Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 187:8e673a65564d
refactoring of storing new instances
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 12 Nov 2012 17:29:11 +0100 |
parents | f68c039b0571 |
children | 090cefdab1d1 |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
0 | 3 * Copyright (C) 2012 Medical Physics Department, CHU of Liege, |
4 * Belgium | |
5 * | |
6 * This program is free software: you can redistribute it and/or | |
7 * modify it under the terms of the GNU General Public License as | |
8 * published by the Free Software Foundation, either version 3 of the | |
9 * License, or (at your option) any later version. | |
136 | 10 * |
11 * In addition, as a special exception, the copyright holders of this | |
12 * program give permission to link the code of its release with the | |
13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
14 * that use the same license as the "OpenSSL" library), and distribute | |
15 * the linked executables. You must obey the GNU General Public License | |
16 * in all respects for all of the code used other than "OpenSSL". If you | |
17 * modify file(s) with this exception, you may extend this exception to | |
18 * your version of the file(s), but you are not obligated to do so. If | |
19 * you do not wish to do so, delete this exception statement from your | |
20 * version. If you delete this exception statement from all source files | |
21 * in the program, then also delete it here. | |
0 | 22 * |
23 * This program is distributed in the hope that it will be useful, but | |
24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
26 * General Public License for more details. | |
27 * | |
28 * You should have received a copy of the GNU General Public License | |
29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
30 **/ | |
31 | |
32 | |
33 #include "ServerIndex.h" | |
34 | |
62 | 35 using namespace Orthanc; |
0 | 36 |
6 | 37 #ifndef NOMINMAX |
2 | 38 #define NOMINMAX |
6 | 39 #endif |
40 | |
8 | 41 #include "EmbeddedResources.h" |
0 | 42 #include "../Core/Toolbox.h" |
43 #include "../Core/Uuid.h" | |
44 #include "../Core/DicomFormat/DicomArray.h" | |
45 #include "../Core/SQLite/Transaction.h" | |
46 #include "FromDcmtkBridge.h" | |
47 | |
48 #include <boost/lexical_cast.hpp> | |
49 #include <stdio.h> | |
108 | 50 #include <glog/logging.h> |
0 | 51 |
62 | 52 namespace Orthanc |
0 | 53 { |
54 namespace Internals | |
55 { | |
56 class DeleteFromFileStorageFunction : public SQLite::IScalarFunction | |
57 { | |
58 private: | |
180
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59 std::auto_ptr<FileStorage> fileStorage_; |
0 | 60 |
61 public: | |
180
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62 DeleteFromFileStorageFunction(const std::string& path) |
0 | 63 { |
180
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64 if (path != ":memory:") |
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65 { |
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66 fileStorage_.reset(new FileStorage(path)); |
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67 } |
0 | 68 } |
69 | |
70 virtual const char* GetName() const | |
71 { | |
72 return "DeleteFromFileStorage"; | |
73 } | |
74 | |
75 virtual unsigned int GetCardinality() const | |
76 { | |
77 return 1; | |
78 } | |
79 | |
80 virtual void Compute(SQLite::FunctionContext& context) | |
81 { | |
180
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82 if (fileStorage_.get() == NULL) |
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83 { |
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84 // In-memory index, for unit tests |
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85 return; |
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86 } |
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87 |
0 | 88 std::string fileUuid = context.GetStringValue(0); |
108 | 89 LOG(INFO) << "Removing file [" << fileUuid << "]"; |
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90 |
0 | 91 if (Toolbox::IsUuid(fileUuid)) |
92 { | |
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93 fileStorage_->Remove(fileUuid); |
0 | 94 } |
95 } | |
96 }; | |
97 | |
98 | |
99 class SignalDeletedLevelFunction : public SQLite::IScalarFunction | |
100 { | |
101 private: | |
102 int remainingLevel_; | |
103 std::string remainingLevelUuid_; | |
104 | |
105 public: | |
106 void Clear() | |
107 { | |
108 remainingLevel_ = std::numeric_limits<int>::max(); | |
109 } | |
110 | |
111 bool HasRemainingLevel() const | |
112 { | |
113 return (remainingLevel_ != 0 && | |
114 remainingLevel_ != std::numeric_limits<int>::max()); | |
115 } | |
116 | |
117 const std::string& GetRemainingLevelUuid() const | |
118 { | |
119 assert(HasRemainingLevel()); | |
120 return remainingLevelUuid_; | |
121 } | |
122 | |
123 const char* GetRemainingLevelType() const | |
124 { | |
125 assert(HasRemainingLevel()); | |
126 switch (remainingLevel_) | |
127 { | |
128 case 1: | |
129 return "patient"; | |
130 case 2: | |
131 return "study"; | |
132 case 3: | |
133 return "series"; | |
134 default: | |
62 | 135 throw OrthancException(ErrorCode_InternalError); |
0 | 136 } |
137 } | |
138 | |
139 virtual const char* GetName() const | |
140 { | |
141 return "SignalDeletedLevel"; | |
142 } | |
143 | |
144 virtual unsigned int GetCardinality() const | |
145 { | |
146 return 2; | |
147 } | |
148 | |
149 virtual void Compute(SQLite::FunctionContext& context) | |
