Mercurial > hg > ltpda
annotate m-toolbox/classes/@ltpda_uo/submit.m @ 40:977eb37f31cb database-connection-manager
User friendlier errors from utils.mysql.connect
| author | Daniele Nicolodi <nicolodi@science.unitn.it> |
|---|---|
| date | Mon, 05 Dec 2011 18:04:03 +0100 |
| parents | d58813ab1b92 |
| children | ca0b8d4dcdb6 |
| rev | line source |
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| 0 | 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. | |
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45 % |
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46 % |
| 0 | 47 |
| 48 | |
| 49 function varargout = submit(varargin) | |
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50 |
| 0 | 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 | |
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56 |
| 0 | 57 import utils.const.* |
| 58 utils.helper.msg(msg.PROC3, 'running %s/%s', mfilename('class'), mfilename); | |
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59 |
| 0 | 60 % collect all AOs |
| 61 [pls, invars, rest] = utils.helper.collect_objects(varargin(:), 'plist'); | |
| 62 [sinfo, invars, objs] = utils.helper.collect_objects(rest(:), 'struct'); | |
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63 |
| 0 | 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 | |
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80 |
| 0 | 81 % rearrange nested objects lists into a single cell array |
| 82 objs = flatten(objs); | |
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83 |
| 0 | 84 if isempty(objs) |
| 85 error('### input at least one object to submit to the repository'); | |
| 86 end | |
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87 |
| 0 | 88 % combine user plist with default |
| 89 pls = fixPlist(pls); | |
| 90 dpl = getDefaultPlist(); | |
| 91 pls = combine(pls, dpl.pset('HOSTNAME', '')); | |
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92 |
| 0 | 93 % for backwards compatibility convert any user supplied sinfo-structure into a plist |
| 94 pls = ltpda_uo.convertSinfo2Plist(pls, sinfo); | |
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95 |
| 0 | 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 | |
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106 |
| 0 | 107 % collect additional informations |
| 108 sinfo = ltpda_uo.submitDialog(pls); | |
| 109 if isempty(sinfo) | |
| 110 [varargout{1}, varargout{2}] = userCanceled(); | |
| 111 return | |
| 112 end | |
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113 |
| 0 | 114 % check completeness of user supplied informations |
| 115 sinfo = checkSinfo(sinfo); | |
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116 |
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117 % database connection |
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118 c = LTPDADatabaseConnectionManager().connect(pls); |
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119 |
| 0 | 120 utils.helper.msg(msg.PROC1, 'submitting %d objects to repository', numel(objs)); |
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121 |
| 0 | 122 try |
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123 % get username and userid |
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124 [username, userid] = utils.repository.getUser(c); |
| 0 | 125 |
| 126 % author of the data: let's take the username | |
| 127 author = username; | |
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128 |
| 0 | 129 % date for the transaction.transdata and objmeta.submitted columns as UTC time string |
| 130 t = time(); | |
| 131 tdate = format(t, 'yyyy-mm-dd HH:MM:SS', 'UTC'); | |
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132 |
| 0 | 133 % machine details |
| 134 prov = provenance(); | |
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135 |
| 0 | 136 % start a transaction. either we submitt all objects or we roll back all changes |
| 137 c.setAutoCommit(false); | |
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138 |
| 0 | 139 % process each object and collect id numbers |
| 140 ids = zeros(numel(objs), 1); cid = []; | |
| 141 for kk = 1:numel(objs) | |
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142 |
| 0 | 143 % this object |
