Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 200:9c58b2b03cf0
refactoring of read operations
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 27 Nov 2012 16:49:22 +0100 |
| parents | dfa2899d9960 |
| children | bee20e978835 |
| rev | line source |
|---|---|
| 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: | |
|
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59 std::auto_ptr<FileStorage> fileStorage_; |
| 0 | 60 |
| 61 public: | |
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62 DeleteFromFileStorageFunction(const std::string& path) |
| 0 | 63 { |
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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 { | |
|
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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 | |
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179 bool ServerIndex::HasInstance(DicomInstanceHasher& hasher) |
| 0 | 180 { |
| 181 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Instances WHERE dicomInstance=?"); | |
| 179 | 182 s.BindString(0, hasher.GetInstanceUid()); |
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183 return s.Step(); |
| 0 | 184 } |
| 185 | |
| 186 | |
| 187 void ServerIndex::RecordChange(const std::string& resourceType, | |
| 188 const std::string& uuid) | |
| 189 { | |
| 190 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Changes VALUES(NULL, ?, ?)"); | |
| 191 s.BindString(0, resourceType); | |
| 192 s.BindString(1, uuid); | |
| 193 s.Run(); | |
| 194 } | |
| 195 | |
| 196 | |
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197 void ServerIndex::CreateInstance(DicomInstanceHasher& hasher, |
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198 const DicomMap& dicomSummary, |
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199 const std::string& fileUuid, |
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200 uint64_t fileSize, |
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201 const std::string& jsonUuid, |
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202 const std::string& remoteAet) |
| 0 | 203 { |
| 82 | 204 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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205 s2.BindString(0, hasher.HashInstance()); |
| 82 | 206 s2.BindInt(1, ResourceType_Instance); |
| 207 s2.Run(); | |
| 208 | |
| 80 | 209 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Instances VALUES(?, ?, ?, ?, ?, ?, ?, ?)"); |
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210 s.BindString(0, hasher.HashInstance()); |
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211 s.BindString(1, hasher.HashSeries()); |
| 179 | 212 s.BindString(2, hasher.GetInstanceUid()); |
| 0 | 213 s.BindString(3, fileUuid); |
| 214 s.BindInt64(4, fileSize); | |
| 215 s.BindString(5, jsonUuid); | |
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216 s.BindString(6, remoteAet); |
| 80 | 217 |
| 218 const DicomValue* indexInSeries; | |
| 219 if ((indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 220 (indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 221 { | |
| 222 s.BindInt(7, boost::lexical_cast<unsigned int>(indexInSeries->AsString())); | |
| 223 } | |
| 224 else | |
| 225 { | |
| 226 s.BindNull(7); | |
| 227 } | |
| 228 | |
| 0 | 229 s.Run(); |
| 230 | |
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231 RecordChange("instances", hasher.HashInstance()); |
| 0 | 232 |
| 233 DicomMap dicom; | |
| 234 dicomSummary.ExtractInstanceInformation(dicom); | |
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235 StoreMainDicomTags(hasher.HashInstance(), dicom); |
| 0 | 236 } |
| 237 | |
| 238 void ServerIndex::RemoveInstance(const std::string& uuid) | |
| 239 { | |
| 240 SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Instances WHERE uuid=?"); | |
| 241 s.BindString(0, uuid); | |
| 242 s.Run(); | |
| 243 } | |
| 244 | |
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245 bool ServerIndex::HasSeries(DicomInstanceHasher& hasher) |
| 0 | 246 { |
| 247 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Series WHERE dicomSeries=?"); | |
| 179 | 248 s.BindString(0, hasher.GetSeriesUid()); |
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249 return s.Step(); |
| 0 | 250 } |
| 251 | |
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252 void ServerIndex::CreateSeries(DicomInstanceHasher& hasher, |
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253 const DicomMap& dicomSummary) |
| 0 | 254 { |
| 82 | 255 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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256 s2.BindString(0, hasher.HashSeries()); |
| 82 | 257 s2.BindInt(1, ResourceType_Series); |
| 258 s2.Run(); | |
| 259 | |
| 77 | 260 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Series VALUES(?, ?, ?, ?)"); |
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261 s.BindString(0, hasher.HashSeries()); |
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262 s.BindString(1, hasher.HashStudy()); |
| 179 | 263 s.BindString(2, hasher.GetSeriesUid()); |
| 80 | 264 |
| 265 const DicomValue* expectedNumberOfInstances; | |
| 84 | 266 if (//(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES)) != NULL || |
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267 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
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268 //(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL || |
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269 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL) |
| 80 | 270 { |
| 271 s.BindInt(3, boost::lexical_cast<unsigned int>(expectedNumberOfInstances->AsString())); | |
| 272 } | |
| 273 else | |
| 274 { | |
| 275 s.BindNull(3); | |
| 276 } | |
| 277 | |
| 0 | 278 s.Run(); |
| 279 | |
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280 RecordChange("series", hasher.HashSeries()); |
| 0 | 281 |
| 282 DicomMap dicom; | |
| 283 dicomSummary.ExtractSeriesInformation(dicom); | |
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284 StoreMainDicomTags(hasher.HashSeries(), dicom); |
| 0 | 285 } |
| 286 | |
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287 bool ServerIndex::HasStudy(DicomInstanceHasher& hasher) |
| 0 | 288 { |
| 289 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Studies WHERE dicomStudy=?"); | |
| 179 | 290 s.BindString(0, hasher.GetStudyUid()); |
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291 return s.Step(); |
