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comparison Odbc/Plugins/OdbcIndex.cpp @ 329:b5fb8b77ce4d

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initial commit of ODBC framework
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 10 Aug 2021 20:08:53 +0200
parents
children 16aac0287485 cd9521e04249
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328:6a49c495c940 329:b5fb8b77ce4d
1 /**
2 * Orthanc - A Lightweight, RESTful DICOM Store
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4 * Department, University Hospital of Liege, Belgium
5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
6 *
7 * This program is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU Affero General Public License
9 * as published by the Free Software Foundation, either version 3 of
10 * the License, or (at your option) any later version.
11 *
12 * This program is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
15 * Affero General Public License for more details.
16 *
17 * You should have received a copy of the GNU Affero General Public License
18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
19 **/
20
21
22 #include "OdbcIndex.h"
23
24 #include "../../Framework/Common/Integer64Value.h"
25 #include "../../Framework/Odbc/OdbcDatabase.h"
26 #include "../../Framework/Plugins/GlobalProperties.h"
27
28 #include <EmbeddedResources.h> // Autogenerated file
29
30 #include <Logging.h>
31 #include <OrthancException.h>
32 #include <Toolbox.h>
33
34 #include <boost/algorithm/string/replace.hpp>
35
36
37 // Some aliases for internal properties
38 static const Orthanc::GlobalProperty GlobalProperty_LastChange = Orthanc::GlobalProperty_DatabaseInternal0;
39
40
41 namespace OrthancDatabases
42 {
43 static int64_t GetSQLiteLastInsert(DatabaseManager& manager)
44 {
45 DatabaseManager::CachedStatement statement(
46 STATEMENT_FROM_HERE, manager, "SELECT LAST_INSERT_ROWID()");
47
48 statement.Execute();
49
50 return statement.ReadInteger64(0);
51 }
52
53
54 static int64_t GetMySQLLastInsert(DatabaseManager& manager)
55 {
56 DatabaseManager::CachedStatement statement(
57 STATEMENT_FROM_HERE, manager, "SELECT LAST_INSERT_ID()");
58
59 statement.Execute();
60
61 return statement.ReadInteger64(0);
62 }
63
64
65 static int64_t GetMSSQLLastInsert(DatabaseManager& manager)
66 {
67 DatabaseManager::CachedStatement statement(
68 STATEMENT_FROM_HERE, manager, "SELECT @@IDENTITY");
69
70 statement.Execute();
71
72 return statement.ReadInteger64(0);
73 }
74
75
76 static void AddPatientToRecyclingOrder(DatabaseManager& manager,
77 int64_t patient)
78 {
79 // In the other database plugins, this is done with a trigger
80
81 std::unique_ptr<DatabaseManager::CachedStatement> statement;
82
83 switch (manager.GetDialect())
84 {
85 case Dialect_SQLite:
86 case Dialect_MySQL:
87 statement.reset(
88 new DatabaseManager::CachedStatement(
89 STATEMENT_FROM_HERE, manager, "INSERT INTO PatientRecyclingOrder VALUES(NULL, ${patient})"));
90 break;
91
92 case Dialect_PostgreSQL:
93 statement.reset(
94 new DatabaseManager::CachedStatement(
95 STATEMENT_FROM_HERE, manager, "INSERT INTO PatientRecyclingOrder VALUES(DEFAULT, ${patient})"));
96 break;
97
98 case Dialect_MSSQL:
99 statement.reset(
100 new DatabaseManager::CachedStatement(
101 STATEMENT_FROM_HERE, manager, "INSERT INTO PatientRecyclingOrder VALUES(${patient})"));
102 break;
103
104 default:
105 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
106 }
107
108 statement->SetParameterType("patient", ValueType_Integer64);
109
110 Dictionary args;
111 args.SetIntegerValue("patient", patient);
112 statement->Execute(args);
113 }
114
115
116 static OrthancPluginResourceType GetParentType(OrthancPluginResourceType level)
117 {
118 switch (level)
119 {
