--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@credentials/credentials.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,183 @@
+classdef credentials
+
+  properties
+
+    hostname = [];
+    database = [];
+    username = [];
+    password = [];
+    expiry = 0;
+
+  end % properties
+
+  methods
+
+    function obj = credentials(hostname, database, username, password)
+    % CREDENTIALS Constructor for credentials objects.
+    %
+    % Those are simple container objects to hold credentials required for
+    % establishing a connection to a database server, in addition to an
+    % expiry time.
+    %
+    % CREDENTIALS(hostname, database, username, password) The constructor can
+    % be called with any number of arguments. The default value for the object
+    % properties is the empty vector.
+
+      switch nargin
+        case 1
+          obj.hostname = hostname;
+        case 2
+          obj.hostname = hostname;
+          obj.database = database;
+        case 3
+          obj.hostname = hostname;
+          obj.database = database;
+          obj.username = username;
+        case 4
+          obj.hostname = hostname;
+          obj.database = database;
+          obj.username = username;
+          obj.password = password;
+      end
+    end
+
+    function str = char(obj, mode)
+    % CHAR Convert a credentials object to string representation.
+    %
+    % It takes an optional second argument that defines the representation to
+    % use. The default is to replace the password, if present, with the YES
+    % string, other possible modes are SHORT where password is omitted, or FULL
+    % where the password is shown at it is.
+
+      if nargin < 2
+        mode = '';
+      end
+      switch mode
+        case 'short'
+          % do not show password
+          frm = 'mysql://%s/%s username=%s';
+          str = sprintf(frm, obj.hostname, obj.database, obj.username);
+        case 'full'
+          % show password
+          frm = 'mysql://%s/%s username=%s password=%s';
+          str = sprintf(frm, obj.hostname, obj.database, obj.username, obj.password);
+        otherwise
+          % by default only show if a password is known
+          passwd = [];
+          if ischar(obj.password)
+            passwd = 'YES';
+          end
+          frm = 'mysql://%s/%s username=%s password=%s';
+          str = sprintf(frm, obj.hostname, obj.database, obj.username, passwd);
+      end
+    end
+
+    function disp(objs)
+    % DISP Overloaded display method for credentials objects.
+    %
+    % Uses the default string representation of the char() method where the
+    % password, if present, is replaced with the string YES.
+
+      for obj = objs
+        disp(['    ' char(obj) char(10)]);
+      end
+    end
+
+    function len = length(obj)
+    % LENGTH Returns the number of not null fields in the object.
+
+      len = 0;
+      if ~isempty(obj.hostname)
+        len = len + 1;
+      end
+      if ~isempty(obj.database)
+        len = len + 1;
+      end
+      if ~isempty(obj.username)
+        len = len + 1;
+      end
+      if ~isempty(obj.password)
+        len = len + 1;
+      end
+    end
+
+    function rv = complete(obj)
+    % COMPLETE Checks if the credentials are complete.
+    %
+    % Credentials object are complete when they contains all the required
+    % information to connect to a database. Namely the HOSTNAME, DATABASE
+    % and USERNAME properties should not be empty, the PASSWORD property is
+    % allowed to be an empty string '' but not [].
+
+      info = {'hostname', 'database', 'username'};
+      for kk = 1:numel(info)
+        if isempty(obj.(info{kk}))
+          rv = false;
+          return;
+        end
+      end
+      if ~ischar(obj.password)
+        rv = false;
+        return;
+      end
+      rv = true;
+    end
+
+    function rv = expired(obj)
+    % EXPIRED Checks if the credentials are expired.
+    %
+    % Credential objects expire when their expiry time is smaller than the
+    % current time in seconds since the epoch, as obtained by the time()
+    % function. Credentials with zero or negative expiry time never expire.
+
+      rv = false;
+      if obj.expiry > 0 && double(time()) > obj.expiry
+        rv = true;
+      end
+    end
+
+    function rv = match(obj, hostname, database, username)
+    % MATCH Check if the credentials object matches the given information.
+    %
+    % MATCH(obj, hostname) Returns true when HOSTANAME parameter match
+    % the object properties.
+    %
+    % MATCH(obj, hostname, database) Returns true when HOSTANAME and
+    % DATABASE parameters match the object properties.
+    %
+    % MATCH(obj, hostname, database, username) Returns true when
+    % HOSTANAME, DATABASE, and USERNAME parameters match the object
+    % properties.
+
+      % default arguments
+      switch nargin
+        case 4
+        case 3
+          username = [];
+        case 2
+          username = [];
+          database = [];
+        otherwise
+          error('### wrong number of parameters');
+      end
+
+      % default return value
+      rv = true;
+
+      if ~strcmp(obj.hostname, hostname)
+        rv = false;
+        return;
+      end
+      if ischar(database) && ~strcmp(obj.database, database)
+        rv = false;
+        return;
+      end
+      if ischar(username) && ~strcmp(obj.username, username)
+        rv = false;
+        return;
+      end
+    end
+
+  end % methods
+
+end
\ No newline at end of file

--- a/m-toolbox/classes/+utils/@jmysql/connect.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/connect.m	Tue Dec 06 19:07:22 2011 +0100
@@ -11,55 +11,15 @@
 % in the LTPDA user preferences.
 %
 % CALL:        conn = connect(hostname)
-%              conn = connect(hostname, dbname)
-%              conn = connect(hostname, dbname, dbuser, dbpass)
+%              conn = connect(hostname, database)
+%              conn = connect(hostname, database, username, password)
 %
 % VERSION:     $Id: connect.m,v 1.13 2011/04/01 08:36:49 hewitson Exp $
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function varargout = connect(varargin)
-  
-  dbuser = '';
-  dbpass = '';
-  dbhost = '';
-  dbname = '';
+function conn = connect(varargin)
+
+  conn = LTPDADatabaseConnectionManager().connect(varargin{:});
   
-  if nargin == 1
-    dbhost = varargin{1};
-  elseif nargin == 2
-    dbhost = varargin{1};
-    dbname = varargin{2};
-  elseif nargin == 3
-    dbhost = varargin{1};
-    dbname = varargin{2};
-  elseif nargin == 4
-    dbhost = varargin{1};
-    dbname = varargin{2};
-    dbuser = varargin{3};
-    dbpass = varargin{4};
-  elseif nargin == 5
-    dbhost = varargin{1};
-    dbname = varargin{2};
-    dbuser = varargin{3};
-    dbpass = varargin{4};
-  end
-  
-  rm = LTPDARepositoryManager();
-  conn = rm.findConnections(dbhost, dbname, dbuser, dbpass);
-  
-  if isempty(conn)
-    conn = rm.newConnection(dbhost, dbname, dbuser, dbpass);
-  end
-  
-  if ~isempty(dbpass) && isempty(char(conn.getPassword))
-    conn.setPassword(dbpass)
-  end
-  
-  % If we have more than one matching connection, let the user choose.
-  if numel(conn) > 1
-    conn = rm.manager.selectConnection([]);
-  end
-  
-  varargout{1} = conn(1);
 end

--- a/m-toolbox/classes/+utils/@jmysql/dbconnTojconn.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-% DBCONNTOJCONN convert a MATLAB database connection to a java db connection.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: DBCONNTOJCONN convert a MATLAB database toolbox connection
-%              to a java db connection.
-%
-% CALL:        jconn = utils.jmysql.dbconnTojconn(dbconn);
-%
-% INPUTS:
-%              dbconn - a database toolbox connecton
-% 
-% OUTPUTS:     
-%              jconn - a connection object like that returned from
-%                     utils.jmysql.connect.
-%
-%
-% VERSION:     $Id: dbconnTojconn.m,v 1.1 2009/07/28 06:46:09 hewitson Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-function jconn = dbconnTojconn(conn)
-  
-  if nargin ~= 1 || ~isa(conn, 'database')
-    error('### The first argument should be a database connection');
-  end
-
-  r = regexp(conn.URL, '//(.+)/', 'tokens');
-  host = r{1};
-  
-  db   = conn.Instance;
-  user = conn.UserName;
-  
-  jconn = utils.jmysql.connect(host, db, user, '');
-  
-  
-  
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/dbquery.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/dbquery.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,27 +1,25 @@
-% DBQUERY query an AO repository database.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: DBQUERY query an AO repository database.
+function varargout = dbquery(conn, varargin)
+% DBQUERY  Query an AO repository database
 %
 % CALL:        info = dbquery(conn);
 %              info = dbquery(conn, query);
 %              info = dbquery(conn, table, query);
 %
 % INPUTS:
-%           conn   - a database connection object such as that returned by
-%                    utils.jmysql.connect().
-%           query  - a valid MySQL query string
-%           table  - a table name
+%
+%    conn  - a database connection object implementing java.sql.Connection
+%   query  - a valid MySQL query string
+%   table  - a table name
 %
 % OUTPUTS:
-%           info - the returned 'info' structure contains the fields from
-%                  each matching record.
+%
+%     info - structure containing fields from each matching record
 %
 % EXAMPLES:
 %
-%   >> info  = utils.jmysql.dbquery(conn, 'select * from objmeta where id>1000 and id<2000');
-%   >> info  = utils.jmysql.dbquery(conn, 'ao',           'id>1000 and id<2000');
-%   >> info  = utils.jmysql.dbquery(conn, 'objmeta',      'name like "x12"');
+%   >> info  = utils.jmysql.dbquery(conn, 'SELECT * FROM objmeta WHERE id>1000 AND id<2000');
+%   >> info  = utils.jmysql.dbquery(conn, 'ao',           'id>1000 AND id<2000');
+%   >> info  = utils.jmysql.dbquery(conn, 'objmeta',      'name LIKE "x12"');
 %   >> info  = utils.jmysql.dbquery(conn, 'users',        'username="aouser"');
 %   >> info  = utils.jmysql.dbquery(conn, 'collections',  'id=3');
 %   >> info  = utils.jmysql.dbquery(conn, 'collections',  'obj_ids="1,2"');
@@ -30,111 +28,65 @@
 %
 %   >> tables  = utils.jmysql.dbquery(conn)
 %
-%   The 'tables' cell-array will contain a list of the tables in the database.
+%   The 'tables' cell-array will contain a list of the tables in the database
 %
 %   >> info  = utils.jmysql.dbquery(conn, query)
 %
-%   The 'info' cell-array will contain the results from the SQL query.
+%   The 'info' cell-array will contain the results from the SQL query
 %
 % VERSION:     $Id: dbquery.m,v 1.2 2010/01/19 20:55:30 ingo Exp $
 %
-% HISTORY:     10-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function varargout = dbquery(varargin)
-
-  conn = varargin{1};
-  if ~isa(conn, 'mpipeline.repository.RepositoryConnection')
-    error('### First input must be a database connection object.');
+  if ~isa(conn, 'java.sql.Connection')
+    error('### first argument should be a java.sql.Connection object');
   end
 
-  if nargin == 1
-    % get table list
-    info = getTableList(conn);
-
-  elseif nargin == 2
-    % execute query
-    info = simpleQuery(conn, varargin{2});
+  switch nargin
+    case 1
+      % get table list
+      try
+        info = utils.mysql.execute(conn, 'SHOW TABLES');
+      catch ex
+        error('### failed to get table list. %s', ex.message);
+      end
 
-  elseif nargin == 3
-    % query a table
-    table    = varargin{2};
-    query    = varargin{3};
-    info = runQuery(conn, table, query);
-  else
-    error('### Incorrect inputs.');
+    case 2
+      % execute query
+      try
+        info = utils.mysql.execute(conn, varargin{1});
+      catch ex
+        error('### failed to execute query. %s', ex.message);
+      end
+
+    case 3
+      % query a table
+      table = varargin{1};
+      query = varargin{2};
+      info = runQuery(conn, table, query);
+
+    otherwise
+      error('### incorrect inputs');
   end
 
   varargout{1} = info;
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get table list
-function info = getTableList(conn)
 
+function info = getFieldList(conn, table)
   info = {};
-  
-  % open a connection
   try
-    q = 'show tables';
-    results = conn.query(q);
-    while results.next
-      info = [info {char(results.getString(1))}];
+    rows = utils.mysql.execute(conn, sprintf('DESCRIBE `%s`', table));
+    for kk = 1:size(rows, 1)
+      info = [info rows(kk,1)];
     end
-  catch
-    error('### Failed to get table list.');
+  catch ex
+    error('### failed to get field list. %s', ex.message);
   end
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get field list
-function info = getFieldList(conn, table)
 
