ltpda: m-toolbox/classes/@ltpda_uo/submit.m comparison

comparison m-toolbox/classes/@ltpda_uo/submit.m @ 20:d58813ab1b92 database-connection-manager

Update ltpda_uo.submit

author	Daniele Nicolodi <nicolodi@science.unitn.it>
date	Mon, 05 Dec 2011 16:20:06 +0100
parents	f0afece42f48
children	ca0b8d4dcdb6

comparison

equal deleted inserted replaced

-:69e3d49b4b0c
+:d58813ab1b92
 % new table in the database. Then this list is passed to validate so that
 % if the 'validate' plist option (which needs to be added) is set to true,
 % then we call validate on the object before submitting. If validate is
 % true, then we set the validated flag in the database after submission if
 % it passes.
 %
 %
 function varargout = submit(varargin)
 % check if this is a call for parameters
 if utils.helper.isinfocall(varargin{:})
 varargout{1} = getInfo(varargin{3});
 return
 end
 import utils.const.*
 utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename);
 % collect all AOs
 [pls,   invars, rest] = utils.helper.collect_objects(varargin(:), 'plist');
 [sinfo, invars, objs] = utils.helper.collect_objects(rest(:),    'struct');
 % identify plists which are only used for the submission process
 mask = false(numel(pls), 1);
 for ii = 1:numel(pls)
 if ~utils.helper.isSubmissionPlist(pls(ii))
 mask(ii) = true;
 end
 % keep all the other as parameters plist
 if sum(~mask)
 pls = combine(pls(~mask));
 end
 % rearrange nested objects lists into a single cell array
 objs = flatten(objs);
 if isempty(objs)
 error('### input at least one object to submit to the repository');
 end
 % combine user plist with default
 pls = fixPlist(pls);
 dpl = getDefaultPlist();
 pls = combine(pls, dpl.pset('HOSTNAME', ''));
 % for backwards compatibility convert any user supplied sinfo-structure into a plist
 pls = ltpda_uo.convertSinfo2Plist(pls, sinfo);
 % read XML submission informations file
 filename = pls.find('sinfo filename');
 if ~isempty(filename)
 try
 pl = fixPlist(utils.xml.read_sinfo_xml(filename));
 pls = combine(pl, pls);
 catch err
 error('### unable to read specified file: %s', filename);
 end
 end
 % collect additional informations
 sinfo = ltpda_uo.submitDialog(pls);
 if isempty(sinfo)
 [varargout{1}, varargout{2}] = userCanceled();
 return
 end
 % check completeness of user supplied informations
 sinfo = checkSinfo(sinfo);
-% user supplied connection
+% database connection
-conn = find(pls, 'conn');
+c = LTPDADatabaseConnectionManager().connect(pls);
-% obtain a connection from the connection manager
-rm = LTPDARepositoryManager();
-if isempty(conn)
-connections = rm.findConnections(pls);
-if isempty(connections)
-% no connection found. create a new one
-conn = rm.newConnection(pls);
-if isempty(conn)
-[varargout{1}, varargout{2}] = userCanceled();
-return
-end
-elseif numel(connections) == 1 && ~utils.prog.yes2true(pls.find('use selector'))
-% found only one connection and we are not forcing the use of the selector
-conn = connections(1);
-else
-% make the user select the desired database connection
-conn = rm.manager.selectConnection([]);
-if isempty(conn)
-[varargout{1}, varargout{2}] = userCanceled();
-return
-end
-end
-end
-% avoid to ask for a password if one was specified in the plist
-if isjava(conn) && ~conn.isConnected()
-passwd = pls.find('password');
-if ~isempty(passwd)
-conn.setPassword(passwd);
-end
-end
-% connect to the database
-if isempty(conn.openConnection())
-error('### unable to connect to the database')
-end
 utils.helper.msg(msg.PROC1, 'submitting %d objects to repository', numel(objs));
 try
-% lock connection to avoid expire during processing
+% get username and userid
-conn.setLocked(true);
+[username, userid] = utils.repository.getUser(c);
-% reload connection table if we have a GUI
-if ~isempty(rm.gui)
-rm.gui.reloadConnectionTable();