150 { | |
151 int level = context.GetIntValue(0); | |
152 if (level < remainingLevel_) | |
153 { | |
154 remainingLevel_ = level; | |
155 remainingLevelUuid_ = context.GetStringValue(1); | |
156 } | |
157 | |
158 //printf("deleted level [%d] [%s]\n", level, context.GetStringValue(1).c_str()); | |
159 } | |
160 }; | |
161 } | |
162 | |
163 | |
164 void ServerIndex::StoreMainDicomTags(const std::string& uuid, | |
165 const DicomMap& map) | |
166 { | |
167 DicomArray flattened(map); | |
168 for (size_t i = 0; i < flattened.GetSize(); i++) | |
169 { | |
138 | 170 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO MainDicomTags VALUES(?, ?, ?, ?)"); |
0 | 171 s.BindString(0, uuid); |
172 s.BindInt(1, flattened.GetElement(i).GetTag().GetGroup()); | |
173 s.BindInt(2, flattened.GetElement(i).GetTag().GetElement()); | |
174 s.BindString(3, flattened.GetElement(i).GetValue().AsString()); | |
175 s.Run(); | |
176 } | |
177 } | |
178 | |
179 bool ServerIndex::GetMainDicomStringTag(std::string& result, | |
180 const std::string& uuid, | |
181 const DicomTag& tag) | |
182 { | |
183 SQLite::Statement s(db_, SQLITE_FROM_HERE, | |
184 "SELECT * FROM MainDicomTags WHERE uuid=? AND tagGroup=? AND tagElement=?"); | |
185 s.BindString(0, uuid); | |
186 s.BindInt(1, tag.GetGroup()); | |
187 s.BindInt(2, tag.GetElement()); | |
188 if (!s.Step()) | |
189 { | |
190 return false; | |
191 } | |
192 | |
193 result = s.ColumnString(0); | |
194 return true; | |
195 } | |
196 | |
197 bool ServerIndex::GetMainDicomIntTag(int& result, | |
198 const std::string& uuid, | |
199 const DicomTag& tag) | |
200 { | |
201 std::string s; | |
202 if (!GetMainDicomStringTag(s, uuid, tag)) | |
203 { | |
204 return false; | |
205 } | |
206 | |
207 try | |
208 { | |
209 result = boost::lexical_cast<int>(s); | |
210 return true; | |
211 } | |
212 catch (boost::bad_lexical_cast) | |
213 { | |
214 return false; | |
215 } | |
216 } | |
217 | |
180
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218 |
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219 bool ServerIndex::HasInstance(DicomInstanceHasher& hasher) |
0 | 220 { |
221 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Instances WHERE dicomInstance=?"); | |
179 | 222 s.BindString(0, hasher.GetInstanceUid()); |
180
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223 return s.Step(); |
0 | 224 } |
225 | |
226 | |
227 void ServerIndex::RecordChange(const std::string& resourceType, | |
228 const std::string& uuid) | |
229 { | |
230 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Changes VALUES(NULL, ?, ?)"); | |
231 s.BindString(0, resourceType); | |
232 s.BindString(1, uuid); | |
233 s.Run(); | |
234 } | |
235 | |
236 | |
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237 void ServerIndex::CreateInstance(DicomInstanceHasher& hasher, |
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238 const DicomMap& dicomSummary, |
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239 const std::string& fileUuid, |
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240 uint64_t fileSize, |
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241 const std::string& jsonUuid, |
187
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242 const std::string& remoteAet) |
0 | 243 { |
82 | 244 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
180
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245 s2.BindString(0, hasher.HashInstance()); |
82 | 246 s2.BindInt(1, ResourceType_Instance); |
247 s2.Run(); | |
248 | |
80 | 249 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Instances VALUES(?, ?, ?, ?, ?, ?, ?, ?)"); |
180
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250 s.BindString(0, hasher.HashInstance()); |
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251 s.BindString(1, hasher.HashSeries()); |
179 | 252 s.BindString(2, hasher.GetInstanceUid()); |
0 | 253 s.BindString(3, fileUuid); |
254 s.BindInt64(4, fileSize); | |
255 s.BindString(5, jsonUuid); | |
187
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256 s.BindString(6, remoteAet); |
80 | 257 |
258 const DicomValue* indexInSeries; | |
259 if ((indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
260 (indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
261 { | |
262 s.BindInt(7, boost::lexical_cast<unsigned int>(indexInSeries->AsString())); | |
263 } | |
264 else | |
265 { | |
266 s.BindNull(7); | |
267 } | |
268 | |
0 | 269 s.Run(); |
270 | |
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271 RecordChange("instances", hasher.HashInstance()); |
0 | 272 |
273 DicomMap dicom; | |
274 dicomSummary.ExtractInstanceInformation(dicom); | |
180
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275 StoreMainDicomTags(hasher.HashInstance(), dicom); |
0 | 276 } |
277 | |
278 void ServerIndex::RemoveInstance(const std::string& uuid) | |
279 { | |
280 SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Instances WHERE uuid=?"); | |
281 s.BindString(0, uuid); | |
282 s.Run(); | |
283 } | |
284 | |
180
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285 bool ServerIndex::HasSeries(DicomInstanceHasher& hasher) |
0 | 286 { |
287 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Series WHERE dicomSeries=?"); | |
179 | 288 s.BindString(0, hasher.GetSeriesUid()); |
180
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289 return s.Step(); |
0 | 290 } |
291 | |
180
