Metacat

Initial checkin of LSID support code for metacat. The LSID support here
provides access to metacat documents through an LSID identifier. The
identifier takes the form:
urn:lsid:ecoinformatics.org:jones:1:1

See http://lsid.sourceforge.net for more details....

Changes in calls made to IndexingQueue class

A version with less number of bugs.

New code for run an indexing queue and indexing thread which runs every 24 hours

Removed the call to indexing function in DBSAXHandler and added a call to indexing function IndexingQueue

removed the indexing code from DBSAXHandler

1. Added code to start the indexing thread.
2. Fixed a bug in the query on xml_nodes and xml_index
3. Added more debug statements
4. Fixed a bug in code which determines namespace

New function which returns the formatted left join query. This is required as Oracle and postgres have different left join syntax

Removed all hard links, and put the jsp page in the same context as the geoserver.

Add more debug info.

Using join query for more efficiency.

Add class as parent class add method.

Add method as parent class adding method.

Add method as parent class adding a method.

Add a method to get doc list query.

Fixed bug to get docid list.

Add more info transfer.

Modified the WARNing message

Fix for bug in the previous commit

Modified the debug levels of debug statements

Add code to handle replication document in xml_document table.

Modification in algo:

1. Find if the root element has prefix (e.g. <eml:eml>). If found, go to step
2, otheriwse go to step 3.

2. Look for xmlns:prefix element to find the ns
(e.g.:xmlns:eml="eml://ecoinformatics.org/eml-2.0.0")
2.a If not found go to step 4...

Bugfix for 2091. Removed the function needValidation(). Added function getPrefix which returns the prefix. And use the following steps to find out the namespace

1. Find if the root element has prefix (e.g. <eml:eml>). If found, go to step
2, otheriwse go to step 3....

Faster script for upgrading oracle database

Add code to handle catalog is null when inserting xml_revisions table.

Add code to handle write record into xml_documents when catalog id is null.

Bugfix to the code which sets parentnodeid in xml_path_index. (Use setInt instead of setFloat)

Added some documentation and did a little cleanup.

Continued work -- now the user can get info on all layers servered by the wms, including the metacat docs.

Removed sql syntax not acceptable by Oracle.

Changed the filter and ldapbase values in getUserInfo so that it works for both NCEAS and LTER ldap

Bug fix in the changes made in previous commit

Added warning to be displayed in the log when document is not inserted.

Interim checkin -- getting the postgis database setup

Modified the login method in the perl metacat client so that status of the user logging is also returned
Earlier if login info was not valid, 0 was returned. And 1 is sent back if login info was valid.

Now, if valid then following values are returned to indicate user status...

Added support in the metacat client for the new function added to MetaCatServlet

Added a new action - getloggedinuserinfo - which returns information about the user in the following format.

<user>
<username>uid=sgarg,o=NCEAS,dc=ecoinformatics,dc=org</username>
<name>Saurabh Garg</name>
<isAdministrator/>
<isMOderator/>
</user>

Removed code entered in previous commit as it is no longer needed

Also in the previous commit, the successful message changed. Now in addtion to the sessionid tag, the following tags also included: <name>[name of the user]</name>, <isModerator> (if is moderator) and <isAdministrator> (if is Administrator)

Added a new function - getUserInfo to AuthInterface and AuthLdap
The function returns a string array for a given username. the array contains the name, organization name and email address of the user. In case of ldap, it is cn, o and mail attributes for ldapbase=username...

Got the metacat datapackage selection (single point) working.

Fixed a bug in QueryGroup which prevented QueryGroup from appending itself to the sql query when no queryTerm is present.

Further work -- added additional layers, added the ability to query AOI. Almost have the js parseing the
correct metacat url, and sme style changes.

Removed unused subroutines that were for testing.

Adding the control-services.pl utility for failover montitoring. From
the README:

This program is designed to run as a script under the Hobbit system
monitoring program (http://hobbitmon.sourceforge.net/). When Hobbit is
configured properly, this script will be called to make changes to the...

Remove debugging.

