Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ArchiveJob.cpp @ 4613:2684544ff03c db-changes
maximum number of database retries for writer collisions is now set by the plugins
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 08 Apr 2021 10:46:12 +0200 |
| parents | ff8170d17d90 |
| children | f7d5372b59b3 |
| rev | line source |
|---|---|
| 2632 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
|
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
| 2632 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * In addition, as a special exception, the copyright holders of this | |
| 13 * program give permission to link the code of its release with the | |
| 14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 15 * that use the same license as the "OpenSSL" library), and distribute | |
| 16 * the linked executables. You must obey the GNU General Public License | |
| 17 * in all respects for all of the code used other than "OpenSSL". If you | |
| 18 * modify file(s) with this exception, you may extend this exception to | |
| 19 * your version of the file(s), but you are not obligated to do so. If | |
| 20 * you do not wish to do so, delete this exception statement from your | |
| 21 * version. If you delete this exception statement from all source files | |
| 22 * in the program, then also delete it here. | |
| 23 * | |
| 24 * This program is distributed in the hope that it will be useful, but | |
| 25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 27 * General Public License for more details. | |
| 28 * | |
| 29 * You should have received a copy of the GNU General Public License | |
| 30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 31 **/ | |
| 32 | |
| 33 | |
| 34 #include "../PrecompiledHeadersServer.h" | |
| 35 #include "ArchiveJob.h" | |
| 36 | |
| 4045 | 37 #include "../../../OrthancFramework/Sources/Cache/SharedArchive.h" |
| 38 #include "../../../OrthancFramework/Sources/Compression/HierarchicalZipWriter.h" | |
| 39 #include "../../../OrthancFramework/Sources/DicomParsing/DicomDirWriter.h" | |
| 40 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" | |
| 41 #include "../../../OrthancFramework/Sources/Logging.h" | |
| 42 #include "../../../OrthancFramework/Sources/OrthancException.h" | |
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43 #include "../OrthancConfiguration.h" |
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44 #include "../ServerContext.h" |
| 2632 | 45 |
| 46 #include <stdio.h> | |
| 47 | |
| 48 #if defined(_MSC_VER) | |
| 49 #define snprintf _snprintf | |
| 50 #endif | |
| 51 | |
| 52 static const uint64_t MEGA_BYTES = 1024 * 1024; | |
| 53 static const uint64_t GIGA_BYTES = 1024 * 1024 * 1024; | |
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54 |
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55 static const char* const MEDIA_IMAGES_FOLDER = "IMAGES"; |
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56 static const char* const KEY_DESCRIPTION = "Description"; |
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57 static const char* const KEY_INSTANCES_COUNT = "InstancesCount"; |
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58 static const char* const KEY_UNCOMPRESSED_SIZE_MB = "UncompressedSizeMB"; |
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59 static const char* const KEY_ARCHIVE_SIZE_MB = "ArchiveSizeMB"; |
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60 static const char* const KEY_TRANSCODE = "Transcode"; |
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61 |
| 2632 | 62 |
| 63 namespace Orthanc | |
| 64 { | |
| 65 static bool IsZip64Required(uint64_t uncompressedSize, | |
| 66 unsigned int countInstances) | |
| 67 { | |
| 68 static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; // Should be large enough to hold DICOMDIR | |
| 69 static const unsigned int FILES_MARGIN = 10; | |
| 70 | |
| 71 /** | |
| 72 * Determine whether ZIP64 is required. Original ZIP format can | |
| 73 * store up to 2GB of data (some implementation supporting up to | |
| 74 * 4GB of data), and up to 65535 files. | |
| 75 * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64 | |
| 76 **/ | |
| 77 | |
| 78 const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES - SAFETY_MARGIN || | |
| 79 countInstances >= 65535 - FILES_MARGIN); | |
| 80 | |
| 81 LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " | |
| 82 << (uncompressedSize / MEGA_BYTES) << "MB using the " | |
| 83 << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; | |
| 84 | |
| 85 return isZip64; | |
| 86 } | |
| 87 | |
| 88 | |
| 89 class ArchiveJob::ResourceIdentifiers : public boost::noncopyable | |
| 90 { | |
| 91 private: | |
| 92 ResourceType level_; | |
| 93 std::string patient_; | |
| 94 std::string study_; | |
| 95 std::string series_; | |
| 96 std::string instance_; | |
| 97 | |
| 98 static void GoToParent(ServerIndex& index, | |
| 99 std::string& current) | |
| 100 { | |
| 101 std::string tmp; | |
| 102 | |
| 103 if (index.LookupParent(tmp, current)) | |
| 104 { | |
| 105 current = tmp; | |
| 106 } | |
| 107 else | |
| 108 { | |
| 109 throw OrthancException(ErrorCode_UnknownResource); | |
| 110 } | |
| 111 } | |
| 112 | |
| 113 | |
| 114 public: | |
| 115 ResourceIdentifiers(ServerIndex& index, | |
| 116 const std::string& publicId) | |
| 117 { | |
| 118 if (!index.LookupResourceType(level_, publicId)) | |
| 119 { | |
| 120 throw OrthancException(ErrorCode_UnknownResource); | |
| 121 } | |
| 122 | |
| 123 std::string current = publicId;; | |
| 124 switch (level_) // Do not add "break" below! | |
| 125 { | |
| 126 case ResourceType_Instance: | |
| 127 instance_ = current; | |
| 128 GoToParent(index, current); | |
| 129 | |
| 130 case ResourceType_Series: | |
| 131 series_ = current; | |
| 132 GoToParent(index, current); | |
| 133 | |
| 134 case ResourceType_Study: | |
| 135 study_ = current; | |
| 136 GoToParent(index, current); | |
| 137 | |
| 138 case ResourceType_Patient: | |
| 139 patient_ = current; | |
| 140 break; | |
| 141 | |
| 142 default: | |
| 143 throw OrthancException(ErrorCode_InternalError); | |
| 144 } | |
| 145 } | |
| 146 | |
| 147 ResourceType GetLevel() const | |
| 148 { | |
| 149 return level_; | |
| 150 } | |
| 151 | |
