Metacat

Fixed a bug in upload function. For online data updates, access was not checked.

Fixed handling of various docid formats.

Code added to handle errors resulting from following urls:
http://metacat.nceas.ucsb.edu/knb/metacat?action2 - no action specified
http://metacat.nceas.ucsb.edu/knb/metacat?action=insert - no docid specified
http://metacat.nceas.ucsb.edu/knb/metacat?action=login - no username specified...

Added check for null condition so that proper error text is returned to user.

Checked to be sure the instance has been initialized in the getDBCOnnection
static method call. Assuming it has been initialized could (and does)
lead to NullPointerExceptions when used outside of the metacat servlet
if the conneciton pool isn't initialized properly.

Reformatted code for readability. It was crazy. Still has problems, but its
better. Will be working on some new methods on monday.

Fixed a bug in access handling when no access is specified.

Added eml-2.0.1 tags for eml processing.

Also fixed a bug. The error returned in case of no revision number specified was just null. Now it says that revision number is required.

Merging in changes made in branch 'dataaccess' by Jing Tao.

Added upload functionality to metacat client for upload online data

Add warning if default harvest list file is not found on disk.

Change relative path to harvestList.xsd schema to allow harvest list editor to run standalone.

Removed some debugging code added in last commit

Added code to read EML2.0.1 into source code.

Improvements to Harvester registration web form.

Add diagnostic output

Get rid of some useless code.

Improve handling of default values.
Call fileNew() if no default Harvest List file is specified.
Improve documentation for default properties.

Add File Validate menu item
Add column to display the row number
Add name of file to the title bar
Load properties from .harvestListEditor in home directory instead
of from metacat.properties

Harvest List Editor, a GUI tool for editing Harvest List XML files

Fixed a bug which was introduced because 'eml2namespace' was replaced by 'eml2_0_0namespace' in metacat.properties

Store session attributes as username and password for consistency with Metacat

Improvements to Harvester registration form

Made initial changes for accepting EML version 2.1.0 in Metacat

Revised the api and ecogrid can use it easily.

Fixed a bug that couldn't find eml2 data format.

Improve Harvester registration login

fixed the bug that couldn't assign access rule for the data file come with morpho.

Change method accessNumberUsed to static method.

Change eml2 to eml200

Change the code when Eml parser name changed.

New class to replace EmlSAXHandler.

Rename this class to Eml200SAXHandler.

Integrate Harvester properties with build.properties and metacat.properties.
Eliminate the need for a separate harvester.properties file.
Improve email message to the site to include more summary information.

Refactored a number of methods to allow for more effective JUnit testing

Changes to comments

Replace Harvester dbDriver property with database property

Added ou also to getprincipal output. So now organizationUnitName is also returned in getprincipal output.

Made changes so that PISCO and NRS trees are also returned in getPrincipals action.

Allow user to set frequency to 0 for testing purposes

Modify schema location

Fixed getprincipals output. Earlier DNs for LTER were in URL form. Now they appear in DN form.
Earlier:
ldap://knb.lternet.edu:389/DN,base
Now:
DN

Have to make changes so that PISCO and NRS also show up.

Fixed two small bugs.

Made changes in XML that is sent back as result of action=getprincipals. Changes are as following:

1. <authSystem> tag contains organization attribute which specifies organization name
2. <user> tag now has <organization> tag which specifies the organization name of the user. This is being generated as null for LTER as of now.

Rename url property to defaultDB

Added the EventLog functionality to the servlet as action=getlog. Valid parameters are ipAddress, principal, docid, event, start, end. All parameters can be repeated except start and end.

Partial implementation of a query facility for the access log. Need to fix problems with the date filtering, and tie this into the servlet action when completed and tested.

Interim checkin of EventLog reporting structure. Still basically incomplete but compiles.

Omit HARVEST_OPERATION_TABLE and store harvest operations in properties file instead

Fixed the returndoctype bug in DBQuery as described in bug 1451. Now,
results are returned even if returndoctype is null, which is the
appropriate behavior.

Implement sending email reports to harvest administrator and site administrator

Patched to make the date-time value insertion work under oracle. Now it
tests fine under both oracle and postgres. Still need to write an
access/query function.

Added additional logging calls for read, upload, insert, update, delete, and
other commands. Now need to get a reporting function working and this
bug 101 will be largely finished.

Modified EventLog to eliminate the separate revision column and instead fold
that into the docid string. Log now includes read events, but need to update
the data sent there.