| 144 obj = objs{kk}; | |
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145 |
| 0 | 146 utils.helper.msg(msg.PROC1, 'submitting object: %s / %s', class(obj), obj.name); |
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147 |
| 0 | 148 % format object creation time as UTC time string |
| 149 if isa(obj, 'plist') | |
| 150 % plist-objects stores creatins time as milli secs since the epoch | |
| 151 created = time().format('yyyy-mm-dd HH:MM:SS', 'UTC'); | |
| 152 else | |
| 153 created = obj.created.format('yyyy-mm-dd HH:MM:SS', 'UTC'); | |
| 154 end | |
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155 |
| 0 | 156 % Set the UUID if it is empty. This should only happen for PLIST |
| 157 % objects. | |
| 158 if isempty(obj.UUID) | |
| 159 obj.UUID = char(java.util.UUID.randomUUID); | |
| 160 end | |
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161 |
| 0 | 162 % create an XML representaion of the object |
| 163 if utils.prog.yes2true(pls.find('binary')); | |
| 164 utils.helper.msg(msg.PROC2, 'binary submit'); | |
| 165 otxt = ['binary submit ' datestr(now)]; | |
| 166 else | |
| 167 utils.helper.msg(msg.PROC2, 'xml submit'); | |
| 168 otxt = utils.prog.obj2xml(obj); | |
| 169 end | |
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170 |
| 0 | 171 % create an MD5 hash of the xml representation |
| 172 md5hash = utils.prog.hash(otxt, 'MD5'); | |
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173 |
| 0 | 174 % create a binary representaion of the object |
| 175 bobj = utils.prog.obj2binary(obj); | |
| 176 if isempty(bobj) | |
| 177 error('### failed to obtain a binary representation'); | |
| 178 end | |
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179 |
| 0 | 180 % submit object to objs table |
| 181 stmt = c.prepareStatement(... | |
| 182 'INSERT INTO objs (xml, hash, uuid) VALUES (?, ?, ?)'); | |
| 183 stmt.setObject(1, otxt); | |
| 184 stmt.setObject(2, char(md5hash)); | |
| 185 stmt.setObject(3, obj.UUID); | |
| 186 stmt.executeUpdate(); | |
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187 |
| 0 | 188 % obtain object id |
| 189 rs = stmt.getGeneratedKeys(); | |
| 190 if rs.next() | |
| 191 objid = rs.getInt(1); | |
| 192 else | |
| 193 objid = []; | |
| 194 end | |
| 195 rs.close(); | |
| 196 stmt.close(); | |
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197 |
| 0 | 198 % insert binary representation |
| 199 stmt = c.prepareStatement(... | |
| 200 'INSERT INTO bobjs (obj_id, mat) VALUES (?,?)'); | |
| 201 stmt.setObject(1, objid); | |
| 202 stmt.setObject(2, bobj); | |
| 203 stmt.execute(); | |
| 204 stmt.close(); | |
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205 |
| 0 | 206 % reference IDs are stored in a CSV string |
| 207 if ischar(sinfo.reference_ids) | |
| 208 refids = sinfo.reference_ids; | |
| 209 else | |
| 210 refids = utils.prog.csv(sinfo.reference_ids); | |
| 211 end | |
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212 |
| 0 | 213 % insert object meta data |
| 214 stmt = c.prepareStatement(... | |
| 215 [ 'INSERT INTO objmeta (obj_id, obj_type, name, created, version, ' ... | |
| 216 'ip, hostname, os, submitted, experiment_title, experiment_desc, ' ... | |
| 217 'reference_ids, additional_comments, additional_authors, keywords, ' ... | |
| 218 'quantity, analysis_desc, author) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)' ]); | |
| 219 stmt.setObject( 1, objid); | |
| 220 stmt.setObject( 2, java.lang.String(class(obj))); | |
| 221 stmt.setObject( 3, java.lang.String(obj.name)); | |
| 222 stmt.setObject( 4, java.lang.String(created)); | |
| 223 stmt.setObject( 5, java.lang.String(getappdata(0, 'ltpda_version'))); | |
| 224 stmt.setObject( 6, java.lang.String(prov.ip)); | |
| 225 stmt.setObject( 7, java.lang.String(prov.hostname)); | |
| 226 stmt.setObject( 8, java.lang.String(prov.os)); | |
| 227 stmt.setObject( 9, java.lang.String(tdate)); | |
| 228 stmt.setObject(10, java.lang.String(sinfo.experiment_title)); | |
| 229 stmt.setObject(11, java.lang.String(sinfo.experiment_description)); | |
| 230 stmt.setObject(12, java.lang.String(refids)); | |
| 231 stmt.setObject(13, java.lang.String(sinfo.additional_comments)); | |