-end
-% look-up user id
-userid   = utils.jmysql.getUserID(conn);
-username = conn.getUsername();
-utils.helper.msg(msg.PROC1, 'got user id %d for user: %s', userid, char(username));
-if userid < 1 || isnan(userid)  || strcmp(userid, 'No Data') || ischar(userid)
-error('### Unknown username.');
-end
 % author of the data: let's take the username
 author = username;
 % date for the transaction.transdata and objmeta.submitted columns as UTC time string
 t     = time();
 tdate = format(t, 'yyyy-mm-dd HH:MM:SS', 'UTC');
 % machine details
 prov = provenance();
-utils.helper.msg(msg.IMPORTANT, 'submitting to %s@%s:%s', ...
-char(conn.getUsername), char(conn.getHostname), char(conn.getDatabase));
-% obtain the underlying connection
-c = conn.getConn();
 % start a transaction. either we submitt all objects or we roll back all changes
 c.setAutoCommit(false);
 % process each object and collect id numbers
 ids = zeros(numel(objs), 1); cid = [];
 for kk = 1:numel(objs)
 % this object
 obj = objs{kk};
 utils.helper.msg(msg.PROC1, 'submitting object: %s / %s', class(obj), obj.name);
 % format object creation time as UTC time string
 if isa(obj, 'plist')
 % plist-objects stores creatins time as milli secs since the epoch
 created = time().format('yyyy-mm-dd HH:MM:SS', 'UTC');
 else
 created = obj.created.format('yyyy-mm-dd HH:MM:SS', 'UTC');
 end
 % Set the UUID if it is empty. This should only happen for PLIST
 % objects.
 if isempty(obj.UUID)
 obj.UUID = char(java.util.UUID.randomUUID);
 end
 % create an XML representaion of the object
 if utils.prog.yes2true(pls.find('binary'));
 utils.helper.msg(msg.PROC2, 'binary submit');
 otxt = ['binary submit ' datestr(now)];
 else
 utils.helper.msg(msg.PROC2, 'xml submit');
 otxt = utils.prog.obj2xml(obj);
 end
 % create an MD5 hash of the xml representation
 md5hash = utils.prog.hash(otxt, 'MD5');
 % create a binary representaion of the object
 bobj = utils.prog.obj2binary(obj);
 if isempty(bobj)
 error('### failed to obtain a binary representation');
 end
 % submit object to objs table
 stmt = c.prepareStatement(...
 'INSERT INTO objs (xml, hash, uuid) VALUES (?, ?, ?)');
 stmt.setObject(1, otxt);
 stmt.setObject(2, char(md5hash));
 stmt.setObject(3, obj.UUID);
 stmt.executeUpdate();
 % obtain object id
 rs = stmt.getGeneratedKeys();
 if rs.next()
 objid = rs.getInt(1);
 else
 objid = [];
 end
 rs.close();
 stmt.close();
 % insert binary representation
 stmt = c.prepareStatement(...
 'INSERT INTO bobjs (obj_id, mat) VALUES (?,?)');
 stmt.setObject(1, objid);
 stmt.setObject(2, bobj);
 stmt.execute();
 stmt.close();
 % reference IDs are stored in a CSV string
 if ischar(sinfo.reference_ids)
 refids = sinfo.reference_ids;
 else
 refids = utils.prog.csv(sinfo.reference_ids);
 end
 % insert object meta data
 stmt = c.prepareStatement(...
 [ 'INSERT INTO objmeta (obj_id, obj_type, name, created, version, ' ...
 'ip, hostname, os, submitted, experiment_title, experiment_desc, ' ...
 'reference_ids, additional_comments, additional_authors, keywords, ' ...
 stmt.setObject(16, java.lang.String(sinfo.quantity));
 stmt.setObject(17, java.lang.String(sinfo.analysis_description));
 stmt.setObject(18, java.lang.String(author));
 stmt.execute();
 stmt.close();
 % update other meta-data tables
-cols = utils.jmysql.execute(c, 'SHOW COLUMNS FROM tsdata');
+cols = utils.mysql.execute(c, 'SHOW COLUMNS FROM tsdata');
 if utils.helper.ismember('obj_id',  cols(:,1))
 % the tsdata table contains an obj id column. use the new database schema
-utils.jmysql.insertObjMetadata(c, obj, objid);
+utils.repository.insertObjMetadata(c, obj, objid);
 else
 % otherwise use the old one
 utils.helper.msg(msg.PROC2, 'using back-compatibility code');
-utils.jmysql.insertObjMetadataV1(c, obj, objid);
+utils.repository.insertObjMetadataV1(c, obj, objid);