| 0 | 292 } |
| 293 | |
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294 void ServerIndex::CreateStudy(DicomInstanceHasher& hasher, |
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295 const DicomMap& dicomSummary) |
| 0 | 296 { |
| 82 | 297 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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298 s2.BindString(0, hasher.HashStudy()); |
| 82 | 299 s2.BindInt(1, ResourceType_Study); |
| 300 s2.Run(); | |
| 301 | |
| 0 | 302 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Studies VALUES(?, ?, ?)"); |
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303 s.BindString(0, hasher.HashStudy()); |
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304 s.BindString(1, hasher.HashPatient()); |
| 179 | 305 s.BindString(2, hasher.GetStudyUid()); |
| 0 | 306 s.Run(); |
| 307 | |
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308 RecordChange("studies", hasher.HashStudy()); |
| 0 | 309 |
| 310 DicomMap dicom; | |
| 311 dicomSummary.ExtractStudyInformation(dicom); | |
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312 StoreMainDicomTags(hasher.HashStudy(), dicom); |
| 0 | 313 } |
| 314 | |
| 315 | |
| 316 | |
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317 bool ServerIndex::HasPatient(DicomInstanceHasher& hasher) |
| 0 | 318 { |
| 319 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Patients WHERE dicomPatientId=?"); | |
| 179 | 320 s.BindString(0,hasher.GetPatientId()); |
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321 return s.Step(); |
| 0 | 322 } |
| 323 | |
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324 void ServerIndex::CreatePatient(DicomInstanceHasher& hasher, |
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325 const DicomMap& dicomSummary) |
| 0 | 326 { |
| 80 | 327 std::string dicomPatientId = dicomSummary.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
| 0 | 328 |
| 82 | 329 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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330 s2.BindString(0, hasher.HashPatient()); |
| 82 | 331 s2.BindInt(1, ResourceType_Patient); |
| 332 s2.Run(); | |
| 333 | |
| 0 | 334 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Patients VALUES(?, ?)"); |
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335 s.BindString(0, hasher.HashPatient()); |
| 0 | 336 s.BindString(1, dicomPatientId); |
| 337 s.Run(); | |
| 338 | |
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339 RecordChange("patients", hasher.HashPatient()); |
| 0 | 340 |
| 341 DicomMap dicom; | |
| 342 dicomSummary.ExtractPatientInformation(dicom); | |
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343 StoreMainDicomTags(hasher.HashPatient(), dicom); |
| 0 | 344 } |
| 345 | |
| 346 | |
| 347 bool ServerIndex::DeleteInternal(Json::Value& target, | |
| 348 const std::string& uuid, | |
| 349 const std::string& tableName) | |
| 350 { | |
| 351 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 352 | |
| 353 deletedLevels_->Clear(); | |
| 354 | |
| 355 SQLite::Statement s(db_, "DELETE FROM " + tableName + " WHERE uuid=?"); | |
| 356 s.BindString(0, uuid); | |
| 357 | |
| 358 if (!s.Run()) | |
| 359 { | |
| 360 return false; | |
| 361 } | |
| 362 | |
| 363 if (db_.GetLastChangeCount() == 0) | |
| 364 { | |
| 365 // Nothing was deleted, inexistent UUID | |
| 366 return false; | |
| 367 } | |
| 368 | |
| 369 if (deletedLevels_->HasRemainingLevel()) | |
| 370 { | |
| 371 std::string type(deletedLevels_->GetRemainingLevelType()); | |
| 372 const std::string& uuid = deletedLevels_->GetRemainingLevelUuid(); | |
| 373 | |
| 374 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 375 target["RemainingAncestor"]["Path"] = "/" + type + "/" + uuid; | |
| 376 target["RemainingAncestor"]["Type"] = type; | |
| 377 target["RemainingAncestor"]["ID"] = uuid; | |
| 378 } | |
| 379 else | |
| 380 { | |
| 381 target["RemainingAncestor"] = Json::nullValue; | |
| 382 } | |
| 383 | |
| 384 return true; | |
| 385 } | |
| 386 | |
| 387 | |
|
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388 namespace Internals |
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389 { |
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390 class ServerIndexListenerTodo : public IServerIndexListener |
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391 { |
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392 public: |
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393 virtual void SignalRemainingAncestor(ResourceType parentType, |
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394 const std::string& publicId) |
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395 { |
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396 LOG(INFO) << "Remaning ancestor \"" << publicId << "\" (" << parentType << ")"; |
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397 } |
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398 |
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399 virtual void SignalFileDeleted(const std::string& fileUuid) |
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400 { |
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401 LOG(INFO) << "Deleted file " << fileUuid; |
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402 } |
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403 |
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404 }; |
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405 } |
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406 |
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407 |
| 0 | 408 ServerIndex::ServerIndex(const std::string& storagePath) |
| 409 { | |
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410 listener2_.reset(new Internals::ServerIndexListenerTodo); |
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411 |
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412 if (storagePath == ":memory:") |
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413 { |
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414 db_.OpenInMemory(); |
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415 db2_.reset(new DatabaseWrapper(*listener2_)); |
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416 } |
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417 else |
| 0 | 418 { |
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419 boost::filesystem::path p = storagePath; |
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420 |