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292 void ServerIndex::CreateSeries(DicomInstanceHasher& hasher, |
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293 const DicomMap& dicomSummary) |
0 | 294 { |
82 | 295 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
180
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296 s2.BindString(0, hasher.HashSeries()); |
82 | 297 s2.BindInt(1, ResourceType_Series); |
298 s2.Run(); | |
299 | |
77 | 300 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Series VALUES(?, ?, ?, ?)"); |
180
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301 s.BindString(0, hasher.HashSeries()); |
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302 s.BindString(1, hasher.HashStudy()); |
179 | 303 s.BindString(2, hasher.GetSeriesUid()); |
80 | 304 |
305 const DicomValue* expectedNumberOfInstances; | |
84 | 306 if (//(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES)) != NULL || |
80 | 307 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
82 | 308 //(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL || |
80 | 309 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL) |
310 { | |
311 s.BindInt(3, boost::lexical_cast<unsigned int>(expectedNumberOfInstances->AsString())); | |
312 } | |
313 else | |
314 { | |
315 s.BindNull(3); | |
316 } | |
317 | |
0 | 318 s.Run(); |
319 | |
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320 RecordChange("series", hasher.HashSeries()); |
0 | 321 |
322 DicomMap dicom; | |
323 dicomSummary.ExtractSeriesInformation(dicom); | |
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324 StoreMainDicomTags(hasher.HashSeries(), dicom); |
0 | 325 } |
326 | |
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327 bool ServerIndex::HasStudy(DicomInstanceHasher& hasher) |
0 | 328 { |
329 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Studies WHERE dicomStudy=?"); | |
179 | 330 s.BindString(0, hasher.GetStudyUid()); |
180
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331 return s.Step(); |
0 | 332 } |
333 | |
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334 void ServerIndex::CreateStudy(DicomInstanceHasher& hasher, |
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335 const DicomMap& dicomSummary) |
0 | 336 { |
82 | 337 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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338 s2.BindString(0, hasher.HashStudy()); |
82 | 339 s2.BindInt(1, ResourceType_Study); |
340 s2.Run(); | |
341 | |
0 | 342 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Studies VALUES(?, ?, ?)"); |
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343 s.BindString(0, hasher.HashStudy()); |
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344 s.BindString(1, hasher.HashPatient()); |
179 | 345 s.BindString(2, hasher.GetStudyUid()); |
0 | 346 s.Run(); |
347 | |
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348 RecordChange("studies", hasher.HashStudy()); |
0 | 349 |
350 DicomMap dicom; | |
351 dicomSummary.ExtractStudyInformation(dicom); | |
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352 StoreMainDicomTags(hasher.HashStudy(), dicom); |
0 | 353 } |
354 | |
355 | |
356 | |
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357 bool ServerIndex::HasPatient(DicomInstanceHasher& hasher) |
0 | 358 { |
359 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Patients WHERE dicomPatientId=?"); | |
179 | 360 s.BindString(0,hasher.GetPatientId()); |
180
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361 return s.Step(); |
0 | 362 } |
363 | |
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364 void ServerIndex::CreatePatient(DicomInstanceHasher& hasher, |
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365 const DicomMap& dicomSummary) |
0 | 366 { |
80 | 367 std::string dicomPatientId = dicomSummary.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
0 | 368 |
82 | 369 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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370 s2.BindString(0, hasher.HashPatient()); |
82 | 371 s2.BindInt(1, ResourceType_Patient); |
372 s2.Run(); | |
373 | |
0 | 374 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Patients VALUES(?, ?)"); |
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375 s.BindString(0, hasher.HashPatient()); |
0 | 376 s.BindString(1, dicomPatientId); |
377 s.Run(); | |
378 | |
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379 RecordChange("patients", hasher.HashPatient()); |
0 | 380 |
381 DicomMap dicom; | |
382 dicomSummary.ExtractPatientInformation(dicom); | |
180
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383 StoreMainDicomTags(hasher.HashPatient(), dicom); |
0 | 384 } |
385 | |
386 | |
387 void ServerIndex::GetMainDicomTags(DicomMap& map, | |
388 const std::string& uuid) | |
389 { | |
390 map.Clear(); | |
391 | |
392 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM MainDicomTags WHERE uuid=?"); | |
393 s.BindString(0, uuid); | |
394 while (s.Step()) | |
395 { | |
396 map.SetValue(s.ColumnInt(1), | |
397 s.ColumnInt(2), | |
398 s.ColumnString(3)); | |
399 } | |
400 } | |
401 | |
402 void ServerIndex::MainDicomTagsToJson(Json::Value& target, | |
403 const std::string& uuid) | |
404 { | |
405 DicomMap map; | |
406 GetMainDicomTags(map, uuid); | |
407 target["MainDicomTags"] = Json::objectValue; | |
408 FromDcmtkBridge::ToJson(target["MainDicomTags"], map); | |