Added some more layers

Fixed the mapbuilder getfeatureinfo function and modified the config. Now the metacat url addresses are available from the rendering.

The index page for the mapbuilder rendering -- running off the geoserver
wms/wfs server.

These are the config files for the mapbuilder rendering app that connects to
geoserver to access the metacat spatial data. The display works but the ability
to get the url to the metacat document is not yet working. This code was
written against the mapbuilder 0.2.0.xx and it is recommended that it be run...

Changes in log levels of some commands mentioned in the previos commit.

Replacing MetaCatUtil.debugMessage or MetaCatUtil.logMetacat call with logMetacat (private Logger object) call

Commited the wrong MetaCatUtil.java file last time. Making the changes again.

1. Replacing MetaCatUtil.debugMessage or MetaCatUtil.logMetacat call with logMetacat (private Logger object) call
  2. Commented out debugMessage()
  3. Removed getLog() and earlier old log4j code...

1. Replacing MetaCatUtil.debugMessage or MetaCatUtil.logMetacat call with logMetacat (private Logger object) call
2. Commented out debugMessage()
3. Removed getLog() and earlier old log4j code
4. Removed formattedDebugMessage

Replacing MetaCatUtil.debugMessage or MetaCatUtil.logMetacat call with logMetacat (private Logger object) call

Add a new sql file to alter control file which from knb backup for new file location

Copy the code to generate xml_path_index from xmltables.sql. xmltables.sql is working, so it may fix the bug.

if moderator is logged into metacat and no option for enable-editing is specified then enable editing by default

Fix for bug 2222. So that correct query is generated when searchmode is 'not-contains'.

Change the method to get access document docid and revision.

Fixed bug which can cause eml beta6 couldn't run access control.

Add rev in get data doc info.

Fixed a bug if one server failed in replication, it will cause another server failed.

Add code to guess the docid's revision in read action.

Remove some debug message.

Fixed bug couldn't delete xml_nodes when moving to xml_nodes_revision in replication.

If skin cfg specified access rights to be included for a certain set of users and groups, then those are entered in the access permissions given.

Fix for bug 2220. And check the cfg file if the eml documents generated should be publically readable or not.

Change the code to make sure DocumentImpl class's constructor should have rev attached.

Remove this file.

Added an attribute to the metacat shapefile called area_coef which is a function
of the areal extent of the datapackage -- so a datapackage which was related to
a global collection would have a large extent, whereas a 3-foot squared plot
would have a small extent. Also fixed a bug related to the ID field that was...

Added a function to strip out the whitespace that was around the bounding
coordinates retrieved from metacat, and also now writing the full set of
bounding coordiantes (east,west,south,north).

bug fix so that error is displayed if station or reserve is not selected

fix for the bug entered in previous fix

Fix for bug in QueryGroup. Didnt check if the QueryGroup returned empty string. E.g. in case of a % search.

Fixed bug in the trigger of xml_path_index table

Fixed bug which currentDocument maybe null.

Fixed bug which currentDocument may be null.

fixe bug which currentDoc maybe null.

Add code to transfer string to date type.

Add function transfer string to date.

Add date info.

Add info about date.

Changes according add data info.

Rewrite replication for revision document.

Add code to get date info

Fixed the bug in xml segment is not correct to express revision document list.

Remove the print out statement.

Fixed some bug in replication.

Added code to enter publication date into the dataset.

Add some drop command and fix the bug in creating xml_path_index table.

Fix for 2214. Allow 0 in coordinates now.

Fix for bug 2215. Error message is displayed if project name is not selected in the nceas skin.

Add code to handle deleted document replication.

Add code to handle replicate the deleted document.

Add method to get revision list in xml_revisions table for a given docid.

Add code to handle replication deleted docs.

Change setString to setInt for ticket account because driver changes.

Fixed a typo.

Refactored the build to use a <path> element for the classpath rather
than ant properties. This makes the classpath easier to manage, but required
changes throughout the build. I think everything should still build fine --
it works for me.

Upgraded the JDBC driver for postgres to the version 8 driver....