Metacat

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.

Add a short sleep when moderator accepts document so system can update. This will make sure correct documents get returned to moderators list.

Change name of writeTempFile to writeTempUploadFile since this instance deals with the temporary upload dir specifically

Added exception to error xml to clarify error to api.

writeTempFile was trying to write the same file as the registry. Changed to write the file to an "upload" subdirectory. Also throws IOException so errors get reported back to api.

Handle sessions with null ids gracefully.

Do not throw exception when skin metadata file is missing. Instead, remove the skin from the available skins list, write an error message to the log and continue on. This was already done for the skins properties file.

Check for null session ID when touching session.

Get the organization list from org.name.<orgname>= property. Add these values back into metacat.properties.

Changing the ChangePassword method to fix password reset broke the password change functionality. Moved the fix (add dc to username) into the handleResetPassword function.

Fix typo after the error message

Include the dc in the user name when connecting to ldap to change password.

Handle non-responsive LDAP referrals without killing the script, but still require the main LDAP to be up.

Add cgiPrefix to the template variables.

Don't worry about checking for user permissions when inserting a new document

Add a few more debugging messages to LDAPweb to help find timeout issues

Do not back up password properties

Only configure skins that are correctly configured in the skins directory.

Check for existance of backup file location at startup time.

Only show the backup configuration screen if the system cannot discover a directory.

A slew of fixes in the process of fixing bug #3679:
- omit port number from the contextUrl if running on 80, looks bad in exposed URLs
- explicitly pass the metacat object to newAccessionNumber, the global definition of the object had introduced a difficult to track bug...

- move moderatorComments into //additionalMetadata/metadata/ as per EML 2.1 (Bug #3679)
- overlay skin-specific email properties on system-level properties (email hostname)

Process affiliated ldap info

Fix problem with failing authentication for creating new accounts. (Bug #3725)