120 case OrthancPluginResourceType_Study:
121 return OrthancPluginResourceType_Patient;
122
123 case OrthancPluginResourceType_Series:
124 return OrthancPluginResourceType_Study;
125
126 case OrthancPluginResourceType_Instance:
127 return OrthancPluginResourceType_Series;
128
129 default:
130 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
131 }
132 }
133
134
135 OdbcIndex::OdbcIndex(OrthancPluginContext* context,
136 const std::string& connectionString) :
137 IndexBackend(context),
138 maxConnectionRetries_(10),
139 connectionRetryInterval_(5),
140 connectionString_(connectionString)
141 {
142 }
143
144
145 void OdbcIndex::SetConnectionRetryInterval(unsigned int seconds)
146 {
147 if (seconds == 0)
148 {
149 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
150 }
151 else
152 {
153 connectionRetryInterval_ = seconds;
154 }
155 }
156
157
158 IDatabaseFactory* OdbcIndex::CreateDatabaseFactory()
159 {
160 return OdbcDatabase::CreateDatabaseFactory(maxConnectionRetries_, connectionRetryInterval_, connectionString_, true);
161 }
162
163
164 void OdbcIndex::ConfigureDatabase(DatabaseManager& manager)
165 {
166 uint32_t expectedVersion = 6;
167
168 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
169 {
170 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
171 }
172
173 // Check the expected version of the database
174 if (expectedVersion != 6)
175 {
176 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
177 << "expecting the DB schema version " << expectedVersion
178 << ", but this plugin is only compatible with version 6";
179 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
180 }
181
182 OdbcDatabase& db = dynamic_cast<OdbcDatabase&>(manager.GetDatabase());
183
184 if (!db.DoesTableExist("resources"))
185 {
186 std::string sql;
187 Orthanc::EmbeddedResources::GetFileResource(sql, Orthanc::EmbeddedResources::ODBC_PREPARE_INDEX);
188
189 switch (db.GetDialect())
190 {
191 case Dialect_SQLite:
192 boost::replace_all(sql, "${LONGTEXT}", "TEXT");
193 boost::replace_all(sql, "${AUTOINCREMENT_TYPE}", "INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT");
194 boost::replace_all(sql, "${AUTOINCREMENT_INSERT}", "NULL, ");
195 break;
196
197 case Dialect_PostgreSQL:
198 boost::replace_all(sql, "${LONGTEXT}", "TEXT");
199 boost::replace_all(sql, "${AUTOINCREMENT_TYPE}", "BIGSERIAL NOT NULL PRIMARY KEY");
200 boost::replace_all(sql, "${AUTOINCREMENT_INSERT}", "DEFAULT, ");
201 break;
202
203 case Dialect_MySQL:
204 boost::replace_all(sql, "${LONGTEXT}", "LONGTEXT");
205 boost::replace_all(sql, "${AUTOINCREMENT_TYPE}", "BIGINT NOT NULL AUTO_INCREMENT PRIMARY KEY");
206 boost::replace_all(sql, "${AUTOINCREMENT_INSERT}", "NULL, ");
207 break;
208
209 case Dialect_MSSQL:
210 /**
211 * cf. OMSSQL-5: Use VARCHAR(MAX) instead of TEXT: (1)
212 * Microsoft issued a warning stating that "ntext, text, and
213 * image data types will be removed in a future version of
214 * SQL Server"
215 * (https://msdn.microsoft.com/en-us/library/ms187993.aspx),
216 * and (2) SQL Server does not support comparison of TEXT
217 * with '=' operator (e.g. in WHERE statements such as
218 * IndexBackend::LookupIdentifier())."
219 **/
220 boost::replace_all(sql, "${LONGTEXT}", "VARCHAR(MAX)");
221 boost::replace_all(sql, "${AUTOINCREMENT_TYPE}", "BIGINT IDENTITY NOT NULL PRIMARY KEY");
222 boost::replace_all(sql, "${AUTOINCREMENT_INSERT}", "");
223 break;
224
225 default:
226 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
227 }
228
229 {
230 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
231
232 db.ExecuteMultiLines(sql);
233
234 if (db.GetDialect() == Dialect_MySQL)
235 {
236 // Switch to the collation that is the default since MySQL
237 // 8.0.1. This must be *after* the creation of the tables.
