Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ArchiveJob.cpp @ 4658:66f6fd77deaf Orthanc-1.9.3
Orthanc-1.9.3
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 07 May 2021 09:22:38 +0200 |
| parents | b02dc8303cf6 |
| children | cdab941fe17d |
| 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; | |
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232 int64_t revision; // ignored |
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233 if (index.LookupAttachment(tmp, revision, id, FileContentType_Dicom)) |
| 2632 | 234 { |
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235 instances_.push_back(Instance(id, tmp.GetUncompressedSize())); |
| 2632 | 236 } |
| 237 } | |
| 238 else | |
| 239 { | |
| 240 resources_[id] = NULL; | |
| 241 } | |
| 242 } | |
| 243 | |
| 244 | |
| 245 public: | |
| 4205 | 246 explicit ArchiveIndex(ResourceType level) : |
| 2632 | 247 level_(level) |
| 248 { | |
| 249 } | |
| 250 | |
| 251 ~ArchiveIndex() | |
| 252 { | |
| 253 for (Resources::iterator it = resources_.begin(); | |
| 254 it != resources_.end(); ++it) | |
| 255 { | |
| 256 delete it->second; | |
| 257 } | |
| 258 } | |
| 259 | |
| 260 | |
| 261 void Add(ServerIndex& index, | |
| 262 const ResourceIdentifiers& resource) | |
| 263 { | |
| 264 const std::string& id = resource.GetIdentifier(level_); | |
| 265 Resources::iterator previous = resources_.find(id); | |
| 266 | |
| 267 if (level_ == ResourceType_Instance) | |
| 268 { | |
| 269 AddResourceToExpand(index, id); | |
| 270 } | |
| 271 else if (resource.GetLevel() == level_) | |
| 272 { | |
| 273 // Mark this resource for further expansion | |
| 274 if (previous != resources_.end()) | |
| 275 { | |
| 276 delete previous->second; | |
| 277 } | |
| 278 | |
| 279 resources_[id] = NULL; | |
| 280 } | |
| 281 else if (previous == resources_.end()) | |
| 282 { | |
| 283 // This is the first time we meet this resource | |
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284 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 285 child->Add(index, resource); |
| 286 resources_[id] = child.release(); | |
| 287 } | |
| 288 else if (previous->second != NULL) | |
| 289 { | |
| 290 previous->second->Add(index, resource); | |
| 291 } | |
| 292 else | |
| 293 { | |
| 294 // Nothing to do: This item is marked for further expansion | |
| 295 } | |
| 296 } | |
| 297 | |
| 298 | |
| 299 void Expand(ServerIndex& index) | |
| 300 { | |
| 301 if (level_ == ResourceType_Instance) | |
| 302 { | |
| 303 // Expanding an instance node makes no sense | |
| 304 return; | |
| 305 } | |
| 306 | |
| 307 for (Resources::iterator it = resources_.begin(); | |
| 308 it != resources_.end(); ++it) | |
| 309 { | |
| 310 if (it->second == NULL) | |
| 311 { | |
| 312 // This is resource is marked for expansion | |
| 313 std::list<std::string> children; | |
| 314 index.GetChildren(children, it->first); | |
| 315 | |
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316 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 317 |
| 318 for (std::list<std::string>::const_iterator | |
| 319 it2 = children.begin(); it2 != children.end(); ++it2) | |
| 320 { | |
| 321 child->AddResourceToExpand(index, *it2); | |
| 322 } | |
| 323 | |
| 324 it->second = child.release(); | |
| 325 } | |
| 326 | |
| 327 assert(it->second != NULL); | |
| 328 it->second->Expand(index); | |
| 329 } | |
| 330 } | |
| 331 | |
| 332 | |
| 333 void Apply(IArchiveVisitor& visitor) const | |
| 334 { | |
| 335 if (level_ == ResourceType_Instance) | |
| 336 { | |
| 337 for (std::list<Instance>::const_iterator | |
| 338 it = instances_.begin(); it != instances_.end(); ++it) | |
| 339 { | |
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340 visitor.AddInstance(it->id_, it->uncompressedSize_); |
| 2632 | 341 } |
| 342 } | |
| 343 else | |
| 344 { | |
| 345 for (Resources::const_iterator it = resources_.begin(); | |
| 346 it != resources_.end(); ++it) | |
| 347 { | |
| 348 assert(it->second != NULL); // There must have been a call to "Expand()" | |
| 349 visitor.Open(level_, it->first); | |
| 350 it->second->Apply(visitor); | |
| 351 visitor.Close(); | |
| 352 } | |
| 353 } | |
| 354 } | |
| 355 }; | |
| 356 | |
| 357 | |
| 358 | |
| 359 class ArchiveJob::ZipCommands : public boost::noncopyable | |
| 360 { | |
| 361 private: | |
| 362 enum Type | |
| 363 { | |
| 364 Type_OpenDirectory, | |
| 365 Type_CloseDirectory, | |
| 366 Type_WriteInstance | |
| 367 }; | |
| 368 | |
| 369 class Command : public boost::noncopyable | |
| 370 { | |
| 371 private: | |
| 372 Type type_; | |
| 373 std::string filename_; | |
| 374 std::string instanceId_; | |
| 375 | |
| 376 public: | |
| 377 explicit Command(Type type) : | |
| 378 type_(type) | |
| 379 { | |
| 380 assert(type_ == Type_CloseDirectory); | |
| 381 } | |
| 382 | |
| 383 Command(Type type, | |
| 384 const std::string& filename) : | |
| 385 type_(type), | |
| 386 filename_(filename) | |
| 387 { | |
| 388 assert(type_ == Type_OpenDirectory); | |
| 389 } | |
| 390 | |
| 391 Command(Type type, | |
| 392 const std::string& filename, | |
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393 const std::string& instanceId) : |
| 2632 | 394 type_(type), |
| 395 filename_(filename), | |
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396 instanceId_(instanceId) |
| 2632 | 397 { |
| 398 assert(type_ == Type_WriteInstance); | |
