Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 201:bee20e978835
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 27 Nov 2012 17:36:19 +0100 |
| parents | 9c58b2b03cf0 |
| children | 1650557bd81a |
| 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 { | |
|
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56 class ServerIndexListenerTodo : public IServerIndexListener |
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57 { |
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58 private: |
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59 FileStorage& fileStorage_; |
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60 bool hasRemainingLevel_; |
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61 ResourceType remainingType_; |
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62 std::string remainingPublicId_; |
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63 |
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64 public: |
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65 ServerIndexListenerTodo(FileStorage& fileStorage) : |
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66 fileStorage_(fileStorage), |
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67 hasRemainingLevel_(false) |
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68 { |
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69 assert(ResourceType_Patient < ResourceType_Study && |
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70 ResourceType_Study < ResourceType_Series && |
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71 ResourceType_Series < ResourceType_Instance); |
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72 } |
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73 |
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74 void Reset() |
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75 { |
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76 hasRemainingLevel_ = false; |
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77 } |
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78 |
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79 virtual void SignalRemainingAncestor(ResourceType parentType, |
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80 const std::string& publicId) |
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81 { |
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82 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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83 |
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84 if (hasRemainingLevel_) |
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85 { |
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86 if (parentType < remainingType_) |
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87 { |
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88 remainingType_ = parentType; |
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89 remainingPublicId_ = publicId; |
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90 } |
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91 } |
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92 else |
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93 { |
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94 hasRemainingLevel_ = true; |
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95 remainingType_ = parentType; |
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96 remainingPublicId_ = publicId; |
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97 } |
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98 } |
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99 |
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100 virtual void SignalFileDeleted(const std::string& fileUuid) |
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101 { |
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102 assert(Toolbox::IsUuid(fileUuid)); |
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103 fileStorage_.Remove(fileUuid); |
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104 } |
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105 |
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106 bool HasRemainingLevel() const |
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107 { |
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108 return hasRemainingLevel_; |
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109 } |
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110 |
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111 ResourceType GetRemainingType() const |
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112 { |
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113 assert(HasRemainingLevel()); |
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114 return remainingType_; |
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115 } |
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116 |
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117 const std::string& GetRemainingPublicId() const |
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118 { |
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119 assert(HasRemainingLevel()); |
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120 return remainingPublicId_; |
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121 } |
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122 }; |
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123 |
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124 |
| 0 | 125 class DeleteFromFileStorageFunction : public SQLite::IScalarFunction |
| 126 { | |
| 127 private: | |
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128 FileStorage& fileStorage_; |
| 0 | 129 |
| 130 public: | |
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131 DeleteFromFileStorageFunction(FileStorage& fileStorage) : |
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132 fileStorage_(fileStorage) |
| 0 | 133 { |
| 134 } | |
| 135 | |
| 136 virtual const char* GetName() const | |
| 137 { | |
| 138 return "DeleteFromFileStorage"; | |
| 139 } | |
| 140 | |
| 141 virtual unsigned int GetCardinality() const | |
| 142 { | |
| 143 return 1; | |
| 144 } | |
| 145 | |
| 146 virtual void Compute(SQLite::FunctionContext& context) | |
| 147 { | |
| 148 std::string fileUuid = context.GetStringValue(0); | |
| 108 | 149 LOG(INFO) << "Removing file [" << fileUuid << "]"; |
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150 |
| 0 | 151 if (Toolbox::IsUuid(fileUuid)) |
| 152 { | |
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153 fileStorage_.Remove(fileUuid); |
| 0 | 154 } |
| 155 } | |
| 156 }; | |
| 157 | |
| 158 | |
| 159 class SignalDeletedLevelFunction : public SQLite::IScalarFunction | |
| 160 { | |
| 161 private: | |
| 162 int remainingLevel_; | |
| 163 std::string remainingLevelUuid_; | |
| 164 | |
| 165 public: | |
| 166 void Clear() | |
| 167 { | |
| 168 remainingLevel_ = std::numeric_limits<int>::max(); | |
| 169 } | |
| 170 | |
| 171 bool HasRemainingLevel() const | |