| 152 const std::string& GetIdentifier(ResourceType level) const | |
| 153 { | |
| 154 // Some sanity check to ensure enumerations are not altered | |
| 155 assert(ResourceType_Patient < ResourceType_Study); | |
| 156 assert(ResourceType_Study < ResourceType_Series); | |
| 157 assert(ResourceType_Series < ResourceType_Instance); | |
| 158 | |
| 159 if (level > level_) | |
| 160 { | |
| 161 throw OrthancException(ErrorCode_InternalError); | |
| 162 } | |
| 163 | |
| 164 switch (level) | |
| 165 { | |
| 166 case ResourceType_Patient: | |
| 167 return patient_; | |
| 168 | |
| 169 case ResourceType_Study: | |
| 170 return study_; | |
| 171 | |
| 172 case ResourceType_Series: | |
| 173 return series_; | |
| 174 | |
| 175 case ResourceType_Instance: | |
| 176 return instance_; | |
| 177 | |
| 178 default: | |
| 179 throw OrthancException(ErrorCode_InternalError); | |
| 180 } | |
| 181 } | |
| 182 }; | |
| 183 | |
| 184 | |
| 185 class ArchiveJob::IArchiveVisitor : public boost::noncopyable | |
| 186 { | |
| 187 public: | |
| 188 virtual ~IArchiveVisitor() | |
| 189 { | |
| 190 } | |
| 191 | |
| 192 virtual void Open(ResourceType level, | |
| 193 const std::string& publicId) = 0; | |
| 194 | |
| 195 virtual void Close() = 0; | |
| 196 | |
| 197 virtual void AddInstance(const std::string& instanceId, | |
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198 uint64_t uncompressedSize) = 0; |
| 2632 | 199 }; |
| 200 | |
| 201 | |
| 202 class ArchiveJob::ArchiveIndex : public boost::noncopyable | |
| 203 { | |
| 204 private: | |
| 205 struct Instance | |
| 206 { | |
| 207 std::string id_; | |
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208 uint64_t uncompressedSize_; |
| 2632 | 209 |
| 210 Instance(const std::string& id, | |
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211 uint64_t uncompressedSize) : |
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212 id_(id), |
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213 uncompressedSize_(uncompressedSize) |
| 2632 | 214 { |
| 215 } | |
| 216 }; | |
| 217 | |
| 218 // A "NULL" value for ArchiveIndex indicates a non-expanded node | |
| 219 typedef std::map<std::string, ArchiveIndex*> Resources; | |
| 220 | |
| 221 ResourceType level_; | |
| 222 Resources resources_; // Only at patient/study/series level | |
| 223 std::list<Instance> instances_; // Only at instance level | |
| 224 | |
| 225 | |
| 226 void AddResourceToExpand(ServerIndex& index, | |
| 227 const std::string& id) | |
| 228 { | |
| 229 if (level_ == ResourceType_Instance) | |
| 230 { | |
| 231 FileInfo tmp; | |
| 232 if (index.LookupAttachment(tmp, id, FileContentType_Dicom)) | |
| 233 { | |
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234 instances_.push_back(Instance(id, tmp.GetUncompressedSize())); |
| 2632 | 235 } |
| 236 } | |
| 237 else | |
| 238 { | |
| 239 resources_[id] = NULL; | |
| 240 } | |
| 241 } | |
| 242 | |
| 243 | |
| 244 public: | |
| 4205 | 245 explicit ArchiveIndex(ResourceType level) : |
| 2632 | 246 level_(level) |
| 247 { | |
| 248 } | |
| 249 | |
| 250 ~ArchiveIndex() | |
| 251 { | |
| 252 for (Resources::iterator it = resources_.begin(); | |
| 253 it != resources_.end(); ++it) | |
| 254 { | |
| 255 delete it->second; | |
| 256 } | |
| 257 } | |
| 258 | |
| 259 | |
| 260 void Add(ServerIndex& index, | |
| 261 const ResourceIdentifiers& resource) | |
| 262 { | |
| 263 const std::string& id = resource.GetIdentifier(level_); | |
| 264 Resources::iterator previous = resources_.find(id); | |
| 265 | |
| 266 if (level_ == ResourceType_Instance) | |
| 267 { | |
| 268 AddResourceToExpand(index, id); | |
| 269 } | |
| 270 else if (resource.GetLevel() == level_) | |
| 271 { | |
| 272 // Mark this resource for further expansion | |
| 273 if (previous != resources_.end()) | |
| 274 { | |
| 275 delete previous->second; | |
| 276 } | |
| 277 | |
| 278 resources_[id] = NULL; | |
| 279 } | |
| 280 else if (previous == resources_.end()) | |
| 281 { | |
| 282 // This is the first time we meet this resource | |
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283 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 284 child->Add(index, resource); |
| 285 resources_[id] = child.release(); | |
| 286 } | |
| 287 else if (previous->second != NULL) | |
| 288 { | |
| 289 previous->second->Add(index, resource); | |
| 290 } | |
| 291 else | |
| 292 { | |
| 293 // Nothing to do: This item is marked for further expansion | |
| 294 } | |
| 295 } | |
| 296 | |
| 297 | |
| 298 void Expand(ServerIndex& index) | |
| 299 { | |
| 300 if (level_ == ResourceType_Instance) | |
| 301 { | |
| 302 // Expanding an instance node makes no sense | |
| 303 return; | |
| 304 } | |
| 305 | |
| 306 for (Resources::iterator it = resources_.begin(); | |
| 307 it != resources_.end(); ++it) | |
| 308 { | |
| 309 if (it->second == NULL) | |
| 310 { | |
| 311 // This is resource is marked for expansion | |
| 312 std::list<std::string> children; | |
| 313 index.GetChildren(children, it->first); | |
| 314 | |
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315 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 316 |
| 317 for (std::list<std::string>::const_iterator | |
| 318 it2 = children.begin(); it2 != children.end(); ++it2) | |
| 319 { | |
| 320 child->AddResourceToExpand(index, *it2); | |
| 321 } | |
| 322 | |
| 323 it->second = child.release(); | |
| 324 } | |
| 325 | |
| 326 assert(it->second != NULL); | |
| 327 it->second->Expand(index); | |
| 328 } | |
| 329 } | |
| 330 | |
| 331 | |
| 332 void Apply(IArchiveVisitor& visitor) const | |
| 333 { | |
| 334 if (level_ == ResourceType_Instance) | |
| 335 { | |
| 336 for (std::list<Instance>::const_iterator | |
| 337 it = instances_.begin(); it != instances_.end(); ++it) | |
| 338 { | |
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339 visitor.AddInstance(it->id_, it->uncompressedSize_); |
| 2632 | 340 } |
| 341 } | |
| 342 else | |
| 343 { | |
| 344 for (Resources::const_iterator it = resources_.begin(); | |
| 345 it != resources_.end(); ++it) | |
| 346 { | |
| 347 assert(it->second != NULL); // There must have been a call to "Expand()" | |
| 348 visitor.Open(level_, it->first); | |
| 349 it->second->Apply(visitor); | |
| 350 visitor.Close(); | |
| 351 } | |
