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author Daniele Nicolodi <nicolodi@science.unitn.it>
date Wed, 23 Nov 2011 19:22:13 +0100
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1 % SUBMIT Submits the given objects to an LTPDA repository
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % DESCRIPTION: Submits the given objects to an LTPDA repository. If multiple
5 % objects are submitted together a corresponding collection entry will be made.
6 %
7 % If not explicitly disabled the user will be prompt for entering submission
8 % metadata and for chosing the database where to submit the objects.
9 %
10 % CALL: [IDS, CIDS] = submit(O1, PL)
11 % [IDS, CIDS] = submit(O1, O2, PL)
12 %
13 % INPUTS: O1, O2, ... - objects to be submitted
14 % PL - plist whih submission and repository informations
15 %
16 % OUTPUTS: IDS - IDs assigned to the submitted objects
17 % CID - ID of the collection entry
18 %
19 % <a href="matlab:utils.helper.displayMethodInfo('ltpda_uo', 'submit')">Parameters Description</a>
20 %
21 % METADATA:
22 %
23 % 'experiment title' - title for the submission (required >4 characters)
24 % 'experiment description' - description of this submission (required >10 characters)
25 % 'analysis description' - description of the analysis performed (required >10 characters)
26 % 'quantity' - the physical quantity represented by the data
27 % 'keywords' - comma-delimited list of keywords
28 % 'reference ids' - comma-delimited list object IDs
29 % 'additional comments' - additional comments
30 % 'additional authors' - additional author names
31 %
32 % VERSION: $Id: submit.m,v 1.91 2011/11/18 08:08:26 mauro Exp $
33 %
34 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
35
36
37 % Notes on submission
38 %
39 % We can check ask the database for a list of allowed modules. This needs a
40 % new table in the database. Then this list is passed to validate so that
41 % if the 'validate' plist option (which needs to be added) is set to true,
42 % then we call validate on the object before submitting. If validate is
43 % true, then we set the validated flag in the database after submission if
44 % it passes.
45 %
46 %
47
48
49 function varargout = submit(varargin)
50
51 % check if this is a call for parameters
52 if utils.helper.isinfocall(varargin{:})
53 varargout{1} = getInfo(varargin{3});
54 return
55 end
56
57 import utils.const.*
58 utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename);
59
60 % collect all AOs
61 [pls, invars, rest] = utils.helper.collect_objects(varargin(:), 'plist');
62 [sinfo, invars, objs] = utils.helper.collect_objects(rest(:), 'struct');
63
64 % identify plists which are only used for the submission process
65 mask = false(numel(pls), 1);
66 for ii = 1:numel(pls)
67 if ~utils.helper.isSubmissionPlist(pls(ii))
68 mask(ii) = true;
69 end
70 end
71 % add all plist that do not look to contain parameters for the
72 % submission to the list of objects submitted to the repository
73 if sum(mask)
74 objs = [objs, {pls(mask)}];
75 end
76 % keep all the other as parameters plist
77 if sum(~mask)
78 pls = combine(pls(~mask));
79 end
80
81 % rearrange nested objects lists into a single cell array
82 objs = flatten(objs);
83
84 if isempty(objs)
85 error('### input at least one object to submit to the repository');
86 end
87
88 % combine user plist with default
89 pls = fixPlist(pls);
90 dpl = getDefaultPlist();
91 pls = combine(pls, dpl.pset('HOSTNAME', ''));
92
93 % for backwards compatibility convert any user supplied sinfo-structure into a plist
94 pls = ltpda_uo.convertSinfo2Plist(pls, sinfo);
95
96 % read XML submission informations file
97 filename = pls.find('sinfo filename');
98 if ~isempty(filename)
99 try
100 pl = fixPlist(utils.xml.read_sinfo_xml(filename));
101 pls = combine(pl, pls);
102 catch err
103 error('### unable to read specified file: %s', filename);
104 end
105 end
106
107 % collect additional informations
108 sinfo = ltpda_uo.submitDialog(pls);
109 if isempty(sinfo)
110 [varargout{1}, varargout{2}] = userCanceled();
111 return
112 end
113
114 % check completeness of user supplied informations
115 sinfo = checkSinfo(sinfo);
116
117 % user supplied connection