| 172 { | |
| 173 return (remainingLevel_ != 0 && | |
| 174 remainingLevel_ != std::numeric_limits<int>::max()); | |
| 175 } | |
| 176 | |
| 177 const std::string& GetRemainingLevelUuid() const | |
| 178 { | |
| 179 assert(HasRemainingLevel()); | |
| 180 return remainingLevelUuid_; | |
| 181 } | |
| 182 | |
| 183 const char* GetRemainingLevelType() const | |
| 184 { | |
| 185 assert(HasRemainingLevel()); | |
| 186 switch (remainingLevel_) | |
| 187 { | |
| 188 case 1: | |
| 189 return "patient"; | |
| 190 case 2: | |
| 191 return "study"; | |
| 192 case 3: | |
| 193 return "series"; | |
| 194 default: | |
| 62 | 195 throw OrthancException(ErrorCode_InternalError); |
| 0 | 196 } |
| 197 } | |
| 198 | |
| 199 virtual const char* GetName() const | |
| 200 { | |
| 201 return "SignalDeletedLevel"; | |
| 202 } | |
| 203 | |
| 204 virtual unsigned int GetCardinality() const | |
| 205 { | |
| 206 return 2; | |
| 207 } | |
| 208 | |
| 209 virtual void Compute(SQLite::FunctionContext& context) | |
| 210 { | |
| 211 int level = context.GetIntValue(0); | |
| 212 if (level < remainingLevel_) | |
| 213 { | |
| 214 remainingLevel_ = level; | |
| 215 remainingLevelUuid_ = context.GetStringValue(1); | |
| 216 } | |
| 217 | |
| 218 //printf("deleted level [%d] [%s]\n", level, context.GetStringValue(1).c_str()); | |
| 219 } | |
| 220 }; | |
| 221 } | |
| 222 | |
| 223 | |
| 224 void ServerIndex::StoreMainDicomTags(const std::string& uuid, | |
| 225 const DicomMap& map) | |
| 226 { | |
| 227 DicomArray flattened(map); | |
| 228 for (size_t i = 0; i < flattened.GetSize(); i++) | |
| 229 { | |
| 138 | 230 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO MainDicomTags VALUES(?, ?, ?, ?)"); |
| 0 | 231 s.BindString(0, uuid); |
| 232 s.BindInt(1, flattened.GetElement(i).GetTag().GetGroup()); | |
| 233 s.BindInt(2, flattened.GetElement(i).GetTag().GetElement()); | |
| 234 s.BindString(3, flattened.GetElement(i).GetValue().AsString()); | |
| 235 s.Run(); | |
| 236 } | |
| 237 } | |
| 238 | |
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239 bool ServerIndex::HasInstance(DicomInstanceHasher& hasher) |
| 0 | 240 { |
| 241 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Instances WHERE dicomInstance=?"); | |
| 179 | 242 s.BindString(0, hasher.GetInstanceUid()); |
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243 return s.Step(); |
| 0 | 244 } |
| 245 | |
| 246 | |
| 247 void ServerIndex::RecordChange(const std::string& resourceType, | |
| 248 const std::string& uuid) | |
| 249 { | |
| 250 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Changes VALUES(NULL, ?, ?)"); | |
| 251 s.BindString(0, resourceType); | |
| 252 s.BindString(1, uuid); | |
| 253 s.Run(); | |
| 254 } | |
| 255 | |
| 256 | |
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257 void ServerIndex::CreateInstance(DicomInstanceHasher& hasher, |
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258 const DicomMap& dicomSummary, |
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259 const std::string& fileUuid, |
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260 uint64_t fileSize, |
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261 const std::string& jsonUuid, |
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262 const std::string& remoteAet) |
| 0 | 263 { |
| 82 | 264 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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265 s2.BindString(0, hasher.HashInstance()); |
| 82 | 266 s2.BindInt(1, ResourceType_Instance); |
| 267 s2.Run(); | |
| 268 | |
| 80 | 269 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Instances VALUES(?, ?, ?, ?, ?, ?, ?, ?)"); |
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270 s.BindString(0, hasher.HashInstance()); |
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271 s.BindString(1, hasher.HashSeries()); |
| 179 | 272 s.BindString(2, hasher.GetInstanceUid()); |
| 0 | 273 s.BindString(3, fileUuid); |
| 274 s.BindInt64(4, fileSize); | |
| 275 s.BindString(5, jsonUuid); | |
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276 s.BindString(6, remoteAet); |
| 80 | 277 |
| 278 const DicomValue* indexInSeries; | |
| 279 if ((indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 280 (indexInSeries = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 281 { | |
| 282 s.BindInt(7, boost::lexical_cast<unsigned int>(indexInSeries->AsString())); | |
| 283 } | |
| 284 else | |
| 285 { | |
| 286 s.BindNull(7); | |
| 287 } | |
| 288 | |
| 0 | 289 s.Run(); |
| 290 | |
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291 RecordChange("instances", hasher.HashInstance()); |
| 0 | 292 |
| 293 DicomMap dicom; | |
| 294 dicomSummary.ExtractInstanceInformation(dicom); | |
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295 StoreMainDicomTags(hasher.HashInstance(), dicom); |
| 0 | 296 } |
| 297 | |
| 298 void ServerIndex::RemoveInstance(const std::string& uuid) | |
| 299 { | |
| 300 SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Instances WHERE uuid=?"); | |
| 301 s.BindString(0, uuid); | |
| 302 s.Run(); | |
| 303 } | |
| 304 | |
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305 bool ServerIndex::HasSeries(DicomInstanceHasher& hasher) |
| 0 | 306 { |
| 307 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Series WHERE dicomSeries=?"); | |
| 179 | 308 s.BindString(0, hasher.GetSeriesUid()); |
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309 return s.Step(); |
| 0 | 310 } |
| 311 | |
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312 void ServerIndex::CreateSeries(DicomInstanceHasher& hasher, |
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313 const DicomMap& dicomSummary) |
| 0 | 314 { |
| 82 | 315 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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316 s2.BindString(0, hasher.HashSeries()); |
| 82 | 317 s2.BindInt(1, ResourceType_Series); |
| 318 s2.Run(); | |
| 319 | |
| 77 | 320 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Series VALUES(?, ?, ?, ?)"); |
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321 s.BindString(0, hasher.HashSeries()); |
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322 s.BindString(1, hasher.HashStudy()); |
| 179 | 323 s.BindString(2, hasher.GetSeriesUid()); |
| 80 | 324 |
| 325 const DicomValue* expectedNumberOfInstances; | |
| 84 | 326 if (//(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_FRAMES)) != NULL || |
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327 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
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328 //(expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL || |
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329 (expectedNumberOfInstances = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL) |
| 80 | 330 { |
| 331 s.BindInt(3, boost::lexical_cast<unsigned int>(expectedNumberOfInstances->AsString())); | |
| 332 } | |
| 333 else | |
| 334 { | |
| 335 s.BindNull(3); | |
| 336 } | |
| 337 | |
| 0 | 338 s.Run(); |
| 339 | |