| 352 } | |
| 353 } | |
| 354 }; | |
| 355 | |
| 356 | |
| 357 | |
| 358 class ArchiveJob::ZipCommands : public boost::noncopyable | |
| 359 { | |
| 360 private: | |
| 361 enum Type | |
| 362 { | |
| 363 Type_OpenDirectory, | |
| 364 Type_CloseDirectory, | |
| 365 Type_WriteInstance | |
| 366 }; | |
| 367 | |
| 368 class Command : public boost::noncopyable | |
| 369 { | |
| 370 private: | |
| 371 Type type_; | |
| 372 std::string filename_; | |
| 373 std::string instanceId_; | |
| 374 | |
| 375 public: | |
| 376 explicit Command(Type type) : | |
| 377 type_(type) | |
| 378 { | |
| 379 assert(type_ == Type_CloseDirectory); | |
| 380 } | |
| 381 | |
| 382 Command(Type type, | |
| 383 const std::string& filename) : | |
| 384 type_(type), | |
| 385 filename_(filename) | |
| 386 { | |
| 387 assert(type_ == Type_OpenDirectory); | |
| 388 } | |
| 389 | |
| 390 Command(Type type, | |
| 391 const std::string& filename, | |
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392 const std::string& instanceId) : |
| 2632 | 393 type_(type), |
| 394 filename_(filename), | |
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395 instanceId_(instanceId) |
| 2632 | 396 { |
| 397 assert(type_ == Type_WriteInstance); | |
| 398 } | |
| 399 | |
| 400 void Apply(HierarchicalZipWriter& writer, | |
| 401 ServerContext& context, | |
| 402 DicomDirWriter* dicomDir, | |
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403 const std::string& dicomDirFolder, |
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404 bool transcode, |
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405 DicomTransferSyntax transferSyntax) const |
| 2632 | 406 { |
| 407 switch (type_) | |
| 408 { | |
| 409 case Type_OpenDirectory: | |
| 410 writer.OpenDirectory(filename_.c_str()); | |
| 411 break; | |
| 412 | |
| 413 case Type_CloseDirectory: | |
| 414 writer.CloseDirectory(); | |
| 415 break; | |
| 416 | |
| 417 case Type_WriteInstance: | |
| 418 { | |
| 419 std::string content; | |
| 420 | |
| 421 try | |
| 422 { | |
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423 context.ReadDicom(content, instanceId_); |
| 2632 | 424 } |
| 425 catch (OrthancException& e) | |
| 426 { | |
| 427 LOG(WARNING) << "An instance was removed after the job was issued: " << instanceId_; | |
| 428 return; | |
| 429 } | |
| 2636 | 430 |
| 431 //boost::this_thread::sleep(boost::posix_time::milliseconds(300)); | |
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432 |
| 2632 | 433 writer.OpenFile(filename_.c_str()); |
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434 |
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435 bool transcodeSuccess = false; |
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436 |
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437 std::unique_ptr<ParsedDicomFile> parsed; |
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438 |
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439 if (transcode) |
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440 { |
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441 // New in Orthanc 1.7.0 |
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442 std::set<DicomTransferSyntax> syntaxes; |
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443 syntaxes.insert(transferSyntax); |
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444 |
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445 IDicomTranscoder::DicomImage source, transcoded; |
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446 source.SetExternalBuffer(content); |
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447 |
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448 if (context.Transcode(transcoded, source, syntaxes, true /* allow new SOP instance UID */)) |
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449 { |
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450 writer.Write(transcoded.GetBufferData(), transcoded.GetBufferSize()); |
| 2632 | 451 |
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452 if (dicomDir != NULL) |
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453 { |
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454 std::unique_ptr<ParsedDicomFile> tmp(transcoded.ReleaseAsParsedDicomFile()); |
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455 dicomDir->Add(dicomDirFolder, filename_, *tmp); |
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456 } |
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457 |
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458 transcodeSuccess = true; |
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459 } |
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460 else |
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461 { |
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462 LOG(INFO) << "Cannot transcode instance " << instanceId_ |
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463 << " to transfer syntax: " << GetTransferSyntaxUid(transferSyntax); |
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464 } |
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465 } |
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466 |
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467 if (!transcodeSuccess) |
| 2632 | 468 { |
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469 writer.Write(content); |
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470 |
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471 if (dicomDir != NULL) |
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472 { |
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473 if (parsed.get() == NULL) |
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474 { |
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475 parsed.reset(new ParsedDicomFile(content)); |
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476 } |
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477 |
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478 dicomDir->Add(dicomDirFolder, filename_, *parsed); |
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479 } |
| 2632 | 480 } |
| 481 | |
| 482 break; | |
| 483 } | |
| 484 | |
| 485 default: | |
| 486 throw OrthancException(ErrorCode_InternalError); | |
| 487 } | |
| 488 } | |
