Metacat

Unix port of transform.bat

Simple DOS batch file to transform an XML document (eg an eml doc) into HTML (or whatever) using an XSLT stylesheet

Eliminate hard-coding of the knb context from the advanced search code. Advanced search servlet determines the metacat context name by reading the metacat.properties file at servlet initialization.

Simple bash script to query metacat (using wget) and transform the XML
resultset into a text file using an XSLT stylesheet.

This is a basic commandline client for resolving LSIDs. It is meant as
a quick and dirty testing utility. It requires the SOAP::Lite,
SOAP::MIME, and MIME::Entity CPAN modules. Run without arguments, it
uses a default LSID and endpoint to resolve. WIth the lsid and endpoint...

Reformatted LSID code for consistency.

Added apache commons logging to the LSID servlet using log4j. Remove println statements.

copy log properties to the deployment for LSID.

Properties for logging in LSID resolver.

Changed search option checkboxes to radio buttons. Restored ant headers. Removed dialog box warnings when changing search options.

changed paragrah style to "intro" for text not in the boxes

unbolded text in boxes and took out the background color for most of the box.

cleaned up formatting - need to test spacing around the table "boxes" , and the boxes alignment

ESA update to Search Feature and cleaning up some formatting - search feature needs testing. Changed <menu> to <ul>
------------------------------------

Error C:\Documents and Settings\Callie\Desktop\metacat\lib\style\skins\esa\index.html "*,*" is not valid value for the "cols" attribute in any of the currently active versions. See the above warnings for more details. 185...

bugfix so that getlastdocid works for postgres

few adjustments added discription of the Morpho software that Margret Conners suggested. trying to fix spacing and alignment problem with "boxes"

modified mod_revise so that Revision Requested is added to the document in additionalMetadata/moderatorComment which can be used by the skin in searching for documents which havnt been requested for revision

Modified the search queries so that moderator doesnt see the documents for which revision is requested

Updated NCEAS Data Repoitory changes - replaced text "auspices" with "as part of" got ride of the text about the data set being reviewed and implemented suggestion from Margret Conners.

added for Morpho Information on NCEAS Data Repository page

New template for displaying results from the accept, reject and revise actions

new variables specifying the esa specific templates

Modified the resultpage to display the message sent in the post request

Following changes:
1. Fixed a bug in checking of contact email address field
2. Added functions to display the result of accept, reject and revise actions
3. Added variable to control if the document creator should be the skin admin
4. a common function to check if the present user is a moderator

Added new variables to the script which creates templates for new skins

Add some servlet mapping for axis.

iNew jar files for LSID soap support.

added 70px left margin to body elements. specified 0px left margins for bodies of header html files

Updates for Moderator header changes - center text and remove double green line

updated the ESA Header with View Documents Pending Moderation changes - centered and placed gray rectange over the top ofthe ViewDocPend gif

Updated changes to Moderation link on header - centered, space under the "underline" removed double green line by adding a gray vector to cover the top of
the ViewDocPend.gif

fix for the access control check - earlier only permission 4 and 7 were checked for read. Now the query checks for permissions 5 and 6 also

Added a new variable to control if admin is made the owner of the document

update for moderator header

Fireworks files for updateing graphics and header code (*.png)

updated to work with the moderator

Modified the xsl so that regular user sees View and Edit button

Modified code to that isModerator param is passed to the xsl which will render the results.

Fixed a bug in the way taxon rank and taxon value were assigned.

Changing the links in the esa header.

Some small bug fixes...

New functions in the dataset registry to support moderation feature needed for ESA

Fixed the bug in the link to view documents pending moderation. The links works now.

add a token to specify the login form template

Changing the table name back to xml_index

a new variable for the moderation email template and change in value of some other variables

Fixes to enable SOAP support for the LSID resolver. Axis now is
installed as a component of the authority context and the services list
is properly displayed. Added the happyaxis.jsp test page to verify that
the axis install is functioning properly.

Minor change to diagnostic output.

Fixed a log bug.

New templates for ESA skin.

loginForm.tmpl is useful in displaying a login form
and esaModNotification is useful in sending notifications to the moderator and the contact

Add a client-side check: if user does not enter any search values, prompt the user with a dialog box to confirm that the user wishes to go ahead with a search for all documents. This is equivalent to the behavior in the simple search box.

Added a hidden input field for siteValue with a value of "ALLSITES". This is a substitute for the siteValue drop-down list that is used at LTER whose default value is also "ALLSITES". Either the hidden input field or the drop-down list should be commented-out, but not both. (This is documented in the internal comments.)

Modify the bean's get() methods that return String values to trim white space off the string prior to returning it. This is so that input fields that contain only white space will not be treated as valid search values.

Updated names of jar files in build.xml for LSID support.

Added axis servlet defs in web.xml

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.