409 } | |
410 | |
411 | |
412 bool ServerIndex::DeleteInternal(Json::Value& target, | |
413 const std::string& uuid, | |
414 const std::string& tableName) | |
415 { | |
416 boost::mutex::scoped_lock scoped_lock(mutex_); | |
417 | |
418 deletedLevels_->Clear(); | |
419 | |
420 SQLite::Statement s(db_, "DELETE FROM " + tableName + " WHERE uuid=?"); | |
421 s.BindString(0, uuid); | |
422 | |
423 if (!s.Run()) | |
424 { | |
425 return false; | |
426 } | |
427 | |
428 if (db_.GetLastChangeCount() == 0) | |
429 { | |
430 // Nothing was deleted, inexistent UUID | |
431 return false; | |
432 } | |
433 | |
434 if (deletedLevels_->HasRemainingLevel()) | |
435 { | |
436 std::string type(deletedLevels_->GetRemainingLevelType()); | |
437 const std::string& uuid = deletedLevels_->GetRemainingLevelUuid(); | |
438 | |
439 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
440 target["RemainingAncestor"]["Path"] = "/" + type + "/" + uuid; | |
441 target["RemainingAncestor"]["Type"] = type; | |
442 target["RemainingAncestor"]["ID"] = uuid; | |
443 } | |
444 else | |
445 { | |
446 target["RemainingAncestor"] = Json::nullValue; | |
447 } | |
448 | |
449 return true; | |
450 } | |
451 | |
452 | |
186
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453 namespace Internals |
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454 { |
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455 class ServerIndexListenerTmp : public IServerIndexListener |
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456 { |
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457 public: |
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458 virtual void SignalRemainingAncestor(ResourceType parentType, |
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459 const std::string& publicId) |
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460 { |
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461 LOG(INFO) << "Remaning ancestor \"" << publicId << "\" (" << parentType << ")"; |
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462 } |
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463 |
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464 virtual void SignalFileDeleted(const std::string& fileUuid) |
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465 { |
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466 LOG(INFO) << "Deleted file " << fileUuid; |
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467 } |
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468 |
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469 }; |
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470 } |
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471 |
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472 |
0 | 473 ServerIndex::ServerIndex(const std::string& storagePath) |
474 { | |
186
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475 listener2_.reset(new Internals::ServerIndexListenerTmp); |
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476 |
180
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477 if (storagePath == ":memory:") |
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478 { |
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479 db_.OpenInMemory(); |
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480 db2_.reset(new DatabaseWrapper(*listener2_)); |
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481 } |
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482 else |
0 | 483 { |
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484 boost::filesystem::path p = storagePath; |
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485 |
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486 try |
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487 { |
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488 boost::filesystem::create_directories(storagePath); |
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489 } |
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490 catch (boost::filesystem::filesystem_error) |
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491 { |
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492 } |
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493 |
186
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494 db2_.reset(new DatabaseWrapper(p.string() + "/index2", *listener2_)); |
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495 |
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496 p /= "index"; |
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497 db_.Open(p.string()); |
0 | 498 } |
499 | |
500 db_.Register(new Internals::DeleteFromFileStorageFunction(storagePath)); | |
501 deletedLevels_ = (Internals::SignalDeletedLevelFunction*) | |
502 db_.Register(new Internals::SignalDeletedLevelFunction); | |
503 | |
504 if (!db_.DoesTableExist("GlobalProperties")) | |
505 { | |
108 | 506 LOG(INFO) << "Creating the database"; |
0 | 507 std::string query; |
508 EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE); | |
509 db_.Execute(query); | |
510 } | |
511 } | |
512 | |
513 | |
187
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514 StoreStatus ServerIndex::Store2(const DicomMap& dicomSummary, |
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515 const std::string& fileUuid, |
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516 uint64_t uncompressedFileSize, |
