Metacat

as John were testing Metacat on postgres,
he discovered that Connection needs more precise check
whether it is open because of db timing outs.
So used to be:
if ( conn null ) { get new connection from db; }
Now changed to:
if ( conn null || conn.isClosed() ) { get new connection from db; }...

fix to view abstract only when abstractpath parameter was specified

put exception handler messages when acc# is not in the correct format as:
<sitecode>.<uniqueid>.[<revisionid>]

fix - added back generate(docid, action) method called from DataFileServer.java where rev is defaulted to 1

- changes to expect revisionid to come from the client on INSERT/UPDATE/DELETE;
now the client should send accession# as:
sitecode.uniqueid.revisionid
INSERT checks if sitecode.uniqueid part does not exist in xml_documents and xml_revisions and revisionid=1...

Tomcat has got configurated mime type mappings, but some are
missing. Thus added support for them in MetaCatServlet as:
File type > MIME type
------------- ----------------
.xml -> "text/xml"
.xsd -> "text/xml"
.dtd -> "text/plain"
.css -> "text/css"...

- merged "getabstract" and "getdatadoc" actions to "read" action;
- put MIME types everywhere for the returned data;
- zip when more than one doc/files were requested or when specified by qformat="zip" parameter;
- get rid of "relation" parameter, instead use "docid" parameter name only - when more that one docid - zip them;...

Changes related to running LDAP servers referred each other in one tree modeling the KNB tree.
Currently there are running LDAP server on dev that holds the KNB root and the NCEAS' s subtree.
It also refers to a subtree modeling the LTER's tree which is held by another LDAP server runnig on alpha .

fixes on getting information from LDAP services

added check to see if a replication server's IP matched it's DNS entry and the entry in the replication table

fixes around getUsers and getGroups.
"getprincipals" action can now produce output like:

<principals>
<group>
<groupname>Administrators<groupname>
<user>
<username>uid=admin,o=NCEAS, c=US<username>
</user>
</group>...

Included back getting the list of users and groups stored in auth scheme
through new action="getprincipals". No extra parameters are needed.
Any logged in users are able to get this information

included missing implementation of getUsers(), getGroups() interfaces

Modifications to allow printing of SQL with and without INDEX option.

added print info and timing info

print the nested statements sql query

included flag in DBQuery to run pathqueries with or without the index,
but for the command line only.

added timing info to main

implemented interface for download of DTD or Schema file from Metacat file system
through the params:
action="getdtdschema"
doctype

- fixed missing replication of public_access
- new attribute catalog_id added in xml_documents and xml_revisions
as a FK to xml_catalog; catalog_id is replicated also

Included check up for <!DOCTYPE ... PUBLIC/SYSTEM ... >
in order to set the validation parser at runtime
In case of:
- no DOCTYPE declaration
- <!DOCTYPE docname>
validation is turned "off"
In case of:
- <!DOCTYPE ... PUBLIC ...>
- <!DOCTYPE ... SYSTEM ...>...

reject writing DTD file if it already exists

there were more mentions of DOCTITLE attr - cleared them

cleared DOCTITLE attribute in xml_documents and xml_revisions
cleared all mentions of doctitle

added new "getaccesscontrol" action for a given docid

fixed white space problem in toXML that was preventing in line end tags from being popped from the stack.

Solving the problem with relication of access file where access files were rejected from the replication servers.
In AccessControlList check for serverCode is included,
so only on the local server the connected user is checked for having "all" permissions on the resources specified in it...

fixed some problems with database connections getting a time out error. Also updated some catch statements

fixed typo

included new servlet parameter "public" specifing public read access for the submitted document
the expected values are "yes" or "no"
public parameter is optional and if it is not specified, means "no"

fixed bug that was accidentally introduced when the change from metacatURL to URL was done.

added location info to catch statements

added precise location information (class.method) to each catch statement so that errors are more easily traced.

removed print statements

fixed typo

included implementation for public "read" access as specified from the access file

fixed introduced problem with preparedStatements

Added license terms to source code files, and cleaned up some javadoc
documentation in a few places.