-  info = {};
-  try
-    q = ['describe ' table];
-    results = conn.query(q);
-    while results.next
-      info = [info {char(results.getObject(1))}];
-    end
-  catch
-    error('### Failed to get field list.');
-  end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get field list
-function info = simpleQuery(conn, q)
-
-  % open a connection
+function info = runQuery(conn, table, query)
   info = {};
-  try
-    results = conn.query(q);
-    mt = results.getMetaData;
-    Ncols = mt.getColumnCount;
-    row = 1;
-    while results.next
-      for kk=1:Ncols
-        info{row,kk} = convertValue(results.getObject(kk));
-      end
-      row = row + 1;
-    end
-    
-  catch ME
-    disp(ME.message)
-    error('### Failed to execute query.');
-  end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Run a query
-function info = runQuery(conn, table, query)
-
-  % Run query
-  info = {};
-
   fields = getFieldList(conn, table);
   f = '';
   fs = {};
@@ -143,22 +95,10 @@
     f  = [f fields{j} ',' ];
     fs = [fs fields(j)];
   end
-  q = sprintf('select %s  from %s where %s', f(1:end-1), table, query);
-  disp(['** QUERY: ' q]);
+  q = sprintf('SELECT %s FROM %s WHERE %s', f(1:end-1), table, query);
   try
-    info = simpleQuery(conn, q);
-  catch
-    error('### Failed to query table.');
+    info = utils.mysql.execute(conn, q);
+  catch ex
+    error('### failed to query table. %s', ex.message);
   end
 end
-
-function val = convertValue(val)
-  
-  switch class(val)
-    case 'java.sql.Timestamp'
-      val = char(val);
-    otherwise
-  end
-end
-
-

--- a/m-toolbox/classes/+utils/@jmysql/execute.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-function rows = execute(conn, query, varargin)
-  % execute the given SQL query with optional parameters varargin
-  % through connection conn. the results are returned in a 2d cell
-  % array
-  %
-  % differs from similar riutines in utils.jmysql by the use of proper
-  % SQL escaping of the query arguments. the connection object should
-  % be an object implementing the java.sql.Connection interface.
-
-  if nargin < 2
-    error('### incorrect usage');
-  end
-  if ~isjava(conn)
-    error('### invalid connection');
-  end
-
-  % return value
-  rows = {};
-
-  % build query
-  stmt = conn.prepareStatement(query);
-  for kk = 1:numel(varargin)
-    stmt.setObject(kk, varargin{kk});
-  end
-
-  % execute query
-  rs = stmt.executeQuery();
-
-  % get results into a cell array
-  ncols = rs.getMetaData.getColumnCount();
-  row = 1;
-  while rs.next()
-    for kk = 1:ncols
-      rows{row,kk} = java2matlab(rs.getObject(kk));
-    end
-    row = row + 1;
-  end
-
-end
-
-function val = java2matlab(val)
-  % matlab converts all base types. just add a conversion for datetime columns
-  switch class(val)
-    case 'java.sql.Timestamp'
-      val = time(plist('time', char(val), 'timezone', 'UTC'));
-  end
-end

--- a/m-toolbox/classes/+utils/@jmysql/getRepositoryVersion.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-% getRepositoryVersion tries to get the version of the repository by
-% inspecting various fields in the database.
-% 
-% ver = utils.jmysql.getRepositoryVersion(conn)
-% 
-% Rules:
-%       objs table contains field 'uuid' => ver = 2.1
-% 
-% else: ver = 2.0;
-% 
-% M Hewitson 11-08-09
-% 
-% $Id: getRepositoryVersion.m,v 1.2 2009/08/11 12:33:19 ingo Exp $
-% 
-
-function ver = getRepositoryVersion(conn)
-  
-  ver = '2.0';
-  
-  q    = ['describe ' char(conn.getDatabase) '.objs'];
-  results = conn.query(q);
-  fields = {};
-  while results.next
-    fields = [fields {char(results.getString(1))}];
-  end
-
-  if utils.helper.ismember('uuid', fields)
-    ver = '2.1';
-  end
-  
-  
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/getUserID.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-% GETUSERID gets the user ID number corresponding to the given user name.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: GETUSERID gets the user ID number corresponding to the
-%              user name that connected to the MySQL database.
-%
-% CALL:        userid = getUserID(conn)
-%
-% VERSION:     $Id: getUserID.m,v 1.1 2008/08/08 11:51:12 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function [userid,dbuser] = getUserID(varargin)
-
-  userid = [];
-  conn = varargin{1};
-  if nargin > 1
-    username = varargin{2};
-  else
-    username = char(conn.getUsername);
-  end
-  try
-    if ~conn.isConnected
-      conn.openConnection;
-    end
-    if conn.isConnected
-      q    = sprintf('select id from users where username="%s"', username);
-      results = conn.query(q);
-      while results.next
-        userid = str2num(char(results.getString(1)));
-      end
-    end
-    dbuser = conn.getUsername;
-        
-  catch
-    warning('!!! Unable to retrieve user ID.');
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/getXdoc.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-% GETXDOC retrieves an object with given id from the LTPDA
-% repository specified by the input database connection. The object is
-% converted from its XML text format to an Xdoc. This can then be converted
-% into an object using the appropriate object constructor.
-%
-% Usage: xdoc = getXdoc(conn, id)
-%
-% Inputs:
-%         conn - a database connection object
-%         id   - the object id
-%
-% Outputs:
-%         xdoc - an Xdoc representation of the object.
-%
-% M Hewitson 30-08-07
-%
-% $Id: getXdoc.m,v 1.2 2009/06/17 11:05:53 ingo Exp $
-%
-%
-
-function xdoc = getXdoc(conn, id)
-
-  xdoc = '';
-  
-  try
-    results = conn.query(sprintf('select xml from objs where id="%d"', id));
-    while results.next
-      objTxt = char(results.getString(1));
-    end
-  catch curs
-    error('### Unable to read xml for ID %d. Server returned %s', id, curs.message);
-  end
-
-  if ~isempty(objTxt) && ~strcmp(objTxt(:), 'No Data')
-    % convert to Java string
-    str = java.lang.String(objTxt);
-    % open stream on this string
-    stream = java.io.StringBufferInputStream(str);
-    % make parser
-    builder = javax.xml.parsers.DocumentBuilderFactory.newInstance.newDocumentBuilder;
-
-    xdoc = builder.parse(stream);
-  else
-    xdoc = [];
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/getsinfo.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/getsinfo.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,79 +1,56 @@
-% GETSINFO This function returns an sinfo object containing many useful information about an object retrieved from the repository
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function sinfo = getsinfo(conn, varargin)
+% GETSINFO  Retrieved objects submission info from the repository.
+%
+% CALL:
 %
-% usage:   sinfo = getsinfo(id, conn)
+%   sinfo = getsinfo(conn, id, id)
 %
-% inputs:  id    = obj_id from objmeta table
-%          conn  = utils.mysql.connect(server, dbname);
+% INPUTS:
+%
+%      id - object ID
+%    conn - repository connection implementing java.sql.Connection
 %
-% outputs: sinfo cell array object containing info about object having the
-%          given obj_id on the repository.
-%          sinfo contains the following fields:
-%          - name
-%          - experiment_title
-%          - experiment_desc
-%          - analysis_desc
-%          - quantity
-%          - additional_authors
-%          - additional_comments
-%          - keywords and reference_ids
+% OUTPUTS:
+%
+%   sinfo - array of sinfo structures containing fields
 %
-%          A Monsky 05-02-2009
-%
-% version: $Id: getsinfo.m,v 1.2 2011/03/29 13:40:16 hewitson Exp $
+%    - name
+%    - experiment_title
+%    - experiment_desc
+%    - analysis_desc
+%    - quantity
+%    - additional_authors
+%    - additional_comments
+%    - keywords
+%    - reference_ids
 %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function [varargout] = getsinfo(varargin)
-  
-  import utils.const.*
-  utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename);
-  
-  % Collect input variable names
-  in_names = cell(size(varargin));
-  for ii = 1:nargin,in_names{ii} = inputname(ii);end
-  
-  % Collect all ids and plists and connections
-  pl = utils.helper.collect_objects(varargin(:), 'plist');
-  id = utils.helper.collect_objects(varargin(:), 'double');
-  conn  = utils.helper.collect_objects(varargin(:), 'mpipeline.repository.RepositoryConnection');
-  
-  if isempty(conn)
-    error('### This method needs a java connection (mpipeline.repository.RepositoryConnection).');
-  end
-  
-  if isempty(id)
-    error('### This method needs at least one object id.');
+% VERSION: $Id: getsinfo.m,v 1.2 2011/03/29 13:40:16 hewitson Exp $
+
+  if ~isa(conn, 'java.sql.Connection')
+    error('### first argument should be a java.sql.Connection object');
   end
-  
-  if nargout == 0
-    error('### lscov can not be used as a modifier method. Please give at least one output');
-  end
-  
-  % combine plists
-  pl = combine(pl, plist());
-  
-  % Algorithm
-  % Get complete experiment information for each input id
+
   sinfo = [];
-  for ii=1:length(id)
-    qall = ['select name,experiment_title,experiment_desc,analysis_desc,quantity, '...
-      'additional_authors,additional_comments,keywords,reference_ids FROM objmeta ' ...
-      sprintf('where objmeta.obj_id=%d',id(ii))];
-    
-    infoall = utils.jmysql.dbquery(conn, qall);
+  for kk = 1:length(varargin)
+
+    q = ['SELECT name, experiment_title, experiment_desc, analysis_desc, ' ...
+         'quantity, additional_authors, additional_comments, keywords, ' ...
+         'reference_ids FROM objmeta WHERE obj_id = ?'];
+
+    info = utils.mysql.execute(conn, q, varargin{kk});
+
     s.conn                    = conn;
-    s.name                    = infoall{1};
-    s.experiment_title        = infoall{2};
-    s.experiment_description  = infoall{3};
-    s.analysis_description    = infoall{4};
-    s.quantity                = infoall{5};
-    s.additional_authors      = infoall{6};
-    s.additional_comments     = infoall{7};
-    s.keywords                = infoall{8};
-    s.reference_ids           = infoall{9};
+    s.name                    = info{1};
+    s.experiment_title        = info{2};
+    s.experiment_description  = info{3};
+    s.analysis_description    = info{4};
+    s.quantity                = info{5};
+    s.additional_authors      = info{6};
+    s.additional_comments     = info{7};
+    s.keywords                = info{8};
+    s.reference_ids           = info{9};
+
     sinfo = [sinfo s];
   end
-  
-  % Set output
-  varargout{1} = sinfo;
+
 end

--- a/m-toolbox/classes/+utils/@jmysql/insert.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-% INSERT inserts values into a single row of a table using JDBC driver
-% specified by the input connection.
-%
-% Usage: message = insert(conn, table, 'field1', value1, 'field2', value2,...)
-%
-% M Hewitson
-%
-% 31-07-07
-%
-% $Id: insert.m,v 1.4 2009/09/16 13:38:58 hewitson Exp $
-%
-
-function message = insert(conn, table, varargin)
-
-  message = '';
-  q = sprintf('INSERT INTO %s SET ',  table);
-  
-  for j=1:2:length(varargin)
-    
-    col = varargin{j};
-    val = varargin{j+1};
-    if isnumeric(val)
-      if ~any(isnan(val))
-        q = [q col '=' num2str(val) ','];
-      end
-    elseif ischar(val)
-      q = [q col '=' '''' val '''' ','];
-    else
-      error('### val class [%s]', class(val))
-    end
-        
-  end
-  
-  q = deblank([q(1:end-1) ';']);
-
-  if length(q) > 50
-    qdisp = [q(1:50) '...'];
-    utils.helper.msg(utils.const.msg.PROC1, 'running query %s', qdisp);
-  else
-    utils.helper.msg(utils.const.msg.PROC1, 'running query %s', q);
-  end
-  
-  try
-    stmt = conn.createStatement;
-    stmt.execute(q);
-  catch Me
-    error('### insert: failed to execute query');
-  end
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/insertObjMetadata.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-function insertObjMetadata(conn, obj, objid)
-  % an utility to insert entries for various object metadata in the
-  % corresponding tables. differs from insertObjMetadataV1() by
-  % the use of the new v3.0 database structure
-  %
-  % MUST BE KEPT IN SYNC WITH updateObjMetadata()
-  %
-  % conn   - Java database connection object
-  % obj    - object
-  % objid  - unique ID of the object in the database
-  %
-  % VERSION:     $Id: insertObjMetadata.m,v 1.9 2011/11/09 18:45:14 mauro Exp $
-  %
-  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-  import utils.const.*
-
-  if nargin < 3
-    error('### incorrect usage');
-  end
-  if ~isjava(conn)
-    error('### incorrect usage');
-  end
-
-  % class of object
-  cl = class(obj);
-  utils.helper.msg(msg.PROC2, 'making meta data entry for %s object', cl);
-
-  switch cl
-    case 'ao'
-
-      % call recursively to insert the data object info
-      utils.jmysql.insertObjMetadata(conn, obj.data, objid);
-
-      % insert the AO info
-      stmt = conn.prepareStatement(...
-        'INSERT INTO ao (obj_id, data_type, description) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(class(obj.data)));
-      
-      desc = obj.description;
-      if length(desc)>65535
-        warning('Object description length exceeded. Truncating to 65535 characters');
-        desc = desc(1:65535);
-      end
-      stmt.setObject(3, java.lang.String(desc));
-      stmt.execute();
-      stmt.close();
-
-    case 'cdata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO cdata (obj_id, yunits) VALUES (?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.execute();
-      stmt.close();
-
-    case 'fsdata'
-
-      % possible bad entries
-      fs = obj.fs;
-      if ~isfinite(fs)
-        fs = [];
-      end
-        
-      stmt = conn.prepareStatement(...
-        'INSERT INTO fsdata (obj_id, xunits, yunits, fs) VALUES (?, ?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(char(obj.xunits)));
-      stmt.setObject(3, java.lang.String(char(obj.yunits)));
-      stmt.setObject(4, fs);
-      stmt.execute();
-      stmt.close();
-
-    case 'tsdata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO tsdata (obj_id, xunits, yunits, fs, t0, nsecs, toffset) VALUES (?, ?, ?, ?, ?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(char(obj.xunits)));
-      stmt.setObject(3, java.lang.String(char(obj.yunits)));
-      stmt.setObject(4, obj.fs);
-      stmt.setObject(5, java.lang.String(format(obj.t0 + obj.toffset/1000, 'yyyy-mm-dd HH:MM:SS', 'UTC')));
-      stmt.setObject(6, obj.nsecs);
-      stmt.setObject(7, obj.toffset);
-      stmt.execute();
-      stmt.close();
-
-    case 'xydata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO xydata (obj_id, xunits, yunits) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(char(obj.xunits)));
-      stmt.setObject(3, java.lang.String(char(obj.yunits)));
-      stmt.execute();
-      stmt.close();
-
-    case 'mfir'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO mfir (obj_id, in_file, fs) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(obj.infile));
-      stmt.setObject(3, obj.fs);
-      stmt.execute();
-      stmt.close();
-
-    case 'miir'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO miir (obj_id, in_file, fs) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(obj.infile));
-      stmt.setObject(3, obj.fs);
-      stmt.execute();
-      stmt.close();
-
-    otherwise
-      utils.helper.msg(msg.PROC2, 'no meta data table for %s object', cl);
-
-  end
-
-end