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517 const std::string& jsonUuid, |
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518 const std::string& remoteAet) |
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519 { |
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520 boost::mutex::scoped_lock scoped_lock(mutex_); |
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521 |
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522 DicomInstanceHasher hasher(dicomSummary); |
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523 |
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524 try |
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525 { |
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526 std::auto_ptr<SQLite::Transaction> t(db2_->StartTransaction()); |
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527 t->Begin(); |
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528 |
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529 int64_t patient, study, series, instance; |
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530 ResourceType type; |
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531 bool isNewSeries = false; |
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532 |
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533 // Do nothing if the instance already exists |
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534 if (db2_->FindResource(hasher.HashInstance(), patient, type)) |
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535 { |
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536 assert(type == ResourceType_Patient); |
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537 return StoreStatus_AlreadyStored; |
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538 } |
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539 |
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540 // Create the patient/study/series/instance hierarchy |
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541 instance = db2_->CreateResource(hasher.HashInstance(), ResourceType_Instance); |
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542 |
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543 if (!db2_->FindResource(hasher.HashSeries(), series, type)) |
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544 { |
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545 // This is a new series |
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546 isNewSeries = true; |
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547 series = db2_->CreateResource(hasher.HashSeries(), ResourceType_Series); |
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548 db2_->AttachChild(series, instance); |
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549 |
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550 if (!db2_->FindResource(hasher.HashStudy(), study, type)) |
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551 { |
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552 // This is a new study |
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553 study = db2_->CreateResource(hasher.HashStudy(), ResourceType_Study); |
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554 db2_->AttachChild(study, series); |
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555 |
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556 if (!db2_->FindResource(hasher.HashPatient(), patient, type)) |
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557 { |
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558 // This is a new patient |
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559 patient = db2_->CreateResource(hasher.HashPatient(), ResourceType_Patient); |
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560 db2_->AttachChild(patient, study); |
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561 } |
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562 else |
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563 { |
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564 assert(type == ResourceType_Patient); |
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565 } |
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566 } |
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567 else |
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568 { |
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569 assert(type == ResourceType_Study); |
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570 } |
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571 } |
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572 else |
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573 { |
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574 assert(type == ResourceType_Series); |
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575 } |
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576 |
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577 // Attach the files to the newly created instance |
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578 db2_->AttachFile(instance, "_dicom", fileUuid, uncompressedFileSize); |
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579 db2_->AttachFile(instance, "_json", jsonUuid, 0); // TODO "0" |
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580 |
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581 // Attach the metadata |