| 399 } | |
| 400 | |
| 401 void Apply(HierarchicalZipWriter& writer, | |
| 402 ServerContext& context, | |
| 403 DicomDirWriter* dicomDir, | |
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404 const std::string& dicomDirFolder, |
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405 bool transcode, |
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406 DicomTransferSyntax transferSyntax) const |
| 2632 | 407 { |
| 408 switch (type_) | |
| 409 { | |
| 410 case Type_OpenDirectory: | |
| 411 writer.OpenDirectory(filename_.c_str()); | |
| 412 break; | |
| 413 | |
| 414 case Type_CloseDirectory: | |
| 415 writer.CloseDirectory(); | |
| 416 break; | |
| 417 | |
| 418 case Type_WriteInstance: | |
| 419 { | |
| 420 std::string content; | |
| 421 | |
| 422 try | |
| 423 { | |
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424 context.ReadDicom(content, instanceId_); |
| 2632 | 425 } |
| 426 catch (OrthancException& e) | |
| 427 { | |
| 428 LOG(WARNING) << "An instance was removed after the job was issued: " << instanceId_; | |
| 429 return; | |
| 430 } | |
| 2636 | 431 |
| 432 //boost::this_thread::sleep(boost::posix_time::milliseconds(300)); | |
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433 |
| 2632 | 434 writer.OpenFile(filename_.c_str()); |
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435 |
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436 bool transcodeSuccess = false; |
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437 |
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438 std::unique_ptr<ParsedDicomFile> parsed; |
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439 |
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440 if (transcode) |
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441 { |
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442 // New in Orthanc 1.7.0 |
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443 std::set<DicomTransferSyntax> syntaxes; |
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444 syntaxes.insert(transferSyntax); |
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445 |
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446 IDicomTranscoder::DicomImage source, transcoded; |
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447 source.SetExternalBuffer(content); |
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448 |
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449 if (context.Transcode(transcoded, source, syntaxes, true /* allow new SOP instance UID */)) |
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450 { |
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451 writer.Write(transcoded.GetBufferData(), transcoded.GetBufferSize()); |
| 2632 | 452 |
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453 if (dicomDir != NULL) |
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454 { |
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455 std::unique_ptr<ParsedDicomFile> tmp(transcoded.ReleaseAsParsedDicomFile()); |
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456 dicomDir->Add(dicomDirFolder, filename_, *tmp); |
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457 } |
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458 |
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459 transcodeSuccess = true; |
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460 } |
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461 else |
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462 { |
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463 LOG(INFO) << "Cannot transcode instance " << instanceId_ |
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464 << " to transfer syntax: " << GetTransferSyntaxUid(transferSyntax); |
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465 } |
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466 } |
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467 |
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468 if (!transcodeSuccess) |
| 2632 | 469 { |
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470 writer.Write(content); |
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471 |
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472 if (dicomDir != NULL) |
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473 { |
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474 if (parsed.get() == NULL) |
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475 { |
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476 parsed.reset(new ParsedDicomFile(content)); |
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477 } |
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478 |
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479 dicomDir->Add(dicomDirFolder, filename_, *parsed); |
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480 } |
| 2632 | 481 } |
| 482 | |
| 483 break; | |
| 484 } | |
| 485 | |
| 486 default: | |
| 487 throw OrthancException(ErrorCode_InternalError); | |
| 488 } | |
| 489 } | |
| 490 }; | |
| 491 | |
| 492 std::deque<Command*> commands_; | |
| 493 uint64_t uncompressedSize_; | |
| 494 unsigned int instancesCount_; | |
| 495 | |
| 496 | |
| 497 void ApplyInternal(HierarchicalZipWriter& writer, | |
| 498 ServerContext& context, | |
| 499 size_t index, | |
| 500 DicomDirWriter* dicomDir, | |
