Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/ArchiveJob.cpp @ 4083:26efd0404d97 framework
integration mainline->framework
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 23 Jun 2020 07:39:42 +0200 |
| parents | 05b8fd21089c |
| children | d962a2996637 |
| 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) 2017-2020 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_TRANSCODE = "Transcode"; |
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60 |
| 2632 | 61 |
| 62 namespace Orthanc | |
| 63 { | |
| 64 static bool IsZip64Required(uint64_t uncompressedSize, | |
| 65 unsigned int countInstances) | |
| 66 { | |
| 67 static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; // Should be large enough to hold DICOMDIR | |
| 68 static const unsigned int FILES_MARGIN = 10; | |
| 69 | |
| 70 /** | |
| 71 * Determine whether ZIP64 is required. Original ZIP format can | |
| 72 * store up to 2GB of data (some implementation supporting up to | |
| 73 * 4GB of data), and up to 65535 files. | |
| 74 * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64 | |
| 75 **/ | |
| 76 | |
| 77 const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES - SAFETY_MARGIN || | |
| 78 countInstances >= 65535 - FILES_MARGIN); | |
| 79 | |
| 80 LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " | |
| 81 << (uncompressedSize / MEGA_BYTES) << "MB using the " | |
| 82 << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; | |
| 83 | |
| 84 return isZip64; | |
| 85 } | |
| 86 | |
| 87 | |
| 88 class ArchiveJob::ResourceIdentifiers : public boost::noncopyable | |
| 89 { | |
| 90 private: | |
| 91 ResourceType level_; | |
| 92 std::string patient_; | |
| 93 std::string study_; | |
| 94 std::string series_; | |
| 95 std::string instance_; | |
| 96 | |
| 97 static void GoToParent(ServerIndex& index, | |
| 98 std::string& current) | |
| 99 { | |
| 100 std::string tmp; | |
| 101 | |
| 102 if (index.LookupParent(tmp, current)) | |
| 103 { | |
| 104 current = tmp; | |
| 105 } | |
| 106 else | |
| 107 { | |
| 108 throw OrthancException(ErrorCode_UnknownResource); | |
| 109 } | |
| 110 } | |
| 111 | |
| 112 | |
| 113 public: | |
| 114 ResourceIdentifiers(ServerIndex& index, | |
| 115 const std::string& publicId) | |
| 116 { | |
| 117 if (!index.LookupResourceType(level_, publicId)) | |
| 118 { | |
| 119 throw OrthancException(ErrorCode_UnknownResource); | |
| 120 } | |
| 121 | |
| 122 std::string current = publicId;; | |
| 123 switch (level_) // Do not add "break" below! | |
| 124 { | |
| 125 case ResourceType_Instance: | |
| 126 instance_ = current; | |
| 127 GoToParent(index, current); | |
| 128 | |
| 129 case ResourceType_Series: | |
| 130 series_ = current; | |
| 131 GoToParent(index, current); | |
| 132 | |
| 133 case ResourceType_Study: | |
| 134 study_ = current; | |
| 135 GoToParent(index, current); | |
| 136 | |
| 137 case ResourceType_Patient: | |
| 138 patient_ = current; | |
| 139 break; | |
| 140 | |
| 141 default: | |
| 142 throw OrthancException(ErrorCode_InternalError); | |
| 143 } | |
| 144 } | |
| 145 | |
| 146 ResourceType GetLevel() const | |
| 147 { | |
| 148 return level_; | |
| 149 } | |
| 150 | |
| 151 const std::string& GetIdentifier(ResourceType level) const | |
| 152 { | |
| 153 // Some sanity check to ensure enumerations are not altered | |
| 154 assert(ResourceType_Patient < ResourceType_Study); | |
| 155 assert(ResourceType_Study < ResourceType_Series); | |
| 156 assert(ResourceType_Series < ResourceType_Instance); | |
| 157 | |
| 158 if (level > level_) | |
| 159 { | |
| 160 throw OrthancException(ErrorCode_InternalError); | |
| 161 } | |
| 162 | |
| 163 switch (level) | |
| 164 { | |
| 165 case ResourceType_Patient: | |
| 166 return patient_; | |
| 167 | |
| 168 case ResourceType_Study: | |
| 169 return study_; | |
| 170 | |
| 171 case ResourceType_Series: | |
| 172 return series_; | |
| 173 | |
| 174 case ResourceType_Instance: | |
| 175 return instance_; | |
| 176 | |
| 177 default: | |
| 178 throw OrthancException(ErrorCode_InternalError); | |
| 179 } | |
| 180 } | |
| 181 }; | |
| 182 | |
| 183 | |
| 184 class ArchiveJob::IArchiveVisitor : public boost::noncopyable | |
| 185 { | |
| 186 public: | |
| 187 virtual ~IArchiveVisitor() | |
| 188 { | |
| 189 } | |
| 190 | |
| 191 virtual void Open(ResourceType level, | |
| 192 const std::string& publicId) = 0; | |
| 193 | |
| 194 virtual void Close() = 0; | |
| 195 | |
| 196 virtual void AddInstance(const std::string& instanceId, | |
| 197 const FileInfo& dicom) = 0; | |
| 198 }; | |
| 199 | |
| 200 | |
| 201 class ArchiveJob::ArchiveIndex : public boost::noncopyable | |
| 202 { | |