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582 db2_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); |
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583 db2_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
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584 |
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585 const DicomValue* value; |
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586 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || |
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587 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) |
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588 { |
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589 db2_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
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590 } |
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591 |
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592 if (isNewSeries) |
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593 { |
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594 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
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595 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL) |
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596 { |
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597 db2_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); |
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598 } |
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599 } |
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600 |
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601 t->Commit(); |
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602 } |
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603 catch (OrthancException& e) |
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604 { |
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605 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
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606 } |
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607 |
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608 return StoreStatus_Failure; |
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609 } |
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610 |
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611 |
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612 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
0 | 613 const std::string& fileUuid, |
614 uint64_t uncompressedFileSize, | |
615 const std::string& jsonUuid, | |
187
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616 const std::string& remoteAet) |
0 | 617 { |
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618 Store2(dicomSummary, fileUuid, uncompressedFileSize, jsonUuid, remoteAet); |
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619 |
0 | 620 boost::mutex::scoped_lock scoped_lock(mutex_); |
621 | |
178 | 622 DicomInstanceHasher hasher(dicomSummary); |
0 | 623 |
624 try | |
625 { | |
626 SQLite::Transaction t(db_); | |
627 t.Begin(); | |
628 | |
180
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629 if (HasInstance(hasher)) |
0 | 630 { |
631 return StoreStatus_AlreadyStored; | |
632 // TODO: Check consistency? | |
633 } | |
634 | |
180
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635 if (HasPatient(hasher)) |
0 | 636 { |
637 // TODO: Check consistency? | |
638 } | |
639 else | |
640 { | |
180
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641 CreatePatient(hasher, dicomSummary); |
0 | 642 } |
643 | |
180
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644 if (HasStudy(hasher)) |
0 | 645 { |
646 // TODO: Check consistency? | |
647 } | |
648 else | |
649 { | |
180
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650 CreateStudy(hasher, dicomSummary); |
0 | 651 } |
652 | |
180
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653 if (HasSeries(hasher)) |
0 | 654 { |
655 // TODO: Check consistency? | |
656 } | |
657 else | |
658 { | |
180
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659 CreateSeries(hasher, dicomSummary); |
0 | 660 } |
661 | |
180
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662 CreateInstance(hasher, dicomSummary, fileUuid, |
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663 uncompressedFileSize, jsonUuid, remoteAet); |
0 | 664 |
665 t.Commit(); | |
666 return StoreStatus_Success; | |
667 //t.Rollback(); | |
668 } | |
62 | 669 catch (OrthancException& e) |
0 | 670 { |
108 | 671 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
0 | 672 } |
673 | |
674 return StoreStatus_Failure; | |
675 } | |
676 | |
677 | |
187
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678 StoreStatus ServerIndex::Store(FileStorage& storage, |
0 | 679 const char* dicomFile, |
680 size_t dicomSize, | |
681 const DicomMap& dicomSummary, | |
682 const Json::Value& dicomJson, | |
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683 const std::string& remoteAet) |
0 | 684 { |
685 std::string fileUuid = storage.Create(dicomFile, dicomSize); | |
686 std::string jsonUuid = storage.Create(dicomJson.toStyledString()); | |
187
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687 StoreStatus status = Store(dicomSummary, fileUuid, dicomSize, jsonUuid, remoteAet); |
0 | 688 |
689 if (status != StoreStatus_Success) | |
690 { | |
