Metacat

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.

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

Add authorization check before scheduling a job in the workflow scheduler

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

Change RequestUtil forwardRequest() method to throw MetacatUtilException.

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

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.

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

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.

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

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

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.

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.

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.

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.

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.

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

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.

Process affiliated ldap info

Fix typos in error messages.