Metacat

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...

Fixed typo in create table syntax (added missing comma) for xml_access table.

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)

CREATE TABLE xml_access (
docid VARCHAR2, -- the document id #
principal_name VARCHAR2, -- name of user, group, etc.
permission NUMBER, -- "read", "write", "all"
perm_type VARCHAR2, -- "allowed" or "denied"
perm_order VARCHAR2 -- "allow first" or "deny first"...

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.

added ticket_counter and deny attributes to xml_access table

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

added needed table fields for storing document location in xml_documents

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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added new server_location field to xml_documents with a foreign key to xml_replication.serverid

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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Changed utility query to include the user_owner field rather than the
title field, which is now obsolete.

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 xml_relation table

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

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.

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"

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....

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 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 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 resource.xsl to the catalog

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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()

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

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