147 | 691 storage.Remove(fileUuid); |
692 storage.Remove(jsonUuid); | |
0 | 693 } |
694 | |
695 switch (status) | |
696 { | |
697 case StoreStatus_Success: | |
187
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698 LOG(WARNING) << "New instance stored"; |
0 | 699 break; |
700 | |
701 case StoreStatus_AlreadyStored: | |
138 | 702 LOG(WARNING) << "Already stored"; |
0 | 703 break; |
704 | |
705 case StoreStatus_Failure: | |
138 | 706 LOG(ERROR) << "Store failure"; |
0 | 707 break; |
708 } | |
709 | |
710 return status; | |
711 } | |
712 | |
187
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713 uint64_t ServerIndex::GetTotalCompressedSize() |
0 | 714 { |
715 boost::mutex::scoped_lock scoped_lock(mutex_); | |
187
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716 return db2_->GetTotalCompressedSize(); |
0 | 717 } |
718 | |
187
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719 uint64_t ServerIndex::GetTotalUncompressedSize() |
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720 { |
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721 boost::mutex::scoped_lock scoped_lock(mutex_); |
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722 return db2_->GetTotalUncompressedSize(); |
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723 } |
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724 |
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725 |
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726 |
0 | 727 |
728 SeriesStatus ServerIndex::GetSeriesStatus(const std::string& seriesUuid) | |
729 { | |
80 | 730 SQLite::Statement s1(db_, SQLITE_FROM_HERE, "SELECT expectedNumberOfInstances FROM Series WHERE uuid=?"); |
731 s1.BindString(0, seriesUuid); | |
82 | 732 if (!s1.Step() || s1.ColumnIsNull(0)) |
80 | 733 { |
734 return SeriesStatus_Unknown; | |
735 } | |
736 | |
737 int numberOfInstances = s1.ColumnInt(0); | |
738 if (numberOfInstances < 0) | |
0 | 739 { |
740 return SeriesStatus_Unknown; | |
741 } | |
742 | |
80 | 743 std::set<int> instances; |
744 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "SELECT indexInSeries FROM Instances WHERE parentSeries=?"); | |
745 s2.BindString(0, seriesUuid); | |
746 while (s2.Step()) | |
747 { | |
748 int index = s2.ColumnInt(0); | |
749 if (index <= 0 || index > numberOfInstances) | |
750 { | |
751 // Out-of-range instance index | |
752 return SeriesStatus_Inconsistent; | |
753 } | |
0 | 754 |
80 | 755 if (instances.find(index) != instances.end()) |
756 { | |
757 // Twice the same instance index | |
758 return SeriesStatus_Inconsistent; | |
759 } | |
760 | |
761 instances.insert(index); | |
762 } | |
763 | |
764 for (int i = 1; i <= numberOfInstances; i++) | |
765 { | |
766 if (instances.find(i) == instances.end()) | |
767 { | |
768 return SeriesStatus_Missing; | |
769 } | |
770 } | |
771 | |
772 return SeriesStatus_Complete; | |
0 | 773 } |
774 | |
775 | |
776 | |
777 bool ServerIndex::GetInstance(Json::Value& result, | |
778 const std::string& instanceUuid) | |
779 { | |
780 assert(result.type() == Json::objectValue); | |
781 boost::mutex::scoped_lock scoped_lock(mutex_); | |
782 | |
80 | 783 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT parentSeries, dicomInstance, fileSize, fileUuid, indexInSeries FROM Instances WHERE uuid=?"); |
0 | 784 s.BindString(0, instanceUuid); |
785 if (!s.Step()) | |
786 { | |
787 return false; | |
788 } | |
789 else | |
790 { | |
791 result["ID"] = instanceUuid; | |
792 result["ParentSeries"] = s.ColumnString(0); | |
793 result["FileSize"] = s.ColumnInt(2); // TODO switch to 64bit with JsonCpp 0.6? | |
794 result["FileUuid"] = s.ColumnString(3); | |
795 MainDicomTagsToJson(result, instanceUuid); | |
80 | 796 |
797 if (s.ColumnIsNull(4)) | |
798 { | |
82 | 799 result["IndexInSeries"] = Json::nullValue; |
80 | 800 } |
801 else | |
802 { | |
803 result["IndexInSeries"] = s.ColumnInt(4); | |
804 } | |
805 | |
0 | 806 return true; |
807 } | |
808 } | |
809 | |
810 | |
811 bool ServerIndex::GetSeries(Json::Value& result, | |
812 const std::string& seriesUuid) | |
813 { | |
814 assert(result.type() == Json::objectValue); | |
815 boost::mutex::scoped_lock scoped_lock(mutex_); | |
816 | |
80 | 817 SQLite::Statement s1(db_, SQLITE_FROM_HERE, "SELECT parentStudy, dicomSeries, expectedNumberOfInstances FROM Series WHERE uuid=?"); |
0 | 818 s1.BindString(0, seriesUuid); |
819 if (!s1.Step()) | |
820 { | |
821 return false; | |
822 } | |
823 | |
824 result["ID"] = seriesUuid; | |
825 result["ParentStudy"] = s1.ColumnString(0); | |
826 MainDicomTagsToJson(result, seriesUuid); | |
827 | |
828 Json::Value instances(Json::arrayValue); | |
829 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Instances WHERE parentSeries=?"); | |
830 s2.BindString(0, seriesUuid); | |
831 while (s2.Step()) | |
832 { | |
833 instances.append(s2.ColumnString(0)); | |
834 } | |
835 | |
836 result["Instances"] = instances; | |
837 | |
80 | 838 if (s1.ColumnIsNull(2)) |
839 { | |
82 | 840 result["ExpectedNumberOfInstances"] = Json::nullValue; |
80 | 841 } |
842 else | |
843 { | |
844 result["ExpectedNumberOfInstances"] = s1.ColumnInt(2); | |
845 } | |
846 | |
847 SeriesStatus status = GetSeriesStatus(seriesUuid); | |
848 | |
849 switch (status) | |
850 { | |
851 case SeriesStatus_Complete: | |
852 result["Status"] = "Complete"; | |
853 break; | |
854 | |
855 case SeriesStatus_Missing: | |
856 result["Status"] = "Missing"; | |
857 break; | |
858 | |