Added License terms to source files, added more documentation to protocol
handler classes.

closed all preparedStatement variables

implementation for multiple <resourceIndentifier> tags under <resource>

removed dependence on MetacatURL for URL handling. Added more flexible support for identifiers in the subject and object fields. They can now be just a docid, an http url or a metacat url.

fixed bug in data file permission checking. (commited wrong file last time)

- turned on the validation in order only valid xml docs comformed to the specified dtd (if any) to be submitted in metacat
- with validation "on" white spaces are reported from ignorableWhitespace() callback, not from characters() (as with validation "off")...

added more documentation

changed getCookie to static

added support for the new abstract class) to handle data file uploading through metnewninterface (actuall

newninterface (actually an abstract class) to handle data file uploading through met

fixed error in logic. sending the filesize as an int terminated by a zero failed when the file size was greater than 256. The filesize is now sent as a string followed by a zero.

added support for the server to return the docid of the newly added data file. Also, now the data stream must be prefixed with the following information: filename <0> sessionid <0> filesize <0>. where the <0> symbol is a byte containing zero. The filesize is sent as an int and the filename and sessionid are sent as strings (in byte form).

unified getting "docid" value from metacat URLs specified in <resourceIdentifier> tags
by using MetaCatUtil.parseQuery() method in the same way as in MetaCatServlet.

fixed error handling and time out issues. Also fixed thread syncronization problem

multiple files with the same names no longer overwrite each other.

fixed minor error

added support for data file upload via a random, authenticated socket.
The action added to metacatServlet is getdataport. A client can send a getdataport request. the server returns a random port number and starts a thread to handle the request on the given random port. The thread will only accept requests from the client that has the session id equal to that of the user that made the getdataport request. the user must be authenticated and logged in to make a getdataport request. Once the port number is received by the client the connection can be made. The first two parameters in the data stream must be the filename, followed by session id. (note that it only wants the session id not the whole cookie and the "JSESSION=" must be stripped from the text.) If the session number is correct, the upload is allowed, the file is written and xml_documents is updated with the new data file information.

added support for data file upload via a random, authenticated socket.

- appling acl through access files only
- clearing around update/delete of access files - to delete the related records from both xml_access and xml_relation tables
- included check for user permissions for setting acl on the resources in the access file
- moved RelationHandler.deleteRelations(docid) down in RelationHandler obj just before the write of the new relations

fixed url error in data download function

Use the new property "accessdoctype" to check if this is access file.
If it is, run AccessControlList for wirting into xml_access and xml_relation tables.
This is the thread that writes XML Index but afterwards.

included support for submition of access files
+ storing the acl info in xml_access table and relationship records in xml_relation table like
<aclfile, "isaclfilefor", recourceIdentifier> for every resource included in the access file

added support to download a data file through metacat using a metacat url or a docid parameter.

updating a package file now updates the relations that are created from it. Also, if you delete a package file, it will delete the relations associated with it.

changed replication interface to make it easier to see the servers.

added support for one way replication

added revision support to the delete function

fixed sql error

cleaned up code

removed package doctype filtering from the resultset.

added comments to top of class

changed accession number schema to <sitecode>.<serialnumber>.<revisionnumber>. DocumentIdentifier.java parses docids into parts for easy manipulation. You can now specifiy a specific revision by asking for document <sitecode>.<serialnumber>.<revisionnumber> or you can get the newest revision by asking for <sitecode>.<serialnumber> or by asking for <sitecode>.<serialnumber>.newest.

fixed typos around acltext and dtdtext params

changed acc# generation to use db sequence instead of timestamp

fixed typo

fixed typo

fixed typo

fixed typo

commented out print statement

fixed typo

problems with passing the connection between objects

problems with passing the connection between objects

overwrite Jivka's overwrite

problem with passing the connection between objects

problem with passing the connection between objects

removed print statement

fixed bug where some relations were not returned because the sql did not take into account an sql that had a directory structure in it.

changed connection handling in the constructor

one more write() method was needed

constructor DBEntityResolver(Connection conn) is needed; cleared by mistake

DBEntityResolver:
- added new parameter dtd for upload on Metacat file system; optional; Reader
- new routines to upload dtd if provided
- systemID of metadata document is used to exctract the filename of new dtd;
- the new dtd is uploaded on Metacat file system as specified by dtdPath property;...

added additional actions to facilitate a web based interface to the replication servlet.

removed the initial connection pool creation step in init()

comment out line in read action that sends a copy of docid prior to returning doc
in XML format (apparent debug statement left in by mistake)

added replication for the xml_catalog table. Right now it is only replicated when the deltaT handler is called. I will add more replication times later.

parser for the xml encoding of the xml_catalog tableing (fi

added a logging system for replication. The log file location is set in metacat.properties

cleaned up code, added more complete documentation of replication algorithms and datastructures.

made replication on insert or update us. Also made a method in AccessionNumber public so that you can tell if an accession number has already been used.e place be

An asynchronous replication handler. This class creates a new thread to handle replication so that the user does not have to wait for replication to take place before he/she sees the result of an insert or update.

updated file locking mechanisms to use revisions instead of dates.

fixed typo, removed extra print statements