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340 RecordChange("series", hasher.HashSeries()); |
| 0 | 341 |
| 342 DicomMap dicom; | |
| 343 dicomSummary.ExtractSeriesInformation(dicom); | |
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344 StoreMainDicomTags(hasher.HashSeries(), dicom); |
| 0 | 345 } |
| 346 | |
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347 bool ServerIndex::HasStudy(DicomInstanceHasher& hasher) |
| 0 | 348 { |
| 349 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Studies WHERE dicomStudy=?"); | |
| 179 | 350 s.BindString(0, hasher.GetStudyUid()); |
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351 return s.Step(); |
| 0 | 352 } |
| 353 | |
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354 void ServerIndex::CreateStudy(DicomInstanceHasher& hasher, |
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355 const DicomMap& dicomSummary) |
| 0 | 356 { |
| 82 | 357 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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358 s2.BindString(0, hasher.HashStudy()); |
| 82 | 359 s2.BindInt(1, ResourceType_Study); |
| 360 s2.Run(); | |
| 361 | |
| 0 | 362 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Studies VALUES(?, ?, ?)"); |
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363 s.BindString(0, hasher.HashStudy()); |
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364 s.BindString(1, hasher.HashPatient()); |
| 179 | 365 s.BindString(2, hasher.GetStudyUid()); |
| 0 | 366 s.Run(); |
| 367 | |
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368 RecordChange("studies", hasher.HashStudy()); |
| 0 | 369 |
| 370 DicomMap dicom; | |
| 371 dicomSummary.ExtractStudyInformation(dicom); | |
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372 StoreMainDicomTags(hasher.HashStudy(), dicom); |
| 0 | 373 } |
| 374 | |
| 375 | |
| 376 | |
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377 bool ServerIndex::HasPatient(DicomInstanceHasher& hasher) |
| 0 | 378 { |
| 379 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid FROM Patients WHERE dicomPatientId=?"); | |
| 179 | 380 s.BindString(0,hasher.GetPatientId()); |
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381 return s.Step(); |
| 0 | 382 } |
| 383 | |
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384 void ServerIndex::CreatePatient(DicomInstanceHasher& hasher, |
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385 const DicomMap& dicomSummary) |
| 0 | 386 { |
| 80 | 387 std::string dicomPatientId = dicomSummary.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
| 0 | 388 |
| 82 | 389 SQLite::Statement s2(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(?, ?)"); |
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390 s2.BindString(0, hasher.HashPatient()); |
| 82 | 391 s2.BindInt(1, ResourceType_Patient); |
| 392 s2.Run(); | |
| 393 | |
| 0 | 394 SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Patients VALUES(?, ?)"); |
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395 s.BindString(0, hasher.HashPatient()); |
| 0 | 396 s.BindString(1, dicomPatientId); |
| 397 s.Run(); | |
| 398 | |
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399 RecordChange("patients", hasher.HashPatient()); |
| 0 | 400 |
| 401 DicomMap dicom; | |
| 402 dicomSummary.ExtractPatientInformation(dicom); | |
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403 StoreMainDicomTags(hasher.HashPatient(), dicom); |
| 0 | 404 } |
| 405 | |
| 406 | |
| 407 bool ServerIndex::DeleteInternal(Json::Value& target, | |
| 408 const std::string& uuid, | |
| 409 const std::string& tableName) | |
| 410 { | |
| 411 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 412 | |
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413 |
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414 { |
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415 listener2_->Reset(); |
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416 |
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417 std::auto_ptr<SQLite::Transaction> t(db2_->StartTransaction()); |
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418 t->Begin(); |
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419 |
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420 int64_t id; |
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421 ResourceType type; |
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422 if (!db2_->LookupResource(uuid, id, type)) |
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423 { |
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424 return false; |
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425 } |
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426 |
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427 db2_->DeleteResource(id); |
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428 |
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429 if (listener2_->HasRemainingLevel()) |
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430 { |
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431 ResourceType type = listener2_->GetRemainingType(); |
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432 const std::string& uuid = listener2_->GetRemainingPublicId(); |
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433 |
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434 target["RemainingAncestor"] = Json::Value(Json::objectValue); |
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435 target["RemainingAncestor"]["Path"] = std::string(GetBasePath(type)) + "/" + uuid; |
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436 target["RemainingAncestor"]["Type"] = ToString(type); |
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437 target["RemainingAncestor"]["ID"] = uuid; |
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438 } |
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439 else |
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440 { |
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441 target["RemainingAncestor"] = Json::nullValue; |
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442 } |
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443 |
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444 std::cout << target << std::endl; |
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445 |
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446 t->Commit(); |
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447 |
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448 return true; |
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449 } |
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450 |
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451 |
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452 |
| 0 | 453 deletedLevels_->Clear(); |
| 454 | |
| 455 SQLite::Statement s(db_, "DELETE FROM " + tableName + " WHERE uuid=?"); | |
| 456 s.BindString(0, uuid); | |
| 457 | |
| 458 if (!s.Run()) | |
| 459 { | |
| 460 return false; | |
| 461 } | |
| 462 | |