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501 const std::string& dicomDirFolder, |
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502 bool transcode, |
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503 DicomTransferSyntax transferSyntax) const |
| 2632 | 504 { |
| 505 if (index >= commands_.size()) | |
| 506 { | |
| 507 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 508 } | |
| 509 | |
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510 commands_[index]->Apply(writer, context, dicomDir, dicomDirFolder, transcode, transferSyntax); |
| 2632 | 511 } |
| 512 | |
| 513 public: | |
| 514 ZipCommands() : | |
| 515 uncompressedSize_(0), | |
| 516 instancesCount_(0) | |
| 517 { | |
| 518 } | |
| 519 | |
| 520 ~ZipCommands() | |
| 521 { | |
| 522 for (std::deque<Command*>::iterator it = commands_.begin(); | |
| 523 it != commands_.end(); ++it) | |
| 524 { | |
| 525 assert(*it != NULL); | |
| 526 delete *it; | |
| 527 } | |
| 528 } | |
| 529 | |
| 530 size_t GetSize() const | |
| 531 { | |
| 532 return commands_.size(); | |
| 533 } | |
| 534 | |
| 535 unsigned int GetInstancesCount() const | |
| 536 { | |
| 537 return instancesCount_; | |
| 538 } | |
| 539 | |
| 540 uint64_t GetUncompressedSize() const | |
| 541 { | |
| 542 return uncompressedSize_; | |
| 543 } | |
| 544 | |
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545 // "media" flavor (with DICOMDIR) |
| 2632 | 546 void Apply(HierarchicalZipWriter& writer, |
| 547 ServerContext& context, | |
| 548 size_t index, | |
| 549 DicomDirWriter& dicomDir, | |
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550 const std::string& dicomDirFolder, |
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551 bool transcode, |
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552 DicomTransferSyntax transferSyntax) const |
| 2632 | 553 { |
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554 ApplyInternal(writer, context, index, &dicomDir, dicomDirFolder, transcode, transferSyntax); |
| 2632 | 555 } |
| 556 | |
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557 // "archive" flavor (without DICOMDIR) |
| 2632 | 558 void Apply(HierarchicalZipWriter& writer, |
| 559 ServerContext& context, | |
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560 size_t index, |
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561 bool transcode, |
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562 DicomTransferSyntax transferSyntax) const |
| 2632 | 563 { |
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564 ApplyInternal(writer, context, index, NULL, "", transcode, transferSyntax); |
| 2632 | 565 } |
| 566 | |
| 567 void AddOpenDirectory(const std::string& filename) | |
| 568 { | |
| 569 commands_.push_back(new Command(Type_OpenDirectory, filename)); | |
| 570 } | |
| 571 | |
| 572 void AddCloseDirectory() | |
| 573 { | |
| 574 commands_.push_back(new Command(Type_CloseDirectory)); | |
| 575 } | |
| 576 | |
| 577 void AddWriteInstance(const std::string& filename, | |
| 578 const std::string& instanceId, | |
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579 uint64_t uncompressedSize) |
| 2632 | 580 { |
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581 commands_.push_back(new Command(Type_WriteInstance, filename, instanceId)); |
| 2632 | 582 instancesCount_ ++; |
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583 uncompressedSize_ += uncompressedSize; |
| 2632 | 584 } |
| 585 | |
| 586 bool IsZip64() const | |
| 587 { | |
| 588 return IsZip64Required(GetUncompressedSize(), GetInstancesCount()); | |
| 589 } | |
| 590 }; | |
| 591 | |
| 592 | |
| 593 | |
| 594 class ArchiveJob::ArchiveIndexVisitor : public IArchiveVisitor | |
| 595 { | |
| 596 private: | |
| 597 ZipCommands& commands_; | |
| 598 ServerContext& context_; | |
| 599 char instanceFormat_[24]; | |
| 600 unsigned int counter_; | |
| 601 | |
| 602 static std::string GetTag(const DicomMap& tags, | |
| 603 const DicomTag& tag) | |
| 604 { | |
| 605 const DicomValue* v = tags.TestAndGetValue(tag); | |
| 606 if (v != NULL && | |
| 607 !v->IsBinary() && | |
| 608 !v->IsNull()) | |
| 609 { | |
| 610 return v->GetContent(); | |
| 611 } | |
| 612 else | |
| 613 { | |
| 614 return ""; | |
| 615 } | |
| 616 } | |
| 617 | |
| 618 public: | |
| 619 ArchiveIndexVisitor(ZipCommands& commands, | |
| 620 ServerContext& context) : | |
| 621 commands_(commands), | |
| 622 context_(context), | |
| 623 counter_(0) | |
| 624 { | |
| 625 if (commands.GetSize() != 0) | |
| 626 { | |
| 627 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 628 } | |
| 629 | |
| 630 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); | |
| 631 } | |
| 632 | |
| 633 virtual void Open(ResourceType level, | |
| 4205 | 634 const std::string& publicId) ORTHANC_OVERRIDE |
| 2632 | 635 { |
| 636 std::string path; | |
| 637 | |
| 638 DicomMap tags; | |
| 639 if (context_.GetIndex().GetMainDicomTags(tags, publicId, level, level)) | |
| 640 { | |
| 641 switch (level) | |
| 642 { | |
| 643 case ResourceType_Patient: | |
| 644 path = GetTag(tags, DICOM_TAG_PATIENT_ID) + " " + GetTag(tags, DICOM_TAG_PATIENT_NAME); | |
| 645 break; | |
| 646 | |
| 647 case ResourceType_Study: | |
| 648 path = GetTag(tags, DICOM_TAG_ACCESSION_NUMBER) + " " + GetTag(tags, DICOM_TAG_STUDY_DESCRIPTION); | |
| 649 break; | |
| 650 | |
| 651 case ResourceType_Series: | |
