Metacat

removing unused search pages (leftover from 'default' skin copy)

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

include links from annotation to the data package metadata

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

include the column name that the measurement is mapped to

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

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

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

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

remove "indus" urls

adding dataone to the login org choice for the dev skin

starting point for semtools skin. augmenting default skin with Annotation documents.
not yet semantically enhanced search capabilities, but you can see a listing of both EML and Annotations on the server.

Commit the change for Madhusudan Gujral from java.net.URL url = new java.net.URL;
to java.net.URL url = new java.net.URL;

Fixed bug the download link didn't work.

Add a mapping between kar xml namespace and karxml.xsl.

Add a style sheet to transform kar xml document.

Change the search query according to the karxml change.

Change the return type from kar to the namespace.

Merge 1.9.2 changes back into the trunk

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

use @class attribute for path queries rather than @name

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

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.

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.

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

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.

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 name of workflowjobid parameter to be workflowjobname which is more accurate

point workflow requests to the new workflow servlet.

Change location of PropertyService to properties directory

Change MetaCatVersion to MetacatVersion

fixes for first installation

Add the ability to delete a scheduled workflow (move status to deleted in database)

Added end time to workflow scheduler.

Propagate the kar id throughout the configuration screens.

Input date formatting changes

override the 10px margin that was added to the EML stylesheet that we are including.

-handle new(?) XPath for the question prompt and include in the CSV download
-sort the multiple choice options

fix name="...." attribute that was causing problems in IE (it was a typo, but not caught in firefox)
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4262

sort workflow run results by:
-date executed (desc)
-tpc name (asc)

sort workflow results by:
-date (desc)
-tpc name (asc)

Add debug statement

Created new AuthStub class to always authenticate.