--- a/m-toolbox/classes/+utils/@jmysql/insertObjMetadataV1.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,142 +0,0 @@
-function id = insertObjMetadataV1(conn, obj, objid)
-  % an utility to insert entries for various object metadata in the
-  % corresponding tables. uses the old v2.1 database schema.
-  %
-  % MUST BE KEPT IN SYNC WITH updateObjMetadataV1()
-  %
-  % conn   - Java database connection object
-  % obj    - object
-  % objid  - unique ID of the object in the database
-  %
-
-  import utils.const.*
-
-  if nargin < 3
-    error('### incorrect usage');
-  end
-  if ~isjava(conn)
-    error('### incorrect usage');
-  end
-
-  % default output value
-  id = [];
-
-  % class of object
-  cl = class(obj);
-  utils.helper.msg(msg.PROC2, 'making meta data entry for %s object', cl);
-
-  switch cl
-    case 'ao'
-
-      % call recursively to insert the data object info
-      dataid = utils.jmysql.insertObjMetadataV1(conn, obj.data, objid);
-
-      % insert the AO info
-      stmt = conn.prepareStatement(...
-        'INSERT INTO ao (obj_id, data_type, data_id, description) VALUES (?, ?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(class(obj.data)));
-      stmt.setObject(3, dataid);
-      desc = obj.description;
-      if length(desc)>65535
-        warning('Object description length exceeded. Truncating to 65535 characters');
-        desc = desc(1:65535);
-      end
-      stmt.setObject(4, java.lang.String(desc));
-      stmt.execute();
-      stmt.close();
-
-    case 'cdata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO cdata (yunits) VALUES (?)');
-      stmt.setObject(1, java.lang.String(char(obj.yunits)));
-      stmt.executeUpdate();
-
-      % obtain generated data id
-      rs = stmt.getGeneratedKeys();
-      rs.next();
-      id = rs.getInt(1);
-      rs.close();
-      stmt.close();
-
-    case 'fsdata'
-
-      % possible bad entries
-      fs = obj.fs;
-      if ~isfinite(fs)
-        fs = [];
-      end
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO fsdata (xunits, yunits, fs) VALUES (?, ?, ?)');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.setObject(3, fs);
-      stmt.executeUpdate();
-
-      % obtain generated data id
-      rs = stmt.getGeneratedKeys();
-      rs.next();
-      id = rs.getInt(1);
-      rs.close();
-      stmt.close();
-
-    case 'tsdata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO tsdata (xunits, yunits, fs, t0, nsecs) VALUES (?, ?, ?, ?, ?)');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.setObject(3, obj.fs);
-      stmt.setObject(4, java.lang.String(format(obj.t0, 'yyyy-mm-dd HH:MM:SS', 'UTC')));
-      stmt.setObject(5, obj.nsecs);
-      stmt.executeUpdate();
-
-      % obtain generated data id
-      rs = stmt.getGeneratedKeys();
-      rs.next();
-      id = rs.getInt(1);
-      rs.close();
-      stmt.close();
-
-    case 'xydata'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO xydata (xunits, yunits) VALUES (?, ?)');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.executeUpdate();
-
-      % obtain generated data id
-      rs = stmt.getGeneratedKeys();
-      rs.next();
-      id = rs.getInt(1);
-      rs.close();
-      stmt.close();
-
-    case 'mfir'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO mfir (obj_id, in_file, fs) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(obj.infile));
-      stmt.setObject(3, obj.fs);
-      stmt.execute();
-      stmt.close();
-
-    case 'miir'
-
-      stmt = conn.prepareStatement(...
-        'INSERT INTO miir (obj_id, in_file, fs) VALUES (?, ?, ?)');
-      stmt.setObject(1, objid);
-      stmt.setObject(2, java.lang.String(obj.infile));
-      stmt.setObject(3, obj.fs);
-      stmt.execute();
-      stmt.close();
-
-    otherwise
-      utils.helper.msg(msg.PROC2, 'no meta data table for %s object', cl);
-
-  end
-end

--- a/m-toolbox/classes/+utils/@jmysql/jconnTodbconn.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-% JCONNTODBCONN convert a java db connection to a MATLAB database
-% connection.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: JCONNTODBCONN convert a java db connection to a MATLAB
-%              database Toolbox connection.
-%
-% CALL:        dbconn = utils.jmysql.jconnTodbconn(jconn);
-%
-% INPUTS:
-%              jconn - a connection object like that returned from
-%                     utils.jmysql.connect.
-% 
-% OUTPUTS:     dbconn - a database toolbox connecton
-%
-%
-% VERSION:     $Id: jconnTodbconn.m,v 1.1 2009/07/28 06:46:09 hewitson Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-function conn = jconnTodbconn(jconn)
-  
-  if nargin ~= 1 || ~isa(jconn, 'mpipeline.repository.RepositoryConnection')
-    error('### The first argument should be a RepositoryConnection');
-  end
-
-  host = char(jconn.getHostname);
-  db   = char(jconn.getDatabase);
-  user = char(jconn.getUsername);
-  pw   = char(jconn.getPassword);
-  
-  dbdriver = getappdata(0, 'mysql_driver');
-  dburl    = sprintf('jdbc:mysql://%s/%s',host,db);
-
-  disp(sprintf('** Connecting to %s as %s...', host, user))
-
-  conn     = database(db,user,pw,dbdriver,dburl);
-  disp('** Connection status:')
-  disp(ping(conn))
-  
-  
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/jmysql.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/jmysql.m	Tue Dec 06 19:07:22 2011 +0100
@@ -25,24 +25,11 @@
     varargout = getsinfo(varargin) % return sinfo structure of repository object
 
     %%% MYSQL TOOLS
-    varargout = connect(varargin) % connects to an LTPDA repository and returns the connection object.
-    varargout = query(varargin) % perform a query on an LTPDA repository and returns the results.
+    varargout = connect(varargin) % connects to an LTPDA repository and returns the connection object
+    varargout = query(varargin) % perform a query on an LTPDA repository and returns the results
     varargout = resultsToCell(varargin) % convert a ResultSet to a cell-array
     varargout = displayResults(varargin) % display a ResultSet in a table
-    varargout = queryDialog(varargin) % show a query builder dialog
-    varargout = submitDialog(varargin) % show a submission dialog
-    varargout = jconnTodbconn(varargin) % convert a java connection to database toolbox connection
-    varargout = dbconnTojconn(varargin) % convert a database toolbox connection to java connection
-    varargout = getUserID(varargin)
-    varargout = getXdoc(varargin)
-    varargout = insert(varargin)
-    varargout = getRepositoryVersion(varargin)
     varargout = dbquery(varargin)
-    varargout = insertObjMetadata(varargin)
-    varargout = updateObjMetadata(varargin)
-    varargout = insertObjMetadataV1(varargin) % back-compatibility for old database schema
-    varargout = updateObjMetadataV1(varargin) % back-compatibility for old database schema
-    varargout = execute(varargin)
 
   end % End static methods
 

--- a/m-toolbox/classes/+utils/@jmysql/query.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/query.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,70 +1,44 @@
-% QUERY query an LTPDA repository.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function varargout = query(conn, query, varargin)
+% QUERY  Query an LTPDA repository.
 %
-% DESCRIPTION: QUERY query an LTPDA repository.
+% DEPRECATED! Use utils.mysql.execute instead!
 %
-% CALL:                     results = query(conn, q)
-%              [results, col_names] = query(conn, q)
+% CALL:                [results] = query(conn, q, varargin)
+%              [results, cnames] = query(conn, q, varargin)
 %
 % INPUTS:
-%              conn - an mpipeline.repository.RepositoryConnection object,
-%                     as is returned by utils.jmysql.connect
-%              q    - a valid MySQL query string
+%
+%      conn  - database connection object implementing java.sql.Connection
+%     query  - a valid SQL query
+%  varargin  - optional query parameters
 %
 % OUTPUTS:
-%                results - a cell-array of the results
-%              col_names - a cell-array of the column names in the query
-%
-% VERSION:     $Id: query.m,v 1.1 2009/07/27 19:46:21 hewitson Exp $
 %
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
+%   results  - a cell-array of the results
+%    cnames  - a cell-array of the column names in the query
 %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+% VERSION: $Id: query.m,v 1.1 2009/07/27 19:46:21 hewitson Exp $
+%
 
-%              (*) the expiry time for MySQL logins is a property of the
-%              LTPDA Toolbox and can be set in the LTPDA Preferences.
-
-
-function varargout = query(varargin)
+  warning('!!! deprecated. use utils.mysql.execute instead');
   
-  prefs = getappdata(0, 'LTPDApreferences');
-  
-  if ~isa(varargin{1}, 'mpipeline.repository.RepositoryConnection')
-    error('### The first argument should be a RepositoryConnection');
+  if ~isa(conn, 'java.sql.Connection')
+    error('### first argument should be a java.sql.Connection object');
   end
   
-  if ~ischar(varargin{2})
-    error('### The second argument should be a query string.');
+  stmt = conn.prepareStatement(query);
+  for kk = 1:numel(varargin)
+    stmt.setObject(kk, varargin{kk});
   end
   
-  % Inputs
-  conn = varargin{1};
-  q    = varargin{2};
-  
-  % Outputs
-  results  = {};
-  colnames = {};
+  % execute query
+  resultSet = stmt.executeQuery();
   
-  % Check connection
-  if ~conn.isConnected
-    conn.openConnection
-  end
-  
-  if ~conn.isConnected
-    conn.display;
-    error('### Failed to open connection');
-    return
-  end
-  
-  resultSet = conn.query(q);
-    
-  % Set outputs
+  % set outputs
   if nargout > 0
     varargout{1} = resultSet;
     if nargout == 2
-      % Get column names from the meta data
+      % get column names from the meta data
       rsm = resultSet.getMetaData;
       Nc = rsm.getColumnCount;
       colnames = cell(1,Nc);