859 case SeriesStatus_Inconsistent: | |
860 result["Status"] = "Inconsistent"; | |
861 break; | |
862 | |
863 default: | |
864 case SeriesStatus_Unknown: | |
865 result["Status"] = "Unknown"; | |
866 break; | |
867 } | |
868 | |
0 | 869 return true; |
870 } | |
871 | |
872 | |
873 bool ServerIndex::GetStudy(Json::Value& result, | |
874 const std::string& studyUuid) | |
875 { | |
876 assert(result.type() == Json::objectValue); | |
877 boost::mutex::scoped_lock scoped_lock(mutex_); | |
878 | |
879 SQLite::Statement s1(db_, SQLITE_FROM_HERE, "SELECT parentPatient, dicomStudy FROM Studies WHERE uuid=?"); | |
880 s1.BindString(0, studyUuid); | |
881 if (!s1.Step()) | |
882 { | |
883 return false; | |
884 } | |
885 | |
886 result["ID"] = studyUuid; | |
887 result["ParentPatient"] = s1.ColumnString(0); | |
888 MainDicomTagsToJson(result, studyUuid); | |
889 | |
890 Json::Value series(Json::arrayValue); | |
891 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Series WHERE parentStudy=?"); | |
892 s2.BindString(0, studyUuid); | |
893 while (s2.Step()) | |
894 { | |
895 series.append(s2.ColumnString(0)); | |
896 } | |
897 | |
898 result["Series"] = series; | |
899 return true; | |
900 } | |
901 | |
902 | |
903 bool ServerIndex::GetPatient(Json::Value& result, | |
904 const std::string& patientUuid) | |
905 { | |
906 assert(result.type() == Json::objectValue); | |
907 boost::mutex::scoped_lock scoped_lock(mutex_); | |
908 | |
909 SQLite::Statement s1(db_, SQLITE_FROM_HERE, "SELECT dicomPatientId FROM Patients WHERE uuid=?"); | |
910 s1.BindString(0, patientUuid); | |
911 if (!s1.Step()) | |
912 { | |
913 return false; | |
914 } | |
915 | |
916 result["ID"] = patientUuid; | |
917 MainDicomTagsToJson(result, patientUuid); | |
918 | |
919 Json::Value studies(Json::arrayValue); | |
920 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Studies WHERE parentPatient=?"); | |
921 s2.BindString(0, patientUuid); | |
922 while (s2.Step()) | |
923 { | |
924 studies.append(s2.ColumnString(0)); | |
925 } | |
926 | |
927 result["Studies"] = studies; | |
928 return true; | |
929 } | |
930 | |
931 | |
932 bool ServerIndex::GetJsonFile(std::string& fileUuid, | |
933 const std::string& instanceUuid) | |
934 { | |
935 boost::mutex::scoped_lock scoped_lock(mutex_); | |
936 | |
937 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT jsonUuid FROM Instances WHERE uuid=?"); | |
938 s.BindString(0, instanceUuid); | |
939 if (s.Step()) | |
940 { | |
941 fileUuid = s.ColumnString(0); | |
942 return true; | |
943 } | |
944 else | |
945 { | |
946 return false; | |
947 } | |
948 } | |
949 | |
950 bool ServerIndex::GetDicomFile(std::string& fileUuid, | |
951 const std::string& instanceUuid) | |
952 { | |
953 boost::mutex::scoped_lock scoped_lock(mutex_); | |
954 | |
955 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT fileUuid FROM Instances WHERE uuid=?"); | |
956 s.BindString(0, instanceUuid); | |
957 if (s.Step()) | |
958 { | |
959 fileUuid = s.ColumnString(0); | |
960 return true; | |
961 } | |
962 else | |
963 { | |
964 return false; | |
965 } | |
966 } | |
967 | |
968 | |
969 void ServerIndex::GetAllUuids(Json::Value& target, | |
970 const std::string& tableName) | |
971 { | |
972 assert(target.type() == Json::arrayValue); | |
973 boost::mutex::scoped_lock scoped_lock(mutex_); | |
974 | |
975 std::string query = "SELECT uuid FROM " + tableName; | |
976 SQLite::Statement s(db_, query); | |
977 while (s.Step()) | |
978 { | |
979 target.append(s.ColumnString(0)); | |
980 } | |
981 } | |
982 | |
983 | |
984 bool ServerIndex::GetChanges(Json::Value& target, | |
985 int64_t since, | |
986 const std::string& filter, | |
987 unsigned int maxResults) | |
988 { | |
989 assert(target.type() == Json::objectValue); | |
990 boost::mutex::scoped_lock scoped_lock(mutex_); | |
991 | |
992 if (filter.size() != 0 && | |
993 filter != "instances" && | |
994 filter != "series" && | |
995 filter != "studies" && | |
996 filter != "patients") | |
997 { | |
998 return false; | |
999 } | |
1000 | |
1001 std::auto_ptr<SQLite::Statement> s; | |
1002 if (filter.size() == 0) | |
1003 { | |
1004 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
1005 "ORDER BY seq LIMIT ?")); | |
1006 s->BindInt64(0, since); | |
1007 s->BindInt(1, maxResults); | |
1008 } | |
1009 else | |
1010 { | |
1011 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
1012 "AND basePath=? ORDER BY seq LIMIT ?")); | |
1013 s->BindInt64(0, since); | |
1014 s->BindString(1, filter); | |
1015 s->BindInt(2, maxResults); | |
1016 } | |
1017 | |
1018 int64_t lastSeq = 0; | |
1019 Json::Value results(Json::arrayValue); | |
1020 while (s->Step()) | |
1021 { | |
1022 int64_t seq = s->ColumnInt64(0); | |
1023 std::string basePath = s->ColumnString(1); | |
1024 std::string uuid = s->ColumnString(2); | |
1025 | |
1026 if (filter.size() == 0 || | |
1027 filter == basePath) | |
1028 { | |
1029 Json::Value change(Json::objectValue); | |
1030 change["Seq"] = static_cast<int>(seq); // TODO JsonCpp in 64bit | |
1031 change["BasePath"] = basePath; | |
1032 change["ID"] = uuid; | |
1033 results.append(change); | |
1034 } | |
1035 | |
1036 if (seq > lastSeq) | |
1037 { | |
1038 lastSeq = seq; | |
1039 } | |
1040 } | |
1041 | |
1042 target["Results"] = results; | |
1043 target["LastSeq"] = static_cast<int>(lastSeq); // TODO JsonCpp in 64bit | |
1044 | |
1045 return true; | |
1046 } | |
82 | 1047 |
0 | 1048 } |