Metacat

Revised handleUploadRequet.

Add three methods into this class. One is named getServerCode, to given a server name, it return server code in xml_replication table.
One named insertServerIntoReplicationTable, if a server is not in the server list, it will insert it.
One is named WriteReplication, this method will be used in forceReplication. It delete the replication code in it.

Delete the control that when action="insert", rev should be 1

Overload a method debugMessage(String msg, int debugLevel)
User can set a debugLevel for this message. If debugLevel is less than the default a value in build.xml, this message will be printed.
If user set a value less than or equals 0, debugLevel will be set automatically to 1. So we can set default value to 0 in build.xml file and close all debug message.

Add two methods getHomeServer and getServerLocation. Given a docid, getHomeServer can get the information of its home host. Given a docid, getServerLocation can return server code for it.

In handleUpdateRequest method, if a metacat was configured to be hub super, it can provide any documents in its database. If the metacat is notsuper, it only provide the documents list which home host is itself.

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

Add a hashtable - server list as a class variable. So programmer have a control to the server list which will be forced to replicate.

Add a hub control in write and writeData method. If hub==super, metacat can replicate any document in its database to any server in server list. If it is not super, metacat only replicate local documents to any server in server list. If a document' home host is not itself, metacat only force replicate the document to the document's home host.

In update method, adding some code to handle replicate data file. Fixed the bug in deleting documents.

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 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 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.

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.

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.

turned debug off for the release

hopefully fixed the connection closed error.

fixed groups error, I hope.

fixed auth bug

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

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.

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.

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.

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

Please check it.

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

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

fixed error I introduced when I got postgres working

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

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.

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

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.

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

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,...

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

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

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...

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....

fixed to get groupnames for a user using any identifying name

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

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#)