Metacat

Added a new URL protocol handler class for the metacat protocol. This
class will replace the current MetacatURL class in a much simpler and
extensible manner. See the documentation for java.net.URLConnection and
java.net.URL for details.

this class allows the parsing of xml data sent by a replication server to assertain document info about a remote document.

added functionality to allow the replication servlet to assertain and insert user and group info into the local database. started implementation of insert replication handler (it is commented out in this commit)

fixed compatibility problem by overloading the write method. Jivka's new parameter (Reader acl) is now defaulted to null if it is not explicitly declared.

added interface to handle a new "acl" parameter bringing the text of a xml access file for a given metadata document
the "acl" parameter is optional and should be sent on INSERT or UPDATE action.

new class for parsing ACL XML file and loading acl data into metacat db

added delete functionality

added support for server_location in the xml_revisions table.

removed inadvertent comments

removed dependence on a server code in the accession number of each document. the file's resident server is now located in xml_documents.server_location.

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now updates the xml_replication last_checked field

updated javadoc documentation

fixed bug/typo

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changed action scheme

Modified pathquery.dtd and QuerySpecification to allow some new constraints
on queries submitted to Metacat. Now, queries can contain an optional
set of <owner> tags that identify the users for which documents should be
returned, and a list of <site> tags constraining the site identifiers...

can now send a file to another server

can now download a document from a server

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Fixed typo in DBSAXHandler debug message.

not needed any more

it is not needed to be here

changes for using SRB v1.1.8 at LTER, NM

changed naming scheme

changed naming scheme

changed naming scheme

servlet to handle metacat replication requests.

a timer based thread that does Delta-T replication checking.

a parser to handle replication xml messages

change for using the db connection

Updated the Javadoc documentation so that the current release can be provided
on the web site.

Fixed problem with AuthInterface, AuthLdap, and AuthMcat where the
sigantures of the methods of these classes were not in agreement, which was
causing AuthLdap to no longer compile. Changed parameter signatures so that
the 'user' parameter is used consistently in all of the methods.

bug fix about util.openDBConnection() for xmlIndex tread

small fix for exception when srbMaster is not running

XSLT transformation on "login" and "logout" action

AuthMcat
- new class for authentication through MCA; implements AuthInterface
AuthSession
- assigning HttpSession obj only after successful athentication;
- cleared isAuthenticated field - not needed
- cleared invalidate() method - not needed
AuthInterface...

Began work on new UI for the KNB web site. It will be the main query
interface from the KNB website.

Fixed the LDAP authentication adapter (AuthLdap.java) so that it now looks up
the distinguished name for a user before attempting to do authentication.
This is because the user's distinguished name can sometimes be based on
their uid attribute, but sometimes be based on their cn (common name)...

merge AUTH_LDAP to the main branch

clear System.exit(0) within the static block

added functionality to return the doctype of a relation in a relationdoctype tag. This information is now returned automatically in the resultset under the path resultset/relation/relationdoctype.

removed debug print statements.

added code for getting stylized related documents

allowed both indexing threads to run without interfering with each other.

fixed bug that caused a nullPointerException when a null resultset was returned.

Changed to prevent the insertion if the provided Accession# is in use as Dan suggested.

removed system.out.printlns

added support for urls of the form "metacat://server.xyz.com?docid=XXX:yy"

Separate thread used for writing into xml_index table.
This cut the time of the response on insert almost in half.
The tread is started afterwards
(on end of document parsing and inserting into xml_nodes) from
DBSAXHandler and uses new(separate) db connection....

This class syncronously indexes any package file that is loaded into the database.r

Added backtrack functionality. Backtracking works by passing a returndoc parameter. There can be more than one. If a document that is hit by a query is not of type returndoc then it searches the database for a related file of type returndoc. If one is found it is displayed, if no relation is found, the original is displayed....

included new method getPoolSize()

added extra timing information to the main() driver method.

fix the small bug with output like:
Fatal processing error

<success>
<docid>null</docid>
</success>
on hadleInsertOrUpdateAction()

writeDocID() not needed any more
throw SAXException from everywhere

on character(cbuf, start, len) included:
if currentNode.getTagName().equals("title")
currentDocument.setTitle(cbuf)
instead of using:
currentDocument.setTitleFromChildElement() in endDocument() call

change Assession# generation to use the same db connection

Updated the download data function. the download data function now pulls a document from the database, zips it up and sends the zip stream to the client. It also zips up any related files. a relation parameter is used to pass related files to the servlet. If only one document should be zipped and sent, a single docid in the param hashtable is sufficient.

changes related to decrease the time of INSERT of document.
With these changes I inserted 200KB file for 3 minutes, 50KB for 50sec.
This is mainly simplifing the DBSAXNode class and
using batching feature of Oracle JDBC driver.