| 463 if (db_.GetLastChangeCount() == 0) | |
| 464 { | |
| 465 // Nothing was deleted, inexistent UUID | |
| 466 return false; | |
| 467 } | |
| 468 | |
| 469 if (deletedLevels_->HasRemainingLevel()) | |
| 470 { | |
| 471 std::string type(deletedLevels_->GetRemainingLevelType()); | |
| 472 const std::string& uuid = deletedLevels_->GetRemainingLevelUuid(); | |
| 473 | |
| 474 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 475 target["RemainingAncestor"]["Path"] = "/" + type + "/" + uuid; | |
| 476 target["RemainingAncestor"]["Type"] = type; | |
| 477 target["RemainingAncestor"]["ID"] = uuid; | |
| 478 } | |
| 479 else | |
| 480 { | |
| 481 target["RemainingAncestor"] = Json::nullValue; | |
| 482 } | |
| 483 | |
| 484 return true; | |
| 485 } | |
| 486 | |
| 487 | |
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488 ServerIndex::ServerIndex(FileStorage& fileStorage, |
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489 const std::string& dbPath) |
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490 { |
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491 listener2_.reset(new Internals::ServerIndexListenerTodo(fileStorage)); |
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492 |
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493 if (dbPath == ":memory:") |
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494 { |
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495 db_.OpenInMemory(); |
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496 db2_.reset(new DatabaseWrapper(*listener2_)); |
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497 } |
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498 else |
| 0 | 499 { |
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500 boost::filesystem::path p = dbPath; |
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501 |
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502 try |
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503 { |
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504 boost::filesystem::create_directories(p); |
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505 } |
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506 catch (boost::filesystem::filesystem_error) |
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507 { |
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508 } |
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509 |
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510 db2_.reset(new DatabaseWrapper(p.string() + "/index2", *listener2_)); |
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511 |
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512 p /= "index"; |
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513 db_.Open(p.string()); |
| 0 | 514 } |
| 515 | |
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516 db_.Register(new Internals::DeleteFromFileStorageFunction(fileStorage)); |
| 0 | 517 deletedLevels_ = (Internals::SignalDeletedLevelFunction*) |
| 518 db_.Register(new Internals::SignalDeletedLevelFunction); | |
| 519 | |
| 520 if (!db_.DoesTableExist("GlobalProperties")) | |
| 521 { | |
| 108 | 522 LOG(INFO) << "Creating the database"; |
| 0 | 523 std::string query; |
| 524 EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE); | |
| 525 db_.Execute(query); | |
| 526 } | |
| 527 } | |
| 528 | |
| 529 | |
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530 StoreStatus ServerIndex::Store2(const DicomMap& dicomSummary, |
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531 const std::string& fileUuid, |
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532 uint64_t uncompressedFileSize, |
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533 const std::string& jsonUuid, |
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534 const std::string& remoteAet) |
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535 { |
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536 boost::mutex::scoped_lock scoped_lock(mutex_); |
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537 |
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538 DicomInstanceHasher hasher(dicomSummary); |
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539 |
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540 try |
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541 { |
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542 std::auto_ptr<SQLite::Transaction> t(db2_->StartTransaction()); |
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543 t->Begin(); |
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544 |
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545 int64_t patient, study, series, instance; |
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546 ResourceType type; |
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547 bool isNewSeries = false; |
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548 |
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549 // Do nothing if the instance already exists |
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550 if (db2_->LookupResource(hasher.HashInstance(), patient, type)) |
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551 { |
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552 assert(type == ResourceType_Instance); |
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553 return StoreStatus_AlreadyStored; |
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554 } |
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555 |
| 190 | 556 // Create the instance |
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557 instance = db2_->CreateResource(hasher.HashInstance(), ResourceType_Instance); |
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558 |
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559 DicomMap dicom; |
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560 dicomSummary.ExtractInstanceInformation(dicom); |
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561 db2_->SetMainDicomTags(instance, dicom); |
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562 |
| 190 | 563 // Create the patient/study/series/instance hierarchy |
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564 if (!db2_->LookupResource(hasher.HashSeries(), series, type)) |
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565 { |
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566 // This is a new series |
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567 isNewSeries = true; |
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568 series = db2_->CreateResource(hasher.HashSeries(), ResourceType_Series); |
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569 dicomSummary.ExtractSeriesInformation(dicom); |
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570 db2_->SetMainDicomTags(series, dicom); |
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571 db2_->AttachChild(series, instance); |
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572 |
|
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573 if (!db2_->LookupResource(hasher.HashStudy(), study, type)) |