| 489 }; | |
| 490 | |
| 491 std::deque<Command*> commands_; | |
| 492 uint64_t uncompressedSize_; | |
| 493 unsigned int instancesCount_; | |
| 494 | |
| 495 | |
| 496 void ApplyInternal(HierarchicalZipWriter& writer, | |
| 497 ServerContext& context, | |
| 498 size_t index, | |
| 499 DicomDirWriter* dicomDir, | |
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500 const std::string& dicomDirFolder, |
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501 bool transcode, |
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502 DicomTransferSyntax transferSyntax) const |
| 2632 | 503 { |
| 504 if (index >= commands_.size()) | |
| 505 { | |
| 506 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 507 } | |
| 508 | |
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509 commands_[index]->Apply(writer, context, dicomDir, dicomDirFolder, transcode, transferSyntax); |
| 2632 | 510 } |
| 511 | |
| 512 public: | |
| 513 ZipCommands() : | |
| 514 uncompressedSize_(0), | |
| 515 instancesCount_(0) | |
| 516 { | |
| 517 } | |
| 518 | |
| 519 ~ZipCommands() | |
| 520 { | |
| 521 for (std::deque<Command*>::iterator it = commands_.begin(); | |
| 522 it != commands_.end(); ++it) | |
| 523 { | |
| 524 assert(*it != NULL); | |
| 525 delete *it; | |
| 526 } | |
| 527 } | |
| 528 | |
| 529 size_t GetSize() const | |
| 530 { | |
| 531 return commands_.size(); | |
| 532 } | |
| 533 | |
| 534 unsigned int GetInstancesCount() const | |
| 535 { | |
| 536 return instancesCount_; | |
| 537 } | |
| 538 | |
| 539 uint64_t GetUncompressedSize() const | |
| 540 { | |
| 541 return uncompressedSize_; | |
| 542 } | |
| 543 | |
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544 // "media" flavor (with DICOMDIR) |
| 2632 | 545 void Apply(HierarchicalZipWriter& writer, |
| 546 ServerContext& context, | |
| 547 size_t index, | |
| 548 DicomDirWriter& dicomDir, | |
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549 const std::string& dicomDirFolder, |
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550 bool transcode, |
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551 DicomTransferSyntax transferSyntax) const |
| 2632 | 552 { |
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553 ApplyInternal(writer, context, index, &dicomDir, dicomDirFolder, transcode, transferSyntax); |
| 2632 | 554 } |
| 555 | |
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556 // "archive" flavor (without DICOMDIR) |
| 2632 | 557 void Apply(HierarchicalZipWriter& writer, |
| 558 ServerContext& context, | |
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559 size_t index, |
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560 bool transcode, |
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561 DicomTransferSyntax transferSyntax) const |
| 2632 | 562 { |
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563 ApplyInternal(writer, context, index, NULL, "", transcode, transferSyntax); |
| 2632 | 564 } |
| 565 | |
| 566 void AddOpenDirectory(const std::string& filename) | |
| 567 { | |
| 568 commands_.push_back(new Command(Type_OpenDirectory, filename)); | |
| 569 } | |
| 570 | |
| 571 void AddCloseDirectory() | |
| 572 { | |
| 573 commands_.push_back(new Command(Type_CloseDirectory)); | |
| 574 } | |
| 575 | |
| 576 void AddWriteInstance(const std::string& filename, | |
| 577 const std::string& instanceId, | |
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578 uint64_t uncompressedSize) |
| 2632 | 579 { |
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580 commands_.push_back(new Command(Type_WriteInstance, filename, instanceId)); |
| 2632 | 581 instancesCount_ ++; |
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582 uncompressedSize_ += uncompressedSize; |
| 2632 | 583 } |
| 584 | |
| 585 bool IsZip64() const | |
| 586 { | |
| 587 return IsZip64Required(GetUncompressedSize(), GetInstancesCount()); | |
| 588 } | |
| 589 }; | |
| 590 | |
| 591 | |
| 592 | |
| 593 class ArchiveJob::ArchiveIndexVisitor : public IArchiveVisitor | |
| 594 { | |
| 595 private: | |
| 596 ZipCommands& commands_; | |
| 597 ServerContext& context_; | |
| 598 char instanceFormat_[24]; | |
| 599 unsigned int counter_; | |
| 600 | |
| 601 static std::string GetTag(const DicomMap& tags, | |
| 602 const DicomTag& tag) | |
| 603 { | |
| 604 const DicomValue* v = tags.TestAndGetValue(tag); | |
| 605 if (v != NULL && | |
| 606 !v->IsBinary() && | |
| 607 !v->IsNull()) | |
| 608 { | |
| 609 return v->GetContent(); | |
| 610 } | |
| 611 else | |
| 612 { | |
| 613 return ""; | |
| 614 } | |
| 615 } | |
| 616 | |
| 617 public: | |
| 618 ArchiveIndexVisitor(ZipCommands& commands, | |
| 619 ServerContext& context) : | |
| 620 commands_(commands), | |
| 621 context_(context), | |
| 622 counter_(0) | |
| 623 { | |
| 624 if (commands.GetSize() != 0) | |
| 625 { | |
| 626 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 627 } | |
| 628 | |
| 629 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); | |
| 630 } | |
| 631 | |
| 632 virtual void Open(ResourceType level, | |
| 4205 | 633 const std::string& publicId) ORTHANC_OVERRIDE |
| 2632 | 634 { |
| 635 std::string path; | |
| 636 | |
| 637 DicomMap tags; | |
| 638 if (context_.GetIndex().GetMainDicomTags(tags, publicId, level, level)) | |
| 639 { | |
| 640 switch (level) | |
| 641 { | |
| 642 case ResourceType_Patient: | |
| 643 path = GetTag(tags, DICOM_TAG_PATIENT_ID) + " " + GetTag(tags, DICOM_TAG_PATIENT_NAME); | |
| 644 break; | |
| 645 | |
| 646 case ResourceType_Study: | |
| 647 path = GetTag(tags, DICOM_TAG_ACCESSION_NUMBER) + " " + GetTag(tags, DICOM_TAG_STUDY_DESCRIPTION); | |
| 648 break; | |
| 649 | |
| 650 case ResourceType_Series: | |
| 651 { | |
| 652 std::string modality = GetTag(tags, DICOM_TAG_MODALITY); | |
| 653 path = modality + " " + GetTag(tags, DICOM_TAG_SERIES_DESCRIPTION); | |
| 654 | |
| 655 if (modality.size() == 0) | |
| 656 { | |
| 657 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); | |
| 658 } | |
| 659 else if (modality.size() == 1) | |
| 660 { | |
| 661 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%%07d.dcm", | |
| 662 toupper(modality[0])); | |
| 663 } | |
| 664 else if (modality.size() >= 2) | |
| 665 { | |
| 666 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%c%%06d.dcm", | |
