Metacat

Fix for a bug in MetacatServlet. Metacat assumed that it is supposed to get the schema information from the second line of the document. This is based
on the assumption that xml decleration will always be present. This is good practice but not required. Hence the fix -> Metacat should ignore the...

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.

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

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...

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.

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

Fixed the way the text query was written.

interim checkin.

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 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.

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.

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

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.

code to handle null pointer exception

Added query for indexing attribute - needed for indexing packageId

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.

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

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.

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.

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

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....

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)

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.

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...