Metacat

fixed my tagging error

some small changes I had to make to get the QAENGINE demo to work right. this should be committing in a branch

We decided that the permission for a user to an access documents is as same as to the data set document(which contains the access document). In order to do this, we need to look-up xml-relation table. If we could find the data set document id, just check the id. If we couldn't find one, we need check if the user is owner. If it is, has permission. Otherwise, doesn't have.

Add a new method getDataSetId to the class. The permission policy for access documents is: the user will have the same permission as data set file. (There is no entry in xml_access table for access document.

Add a throwing exception in hasPermission and hasReadPermission methods.

Add a throwing exception in haspermission method.

A constructor for this class was added. In the new constructor, user can specify the revision number he want to update. In method writeDocumentToDB, when a update action happend, the rev number would not automatictlly to add one, but it can go to specified number. This is for bug 417.

A constructor was added to this class. In this constructor, user can specify the revision number he want to update. And the number can be passed into a DocumentImpl object constructor in startElement method. But the number should be greater than current number in database.

A method named getLastRevisionNumber was added. And condition for checking accession number was revised too. Now metacat wouldn't refuse a revsion number which is 2 or more greater than current revision number in the database. This is for bug 417.

Access document was added to exported data package too.

The method - hasAllowRule was revised. If a action -read or update was approved, all ticket count of allow rule entries for this action will minus one if the entries have ticket count number (not null).

The two hasPermission methods were rewritten. Some logic bugs were fixed. Now user, public and group will not be checked speratedly, but they will be check together as string array. In order to do this, private methods isAccessDocument, containDocumentOwner, isAllowFirst, hasAllowRule, hasExplicitDenyRule, hasImplicitDenyRule, and createUsersPackage were added.

In method transformXMLDocument, if no style sheet registered was found for the input document, the document will be send back, rather than use util.DebugMessge to print.

Only delete some incorrect comment.

When user request a data package, the old version documents would be exported. Only export the request one.

During the export function. Every document will be check if the user has the permission to read or not.

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 method named hasReadPermission was added. The method will check if a user has permission toread a xml document.

A new method named hasPermissionToExportPackage was added. So when MetaCat handle export action, it will check if user has permission to read the data package. If it has, MetaCat will export a zip output stream to it. Otherwise, MetaCat will be through a exception.

Code to handle "read" permission was changed in hasPermission method. The old code used old way to look up the public_access field in xml_documents table.

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...

Two metacat util methods were add. One is getDocIdFromString and the other is getVersionFromString. They output a docid and revision if a string like str1.str2.str3. were passed to them.

A method named transformXmlDocument were overload. It transform an XML document to StringWriter using the stylesheet reference from the db.

A public method named getZippedPackage() and other relative private methods were add to this class. The public method can give a zip output stream if a docid and other parameters were passed to it.

A property named "morpho" was added. It is the path for morpho.jar. (Now, in DBQuery class some morpho package class are used). Morpho was added to cpath too. During the "install", morpho willbe copy to the target too.

In QBQuery class some classes - Triple and TripleCollection, which come from morpho package wereused. So morpho.jar was added to metacat libray. The reseaon to use these class is xml document need to be parsed and get docids' relationship.

Adding the style sheet of html file in zip data package for morpho to metacat.
So the html summary file can have the same style in morpho and metacat zip package.

Adding a new doctype and its publicid="-//NCEAS//eml-generic//EN".
It connects http://server@style-path@/generic-morpho.xsl.
So the html files in zip data package have the same style sheet for both morpho and metacat.

Some code format problem was fixed.

The bug was fixed.
After a referral exception happend, we should set enviroment properties again before creating a contex. These environment properties include PROVIDER_URL, SECURITY_PRINCIPLE, SECURITY_CREDENTIALS, REFERRAL, and INITIAL_CONTEXT_FACOTRY. Otherwise, you couldn't get a naming exception.