--- a/m-toolbox/classes/+utils/@jmysql/queryDialog.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-% QUERYDIALOG a visual query builder for querying an LTPDA repository.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: QUERYDIALOG a visual query builder for querying an LTPDA
-%              repository.
-%
-% CALL:        utils.jmysql.queryDialog();
-%              utils.jmysql.queryDialog(conn);
-%
-% INPUTS:
-%              conn - a connection object like that returned from
-%                     utils.jmysql.connect.
-%
-%
-% VERSION:     $Id: queryDialog.m,v 1.2 2009/09/22 14:40:07 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-function  queryDialog(varargin)
-  
-  if nargin == 1 && ~isa(varargin{1}, 'mpipeline.repository.RepositoryConnection')
-    error('### The first argument should be empty or a RepositoryConnection');
-  end
-  
-  
-  % Inputs
-  conn = [];
-  if nargin > 0
-    conn  = varargin{1};
-  end
-  
-  if isempty(conn)
-    conn = utils.jmysql.connect();
-  end
-  
-  if ~conn.isConnected
-    conn.openConnection
-  end
-  
-  if ~conn.isConnected
-    error('### Failed to connect to repository.');
-  end
-  
-  % open a query dialog
-  if nargin == 0
-    closeConnectionOnExit = true;
-  else
-    closeConnectionOnExit = false;
-  end
-  warning('off', 'MATLAB:JavaEDTAutoDelegation');
-  qrd = mpipeline.repository.RepositoryQueryDialog([], false, conn, false, closeConnectionOnExit);
-  qrd.setVisible(true)
-  warning('off', 'MATLAB:JavaEDTAutoDelegation');
-  
-  
-  
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/resultsToCell.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@jmysql/resultsToCell.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,58 +1,67 @@
-% RESULTSTOCELL converts a java sql ResultSet to a cell-array
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function varargout = resultsToCell(resultSet)
+% RESULTSTOCELL  Converts a java.sql.ResultSet to a cell array
 %
-% DESCRIPTION: RESULTSTOCELL converts a java sql ResultSet to a cell-array.
+% DEPRECATED! Use utils.mysql.execute instead!
 %
-% CALL:        [results, colnames] = utils.jmysql.resultsToCell(resultSet);
+% CALL:
+%
+%   [results, colnames] = utils.jmysql.resultsToCell(rs);
 %
 % INPUTS:
-%              resultSet - a result set like that returned from
-%                          utils.jmysql.query
+%
+%   rs       - a java.sql.ResultSet like that returned from utils.jmysql.query
 %
 % OUTPUTS:
-%              results      - a cell array of results
-%              col_names    - a cell array of column names
 %
+%   results  - a cell array of results
+%   colnames - a cell array of column names
 %
-% VERSION:     $Id: resultsToCell.m,v 1.1 2009/07/27 19:46:21 hewitson Exp $
+% VERSION: $Id: resultsToCell.m,v 1.1 2009/07/27 19:46:21 hewitson Exp $
 %
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+  warning('!!! deprecated. use utils.mysql.execute instead');
+  
+  if ~isa(resultSet, 'java.sql.ResultSet')
+    error('### first argument should be a java.sql.ResultSet');
+  end
 
+  % get results into a cell array
+  md = rs.getMetaData();
+  nc = md.getColumnCount();
+  row = 1;
+  while rs.next()
+    for kk = 1:nc
+      % convert to matlab objects
+      rows{row, kk} = java2matlab(rs.getObject(kk));
+    end
+    row = row + 1;
+  end
+      
+  % get column names
+  names = cell(1, nc);
+  for kk = 1:nc
+    names{kk} = char(md.getColumnName(kk));
+  end
+      
+  % assign output
+  switch nargout
+    case 0
+      varargout{1} = rows;
+    case 1
+      varargout{1} = rows;
+    case 2
+      varargout{1} = names;
+      varargout{2} = rows;
+    otherwise
+      error('### too many output arguments');
+  end      
+end
 
 
-function varargout = resultsToCell(varargin)
-  
-  prefs = getappdata(0, 'LTPDApreferences');
-  
-  if ~isa(varargin{1}, 'java.sql.ResultSet')
-    error('### The first argument should be a ResultSet');
+function val = java2matlab(val)
+  % matlab converts all base types. just add a conversion for datetime columns
+  switch class(val)
+    case 'java.sql.Timestamp'
+      val = time(plist('time', char(val), 'timezone', 'UTC'));
   end
-  
-  % Inputs
-  resultSet  = varargin{1};
-  
-  os = mpipeline.repository.RepositoryConnection.resultSetToObjectArray(resultSet);
-  disp(sprintf('*** converted result set: [%dx%d]', numel(os), numel(os(1))));
-  
-  % Set outputs
-  if nargout > 0
-    varargout{1} = cell(os);
-    if nargout == 2
-      % Get column names from the meta data
-      rsm = resultSet.getMetaData;
-      Nc = rsm.getColumnCount;
-      colnames = cell(1,Nc);
-      for kk=1:Nc
-        colnames{kk} = char(rsm.getColumnName(kk));
-      end
-      
-      varargout{2} = colnames;
-    end
-  end
-  
-  
 end
-

--- a/m-toolbox/classes/+utils/@jmysql/submitDialog.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-% SUBMITDIALOG a submission dialog for submitting objects an LTPDA repository.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: SUBMITDIALOG a submission dialog for submitting objects an
-%              LTPDA repository.
-%
-% CALL:        sinfo = utils.jmysql.submitDialog();
-%              sinfo = utils.jmysql.submitDialog(conn);
-%              sinfo = utils.jmysql.submitDialog(conn,sinfo);
-%
-% INPUTS:
-%              conn  - a connection object like that returned from
-%                      utils.jmysql.connect.
-%              sinfo - an sinfo structure to pre-populate the entry fields
-%
-% OUTPUTS: 
-%              sinfo - an sinfo structure suitable to pass to submit
-% 
-% NOTE: the sinfo object contains a valid and connected database connection
-% object. It is up to the caller to close this connection when it is no
-% longer required.
-% 
-% NOTE: if an input connection is provided, this is not closed by this
-% process.
-%
-% VERSION:     $Id: submitDialog.m,v 1.4 2009/10/02 09:19:50 hewitson Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-function sinfo = submitDialog(varargin)
-  
-  if nargin > 0 && ~isa(varargin{1}, 'mpipeline.repository.RepositoryConnection')
-    error('### The first argument should be empty or a RepositoryConnection');
-  end
-  
-  isinfo = [];
-  
-  if nargin == 2 && isstruct(varargin{2})
-    isinfo = varargin{2};
-  end
-  
-  % Inputs
-  conn = [];
-  if nargin > 0
-    conn  = varargin{1};
-  end
-
-  % Check the connection
-  if ~isempty(conn)
-    closeConnection = false;
-    if ~conn.isConnected
-      conn.openConnection
-    end
-    if ~conn.isConnected
-      error('### Failed to connect to repository.');
-    end
-  else
-    closeConnection = true;
-  end
-  
-  % Get host list
-  prefs = getappdata(0, 'LTPDApreferences');
-  hosts = java.util.ArrayList();
-  servers = prefs.repository.servers;
-  for kk=1:numel(servers)
-    hosts.add(servers{kk});
-  end
-  
-  jisinfo = [];
-  if ~isempty(isinfo) 
-    
-    jisinfo = mpipeline.repository.SubmissionInfo([]);
-    jisinfo.setExperimentTitle(isinfo.experiment_title);
-    jisinfo.setExperimentDescription(isinfo.experiment_description);
-    jisinfo.setAnalysisDescription(isinfo.analysis_description);
-    jisinfo.setQuantity(isinfo.quantity);
-    jisinfo.setKeywords(isinfo.keywords);
-    jisinfo.setReferenceIDs(isinfo.reference_ids);
-    jisinfo.setAdditionalComments(isinfo.additional_comments);
-    jisinfo.setAdditionalAuthors(isinfo.additional_authors);
-    
-  end
-  
-  % Open submit dialog
-  warning('off', 'MATLAB:JavaEDTAutoDelegation');
-  srd = mpipeline.repository.SubmitInfoDialog([], jisinfo, hosts, conn);
-  srd.setVisible(true)
-  warning('on', 'MATLAB:JavaEDTAutoDelegation');
-  
-  sinfo = [];
-  if ~srd.isCancelled
-    
-    jsinfo = srd.getSubmissionInfo;
-    sinfo.experiment_title       = char(jsinfo.getExperimentTitle);
-    sinfo.experiment_description = char(jsinfo.getExperimentDescription);
-    sinfo.analysis_description   = char(jsinfo.getAnalysisDescription);
-    sinfo.quantity               = char(jsinfo.getQuantity);
-    sinfo.keywords               = char(jsinfo.getKeywords);
-    sinfo.reference_ids          = char(jsinfo.getReferenceIDs);
-    sinfo.additional_comments    = char(jsinfo.getAdditionalComments);
-    sinfo.additional_authors     = char(jsinfo.getAdditionalAuthors);
-    
-    jconn = srd.getRepoConnection;    
-    sinfo.conn = jconn; %utils.jmysql.jconnTodbconn(jconn);    
-    if closeConnection
-      jconn.closeConnection;
-    end
-  end
-  
-end
-

--- a/m-toolbox/classes/+utils/@jmysql/updateObjMetadata.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-function updateObjMetadata(conn, obj, objid)
-  % an utility to update entries for various object metadata in the
-  % corresponding tables. differs from insertObjMetadataV1() by
-  % the use of the new v3.0 database structure
-  %
-  % MUST BE KEPT IN SYNC WITH insertObjMetadata()
-  %
-  % conn   - Java database connection object
-  % obj    - object
-  % objid  - unique ID of the object in the database
-  %
-  % VERSION:     $Id: updateObjMetadata.m,v 1.7 2011/11/09 18:47:04 mauro Exp $
-  %
-  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-  import utils.const.*
-
-  if nargin < 3
-    error('### incorrect usage');
-  end
-  if ~isjava(conn)
-    error('### incorrect usage');
-  end
-
-  % class of object
-  cl = class(obj);
-  utils.helper.msg(msg.PROC2, 'making meta data entry for %s object', cl);
-
-  switch cl
-    case 'ao'
-
-      % call recursively to insert the data object info
-      utils.jmysql.updateObjMetadata(conn, obj.data, objid);
-
-      % insert the AO info
-      stmt = conn.prepareStatement(...
-        'UPDATE ao SET data_type=?, description=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(class(obj.data)));
-      desc = obj.description;
-      if length(desc)>65535
-        warning('Object description length exceeded. Truncating to 65535 characters');
-        desc = desc(1:65535);
-      end
-      stmt.setObject(2, java.lang.String(desc));
-      stmt.setObject(3, objid);
-      stmt.executeUpdate();
-      stmt.close();
-
-    case 'cdata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE cdata SET yunits=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(char(obj.yunits)));
-      stmt.setObject(2, objid);
-      stmt.executeUpdate();
-      stmt.close();
-
-    case 'fsdata'
-
-      % possible bad entries
-      fs = obj.fs;
-      if ~isfinite(fs)
-        fs = [];
-      end
-        
-      stmt = conn.prepareStatement(...
-        'UPDATE fsdata SET xunits=?, yunits=?, fs=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.setObject(3, fs);
-      stmt.setObject(4, objid);
-      stmt.executeUpdate();
-      stmt.close();
-
-    case 'tsdata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE tsdata SET xunits=?, yunits=?, fs=?, t0=?, nsecs=?, toffset=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.setObject(3, obj.fs);
-      stmt.setObject(4, java.lang.String(format(obj.t0 + obj.toffset/1000, 'yyyy-mm-dd HH:MM:SS', 'UTC')));
-      stmt.setObject(5, obj.nsecs);
-      stmt.setObject(6, obj.toffset);
-      stmt.setObject(7, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'xydata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE xydata SET xunits=?, yunits=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(char(obj.xunits)));
-      stmt.setObject(2, java.lang.String(char(obj.yunits)));
-      stmt.setObject(3, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'mfir'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE mfir SET in_file=?, fs=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(obj.infile));
-      stmt.setObject(2, obj.fs);
-      stmt.setObject(3, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'miir'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE miir SET in_file=?, fs=? WHERE obj_id = ?');
-      stmt.setObject(1, java.lang.String(obj.infile));
-      stmt.setObject(2, obj.fs);
-      stmt.setObject(3, objid);
-      stmt.execute();
-      stmt.close();
-
-    otherwise
-      utils.helper.msg(msg.PROC2, 'no meta data table for %s object', cl);
-
-  end
-
-end

