Metacat

Making parser to handle datafile attribute in parsing updated doclist.

Add a new attribute in updated doc list: data file. So from this attribute, we can tell which document is a data file.

In writeDataFile method, using getDataFileLockGrant(docid) replace getDataFileLockGrant(docid, serverCode). The latter will cause a problem

Add a new variable datafileflag. This variable will indicate if a document is a data file in updated documents list in replication.

Add two controls for handle replication server list is empty and updated document list is empty

Using DocumentImpl.writeDataFile method in handleReplicateDataFileRequest. Make code simple.

Add a control to handle if the server list is empty.

Add a method named writeDataFile. This method will register data file into xml_documents table and save a input stream to a file.

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

Adding a control which can turn on or off replcation data file.

Add method getDataFileLockGrant(). This method will check if xml-document of data file can be store into database.

Add some new format.

changed .highlight style so font-size attribute is 1em instead of -1. Original -1 setting was not NN4 compatible

Add two method: handleGetDataFileRequest and handleForceReplicateDataFile. The two methods will handle data file replication.

Adding handle force replication data file part.

Add a new method named unRegisterDocument. This method will delete the record in xml_document table which is for a data file

Figure out the configuration issue about replication. If metacat was configured to set replication off in build.xml, it will reject replication.

Adding a method named handleGetDataFileRequest. User can download data file from replcication now.

Change replication and replicationdata to be tokens

Adding two properties: replication and replicationdata. Administor can config build.xml instead of metacat.properties file.

Add two variable: replication and replicationdata.
If administrator set replication on, replication will work. Set it off, it stop.
If administrator set both replication and replicationdata on, metacat will replicate both meta data and data. If replication is set on and replciationdata set off, metacat only replicate meta data.

Currently, some document in xml_document table doesn't have entries in
xml_access table. This is okay during the old access policy.
But we changed the access policy( see bug 437 ) and if there is no entry in
xml_access table, except owner, other person can not access it....

Fixed the bug that handle force replication

Fixed the bug that to handle forceReplication action

Add a method named getLocalReplicationServerName

Fixed the bug metacat will set server location to 1, no matter it is.

Fixed the getall didn't work. Now local host can insert or update documents from remote host.
But still there some problem on force replcation.

Adding a variable "context " here.

Adding a new token "context" in it.

Token for the server is changed to correct one.

Fixed getGroup method return a exception and cause authenticate failed.

Fixed the getIdentifyingName() sub so that it properly looks up someones
DN if passed in a DN that is an alias. This is mainly important for
sites like PISCO that use a different root to their tree than the
ecoinformatics.org tree. Now we can successfully authenticate againast...

Some changes for pisco.

updated some spelling and grammar errors

turned debug off for the release

hopefully fixed the connection closed error.

fixed groups error, I hope.

Removed obsoleted marine files. See the new "marine" module for
relevant copies of these files.

New stylesheet that is specific to the KNB website.

replaced dev.nceas.ucsb.edu with server in the marine index file

changed some values for the release

changed some values for the release

updated data directory note

When Metacat installed, it can automatically create data directory for data file.

updated build file. fixed the dist target so it doesn't copy the build directory into the distro.

fixed auth bug

Adding a note for user. The user should make a directory under 'webapps/context/'.
The user should have write permission for this directory.

updated for 1.1.0

Update the install instruction.

changed version number from 1.1 to 1.1.0

changed version number from 1.1 to 1.1.0

fixed some things for release 1.1

fixed some things for release 1.1

Change description for access control in readme file from "aplly" to "not aplly".

changed some minor points in the readme.

Update README for 1.1 release.

updated authldap to get the groups to work (king of)

Change every "http://server to "systemidserver". It will look like:
INSERT INTO xml_catalog (entry_type, public_id, system_id)
VALUES ('DTD', '-//ecoinformatics.org//eml-software-eml-version//EN',
'systemidserver@html-path@/dtd/eml-software-eml-version.dtd')

Change every "http://server" in target to "systemidserver". It will look
like that:
<target
publicid="-//W3C//HTML//EN">systemidserver@style-path@/resultset.xsl</target>

Add a property named systemidserver, its value="http://host.domainname:8080"
Add a token named systemidserver too.

Method getGourps was revised. Attributes variables were set there. Other wise, when it caught a referral exception and started a thread, this will caused a exception problem. When string array groups were returned by method getGroups in getPrincipals method, we should check if the groups is null or not. Otherwise it will cause a exception problem. This revise is for bug 445.

In hasPermission method, a situation was considered: if no user and group, the permssion will be true. This is for the command line invocation.

This is sample JUnit test file for MetacatURL class. In this file, getProtocol, toString and getParam methods are tested.

This script file can run serials queries and print out the running time.

In order to test query performance. We need add lots of documents to database. This script file can add couple documents to database by for loop.

Add a target - test in the file. Now user can type "ant test" to run the test class extends from JUnit.

Method endElement in AccessControList was revised. A feature that put access document itset into xml_access was added.

In hasPermission method, a rule for access document is implements. If user want to write a access document, it should hhave "all" permission.
The permission for access document now is looking up in xml_access table directly, rather get same permission to data set document.

In order to increase data file docid, method registerDocument was revised. Now it not only insert a new data file record to xml_documents table, but also can update the data file documents. Moreover, it can archieve the old version to xml_revisions table. Two other private methods were added to handl these futures: deleteXMLDocuments and getLatestRevisionNumber.

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...