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421 try |
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422 { |
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423 boost::filesystem::create_directories(storagePath); |
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424 } |
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425 catch (boost::filesystem::filesystem_error) |
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426 { |
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427 } |
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428 |
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429 db2_.reset(new DatabaseWrapper(p.string() + "/index2", *listener2_)); |
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430 |
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431 p /= "index"; |
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432 db_.Open(p.string()); |
| 0 | 433 } |
| 434 | |
| 435 db_.Register(new Internals::DeleteFromFileStorageFunction(storagePath)); | |
| 436 deletedLevels_ = (Internals::SignalDeletedLevelFunction*) | |
| 437 db_.Register(new Internals::SignalDeletedLevelFunction); | |
| 438 | |
| 439 if (!db_.DoesTableExist("GlobalProperties")) | |
| 440 { | |
| 108 | 441 LOG(INFO) << "Creating the database"; |
| 0 | 442 std::string query; |
| 443 EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE); | |
| 444 db_.Execute(query); | |
| 445 } | |
| 446 } | |
| 447 | |
| 448 | |
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449 StoreStatus ServerIndex::Store2(const DicomMap& dicomSummary, |
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450 const std::string& fileUuid, |
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451 uint64_t uncompressedFileSize, |
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452 const std::string& jsonUuid, |
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453 const std::string& remoteAet) |
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454 { |
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455 boost::mutex::scoped_lock scoped_lock(mutex_); |
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456 |
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457 DicomInstanceHasher hasher(dicomSummary); |
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458 |
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459 try |
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460 { |
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461 std::auto_ptr<SQLite::Transaction> t(db2_->StartTransaction()); |
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462 t->Begin(); |
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463 |
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464 int64_t patient, study, series, instance; |
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465 ResourceType type; |
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466 bool isNewSeries = false; |
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467 |
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468 // Do nothing if the instance already exists |
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469 if (db2_->LookupResource(hasher.HashInstance(), patient, type)) |
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470 { |
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471 assert(type == ResourceType_Instance); |
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472 return StoreStatus_AlreadyStored; |
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473 } |
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474 |
| 190 | 475 // Create the instance |
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476 instance = db2_->CreateResource(hasher.HashInstance(), ResourceType_Instance); |
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477 |
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478 DicomMap dicom; |
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479 dicomSummary.ExtractInstanceInformation(dicom); |
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480 db2_->SetMainDicomTags(instance, dicom); |
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481 |
| 190 | 482 // Create the patient/study/series/instance hierarchy |
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483 if (!db2_->LookupResource(hasher.HashSeries(), series, type)) |
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484 { |
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485 // This is a new series |
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486 isNewSeries = true; |
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487 series = db2_->CreateResource(hasher.HashSeries(), ResourceType_Series); |
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488 dicomSummary.ExtractSeriesInformation(dicom); |
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489 db2_->SetMainDicomTags(series, dicom); |
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490 db2_->AttachChild(series, instance); |
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491 |
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492 if (!db2_->LookupResource(hasher.HashStudy(), study, type)) |
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493 { |
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494 // This is a new study |
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495 study = db2_->CreateResource(hasher.HashStudy(), ResourceType_Study); |
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496 dicomSummary.ExtractStudyInformation(dicom); |
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497 db2_->SetMainDicomTags(study, dicom); |
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498 db2_->AttachChild(study, series); |
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499 |
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500 if (!db2_->LookupResource(hasher.HashPatient(), patient, type)) |
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501 { |
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502 // This is a new patient |
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503 patient = db2_->CreateResource(hasher.HashPatient(), ResourceType_Patient); |
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504 dicomSummary.ExtractPatientInformation(dicom); |
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505 db2_->SetMainDicomTags(patient, dicom); |
