Metacat

moving metacat docs to xmltodb

Improvements to the build process that make it easier to install the DTDs
form EML. There are now three new targets in the build.xml file:

getdtd: uses cvs to get a working copy of a tagged release of eml
  instdtd: copies the DTDs from the build directory to the install directory...

Removed all of the redundant/obsolete copies of eml dtds from the
metacat module. Now one must get the dtds from the mdstandards/eml
module instead. This is doen to ensure that the DTDs installed are up to
date.

Note that I am adding build support into the build.xml file for automatically...

Updated the SQL for loading DTD references to use the correct file
names and paths and identifiers.

updated for new eml release

Fixed the getUsers() and getPrincipals() methods so that they no longer
fail when large result sets are requested. The problem was that the
LDAP server was returning a "size limit exceeded" message when the resultset
from the query exceeded the default limit of 500 entries. Now we...

Re-enabled referrals which I had turned off for debugging purposes.

Modified AuthLdap to fix the may problems associated with group and user
queries. Now the getGroups() and getUsers() methods work as advertised,
and there is a test of each of the methods in "main" for testing purposes.
Simplified the class substantially. Fixed the getAttributes method as...

fixed error where person with 'all' permission could not update the access file.

fixed error where person with 'all' permission could not update the access file.

fixed referral catching mechanism in authLdap.ldapAuthenticate() so that it will refer through a bunch of linked servers instead of just one....I still haven't figured out why the getGroups method wont work.

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

I think i have fixed the ldap referral bug. the test lter account that david made for me works, however I would like matt or someone more knowedgeable with ldap to please check my code. the changes I made are around line 200 of AuthLdap. I put a comment in the source where the code needs to be checked.

Fix for bug #309 so that Metacat will now follow LDAP referrals. Previously
the default was to ignore referrals. Now we explictly set the JNDI
Context.REFERRAL value to the value in the metacat.propert "referral".
The metacat.properties file has been modified to add the "referral" property,...

updated web.xml file for the download servlet

added new permission 'changepermission' and made 'all' inclusive for all permissions

README and build changes in preparation for the 1.0.0 release of Metacat.
The files contributing to this release are being tagged in CVS as
"METACAT_1_0_0".

Updated the knb.xml configuration to use the new public IDs associated with
eml beta 4.

fixed access control bug. the character data in the sax parser was not getting trimmed and causing problems. also fixed hard coded eml-dataset public id in the web index file

Added new beta5 version of eml-software dtd, and added to catalog.

added new docid to returndoc for web form

changed package and access file doctype

took out hard coded paths for style dirs

removed the stylesheet sql script since we don't need it anymore

Added new DTD files for the new release of EML. Changed the naming
convention for all new DTDs, so the public IDs are now consistently
versioned.

Updated metacat login semantics. Now, metacat assumes the username passed
in is the 'full' distinguished name of the user. If that fails, then
instead it tries looking up the string and seeing if it can determine
what the DN is, then uses it. The preferred method of logging in via...

New version of the IE5 stylesheet that is XSLT 1.0 compliant.

CHanged style-set handling for case when a stylesheet for a specific
doctype has not been registered. Now we are using a simple "ascii tree"
view of the XML document. I'm hoping we can get a nicer generic display
set up over the long run, but for now this handles the basics.

Removed all DTDs from the metacat module in anticipation of getting
them from the standard "mdstandards/eml" module. This will mean
that an update to the build script is necessary in order to copy and rename
the dtds from the eml module.

Updated build.xml and README for a Beta 3 release. This is a temporary
release until the full Release 1.0 is produced next week.

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....

default css stylesheet so that metacat will look right

removed errant comment that was causing an error in the xml_documents table

fixed to get groupnames for a user using any identifying name

added insert statement for eml-attribute-2.0.dtd entry in xml_catalog

for action=servercontrol&subaction=add
added function for downloading of the certificate file
from the specified URL of the source server
and uploading it onto this server

added input box in replMain web page for downloading of the certificate file
from the specified URL of the source server
added new metacat property "certPath" for uploading the certificate file onto destination server

server property is used in replication thus
it should include the SSL port number

changes in replication to use https

fix around one way replication:
when server A sends document to the servers in its list of replication servers with replicate=1 in xml_replication table,
the server B received the document does NOT need the opposite check on its end.

fixed error:
writing on the replication server required the whole acc# (including the rev#)

Fixed bug in metacat where an Exception was thrown when a search returned
an empty resultset. Now we avoid the function call that threw the exeption.

Minor bug fixes following change in style handling. Fixed image locations,
cleaned up main resultset stylesheet.