118 conn = find(pls, 'conn');
119
120 % obtain a connection from the connection manager
121 rm = LTPDARepositoryManager();
122
123 if isempty(conn)
124 connections = rm.findConnections(pls);
125 if isempty(connections)
126 % no connection found. create a new one
127 conn = rm.newConnection(pls);
128 if isempty(conn)
129 [varargout{1}, varargout{2}] = userCanceled();
130 return
131 end
132 elseif numel(connections) == 1 && ~utils.prog.yes2true(pls.find('use selector'))
133 % found only one connection and we are not forcing the use of the selector
134 conn = connections(1);
135 else
136 % make the user select the desired database connection
137 conn = rm.manager.selectConnection([]);
138 if isempty(conn)
139 [varargout{1}, varargout{2}] = userCanceled();
140 return
141 end
142 end
143 end
144
145 % avoid to ask for a password if one was specified in the plist
146 if isjava(conn) && ~conn.isConnected()
147 passwd = pls.find('password');
148 if ~isempty(passwd)
149 conn.setPassword(passwd);
150 end
151 end
152
153 % connect to the database
154 if isempty(conn.openConnection())
155 error('### unable to connect to the database')
156 end
157
158 utils.helper.msg(msg.PROC1, 'submitting %d objects to repository', numel(objs));
159
160 try
161 % lock connection to avoid expire during processing
162 conn.setLocked(true);
163
164 % reload connection table if we have a GUI
165 if ~isempty(rm.gui)
166 rm.gui.reloadConnectionTable();
167 end
168
169 % look-up user id
170 userid = utils.jmysql.getUserID(conn);
171 username = conn.getUsername();
172
173 utils.helper.msg(msg.PROC1, 'got user id %d for user: %s', userid, char(username));
174 if userid < 1 || isnan(userid) || strcmp(userid, 'No Data') || ischar(userid)
175 error('### Unknown username.');
176 end
177
178 % author of the data: let's take the username
179 author = username;
180
181 % date for the transaction.transdata and objmeta.submitted columns as UTC time string
182 t = time();
183 tdate = format(t, 'yyyy-mm-dd HH:MM:SS', 'UTC');
184
185 % machine details
186 prov = provenance();
187
188 utils.helper.msg(msg.IMPORTANT, 'submitting to %s@%s:%s', ...
189 char(conn.getUsername), char(conn.getHostname), char(conn.getDatabase));
190
191 % obtain the underlying connection
192 c = conn.getConn();
193
194 % start a transaction. either we submitt all objects or we roll back all changes
195 c.setAutoCommit(false);
196
197 % process each object and collect id numbers
198 ids = zeros(numel(objs), 1); cid = [];
199 for kk = 1:numel(objs)
200
201 % this object
202 obj = objs{kk};
203
204 utils.helper.msg(msg.PROC1, 'submitting object: %s / %s', class(obj), obj.name);
205
206 % format object creation time as UTC time string
207 if isa(obj, 'plist')
208 % plist-objects stores creatins time as milli secs since the epoch
209 created = time().format('yyyy-mm-dd HH:MM:SS', 'UTC');
210 else
211 created = obj.created.format('yyyy-mm-dd HH:MM:SS', 'UTC');
212 end
213
214 % Set the UUID if it is empty. This should only happen for PLIST
215 % objects.
216 if isempty(obj.UUID)
217 obj.UUID = char(java.util.UUID.randomUUID);
218 end
219
220 % create an XML representaion of the object
221 if utils.prog.yes2true(pls.find('binary'));
222 utils.helper.msg(msg.PROC2, 'binary submit');
223 otxt = ['binary submit ' datestr(now)];
224 else
225 utils.helper.msg(msg.PROC2, 'xml submit');
226 otxt = utils.prog.obj2xml(obj);
227 end
228
229 % create an MD5 hash of the xml representation
230 md5hash = utils.prog.hash(otxt, 'MD5');
231
232 % create a binary representaion of the object
233 bobj = utils.prog.obj2binary(obj);
234 if isempty(bobj)
235 error('### failed to obtain a binary representation');
236 end
237
238 % submit object to objs table
239 stmt = c.prepareStatement(...
240 'INSERT INTO objs (xml, hash, uuid) VALUES (?, ?, ?)');
241 stmt.setObject(1, otxt);
242 stmt.setObject(2, char(md5hash));
243 stmt.setObject(3, obj.UUID);
244 stmt.executeUpdate();
245
246 % obtain object id
247 rs = stmt.getGeneratedKeys();
248 if rs.next()
249 objid = rs.getInt(1);
250 else
251 objid = [];
252 end
253 rs.close();
254 stmt.close();
255
256 % insert binary representation
257 stmt = c.prepareStatement(...