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506 db2_->AttachChild(patient, study); |
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507 } |
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508 else |
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509 { |
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510 assert(type == ResourceType_Patient); |
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511 db2_->AttachChild(patient, study); |
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512 } |
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513 } |
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514 else |
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515 { |
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516 assert(type == ResourceType_Study); |
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517 db2_->AttachChild(study, series); |
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518 } |
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519 } |
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520 else |
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521 { |
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522 assert(type == ResourceType_Series); |
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523 db2_->AttachChild(series, instance); |
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524 } |
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525 |
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526 // Attach the files to the newly created instance |
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527 db2_->AttachFile(instance, AttachedFileType_Dicom, fileUuid, uncompressedFileSize); |
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528 db2_->AttachFile(instance, AttachedFileType_Json, jsonUuid, 0); // TODO "0" |
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529 |
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530 // Attach the metadata |
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531 db2_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); |
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532 db2_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
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533 |
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534 const DicomValue* value; |
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535 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || |
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536 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) |
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537 { |
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538 db2_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
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539 } |
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540 |
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541 if (isNewSeries) |
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542 { |
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543 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
|
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544 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL || |
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545 (value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) |
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546 { |
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547 db2_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); |
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548 } |
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549 } |
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550 |
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551 t->Commit(); |
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552 } |
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553 catch (OrthancException& e) |
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554 { |
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555 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
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556 } |
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557 |
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558 return StoreStatus_Failure; |
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559 } |
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560 |
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561 |
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562 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
| 0 | 563 const std::string& fileUuid, |
| 564 uint64_t uncompressedFileSize, | |
| 565 const std::string& jsonUuid, | |
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566 const std::string& remoteAet) |
| 0 | 567 { |
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568 Store2(dicomSummary, fileUuid, uncompressedFileSize, jsonUuid, remoteAet); |
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569 |
| 0 | 570 boost::mutex::scoped_lock scoped_lock(mutex_); |
| 571 | |
| 178 | 572 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 573 |
| 574 try | |
| 575 { | |
| 576 SQLite::Transaction t(db_); | |
| 577 t.Begin(); | |
| 578 | |
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579 if (HasInstance(hasher)) |
| 0 | 580 { |
| 581 return StoreStatus_AlreadyStored; | |
| 582 // TODO: Check consistency? | |
| 583 } | |
| 584 | |
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585 if (HasPatient(hasher)) |
| 0 | 586 { |
| 587 // TODO: Check consistency? | |
| 588 } | |
| 589 else | |
| 590 { | |
|
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591 CreatePatient(hasher, dicomSummary); |
| 0 | 592 } |
| 593 | |
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594 if (HasStudy(hasher)) |
| 0 | 595 { |
| 596 // TODO: Check consistency? | |
| 597 } | |
| 598 else | |
| 599 { | |
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600 CreateStudy(hasher, dicomSummary); |
| 0 | 601 } |
| 602 | |
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603 if (HasSeries(hasher)) |
| 0 | 604 { |
| 605 // TODO: Check consistency? | |
| 606 } | |
| 607 else | |
| 608 { | |
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609 CreateSeries(hasher, dicomSummary); |
| 0 | 610 } |
| 611 | |
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612 CreateInstance(hasher, dicomSummary, fileUuid, |