--- a/m-toolbox/classes/+utils/@jmysql/updateObjMetadataV1.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,137 +0,0 @@
-function id = updateObjMetadataV1(conn, obj, objid)
-  % an utility to update entries for various object metadata in the
-  % corresponding tables. uses the old v2.1 database schema.
-  %
-  % MUST BE KEPT IN SYNC WITH insertObjMetadataV1()
-  %
-  % conn   - Java database connection object
-  % obj    - object
-  % objid  - unique ID of the object in the database
-  %
-
-  import utils.const.*
-
-  if nargin < 3
-    error('### incorrect usage');
-  end
-  if ~isjava(conn)
-    error('### incorrect usage');
-  end
-
-  % default return value
-  id = [];
-  
-  % class of object
-  cl = class(obj);
-  utils.helper.msg(msg.PROC2, 'making meta data entry for %s object', cl);
-
-  switch cl
-    case 'ao'
-
-      % get data type and id
-      stmt = conn.prepareStatement(...
-        'SELECT data_id, data_type FROM ao WHERE obj_id = ?');
-      stmt.setObject(1, objid);
-      rs = stmt.executeQuery();
-      rs.next();
-      dataid = rs.getInt(1);
-      datatype = rs.getString(2);
-      rs.close();
-      stmt.close();
-      
-      % check if the data type is consistent
-      if ~strcmp(datatype, class(obj.data))
-        error('### cannot update an object with one having a different data type');
-      end
-        
-      % call recursively to insert the data object info
-      id = utils.jmysql.updateObjMetadataV1(conn, obj.data, dataid);
-
-      % update ao description
-      stmt = conn.prepareStatement(...
-        'UPDATE ao SET description=? WHERE obj_id = ?');
-      desc = obj.description;
-      if length(desc)>65535
-        warning('Object description length exceeded. Truncating to 65535 characters');
-        desc = desc(1:65535);
-      end
-      stmt.setObject(1, desc);
-      stmt.setObject(2, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'cdata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE cdata SET yunits=? WHERE id = ?');
-      stmt.setObject(1, char(obj.yunits));
-      stmt.setObject(2, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'fsdata'
-
-      % possible bad entries
-      fs = obj.fs;
-      if ~isfinite(fs)
-        fs = [];
-      end
-        
-      stmt = conn.prepareStatement(...
-        'UPDATE fsdata SET xunits=?, yunits=?, fs=? WHERE id = ?');
-      stmt.setObject(1, char(obj.xunits));
-      stmt.setObject(2, char(obj.yunits));
-      stmt.setObject(3, fs);
-      stmt.setObject(4, objid);      
-      stmt.execute();
-      stmt.close();
-
-    case 'tsdata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE tsdata SET xunits=?, yunits=?, fs=?, t0=?, nsecs=? WHERE id = ?');
-      stmt.setObject(1, char(obj.xunits));
-      stmt.setObject(2, char(obj.yunits));
-      stmt.setObject(3, obj.fs);
-      stmt.setObject(4, format(obj.t0, 'yyyy-mm-dd HH:MM:SS', 'UTC'));
-      stmt.setObject(5, obj.nsecs);
-      stmt.setObject(6, objid);      
-      stmt.execute();
-      stmt.close();
-
-    case 'xydata'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE xydata SET xunits=?, yunits=? WHERE id = ?');
-      stmt.setObject(1, char(obj.xunits));
-      stmt.setObject(2, char(obj.yunits));
-      stmt.setObject(3, objid);      
-      stmt.execute();
-      stmt.close();
-
-    case 'mfir'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE mfir SET in_file=?, fs=? WHERE obj_id = ?');
-      stmt.setObject(1, obj.infile);
-      stmt.setObject(2, obj.fs);
-      stmt.setObject(3, objid);
-      stmt.execute();
-      stmt.close();
-
-    case 'miir'
-
-      stmt = conn.prepareStatement(...
-        'UPDATE miir SET in_file=?, fs=? WHERE obj_id = ?');
-      stmt.setObject(1, obj.infile);
-      stmt.setObject(2, obj.fs);
-      stmt.setObject(3, objid);      
-      stmt.execute();
-      stmt.close();
-
-    otherwise
-      utils.helper.msg(msg.PROC2, 'no meta data table for %s object', cl);
-
-  end
-
-end

--- a/m-toolbox/classes/+utils/@mysql/connect.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@mysql/connect.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,189 +1,50 @@
-% CONNECT connects to an LTPDA repository and returns the connection object.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function conn = connect(hostname, database, username, password)
+% CONNECT Opens a connection to the given database.
 %
-% DESCRIPTION: CONNECT connects to an LTPDA repository and returns the
-%              connection object.
-% 
-%              CONNECT stores a persistent set of logins where a login has
-%              the fields:
-%                  'hostname' - the hostname of the MySQL server
-%                  'db'       - the name of the database
-%                  'user'     - the username for connection to this db
-%                  'passwd'   - the password for this user
-% 
-%              If a login for the requested hostname and db doesn't exist,
-%              or if the existing login is too old (*) then the user is
-%              prompted to log in again.
-%               
-%              (*) the expiry time for MySQL logins is set to 30s.
+% CALL:
+%
+%   conn = utils.mysql.connect(hostname, database, username, password)
 %
-% CALL:        conn = connect(hostname)  % connects to 'test' database
-%              conn = connect(hostname, dbname)  % dialog prompt for username and password
-%              [conn, password] = connect(hostname, dbname) % return password to caller
-%              conn = connect(hostname, dbname, dbuser, dbpass) % connect with explicit username and password
+% This function returns a Java java.sql.Connection object.
 %
-% VERSION:     $Id: connect.m,v 1.8 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% On authetication error an utils:mysql:connect:AccessDenied exception
+% is thrown. On other errors an utils:mysql:connect:ConnectionError
+% exception is thrown.
 
-
-%              (*) the expiry time for MySQL logins is a property of the
-%              LTPDA Toolbox and can be set in the LTPDA Preferences.
-
-
-function varargout = connect(varargin)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  if nargin < 1
-    error('### Incorrect inputs')
-  end
+  % informative message
+  import utils.const.*
+  utils.helper.msg(msg.PROC1, 'connection to mysql://%s/%s username=%s', hostname, database, username);
 
-  persistent logins;
-  
-  prefs = getappdata(0, 'LTPDApreferences');
-  expTime = prefs.repository.loginExpiry;
-  
-  dbuser = '';
-  dbpass = '';
+  % connection credential
+  uri = sprintf('jdbc:mysql://%s/%s', hostname, database);
+  db = javaObject('com.mysql.jdbc.Driver');
+  pl = javaObject('java.util.Properties');
+  pl.setProperty(db.USER_PROPERTY_KEY, username);
+  pl.setProperty(db.PASSWORD_PROPERTY_KEY, password);
 
-  force = false;
-  if nargin == 1
-    dbhost = varargin{1};
-    dbname = 'test';
-  elseif nargin == 2
-    dbhost = varargin{1};
-    dbname = varargin{2};
-  elseif nargin == 3
-    dbhost = varargin{1};
-    dbname = varargin{2};
-    force = varargin{3};
-  elseif nargin == 4
-    dbhost = varargin{1};
-    dbname = varargin{2};
-    dbuser = varargin{3};
-    dbpass = varargin{4};
-  elseif nargin == 5
-    dbhost = varargin{1};
-    dbname = varargin{2};
-    dbuser = varargin{3};
-    dbpass = varargin{4};
-    force = varargin{5};
-  end
-  
-  if isempty(logins)
-    % Prompt for username and password
-    [dbuser, dbpass] = getlogin(dbhost, dbname, dbuser, dbpass, force);
-        
-    % in the case the user clicks cancel
-    if ~ischar(dbuser) && ~ischar(dbpass)
-      if (dbuser == -1 && dbpass == -1)
-        varargout{1} = -1;
-        varargout{2} = -1;
-        return
+  try
+    % connect
+    conn = db.connect(uri, pl);
+  catch ex
+    % exceptions handling in matlab sucks
+    if strcmp(ex.identifier, 'MATLAB:Java:GenericException')
+      % extract exception class and message
+      lines = regexp(ex.message, '\n', 'split');
+      p = strfind(lines{2}, ': ');
+      id = lines{2}(1:p(1)-1);
+      message = lines{2}(p(1)+2:end);
+      % some notable cases
+      switch id
+        case 'java.sql.SQLException'
+          throwAsCaller(MException('utils:mysql:connect:AccessDenied', '### access denied: %s', message))
+        case 'com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException'
+          throwAsCaller(MException('utils:mysql:connect:ConnectionError', '### connection error: %s. check database name', message))
+        case 'com.mysql.jdbc.exceptions.jdbc4.CommunicationsException'
+          throwAsCaller(MException('utils:mysql:connect:ConnectionError', '### connection error: %s. check hostname', message))
       end
+      % user friendlier exception
+      throwAsCaller(MException('utils:mysql:connect:ConnectionError', '### connection error: %s: %s', id, message))
     end
-    
-    % Create a new login
-    login.hostname = dbhost;
-    login.db       = dbname;
-    login.user     = dbuser;
-    login.passwd   = dbpass;
-    login.ts       = now;
-    
-    % store this login
-    logins = [logins login];
-    
-  else
-    % look for a login to this hostname/db
-    loginFound = false;
-    for kk=1:numel(logins)
-      login = logins(kk);
-      dt = (now - login.ts) * 86400; % [s]
-      if strcmp(login.hostname, dbhost) && strcmp(login.db, dbname)
-        if dt < expTime
-          % get the username and password from here
-          dbuser = login.user;
-          dbpass = login.passwd;
-          logins(kk).ts = now;
-          loginFound = true;
-          break;
-        end
-      end
-    end    
-    
-    % If we didn't find a login then create a new one
-    if force || isempty(dbuser) || isempty(dbpass)
-      [dbuser, dbpass] = getlogin(dbhost, dbname, dbuser, dbpass, force);
-      
-      % Create a new login
-      login.hostname = dbhost;
-      login.db       = dbname;
-      login.user     = dbuser;
-      login.passwd   = dbpass;
-      login.ts       = now;
-      
-      % store this login
-      if ~loginFound
-        logins = [logins login];      
-      end
-    end
-    
+    rethrow(ex);
   end
-  
-  %% return if we don't have a dbuser
-  if isempty(dbuser)
-    return
-  end
-  
-  %% Database settings
-  dbdriver = getappdata(0, 'mysql_driver');
-  dburl    = sprintf('jdbc:mysql://%s/%s',dbhost,dbname);
-
-  disp(sprintf('** Connecting to %s as %s...', dbhost, dbuser))
-
-  conn     = database(dbname,dbuser,dbpass,dbdriver,dburl);
-  disp('** Connection status:')
-  disp(ping(conn))
-
-  % Set outputs
-  if nargout > 0
-    varargout{1} = conn;
-    if nargout == 2
-      varargout{2} = dbpass;
-    end
-  end
-
 end
-
-function [dbuser, dbpass] = getlogin(dbhost, dbname, dbuser, dbpass, force)
-      
-    % first try defaults
-    if isempty(dbuser)
-      dbuser = getappdata(0, 'ltpda_repo_user');
-    end
-    if isempty(dbpass)
-      dbpass = getappdata(0, 'ltpda_repo_pass');
-    end
-    
-    % then log-in dialog
-    if force || isempty(dbuser) || isempty(dbpass)
-
-        ld = logindialog.LoginDialog([], true);
-        ld.setVisible(true)
-        if ~ld.isCancelled
-            dbuser = char(ld.getUsername);
-            dbpass = [char(ld.getPassword)]'; % for some reason we get a column here, so transpose.
-        end
-
-      if isempty(dbuser) || isempty(dbpass)
-        warning('!!! Login process cancelled.');
-        dbuser = -1;
-        dbpass = -1;
-        return
-      end
-    end
-    
-end

--- a/m-toolbox/classes/+utils/@mysql/dbquery.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-% DBQUERY query an AO repository database.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: DBQUERY query an AO repository database.
-%
-% CALL:        info = dbquery(conn);
-%              info = dbquery(conn, query);
-%              info = dbquery(conn, table, query);
-%
-% INPUTS:
-%           conn   - a database connection object such as that returned by
-%                    utils.mysql.connect().
-%           query  - a valid MySQL query string
-%           table  - a table name
-%
-% OUTPUTS:
-%           info - the returned 'info' structure contains the fields from
-%                  each matching record.
-%
-% EXAMPLES:
-%
-%   >> info  = dbquery(conn, 'select * from objmeta where id>1000 and id<2000');
-%   >> info  = dbquery(conn, 'ao',           'id>1000 and id<2000');
-%   >> info  = dbquery(conn, 'objmeta',      'name like "x12"');
-%   >> info  = dbquery(conn, 'users',        'username="aouser"');
-%   >> info  = dbquery(conn, 'collections',  'id=3');
-%   >> info  = dbquery(conn, 'collections',  'obj_ids="1,2"');
-%   >> info  = dbquery(conn, 'transactions', 'user_id=3');
-%   >> info  = dbquery(conn, 'transactions', 'obj_id=56');
-%
-%   >> info  = dbquery(conn)
-%
-%   The 'info' structure will contain a list of the tables in the database.
-%
-%   >> info  = dbquery(conn, query)
-%
-%   The 'info' structure will contain a list of records resulting from the SQL query.
-%
-% VERSION:     $Id: dbquery.m,v 1.2 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     10-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function varargout = dbquery(varargin)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  conn = varargin{1};
-  if ~isa(conn, 'database')
-    error('### First input must be a database connection object.');
-  end
-
-  if nargin == 1
-    % get table list
-    info = getTableList(conn);
-
-  elseif nargin == 2
-    % execute query
-    info = simpleQuery(conn, varargin{2});
-
-  elseif nargin == 3
-    % query a table
-    table    = varargin{2};
-    query    = varargin{3};
-    info = runQuery(conn, table, query);
-  else
-    error('### Incorrect inputs.');
-  end
-
-  varargout{1} = info;
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get table list
-function info = getTableList(conn)
-
-  % open a connection
-  try
-    curs = exec(conn, 'show tables');
-    curs = fetch(curs);
-    info = curs.Data;
-    close(curs);
-  catch
-    error('### Failed to get table list. Server returned: %s', curs.Message);
-  end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get field list
-function info = getFieldList(conn, table)
-
-  try
-    curs = exec(conn, sprintf('describe %s', table));
-    curs = fetch(curs);
-    info = curs.Data;
-    close(curs);
-  catch
-    error('### Failed to get field list. Server returned: %s', curs.Message);
-  end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Get field list
-function info = simpleQuery(conn, q)
-
-  % open a connection
-
-  try
-    curs = exec(conn, sprintf('%s', q));
-    curs = fetch(curs);
-    info = curs.Data;
-    close(curs);
-  catch
-    error('### Failed to execute query. Server returned: %s', curs.Message);
-  end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Run a query
-function info = runQuery(conn, table, query)
-
-  % Run query
-  info = [];
-
-  fieldlist = getFieldList(conn, table);
-  fields  = fieldlist(:,1);
-  f = '';
-  fs = {};
-  for j=1:length(fields)
-    % special cases
-    f  = [f fields{j} ',' ];
-    fs = [fs fields(j)];
-  end
-  q = sprintf('select %s  from %s where %s', f(1:end-1), table, query);
-  disp(['** QUERY: ' q]);
-  try
-    curs = exec(conn, q);
-    curs = fetch(curs);
-    info = curs.Data;
-    close(curs);
-  catch
-    error('### Failed to query table. Server returned: %s', curs.Message);
-  end
-end
-
-