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...

small fix to enable resolving external entities included in the DTD;
external entities are now resolved successfully by DBEntityResolver using the specified system ids
and thus there no need of registering the relative system ids,
This is because EntityResolver uses its internal implementation to map the relative system ids to the...

Removed the requirement that the relationship for ACL associations be
"isRelatedTo". Now the relationship in the triple can be anything, like
"describes access control rules for". This doesn't affect the ACL
processing because it is based on the ACL document type, not the...

More fully completed the eml-dataset XSLT stylesheet for translating
into HTML format. Now more of the relevant fields are completed, and
the coverages are shown. Still need to systematically address every
field that could be present, but I hit the major ones.

Added new filter for style-path

Modified metacat stylesheets to now use a "style-path" filter for setting
the path to XSL and CSS style sheets. this allows the style
location to be configured independently of the main web url for metacat
links.

changes to store namespace prefixes separately from the local names of nodes (elements and attributes)
in xml_nodes.nodeprefix column

added nodeprefix column to xml_nodes table for storing of namespace prefixes per nodes

Updated index page to launch proper initial query.

Updated stylesheet to reflect the new eml2 schema.

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 Namespaces.
Metacat now can store and retrieve XML documents with Namespaces.
Namespace is stored as separate record in xml_nodes table with type "NAMESPACE"
where nodename is the prefix and nodedata is the uri of the namespace.

fixed an error of NullPointerException

- when the Access file goes first before the Package file (eml-dataset-2.0)
relations are not available in xml_relation, thus updated the code
to check and run ACL also after the Package file is saved.
- cut out the rev# from subject and object in xml_relation as needed by ACL...

fixed error with out of cursors error because pstmts were not getting closed in DBQuery

Updated build file to resotre changes that were lost when version
1.54 was committed.

look for relationship "isRelatedTo" b' that is the word that is used in the triples

Fixed returndoctype param.

Updated stylesheet to use new package returndoc type for searches
(eml-dataset-2.0).

updated with the new eml modules

changed web-base-url to http://knb.ecoinformatics.org

made ant copy the dtds

added new dtds

dtds that have entities removed for morpho/metacat compatibility

Clean up after building distribution.

Updated build.xml with new targets to create metacat distributions.
Run "ant dist" to create a non-source distribution and "ant distsrc"
to create a source distribution. Best if this is run on a clean
checkout to be sure not to include extraneous files that are not in CVS.

Updated README file for the beta2 release. Added list of known issues,
which will need to be edited for the final release.

fixed the compilation bug about the change of group parameter in DocumentImpl.write()

changed accessdoctype=-//NCEAS//eml-access-2.0//EN
b' AccessControlList is changed to use eml-access-2.0.dtd already

added support for multiple group membership

Changed the constructors so that the nodeRecordList is automatically
retrieved by the DocumentImpl(Connection,String) constructor. this
restores its earlier behavior, but the implementation is totally
done by DocumentImpl(Connection,String,boolean).

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...

Simplified ReplicationHandler:
It is run now in the same thread started from DBSAXHandler;
thus the same connection opened in that thread is used,
i.e. no need for new connection and no complains as "Connection is closed" in ReplicationHandler;
"Connection is closed" error happens when in the current thread there are try to use connection opened in another thread,...

tests made on Oracle and SQL Server.

support for the new terms included in pathquery.dtd

included new terms for searchmode:
equals (former matches-exactly)
isnot-equal
less-than
greater-than
less-than-equals
greater-than-equals

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

don't need to override the old meta_file_id tags with docid without rev
since Morpho inserts docids before sending the docs to Metacat

added the new software module

added constructor in DocumentImpl for use in DBQuery.findDocuments();
this new constructor is used with getDocumentInfo() to get the doc info only;
because the other constructor builds the whole xml doc which is not needed here and time consuming;
this happens on backtracking only.

updated script with new eml20 dtds

fixed bug - hardcoded LDAP URL

made use of the new property for ldaps url;
it is used for secure connection to LDAP server listening on second port 636 by default with SSL sockets;
it is used from Metacat for the authetication process only;
all the rest communications with LDAP server are made on the default port 389 with plain sockets

new property for ldaps:// url for LDAP connection over SSL;
it is set on second port - by default 636;
for plain LDAP communications the default port 389 is used.

moved delete from xml_relation before delete from xml_documents
because of the parent-child relation b/w these 2 tables

cleared the text under the figure; should go in the Word text

EPS files saved as AdobeIllustrator v7.0

EPS file for the IC paper

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

changes according to bug# 234 - metacat accession # handling, done

changed all mentions of DBAdapter to the new name AbstractDatabase

changed all mentions of DBAdapter to the new name AbstractDatabase

changed dbAdapter property to edu...OracleAdapter