Metacat

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.

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).

Merge 1.9.2 changes back into the trunk

Adding commons-io jar for the IOUtils utilities for stream manipulation.

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...

Excluding the Maven ant tasks jar from the metacat war distribution because
it is not needed (its only used to build dataone-service at build time, and
is unused at runtime), and it conflicts with jar files checked in for Spring
as part of the geoserver install. Also updated dataone interface...

Modified the build.xml to include a new task for building the dataone
service api package, which generates a jar file that is put into lib. This
task depends on maven being installed in maven.home, and depends on the
DataONE service_api being checed out in a sibling directory to the build....

Adding a new property to be used as an identifier prefix by default.

Modified table structure to change identifiers table (previously unused) to
represent a mapping between arbitrary string identifiers and metacat docids.
More information in https://trac.dataone.org/ticket/361. Modifications to
Oracle schemas were made but not tested.

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

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...

Populate esa home links with skin property value

change dropdown select event to work on IE.

Fix main cross browser gui compatibility issues in sanparks tpc skin.

Fix main cross browser gui compatibility issues in sanparks tpc skin.

Remove commas from the end of lists because they break IE

remove the "optional" tip since it is not currently optional

add properties expected by the DB property service

use @class attribute for path queries rather than @name

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

add parc-moderators to config.username

I've added the PARC and PISCO organizations to the delete and confirm form templates for the data registry application.

remove registry.config.username value

added a commented out line for auth.moderators for the parc system. This will get uncommented on the parc system and the existing auth.moderators will be commented out.

I've removed the value for the PARC registry.config.site property since it isn't appropriate to this skin, and causes the registry CGI to produce two organization creator elements with the same value.

hard code parc home url

Redirect data.palmyraresearch.org to parc skin

I've added the PARC organization to the login form template.

I've replaced hard-coded URL strings in the PARC skin files with their appropriate variables in JSP, TT2, and XSL.

This updates the Registry login form to handle PARC logins. I've changed the template to load the PARC header and footer if the cfg = parc.

added parc to list of available skins.

I'm adding two PARC-specific templates to the CGI templates directory. This is a temporary addition, since these templates should reside in the PARC skin. However, the NCEAS skin has templates in this location as well, and all four files will be relocated once bug #4573 has been resolved where the register and ldapweb CGIs change.

I'm adding the spatial support files for the PARC skin. At the moment, the spatial option in the skin is not being used, but these files have been modified slightly from the NCEAS skin version in branding only.

I've added in the XSL stylesheets for the PARC skin. The parc, parc-eml, parc-common and login stylesheets have been changed slightly for PARC branding.

I'm adding the settings and map JSPs. These are placeholder files since the map is not used in the PARC skin, and the settings file merely import common settings for the skin, but doesn't modify any of the interface settings.

These are the minimal images used in the PARC skin layout. The research banner comes from the research section of the PARC website.

I've added the PARC CSS file, which uses colors and images found at the PARC website.

These are the index files for the PARC skin. The html file provides the standard redirect to the JSP. The JSP has been PARC branded, and the layout has changed slightly to work with the http://www.palmyraresearch.org website layout (e.g. some navigation links have been removed).

Here are the three javascript libraries associated with the PARC skin. The only real changes are in the search.js file, where metacat searches have absolute XPaths in the search criteria. The return fields remain as relative XPaths to be consistent with the rendering code for the skin.

I'm adding the parc.cfg configuration file, which is effectively a copy of the nceas.cfg file.

This is the PARC XML configuration file. I've removed the EML beta 4-6 doctype identifiers since this skin will only deal with EML 2.1.0 documents.

I'm adding the Metacat metadata properties file for the PARC installation.

I'm adding the properties file configured for the Palmyra Atoll Research Consortium's installation.

I'm adding in the parc directory, which will contain the skin for the Palmyra Atoll Research Consortium.

special handling for RDF namespace documents (semtools project)

Start to fix I.E. gui issues

check for IE6 and show warning if they are using it

Remove seconds and minutes values from workflow scheduler and add weeks and months.

Include kar id in delete url parameters so resultset will render after delete

add id attributes for form elements (in case IE6 needed them) but it appears they are not required

add the "value" attribute for metadata tag downloads

add code block (commented out) to use in case "?column?" headers become an issue.

handle repeating "?column?" headers - somewhat naively, but consistent

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

Create workflow access pages

correct the metadata matrix for "transposed" data download
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4452

order the unions by width
addresses this bug:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4376

order the unions by width
addresses this bug:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4376

order the unions by width
addresses this bug:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4376

include at least one metadata field and then include any that are additional (_2, _3....etc)
bug #4452

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

allow user to specify the data columns included for the transpose data set (score, response, response file).
decided in today's CC

Only allow workflows with kars that have user write permissions to be scheduled.

Add authorization check before scheduling a job in the workflow scheduler

submit a form into a div via ajax using either form id or form object

move worflow page sections from common into the sanparks skin files

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

choices for metadata tags to include:
1-10, increments of 1; 11-50 increments of 10

add "responsefile" column as data in the transpose
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4412

include input selection for the number of metadata fields to download
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4414

include more than just the first metadata field for questions
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4414

include download link instead of an ecogrid pointer
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4412

include ecogrid link to the external file in downloaded data

do not search across items when simply "browsing all"

comment out a debugging alert() call

use keyword field for both assessments and assessment items
remove unused query options that were in place for the mock up UI
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4387

search across items as well as assessments
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4387
note: you can switch this feature off using the checkbox provided in the search form. the search can be slow otherwise

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

change to DM that preserve the order of the attributes being selected

include latest datamanager changes - notably the performance enhancement regarding attributes and table creation

do not use the jdk logging - this was being used with the datamanager for some reason (but not the rest of metacat).
we use log4j...

Add code from Bill Baker, which uses certficate to login metacat.

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

Add session Validation action and session timeout functionality.

remove base dir definitions from configuration

point workflow requests to the new workflow servlet.

Move workflow scheduler lib files into their own directory

Remove metacat web servlet that was added last week

Change location of PropertyService to properties directory

Persist skin properties across installations

Change MetaCatVersion to MetacatVersion

includes ability to select null attributes for unions

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem: * Add documentation files to the 'docs/dev/oaipmh' directory. * Delete two obsolete files. * Modify class description comment in MetacatRecordFactory.java

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem. Develop harvester component of the OAI-PMH harvester/provider pair. * Terminate harvest if login failed. * Add runHarvester.sh shell script

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem. Develop harvester component of the OAI-PMH harvester/provider pair.

fixes for first installation

include first as an available skin

Fix references to db classes that were moved and refactoring missed.

Create database and shared directories for database management code and shared code respectively.

Create replication directory. Move replication code there. Use log4j for replication logging (rollingfileappender). Beef up replication logging and error control.