| 652 { | |
| 653 std::string modality = GetTag(tags, DICOM_TAG_MODALITY); | |
| 654 path = modality + " " + GetTag(tags, DICOM_TAG_SERIES_DESCRIPTION); | |
| 655 | |
| 656 if (modality.size() == 0) | |
| 657 { | |
| 658 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); | |
| 659 } | |
| 660 else if (modality.size() == 1) | |
| 661 { | |
| 662 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%%07d.dcm", | |
| 663 toupper(modality[0])); | |
| 664 } | |
| 665 else if (modality.size() >= 2) | |
| 666 { | |
| 667 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%c%%06d.dcm", | |
| 668 toupper(modality[0]), toupper(modality[1])); | |
| 669 } | |
| 670 | |
| 671 counter_ = 0; | |
| 672 | |
| 673 break; | |
| 674 } | |
| 675 | |
| 676 default: | |
| 677 throw OrthancException(ErrorCode_InternalError); | |
| 678 } | |
| 679 } | |
| 680 | |
| 681 path = Toolbox::StripSpaces(Toolbox::ConvertToAscii(path)); | |
| 682 | |
| 683 if (path.empty()) | |
| 684 { | |
| 685 path = std::string("Unknown ") + EnumerationToString(level); | |
| 686 } | |
| 687 | |
| 688 commands_.AddOpenDirectory(path.c_str()); | |
| 689 } | |
| 690 | |
| 4205 | 691 virtual void Close() ORTHANC_OVERRIDE |
| 2632 | 692 { |
| 693 commands_.AddCloseDirectory(); | |
| 694 } | |
| 695 | |
| 696 virtual void AddInstance(const std::string& instanceId, | |
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697 uint64_t uncompressedSize) ORTHANC_OVERRIDE |
| 2632 | 698 { |
| 699 char filename[24]; | |
| 700 snprintf(filename, sizeof(filename) - 1, instanceFormat_, counter_); | |
| 701 counter_ ++; | |
| 702 | |
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703 commands_.AddWriteInstance(filename, instanceId, uncompressedSize); |
| 2632 | 704 } |
| 705 }; | |
| 706 | |
| 707 | |
| 708 class ArchiveJob::MediaIndexVisitor : public IArchiveVisitor | |
| 709 { | |
| 710 private: | |
| 711 ZipCommands& commands_; | |
| 712 unsigned int counter_; | |
| 713 | |
| 714 public: | |
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715 explicit MediaIndexVisitor(ZipCommands& commands) : |
| 2632 | 716 commands_(commands), |
| 717 counter_(0) | |
| 718 { | |
| 719 } | |
| 720 | |
| 721 virtual void Open(ResourceType level, | |
| 4205 | 722 const std::string& publicId) ORTHANC_OVERRIDE |
| 2632 | 723 { |
| 724 } | |
| 725 | |
| 4205 | 726 virtual void Close() ORTHANC_OVERRIDE |
| 2632 | 727 { |
| 728 } | |
| 729 | |
| 730 virtual void AddInstance(const std::string& instanceId, | |
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731 uint64_t uncompressedSize) ORTHANC_OVERRIDE |
| 2632 | 732 { |
| 733 // "DICOM restricts the filenames on DICOM media to 8 | |
| 734 // characters (some systems wrongly use 8.3, but this does not | |
| 735 // conform to the standard)." | |
| 736 std::string filename = "IM" + boost::lexical_cast<std::string>(counter_); | |
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737 commands_.AddWriteInstance(filename, instanceId, uncompressedSize); |
| 2632 | 738 |
| 739 counter_ ++; | |
| 740 } | |
| 741 }; | |
| 742 | |
| 743 | |
| 744 class ArchiveJob::ZipWriterIterator : public boost::noncopyable | |
| 745 { | |
| 746 private: | |
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747 ServerContext& context_; |
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748 ZipCommands commands_; |
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749 std::unique_ptr<HierarchicalZipWriter> zip_; |
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750 std::unique_ptr<DicomDirWriter> dicomDir_; |
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751 bool isMedia_; |
| 2632 | 752 |
| 753 public: | |
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754 ZipWriterIterator(const TemporaryFile& target, |
| 2632 | 755 ServerContext& context, |
| 756 ArchiveIndex& archive, | |
| 757 bool isMedia, | |
| 758 bool enableExtendedSopClass) : | |
| 759 context_(context), | |
| 760 isMedia_(isMedia) | |
| 761 { | |
| 762 if (isMedia) | |
| 763 { | |
| 4588 | 764 MediaIndexVisitor visitor(commands_); |
| 2632 | 765 archive.Expand(context.GetIndex()); |
| 766 | |
| 767 commands_.AddOpenDirectory(MEDIA_IMAGES_FOLDER); | |
| 768 archive.Apply(visitor); | |
| 769 commands_.AddCloseDirectory(); | |
| 770 | |
| 771 dicomDir_.reset(new DicomDirWriter); | |
| 772 dicomDir_->EnableExtendedSopClass(enableExtendedSopClass); | |
| 773 } | |
| 774 else | |
| 775 { | |
| 776 ArchiveIndexVisitor visitor(commands_, context); | |
| 777 archive.Expand(context.GetIndex()); | |
| 778 archive.Apply(visitor); | |
| 779 } | |
| 780 | |
| 781 zip_.reset(new HierarchicalZipWriter(target.GetPath().c_str())); | |
| 782 zip_->SetZip64(commands_.IsZip64()); | |
| 783 } | |
| 784 | |
| 785 size_t GetStepsCount() const | |
| 786 { | |
| 787 return commands_.GetSize() + 1; | |
| 788 } | |
| 789 | |
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790 void RunStep(size_t index, |
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791 bool transcode, |
|
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792 DicomTransferSyntax transferSyntax) |
| 2632 | 793 { |
| 794 if (index > commands_.GetSize()) | |
| 795 { | |
| 796 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 797 } | |
| 798 else if (index == commands_.GetSize()) | |
| 799 { | |
| 800 // Last step: Add the DICOMDIR | |