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574 { |
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575 // This is a new study |
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576 study = db2_->CreateResource(hasher.HashStudy(), ResourceType_Study); |
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577 dicomSummary.ExtractStudyInformation(dicom); |
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578 db2_->SetMainDicomTags(study, dicom); |
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579 db2_->AttachChild(study, series); |
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580 |
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581 if (!db2_->LookupResource(hasher.HashPatient(), patient, type)) |
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582 { |
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583 // This is a new patient |
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584 patient = db2_->CreateResource(hasher.HashPatient(), ResourceType_Patient); |
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585 dicomSummary.ExtractPatientInformation(dicom); |
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586 db2_->SetMainDicomTags(patient, dicom); |
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587 db2_->AttachChild(patient, study); |
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588 } |
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589 else |
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590 { |
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591 assert(type == ResourceType_Patient); |
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592 db2_->AttachChild(patient, study); |
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593 } |
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594 } |
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595 else |
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596 { |
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597 assert(type == ResourceType_Study); |
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598 db2_->AttachChild(study, series); |
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599 } |
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600 } |
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601 else |
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602 { |
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603 assert(type == ResourceType_Series); |
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604 db2_->AttachChild(series, instance); |
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605 } |
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606 |
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607 // Attach the files to the newly created instance |
|
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608 db2_->AttachFile(instance, AttachedFileType_Dicom, fileUuid, uncompressedFileSize); |
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609 db2_->AttachFile(instance, AttachedFileType_Json, jsonUuid, 0); // TODO "0" |
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610 |
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611 // Attach the metadata |
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612 db2_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); |
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613 db2_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
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614 |
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615 const DicomValue* value; |
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616 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || |
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617 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) |
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618 { |
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619 db2_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
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620 } |
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621 |
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622 if (isNewSeries) |
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623 { |
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624 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || |
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625 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL || |
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626 (value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) |
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627 { |
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628 db2_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); |
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629 } |
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630 } |
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631 |
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632 t->Commit(); |
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633 } |
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634 catch (OrthancException& e) |
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635 { |
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636 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
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637 } |
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638 |
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639 return StoreStatus_Failure; |
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640 } |
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641 |
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642 |
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643 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
| 0 | 644 const std::string& fileUuid, |
| 645 uint64_t uncompressedFileSize, | |
| 646 const std::string& jsonUuid, | |
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647 const std::string& remoteAet) |
| 0 | 648 { |
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649 Store2(dicomSummary, fileUuid, uncompressedFileSize, jsonUuid, remoteAet); |
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650 |
| 0 | 651 boost::mutex::scoped_lock scoped_lock(mutex_); |
| 652 | |
| 178 | 653 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 654 |
| 655 try | |
| 656 { | |
| 657 SQLite::Transaction t(db_); | |
| 658 t.Begin(); | |
| 659 | |
|
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660 if (HasInstance(hasher)) |
| 0 | 661 { |
| 662 return StoreStatus_AlreadyStored; | |
| 663 // TODO: Check consistency? | |
| 664 } | |
| 665 | |
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666 if (HasPatient(hasher)) |
| 0 | 667 { |
| 668 // TODO: Check consistency? | |
| 669 } | |
| 670 else | |
| 671 { | |
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672 CreatePatient(hasher, dicomSummary); |
| 0 | 673 } |
| 674 | |
