Metacat

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.

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

add method name to log statements

fix spelling of word additional

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.

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

Change warn messages to info

beef up error log messages

Make sure session data exists before extracting information

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

Beefed up the logging

remove registry.config.username value

Start to flesh out the eclipse metacat setup document

Create some basic workflow scheduler system installation documents

When comparing lat and long ranges, make sure the values have content first. Perl values with no content = 0.

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

change unregister error message to be an info message

fix file name reference for skin configuration file

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.

Fix errors in workflow scheduler unit test

Create database scripts for workflow scheduler

Do not register the session service

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

add connection serial number where it was missing.

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 ability to schedule daily, weekly and monthly jobs.

Format and add comments.

Beef up comments

add method to read test file from disk

add getaccesscontrol and setaccess api calls

Add access api test and supporting files

handle ben's change to the metacat client read api because it returns inputstream now

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

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

Add success message to metacat response for setaccess action

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

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

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

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

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

Use OR to add permissions, not AND

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

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.

change location of accesscontrolinterface

Removed some old commented out code

Remove unneeded references to Timer

SMS-related addition: retrieve docids for a given doctype

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....

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

Move access control source to it's own directory.

Move access control source to it's own directory.

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

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

Include the authorization service stub jars in workflow scheduler build

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

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

Remove commented out sections

Add authorization functionality

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

Add user name to SessionData object

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

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

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