Modified SQL scripts to add the new access_log table. I've partially tested this under postgres but have not yet tested under oracle.

Reformatted code for readability and consistency.

Added javadoc that was missing for the EventLogData class.

Added classes for basic event logging support. These classes write log entries to the database connection. Still to do: query the event log, write oracle sql code (postgres is done), possibly allow the log to be archived to a text file, and possibly do the dtabase writes asynchronously via a caching mechanism.

Made change in result tag that is returned in getprincipals action. Replaced userdn with username.

Added GPL license text to harvester source files.

Fixed a bug the text filed in path xml query maybe splited.

Fixed a bug if a document already has index, but now metacat doesn't use index. If you try to delete this one, will cause error.

Clean up some code.

Revise the handle query and squery method, not finished yet.

Add a new transform method.

Add a new transferm method for string reader.

Implement harvester scheduing capabilities and sending email reports to the Harvester Administrator

Validate user input data in registration servlet

Improve authorization logic for single file uload servlet

Add delete capability to single file upload servlet

Set content type properly for getversion action.

Added a simple action for finding out the current metacat version. The information is pulled from the property file, so be sure to update the version in the property file before shipping a release.

Fixed a bug in the new recursive SQL statements that prevented them from operating on oracle. Now they should work on both oracle and postgres.

Reformatted source for readability and conformance.

Excluded the update of the xml_index table in insert,update, and delete if the usexmlindex option is set to false.

Reformatted DBQuery.java for readability and consistency.

Changed printAttributeQuery() to no longer depend on the xml_index table. Now, if useXMLIndex is false, the method will use a recursive query on xml_nodes to match paths instead of using xml_index.

Some refactoring of the printExtendedSQL()
methods to eliminate redundancy in the code and
to provide more readable documentation.

Moved decision about whether to use xml_index for
query to the metacat.properties as "usexmlindex". Default
is now false. Still have some refactoring to do to remove a
few more uses of the xml_index table.

Created new printExtendedSQL function that can get the extended
return fields using only xml_nodes and not xml_index. One
step closer to eliminating the dependence ofn xml_index.

Created test class QuerySpecificationTest and started process of removing the xml_index from the QuerySpecification code. Reformatted some classes for readability.

Removed the "getdataguide" action as it was always experimental and is no longer used in metacat or morpho.

removed the 3 versions of printPackageSQL which are no longer used by metacat. This eliminates some dependency on xml_index.

Implement Harvester Registration Servlet

Additional scheduling logic

Changes to Harvester properties

Changes to log entries

Made changes in these three files so that getPrincipal returns back more details about users and groups. Users now contain userDN, user Name and user Email. Groups now contain Group name and Group description. So some function calls which returned single string array earlier now returns multiple string arrays. AuthSession.java called one of these functions - so accordingly changes were made to fix that part of the code.

Fixed the bug for sessionid storing, revision couldn't be zero and Ldap DN is case sensitive.

Replaced Hash table with Vector of Vector datastructure in getting <param> from Query. This was done so that the results are represented in same order as they appeared in the document.

Fixed bug that version could not be zero in replication.

Additional Harvester development

Additional development of Harvester implementation

Harvester source files

Restoring AuthLdap to previous search filter. Determined that the problem was
a missing o: attribute in the UCNRS LDAP directory. Adding it in makes the old
method work. The change I had made caused some confusion about authentication
because using just uid for a filter caused too many return dn's, and it was just...

Modified LDAP authentication to support a lookup for the NRS system. If
the auth on the provided string fails as a DN, try to look up a new
DN based on the UID. If we get a match, use that DN for auth and see
if that works. This allows us to use a referral within the...

Enabled stylesheet parameters to be passed through metacat even when the
'query' function is called. Previously, query would interpret all
parameters except a few hardcoded ones to be pathexpressions that should be
built into a squery. Now, metacat.properties contains a new configuration...

Moved the metacat.properties file from the jar file to now be located in
the tomcat context directory in WEB-INF. Now the metacat configuration is
editable in place. This change depends on a new Options.java class in the
utilities module, so be sure you do a "clean" build in metacat so that you...

Improvements to Harvester single file upload servlets

This is the merge from the branch WEB_UI_REDESIGN_BRANCH back into the head.
The only files that have been removed are those in lib/style/eml2; other files
that have been cvs removed (only from lib/ and lib/style) have been re-added
elsewhere (i.e. moved from one directory to another)....