| 232 stmt.setObject(14, java.lang.String(sinfo.additional_authors)); | |
| 233 stmt.setObject(15, java.lang.String(sinfo.keywords)); | |
| 234 stmt.setObject(16, java.lang.String(sinfo.quantity)); | |
| 235 stmt.setObject(17, java.lang.String(sinfo.analysis_description)); | |
| 236 stmt.setObject(18, java.lang.String(author)); | |
| 237 stmt.execute(); | |
| 238 stmt.close(); | |
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239 |
| 0 | 240 % update other meta-data tables |
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241 cols = utils.mysql.execute(c, 'SHOW COLUMNS FROM tsdata'); |
| 0 | 242 if utils.helper.ismember('obj_id', cols(:,1)) |
| 243 % the tsdata table contains an obj id column. use the new database schema | |
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244 utils.repository.insertObjMetadata(c, obj, objid); |
| 0 | 245 else |
| 246 % otherwise use the old one | |
| 247 utils.helper.msg(msg.PROC2, 'using back-compatibility code'); | |
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248 utils.repository.insertObjMetadataV1(c, obj, objid); |
| 0 | 249 end |
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250 |
| 0 | 251 % update transactions table |
| 252 stmt = c.prepareStatement(... | |
| 253 'INSERT INTO transactions (obj_id, user_id, transdate, direction) VALUES (?, ?, ?, ?)'); | |
| 254 stmt.setObject(1, objid); | |
| 255 stmt.setObject(2, userid); | |
| 256 stmt.setObject(3, java.lang.String(tdate)); | |
| 257 stmt.setObject(4, java.lang.String('in')); | |
| 258 stmt.execute(); | |
| 259 stmt.close(); | |
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260 |
| 0 | 261 % collect the id of the submitted object |
| 262 ids(kk) = objid; | |
| 263 end | |
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264 |
| 0 | 265 % make collection entry |
| 266 if numel(objs) > 1 | |
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267 |
| 0 | 268 % insert record into collections table |
| 269 stmt = c.prepareStatement(... | |
| 270 'INSERT INTO collections (nobjs, obj_ids) VALUES (?, ?)'); | |
| 271 stmt.setObject(1, length(ids)); | |
| 272 stmt.setObject(2, java.lang.String(utils.prog.csv(ids))); | |
| 273 stmt.executeUpdate(); | |
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274 |
| 0 | 275 % obtain collection id |
| 276 rs = stmt.getGeneratedKeys(); | |
| 277 if rs.next() | |
| 278 cid = rs.getInt(1); | |
| 279 else | |
| 280 cid = []; | |
| 281 end | |
| 282 rs.close(); | |
| 283 stmt.close(); | |
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284 |
| 0 | 285 end |
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286 |
| 0 | 287 catch ex |
| 288 utils.helper.msg(msg.IMPORTANT, 'submission error. no object submitted') | |
| 289 c.close() | |
| 290 rethrow(ex) | |
| 291 end | |
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292 |
| 0 | 293 % commit the transaction |
| 294 c.commit(); | |
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295 |
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296 % close the connection if we own it |
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297 if isempty(find(pls, 'conn')) |
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298 c.close(); |
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299 end |
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300 |
| 0 | 301 % report IDs of the inserted objects |
| 302 for kk = 1:numel(objs) | |
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303 utils.helper.msg(msg.IMPORTANT, 'submitted %s object with ID: %d UUID: %s name: %s', ... |
| 0 | 304 class(objs{kk}), ids(kk), objs{kk}.UUID, objs{kk}.name); |
| 305 end | |
| 306 if ~isempty(cid) | |
| 307 utils.helper.msg(msg.IMPORTANT, 'made collection entry with ID: %d', cid); | |
| 308 end | |
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309 |
| 0 | 310 % pass back outputs |
| 311 if nargout > 0 | |
| 312 varargout{1} = ids; | |
| 313 end | |
| 314 if nargout > 1 | |
| 315 varargout{2} = cid; | |
| 316 end | |
| 317 end | |
| 318 | |
| 319 | |
| 320 function varargout = userCanceled() | |
| 321 % signal that the user cancelled the submission | |
| 322 import utils.const.* | |
| 323 utils.helper.msg(msg.PROC1, 'user cancelled'); | |
| 324 varargout{1} = []; | |