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@mysql/execute.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,108 @@
+function varargout = execute(conn, query, varargin)
+% EXECUTE Execute the given QUERY with optional parameters VARARGIN
+% substituted for the '?' placeholders through connection CONN. In the
+% case of data manupulation queries returns the update count. In case
+% of data retrival queries returns a 2D cell array with the query
+% results and optionally a cell array with column names.
+%
+% CALL:
+%
+%          [rows] = utils.mysql.execute(conn, query, varargin)
+%   [rows, names] = utils.mysql.execute(conn, query, varargin)
+%
+% PARAMETERS:
+%
+%      conn -  an object implementing the java.sql.Connection interface
+%     query -  SQL query string. ? are substituted with PARAMS values
+%  varargin -  query parameters
+%
+% RETURNS:
+%
+%      rows -  update count in the case of data manipulation queries
+%              or 2D cell array with query resutls in the case of
+%              data retrival queries
+%     names -  names of the columns in the result set
+%
+
+  % check parameters
+  if nargin < 2
+    error('### incorrect usage');
+  end
+  if ~isa(conn, 'java.sql.Connection')
+    error('### invalid connection');
+  end
+
+  % build query
+  stmt = conn.prepareStatement(query);
+  for kk = 1:numel(varargin)
+    stmt.setObject(kk, matlab2sql(varargin{kk}));
+  end
+
+  % execute query
+  rv = stmt.execute();
+
+  switch rv
+    case 0
+      % we have an update count
+      varargout{1} = stmt.getUpdateCount();
+    case 1
+      % we have a result set
+      rs = stmt.getResultSet();
+
+      % get results into a cell array
+      md = rs.getMetaData();
+      nc = md.getColumnCount();
+      row = 1;
+      rows = {};
+      while rs.next()
+        for kk = 1:nc
+          % convert to matlab objects
+          rows{row, kk} = java2matlab(rs.getObject(kk));
+        end
+        row = row + 1;
+      end
+
+      % get column names
+      names = cell(1, nc);
+      for kk = 1:nc
+        names{kk} = char(md.getColumnName(kk));
+      end
+
+      % assign output
+      switch nargout
+        case 0
+          varargout{1} = rows;
+        case 1
+          varargout{1} = rows;
+        case 2
+          varargout{1} = names;
+          varargout{2} = rows;
+        otherwise
+          error('### too many output arguments');
+      end
+
+    otherwise
+      erorr('### error');
+  end
+end
+
+
+function val = matlab2sql(val)
+  switch class(val)
+    case 'char'
+      % matlab converts length one strings to the wrong java type
+      val = java.lang.String(val);
+    case 'time'
+      % convert time objects to strings
+      val = val.format('yyyy-mm-dd HH:MM:SS', 'UTC');
+  end
+end
+
+
+function val = java2matlab(val)
+  % matlab converts all base types. just add a conversion for datetime columns
+  switch class(val)
+    case 'java.sql.Timestamp'
+      val = time(plist('time', char(val), 'timezone', 'UTC'));
+  end
+end

--- a/m-toolbox/classes/+utils/@mysql/getAOsInTimeSpan.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,196 +0,0 @@
-% GETAOSINTIMESPAN performs high-level queries to retrieve AOs from an LTPDA repository.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: GETAOSINTIMESPAN performs high-level queries to retrieve AOs
-%              from an LTPDA repository. The AOs for that channel in that time-span
-%              are joined together and then split on the requested
-%              interval. The resulting AO covers the requested interval,
-%              assuming that the repositoy contains a contiguos set of AOs
-%              spanning the requested time.
-%
-% CALL:        b = getAOsInTimeSpan(pl)
-%
-% INPUTS:      pl - a plist containing parameters as described below
-%
-% OUTPUTS:     b  - a vector of AOs resulting from the query
-%
-% PARAMETERS:
-%
-%     choose from
-%              'hostname'       - hostname/IP address of LTPDA Repository
-%              'database'       - the name of the database to query
-%          or
-%              'conn'           - a database connection object
-%
-%    in addition, we need
-%              'binary'         - retrieve binary data (true or false)
-%              'channels'       - a cell array of AO names
-%              'timespan'       - a timespan object to specify the
-%                                 time-interval of interest
-%
-% The timespan is applied start <= data < end.
-%
-% OPTIONAL PARAMETERS:
-%
-%    further restrict the search with the following conditions
-%
-%               'username'   - specify the username of the person who
-%                              submitted the AO
-%               'submitted'  - specify the date the AO was submitted
-%
-% EXAMPLES:
-%
-% 1) Find all AOs which are called 'ChannelX' submitted after 1st May 2007
-%
-%    pl = plist('hostname', 'localhost', 'database', 'ltpda_test', ...
-%               'channels', {'channelX'}, ...
-%               'timespan', timespan('2007-05-01 00:00:00', '3000-01-01 12:34:50', ...
-%               );
-%
-%    a = getAOsInTimeSpan(pl);
-%
-% 2) Find all AOs for ChannelX and ChannelY on 1st May 2007 submitted by
-%    hewitson
-%
-%    pl = plist('hostname', 'localhost', 'database', 'ltpda_test', ...
-%               'channels', {'channelX'}, ...
-%               'timespan', timespan('2007-05-01 00:00:00', '2007-05-02 00:00:00', ...
-%               'username', 'hewitson');
-%
-%    a = getAOsInTimeSpan(pl);
-%
-% VERSION:     $Id: getAOsInTimeSpan.m,v 1.3 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     25-02-08 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function varargout = getAOsInTimeSpan(varargin)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my AO model retrieve_in_timespan');
-  % Collect input ao's, plist's and ao variable names
-  in_names = {};
-  for ii = 1:nargin
-    in_names{end+1} = inputname(ii);
-  end
-  [pl, pl_invars] = utils.helper.collect_objects(varargin(:), 'plist', in_names);
-
-  % Process the input plist
-  conn     = find(pl, 'conn');
-  hostname = find(pl, 'hostname');
-  database = find(pl, 'database');
-  channels = find(pl, 'channels');
-  tspan    = find(pl, 'timespan');
-  useBinary = find(pl, 'binary');
-
-  % Check inputs
-  if isempty(hostname) || ~ischar(hostname)
-    if isempty(conn) || ~isa(conn, 'database')
-      error(sprintf('### Plist should contain ''hostname'' and ''database'' parameters,\n or a ''conn'' parameter.'));
-    end
-  end
-  if isempty(database) || ~ischar(database)
-    if isempty(conn) || ~isa(conn, 'database')
-      error(sprintf('### Plist should contain ''hostname'' and ''database'' parameters,\n or a ''conn'' parameter.'));
-    end
-  end
-  if isempty(channels)
-    error('### Plist should contain a ''channels'' parameter.');
-  end
-  if isempty(tspan) || ~isa(tspan, 'timespan')
-    error('### Plist should contain a ''timespan'' parameter.');
-  end
-
-  % Check the channels value is a cell
-  if ~iscell(channels)
-    channels = {channels};
-  end
-
-  % Get a connection to the database
-  iConnected = 0;
-  if ~isa(conn, 'database')
-    % then we connect
-    try
-      conn = utils.mysql.connect(hostname, database);
-      iConnected = 1;
-    catch
-      error('### Failed to connect to server: %s/%s', hostname, database);
-    end
-  end
-
-  % Collect the data
-  try
-    aout =  hlq(conn, channels, tspan, useBinary);
-  catch
-    lasterr
-    % Do we need to close database connection?
-    if iConnected
-      close(conn);
-    end
-    error('### Error retrieving objects.');
-  end
-
-  % Do we need to close database connection?
-  if iConnected
-    close(conn);
-  end
-
-  % set outputs
-  varargout{1} = aout;
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% A prototype for the kind of high-level query functions we might need
-function objsOut = hlq(conn, channels, ts, useBinary)
-
-  % prepare output
-  objsOut = [];
-
-  % Loop over the channels
-  for j=1:length(channels)
-
-    % this channel
-    channel = channels{j};
-
-    % the query
-    q =      ['select objmeta.obj_id from objmeta,ao,tsdata ' ...
-      'where objmeta.obj_id=ao.obj_id ' ...
-      'and ao.data_id=tsdata.id ' ...
-      sprintf('and objmeta.name=''%s''', channel) ...
-      sprintf('and tsdata.t0+INTERVAL tsdata.nsecs SECOND  >= ''%s''', char(ts.startT)) ...
-      sprintf('and tsdata.t0 <= ''%s''', char(ts.endT))];
-
-    % execute query
-    info = utils.mysql.dbquery(conn, q);
-
-    % collect objects
-    if useBinary
-      objs = ltpda_uo.retrieve(conn, 'binary', [info{:}]);
-    else
-      objs = ltpda_uo.retrieve(conn, [info{:}]);
-    end
-    
-    % join these up
-    ojn = join([objs{:}]);
-
-    % split out the bit we want
-    os = split(ojn, plist('split_type', 'interval', 'timespan', ts));
-
-    % add to outputs
-    objsOut = [objsOut os];
-  end % end loop over channels
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Returns the default plist
-function pl = getDefaultPlist(varargin)
-
-  pl = plist('hostname', 'localhost', ...
-    'database', 'ltpda_test',  ...
-    'channels', {'chan1', 'chan2'}, ...
-    'timespan', timespan('1970-01-01 00:00:00', '2010-10-12 12:45:32') ...
-    );
-end
-
-

--- a/m-toolbox/classes/+utils/@mysql/getMD5hash.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-% GETMD5HASH gets the md5 hash string of a given object ID.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: GETMD5HASH gets the md5 hash string of a given object ID.
-%
-% CALL:        h = getMD5hash(conn, id)
-%
-% VERSION:     $Id: getMD5hash.m,v 1.2 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function h = getMD5hash(conn, id)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  q    = sprintf('select hash from objs where id="%d"', id);
-  curs = exec(conn, q);
-  curs = fetch(curs);
-  h = curs.Data{1};
-  close(curs);
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getMaxId.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-% GETMAXID get the maximum Id from the objs table.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: GETMAXID get the maximum Id from the objs table.
-%
-% CALL:        id = getMaxId()
-%
-% VERSION:     $Id: getMaxId.m,v 1.2 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function id = getMaxId(conn)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  q    = 'select max(id) from objs';
-  curs = exec(conn, q);
-  curs = fetch(curs);
-  id   = curs.Data{1};
-  close(curs);
-
-  if isnan(id)
-    id = 0;
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getObjIds.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-% GETOBJIDS gets a list of object ids from a given collection id.
-%
-% Usage: ids = getObjIds(conn,cid);
-%
-% Inputs:
-%     conn - a database connection object
-%     cid  - a collection id
-%
-% Outputs:
-%     ids  - a list of object ids
-%
-% M Hewitson 30-08-07
-%
-% $Id: getObjIds.m,v 1.2 2010/01/22 12:46:08 ingo Exp $
-%
-
-function ids = getObjIds(conn, cid)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  try
-    curs    = exec(conn, sprintf('select obj_ids from collections where id="%d"', cid));
-    curs    = fetch(curs);
-    ids     = str2num(curs.Data{1});
-    close(curs);
-  catch
-    error('### Unable to determine object IDs from collection ID. Server returned %s', curs.Message);
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getObjType.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-% GETOBJTYPE gets the object type associated with the given object id.
-%
-% Usage: ids = getObjType(conn,id);
-%
-% Inputs:
-%     conn - a database connection object
-%     id   - an object id
-%
-% Outputs:
-%     type - the type of this object
-%
-% M Hewitson 30-08-07
-%
-% $Id: getObjType.m,v 1.2 2010/01/22 12:46:08 ingo Exp $
-%
-
-function type = getObjType(conn, id)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  try
-    curs    = exec(conn, sprintf('select obj_type from objmeta where obj_id="%d"', id));
-    curs    = fetch(curs);
-    type    = curs.Data{1};
-    close(curs);
-  catch
-    warning('!!! Unable to get object type for ID %d. [Server returned: %s]', id, curs.Message);
-    type = '';
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getRepositoryVersion.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-% getRepositoryVersion tries to get the version of the repository by
-% inspecting various fields in the database.
-% 
-% ver = utils.mysql.getRepositoryVersion(conn)
-% 
-% Rules:
-%       objs table contains field 'uuid' => ver = 2.1
-% 
-% else: ver = 2.0;
-% 
-% M Hewitson 11-08-09
-% 
-% $Id: getRepositoryVersion.m,v 1.3 2010/01/22 12:46:08 ingo Exp $
-% 
-
-function ver = getRepositoryVersion(conn)
-  
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  ver = '2.0';
-  
-  q    = ['describe ' conn.Instance '.objs'];
-  curs = exec(conn, q);
-  curs = fetch(curs);
-  
-  if utils.helper.ismember('uuid', curs.Data(:,1))
-    ver = '2.1';
-  end
-  
-  
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getUserID.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-% GETUSERID gets the user ID number corresponding to the given user name.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: GETUSERID gets the user ID number corresponding to the
-%              user name that connected to the MySQL database.
-%
-% CALL:        userid = getUserID(conn)
-%
-% VERSION:     $Id: getUserID.m,v 1.3 2010/01/22 12:46:08 ingo Exp $
-%
-% HISTORY:     24-05-2007 M Hewitson
-%                 Creation
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function [userid,dbuser] = getUserID(conn, username)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-
-  userid = [];
-  try
-    q    = sprintf('select id from users where username="%s"', conn.Username);
-    curs = exec(conn, q);
-    curs = fetch(curs);
-    userid = curs.Data{1};
-    close(curs);
-  catch curs
-    warning('!!! Unable to retrieve user ID. [Server returned: %s]', curs.message);
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getXdoc.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-% GETXDOC retrieves an object with given id from the LTPDA
-% repository specified by the input database connection. The object is
-% converted from its XML text format to an Xdoc. This can then be converted
-% into an object using the appropriate object constructor.
-%
-% Usage: xdoc = getXdoc(conn, id)
-%
-% Inputs:
-%         conn - a database connection object
-%         id   - the object id
-%
-% Outputs:
-%         xdoc - an Xdoc representation of the object.
-%
-% M Hewitson 30-08-07
-%
-% $Id: getXdoc.m,v 1.3 2010/01/22 12:46:08 ingo Exp $
-%
-%
-
-function xdoc = getXdoc(conn, id)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-
-  try
-    curs    = exec(conn, sprintf('select xml from objs where id="%d"', id));
-    curs    = fetch(curs);
-    objTxt  = char([curs.Data{1}].');
-    close(curs);
-  catch
-    error('### Unable to read xml for ID %d. Server returned %s', id, curs.Message);
-  end
-
-  if ~isempty(objTxt) && ~strcmp(objTxt(:), 'No Data')
-    % convert to Java string
-    str = java.lang.String(objTxt);
-    % open stream on this string
-    stream = java.io.StringBufferInputStream(str);
-    % make parser
-    builder = javax.xml.parsers.DocumentBuilderFactory.newInstance.newDocumentBuilder;
-
-    xdoc = builder.parse(stream);
-  else
-    xdoc = [];
-  end
-
-end
-

