Metacat

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.

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.