This allows for the easy handling of metacat:// urls. The documentation in the source code explains the specification for the url in detail.

Added functionality for package specifications. metacatservlet now contains a new action called getrelateddocument that handles retrieving related documents using the metacatURL specification (metacatURL.java). DBQuery contains new code in runQuery that embeds relation tags in the returned hashtable describing the documents related to each docid. querySpecification contains a new method which prints the sql that does the relation query.

store generated Access# in meta_file_id tag if there are any

fix bug in toXML() about getting output of XML document like:
<paragraph

added parentnodeid to xml_index

fix for "Document not found" err message on "getdocument" action

fix for "public" authentication

removed print statments

fixed xml tag error in squer

fixed bug in handleSQuery that returned the tag in the <query> tag of a resultset.
BugID:
Submitted by:
Reviewed by:

added check from "read" permission on "query" and "squery" actions
for connected user or for "public" connection

added support for getabstract action

Added a method called getNodeContent which retrieves the content of a node in a document. If there are more than one nodes with the same name returned, it returns an array with all of the data.

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Modified MetaCatServlet to use the new DocumentImpl.toXml() method for
efficiency of reading documents. See bugzilla bug #111 for an explanation.

Fixed document reading bug (bugzilla bug #111) so that reading documents
is no longer a power function of the number of nodes in the document
(which used to be the case). Now, reading a document occurs entirely
within DocumentImpl, by making a single SQL call to get the document data,...

change the 2 executions in archiveDocRevision()
with 1 statement:
"insert into xml_revisions
select ... from xml_documents where docid = ..."

small changes on hasWritePermission()

storing user_owner and user_updated where needed
new function in DocumentImpl checking for "write" perm on UPDATE or DELETE
added delete from xml_index of the old version of docid on UPDATE

this file is no longer used.

changed xslf for new returnfield scheme. the returnfields are now returned as <param name="<returnfield>"> tags.
hThe sql for the returnfield query was redone to fix a previous problem with slow queries

cleared static methods in AccessionNumber classes for fixing bug found
when multiple requests to the servlet at a time.

Minor update to remove unneeded constructor in DocumentImpl class.

for getDoctypes() added
WHERE entry_type='DTD' condition in the select statement

Changes with Srb authentication: including quering of Srb/MCAT during the Srb connection for:
- groupname of connected user
- list of groups and users in MCAT for ACL function for MetaCat

Continued code redesign for the DocumentImpl class. Now the "delete" and
"write" methods are static, so a DocumentImpl objject need not be created
in order to initiate a INSERT, UPDATE, or DELETE action (it is created
implicitly by the DBSAXHandler). When doing a "READ" action, one still...

Folded the functionality from DBWriter into DocumentImpl, continuing the
work started earlir to create a more DOM-like model for the classes, in
which a single DocumentImpl class handles both reading and writing of
documents to the database. Modified shell scripts and MetaCatServlet to...

changed the field names to be case-sensitive in the returnfields

added support for the returnfield parameter
-QuerySpecification now sets a flag (containsExtendedSQL) when there are returnfield items in the pathquery document.
the accessor method containsExtendedSQL() can be called by other classes to check for extended return parameters...

added support for the returnfield parameter
-added the dynamic parameters to the returned hash table of documents

added support for the returnfield parameter

Folded the functionality from DBSAXDocument into the DocumentImpl class.
Now DocumentImpl handles both the reads and the writes to the database.
Eventually, it will implment the full DOM Document interface. Eliminated
the DBSAXDocument.java file as it is no longer relevant....

Removed DBReader.java because the functionality of that class has been
replaced by the more efficient DocumentImpl class.

Created new class "DocumentImpl" which represents an XML Document. This
document will eventually implment the DOM Document interface. For now,
it implments all of the functionality that was present in DBReader, plus
cuts down on the number of database calls required to read a document. And...

Updated documentation for NodeComparator.java.

Modified the DBReader and ElementNode classes to more efficiently read
documents from the database. In the old implementation, a db connection
was opened for each and every node in a document, recursively fromthe root
node. In the new implementation, all of the data from xml_nodes is...

marineServlet now overrides the transformQuery() function to allow it to put the values back into the text boxes of the xsl stylesheet rendered form.

-fixed the bug where a pathquery document was not valid inside of the <query> tags in a resultset document.
-provided override support for a new function called transformQuery() which allows specific applications to
customize what is returned in the <query> tag

Fixed small bug in transforming the document to HTML. If there was
no stylesheet for a given doctype, and so the transformation couldn't
occur, the XML doc was returned, but the content-type was still set
(incorrectly) to html. Now it is not set to text/html when an xml doc is...