238 db.ExecuteMultiLines("ALTER DATABASE CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci");
239 }
240
241 t.Commit();
242 }
243 }
244 }
245
246
247 int64_t OdbcIndex::CreateResource(DatabaseManager& manager,
248 const char* publicId,
249 OrthancPluginResourceType type)
250 {
251 Dictionary args;
252 args.SetUtf8Value("id", publicId);
253 args.SetIntegerValue("type", static_cast<int>(type));
254
255 switch (manager.GetDatabase().GetDialect())
256 {
257 case Dialect_SQLite:
258 {
259 {
260 DatabaseManager::CachedStatement statement(
261 STATEMENT_FROM_HERE, manager, "INSERT INTO Resources VALUES(NULL, ${type}, ${id}, NULL)");
262
263 statement.SetParameterType("id", ValueType_Utf8String);
264 statement.SetParameterType("type", ValueType_Integer64);
265 statement.Execute(args);
266 }
267
268 // Must be out of the scope of "DatabaseManager::CachedStatement"
269 const int64_t id = GetSQLiteLastInsert(manager);
270
271 if (type == OrthancPluginResourceType_Patient)
272 {
273 AddPatientToRecyclingOrder(manager, id);
274 }
275
276 return id;
277 }
278
279 case Dialect_PostgreSQL:
280 {
281 int64_t id;
282
283 {
284 DatabaseManager::CachedStatement statement(
285 STATEMENT_FROM_HERE, manager,
286 "INSERT INTO Resources VALUES(DEFAULT, ${type}, ${id}, NULL) RETURNING internalId");
287
288 statement.SetParameterType("id", ValueType_Utf8String);
289 statement.SetParameterType("type", ValueType_Integer64);
290 statement.Execute(args);
291 id = statement.ReadInteger64(0);
292 }
293
294 if (type == OrthancPluginResourceType_Patient)
295 {
296 AddPatientToRecyclingOrder(manager, id);
297 }
298
299 return id;
300 }
301
302 case Dialect_MySQL:
303 {
304 {
305 DatabaseManager::CachedStatement statement(
306 STATEMENT_FROM_HERE, manager, "INSERT INTO Resources VALUES(NULL, ${type}, ${id}, NULL)");
307
308 statement.SetParameterType("id", ValueType_Utf8String);
309 statement.SetParameterType("type", ValueType_Integer64);
310 statement.Execute(args);
311 }
312
313 // Must be out of the scope of "DatabaseManager::CachedStatement"
314 const int64_t id = GetMySQLLastInsert(manager);
315
316 if (type == OrthancPluginResourceType_Patient)
317 {
318 AddPatientToRecyclingOrder(manager, id);
319 }
320
321 return id;
322 }
323
324 case Dialect_MSSQL:
325 {
326 {
327 DatabaseManager::CachedStatement statement(
328 STATEMENT_FROM_HERE, manager, "INSERT INTO Resources VALUES(${type}, ${id}, NULL)");
329
330 statement.SetParameterType("id", ValueType_Utf8String);
331 statement.SetParameterType("type", ValueType_Integer64);
332 statement.Execute(args);
333 }
334
335 // Must be out of the scope of "DatabaseManager::CachedStatement"
336 const int64_t id = GetMSSQLLastInsert(manager);
337
338 if (type == OrthancPluginResourceType_Patient)
339 {
340 AddPatientToRecyclingOrder(manager, id);
341 }
342
343 return id;
344 }
345
346 default:
347 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
348 }
349 }
350
351
352 void OdbcIndex::DeleteResource(IDatabaseBackendOutput& output,
353 DatabaseManager& manager,
354 int64_t id)
355 {
356 /**
357 * Contrarily to PostgreSQL and SQLite, the MySQL dialect
358 * doesn't support cascaded delete inside the same
359 * table. Furthermore, for maximum portability, we don't use
360 * triggers in the ODBC plugins. We therefore implement a custom
361 * version of this deletion.
