Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 205:6ab754744446
logging of completed series
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 28 Nov 2012 11:34:54 +0100 |
parents | 7f4acf490179 |
children | 4453a010d0db |
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 { | |
202 | 56 class ServerIndexListener : public IServerIndexListener |
201
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57 { |
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58 private: |
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59 FileStorage& fileStorage_; |
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60 bool hasRemainingLevel_; |
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61 ResourceType remainingType_; |
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62 std::string remainingPublicId_; |
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63 |
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64 public: |
202 | 65 ServerIndexListener(FileStorage& fileStorage) : |
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66 fileStorage_(fileStorage), |
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67 hasRemainingLevel_(false) |
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68 { |
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69 assert(ResourceType_Patient < ResourceType_Study && |
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70 ResourceType_Study < ResourceType_Series && |
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71 ResourceType_Series < ResourceType_Instance); |
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72 } |
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73 |
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74 void Reset() |
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75 { |
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76 hasRemainingLevel_ = false; |
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77 } |
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78 |
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79 virtual void SignalRemainingAncestor(ResourceType parentType, |
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80 const std::string& publicId) |
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81 { |
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82 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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83 |
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84 if (hasRemainingLevel_) |
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85 { |
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86 if (parentType < remainingType_) |
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87 { |
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88 remainingType_ = parentType; |
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89 remainingPublicId_ = publicId; |
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90 } |
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91 } |
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92 else |
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93 { |
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94 hasRemainingLevel_ = true; |
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95 remainingType_ = parentType; |
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96 remainingPublicId_ = publicId; |
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97 } |
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98 } |
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99 |
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100 virtual void SignalFileDeleted(const std::string& fileUuid) |
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101 { |
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102 assert(Toolbox::IsUuid(fileUuid)); |
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103 fileStorage_.Remove(fileUuid); |
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104 } |
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105 |
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106 bool HasRemainingLevel() const |
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107 { |
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108 return hasRemainingLevel_; |
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109 } |
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110 |
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111 ResourceType GetRemainingType() const |
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112 { |
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113 assert(HasRemainingLevel()); |
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114 return remainingType_; |
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115 } |
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116 |
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117 const std::string& GetRemainingPublicId() const |
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118 { |
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119 assert(HasRemainingLevel()); |
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120 return remainingPublicId_; |
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121 } |
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122 }; |
0 | 123 } |
124 | |
125 | |
126 bool ServerIndex::DeleteInternal(Json::Value& target, | |
127 const std::string& uuid, | |
202 | 128 ResourceType expectedType) |
0 | 129 { |
130 boost::mutex::scoped_lock scoped_lock(mutex_); | |
131 | |
202 | 132 listener_->Reset(); |
201
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133 |
202 | 134 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
135 t->Begin(); | |
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136 |
202 | 137 int64_t id; |
138 ResourceType type; | |
139 if (!db_->LookupResource(uuid, id, type) || | |
140 expectedType != type) | |
0 | 141 { |
142 return false; | |
143 } | |
202 | 144 |
145 db_->DeleteResource(id); | |
0 | 146 |
202 | 147 if (listener_->HasRemainingLevel()) |
0 | 148 { |
202 | 149 ResourceType type = listener_->GetRemainingType(); |
150 const std::string& uuid = listener_->GetRemainingPublicId(); | |
0 | 151 |
152 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
204 | 153 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
202 | 154 target["RemainingAncestor"]["Type"] = ToString(type); |
0 | 155 target["RemainingAncestor"]["ID"] = uuid; |
156 } | |
157 else | |
158 { | |
159 target["RemainingAncestor"] = Json::nullValue; | |
160 } | |
161 | |
202 | 162 t->Commit(); |
163 | |
0 | 164 return true; |
165 } | |
166 | |
167 | |
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168 ServerIndex::ServerIndex(FileStorage& fileStorage, |
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169 const std::string& dbPath) |
186
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170 { |
202 | 171 listener_.reset(new Internals::ServerIndexListener(fileStorage)); |
186
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172 |
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173 if (dbPath == ":memory:") |
180
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174 { |
202 | 175 db_.reset(new DatabaseWrapper(*listener_)); |
180
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176 } |