--- a/m-toolbox/classes/+utils/@mysql/getsinfo.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-% GETSINFO This function returns an sinfo object containing many useful information about an object retrieved from the repository
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% usage:   sinfo = getsinfo(id, conn)
-%
-% inputs:  id    = obj_id from objmeta table
-%          conn  = utils.mysql.connect(server, dbname);
-%
-% outputs: sinfo cell array object containing info about object having the
-%          given obj_id on the repository.
-%          sinfo contains the following fields:
-%          - name
-%          - experiment_title
-%          - experiment_desc
-%          - analysis_desc
-%          - quantity
-%          - additional_authors
-%          - additional_comments
-%          - keywords and reference_ids
-%
-%          A Monsky 05-02-2009
-%
-% version: $Id: getsinfo.m,v 1.6 2011/03/29 13:40:17 hewitson Exp $
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function [varargout] = getsinfo(varargin)
-  
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-
-  import utils.const.*
-  utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename);
-  
-  % Collect input variable names
-  in_names = cell(size(varargin));
-  for ii = 1:nargin,in_names{ii} = inputname(ii);end
-  
-  % Collect all ids and plists and connections
-  pl = utils.helper.collect_objects(varargin(:), 'plist');
-  id = utils.helper.collect_objects(varargin(:), 'double');
-  conn  = utils.helper.collect_objects(varargin(:), 'database');
-  
-  if isempty(conn)
-    error('### This method needs a MATLAB connection.');
-  end
-  
-  if isempty(id)
-    error('### This method needs at least one object id.');
-  end
-  
-  if nargout == 0
-    error('### lscov can not be used as a modifier method. Please give at least one output');
-  end
-  
-  % combine plists
-  pl = combine(pl, plist());
-  
-  % Algorithm
-  % Get complete experiment information for each input id
-  sinfo = [];
-  for ii=1:length(id)
-    qall = ['select name,experiment_title,experiment_desc,analysis_desc,quantity, '...
-      'additional_authors,additional_comments,keywords,reference_ids FROM objmeta ' ...
-      sprintf('where objmeta.obj_id=%d',id(ii))];
-    
-    infoall = utils.mysql.dbquery(conn, qall);
-    s.conn                    = conn;
-    s.name                    = infoall{1};
-    s.experiment_title        = infoall{2};
-    s.experiment_description  = infoall{3};
-    s.analysis_description    = infoall{4};
-    s.quantity                = infoall{5};
-    s.additional_authors      = infoall{6};
-    s.additional_comments     = infoall{7};
-    s.keywords                = infoall{8};
-    s.reference_ids           = infoall{9};
-    sinfo = [sinfo s];
-  end
-  
-  % Set output
-  varargout{1} = sinfo;
-end

--- a/m-toolbox/classes/+utils/@mysql/insert.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-% INSERT inserts values into a single row of a table using JDBC driver
-% specified by the input connection.
-%
-% Usage: message = insert(conn, table, 'field1', value1, 'field2', value2,...)
-%
-% M Hewitson
-%
-% 31-07-07
-%
-% $Id: insert.m,v 1.6 2010/01/22 12:46:08 ingo Exp $
-%
-
-function message = insert(conn, table, varargin)
-
-  error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-  
-  q = sprintf('INSERT INTO %s SET ',  table);
-  
-  for j=1:2:length(varargin)
-    
-    col = varargin{j};
-    val = varargin{j+1};
-    if isnumeric(val)
-      if ~any(isnan(val))
-        q = [q col '=' num2str(val) ','];
-      end
-    elseif ischar(val)
-      q = [q col '=' '''' val '''' ','];
-    else
-      error('### val class [%s]', class(val))
-    end
-        
-  end
-  
-  q = deblank([q(1:end-1) ';']);
-
-  utils.helper.msg(utils.const.msg.PROC1, 'running query %s', q);
-  
-  try
-    curs = exec(conn, q);
-    message = curs.Message;
-    close(curs);
-  catch
-    error('### insert: failed to execute query: %s\nServer returned %s', q, curs.Message);
-  end
-end
-

--- a/m-toolbox/classes/+utils/@mysql/logindlg.m	Tue Dec 06 18:42:11 2011 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-function [varargout]=logindlg(varargin)
-   % LOGINDLG   Dialog for visually secure login.
-   %
-   % Author: Jeremy Smith
-   % Date: September 24, 2005
-   % Last Edit: July 7, 2006
-   % Version: 1.2
-   % Tested on: Matlab 7.0.4.365 (R14) Service Pack 2 and Matlab 7.1 SP 3
-   % Description: custom login dialog because Matlab doesn't have an option
-   %       for characters in an edit field to be replaced by asterixes
-   %       (password security)
-   %
-   % =======================================================================
-   % ============== UPDATED FOR USE WITH LTPDA PACKAGE =====================
-   % =======================================================================
-   %
-   % The function now has a fixed supported syntax to call:
-   %          [login password] = loginLTPDA('userID','password')
-   % or
-   %          [login password] = loginLTPDA('','')
-   %
-   % It will only accept 2 string inputs and it will provide 2 string
-   % outputs.
-   % If 2 empty strings are passed the edit fields will be empty, otherwise
-   % they'll show as defaults the strings passed.
-   %
-   %   $Id: logindlg.m,v 1.4 2010/01/22 12:46:08 ingo Exp $
-
-   error('### Obsolete as of LTPDA version 2.2. Replaced my the utils class jmysql (utils.jmysql.%s)', mfilename());
-   
-   Login    = varargin{1};
-   password = varargin{2};
-   for i=1:numel(password), passwordHidden(i)='*'; end
-   if ~exist('passwordHidden','var'), passwordHidden = ''; end
-
-   set(0,'Units','pixels')
-   Screen = get(0,'screensize');
-   loginSize = [230 130];
-   Position = [(Screen(3)-loginSize(1))/2 (Screen(4)-loginSize(2))/2 loginSize];
-
-
-   % Create the GUI
-   gui.main = dialog('HandleVisibility','on',...
-      'Color','white',...
-      'IntegerHandle','off',...
-      'Menubar','none',...
-      'Name','LTPDA Login',...
-      'NumberTitle','off',...
-      'Name','Login',...
-      'Tag','logindlg',...
-      'Units','pixels',...
-      'Userdata','logindlg',...
-      'Position',Position);
-
-   set(gui.main,'Closerequestfcn',{@Cancel,gui.main},'Keypressfcn',{@Escape,gui.main})
-
-   FONTSIZE = 12;
-   
-   % Texts
-   gui.login_text = uicontrol(gui.main,'Style','text','BackgroundColor','white','FontSize',FONTSIZE,'HorizontalAlign','center','Units','pixels','String','Login','Position',[0 105 Position(3) 20]);
-   gui.password_text = uicontrol(gui.main,'Style','text','BackgroundColor','white','FontSize',FONTSIZE,'HorizontalAlign','center','Units','pixels','String','Password','Position',[0 60 Position(3) 20]);
-
-   % Edits
-   gui.edit1 = uicontrol(gui.main,'Tag','userid','Style','edit','FontSize',FONTSIZE,'HorizontalAlign','center','BackgroundColor','white','Units','pixels','String',Login,'KeyPressfcn',{@KeyPress_Func2,gui.main},'Position',[5 85 Position(3)-10 24],'Userdata',0);
-   gui.edit2 = uicontrol(gui.main,'Tag','password','Style','edit','FontSize',FONTSIZE,'HorizontalAlign','center','BackgroundColor','white','Units','pixels','String',passwordHidden,'Position',[5 40 Position(3)-10 24],'KeyPressfcn',{@KeyPress_Function,gui.main},'Userdata',password);
-
-   % Buttons
-   buttonSize = [75 26];
-   gui.OK = uicontrol(gui.main,'Style','push','FontSize',FONTSIZE,'Units','pixels','String','OK','Position',[Position(3)/2-buttonSize(1)-1 5 buttonSize],'KeyPressFcn',{@OKReturn,gui.main},'Callback',{@OK,gui.main});
-   gui.Cancel = uicontrol(gui.main,'Style','push','FontSize',FONTSIZE,'Units','pixels','String','Cancel','Position',[Position(3)/2+1 5 buttonSize],'KeyPressFcn',{@CancelReturn,gui.main},'Callback',{@Cancel,gui.main});
-
-   % Images
-   logosize = [31,31];
-   dimension = [5 3 logosize];
-   logo = axes('Parent',gui.main,'Units','pixels','Position',dimension);
-   image(imread('buttonyes.jpg'),'Parent',logo);
-   axis(logo,'off');
-   logosize = [31,31];
-   dimension = [Position(3)-logosize(1)-5 3 logosize];
-   logo = axes('Parent',gui.main,'Units','pixels','Position',dimension);
-   image(imread('buttonno.jpg'),'Parent',logo);
-   axis(logo,'off');
-   
-   setappdata(0,'logindlg',gui) % Save handle data
-   setappdata(gui.main,'Check',0) % Error check setup. If Check remains 0 an empty cell array will be returned
-
-   uicontrol(gui.edit1) % Make the first edit box active
-   % uicontrol(gui.OK) % Make the OK button active
-
-   % Pause the GUI and wait for a button to be pressed
-   uiwait(gui.main)
-   
-   try if varargin{3}, welcome2LTPDA(varargin{4},varargin{5}); pause(1); end; catch end
-
-   Check = getappdata(gui.main,'Check'); % Check to see if a button was pressed
-
-   % Format output
-   if Check == 1
-      Login = get(gui.edit1,'String');
-      Password = get(gui.edit2,'Userdata');
-
-      varargout(1) = {Login};
-      varargout(2) = {Password};
-   else % If OK wasn't pressed output empty fields
-      varargout(1) = {''};
-      varargout(2) = {''};
-   end
-
-   delete(gui.main) % Close the GUI
-   setappdata(0,'logindlg',[]) % Erase handles from memory
-
-   %% Hide Password
-function KeyPress_Function(h,eventdata,fig)
-   % Function to replace all characters in the password edit box with
-   % asterixes
-   password = get(h,'Userdata');
-   key = get(fig,'currentkey');
-
-   switch key
-      case 'backspace'
-         password = password(1:end-1); % Delete the last character in the password
-      case 'return'  % This cannot be done through callback without making tab to the same thing
-         gui = getappdata(0,'logindlg');
-         OK([],[],gui.main);
-      case 'tab'  % Avoid tab triggering the OK button
-         gui = getappdata(0,'logindlg');
-         uicontrol(gui.OK);
-      otherwise
-         password = [password get(fig,'currentcharacter')]; % Add the typed character to the password
-   end
-
-   SizePass = size(password); % Find the number of asterixes
-   if SizePass(2) > 0
-      asterix(1,1:SizePass(2)) = '*'; % Create a string of asterixes the same size as the password
-      set(h,'String',asterix) % Set the text in the password edit box to the asterix string
-   else
-      set(h,'String','')
-   end
-
-   set(h,'Userdata',password) % Store the password in its current state
-
-function KeyPress_Func2(h,eventdata,fig)
-   % To check whenever the user press Enter
-   if ~isempty(get(fig,'CurrentCharacter')) && real(get(fig,'CurrentCharacter'))==13 && get(h,'UserData')==0
-      setappdata(fig,'Check',1)
-      uiresume(fig)
-   elseif real(get(fig,'CurrentCharacter'))==13
-      uicontrol(findobj(gcf,'Tag','password'))
-   else
-      set(h,'UserData',1)
-   end
-
-   %% Cancel
-function Cancel(h,eventdata,fig)
-   uiresume(fig)
-
-   %% OK
-function OK(h,eventdata,fig)
-   % Set the check and resume
-   setappdata(fig,'Check',1)
-   uiresume(fig)
-
-function CancelReturn(h,eventdata,fig)
-   if real(get(fig,'CurrentCharacter'))==13
-      uiresume(fig)
-   end
-
-   %% OK
-function OKReturn(h,eventdata,fig)
-   % Set the check and resume
-   if real(get(fig,'CurrentCharacter'))==13
-      setappdata(fig,'Check',1)
-      uiresume(fig)
-   end
-
-   %% Escape
-function Escape(h,eventdata,fig)
-   % Close the login if the escape button is pushed and neither edit box is
-   % active
-   key = get(fig,'currentkey');
-
-   if isempty(strfind(key,'escape')) == 0 && h == fig
-      Cancel([],[],fig)
-   end
\ No newline at end of file