| 325 varargout{2} = []; | |
| 326 end | |
| 327 | |
| 328 | |
| 329 function sinfo = checkSinfo(sinfo) | |
| 330 % check sinfo structure | |
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331 |
| 0 | 332 import utils.const.* |
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333 |
| 0 | 334 % fieldnames |
| 335 mainfields = {'experiment_title', 'experiment_description', 'analysis_description'}; | |
| 336 extrafields = {'quantity', 'keywords', 'reference_ids', 'additional_comments', 'author', 'additional_authors'}; | |
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337 |
| 0 | 338 % fieldnames of the input structure |
| 339 fnames = fieldnames(sinfo); | |
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340 |
| 0 | 341 % check mandatory fields |
| 342 for jj = 1:length(mainfields) | |
| 343 if ~ismember(fnames, mainfields{jj}) | |
| 344 error('### the sinfo structure should contain a ''%s'' field', mainfields{jj}); | |
| 345 end | |
| 346 end | |
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347 |
| 0 | 348 % check extra fields |
| 349 for jj = 1:length(extrafields) | |
| 350 if ~ismember(fnames, extrafields{jj}) | |
| 351 utils.helper.msg(msg.PROC2, 'setting default for field %s', extrafields{jj}); | |
| 352 sinfo.(extrafields{jj}) = ''; | |
| 353 end | |
| 354 end | |
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355 |
| 0 | 356 % additional checks |
| 357 if length(sinfo.experiment_title) < 5 | |
| 358 error('### ''experiment title'' should be at least 5 characters long'); | |
| 359 end | |
| 360 if length(sinfo.experiment_description) < 10 | |
| 361 error('### ''experiment description'' should be at least 10 characters long'); | |
| 362 end | |
| 363 if length(sinfo.analysis_description) < 10 | |
| 364 error('### ''analysis description'' should be at least 10 characters long'); | |
| 365 end | |
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366 |
| 0 | 367 end |
| 368 | |
| 369 | |
| 370 function ii = getInfo(varargin) | |
| 371 if nargin == 1 && strcmpi(varargin{1}, 'None') | |
| 372 sets = {}; | |
| 373 pl = []; | |
| 374 else | |
| 375 sets = {'Default'}; | |
| 376 pl = getDefaultPlist(); | |
| 377 end | |
| 378 % Build info object | |
| 379 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); | |
| 380 ii.setModifier(false); | |
| 381 end | |
| 382 | |
| 383 | |
| 384 function plout = getDefaultPlist() | |
| 385 persistent pl; | |
| 386 if ~exist('pl', 'var') || isempty(pl) | |
| 387 pl = buildplist(); | |
| 388 end | |
| 389 plout = pl; | |
| 390 end | |
| 391 | |
| 392 function plo = buildplist() | |
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393 |
| 0 | 394 plo = plist.TO_REPOSITORY_PLIST; |
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395 |
| 0 | 396 p = param({'sinfo filename', 'Path to an XML file containing submission metadata'}, paramValue.EMPTY_STRING); |
| 397 plo.append(p); | |
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398 |
| 0 | 399 p = param({'binary', 'Submit only binary version of the objects'}, paramValue.FALSE_TRUE); |
| 400 plo.append(p); | |
| 401 end | |
| 402 | |
| 403 | |
| 404 function pl = fixPlist(pl) | |
| 405 % accept parameters where words are separated either by spaces or underscore | |
| 406 if ~isempty(pl) | |
| 407 for ii = 1:pl.nparams | |
| 408 pl.params(ii).setKey(strrep(pl.params(ii).key, '_', ' ')); | |
| 409 end | |
| 410 end | |
| 411 end | |
| 412 | |
| 413 | |
| 414 function flat = flatten(objs) | |
| 415 % flatten nested lists into a single cell array | |
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416 |
| 0 | 417 flat = {}; |
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418 |
| 0 | 419 while iscell(objs) && numel(objs) == 1 |
| 420 objs = objs{1}; | |
| 421 end | |
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422 |
| 0 | 423 if numel(objs) == 1 |
| 424 flat = {objs}; | |
| 425 return; | |
| 426 end | |
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427 |
| 0 | 428 for jj = 1:numel(objs) |
| 429 obj = flatten(objs(jj)); | |
| 430 for kk = 1:numel(obj) | |
| 431 flat = [ flat obj(kk) ]; | |
| 432 end | |
| 433 end | |
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434 |
| 0 | 435 end |