Metacat

If the sessionid is null and user will be treated as public.

Fixed the bug that if path query without xml declaration will cause a non well-formed result doc.

Change string to stringreader to save memory.

got interservlet session handling working.

fixed errors with jing and my merges

changes to make session management between monarch and metacat work.

Revise the code for read from metcat.

Add code to hanlder wirte and update funtion.

Get the file size limit from property rather than hard code.

Revise code to decide use which parser.

Add contenttypeprovider when read a data file.

Finished the implementation for action readinlinedata. The prototype is action=readinlinedata&inlinedataid=eml.23.1.1

Set default content type for data file.

Add a new action readilninedata for metacat. By this action, user can read inline data only.

Add a flag in read action that the user want inline data in xml document or not.

Add eml parser checking here.

Add code to handle validate xml instance by noNamespaceSchemaLocation.

Just now made a wrong sumbit and revise it.

Add access query for control the return fields.

Change the calling method.

Chane a info for output.

Set a condition to for setting eml2 parser.

Change schemalocationkeywords constant from private to public and it can be reused.

Add schema validation parameter here.

Change some output for inser documents.

Create a action setaccess for assign access rule to single file.

Merge code from branch monarch.

Change the code for validation.

Add some debug message for displaying search time.

Add a control for readForRemoteServer is only for data file.

Merge cvs branch replication to cvs head.

Add code to shrink connection pool size. If all connections are free.

Merge DBConnection branch to head.

Change back to Connection. DBConnection will store in cvs branch..

Add DBConnectionPool object in servlet's init method and DBConnectionPool's release method in servlet's destory method.

Add control to send data or not

Add a control to get data file granted in handleUploadMethod.

Delete a some useless code for connection pool

Revised handleUploadRequet.

Adding a hub control to data file in handleUpLoad method. Data file was changed can be replicate to all server or only home host.

Adding a new feature that in uploaddatafile that the datafile can be replicated.

Only delete some incorrect comment.

The feature of check permission before Metacat handle a "read" action. If user doesn't have permission, its request will be rejected.
After creating a DocumentImpl object. A method named hasReadPermission in that class will be called to make sure the user has permission to read it.

A new action named export was add to it. This action will export a zip output stream for a data package. In the zip output stream, meta data documents, data files and a html summary file are include. The stucture will looks like:
package----/metadata/metadata docments...

updated metacat so that the xmlparserv2.jar file is no longer needed. replaced all of teh oracle xml processing with xalan and xerces.

fixed the error where the ldap authenticate took 15 seconds to execute

Fixed the function to return the max id for a given scope. Now the function
takes a parameter named 'scope' and returns the largest docid that has been
used under that scope in this metacat instance (it used to return the most
recently created docid, which is clearly different). For compatibility with...

fixed bug where the whole filename of a data file was not appended to the file input stream so metacat just returned a null document

Fixed problem with metacat handleReadAction where the OutputStream from the
response object was closed and an attempt to reopen a PrintWriter was made
on the same response, which is illegal. Now the OutputStream is converted
to a PrintWriter in order to write the XML error message back to the client....

Added support for multiple user interfaces by enabling style sheet
transformations to be configured from within metacat rather than
from in the database. Now, metacat uses the qformat parameter to determine
a "style set", which is mapped to an xml configuration file that...

Revised build.xml and metacat.properties to make it easier to
install alternative stylesheets for metacat. In the process,
replaced the deprecated copydir and copyfile commands in build.xml
with appropriate "copy" commands.

added support for multiple group membership

Added fix to DocumentImpl that showed problems when the DocumentImpl(conn)
constructor was called. Now there is a new constructor:
DocumentImpl(Connection, String, boolean)
where the boolean value is used to determine if the nodeset should be
read a t the time the cosntructor is called. if false, then...

Completely removed the socket-server feature that used to provide
file upload. It is now replaced by multipart/form-data over http.

Modified Metacat to support large data file uploads. This is accomplished
by supporting a new content type for data sent to metacat:
multipart/form-data
which allows multiple files to be sent in a standard MIME format. The
MetacatServlet.handleGetOrPost() method now checks the incoming content...

