Metacat

Changed target of the javadoc builds to the build/docs/apiDocs directory
so that we no loger version track the javadoc html files -- they changes
too much between each of the times we would generate them. Also, removed
the old javadoc documentation that was found in the "docs" subdirectory.

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

not needed

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...

added "qformat=html" form parameter for "login" and "logout" actions

changed action's value:
"Login" to "login"
"Logout" to "logout"

Modified stylesheets to use the default.css file from the new KNB web site.
Also, provided a new resultset.xsl that represents a simple freetext query
of the KNB data repository. Updated build.xml to relect the location of the
new css stylesheet.

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

Fixed typo in stylesheet.

More user interface changes to the HTML MARINE interface. Minor
rearrangement of columns, some link changes.

Replaced imagemap with anchor links in the web interface to simplify the
rearrangement of the interface. This new feature uses javascript to
submit the form when the link is clicked.

Various changes to improve consistency of the MARINE and METACAT user
interfaces as presented through the XSL->HTML conversions. Eliminated
one (extraneous) copy of the rowcol.css style sheet in favor of sharing
a single css stylesheet in xmltodb/lib/style/rowcol.css. Modified all...

Included script for insert of all eml dtds.

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.

added ability to enterpret relationdoctype tag.

added new linkage to the title in the table

removed debug print statements.

added code for getting stylized related documents

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

made package changes

- cleared copyfile of marine.properties since it is no longer in use
- added copyfile of srbProps.properties from xmltodb/lib to the servlet classpath
same like metacat.properties

moved it from src/edu/ucsb/nceas/metacat dir to here

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

changed the look of relations

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

removed system.out.printlns

added a "server" parameter which tells the system the path to the server on which metacat is running. This is used for metacat:// urls.

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

added package and resource data and structures

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....

added new fields

added support for returndoc handling.

added a packagedoctype parameter so that the servlet knows what kind of doctype a package

updated for returndoc field

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.

updated this style sheet to display only resource documents and their related files. Also added hidden input params to the images on the left so that the related document info is sent back to the servlet when documentation or an abstract is requested.

this stylesheet now processes relation information.

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 table

added parentnodeid to xml_index

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

fix for "public" authentication

xml_documents.public_access modified to be
NUMBER DEFAULT 1
ie all documents to have public access by default

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

3 indexes added on:
xml_nodes (rootnodeid)
xml_nodes (parentnodeid)
xml_documents (docid, doctype)

sql file defining the table structure for eml-package data.

added documentation and cleaned up the markup.

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.

Added support for viewabstract

added resource.xsl to the catalog

no message

style sheet for resource documents

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

Updated the test.xml file to use more XML features for testing insert,
update, and read functions of DocumentImpl. Now the document contains
comments and processing instructions.

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()

get rid of the FK in xml_acess table that points to xm_documents.docid
since xml_access.docid(s) point to current and revised documents
(ie xml_documents.docid and xml_revisions.docid)

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

changed xslf for new resultfield scheme

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

changed paths in returnfield parameters

added alt tags

added alt tag

new graphics and their adobe illustrator vector files

changed colors and layout

Minor update to remove unneeded constructor in DocumentImpl class.

new table xml_access and new attrs to xml_documents for ACL

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

fixed typ-o

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

update of build.xml based on Matt's recommendations

added an image-path property to get around the messed up images when loading images from tomcat. To add your own image directory,
create a directory under /opt/httpd/html/img/ and add the path to the image-path property in build.xml. Then all img tags in your documents...

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...