362 **/
363
364 ClearDeletedFiles(manager);
365 ClearDeletedResources(manager);
366
367 OrthancPluginResourceType type;
368 bool hasParent;
369 int64_t parentId;
370
371 {
372 DatabaseManager::CachedStatement lookupResource(
373 STATEMENT_FROM_HERE, manager,
374 "SELECT resourceType, parentId FROM Resources WHERE internalId=${id}");
375 lookupResource.SetParameterType("id", ValueType_Integer64);
376
377 Dictionary args;
378 args.SetIntegerValue("id", id);
379 lookupResource.Execute(args);
380
381 if (lookupResource.IsDone())
382 {
383 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
384 }
385
386 type = static_cast<OrthancPluginResourceType>(lookupResource.ReadInteger32(0));
387
388 if (lookupResource.GetResultField(1).GetType() == ValueType_Null)
389 {
390 hasParent = false;
391 }
392 else
393 {
394 hasParent = true;
395 parentId = lookupResource.ReadInteger64(1);
396 }
397 }
398
399 {
400 DatabaseManager::CachedStatement scheduleRootDeletion(
401 STATEMENT_FROM_HERE, manager,
402 "INSERT INTO DeletedResources SELECT internalId, resourceType, publicId "
403 "FROM Resources WHERE Resources.internalId = ${id}");
404 scheduleRootDeletion.SetParameterType("id", ValueType_Integer64);
405
406 Dictionary args;
407 args.SetIntegerValue("id", id);
408 scheduleRootDeletion.Execute(args);
409 }
410
411 {
412 const std::string scheduleChildrenDeletion =
413 "INSERT INTO DeletedResources SELECT Resources.internalId, Resources.resourceType, Resources.publicId "
414 "FROM Resources INNER JOIN DeletedResources ON Resources.parentId = DeletedResources.internalId "
415 "WHERE Resources.resourceType = ${level}";
416
417 switch (type)
418 {
419 /**
420 * WARNING: Don't add "break" or reorder cases below.
421 **/
422
423 case OrthancPluginResourceType_Patient:
424 {
425 DatabaseManager::CachedStatement statement(STATEMENT_FROM_HERE, manager, scheduleChildrenDeletion);
426 statement.SetParameterType("level", ValueType_Integer64);
427
428 Dictionary args;
429 args.SetIntegerValue("level", OrthancPluginResourceType_Study);
430 statement.Execute(args);
431 }
432
433 case OrthancPluginResourceType_Study:
434 {
435 DatabaseManager::CachedStatement statement(STATEMENT_FROM_HERE, manager, scheduleChildrenDeletion);
436 statement.SetParameterType("level", ValueType_Integer64);
437
438 Dictionary args;
439 args.SetIntegerValue("level", OrthancPluginResourceType_Series);
440 statement.Execute(args);
441 }
442
443 case OrthancPluginResourceType_Series:
444 {
445 DatabaseManager::CachedStatement statement(STATEMENT_FROM_HERE, manager, scheduleChildrenDeletion);
446 statement.SetParameterType("level", ValueType_Integer64);
447
448 Dictionary args;
449 args.SetIntegerValue("level", OrthancPluginResourceType_Instance);
450 statement.Execute(args);
451 }
452
453 case OrthancPluginResourceType_Instance:
454 // No child
455 break;
456
457 default:
458 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
459 }
460 }
461
462 bool hasRemainingAncestor = false;
463 std::string remainingAncestor;
464 OrthancPluginResourceType ancestorType;
465
466 if (hasParent)
467 {
468 int64_t currentAncestor = parentId;
469 int64_t currentResource = id;
470 OrthancPluginResourceType currentType = type;
471
472 for (;;)
473 {
474 bool hasSiblings;
475
476 {