258 'INSERT INTO bobjs (obj_id, mat) VALUES (?,?)');
259 stmt.setObject(1, objid);
260 stmt.setObject(2, bobj);
261 stmt.execute();
262 stmt.close();
263
264 % reference IDs are stored in a CSV string
265 if ischar(sinfo.reference_ids)
266 refids = sinfo.reference_ids;
267 else
268 refids = utils.prog.csv(sinfo.reference_ids);
269 end
270
271 % insert object meta data
272 stmt = c.prepareStatement(...
273 [ 'INSERT INTO objmeta (obj_id, obj_type, name, created, version, ' ...
274 'ip, hostname, os, submitted, experiment_title, experiment_desc, ' ...
275 'reference_ids, additional_comments, additional_authors, keywords, ' ...
276 'quantity, analysis_desc, author) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)' ]);
277 stmt.setObject( 1, objid);
278 stmt.setObject( 2, java.lang.String(class(obj)));
279 stmt.setObject( 3, java.lang.String(obj.name));
280 stmt.setObject( 4, java.lang.String(created));
281 stmt.setObject( 5, java.lang.String(getappdata(0, 'ltpda_version')));
282 stmt.setObject( 6, java.lang.String(prov.ip));
283 stmt.setObject( 7, java.lang.String(prov.hostname));
284 stmt.setObject( 8, java.lang.String(prov.os));
285 stmt.setObject( 9, java.lang.String(tdate));
286 stmt.setObject(10, java.lang.String(sinfo.experiment_title));
287 stmt.setObject(11, java.lang.String(sinfo.experiment_description));
288 stmt.setObject(12, java.lang.String(refids));
289 stmt.setObject(13, java.lang.String(sinfo.additional_comments));
290 stmt.setObject(14, java.lang.String(sinfo.additional_authors));
291 stmt.setObject(15, java.lang.String(sinfo.keywords));
292 stmt.setObject(16, java.lang.String(sinfo.quantity));
293 stmt.setObject(17, java.lang.String(sinfo.analysis_description));
294 stmt.setObject(18, java.lang.String(author));
295 stmt.execute();
296 stmt.close();
297
298 % update other meta-data tables
299 cols = utils.jmysql.execute(c, 'SHOW COLUMNS FROM tsdata');
300 if utils.helper.ismember('obj_id', cols(:,1))
301 % the tsdata table contains an obj id column. use the new database schema
302 utils.jmysql.insertObjMetadata(c, obj, objid);
303 else
304 % otherwise use the old one
305 utils.helper.msg(msg.PROC2, 'using back-compatibility code');
306 utils.jmysql.insertObjMetadataV1(c, obj, objid);
307 end
308
309 % update transactions table
310 stmt = c.prepareStatement(...
311 'INSERT INTO transactions (obj_id, user_id, transdate, direction) VALUES (?, ?, ?, ?)');
312 stmt.setObject(1, objid);
313 stmt.setObject(2, userid);
314 stmt.setObject(3, java.lang.String(tdate));
315 stmt.setObject(4, java.lang.String('in'));
316 stmt.execute();
317 stmt.close();
318
319 % collect the id of the submitted object
320 ids(kk) = objid;
321 end
322
323 % make collection entry
324 if numel(objs) > 1
325
326 % insert record into collections table
327 stmt = c.prepareStatement(...
328 'INSERT INTO collections (nobjs, obj_ids) VALUES (?, ?)');
329 stmt.setObject(1, length(ids));
330 stmt.setObject(2, java.lang.String(utils.prog.csv(ids)));
331 stmt.executeUpdate();
332
333 % obtain collection id
334 rs = stmt.getGeneratedKeys();
335 if rs.next()
336 cid = rs.getInt(1);
337 else
338 cid = [];
339 end
340 rs.close();
341 stmt.close();
342
343 end
344
345 catch ex
346 utils.helper.msg(msg.IMPORTANT, 'submission error. no object submitted')
347 c.close()
348 conn.setLocked(false);
349 rethrow(ex)
350 end
351
352 % commit the transaction
353 c.commit();
354
355 % report IDs of the inserted objects
356 for kk = 1:numel(objs)
357 utils.helper.msg(msg.IMPORTANT, 'submitted %s object with ID: %d, UUID: %s, name: %s', ...