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613 uncompressedFileSize, jsonUuid, remoteAet); |
| 0 | 614 |
| 615 t.Commit(); | |
| 616 return StoreStatus_Success; | |
| 617 //t.Rollback(); | |
| 618 } | |
| 62 | 619 catch (OrthancException& e) |
| 0 | 620 { |
| 108 | 621 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
| 0 | 622 } |
| 623 | |
| 624 return StoreStatus_Failure; | |
| 625 } | |
| 626 | |
| 627 | |
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628 StoreStatus ServerIndex::Store(FileStorage& storage, |
| 0 | 629 const char* dicomFile, |
| 630 size_t dicomSize, | |
| 631 const DicomMap& dicomSummary, | |
| 632 const Json::Value& dicomJson, | |
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633 const std::string& remoteAet) |
| 0 | 634 { |
| 635 std::string fileUuid = storage.Create(dicomFile, dicomSize); | |
| 636 std::string jsonUuid = storage.Create(dicomJson.toStyledString()); | |
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637 StoreStatus status = Store(dicomSummary, fileUuid, dicomSize, jsonUuid, remoteAet); |
| 0 | 638 |
| 639 if (status != StoreStatus_Success) | |
| 640 { | |
| 147 | 641 storage.Remove(fileUuid); |
| 642 storage.Remove(jsonUuid); | |
| 0 | 643 } |
| 644 | |
| 645 switch (status) | |
| 646 { | |
| 647 case StoreStatus_Success: | |
|
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648 LOG(INFO) << "New instance stored"; |
| 0 | 649 break; |
| 650 | |
| 651 case StoreStatus_AlreadyStored: | |
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652 LOG(INFO) << "Already stored"; |
| 0 | 653 break; |
| 654 | |
| 655 case StoreStatus_Failure: | |
| 138 | 656 LOG(ERROR) << "Store failure"; |
| 0 | 657 break; |
| 658 } | |
| 659 | |
| 660 return status; | |
| 661 } | |
| 662 | |
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663 uint64_t ServerIndex::GetTotalCompressedSize() |
| 0 | 664 { |
| 665 boost::mutex::scoped_lock scoped_lock(mutex_); | |
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666 return db2_->GetTotalCompressedSize(); |
| 0 | 667 } |
| 668 | |
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669 uint64_t ServerIndex::GetTotalUncompressedSize() |
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670 { |
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671 boost::mutex::scoped_lock scoped_lock(mutex_); |
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672 return db2_->GetTotalUncompressedSize(); |
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673 } |
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674 |
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675 |
| 199 | 676 SeriesStatus ServerIndex::GetSeriesStatus(int id) |
| 677 { | |
| 678 // Get the expected number of instances in this series (from the metadata) | |
| 679 std::string s = db2_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); | |
| 680 | |
| 681 size_t expected; | |
| 682 try | |
| 683 { | |
| 684 expected = boost::lexical_cast<size_t>(s); | |
| 685 if (expected < 0) | |
| 686 { | |
| 687 return SeriesStatus_Unknown; | |
| 688 } | |
| 689 } | |
| 690 catch (boost::bad_lexical_cast&) | |
| 691 { | |
| 692 return SeriesStatus_Unknown; | |
| 693 } | |
| 694 | |
| 695 // Loop over the instances of this series | |
| 696 std::list<int64_t> children; | |
| 697 db2_->GetChildrenInternalId(children, id); | |
| 698 | |
| 699 std::set<size_t> instances; | |
| 700 for (std::list<int64_t>::const_iterator | |
| 701 it = children.begin(); it != children.end(); it++) | |
| 702 { | |
| 703 // Get the index of this instance in the series | |
| 704 s = db2_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); | |
| 705 size_t index; | |
| 706 try | |
| 707 { | |
| 708 index = boost::lexical_cast<size_t>(s); | |
| 709 } | |
| 710 catch (boost::bad_lexical_cast&) | |
| 711 { | |
| 712 return SeriesStatus_Unknown; | |
| 713 } | |
| 714 | |
| 715 if (index <= 0 || index > expected) | |
| 716 { | |
| 717 // Out-of-range instance index | |
| 718 return SeriesStatus_Inconsistent; | |
| 719 } | |
| 720 | |
| 721 if (instances.find(index) != instances.end()) | |
| 722 { | |
| 723 // Twice the same instance index | |
| 724 return SeriesStatus_Inconsistent; | |
| 725 } | |
| 726 | |
| 727 instances.insert(index); | |
| 728 } | |
| 729 | |
| 730 if (instances.size() == expected) | |
| 731 { | |
| 732 return SeriesStatus_Complete; | |
| 733 } | |
| 734 else | |
| 735 { | |
| 736 return SeriesStatus_Missing; | |
| 737 } | |
| 738 } | |
| 739 | |
| 740 | |
| 741 | |
|
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742 void ServerIndex::MainDicomTagsToJson2(Json::Value& target, |
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743 int64_t resourceId) |
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744 { |
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745 DicomMap tags; |
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746 db2_->GetMainDicomTags(tags, resourceId); |
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747 target["MainDicomTags"] = Json::objectValue; |
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748 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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749 } |
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750 |
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751 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 752 const std::string& publicId, |
| 753 ResourceType expectedType) | |
|
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754 { |
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755 result = Json::objectValue; |
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756 |
| 199 | 757 boost::mutex::scoped_lock scoped_lock(mutex_); |
| 758 | |
|
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759 // Lookup for the requested resource |
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760 int64_t id; |
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761 ResourceType type; |
| 199 | 762 if (!db2_->LookupResource(publicId, id, type) || |
| 763 type != expectedType) | |
|
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764 { |
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765 return false; |
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766 } |
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767 |
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768 // Find the parent resource (if it exists) |
