Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 187:8e673a65564d
refactoring of storing new instances
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 12 Nov 2012 17:29:11 +0100 |
| parents | f68c039b0571 |
| children | 090cefdab1d1 |
| 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 | |
| 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 | |
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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()); |
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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, |
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242 const std::string& remoteAet) |
| 0 | 243 { |
| 82 | 244 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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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(?, ?, ?, ?, ?, ?, ?, ?)"); |
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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); | |
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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); | |
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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 | |
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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()); |
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289 return s.Step(); |
| 0 | 290 } |
| 291 | |
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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(?, ?)"); |
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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(?, ?, ?, ?)"); |
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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()); |
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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()); |
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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); | |
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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 | |
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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 { | |
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475 listener2_.reset(new Internals::ServerIndexListenerTmp); |
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476 |
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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 |
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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 | |
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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, | |
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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 | |
|
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629 if (HasInstance(hasher)) |
| 0 | 630 { |
| 631 return StoreStatus_AlreadyStored; | |
| 632 // TODO: Check consistency? | |
| 633 } | |
| 634 | |
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635 if (HasPatient(hasher)) |
| 0 | 636 { |
| 637 // TODO: Check consistency? | |
| 638 } | |
| 639 else | |
| 640 { | |
|
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641 CreatePatient(hasher, dicomSummary); |
| 0 | 642 } |
| 643 | |
|
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644 if (HasStudy(hasher)) |
| 0 | 645 { |
| 646 // TODO: Check consistency? | |
| 647 } | |
| 648 else | |
| 649 { | |
|
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650 CreateStudy(hasher, dicomSummary); |
| 0 | 651 } |
| 652 | |
|
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653 if (HasSeries(hasher)) |
| 0 | 654 { |
| 655 // TODO: Check consistency? | |
| 656 } | |
| 657 else | |
| 658 { | |
|
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659 CreateSeries(hasher, dicomSummary); |
| 0 | 660 } |
| 661 | |
|
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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 | |
|
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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()); | |
|
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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: | |
|
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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 | |
|
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713 uint64_t ServerIndex::GetTotalCompressedSize() |
| 0 | 714 { |
| 715 boost::mutex::scoped_lock scoped_lock(mutex_); | |
|
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716 return db2_->GetTotalCompressedSize(); |
| 0 | 717 } |
| 718 | |
|
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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 } |