358 class(objs{kk}), ids(kk), objs{kk}.UUID, objs{kk}.name);
359 end
360 if ~isempty(cid)
361 utils.helper.msg(msg.IMPORTANT, 'made collection entry with ID: %d', cid);
362 end
363
364 % unlock connection expire
365 conn.setLocked(false);
366
367 % reset timer
368 LTPDARepositoryManager.resetTimer(rm.timerClearPass, conn);
369 LTPDARepositoryManager.resetTimer(rm.timerDisconnect, conn);
370
371 % pass back outputs
372 if nargout > 0
373 varargout{1} = ids;
374 end
375 if nargout > 1
376 varargout{2} = cid;
377 end
378 end
379
380
381 function varargout = userCanceled()
382 % signal that the user cancelled the submission
383 import utils.const.*
384 utils.helper.msg(msg.PROC1, 'user cancelled');
385 varargout{1} = [];
386 varargout{2} = [];
387 end
388
389
390 function sinfo = checkSinfo(sinfo)
391 % check sinfo structure
392
393 import utils.const.*
394
395 % fieldnames
396 mainfields = {'experiment_title', 'experiment_description', 'analysis_description'};
397 extrafields = {'quantity', 'keywords', 'reference_ids', 'additional_comments', 'author', 'additional_authors'};
398
399 % fieldnames of the input structure
400 fnames = fieldnames(sinfo);
401
402 % check mandatory fields
403 for jj = 1:length(mainfields)
404 if ~ismember(fnames, mainfields{jj})
405 error('### the sinfo structure should contain a ''%s'' field', mainfields{jj});
406 end
407 end
408
409 % check extra fields
410 for jj = 1:length(extrafields)
411 if ~ismember(fnames, extrafields{jj})
412 utils.helper.msg(msg.PROC2, 'setting default for field %s', extrafields{jj});
413 sinfo.(extrafields{jj}) = '';
414 end
415 end
416
417 % additional checks
418 if length(sinfo.experiment_title) < 5
419 error('### ''experiment title'' should be at least 5 characters long');
420 end
421 if length(sinfo.experiment_description) < 10
422 error('### ''experiment description'' should be at least 10 characters long');
423 end
424 if length(sinfo.analysis_description) < 10
425 error('### ''analysis description'' should be at least 10 characters long');
426 end
427
428 end
429
430
431 function ii = getInfo(varargin)
432 if nargin == 1 && strcmpi(varargin{1}, 'None')
433 sets = {};
434 pl = [];
435 else
436 sets = {'Default'};
437 pl = getDefaultPlist();
438 end
439 % Build info object
440 ii = minfo(mfilename, 'ltpda_uo', 'ltpda', utils.const.categories.internal, '$Id: submit.m,v 1.91 2011/11/18 08:08:26 mauro Exp $', sets, pl);
441 ii.setModifier(false);
442 end
443
444
445 function plout = getDefaultPlist()
446 persistent pl;
447 if ~exist('pl', 'var') || isempty(pl)
448 pl = buildplist();
449 end
450 plout = pl;
451 end
452
453 function plo = buildplist()
454
455 plo = plist.TO_REPOSITORY_PLIST;
456
457 p = param({'sinfo filename', 'Path to an XML file containing submission metadata'}, paramValue.EMPTY_STRING);
458 plo.append(p);
459
460 p = param({'binary', 'Submit only binary version of the objects'}, paramValue.FALSE_TRUE);
461 plo.append(p);
462 end
463
464
465 function pl = fixPlist(pl)
466 % accept parameters where words are separated either by spaces or underscore
467 if ~isempty(pl)
468 for ii = 1:pl.nparams
469 pl.params(ii).setKey(strrep(pl.params(ii).key, '_', ' '));
470 end
471 end
472 end
473
474
475 function flat = flatten(objs)
476 % flatten nested lists into a single cell array
477
478 flat = {};
479
480 while iscell(objs) && numel(objs) == 1
481 objs = objs{1};
482 end
483
484 if numel(objs) == 1
485 flat = {objs};
486 return;
487 end
488
489 for jj = 1:numel(objs)
490 obj = flatten(objs(jj));
491 for kk = 1:numel(obj)
492 flat = [ flat obj(kk) ];
493 end
494 end
495
496 end