| 801 if (isMedia_) | |
| 802 { | |
| 803 assert(dicomDir_.get() != NULL); | |
| 804 std::string s; | |
| 805 dicomDir_->Encode(s); | |
| 806 | |
| 807 zip_->OpenFile("DICOMDIR"); | |
| 808 zip_->Write(s); | |
| 809 } | |
| 810 } | |
| 811 else | |
| 812 { | |
| 813 if (isMedia_) | |
| 814 { | |
| 815 assert(dicomDir_.get() != NULL); | |
|
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816 commands_.Apply(*zip_, context_, index, *dicomDir_, |
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817 MEDIA_IMAGES_FOLDER, transcode, transferSyntax); |
| 2632 | 818 } |
| 819 else | |
| 820 { | |
| 821 assert(dicomDir_.get() == NULL); | |
|
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822 commands_.Apply(*zip_, context_, index, transcode, transferSyntax); |
| 2632 | 823 } |
| 824 } | |
| 825 } | |
| 826 | |
| 827 unsigned int GetInstancesCount() const | |
| 828 { | |
| 829 return commands_.GetInstancesCount(); | |
| 830 } | |
| 831 | |
| 832 uint64_t GetUncompressedSize() const | |
| 833 { | |
| 834 return commands_.GetUncompressedSize(); | |
| 835 } | |
| 836 }; | |
| 837 | |
| 838 | |
| 2966 | 839 ArchiveJob::ArchiveJob(ServerContext& context, |
| 2632 | 840 bool isMedia, |
| 841 bool enableExtendedSopClass) : | |
| 842 context_(context), | |
| 843 archive_(new ArchiveIndex(ResourceType_Patient)), // root | |
| 844 isMedia_(isMedia), | |
| 845 enableExtendedSopClass_(enableExtendedSopClass), | |
| 846 currentStep_(0), | |
| 847 instancesCount_(0), | |
|
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848 uncompressedSize_(0), |
|
4341
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849 archiveSize_(0), |
|
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850 transcode_(false), |
|
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851 transferSyntax_(DicomTransferSyntax_LittleEndianImplicit) |
| 2632 | 852 { |
| 2966 | 853 } |
| 854 | |
|
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855 |
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856 ArchiveJob::~ArchiveJob() |
|
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857 { |
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858 if (!mediaArchiveId_.empty()) |
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859 { |
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860 context_.GetMediaArchive().Remove(mediaArchiveId_); |
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861 } |
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862 } |
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863 |
| 2966 | 864 |
| 865 void ArchiveJob::SetSynchronousTarget(boost::shared_ptr<TemporaryFile>& target) | |
| 866 { | |
| 867 if (target.get() == NULL) | |
| 2632 | 868 { |
| 869 throw OrthancException(ErrorCode_NullPointer); | |
| 870 } | |
|
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871 else if (writer_.get() != NULL || // Already started |
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872 synchronousTarget_.get() != NULL || |
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873 asynchronousTarget_.get() != NULL) |
| 2966 | 874 { |
| 875 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 876 } | |
| 877 else | |
| 878 { | |
| 879 synchronousTarget_ = target; | |
| 880 } | |
| 2632 | 881 } |
| 882 | |
| 883 | |
|
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884 void ArchiveJob::SetDescription(const std::string& description) |
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885 { |
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886 if (writer_.get() != NULL) // Already started |
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887 { |
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888 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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889 } |
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890 else |
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891 { |
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892 description_ = description; |
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893 } |
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894 } |
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895 |
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896 |
| 2632 | 897 void ArchiveJob::AddResource(const std::string& publicId) |
| 898 { | |
| 899 if (writer_.get() != NULL) // Already started | |
| 900 { | |
| 901 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 902 } | |
|
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903 else |
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904 { |
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|
905 ResourceIdentifiers resource(context_.GetIndex(), publicId); |
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906 archive_->Add(context_.GetIndex(), resource); |
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|
907 } |
| 2632 | 908 } |
| 909 | |
|
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|
910 |
|
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911 void ArchiveJob::SetTranscode(DicomTransferSyntax transferSyntax) |
|
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912 { |
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913 if (writer_.get() != NULL) // Already started |
|
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914 { |
|