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769 if (type != ResourceType_Patient) |
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770 { |
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771 int64_t parentId; |
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772 if (!db2_->LookupParent(parentId, id)) |
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773 { |
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774 throw OrthancException(ErrorCode_InternalError); |
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775 } |
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776 |
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777 std::string parent = db2_->GetPublicId(parentId); |
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778 |
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779 switch (type) |
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780 { |
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781 case ResourceType_Study: |
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782 result["ParentPatient"] = parent; |
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783 break; |
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784 |
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785 case ResourceType_Series: |
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786 result["ParentStudy"] = parent; |
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787 break; |
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788 |
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789 case ResourceType_Instance: |
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790 result["ParentSeries"] = parent; |
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791 break; |
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792 |
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793 default: |
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794 throw OrthancException(ErrorCode_InternalError); |
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795 } |
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796 } |
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797 |
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798 // List the children resources |
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799 std::list<std::string> children; |
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800 db2_->GetChildrenPublicId(children, id); |
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801 |
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802 if (type != ResourceType_Instance) |
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803 { |
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804 Json::Value c = Json::arrayValue; |
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805 |
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806 for (std::list<std::string>::const_iterator |
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807 it = children.begin(); it != children.end(); it++) |
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808 { |
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809 c.append(*it); |
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810 } |
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811 |
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812 switch (type) |
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813 { |
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814 case ResourceType_Patient: |
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815 result["Studies"] = c; |
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816 break; |
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817 |
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818 case ResourceType_Study: |
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819 result["Series"] = c; |
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820 break; |
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821 |
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822 case ResourceType_Series: |
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823 result["Instances"] = c; |
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824 break; |
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825 |
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826 default: |
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827 throw OrthancException(ErrorCode_InternalError); |
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828 } |
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829 } |
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830 |
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831 // Set the resource type |
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832 switch (type) |
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833 { |
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834 case ResourceType_Patient: |
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835 result["Type"] = "Patient"; |
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836 break; |
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837 |
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838 case ResourceType_Study: |
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839 result["Type"] = "Study"; |
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840 break; |
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841 |
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842 case ResourceType_Series: |
| 199 | 843 { |
|
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844 result["Type"] = "Series"; |
| 199 | 845 result["Status"] = ToString(GetSeriesStatus(id)); |
| 846 | |
|
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847 int i; |
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848 if (db2_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
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849 result["ExpectedNumberOfInstances"] = i; |
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850 else |
| 199 | 851 result["ExpectedNumberOfInstances"] = Json::nullValue; |
|
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852 |
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853 break; |
| 199 | 854 } |
|
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855 |
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856 case ResourceType_Instance: |
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857 { |
