Metacat

New libraries for axis 1.3.

New SQL tables and db upgrade scripts that define a new table stucture for identifiers and delete the previously unused accession_number table. This is in anticipation of supporting LSID identifiers. Currently these tables are unused by the servlet but are in place for discussion.

Cleaned up AccessionNumber class to get rid of unused methods. It seems the entire accession_number table is no longer used but has not been deleted from the build. Will do in subsequent commit.

1. Modified buildIndex() so that only one connection is used for both indexing nodes and indexing paths.
2. Modified the indexing algo so that indexing of paths is done while nodes are being indexed. Results in a much faster indexing algo
3. Replaced access to NodeRecord.<variable> with NodeRecord.<getVariable>

Change the code level of the MetacatHasDoc harvester operation from "Warning" to "Info". This is to reduce the amount of diagnostic output generated in the email reports to the site contact.

Change the maximum code level reported to the site contact from "info" to "notice". This is to reduce the amount of diagnostic output generated in the email reports to the site contact. Diagnositcs of type "error", "warning", and "notice" will be sent to the site contact, while messages of type "info" and "debug" will not (but they will still be sent to the Harvester Administrator).

Modified the way checkDocumentTable is accessed. Also removed the while loop from the checkDocumentTable. Now if the document is not found, the thread goes to sleep - instead of checking again. (In hope of a more bugfree code)

Replaced access to NodeRecord.<variable> with NodeRecord.<getVariable>

1. Changed teh access modifier from public to private for variables
2. Added a new variable for nodedatanumerical
3. added a new constructor

Moved printMessage statements to inside the if loop so that they are not printed each time getInstance is called

Bug #2207. Metacat Advanced Search interface.
Improvements to Advanced Search form:
(1) Delete keywordSearch() function. Not used in advanced search form.
(2) Re-initialize hidden form values for geographic boundaries.
(3) Change table width to 100% so horizontal rules will span the full width....

Using xml_path_index instead of xml_index to find documents which havnt been indexed.

Replaced hardcoded namespaces with variable defined in metacat.properties

Replaced hardcoded link with ant token

Modified links for the Accept, Delete and Review buttons

Replaced hyperion.nceas.ucsb.edu with mailhost

a new variable for the namepsaces to be indexed

Changed logMetacat to be a local variable in MetaCatServlet to avoid any potential threading issues.

Metacat has had problems with threading issues when accessed from ecogrid. These problems may stem from the use of shared global variables within the servlet that are not protected against threading problems. We used a lot of these, which I am eliminating in this commit. Besides final variables used as constants (which are not a problem), now there are only three unprotected variables (sessionHash, logMetacat, and conn) which are harder to eliminate. I will be discussiong this with Sid tomorrow to see how to eliminate them.

Fixed the bug that replicate data file failed that the documents records wouldn't be deleted.

the parameter of method getRevisionTableReList is docidWithoutRev.

Fixed bug that data file upload failed, record couldn't be deleted.

Bug #2207. Add new build target, advancedsearchjar. This allows the Advanced Search engine to be built as a library for use in other web applications. This is important because LTER is currently using a separate web application for its interface to the Metacat data catalog, so the library allows the search engine to be used both inside and outside Metacat. Eventually LTER would like to fully re-integrate its Metacat interface with the lter skin, so eventually the need for this build target may go away.

Bug #2207. Enable hyperlink to the Advanced Search form.

Bug #2207. New JSPs added to the default skin to support Metacat Advanced Search interface.

Bug #2207. Add new CSS class to set the correct iframe sizes for the Advanced Search box.

Bug #2207. Add two new JavaScript variables to support Metacat Advanced Search interface.

Bug #2207. Add new JavaScript function to support Metacat Advanced Search interface.

Bug #2207. Add AdvancedSearchServlet to support Metacat Advanced Search interface.

Bug #2207: Implementation of the Metacat Advanced Search engine.

Fixed a bug in log

Fixed log bug when xml_revision updated failed.

Removed extra package declaration in LSID java file.

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....

Add new index value for distribution url.

Added parameter to specify how long the indexing Thread should wait for the docid to show up in xml_documents

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

new variables defined for the indexing threads.

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 new command to create no-password key.

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

Updated list of coordinates for OBFS sites

(Commit for Veronique Connolly by Saurabh Garg)

Bugfix in the searches done from the skin webpages...

Updated list of coordinates for UCNRS sites

(Commit for Veronique Connolly by Saurabh Garg)

Change in obfs homepage so that search uses a radio button instead of check box

Change in nrs homepage so that search uses a radio button instead of check box

Change in nceas homepage so that search uses a radio button instead of check box

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

Bugfix in the query sent to metacat

Bugfix in the metacat query generated in javascript

Bug fix in the changes made in previous commit

changed old link for Long-Term Studies Section to current link

this file is used in Fireworks to make the header and the slices

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

1. useSiteCoord option is made avaiable again
2. contact email address can be made required.

Interim checkin -- getting the postgis database setup

Added lter to list of orgs.

New changes in the esa skin so that includes the moderator functionality and login/logout functionality

These are all header updates to include the login and logout for the ESA Header links. I left the original Header and named it headerOld.html and saved the Slices
that go with it too. (the ESAHomeLogo.gif file might be overwritten) The code for
the header to work with the Logout slice and roll over is in the file headerLogout.htm. <td><a href="#" target="_top" onMouseOut="MM_swapImgRestore();" onMouseOver="MM_swapImage('ESALogout','','ESAHeaderSlices/RollOvers/ESALogoutR.gif',1);"><img name="ESALogout" src="ESAHeaderSlices/ESALogout.gif" width="57" height="17" border="0" alt="Logout"></a></td> The code for the login slice and rollover is in the header.htm file <td><a href="#" target="_top" onMouseOut="MM_swapImgRestore();" onMouseOver="MM_swapImage('ESALogin','','ESAHeaderSlices/RollOvers/ESALoginR.gif',1);"><img name="ESALogin" src="ESAHeaderSlices/ESALogin.gif" width="57" height="17" border="0" alt="Login"></a></td>

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.