Metacat

Fix for bug# 2371

Modified code so that database is queried just once when a document is read. Currently the read is being done in the constructor and then again in
the function.

Two changes to Metacat Harvester implementation:

(1) Removed call to deprecated Thread.stop() method. Added boolean class variable, Harvester.keepRunning. When the thread is destroyed, set Harvester.keepRunning to false.

(2) Access the harvestList.xsd schema file by finding it locally in the web application rather than via a URL to cvs.ecoinformatics.org.

added function to get list of projects for NCEAS from a given project list

fixed bugs in teh client that were preventing the lsid service from working right

modified the client so it will work consistently with the web service

updated the client so it throws a DocumentNotFoundException if you attempt to read a docuemnt that doesn't exist

Missed a period.

Patch to make the getLastDocid function actually work on the text node.

Patch for making getlastdocid work when the identifier is a large number
greater than can be encompassed by an int. Now it uses a long to
represent the number, which doesn't solve the problem but probably does
make it work for the vast majority of cases.

Added ref to the FGDC schema that I forgot to check in earlier.

Added new function getLastDocid to the metacat client so that it is
accessible to clients that need it.

dded TLS support to the ldapweb.cgi script, cleaned up some TempToolkit
template processing so that the results display CSS properly, and some minor
formatting issues. The TLS support should probably be enabled only if the
server supports it, which can be queried with supported_extensions, but for...

Changes in the spatial query. The spatial query can be generated on the client side in form of an squery rather than specifically creating one on the server side.
Commented out the code which creates spatial query based on the coordinates sent to Metacat. Instead of that, a temporary method was added which creates the squery...

Removing the comments from postgres upgrade script as ant upgrade fails because of these.

fixed a bug with postgres 8.1.6 where the sequence must be created before the table is created.

iModified code -- the booleans werent really getting tested :(

iModified the switch to turn/off the spatial searching.:wq

Fixed a bug in the query system.

Now this page is in an expandable drawer.

Some style changes and small changes to the spatial querying system.

Updated style for the kruger soils layer.

Fixed the way the text query was written.

Adding maps for the world frame.

This is the internal frame for the africa view.

interim checkin.

This is the mapbuilder app that will be used in the kroger demo.

Initial support for displaying FGDC metadata documents in metacat.
Added new returndoctype and returnfields to all query forms in the knp
skin to allow FGDC documents to display in the resultsets. Need to add
these to the other skins as well, and to clean up the FGDC stylesheet to...

Patched to fix regression bug that prevented insertion of documents
without a DOCTYPE or namespace declaration due to an
ArrayOutOfBoundsException. Now these documents can be inserted, which
is useful for inserting FGDC documents that frequently do not have a...

modified the code to return the correct metacat resltset.

Modified the way the results page is displayed.

Fix in getNamespace function. Bug reported by Margaret in testing for cases where no namespace is specified.

This is a utility class for generating a pathquery document from an array of docids that one wants to query for. Its hacked together in that the default query parameters are all hardcoded into the class, which is obviously wrong. Need to figure out where those default params should be derived from.

Integration of new shapefile writers (r. reeves code) with MSO.

Continued integration of the spataial stuff with the metacat servlet.

Integration of the metacat servlet with the spatial option -- rubberbanding is implemented too.

adding changes that pmark made, and some small changes that I made.

Implementation of the rubber-bad query that PMARK has implemented through the UI.

metacat spatial option code -- code that produces layers depending on the
metacat transaction.

Adding a page that'll be returned when a user issues a metacat query.

fixed the index jsp to do the redirection to the given skin's html (the all
seem to have html pages, yet not all have jsp's). Started implementing the
display of eml docs with bounding coordinates as boxes.

Got rid of some debugging.

bugfixes to teh previous commit... cleaner exit for the indexing thread

Added a flag for indexing threads so that they exit once Metacat has unloaded.

Added checks for null pointers and changed the name of the config file

Using java.util.Property instead of Options. Options is a singleton class. Hence it cant be used for reading skin property files without changing it into a non-singleton class

variable for showing instructions

Making changes for passing the params to the xsl for skins.

Remove CR characters from end of line. Formatting changes only, no functional changes.

Modified the lsid code to lookup document type-appropriate stylesheets from
the lsid prooperties file.

added code to give access to moderator group on the review document

Added template for getting the review

Made changes so that the user is prompted to login before entering a dataset

Added functionality for storing comments and displaying them. Also added functionality for reading the eml document.

hardcoded the organization as unaffiliated

bugfixes in previous code and added functionality to store reviews on various documents...

Added setaccess method

code to handle null pointer exception

Added query for indexing attribute - needed for indexing packageId

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.

bugfix so that getlastdocid works for postgres

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

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

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

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

Some small bug fixes...

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

Changing the table name back to xml_index

Minor change to diagnostic output.

Fixed a log bug.

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.

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 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

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

Replaced hardcoded namespaces with variable defined in metacat.properties

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: 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....

Changes in calls made to IndexingQueue class

A version with less number of bugs.