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675 if (HasStudy(hasher)) |
| 0 | 676 { |
| 677 // TODO: Check consistency? | |
| 678 } | |
| 679 else | |
| 680 { | |
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681 CreateStudy(hasher, dicomSummary); |
| 0 | 682 } |
| 683 | |
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684 if (HasSeries(hasher)) |
| 0 | 685 { |
| 686 // TODO: Check consistency? | |
| 687 } | |
| 688 else | |
| 689 { | |
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690 CreateSeries(hasher, dicomSummary); |
| 0 | 691 } |
| 692 | |
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693 CreateInstance(hasher, dicomSummary, fileUuid, |
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694 uncompressedFileSize, jsonUuid, remoteAet); |
| 0 | 695 |
| 696 t.Commit(); | |
| 697 return StoreStatus_Success; | |
| 698 //t.Rollback(); | |
| 699 } | |
| 62 | 700 catch (OrthancException& e) |
| 0 | 701 { |
| 108 | 702 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" << " " << db_.GetErrorMessage(); |
| 0 | 703 } |
| 704 | |
| 705 return StoreStatus_Failure; | |
| 706 } | |
| 707 | |
| 708 | |
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709 StoreStatus ServerIndex::Store(FileStorage& storage, |
| 0 | 710 const char* dicomFile, |
| 711 size_t dicomSize, | |
| 712 const DicomMap& dicomSummary, | |
| 713 const Json::Value& dicomJson, | |
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714 const std::string& remoteAet) |
| 0 | 715 { |
| 716 std::string fileUuid = storage.Create(dicomFile, dicomSize); | |
| 717 std::string jsonUuid = storage.Create(dicomJson.toStyledString()); | |
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718 StoreStatus status = Store(dicomSummary, fileUuid, dicomSize, jsonUuid, remoteAet); |
| 0 | 719 |
| 720 if (status != StoreStatus_Success) | |
| 721 { | |
| 147 | 722 storage.Remove(fileUuid); |
| 723 storage.Remove(jsonUuid); | |
| 0 | 724 } |
| 725 | |
| 726 switch (status) | |
| 727 { | |
| 728 case StoreStatus_Success: | |
|
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729 LOG(INFO) << "New instance stored"; |
| 0 | 730 break; |
| 731 | |
| 732 case StoreStatus_AlreadyStored: | |
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733 LOG(INFO) << "Already stored"; |
| 0 | 734 break; |
| 735 | |
| 736 case StoreStatus_Failure: | |
| 138 | 737 LOG(ERROR) << "Store failure"; |
| 0 | 738 break; |
| 739 } | |
| 740 | |
| 741 return status; | |
| 742 } | |
| 743 | |
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744 uint64_t ServerIndex::GetTotalCompressedSize() |
| 0 | 745 { |
| 746 boost::mutex::scoped_lock scoped_lock(mutex_); | |
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747 return db2_->GetTotalCompressedSize(); |
| 0 | 748 } |
| 749 | |
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750 uint64_t ServerIndex::GetTotalUncompressedSize() |
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751 { |
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752 boost::mutex::scoped_lock scoped_lock(mutex_); |
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753 return db2_->GetTotalUncompressedSize(); |
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754 } |
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755 |
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756 |
| 199 | 757 SeriesStatus ServerIndex::GetSeriesStatus(int id) |
| 758 { | |
| 759 // Get the expected number of instances in this series (from the metadata) | |
| 760 std::string s = db2_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); | |
| 761 | |
| 762 size_t expected; | |
| 763 try | |
| 764 { | |
| 765 expected = boost::lexical_cast<size_t>(s); | |
| 766 if (expected < 0) | |
| 767 { | |
| 768 return SeriesStatus_Unknown; | |
| 769 } | |
| 770 } | |
| 771 catch (boost::bad_lexical_cast&) | |
| 772 { | |
| 773 return SeriesStatus_Unknown; | |
| 774 } | |
| 775 | |
| 776 // Loop over the instances of this series | |
| 777 std::list<int64_t> children; | |
| 778 db2_->GetChildrenInternalId(children, id); | |
| 779 | |
| 780 std::set<size_t> instances; | |
| 781 for (std::list<int64_t>::const_iterator | |
| 782 it = children.begin(); it != children.end(); it++) | |
| 783 { | |
| 784 // Get the index of this instance in the series | |
| 785 s = db2_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); | |
| 786 size_t index; | |
| 787 try | |
| 788 { | |
| 789 index = boost::lexical_cast<size_t>(s); | |
| 790 } | |
| 791 catch (boost::bad_lexical_cast&) | |
| 792 { | |
| 793 return SeriesStatus_Unknown; | |
| 794 } | |
| 795 | |
| 796 if (index <= 0 || index > expected) | |
| 797 { | |
| 798 // Out-of-range instance index | |
| 799 return SeriesStatus_Inconsistent; | |
| 800 } | |
| 801 | |
| 802 if (instances.find(index) != instances.end()) | |
| 803 { | |
| 804 // Twice the same instance index | |
| 805 return SeriesStatus_Inconsistent; | |
| 806 } | |
| 807 | |
| 808 instances.insert(index); | |
| 809 } | |
| 810 | |
| 811 if (instances.size() == expected) | |
| 812 { | |
| 813 return SeriesStatus_Complete; | |
| 814 } | |
| 815 else | |
| 816 { | |
| 817 return SeriesStatus_Missing; | |
| 818 } | |
| 819 } | |
| 820 | |
| 821 | |
| 822 | |
|
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823 void ServerIndex::MainDicomTagsToJson2(Json::Value& target, |
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824 int64_t resourceId) |
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825 { |
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826 DicomMap tags; |
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827 db2_->GetMainDicomTags(tags, resourceId); |
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828 target["MainDicomTags"] = Json::objectValue; |
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829 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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830 } |
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831 |
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832 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 833 const std::string& publicId, |
| 834 ResourceType expectedType) | |
|
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835 { |
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836 result = Json::objectValue; |
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837 |
| 199 | 838 boost::mutex::scoped_lock scoped_lock(mutex_); |
| 839 | |
|
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840 // Lookup for the requested resource |
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841 int64_t id; |
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842 ResourceType type; |
| 199 | 843 if (!db2_->LookupResource(publicId, id, type) || |
| 844 type != expectedType) | |
|
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845 { |
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846 return false; |
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847 } |
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848 |