477 std::string suffix;
478 if (manager.GetDialect() == Dialect_MSSQL)
479 {
480 suffix = "ORDER BY internalId OFFSET 0 ROWS FETCH FIRST 1 ROWS ONLY";
481 }
482 else
483 {
484 suffix = "LIMIT 1";
485 }
486
487 DatabaseManager::CachedStatement lookupSiblings(
488 STATEMENT_FROM_HERE, manager,
489 "SELECT internalId FROM Resources WHERE parentId = ${parent} AND internalId <> ${id} " + suffix);
490
491 lookupSiblings.SetParameterType("parent", ValueType_Integer64);
492 lookupSiblings.SetParameterType("id", ValueType_Integer64);
493
494 Dictionary args;
495 args.SetIntegerValue("parent", currentAncestor);
496 args.SetIntegerValue("id", currentResource);
497 lookupSiblings.Execute(args);
498
499 hasSiblings = !lookupSiblings.IsDone();
500 }
501
502 if (hasSiblings)
503 {
504 // There remains some sibling: Signal this remaining ancestor
505 hasRemainingAncestor = true;
506 remainingAncestor = GetPublicId(manager, currentAncestor);
507 ancestorType = GetParentType(currentType);
508 break;
509 }
510 else
511 {
512 // No sibling remaining: This parent resource must be deleted
513 {
514 DatabaseManager::CachedStatement addDeletedResource(
515 STATEMENT_FROM_HERE, manager,
516 "INSERT INTO DeletedResources SELECT internalId, resourceType, publicId "
517 "FROM Resources WHERE internalId=${id}");
518 addDeletedResource.SetParameterType("id", ValueType_Integer64);
519
520 Dictionary args;
521 args.SetIntegerValue("id", currentAncestor);
522 addDeletedResource.Execute(args);
523 }
524
525 int64_t tmp;
526 if (LookupParent(tmp, manager, currentAncestor))
527 {
528 currentResource = currentAncestor;
529 currentAncestor = tmp;
530 currentType = GetParentType(currentType);
531 }
532 else
533 {
534 assert(currentType == OrthancPluginResourceType_Study);
535 break;
536 }
537 }
538 }
539 }
540
541 {
542 // This is implemented by triggers in the PostgreSQL and MySQL plugins
543 DatabaseManager::CachedStatement lookupDeletedAttachments(
544 STATEMENT_FROM_HERE, manager,
545 "INSERT INTO DeletedFiles SELECT AttachedFiles.* FROM AttachedFiles "
546 "INNER JOIN DeletedResources ON AttachedFiles.id = DeletedResources.internalId");
547 lookupDeletedAttachments.Execute();
548 }
549
550 {
551 // Note that the attachments are automatically deleted by DELETE CASCADE
552 DatabaseManager::CachedStatement applyResourcesDeletion(
553 STATEMENT_FROM_HERE, manager,
554 "DELETE FROM Resources WHERE internalId IN (SELECT internalId FROM DeletedResources)");
555 applyResourcesDeletion.Execute();
556 }
557
558 SignalDeletedResources(output, manager);
559 SignalDeletedFiles(output, manager);
560
561 if (hasRemainingAncestor)
562 {
563 assert(!remainingAncestor.empty());
564 output.SignalRemainingAncestor(remainingAncestor, ancestorType);
565 }
566 }
567
568
569 static void ExecuteLogChange(DatabaseManager::CachedStatement& statement,
570 const Dictionary& args)
571 {
572 statement.SetParameterType("changeType", ValueType_Integer64);
573 statement.SetParameterType("id", ValueType_Integer64);
574 statement.SetParameterType("resourceType", ValueType_Integer64);
575 statement.SetParameterType("date", ValueType_Utf8String);
576 statement.Execute(args);
577 }
578
579
580 void OdbcIndex::LogChange(DatabaseManager& manager,
581 int32_t changeType,