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915 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
|
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916 } |
|
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917 else |
|
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|
918 { |
|
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919 transcode_ = true; |
|
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920 transferSyntax_ = transferSyntax; |
|
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921 } |
|
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922 } |
|
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|
923 |
| 2632 | 924 |
|
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diff
changeset
|
925 void ArchiveJob::Reset() |
| 2632 | 926 { |
| 2955 | 927 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
| 928 "Cannot resubmit the creation of an archive"); | |
| 2632 | 929 } |
| 930 | |
| 931 | |
| 932 void ArchiveJob::Start() | |
| 933 { | |
|
4641
b02dc8303cf6
Fixed the lifetime of temporary files associated with jobs that create ZIP archive/media
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4627
diff
changeset
|
934 TemporaryFile* target = NULL; // (*) |
|
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|
935 |
| 2966 | 936 if (synchronousTarget_.get() == NULL) |
| 937 { | |
|
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|
938 { |
|
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|
939 OrthancConfiguration::ReaderLock lock; |
|
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|
940 asynchronousTarget_.reset(lock.GetConfiguration().CreateTemporaryFile()); |
|
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|
941 } |
|
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|
942 |
|
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|
943 target = asynchronousTarget_.get(); |
|
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|
944 } |
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|
945 else |
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|
946 { |
|
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|
947 target = synchronousTarget_.get(); |
| 2966 | 948 } |
|
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|
949 |
|
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|
950 assert(target != NULL); |
|
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changeset
|
951 target->Touch(); // Make sure we can write to the temporary file |
| 2966 | 952 |
| 2632 | 953 if (writer_.get() != NULL) |
| 954 { | |
| 955 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 956 } | |
| 957 | |
|
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changeset
|
958 writer_.reset(new ZipWriterIterator(*target, context_, *archive_, |
| 2632 | 959 isMedia_, enableExtendedSopClass_)); |
| 960 | |
| 961 instancesCount_ = writer_->GetInstancesCount(); | |
| 962 uncompressedSize_ = writer_->GetUncompressedSize(); | |
| 963 } | |
| 964 | |
|
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|
965 |
|
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changeset
|
966 |
|
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|
967 namespace |
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|
968 { |
|
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|
969 class DynamicTemporaryFile : public IDynamicObject |
|
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|
970 { |
|
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|
971 private: |
|
3712
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replacing std::auto_ptr by std::unique_ptr
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diff
changeset
|
972 std::unique_ptr<TemporaryFile> file_; |
|
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|
973 |
|
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diff
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|
974 public: |
| 4205 | 975 explicit DynamicTemporaryFile(TemporaryFile* f) : file_(f) |
|
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changeset
|
976 { |
|
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changeset
|
977 if (f == NULL) |
|
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|
978 { |
|
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|
979 throw OrthancException(ErrorCode_NullPointer); |
|
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|
980 } |
|
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|
981 } |
|
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|
982 |
|
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changeset
|
983 const TemporaryFile& GetFile() const |
|
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|
984 { |
|
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diff
changeset
|
985 assert(file_.get() != NULL); |
|
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986 return *file_; |
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987 } |
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988 }; |
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989 } |
| 2632 | 990 |
|
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991 |
|
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992 void ArchiveJob::RefreshArchiveSize() |
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993 { |
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994 if (synchronousTarget_.get() != NULL) |