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849 // Find the parent resource (if it exists) |
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850 if (type != ResourceType_Patient) |
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851 { |
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852 int64_t parentId; |
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853 if (!db2_->LookupParent(parentId, id)) |
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854 { |
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855 throw OrthancException(ErrorCode_InternalError); |
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856 } |
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857 |
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858 std::string parent = db2_->GetPublicId(parentId); |
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859 |
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860 switch (type) |
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861 { |
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862 case ResourceType_Study: |
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863 result["ParentPatient"] = parent; |
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864 break; |
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865 |
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866 case ResourceType_Series: |
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867 result["ParentStudy"] = parent; |
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868 break; |
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869 |
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870 case ResourceType_Instance: |
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871 result["ParentSeries"] = parent; |
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872 break; |
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|
873 |
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874 default: |
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875 throw OrthancException(ErrorCode_InternalError); |
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876 } |
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|
877 } |
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|
878 |
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|
879 // List the children resources |
|
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880 std::list<std::string> children; |
|
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881 db2_->GetChildrenPublicId(children, id); |
|
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882 |
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883 if (type != ResourceType_Instance) |
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884 { |
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|
885 Json::Value c = Json::arrayValue; |
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886 |
|
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|
887 for (std::list<std::string>::const_iterator |
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888 it = children.begin(); it != children.end(); it++) |
|
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|
889 { |
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890 c.append(*it); |
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891 } |
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|
892 |
|
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|
893 switch (type) |
|
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|
894 { |
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895 case ResourceType_Patient: |
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896 result["Studies"] = c; |
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897 break; |
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|
898 |
|
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|
899 case ResourceType_Study: |
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900 result["Series"] = c; |
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901 break; |
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|
902 |
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|
903 case ResourceType_Series: |
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904 result["Instances"] = c; |
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905 break; |
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|
906 |
|
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|
907 default: |
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|
908 throw OrthancException(ErrorCode_InternalError); |
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909 } |
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|
910 } |
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|
911 |
|
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|
912 // Set the resource type |
|
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|
913 switch (type) |
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|
914 { |
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|
915 case ResourceType_Patient: |
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916 result["Type"] = "Patient"; |
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|
917 break; |
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|
918 |
|
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|
919 case ResourceType_Study: |
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|
920 result["Type"] = "Study"; |
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|
921 break; |
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|
922 |
|
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|
923 case ResourceType_Series: |
| 199 | 924 { |
|
198
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|
925 result["Type"] = "Series"; |
| 199 | 926 result["Status"] = ToString(GetSeriesStatus(id)); |
| 927 | |
|
200
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changeset
|
928 int i; |
|
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|
929 if (db2_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
|
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|
930 result["ExpectedNumberOfInstances"] = i; |
|
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|
931 else |
| 199 | 932 result["ExpectedNumberOfInstances"] = Json::nullValue; |
|
200
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changeset
|
933 |
|
198
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|
934 break; |
| 199 | 935 } |
|
198
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|
936 |
|
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|
937 case ResourceType_Instance: |
|
200
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diff
changeset
|
938 { |
|
198
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|
939 result["Type"] = "Instance"; |
|
200
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diff
changeset
|
940 |
|
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diff
changeset
|
941 std::string fileUuid; |
|
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diff