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=248
Included utility function about gettig the latest docid for a user:
DBUtil.getLastDocid(username).
Metacat parameters:
action='getlastdocid'
username

fixed error with exception handling in metacat servlet and added new dtds to the sql script

Fixed bug in metacat where return doctypes were not being properly
back traced. Changed DBQuery.findDocuments() so that it no longer
takes a returndoc array, but instead retrieves the returndoc array
fromthe QUERYSpecification. The QuerySpecification was augmented...

Added ability to process multiple "returndoc" elements in
a pathquery document. Now, any query hit will be back traced to an
associated package if that package is listed in one of the
"returndoctype" elements.

Modifications that change the package handling behavior of metacat. Package
membership is now determined by an identifier being used as either the subject
or object in a triple. One can not request arbitrary returndocs -- only
those types that have package information embedded can be "returndoctype"...

fix to view abstract only when abstractpath parameter was specified

Tomcat has got configurated mime type mappings, but some are
missing. Thus added support for them in MetaCatServlet as:
File type > MIME type
------------- ----------------
.xml -> "text/xml"
.xsd -> "text/xml"
.dtd -> "text/plain"
.css -> "text/css"...

- merged "getabstract" and "getdatadoc" actions to "read" action;
- put MIME types everywhere for the returned data;
- zip when more than one doc/files were requested or when specified by qformat="zip" parameter;
- get rid of "relation" parameter, instead use "docid" parameter name only - when more that one docid - zip them;...

Included back getting the list of users and groups stored in auth scheme
through new action="getprincipals". No extra parameters are needed.
Any logged in users are able to get this information

implemented interface for download of DTD or Schema file from Metacat file system
through the params:
action="getdtdschema"
doctype

Included check up for <!DOCTYPE ... PUBLIC/SYSTEM ... >
in order to set the validation parser at runtime
In case of:
- no DOCTYPE declaration
- <!DOCTYPE docname>
validation is turned "off"
In case of:
- <!DOCTYPE ... PUBLIC ...>
- <!DOCTYPE ... SYSTEM ...>...

added new "getaccesscontrol" action for a given docid

included new servlet parameter "public" specifing public read access for the submitted document
the expected values are "yes" or "no"
public parameter is optional and if it is not specified, means "no"

added precise location information (class.method) to each catch statement so that errors are more easily traced.

fixed typo

Added license terms to source code files, and cleaned up some javadoc
documentation in a few places.

closed all preparedStatement variables

fixed bug in data file permission checking. (commited wrong file last time)

fixed minor error

added support for data file upload via a random, authenticated socket.
The action added to metacatServlet is getdataport. A client can send a getdataport request. the server returns a random port number and starts a thread to handle the request on the given random port. The thread will only accept requests from the client that has the session id equal to that of the user that made the getdataport request. the user must be authenticated and logged in to make a getdataport request. Once the port number is received by the client the connection can be made. The first two parameters in the data stream must be the filename, followed by session id. (note that it only wants the session id not the whole cookie and the "JSESSION=" must be stripped from the text.) If the session number is correct, the upload is allowed, the file is written and xml_documents is updated with the new data file information.

fixed url error in data download function

added support to download a data file through metacat using a metacat url or a docid parameter.

cleaned up code

fixed typos around acltext and dtdtext params

fixed typo

DBEntityResolver:
- added new parameter dtd for upload on Metacat file system; optional; Reader
- new routines to upload dtd if provided
- systemID of metadata document is used to exctract the filename of new dtd;
- the new dtd is uploaded on Metacat file system as specified by dtdPath property;...

removed the initial connection pool creation step in init()

comment out line in read action that sends a copy of docid prior to returning doc
in XML format (apparent debug statement left in by mistake)

Modified stylesheets and server code to use a single "read" action instead
of the earlier "getdocument" and "getrelateddocument" actions. In the
process, developed and started to utilize a new suite of URL "protocol
handlers" that are in the package "edu.ucsb.nceas.protocols" and handle...

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.

changed naming scheme

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.

merge AUTH_LDAP to the main branch

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.

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

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....

fix the small bug with output like:
Fatal processing error

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

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.

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.

removed print statments