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995 { |
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996 archiveSize_ = synchronousTarget_->GetFileSize(); |
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997 } |
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998 |
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999 if (asynchronousTarget_.get() != NULL) |
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1000 { |
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1001 archiveSize_ = asynchronousTarget_->GetFileSize(); |
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1002 } |
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1003 } |
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1004 |
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1005 |
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1006 void ArchiveJob::FinalizeTarget() |
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1007 { |
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1008 writer_.reset(); // Flush all the results |
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1009 |
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1010 RefreshArchiveSize(); |
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1011 |
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1012 if (synchronousTarget_.get() != NULL) |
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1013 { |
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1014 /** |
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1015 * Synchronous behavior: Release the reference to the temporary |
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1016 * file. It is now up to the caller to deal with the shared |
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1017 * pointer. This is a fix in Orthanc 1.9.3. |
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1018 * https://groups.google.com/g/orthanc-users/c/tpP2fkRAd9o/m/5SGpEHbGCQAJ |
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1019 **/ |
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1020 synchronousTarget_.reset(); |
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1021 } |
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1022 |
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1023 if (asynchronousTarget_.get() != NULL) |
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1024 { |
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1025 // Asynchronous behavior: Move the resulting file into the media archive |
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1026 mediaArchiveId_ = context_.GetMediaArchive().Add( |
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1027 new DynamicTemporaryFile(asynchronousTarget_.release())); |
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1028 } |
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1029 } |
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1030 |
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1031 |
|
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1032 JobStepResult ArchiveJob::Step(const std::string& jobId) |
| 2632 | 1033 { |
| 1034 assert(writer_.get() != NULL); | |
| 1035 | |
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1036 if (synchronousTarget_.get() != NULL && |
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1037 synchronousTarget_.unique()) |
| 2632 | 1038 { |
| 1039 LOG(WARNING) << "A client has disconnected while creating an archive"; | |
|
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1040 return JobStepResult::Failure(ErrorCode_NetworkProtocol, |
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1041 "A client has disconnected while creating an archive"); |
| 2632 | 1042 } |
|
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1043 |
| 2632 | 1044 if (writer_->GetStepsCount() == 0) |
| 1045 { | |
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1046 FinalizeTarget(); |
| 2632 | 1047 return JobStepResult::Success(); |
| 1048 } | |
| 1049 else | |
| 1050 { | |
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1051 writer_->RunStep(currentStep_, transcode_, transferSyntax_); |
| 2632 | 1052 |
| 1053 currentStep_ ++; | |
| 1054 | |
| 1055 if (currentStep_ == writer_->GetStepsCount()) | |
| 1056 { | |
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1057 FinalizeTarget(); |
| 2632 | 1058 return JobStepResult::Success(); |
| 1059 } | |
| 1060 else | |
| 1061 { | |
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1062 RefreshArchiveSize(); |
| 2632 | 1063 return JobStepResult::Continue(); |
| 1064 } | |
| 1065 } | |
| 1066 } | |
| 1067 | |
| 1068 | |
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1069 void ArchiveJob::Stop(JobStopReason reason) |
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1070 { |
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1071 /** |
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1072 * New in Orthanc 1.9.3: Remove the temporary file associated with |
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1073 * the job as soon as its job gets canceled (especially visible in |
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1074 * asynchronous mode). |
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1075 **/ |
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1076 if (reason == JobStopReason_Canceled || |