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177 else |
0 | 178 { |
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179 boost::filesystem::path p = dbPath; |
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180 |
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181 try |
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182 { |
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183 boost::filesystem::create_directories(p); |
180
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184 } |
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185 catch (boost::filesystem::filesystem_error) |
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186 { |
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187 } |
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188 |
202 | 189 db_.reset(new DatabaseWrapper(p.string() + "/index", *listener_)); |
0 | 190 } |
191 } | |
192 | |
193 | |
187
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194 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
0 | 195 const std::string& fileUuid, |
196 uint64_t uncompressedFileSize, | |
197 const std::string& jsonUuid, | |
187
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198 const std::string& remoteAet) |
0 | 199 { |
200 boost::mutex::scoped_lock scoped_lock(mutex_); | |
201 | |
178 | 202 DicomInstanceHasher hasher(dicomSummary); |
0 | 203 |
204 try | |
205 { | |
202 | 206 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
207 t->Begin(); | |
0 | 208 |
202 | 209 int64_t patient, study, series, instance; |
210 ResourceType type; | |
211 bool isNewSeries = false; | |
212 | |
213 // Do nothing if the instance already exists | |
214 if (db_->LookupResource(hasher.HashInstance(), patient, type)) | |
0 | 215 { |
202 | 216 assert(type == ResourceType_Instance); |
0 | 217 return StoreStatus_AlreadyStored; |
218 } | |
219 | |
202 | 220 // Create the instance |
221 instance = db_->CreateResource(hasher.HashInstance(), ResourceType_Instance); | |
222 | |
223 DicomMap dicom; | |
224 dicomSummary.ExtractInstanceInformation(dicom); | |
225 db_->SetMainDicomTags(instance, dicom); | |
226 | |
227 // Create the patient/study/series/instance hierarchy | |
228 if (!db_->LookupResource(hasher.HashSeries(), series, type)) | |
0 | 229 { |
202 | 230 // This is a new series |
231 isNewSeries = true; | |
232 series = db_->CreateResource(hasher.HashSeries(), ResourceType_Series); | |
233 dicomSummary.ExtractSeriesInformation(dicom); | |
234 db_->SetMainDicomTags(series, dicom); | |
235 db_->AttachChild(series, instance); | |
236 | |
237 if (!db_->LookupResource(hasher.HashStudy(), study, type)) | |
238 { | |
239 // This is a new study | |
240 study = db_->CreateResource(hasher.HashStudy(), ResourceType_Study); | |
241 dicomSummary.ExtractStudyInformation(dicom); | |
242 db_->SetMainDicomTags(study, dicom); | |
243 db_->AttachChild(study, series); | |
244 | |
245 if (!db_->LookupResource(hasher.HashPatient(), patient, type)) | |
246 { | |
247 // This is a new patient | |
248 patient = db_->CreateResource(hasher.HashPatient(), ResourceType_Patient); | |
249 dicomSummary.ExtractPatientInformation(dicom); | |
250 db_->SetMainDicomTags(patient, dicom); | |
251 db_->AttachChild(patient, study); | |
252 } | |
253 else | |
254 { | |
255 assert(type == ResourceType_Patient); | |
256 db_->AttachChild(patient, study); | |
257 } | |
258 } | |
259 else | |
260 { | |
261 assert(type == ResourceType_Study); | |
262 db_->AttachChild(study, series); | |
263 } | |
0 | 264 } |
265 else | |
266 { | |
202 | 267 assert(type == ResourceType_Series); |
268 db_->AttachChild(series, instance); | |
0 | 269 } |
270 | |
202 | 271 // Attach the files to the newly created instance |
272 db_->AttachFile(instance, AttachedFileType_Dicom, fileUuid, uncompressedFileSize); | |
273 db_->AttachFile(instance, AttachedFileType_Json, jsonUuid, 0); // TODO "0" | |
274 | |
275 // Attach the metadata | |
276 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); | |
277 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); | |
278 | |
279 const DicomValue* value; | |
280 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
281 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
0 | 282 { |
202 | 283 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
0 | 284 } |
285 | |
202 | 286 if (isNewSeries) |
287 { | |
288 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || | |
289 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL || | |
290 (value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
291 { | |
292 db_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); | |
293 } | |
294 } | |
295 | |
205
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296 // Check whether the series of this new instance is now completed |
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297 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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298 if (seriesStatus == SeriesStatus_Complete) |
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299 { |
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300 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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301 } |
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302 |
202 | 303 t->Commit(); |
304 | |
0 | 305 return StoreStatus_Success; |
306 } | |
62 | 307 catch (OrthancException& e) |
0 | 308 { |
202 | 309 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_->GetErrorMessage(); |
0 | 310 } |
311 | |
312 return StoreStatus_Failure; | |
313 } | |
314 | |
315 | |
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316 StoreStatus ServerIndex::Store(FileStorage& storage, |
0 | 317 const char* dicomFile, |
318 size_t dicomSize, | |
319 const DicomMap& dicomSummary, | |
320 const Json::Value& dicomJson, | |
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321 const std::string& remoteAet) |
0 | 322 { |
323 std::string fileUuid = storage.Create(dicomFile, dicomSize); | |
324 std::string jsonUuid = storage.Create(dicomJson.toStyledString()); | |
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325 StoreStatus status = Store(dicomSummary, fileUuid, dicomSize, jsonUuid, remoteAet); |
0 | 326 |
327 if (status != StoreStatus_Success) | |
328 { | |
147 | 329 storage.Remove(fileUuid); |
330 storage.Remove(jsonUuid); | |
0 | 331 } |
332 | |
333 switch (status) | |
334 { | |
335 case StoreStatus_Success: | |
194
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336 LOG(INFO) << "New instance stored"; |
0 | 337 break; |
338 | |
339 case StoreStatus_AlreadyStored: | |
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340 LOG(INFO) << "Already stored"; |
0 | 341 break; |
342 | |
343 case StoreStatus_Failure: | |
138 | 344 LOG(ERROR) << "Store failure"; |
0 | 345 break; |
346 } | |
347 | |
348 return status; | |
349 } | |
350 | |
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351 uint64_t ServerIndex::GetTotalCompressedSize() |
0 | 352 { |
353 boost::mutex::scoped_lock scoped_lock(mutex_); | |
202 | 354 return db_->GetTotalCompressedSize(); |
0 | 355 } |
356 | |
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357 uint64_t ServerIndex::GetTotalUncompressedSize() |
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358 { |