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858 result["Type"] = "Instance"; |
|
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859 |
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860 std::string fileUuid; |
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861 uint64_t uncompressedSize; |
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862 if (!db2_->LookupFile(id, AttachedFileType_Dicom, fileUuid, uncompressedSize)) |
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863 { |
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864 throw OrthancException(ErrorCode_InternalError); |
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865 } |
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866 |
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867 result["FileSize"] = static_cast<unsigned int>(uncompressedSize); |
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868 result["FileUuid"] = fileUuid; |
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869 |
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870 int i; |
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871 if (db2_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
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872 result["IndexInSeries"] = i; |
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873 else |
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874 result["IndexInSeries"] = Json::nullValue; |
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875 |
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876 break; |
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877 } |
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878 |
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879 default: |
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880 throw OrthancException(ErrorCode_InternalError); |
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881 } |
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882 |
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883 // Record the remaining information |
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884 result["ID"] = publicId; |
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885 MainDicomTagsToJson2(result, id); |
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886 |
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887 return true; |
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888 } |
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889 |
| 0 | 890 |
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891 bool ServerIndex::GetFile(std::string& fileUuid, |
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892 CompressionType& compressionType, |
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893 const std::string& instanceUuid, |
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894 AttachedFileType contentType) |
| 0 | 895 { |
| 896 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 897 | |
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898 int64_t id; |
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899 ResourceType type; |
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900 if (!db2_->LookupResource(instanceUuid, id, type) || |
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901 type != ResourceType_Instance) |
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902 { |
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903 throw OrthancException(ErrorCode_InternalError); |
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904 } |
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905 |
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906 uint64_t compressedSize, uncompressedSize; |
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907 |
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908 return db2_->LookupFile(id, contentType, fileUuid, compressedSize, uncompressedSize, compressionType); |
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909 } |
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910 |
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911 |
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912 |
| 0 | 913 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 914 ResourceType resourceType) |
| 0 | 915 { |
| 190 | 916 boost::mutex::scoped_lock scoped_lock(mutex_); |
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917 db2_->GetAllPublicIds(target, resourceType); |
| 0 | 918 } |
| 919 | |
| 920 | |
| 921 bool ServerIndex::GetChanges(Json::Value& target, | |
| 922 int64_t since, | |
| 923 const std::string& filter, | |
| 924 unsigned int maxResults) | |
| 925 { | |
| 926 assert(target.type() == Json::objectValue); | |
| 927 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 928 | |
| 929 if (filter.size() != 0 && | |
| 930 filter != "instances" && | |
| 931 filter != "series" && | |
| 932 filter != "studies" && | |
| 933 filter != "patients") | |
| 934 { | |
| 935 return false; | |
| 936 } | |
| 937 | |
| 938 std::auto_ptr<SQLite::Statement> s; | |
| 939 if (filter.size() == 0) | |
| 940 { | |
| 941 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
| 942 "ORDER BY seq LIMIT ?")); | |
| 943 s->BindInt64(0, since); | |
| 944 s->BindInt(1, maxResults); | |
| 945 } | |
| 946 else | |
| 947 { | |
| 948 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
| 949 "AND basePath=? ORDER BY seq LIMIT ?")); | |
| 950 s->BindInt64(0, since); | |
| 951 s->BindString(1, filter); | |
| 952 s->BindInt(2, maxResults); | |
| 953 } | |
| 954 | |
| 955 int64_t lastSeq = 0; | |
| 956 Json::Value results(Json::arrayValue); | |
| 957 while (s->Step()) | |
| 958 { | |
| 959 int64_t seq = s->ColumnInt64(0); | |
| 960 std::string basePath = s->ColumnString(1); | |
| 961 std::string uuid = s->ColumnString(2); | |
| 962 | |
| 963 if (filter.size() == 0 || | |
| 964 filter == basePath) | |
| 965 { | |
| 966 Json::Value change(Json::objectValue); | |
| 967 change["Seq"] = static_cast<int>(seq); // TODO JsonCpp in 64bit | |
| 968 change["BasePath"] = basePath; | |
| 969 change["ID"] = uuid; | |
| 970 results.append(change); | |
| 971 } | |
| 972 | |
| 973 if (seq > lastSeq) | |
| 974 { | |
| 975 lastSeq = seq; | |
| 976 } | |
| 977 } | |
| 978 | |
| 979 target["Results"] = results; | |
| 980 target["LastSeq"] = static_cast<int>(lastSeq); // TODO JsonCpp in 64bit | |
| 981 | |
| 982 return true; | |
| 983 } | |
| 82 | 984 |
| 0 | 985 } |