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1077 reason == JobStopReason_Failure || |
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1078 reason == JobStopReason_Retry) |
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1079 { |
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1080 // First delete the writer, as it holds a reference to "(a)synchronousTarget_", cf. (*) |
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1081 writer_.reset(); |
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1082 |
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1083 synchronousTarget_.reset(); |
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1084 asynchronousTarget_.reset(); |
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1085 } |
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1086 } |
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1087 |
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1088 |
| 2632 | 1089 float ArchiveJob::GetProgress() |
| 1090 { | |
| 1091 if (writer_.get() == NULL || | |
| 1092 writer_->GetStepsCount() == 0) | |
| 1093 { | |
| 1094 return 1; | |
| 1095 } | |
| 1096 else | |
| 1097 { | |
| 1098 return (static_cast<float>(currentStep_) / | |
| 1099 static_cast<float>(writer_->GetStepsCount() - 1)); | |
| 1100 } | |
| 1101 } | |
| 1102 | |
| 1103 | |
| 1104 void ArchiveJob::GetJobType(std::string& target) | |
| 1105 { | |
| 1106 if (isMedia_) | |
| 1107 { | |
| 1108 target = "Media"; | |
| 1109 } | |
| 1110 else | |
| 1111 { | |
| 1112 target = "Archive"; | |
| 1113 } | |
| 1114 } | |
| 1115 | |
|
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1116 |
| 2632 | 1117 void ArchiveJob::GetPublicContent(Json::Value& value) |
| 1118 { | |
|
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1119 value = Json::objectValue; |
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1120 value[KEY_DESCRIPTION] = description_; |
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1121 value[KEY_INSTANCES_COUNT] = instancesCount_; |
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1122 value[KEY_UNCOMPRESSED_SIZE_MB] = |
| 2643 | 1123 static_cast<unsigned int>(uncompressedSize_ / MEGA_BYTES); |
|
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1124 value[KEY_ARCHIVE_SIZE_MB] = |
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1125 static_cast<unsigned int>(archiveSize_ / MEGA_BYTES); |
|
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1126 |
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1127 if (transcode_) |
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1128 { |
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1129 value[KEY_TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
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1130 } |
| 2632 | 1131 } |
|
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1132 |
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1133 |
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1134 bool ArchiveJob::GetOutput(std::string& output, |
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1135 MimeType& mime, |
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Sebastien Jodogne <s.jodogne@gmail.com>
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1136 const std::string& key) |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1137 { |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1138 if (key == "archive" && |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1139 !mediaArchiveId_.empty()) |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
2966
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changeset
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1140 { |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1141 SharedArchive::Accessor accessor(context_.GetMediaArchive(), mediaArchiveId_); |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1142 |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1143 if (accessor.IsValid()) |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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changeset
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1144 { |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1145 const DynamicTemporaryFile& f = dynamic_cast<DynamicTemporaryFile&>(accessor.GetItem()); |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1146 f.GetFile().Read(output); |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1147 mime = MimeType_Zip; |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1148 return true; |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1149 } |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1150 else |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1151 { |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1152 return false; |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1153 } |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1154 } |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1155 else |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1156 { |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1157 return false; |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1158 } |
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cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1159 } |
| 2632 | 1160 } |