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359 boost::mutex::scoped_lock scoped_lock(mutex_); |
202 | 360 return db_->GetTotalUncompressedSize(); |
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361 } |
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362 |
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363 |
199 | 364 SeriesStatus ServerIndex::GetSeriesStatus(int id) |
365 { | |
366 // Get the expected number of instances in this series (from the metadata) | |
202 | 367 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
199 | 368 |
369 size_t expected; | |
370 try | |
371 { | |
372 expected = boost::lexical_cast<size_t>(s); | |
373 if (expected < 0) | |
374 { | |
375 return SeriesStatus_Unknown; | |
376 } | |
377 } | |
378 catch (boost::bad_lexical_cast&) | |
379 { | |
380 return SeriesStatus_Unknown; | |
381 } | |
382 | |
383 // Loop over the instances of this series | |
384 std::list<int64_t> children; | |
202 | 385 db_->GetChildrenInternalId(children, id); |
199 | 386 |
387 std::set<size_t> instances; | |
388 for (std::list<int64_t>::const_iterator | |
389 it = children.begin(); it != children.end(); it++) | |
390 { | |
391 // Get the index of this instance in the series | |
202 | 392 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
199 | 393 size_t index; |
394 try | |
395 { | |
396 index = boost::lexical_cast<size_t>(s); | |
397 } | |
398 catch (boost::bad_lexical_cast&) | |
399 { | |
400 return SeriesStatus_Unknown; | |
401 } | |
402 | |
403 if (index <= 0 || index > expected) | |
404 { | |
405 // Out-of-range instance index | |
406 return SeriesStatus_Inconsistent; | |
407 } | |
408 | |
409 if (instances.find(index) != instances.end()) | |
410 { | |
411 // Twice the same instance index | |
412 return SeriesStatus_Inconsistent; | |
413 } | |
414 | |
415 instances.insert(index); | |
416 } | |
417 | |
418 if (instances.size() == expected) | |
419 { | |
420 return SeriesStatus_Complete; | |
421 } | |
422 else | |
423 { | |
424 return SeriesStatus_Missing; | |
425 } | |
426 } | |
427 | |
428 | |
429 | |
202 | 430 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
431 int64_t resourceId) | |
198
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432 { |
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433 DicomMap tags; |
202 | 434 db_->GetMainDicomTags(tags, resourceId); |
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435 target["MainDicomTags"] = Json::objectValue; |
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436 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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437 } |
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438 |
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439 bool ServerIndex::LookupResource(Json::Value& result, |
199 | 440 const std::string& publicId, |
441 ResourceType expectedType) | |
198
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442 { |
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443 result = Json::objectValue; |
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444 |
199 | 445 boost::mutex::scoped_lock scoped_lock(mutex_); |
446 | |
198
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447 // Lookup for the requested resource |
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448 int64_t id; |
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449 ResourceType type; |
202 | 450 if (!db_->LookupResource(publicId, id, type) || |
199 | 451 type != expectedType) |
198
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452 { |
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453 return false; |
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454 } |
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455 |
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456 // Find the parent resource (if it exists) |
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457 if (type != ResourceType_Patient) |
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458 { |
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459 int64_t parentId; |
202 | 460 if (!db_->LookupParent(parentId, id)) |
198
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461 { |
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462 throw OrthancException(ErrorCode_InternalError); |
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463 } |
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464 |
202 | 465 std::string parent = db_->GetPublicId(parentId); |
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466 |
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467 switch (type) |
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468 { |
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469 case ResourceType_Study: |
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470 result["ParentPatient"] = parent; |
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471 break; |
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472 |
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473 case ResourceType_Series: |
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474 result["ParentStudy"] = parent; |
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475 break; |
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476 |
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477 case ResourceType_Instance: |
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478 result["ParentSeries"] = parent; |
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479 break; |
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480 |
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481 default: |
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482 throw OrthancException(ErrorCode_InternalError); |
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483 } |
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484 } |
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485 |
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486 // List the children resources |
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487 std::list<std::string> children; |
202 | 488 db_->GetChildrenPublicId(children, id); |
198
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489 |
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490 if (type != ResourceType_Instance) |
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491 { |
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492 Json::Value c = Json::arrayValue; |
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493 |
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494 for (std::list<std::string>::const_iterator |
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495 it = children.begin(); it != children.end(); it++) |
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496 { |
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497 c.append(*it); |
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498 } |
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499 |
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500 switch (type) |
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501 { |
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502 case ResourceType_Patient: |
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503 result["Studies"] = c; |
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504 break; |