582 int64_t resourceId,
583 OrthancPluginResourceType resourceType,
584 const char* date)
585 {
586 Dictionary args;
587 args.SetIntegerValue("changeType", changeType);
588 args.SetIntegerValue("id", resourceId);
589 args.SetIntegerValue("resourceType", resourceType);
590 args.SetUtf8Value("date", date);
591
592 int64_t seq;
593
594 switch (manager.GetDatabase().GetDialect())
595 {
596 case Dialect_SQLite:
597 {
598 DatabaseManager::CachedStatement statement(
599 STATEMENT_FROM_HERE, manager,
600 "INSERT INTO Changes VALUES(NULL, ${changeType}, ${id}, ${resourceType}, ${date})");
601 ExecuteLogChange(statement, args);
602 seq = GetSQLiteLastInsert(manager);
603 break;
604 }
605
606 case Dialect_PostgreSQL:
607 {
608 DatabaseManager::CachedStatement statement(
609 STATEMENT_FROM_HERE, manager,
610 "INSERT INTO Changes VALUES(DEFAULT, ${changeType}, ${id}, ${resourceType}, ${date}) RETURNING seq");
611 ExecuteLogChange(statement, args);
612 seq = statement.ReadInteger64(0);
613 break;
614 }
615
616 case Dialect_MySQL:
617 {
618 DatabaseManager::CachedStatement statement(
619 STATEMENT_FROM_HERE, manager,
620 "INSERT INTO Changes VALUES(NULL, ${changeType}, ${id}, ${resourceType}, ${date})");
621 ExecuteLogChange(statement, args);
622 seq = GetMySQLLastInsert(manager);
623 break;
624 }
625
626 case Dialect_MSSQL:
627 {
628 DatabaseManager::CachedStatement statement(
629 STATEMENT_FROM_HERE, manager,
630 "INSERT INTO Changes VALUES(${changeType}, ${id}, ${resourceType}, ${date})");
631 ExecuteLogChange(statement, args);
632 seq = GetMSSQLLastInsert(manager);
633 break;
634 }
635
636 default:
637 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
638 }
639
640 std::string value = boost::lexical_cast<std::string>(seq);
641 SetGlobalProperty(manager, MISSING_SERVER_IDENTIFIER, GlobalProperty_LastChange, value.c_str());
642 }
643
644
645 int64_t OdbcIndex::GetLastChangeIndex(DatabaseManager& manager)
646 {
647 std::string value;
648
649 if (LookupGlobalProperty(value, manager, MISSING_SERVER_IDENTIFIER, GlobalProperty_LastChange))
650 {
651 return boost::lexical_cast<int64_t>(value);
652 }
653 else
654 {
655 return 0;
656 }
657 }
658
659
660 void OdbcIndex::DeleteAttachment(IDatabaseBackendOutput& output,
661 DatabaseManager& manager,
662 int64_t id,
663 int32_t attachment)
664 {
665 ClearDeletedFiles(manager);
666
667 Dictionary args;
668 args.SetIntegerValue("id", id);
669 args.SetIntegerValue("type", static_cast<int>(attachment));
670
671 {
672 // This is implemented by triggers in the PostgreSQL and MySQL plugins
673 DatabaseManager::CachedStatement statement(
674 STATEMENT_FROM_HERE, manager,
675 "INSERT INTO DeletedFiles SELECT * FROM AttachedFiles WHERE id=${id} AND fileType=${type}");
676
677 statement.SetParameterType("id", ValueType_Integer64);
678 statement.SetParameterType("type", ValueType_Integer64);
679 statement.Execute(args);
680 }
681
682 {
683 DatabaseManager::CachedStatement statement(
684 STATEMENT_FROM_HERE, manager,
685 "DELETE FROM AttachedFiles WHERE id=${id} AND fileType=${type}");
686
687 statement.SetParameterType("id", ValueType_Integer64);
688 statement.SetParameterType("type", ValueType_Integer64);
689 statement.Execute(args);
690 }
691
692 SignalDeletedFiles(output, manager);
693 }
694 }