| 667 toupper(modality[0]), toupper(modality[1])); | |
| 668 } | |
| 669 | |
| 670 counter_ = 0; | |
| 671 | |
| 672 break; | |
| 673 } | |
| 674 | |
| 675 default: | |
| 676 throw OrthancException(ErrorCode_InternalError); | |
| 677 } | |
| 678 } | |
| 679 | |
| 680 path = Toolbox::StripSpaces(Toolbox::ConvertToAscii(path)); | |
| 681 | |
| 682 if (path.empty()) | |
| 683 { | |
| 684 path = std::string("Unknown ") + EnumerationToString(level); | |
| 685 } | |
| 686 | |
| 687 commands_.AddOpenDirectory(path.c_str()); | |
| 688 } | |
| 689 | |
| 4205 | 690 virtual void Close() ORTHANC_OVERRIDE |
| 2632 | 691 { |
| 692 commands_.AddCloseDirectory(); | |
| 693 } | |
| 694 | |
| 695 virtual void AddInstance(const std::string& instanceId, | |
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696 uint64_t uncompressedSize) ORTHANC_OVERRIDE |
| 2632 | 697 { |
| 698 char filename[24]; | |
| 699 snprintf(filename, sizeof(filename) - 1, instanceFormat_, counter_); | |
| 700 counter_ ++; | |
| 701 | |
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702 commands_.AddWriteInstance(filename, instanceId, uncompressedSize); |
| 2632 | 703 } |
| 704 }; | |
| 705 | |
| 706 | |
| 707 class ArchiveJob::MediaIndexVisitor : public IArchiveVisitor | |
| 708 { | |
| 709 private: | |
| 710 ZipCommands& commands_; | |
| 711 unsigned int counter_; | |
| 712 | |
| 713 public: | |
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714 explicit MediaIndexVisitor(ZipCommands& commands) : |
| 2632 | 715 commands_(commands), |
| 716 counter_(0) | |
| 717 { | |
| 718 } | |
| 719 | |
| 720 virtual void Open(ResourceType level, | |
| 4205 | 721 const std::string& publicId) ORTHANC_OVERRIDE |
| 2632 | 722 { |
| 723 } | |
| 724 | |
| 4205 | 725 virtual void Close() ORTHANC_OVERRIDE |
| 2632 | 726 { |
| 727 } | |
| 728 | |
| 729 virtual void AddInstance(const std::string& instanceId, | |
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730 uint64_t uncompressedSize) ORTHANC_OVERRIDE |
| 2632 | 731 { |
| 732 // "DICOM restricts the filenames on DICOM media to 8 | |
| 733 // characters (some systems wrongly use 8.3, but this does not | |
| 734 // conform to the standard)." | |
| 735 std::string filename = "IM" + boost::lexical_cast<std::string>(counter_); | |
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736 commands_.AddWriteInstance(filename, instanceId, uncompressedSize); |
| 2632 | 737 |
| 738 counter_ ++; | |
| 739 } | |
| 740 }; | |
| 741 | |
| 742 | |
| 743 class ArchiveJob::ZipWriterIterator : public boost::noncopyable | |
| 744 { | |
| 745 private: | |
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746 ServerContext& context_; |
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747 ZipCommands commands_; |
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748 std::unique_ptr<HierarchicalZipWriter> zip_; |
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749 std::unique_ptr<DicomDirWriter> dicomDir_; |
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750 bool isMedia_; |
| 2632 | 751 |
| 752 public: | |
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753 ZipWriterIterator(const TemporaryFile& target, |
| 2632 | 754 ServerContext& context, |
| 755 ArchiveIndex& archive, | |
| 756 bool isMedia, | |
| 757 bool enableExtendedSopClass) : | |
| 758 context_(context), | |
| 759 isMedia_(isMedia) | |
| 760 { | |
| 761 if (isMedia) | |
| 762 { | |
| 4588 | 763 MediaIndexVisitor visitor(commands_); |
| 2632 | 764 archive.Expand(context.GetIndex()); |
| 765 | |
| 766 commands_.AddOpenDirectory(MEDIA_IMAGES_FOLDER); | |
| 767 archive.Apply(visitor); | |
| 768 commands_.AddCloseDirectory(); | |
| 769 | |
| 770 dicomDir_.reset(new DicomDirWriter); | |
| 771 dicomDir_->EnableExtendedSopClass(enableExtendedSopClass); | |
| 772 } | |
| 773 else | |
| 774 { | |
| 775 ArchiveIndexVisitor visitor(commands_, context); | |
| 776 archive.Expand(context.GetIndex()); | |
| 777 archive.Apply(visitor); | |
| 778 } | |
| 779 | |
| 780 zip_.reset(new HierarchicalZipWriter(target.GetPath().c_str())); | |
| 781 zip_->SetZip64(commands_.IsZip64()); | |
| 782 } | |
| 783 | |
| 784 size_t GetStepsCount() const | |
| 785 { | |
| 786 return commands_.GetSize() + 1; | |
| 787 } | |
| 788 | |
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789 void RunStep(size_t index, |
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790 bool transcode, |
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791 DicomTransferSyntax transferSyntax) |
| 2632 | 792 { |
| 793 if (index > commands_.GetSize()) | |
| 794 { | |
| 795 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 796 } | |
| 797 else if (index == commands_.GetSize()) | |
| 798 { | |
| 799 // Last step: Add the DICOMDIR | |
| 800 if (isMedia_) | |
| 801 { | |
| 802 assert(dicomDir_.get() != NULL); | |
| 803 std::string s; | |
| 804 dicomDir_->Encode(s); | |
| 805 | |
| 806 zip_->OpenFile("DICOMDIR"); | |
| 807 zip_->Write(s); | |
| 808 } | |
| 809 } | |
| 810 else | |
| 811 { | |
| 812 if (isMedia_) | |
| 813 { | |
| 814 assert(dicomDir_.get() != NULL); | |
|
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|
815 commands_.Apply(*zip_, context_, index, *dicomDir_, |
|
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|
816 MEDIA_IMAGES_FOLDER, transcode, transferSyntax); |
| 2632 | 817 } |
| 818 else | |
| 819 { | |
| 820 assert(dicomDir_.get() == NULL); | |
|
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821 commands_.Apply(*zip_, context_, index, transcode, transferSyntax); |
| 2632 | 822 } |
| 823 } | |
| 824 } | |
| 825 | |
| 826 unsigned int GetInstancesCount() const | |
| 827 { | |
| 828 return commands_.GetInstancesCount(); | |
| 829 } | |
| 830 | |
| 831 uint64_t GetUncompressedSize() const | |
| 832 { | |
| 833 return commands_.GetUncompressedSize(); | |
| 834 } | |
| 835 }; | |
| 836 | |
| 837 | |
| 2966 | 838 ArchiveJob::ArchiveJob(ServerContext& context, |
| 2632 | 839 bool isMedia, |
| 840 bool enableExtendedSopClass) : | |
| 841 context_(context), | |
| 842 archive_(new ArchiveIndex(ResourceType_Patient)), // root | |
| 843 isMedia_(isMedia), | |
| 844 enableExtendedSopClass_(enableExtendedSopClass), | |
| 845 currentStep_(0), | |