changeset
|
942 uint64_t uncompressedSize; |
|
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diff
changeset
|
943 if (!db2_->LookupFile(id, AttachedFileType_Dicom, fileUuid, uncompressedSize)) |
|
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diff
changeset
|
944 { |
|
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diff
changeset
|
945 throw OrthancException(ErrorCode_InternalError); |
|
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199
diff
changeset
|
946 } |
|
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diff
changeset
|
947 |
|
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diff
changeset
|
948 result["FileSize"] = static_cast<unsigned int>(uncompressedSize); |
|
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diff
changeset
|
949 result["FileUuid"] = fileUuid; |
|
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199
diff
changeset
|
950 |
|
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diff
changeset
|
951 int i; |
|
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diff
changeset
|
952 if (db2_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
|
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diff
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|
953 result["IndexInSeries"] = i; |
|
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diff
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|
954 else |
|
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diff
changeset
|
955 result["IndexInSeries"] = Json::nullValue; |
|
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199
diff
changeset
|
956 |
|
198
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|
957 break; |
|
200
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diff
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|
958 } |
|
198
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|
959 |
|
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|
960 default: |
|
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|
961 throw OrthancException(ErrorCode_InternalError); |
|
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|
962 } |
|
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|
963 |
|
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|
964 // Record the remaining information |
|
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|
965 result["ID"] = publicId; |
|
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|
966 MainDicomTagsToJson2(result, id); |
|
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967 |
|
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|
968 return true; |
|
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|
969 } |
|
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|
970 |
| 0 | 971 |
|
193
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changeset
|
972 bool ServerIndex::GetFile(std::string& fileUuid, |
|
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|
973 CompressionType& compressionType, |
|
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|
974 const std::string& instanceUuid, |
|
197
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diff
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|
975 AttachedFileType contentType) |
| 0 | 976 { |
| 977 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 978 | |
|
193
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changeset
|
979 int64_t id; |
|
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diff
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|
980 ResourceType type; |
|
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|
981 if (!db2_->LookupResource(instanceUuid, id, type) || |
|
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changeset
|
982 type != ResourceType_Instance) |
|
192
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diff
changeset
|
983 { |
|
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diff
changeset
|
984 throw OrthancException(ErrorCode_InternalError); |
|
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diff
changeset
|
985 } |
|
193
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diff
changeset
|
986 |
|
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987 uint64_t compressedSize, uncompressedSize; |
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988 |
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989 return db2_->LookupFile(id, contentType, fileUuid, compressedSize, uncompressedSize, compressionType); |
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990 } |
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991 |
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992 |
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993 |
| 0 | 994 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 995 ResourceType resourceType) |
| 0 | 996 { |
| 190 | 997 boost::mutex::scoped_lock scoped_lock(mutex_); |
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998 db2_->GetAllPublicIds(target, resourceType); |
| 0 | 999 } |
| 1000 | |
| 1001 | |
| 1002 bool ServerIndex::GetChanges(Json::Value& target, | |
| 1003 int64_t since, | |
| 1004 const std::string& filter, | |
| 1005 unsigned int maxResults) | |
| 1006 { | |
| 1007 assert(target.type() == Json::objectValue); | |
| 1008 boost::mutex::scoped_lock scoped_lock(mutex_); | |
| 1009 | |
| 1010 if (filter.size() != 0 && | |
| 1011 filter != "instances" && | |
| 1012 filter != "series" && | |
| 1013 filter != "studies" && | |
| 1014 filter != "patients") | |
| 1015 { | |
| 1016 return false; | |
| 1017 } | |
| 1018 | |
| 1019 std::auto_ptr<SQLite::Statement> s; | |
| 1020 if (filter.size() == 0) | |
| 1021 { | |
| 1022 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
| 1023 "ORDER BY seq LIMIT ?")); | |
| 1024 s->BindInt64(0, since); | |
| 1025 s->BindInt(1, maxResults); | |
| 1026 } | |
| 1027 else | |
| 1028 { | |
| 1029 s.reset(new SQLite::Statement(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? " | |
| 1030 "AND basePath=? ORDER BY seq LIMIT ?")); | |
| 1031 s->BindInt64(0, since); | |
| 1032 s->BindString(1, filter); | |
| 1033 s->BindInt(2, maxResults); | |
| 1034 } | |
| 1035 | |
| 1036 int64_t lastSeq = 0; | |
| 1037 Json::Value results(Json::arrayValue); | |
| 1038 while (s->Step()) | |
| 1039 { | |
| 1040 int64_t seq = s->ColumnInt64(0); | |
| 1041 std::string basePath = s->ColumnString(1); | |
| 1042 std::string uuid = s->ColumnString(2); | |
| 1043 | |
| 1044 if (filter.size() == 0 || | |
| 1045 filter == basePath) | |
| 1046 { | |
| 1047 Json::Value change(Json::objectValue); | |
| 1048 change["Seq"] = static_cast<int>(seq); // TODO JsonCpp in 64bit | |
| 1049 change["BasePath"] = basePath; | |
| 1050 change["ID"] = uuid; | |
| 1051 results.append(change); | |
| 1052 } | |
| 1053 | |
| 1054 if (seq > lastSeq) | |
| 1055 { | |
| 1056 lastSeq = seq; | |
| 1057 } | |
| 1058 } | |
| 1059 | |
| 1060 target["Results"] = results; | |
| 1061 target["LastSeq"] = static_cast<int>(lastSeq); // TODO JsonCpp in 64bit | |
| 1062 | |
| 1063 return true; | |
| 1064 } | |
| 82 | 1065 |
| 0 | 1066 } |