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505 |
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506 case ResourceType_Study: |
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507 result["Series"] = c; |
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508 break; |
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509 |
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510 case ResourceType_Series: |
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511 result["Instances"] = c; |
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512 break; |
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513 |
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514 default: |
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515 throw OrthancException(ErrorCode_InternalError); |
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516 } |
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517 } |
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518 |
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519 // Set the resource type |
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520 switch (type) |
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521 { |
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522 case ResourceType_Patient: |
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523 result["Type"] = "Patient"; |
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524 break; |
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525 |
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526 case ResourceType_Study: |
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527 result["Type"] = "Study"; |
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528 break; |
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529 |
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530 case ResourceType_Series: |
199 | 531 { |
198
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532 result["Type"] = "Series"; |
199 | 533 result["Status"] = ToString(GetSeriesStatus(id)); |
534 | |
200
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535 int i; |
202 | 536 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
200
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537 result["ExpectedNumberOfInstances"] = i; |
202 | 538 else |
199 | 539 result["ExpectedNumberOfInstances"] = Json::nullValue; |
200
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540 |
198
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541 break; |
199 | 542 } |
198
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543 |
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544 case ResourceType_Instance: |
200
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545 { |
198
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546 result["Type"] = "Instance"; |
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547 |
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548 std::string fileUuid; |
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549 uint64_t uncompressedSize; |
202 | 550 if (!db_->LookupFile(id, AttachedFileType_Dicom, fileUuid, uncompressedSize)) |
200
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551 { |
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552 throw OrthancException(ErrorCode_InternalError); |
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553 } |
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554 |
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555 result["FileSize"] = static_cast<unsigned int>(uncompressedSize); |
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556 result["FileUuid"] = fileUuid; |
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557 |
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558 int i; |
202 | 559 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
200
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560 result["IndexInSeries"] = i; |
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561 else |
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562 result["IndexInSeries"] = Json::nullValue; |
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563 |
198
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564 break; |
200
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565 } |
198
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566 |
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567 default: |
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568 throw OrthancException(ErrorCode_InternalError); |
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569 } |
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570 |
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571 // Record the remaining information |
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572 result["ID"] = publicId; |
202 | 573 MainDicomTagsToJson(result, id); |
198
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574 |
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575 return true; |
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576 } |
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577 |
0 | 578 |
193
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579 bool ServerIndex::GetFile(std::string& fileUuid, |
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580 CompressionType& compressionType, |
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581 const std::string& instanceUuid, |
197
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582 AttachedFileType contentType) |
0 | 583 { |
584 boost::mutex::scoped_lock scoped_lock(mutex_); | |
585 | |
193
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586 int64_t id; |
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587 ResourceType type; |
202 | 588 if (!db_->LookupResource(instanceUuid, id, type) || |
193
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589 type != ResourceType_Instance) |
192
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590 { |
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591 throw OrthancException(ErrorCode_InternalError); |
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592 } |
193
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593 |
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594 uint64_t compressedSize, uncompressedSize; |
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595 |
202 | 596 return db_->LookupFile(id, contentType, fileUuid, compressedSize, uncompressedSize, compressionType); |
192
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597 } |
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598 |
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599 |
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600 |
0 | 601 void ServerIndex::GetAllUuids(Json::Value& target, |
190 | 602 ResourceType resourceType) |
0 | 603 { |
190 | 604 boost::mutex::scoped_lock scoped_lock(mutex_); |
202 | 605 db_->GetAllPublicIds(target, resourceType); |
0 | 606 } |
607 | |
608 | |
609 bool ServerIndex::GetChanges(Json::Value& target, | |
204 | 610 int64_t since, |
0 | 611 unsigned int maxResults) |
612 { | |
613 boost::mutex::scoped_lock scoped_lock(mutex_); | |
614 | |
204 | 615 db_->GetChanges(target, since, maxResults); |
0 | 616 |
204 | 617 return true; |
0 | 618 } |
619 } |