| 846 instancesCount_(0), | |
|
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847 uncompressedSize_(0), |
|
4341
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Archive/media jobs report the size of the created ZIP file in content field "ArchiveSizeMB"
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|
848 archiveSize_(0), |
|
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849 transcode_(false), |
|
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850 transferSyntax_(DicomTransferSyntax_LittleEndianImplicit) |
| 2632 | 851 { |
| 2966 | 852 } |
| 853 | |
|
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|
854 |
|
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855 ArchiveJob::~ArchiveJob() |
|
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856 { |
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857 if (!mediaArchiveId_.empty()) |
|
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858 { |
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859 context_.GetMediaArchive().Remove(mediaArchiveId_); |
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|
860 } |
|
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|
861 } |
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|
862 |
| 2966 | 863 |
| 864 void ArchiveJob::SetSynchronousTarget(boost::shared_ptr<TemporaryFile>& target) | |
| 865 { | |
| 866 if (target.get() == NULL) | |
| 2632 | 867 { |
| 868 throw OrthancException(ErrorCode_NullPointer); | |
| 869 } | |
|
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870 else if (writer_.get() != NULL || // Already started |
|
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|
871 synchronousTarget_.get() != NULL || |
|
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|
872 asynchronousTarget_.get() != NULL) |
| 2966 | 873 { |
| 874 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 875 } | |
| 876 else | |
| 877 { | |
| 878 synchronousTarget_ = target; | |
| 879 } | |
| 2632 | 880 } |
| 881 | |
| 882 | |
|
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|
883 void ArchiveJob::SetDescription(const std::string& description) |
|
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|
884 { |
|
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885 if (writer_.get() != NULL) // Already started |
|
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886 { |
|
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887 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
|
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888 } |
|
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|
889 else |
|
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|
890 { |
|
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|
891 description_ = description; |
|
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|
892 } |
|
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|
893 } |
|
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|
894 |
|
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|
895 |
| 2632 | 896 void ArchiveJob::AddResource(const std::string& publicId) |
| 897 { | |
| 898 if (writer_.get() != NULL) // Already started | |
| 899 { | |
| 900 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 901 } | |
|
2976
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|
902 else |
|
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|
903 { |
|
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|
904 ResourceIdentifiers resource(context_.GetIndex(), publicId); |
|
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|
905 archive_->Add(context_.GetIndex(), resource); |
|
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|
906 } |
| 2632 | 907 } |
| 908 | |
|
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|
909 |
|
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changeset
|
910 void ArchiveJob::SetTranscode(DicomTransferSyntax transferSyntax) |
|
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|
911 { |
|
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|
912 if (writer_.get() != NULL) // Already started |
|
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|
913 { |
|
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|
914 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
|
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|
915 } |
|
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|
916 else |
|
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changeset
|
917 { |
|
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changeset
|
918 transcode_ = true; |
|
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|
919 transferSyntax_ = transferSyntax; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
920 } |
|
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transcoding ZIP archive and media
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changeset
|
921 } |
|
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diff
changeset
|
922 |
| 2632 | 923 |
|
2812
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improved naming of methods in IJob
Sebastien Jodogne <s.jodogne@gmail.com>
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2730
diff
changeset
|
924 void ArchiveJob::Reset() |
| 2632 | 925 { |
| 2955 | 926 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
| 927 "Cannot resubmit the creation of an archive"); | |
| 2632 | 928 } |
| 929 | |
| 930 | |
| 931 void ArchiveJob::Start() | |
| 932 { | |
|
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2966
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changeset
|
933 TemporaryFile* target = NULL; |
|
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diff
changeset
|
934 |
| 2966 | 935 if (synchronousTarget_.get() == NULL) |
| 936 { | |
|
3181
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
937 { |
|
6fd38327e777
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
938 OrthancConfiguration::ReaderLock lock; |
|
6fd38327e777
Fix issue #130 (Orthanc failed to start when /tmp partition was full)
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
939 asynchronousTarget_.reset(lock.GetConfiguration().CreateTemporaryFile()); |
|
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|
940 } |
|
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changeset