--- a/m-toolbox/classes/+utils/@mysql/mysql.m	Tue Dec 06 18:42:11 2011 +0100
+++ b/m-toolbox/classes/+utils/@mysql/mysql.m	Tue Dec 06 19:07:22 2011 +0100
@@ -1,73 +1,11 @@
-% MYSQL class for tools to manipulate the current object/figure/axis.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% DESCRIPTION: MYSQL class for tools to manipulate the current
-%              object/figure/axis.
-%
-% MYSQL METHODS:
-%
-%     Static methods:
-%       yticks      - Set the input vector as the y-ticks of the current axis
-%       %%% GENERAL TOOLS
-%       logindlg          - creates a login dialog box.
-%       dbquery           - query an AO repository database.
-%       getAOsInTimeSpan  - performs high-level queries to retrieve AOs from
-%                           a LTPDA repository.
-%       insert            - inserts values into a single row of a table using
-%                           JDBC driver specified by the input connection.
-%
-%       %%% MYSQL TOOLS
-%       connect           - connects to an LTPDA repository and returns
-%                           the connection object.
-%       getMaxId          - get the maximum Id from the objs table.
-%       getMD5hash        - gets the md5 hash string of a given object ID.
-%       getObjIds         - gets a list of object ids from a given collection id.
-%       getObjType        - gets the object type associated with the given object id.
-%       getUserID         - gets the user ID number corresponding to the given
-%                           user name.
-%       getXdoc           - retrieves an object with given id from the
-%                           LTPDA repository
-%
-% HELP:        To see the available static methods, call
-%              >> methods utils.mysql
-%
-% HISTORY:     26-05-2008 Diepholz
-%                 Creation
-%
-% VERSION:     $Id: mysql.m,v 1.3 2009/08/11 12:02:46 hewitson Exp $
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+classdef mysql
+% UTILS.MYSQL  MySQL database utilities.
 
-classdef mysql
-
-  %------------------------------------------------
-  %--------- Declaration of Static methods --------
-  %------------------------------------------------
   methods (Static)
 
-    %-------------------------------------------------------------
-    % List other methods
-    %-------------------------------------------------------------
+    conn = connect(hostname, database, username, password);
+    varargout = execute(conn, query, varargin);
 
-    %%% GENERAL TOOLS
-	varargout = getsinfo(varargin) % return sinfo structure of repository object
-    varargout = logindlg(varargin) % creates a login dialog box.
-    varargout = dbquery(varargin)  % query an AO repository database.
-    varargout = getAOsInTimeSpan(varargin) % performs high-level queries to retrieve AOs from an LTPDA repository.
-    message   = insert(conn, table, varargin) % inserts values into a single row of a table using JDBC driver specified by the input connection.
-    varargout = getRepositoryVersion(varargin);
-    
-    
-    %%% MYSQL TOOLS
-    varargout = connect(varargin) % connects to an LTPDA repository and returns the connection object.
-    id   = getMaxId(conn)         % get the maximum Id from the objs table.
-    h    = getMD5hash(conn, id)   % gets the md5 hash string of a given object ID.
-    ids  = getObjIds(conn, cid)   % gets a list of object ids from a given collection id.
-    type = getObjType(conn, id)   % gets the object type associated with the given object id.
-    [userid,dbuser] = getUserID(conn, username) % gets the user ID number corresponding to the given user name.
-    xdoc = getXdoc(conn, id)      % retrieves an object with given id from the LTPDA repository
-
-  end % End static methods
+  end % static methods
 
 end
-

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@repository/adjustPlist.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,37 @@
+function adjustPlist(conn, pl)
+% ADJUSTPLIST(CONN, PL) Removes CONN, USERNAME, PASSWORD parameters
+% from plist PL, and adds or or substitutes HOSTNAME and DATABASE
+% parameters with the ones used to establish connection CONN.
+%
+% The resulting plist may be used to set object history.
+
+  % check parameters
+  if ~isa(conn, 'java.sql.Connection')
+    error('### invalid call');
+  end
+  if ~isa(pl, 'plist')
+    error('### invalid call');
+  end
+
+  % get connection parameters
+  r = '^jdbc:mysql://(?<hostname>.+)/(?<database>.+)$';
+  c = regexp(char(conn.getMetaData().getURL()), r, 'names');
+
+  % remove unwanted parameters
+  prem(pl, 'conn');
+  prem(pl, 'username');
+  prem(pl, 'password');
+
+  % add essentials connections parameters
+  pset(pl, 'hostname', c.hostname);
+  pset(pl, 'database', c.database);
+
+end
+
+
+function prem(pl, key)
+% PREM Remove parameter KEY if present in plist PL.
+  if isparam(pl, key)
+    remove(pl, key);
+  end
+end

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@repository/getCollectionIDs.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,26 @@
+function ids = getCollectionIDs(conn, cid)
+% GETCOLLECTIONIDS  Return the IDs of the object composing a collection.
+%
+% CALL:
+%
+%   ids = utils.repository.getCollectionIDs(conn, cid)
+%
+% PARAMETERS:
+%
+%   CONN   database connection implementing java.sql.Connection
+%   CID    collection id
+%
+
+  rows = utils.mysql.execute(conn, 'SELECT nobjs, obj_ids FROM collections WHERE id = ?', cid);
+  if isempty(rows)
+    error('### collection %d not found', cid);
+  end
+  nobjs = rows{1};
+  ids = strread(rows{2}, '%d', 'delimiter', ',');
+  if length(ids) ~= nobjs
+    error('### inconsistent collection description');
+  end
+  % transform column vector in row vector
+  ids = ids';
+  
+end

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@repository/getObjectType.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,20 @@
+function type = getObjectType(conn, id)
+% GETOBJECTTYPE  Return the type of the object.
+%
+% CALL:
+%
+%   ids = utils.repository.getObjectType(conn, cid)
+%
+% PARAMETERS:
+%
+%   CONN   database connection implementing java.sql.Connection
+%   ID     object id
+%
+
+  rows = utils.mysql.execute(conn, 'SELECT obj_type FROM objmeta WHERE obj_id = ?', id);
+  if isempty(rows)
+    error('### object %d not found', id);
+  end
+  type = rows{1};
+  
+end

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@repository/getUser.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,20 @@
+function [username, userid] = getUser(conn)
+% GETUSER  Return username and userid of the current database user.
+%
+% CALL:
+%
+%   [username, userid] = utils.repository.getUser(conn)
+%
+
+  % current database user
+  rows = utils.mysql.execute(conn, 'SELECT SUBSTRING_INDEX(USER(),''@'',1)');
+  username = rows{1};
+
+  % userid
+  rows = utils.mysql.execute(conn, 'SELECT id FROM users WHERE username = ?', username);
+  if isempty(rows)
+    error('### could not determine user id');
+  end
+  userid = rows{1};
+
+end

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/m-toolbox/classes/+utils/@repository/insertObjMetadata.m	Tue Dec 06 19:07:22 2011 +0100
@@ -0,0 +1,124 @@
+function insertObjMetadata(conn, obj, objid)
+% an utility to insert entries for various object metadata in the
+% corresponding tables. differs from insertObjMetadataV1() by
+% the use of the new v3.0 database structure
+%
+% MUST BE KEPT IN SYNC WITH updateObjMetadata()
+%
+% conn   - Java database connection object
+% obj    - object
+% objid  - unique ID of the object in the database
+%
+% VERSION:     $Id: insertObjMetadata.m,v 1.9 2011/11/09 18:45:14 mauro Exp $
+%
+
+  import utils.const.*
+
+  if nargin < 3
+    error('### incorrect usage');
+  end
+  if ~isjava(conn)
+    error('### incorrect usage');
+  end
+
+  % class of object
+  cl = class(obj);
+  utils.helper.msg(msg.PROC2, 'making meta data entry for %s object', cl);
+
+  switch cl
+    case 'ao'
+
+      % call recursively to insert the data object info
+      utils.repository.insertObjMetadata(conn, obj.data, objid);
+
+      % insert the AO info
+      stmt = conn.prepareStatement(...
+        'INSERT INTO ao (obj_id, data_type, description) VALUES (?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(class(obj.data)));
+      
+      desc = obj.description;
+      if length(desc)>65535
+        warning('Object description length exceeded. Truncating to 65535 characters');
+        desc = desc(1:65535);
+      end
+      stmt.setObject(3, java.lang.String(desc));
+      stmt.execute();
+      stmt.close();
+
+    case 'cdata'
+
+      stmt = conn.prepareStatement(...
+        'INSERT INTO cdata (obj_id, yunits) VALUES (?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(char(obj.yunits)));
+      stmt.execute();
+      stmt.close();
+
+    case 'fsdata'
+
+      % possible bad entries
+      fs = obj.fs;
+      if ~isfinite(fs)
+        fs = [];
+      end
+        
+      stmt = conn.prepareStatement(...
+        'INSERT INTO fsdata (obj_id, xunits, yunits, fs) VALUES (?, ?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(char(obj.xunits)));
+      stmt.setObject(3, java.lang.String(char(obj.yunits)));
+      stmt.setObject(4, fs);
+      stmt.execute();
+      stmt.close();
+
+    case 'tsdata'
+
+      stmt = conn.prepareStatement(...
+        'INSERT INTO tsdata (obj_id, xunits, yunits, fs, t0, nsecs, toffset) VALUES (?, ?, ?, ?, ?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(char(obj.xunits)));
+      stmt.setObject(3, java.lang.String(char(obj.yunits)));
+      stmt.setObject(4, obj.fs);
+      stmt.setObject(5, java.lang.String(format(obj.t0 + obj.toffset/1000, 'yyyy-mm-dd HH:MM:SS', 'UTC')));
+      stmt.setObject(6, obj.nsecs);
+      stmt.setObject(7, obj.toffset);
+      stmt.execute();
+      stmt.close();
+
+    case 'xydata'
+
+      stmt = conn.prepareStatement(...
+        'INSERT INTO xydata (obj_id, xunits, yunits) VALUES (?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(char(obj.xunits)));
+      stmt.setObject(3, java.lang.String(char(obj.yunits)));
+      stmt.execute();
+      stmt.close();
+
+    case 'mfir'
+
+      stmt = conn.prepareStatement(...
+        'INSERT INTO mfir (obj_id, in_file, fs) VALUES (?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(obj.infile));
+      stmt.setObject(3, obj.fs);
+      stmt.execute();
+      stmt.close();
+
+    case 'miir'
+
+      stmt = conn.prepareStatement(...
+        'INSERT INTO miir (obj_id, in_file, fs) VALUES (?, ?, ?)');
+      stmt.setObject(1, objid);
+      stmt.setObject(2, java.lang.String(obj.infile));
+      stmt.setObject(3, obj.fs);
+      stmt.execute();
+      stmt.close();
+
+    otherwise
+      utils.helper.msg(msg.PROC2, 'no meta data table for %s object', cl);
+
+  end
+
+end