Removed an obsolete filter fromthe build.xml file.

Updated installation instructions to reflect the new procedures involved
with the changes to build.xml.

Modified the build.xml file to make it easier to set up the configuration.
There is now a "config" target in which all of the properties that are usually
modified are located. Also, now one sets the location of tomcat and the
webapps dir, and chooses a name for the tomcat context, and everything else...

Authentication bug was fixed (bug 408).
However, it needs to test if referral cotaining a referral.

xerces.jar was update to 1.4.4

Please check it.

In order to fix bug 408 (authentication), some important variables' values
were followed.

took my password out of the build file

integrated the postgres and oracle properties into one build file. now, if you want to switch between oracle and postgres, you just change the 'depends' attribute in the 'init' target. also, I fixed the path to the servlet.jar file to match up with where tomcat now stores it (lib/common/servlet.jar instead of lib/servlet.jar).

Modified the build file to point at the proper eml directory so that the
"getdtd" target can find the right files to be checked out.

Committed changes to the build file so that it properly copies the Xalan
jar files instead of the oracle xml parser which has been eliminated.

Added qformat parameter for switching css stylesheets.

Fixed bug in login.xsl that was preventing a successful xslt transform. Now
successful logins redirect correctly, unsuccessful ones redirect to the
login page again.

Set the qformat parameter so the stylesheets can use it for conditional
processing.

Added new stylesheets for displaying the eml-attribute and eml-entity modules.

Changed the link urls in the eml-dataset display stylesheet to use the
default style-set as set in the build file rather than hard-coding the
value 'html'. This allows more flexibility in switching styles, for example
when setting up the marine, nrs, and obfs sites.

fixed error with dist target so that it now copies the source correctly

updated all of the returndoctypes so that emlbeta4 and emlbeta6 will show up in the resultset.

fixed error I introduced when I got postgres working

changed dtd dir

changed the datadir again

changed datadir variable from install-dir to installdir

removed old properties

fixed minor error

made postgres db name independent from my name

we no longer need this jar file. all of its functionality was replaced by xalan.

jar files for xalan

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

fixed typo in web.xml file

updated the web.xml file. took out download servlet and marineservlet.

jar files needed for metacat.

• empty log message ***

created dummy versions of the oracle and postgres build files

readded the oracle stuff to te build file

made a ton of changes related to keeping oracle SQL code out of the main classes. fixed a bug where the timing of the index thread was off so when it went to index a document, the document was not already in xml_documents thus breaking the FK relation between xml_documents and xml_index. I think that bug might be the reason for the blank resultset screens in morpho. made the postgres implementation much more robust.

updated postgres sql script so that it creates the same table structure as the oracle script. removed a bunch of \t tabs that were messing things up

removed because this is no longer used. it was causing a compile error when using postgres because it directly imports the oracle driver.

updated for new release

fixed bug with ampersands in the returned relations in the resultset.

added a manual timeout to counteract the hideously long ldap time out that is encountered when a referred ldap server is down.

fixed a couple bugs with doctypes that I found while setting up a demo

new README for 1.0.2

new build file with updated release number

updated the referral mechanism so that metacat doesn't crash when a referral server is not available

made it so we can now use multiple accessfilestypes and packagdfiletypes in the metacat.properties file. Also fixed a bug introduced when the 'http://' was removed from behind the server name in the loaddtd.sql script and the knb.xml file

Updated properties to reflect the new EML version.

Added new dtd to style-set config file.

More changes to build process. No longer need the instdtd target
because it is handled by the install target. Updated installation
instructions accordingly.

Updated documentation to reflect new installprocess.

Modified build.xml to properly copy the docs into the distribution, which
required some changes in the ant token filtering scheme.

updated documentation. removed a lot of typos and updated all of the new stuff for the new release

Updated the installation doc to reflect the new install procedure.

Updated build.xml to improve dtd handling so that DTDs can be included in
the distribution.

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