|
941 |
|
2976
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diff
changeset
|
942 target = asynchronousTarget_.get(); |
|
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|
943 } |
|
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|
944 else |
|
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|
945 { |
|
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diff
changeset
|
946 target = synchronousTarget_.get(); |
| 2966 | 947 } |
|
3181
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changeset
|
948 |
|
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diff
changeset
|
949 assert(target != NULL); |
|
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diff
changeset
|
950 target->Touch(); // Make sure we can write to the temporary file |
| 2966 | 951 |
| 2632 | 952 if (writer_.get() != NULL) |
| 953 { | |
| 954 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 955 } | |
| 956 | |
|
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diff
changeset
|
957 writer_.reset(new ZipWriterIterator(*target, context_, *archive_, |
| 2632 | 958 isMedia_, enableExtendedSopClass_)); |
| 959 | |
| 960 instancesCount_ = writer_->GetInstancesCount(); | |
| 961 uncompressedSize_ = writer_->GetUncompressedSize(); | |
| 962 } | |
| 963 | |
|
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changeset
|
964 |
|
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diff
changeset
|
965 |
|
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diff
changeset
|
966 namespace |
|
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diff
changeset
|
967 { |
|
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diff
changeset
|
968 class DynamicTemporaryFile : public IDynamicObject |
|
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changeset
|
969 { |
|
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diff
changeset
|
970 private: |
|
3712
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replacing std::auto_ptr by std::unique_ptr
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3640
diff
changeset
|
971 std::unique_ptr<TemporaryFile> file_; |
|
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changeset
|
972 |
|
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diff
changeset
|
973 public: |
| 4205 | 974 explicit DynamicTemporaryFile(TemporaryFile* f) : file_(f) |
|
2976
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changeset
|
975 { |
|
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diff
changeset
|
976 if (f == NULL) |
|
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changeset
|
977 { |
|
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diff
changeset
|
978 throw OrthancException(ErrorCode_NullPointer); |
|
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changeset
|
979 } |
|
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diff
changeset
|
980 } |
|
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diff
changeset
|
981 |
|
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diff
changeset
|
982 const TemporaryFile& GetFile() const |
|
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changeset
|
983 { |
|
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diff
changeset
|
984 assert(file_.get() != NULL); |
|
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diff
changeset
|
985 return *file_; |
|
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986 } |
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987 }; |
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Asynchronous generation of ZIP archives and DICOM medias
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|
988 } |
| 2632 | 989 |
|
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|
990 |
|
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991 void ArchiveJob::RefreshArchiveSize() |
|
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992 { |
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993 if (synchronousTarget_.get() != NULL) |
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994 { |
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995 archiveSize_ = synchronousTarget_->GetFileSize(); |
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996 } |
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997 |
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998 if (asynchronousTarget_.get() != NULL) |
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999 { |
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|
1000 archiveSize_ = asynchronousTarget_->GetFileSize(); |
|
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1001 } |
|
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1002 } |
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Archive/media jobs report the size of the created ZIP file in content field "ArchiveSizeMB"
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1003 |
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1004 |
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1005 void ArchiveJob::FinalizeTarget() |
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1006 { |
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1007 writer_.reset(); // Flush all the results |
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1008 |
|
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1009 RefreshArchiveSize(); |
|
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1010 |
|
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1011 if (asynchronousTarget_.get() != NULL) |
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1012 { |
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1013 // Asynchronous behavior: Move the resulting file into the media archive |
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1014 mediaArchiveId_ = context_.GetMediaArchive().Add( |
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1015 new DynamicTemporaryFile(asynchronousTarget_.release())); |
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1016 } |
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1017 } |
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Asynchronous generation of ZIP archives and DICOM medias
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|
1018 |
