Metacat

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

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

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

Make some error messages more understandable

add performance debugging statements for dataquery action

remove web directory

Remove the recently created metacat web servlet

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

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

change pw.println to print to remove newline at end of url

Add unshedulejob to base class

Add session Validation action and session timeout functionality.

Fix spelling in debug statement

Added workflow scheduler directory with supporting files

Make properties handlers implement an interface so you can use configurable or non-configurable properties.

Change location of PropertyService to properties directory

Change location of PropertyService to properties directory

Add Content_type line so debug prints

Persist skin properties across installations

Change MetaCatVersion to MetacatVersion

Rename MetaCat to Metacat

Move document specific utilities to DocumentUtil from MetacatUtil. This makes it easier to define a layer between the core metacat services and the rest of the code.

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem: * Remove import of deleted class

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.

Updated comments to more accurately reflect the API

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.

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.

Populate admin login user dropdown with configured admins

Input date formatting changes

Use context url instead of server IP. Server IP breaks if the server does not have an externally facing IP (behind a proxy server)

Implement fix for Bug #4245: Harvester command line scripts don't execute.

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem
Check to see whether metacat database has changed since last refresh date, and if it has, refresh catalog objects in memory.

Add a new line for NameVirtualHost. Otherwise, the host will fail.

Fix issue where every scheduled job gets the same parameters.

Created new AuthStub class to always authenticate.

Implement stop method in services. Stop all services when shutting down metacat. This primarily keeps scheduler from hanging with open threads.

Catch exception that was leaving shape files open. Roll back transaction in this case.

Catch exception when schema exists in db but not on disk. Try to get the schema before throwing exception

remove this file. This is now handled in db update scripts.

Add upgrade scripts for 1.9.2 (scheduler tables)

Handle extracting a docid from a urn (lsid) during a read action

Beef up comments

kepler workflow execution engine client classes

Workflow scheduler and archiving fixes for TPC workflow engine

Added generic scheduler and workflow scheduling functionality.

Add scheduler and workflow schedule functionality

Add scheduler and workflow schedule functionality

Add archival read funtionality (jar/kar/war files)

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem
1. Refactor the 'eml' metadataPrefix into a distinct metadataPrefix value (and corresponding crosswalk class) for each EML version:
eml-2.0.0, eml-2.0.1, eml-2.1.0. (In recent VTC discussion, we decided not to add support for the older 'beta' versions of EML 2.0.0.)...

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem
1. When building the Metacat OAI-PMH catalog, modify the database query to search only for documents with public read access.
2. Change syntax used for identifiers in the repository to LSID format instead of using a URL to a specific repository....

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem
Add support for request parameter "metadataPrefix=eml". This returns EML 2.1.0 records in an OAI-PMH format. EML 2.0.0 and 2.0.1 documents are first transformed to EML 2.1.0 using the eml201to210.xsl stylesheet that is packaged with the EML Utilities.

Begin development for Bug 3835: Design and implement OAI-PMH compliant harvest subsystem

In AuthSession, I've modified the formatOutput() method to include both the email and organization values found in the userInfo array. On successful login(), this changes the returned xml to include <email> and <organization> elements if they exist in the userInfo array. This information is useful to web client applications that need to show login status beyond just the users full name.

Add ssl virtualhost. Change non-ssl to work with ssl.

Further fixes to handle mixed-file uploads:
- set the fileCount object based on upCount existing files
- use ucount only if it exists; remove debugging'
- the entry form javascript now correctly tracks the file numbers, and can be relied on instead of using upCount...

Display helpful error message when user lacks permissions to edit a document, supress the 'use Morpho' message (closes Bug #3928)

Three small fixes:
- 'salutation' was misspelled and wasn't picked up correctly in document modificiation
- keyword handling wasn't setting the thesaurus correctly
- check against the full list of moderators for the ACL validation

Adding back fix for editing documents with multiple keywords, closing #3929

Update version to 1.9.1. Add nrs ldap properties to configuration.

remove DataTranspose from core metacat - only used in FIRST skin for this 1.9.1 release

Include hack for UCNRS organization properties.

- build up username using base if username isn't fully qualified (e.g. cn=Manager,dc=ecoinformatics,dc=org)
- additional debugging statements for changePassword

- fix error reporting for failed password reset request
- automatically generate necessary LDAP parameters from our defaults,
included in auth.base and unaffiliated properties. This won't work for
skins such as UCNRS with a different base, which still need to be ...

- reformat header
- add debugging for getLdapEntry searches
- add 'filter' parameter for organizations

Provide improved contextUrl, provide proper URL in password reset message body

Accidentally removed ACCESS constant declaration. Restored.

Roll back replication user changes. Fix code that converts access levels to integer and to text.

Introduce replication user. Use the fileutil writer methods instead of writing directly.

new datamanager feature!
Pivot a result set (rows to columns).
Handles simplest case:
-single id column (observation)
-single pivot column (pivot)

Beef up exception handling from file utilities. Move UtilException to MetacatUtilException to eliminate conflict with similar exception in utility package.

Do not read or write zero length documents to/from disk

Handle all places where ldap may be null

enclose more references to ldap and mesg in the if (ldap) statement.

made mesg var global to function.

left off ;

Do not try to use non-existant ldap object if ldap server is down.

Use only one eml common stylesheet directory for all post 2.0.0 beta versions of eml. Point all eml versions to that directory in skin xml files.

distribute perl autosplit.ix file with metacat. change tomcat startup script output to echos.

Add db rollback scripts

update workers.properties with more standard ajp13 worker name (not used until apt-get install project)

Format indexPaths in metacat.properties. Remove from build.properties and build.xml. Move indexPath list getter from MetacatUtil to SystemUtil.

Replace System.out.println statements with logMetacat statements.

moved file from metacat/bin to metacat/src/scripts/bash since eclipse uses <project>/bin as a default build directory and these files will consistently get blown away locally by eclipse.

Replace System.out.println statements with logMetacat statements.

Update replication documentation and fix code so that replication log is available.

Separate the concept of a backup file location and a metacat external directory location. These can be totally different.

Fixes include:
-Overwriting existing DTDs on the filesystem if they exist and registration in the DB failed
-only registering a DTD once

do not include the column name when inserting into an auto-increment column

Make sure and write the shortcut to the backup directory to a directory in the users home.

Add the service registration xml schema to the database. The ecogrid build will add the schema files to the application (see seek)

Allow for backup properties to be written to context based subdirectory of the external configuration directory. This allow multiple instances of metacat to be run side by side.