Metacat

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

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

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.

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.

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

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

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

use same xercesImpl as geoserver (2.4)

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

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

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

don't include the semtools plugin in the default config

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

new values for mets namespace

added METS schemas to db scripts

added METS schema to the catalog

moved the dataone types to the metacat.properties file

updated for new dataone jars

changes to work with new dataone jars

removing old service api jar

new dataone jars

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).

include 1.9.3 upgrade script in trunk

updated folder name for schemas

added explicit 200 codes to ResourceHandler

use localhost as defaults for the properties

print the workflow server name

added better logging and http code setting

changed metacat to get the new version of the d1 schemas

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

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

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

add 1.9.3 upgrade scripts to trunk

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

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

Merge 1.9.3 branch to the trunk.

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

re-added some code inadvertently removed

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

added a todo

new todos from code review with roger

merging changes from branch

merging test changes into the trunk

remove "indus" urls

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

added TODOs and cleaned up the code a bit

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

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

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

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

reformatting logs for robert

added another logging statement

added replicate log statements with the guid and localId

fixed update bug I introduced yesterday while fixing replication

hopefully fixed bug with systemmetadata replication

debug statements in dbsaxhandler

still working on getting guid problems fixed with replication

fixed identifier manager problem with getting guid for systememtadaa doc

fixing problems with replication and systemmetadata

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

fixed yet another null sessionData bug

Fixed spelling error.

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

Reformatted code to fix indenting.

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

fixed problems with access control on sysmeta

fix for set access bug

fixes for the access control setting for sysmeta

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

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

hopefully fixed get bug where session was null

adding dataone to the login org choice for the dev skin

reverting accidental cahgnes

fixing another null auth token bug

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.

changing d1 log format

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

removing println

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

fix for null session bug

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

updated for date format that supports time zones correctly.

changed date comparison to compare to gmt only

fixed NPE with sessionData

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

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

fixed bug where null session data was not treated properly.

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

add back all tests

fixing date formatting and timezone issues

fixed bug with log processing

fixed some bugs in time handling for listObjects and getLogRecords

bug fix to handle nulls

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

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

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

fixed query for listObjects so that paging works as advertised.

formatting

fixed error with listObjects and get.

got the crud test to pass on knb-mn, now need to figure out why the rest service still isn't working