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|
1019 |
|
3658
2d90dd30858c
providing job ID to the IJob::Step() methods
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1020 JobStepResult ArchiveJob::Step(const std::string& jobId) |
| 2632 | 1021 { |
| 1022 assert(writer_.get() != NULL); | |
| 1023 | |
|
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1024 if (synchronousTarget_.get() != NULL && |
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Asynchronous generation of ZIP archives and DICOM medias
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|
1025 synchronousTarget_.unique()) |
| 2632 | 1026 { |
| 1027 LOG(WARNING) << "A client has disconnected while creating an archive"; | |
|
3240
e44e0127e553
Fix issue #134 (/patient/modify gives 500, should really be 400)
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|
1028 return JobStepResult::Failure(ErrorCode_NetworkProtocol, |
|
e44e0127e553
Fix issue #134 (/patient/modify gives 500, should really be 400)
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|
1029 "A client has disconnected while creating an archive"); |
| 2632 | 1030 } |
|
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changeset
|
1031 |
| 2632 | 1032 if (writer_->GetStepsCount() == 0) |
| 1033 { | |
|
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|
1034 FinalizeTarget(); |
| 2632 | 1035 return JobStepResult::Success(); |
| 1036 } | |
| 1037 else | |
| 1038 { | |
|
3913
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transcoding ZIP archive and media
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|
1039 writer_->RunStep(currentStep_, transcode_, transferSyntax_); |
| 2632 | 1040 |
| 1041 currentStep_ ++; | |
| 1042 | |
| 1043 if (currentStep_ == writer_->GetStepsCount()) | |
| 1044 { | |
|
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|
1045 FinalizeTarget(); |
| 2632 | 1046 return JobStepResult::Success(); |
| 1047 } | |
| 1048 else | |
| 1049 { | |
|
4341
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changeset
|
1050 RefreshArchiveSize(); |
| 2632 | 1051 return JobStepResult::Continue(); |
| 1052 } | |
| 1053 } | |
| 1054 } | |
| 1055 | |
| 1056 | |
| 1057 float ArchiveJob::GetProgress() | |
| 1058 { | |
| 1059 if (writer_.get() == NULL || | |
| 1060 writer_->GetStepsCount() == 0) | |
| 1061 { | |
| 1062 return 1; | |
| 1063 } | |
| 1064 else | |
| 1065 { | |
| 1066 return (static_cast<float>(currentStep_) / | |
| 1067 static_cast<float>(writer_->GetStepsCount() - 1)); | |
| 1068 } | |
| 1069 } | |
| 1070 | |
| 1071 | |
| 1072 void ArchiveJob::GetJobType(std::string& target) | |
| 1073 { | |
| 1074 if (isMedia_) | |
| 1075 { | |
| 1076 target = "Media"; | |
| 1077 } | |
| 1078 else | |
| 1079 { | |
| 1080 target = "Archive"; | |
| 1081 } | |
| 1082 } | |
| 1083 | |
|
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|
1084 |
| 2632 | 1085 void ArchiveJob::GetPublicContent(Json::Value& value) |
| 1086 { | |
|
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|
1087 value = Json::objectValue; |
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|
1088 value[KEY_DESCRIPTION] = description_; |
|
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|
1089 value[KEY_INSTANCES_COUNT] = instancesCount_; |
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|
1090 value[KEY_UNCOMPRESSED_SIZE_MB] = |
| 2643 | 1091 static_cast<unsigned int>(uncompressedSize_ / MEGA_BYTES); |
|
4341
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|
1092 value[KEY_ARCHIVE_SIZE_MB] = |
|
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|
1093 static_cast<unsigned int>(archiveSize_ / MEGA_BYTES); |
|
3913
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1094 |
|
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|
1095 if (transcode_) |
|
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|
1096 { |
|
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|
1097 value[KEY_TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
|
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|
1098 } |
| 2632 | 1099 } |
|
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|
1100 |
|
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|
1101 |
|
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|
1102 bool ArchiveJob::GetOutput(std::string& output, |
|
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1103 MimeType& mime, |
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1104 const std::string& key) |
|
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1105 { |
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|
1106 if (key == "archive" && |
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|
1107 !mediaArchiveId_.empty()) |
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1108 { |
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|
1109 SharedArchive::Accessor accessor(context_.GetMediaArchive(), mediaArchiveId_); |
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1110 |
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1111 if (accessor.IsValid()) |
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|
1112 { |
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1113 const DynamicTemporaryFile& f = dynamic_cast<DynamicTemporaryFile&>(accessor.GetItem()); |
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1114 f.GetFile().Read(output); |
|
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1115 mime = MimeType_Zip; |
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1116 return true; |
|
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1117 } |
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1118 else |
|
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1119 { |
|
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1120 return false; |
|
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|
1121 } |
|
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|
1122 } |
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1123 else |
|
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|
1124 { |
|
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1125 return false; |
|
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|
1126 } |
|
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|
1127 } |
| 2632 | 1128 } |