 end
 % update transactions table
 stmt = c.prepareStatement(...
 'INSERT INTO transactions (obj_id, user_id, transdate, direction) VALUES (?, ?, ?, ?)');
 stmt.setObject(1, objid);
 stmt.setObject(2, userid);
 stmt.setObject(3, java.lang.String(tdate));
 stmt.setObject(4, java.lang.String('in'));
 stmt.execute();
 stmt.close();
 % collect the id of the submitted object
 ids(kk) = objid;
 end
 % make collection entry
 if numel(objs) > 1
 % insert record into collections table
 stmt = c.prepareStatement(...
 'INSERT INTO collections (nobjs, obj_ids) VALUES (?, ?)');
 stmt.setObject(1, length(ids));
 stmt.setObject(2, java.lang.String(utils.prog.csv(ids)));
 stmt.executeUpdate();
 % obtain collection id
 rs = stmt.getGeneratedKeys();
 if rs.next()
 cid = rs.getInt(1);
 else
 cid = [];
 end
 rs.close();
 stmt.close();
 end
 catch ex
 utils.helper.msg(msg.IMPORTANT, 'submission error. no object submitted')
 c.close()
-conn.setLocked(false);
 rethrow(ex)
 end
 % commit the transaction
 c.commit();
+% close the connection if we own it
+if isempty(find(pls, 'conn'))
+c.close();
+end
 % report IDs of the inserted objects
 for kk = 1:numel(objs)
-utils.helper.msg(msg.IMPORTANT, 'submitted %s object with ID: %d, UUID: %s, name: %s', ...
+utils.helper.msg(msg.IMPORTANT, 'submitted %s object with ID: %d UUID: %s name: %s', ...
 class(objs{kk}), ids(kk), objs{kk}.UUID, objs{kk}.name);
 end
 if ~isempty(cid)
 utils.helper.msg(msg.IMPORTANT, 'made collection entry with ID: %d', cid);
 end
-% unlock connection expire
-conn.setLocked(false);
-% reset timer
-LTPDARepositoryManager.resetTimer(rm.timerClearPass, conn);
-LTPDARepositoryManager.resetTimer(rm.timerDisconnect, conn);
 % pass back outputs
 if nargout > 0
 varargout{1} = ids;
 end
 if nargout > 1
 end
 function sinfo = checkSinfo(sinfo)
 % check sinfo structure
 import utils.const.*
 % fieldnames
 mainfields = {'experiment_title', 'experiment_description', 'analysis_description'};
 extrafields = {'quantity', 'keywords', 'reference_ids', 'additional_comments', 'author', 'additional_authors'};
 % fieldnames of the input structure
 fnames = fieldnames(sinfo);
 % check mandatory fields
 for jj = 1:length(mainfields)
 if ~ismember(fnames, mainfields{jj})
 error('### the sinfo structure should contain a ''%s'' field', mainfields{jj});
 end
 end
 % check extra fields
 for jj = 1:length(extrafields)
 if ~ismember(fnames, extrafields{jj})
 utils.helper.msg(msg.PROC2, 'setting default for field %s', extrafields{jj});
 sinfo.(extrafields{jj}) = '';
 end
 end
 % additional checks
 if length(sinfo.experiment_title) < 5
 error('### ''experiment title'' should be at least 5 characters long');
 end
 if length(sinfo.experiment_description) < 10
 error('### ''experiment description'' should be at least 10 characters long');
 end
 if length(sinfo.analysis_description) < 10
 error('### ''analysis description'' should be at least 10 characters long');
 end
 end
 function ii = getInfo(varargin)
 if nargin == 1 && strcmpi(varargin{1}, 'None')
 end
 plout = pl;
 end
 function plo = buildplist()
 plo = plist.TO_REPOSITORY_PLIST;
 p = param({'sinfo filename', 'Path to an XML file containing submission metadata'}, paramValue.EMPTY_STRING);
 plo.append(p);
 p = param({'binary', 'Submit only binary version of the objects'}, paramValue.FALSE_TRUE);
 plo.append(p);
 end
 end
 function flat = flatten(objs)
 % flatten nested lists into a single cell array
 flat = {};
 while iscell(objs) && numel(objs) == 1
 objs = objs{1};
 end
 if numel(objs) == 1
 flat = {objs};
 return;
 end
 for jj = 1:numel(objs)
 obj = flatten(objs(jj));
 for kk = 1:numel(obj)
 flat = [ flat obj(kk) ];
 end
 end
 end

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comparison m-toolbox/classes/@ltpda_uo/submit.m @ 20:d58813ab1b92 database-connection-manager