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 archival read funtionality (jar/kar/war files)
Bug 3835: Design and implement OAI-PMH compliant harvest subsystem1. 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 subsystem1. 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 subsystemAdd 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.
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.
Move the logMetacat global
Only check user permissions for online data if the data already exists.
Get the metacat url from the SystemUtil.
Add back the auth.base variable to metacat.properties. Use this variable when creating ldap distinguished name.
Try to create the backup directories before creating th ebackup files.
Create a propertyService.getTestInstance method to facilitate unit tests
Add external (backup) directory discovery methods.
Remove org configuration methods since they are not used. Get the backup configuration directories when doing a bypass. Implement the refresh method.
This service now holds a registry of active services. Refreshing of services must go through this class. Also holds some common values that are discovered via servlet context.
Implement refresh methods inherited from base class
Remove the configuration directory from the PropertyService constructor
Do not worry about creating backup directories here
Use configured backup dir when discovering data directories
Handle backup configuration action
Class to support backup directory configuration
Deleted this file. Organization level configuration is not used.
Renamed MetaCatUtil to MetacatUtil
Move global connection variable setters into the constructor so they are retrieved every time we get a new dbConnetion object
Robustly handle file naming as per bug #2566 and the feedback of the scientific programmers (http://tinyurl.com/4n4jve).
revert the changes for: -- On update, check if the accession number exists in the db. If not, change the action to insert.
Quote filenames as per RFC2616 (http://www.w3.org/Protocols/rfc2616/rfc2616-sec19.html#sec19.5.1), this prevents filename truncation on Firefox for files with spaces within the names (part of #2566).
On update, check if the accession number exists in the db. If not, change the action to insert.
Use a distributionSection object to hold a distribution and it's access.
move readerToString function to StringUtil class in utilities module.
Holds all the information for a single distribution in eml.
Change Inlinedatafilename to datafilename, since it can be the name of a regular data file
Add method to save transforming message into files.
Use a while loop to replace if.
Add code to go through eml201 document list to transform them to eml210.
Add a new class which will transform eml201 and eml 200 to eml210.
Correct the pathing for the schema directories based on OS. Leave them in the database with linux style paths (forward slashes) since the values are also used to create urls.
Discover the external (backup) directory based on OS
Add debug statements
catch and report missing skins configuration files.
Catch login errors and report the details via an exception.
Added code to populate moderators from metacat.properties
Add release info property to provide a brief description of the release (release candidate info mostly)
Remove application.default-style from the global configuration screen and activate it in the skins configuration.
Update metacat api documentation
Rename LDAPUtil to AuthUtil
This handles the configuration login form
Rename LDAPAdmin to AuthAdmin
Add a getAttributes method to pass through the getAttributes defined in the AuthInterface.
change generic authentication properties from ldap.* to auth.*
Added this class to be able to test multiple authentication strategies