login org choice for the dev skin

5437 07/19/2010 02:15 PM berkley

reverting accidental cahgnes

5436 07/19/2010 02:02 PM berkley

fixing another null auth token bug

5435 07/14/2010 12:13 PM ben leinfelder

add a note about not shipping with Oracle JDBC jar.
remove "8i" from the Oracle references throughout the doc so as not to indicate it is a requirement that precludes more recent versions.

5434 07/12/2010 01:41 PM berkley

changing d1 log format

5433 07/12/2010 11:33 AM berkley

added code to make sure the localId and guid get added to get and create d1 logs

5432 07/12/2010 10:55 AM berkley

removing println

5431 07/09/2010 10:14 AM berkley

fixed more NPE problems with sessionData. hopefully got them all this time

5430 07/08/2010 08:51 AM berkley

fix for null session bug

5429 07/07/2010 04:00 PM berkley

hudson tests are now running. needed date conversions. still more work to do with systemmetadata date format.

5428 07/07/2010 03:22 PM berkley

updated for date format that supports time zones correctly.

5427 07/07/2010 10:53 AM berkley

changed date comparison to compare to gmt only

5426 07/07/2010 09:32 AM berkley

fixed NPE with sessionData

5425 07/06/2010 03:23 PM berkley

added some new error handling to work around this issue https://trac.dataone.org/ticket/706

5424 07/06/2010 11:58 AM berkley

fixed bug in access control where the sessionid was not correctly passed along so changes of privileges were not being made

5423 07/06/2010 10:14 AM berkley

fixed bug where null session data was not treated properly.

5422 07/02/2010 01:08 PM ben leinfelder

Correct log warning message - not "Account" but "Accession" number

5421 06/30/2010 03:35 PM berkley

add back all tests

5420 06/30/2010 03:28 PM berkley

fixing date formatting and timezone issues

5419 06/30/2010 02:03 PM berkley

fixed bug with log processing

5418 06/30/2010 01:48 PM berkley

fixed some bugs in time handling for listObjects and getLogRecords

5417 06/30/2010 11:37 AM berkley

bug fix to handle nulls

5416 06/30/2010 11:27 AM berkley

fixed bug in getLogRecords where the wrong id was getting set as the identifier

5415 06/30/2010 09:35 AM berkley

added new exception handling to serialize number format exceptions for rest calls

5414 06/29/2010 11:44 AM berkley

fixed listObject bugs, added params to the listObjects rest interface, consolidated the date format passed in params