| 203 private: | |
| 204 struct Instance | |
| 205 { | |
| 206 std::string id_; | |
| 207 FileInfo dicom_; | |
| 208 | |
| 209 Instance(const std::string& id, | |
| 210 const FileInfo& dicom) : | |
| 211 id_(id), dicom_(dicom) | |
| 212 { | |
| 213 } | |
| 214 }; | |
| 215 | |
| 216 // A "NULL" value for ArchiveIndex indicates a non-expanded node | |
| 217 typedef std::map<std::string, ArchiveIndex*> Resources; | |
| 218 | |
| 219 ResourceType level_; | |
| 220 Resources resources_; // Only at patient/study/series level | |
| 221 std::list<Instance> instances_; // Only at instance level | |
| 222 | |
| 223 | |
| 224 void AddResourceToExpand(ServerIndex& index, | |
| 225 const std::string& id) | |
| 226 { | |
| 227 if (level_ == ResourceType_Instance) | |
| 228 { | |
| 229 FileInfo tmp; | |
| 230 if (index.LookupAttachment(tmp, id, FileContentType_Dicom)) | |
| 231 { | |
| 232 instances_.push_back(Instance(id, tmp)); | |
| 233 } | |
| 234 } | |
| 235 else | |
| 236 { | |
| 237 resources_[id] = NULL; | |
| 238 } | |
| 239 } | |
| 240 | |
| 241 | |
| 242 public: | |
| 243 ArchiveIndex(ResourceType level) : | |
| 244 level_(level) | |
| 245 { | |
| 246 } | |
| 247 | |
| 248 ~ArchiveIndex() | |
| 249 { | |
| 250 for (Resources::iterator it = resources_.begin(); | |
| 251 it != resources_.end(); ++it) | |
| 252 { | |
| 253 delete it->second; | |
| 254 } | |
| 255 } | |
| 256 | |
| 257 | |
| 258 void Add(ServerIndex& index, | |
| 259 const ResourceIdentifiers& resource) | |
| 260 { | |
| 261 const std::string& id = resource.GetIdentifier(level_); | |
| 262 Resources::iterator previous = resources_.find(id); | |
| 263 | |
| 264 if (level_ == ResourceType_Instance) | |
| 265 { | |
| 266 AddResourceToExpand(index, id); | |
| 267 } | |
| 268 else if (resource.GetLevel() == level_) | |
| 269 { | |
| 270 // Mark this resource for further expansion | |
| 271 if (previous != resources_.end()) | |
| 272 { | |
| 273 delete previous->second; | |
| 274 } | |
| 275 | |
| 276 resources_[id] = NULL; | |
| 277 } | |
| 278 else if (previous == resources_.end()) | |
| 279 { | |
| 280 // This is the first time we meet this resource | |
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281 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 282 child->Add(index, resource); |
| 283 resources_[id] = child.release(); | |
| 284 } | |
| 285 else if (previous->second != NULL) | |
| 286 { | |
| 287 previous->second->Add(index, resource); | |
| 288 } | |
| 289 else | |
| 290 { | |
| 291 // Nothing to do: This item is marked for further expansion | |
| 292 } | |
| 293 } | |
| 294 | |
| 295 | |
| 296 void Expand(ServerIndex& index) | |
| 297 { | |
| 298 if (level_ == ResourceType_Instance) | |
| 299 { | |
| 300 // Expanding an instance node makes no sense | |
| 301 return; | |
| 302 } | |
| 303 | |
| 304 for (Resources::iterator it = resources_.begin(); | |
| 305 it != resources_.end(); ++it) | |
| 306 { | |
| 307 if (it->second == NULL) | |
| 308 { | |
| 309 // This is resource is marked for expansion | |
| 310 std::list<std::string> children; | |
| 311 index.GetChildren(children, it->first); | |
| 312 | |
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313 std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
| 2632 | 314 |
| 315 for (std::list<std::string>::const_iterator | |
| 316 it2 = children.begin(); it2 != children.end(); ++it2) | |
| 317 { | |
| 318 child->AddResourceToExpand(index, *it2); | |
| 319 } | |
| 320 | |
| 321 it->second = child.release(); | |
| 322 } | |
| 323 | |
| 324 assert(it->second != NULL); | |
| 325 it->second->Expand(index); | |
| 326 } | |
| 327 } | |
| 328 | |
| 329 | |
| 330 void Apply(IArchiveVisitor& visitor) const | |
| 331 { | |
| 332 if (level_ == ResourceType_Instance) | |
| 333 { | |
| 334 for (std::list<Instance>::const_iterator | |
| 335 it = instances_.begin(); it != instances_.end(); ++it) | |
| 336 { | |
| 337 visitor.AddInstance(it->id_, it->dicom_); | |
| 338 } | |
| 339 } | |
| 340 else | |
| 341 { | |
| 342 for (Resources::const_iterator it = resources_.begin(); | |
| 343 it != resources_.end(); ++it) | |
| 344 { | |
| 345 assert(it->second != NULL); // There must have been a call to "Expand()" | |
| 346 visitor.Open(level_, it->first); | |
| 347 it->second->Apply(visitor); | |
| 348 visitor.Close(); | |
| 349 } | |
| 350 } | |
| 351 } | |
| 352 }; | |
| 353 | |
| 354 | |
| 355 | |
| 356 class ArchiveJob::ZipCommands : public boost::noncopyable | |
| 357 { | |
| 358 private: | |
| 359 enum Type | |
| 360 { | |
| 361 Type_OpenDirectory, | |
| 362 Type_CloseDirectory, | |
| 363 Type_WriteInstance | |
| 364 }; | |
| 365 | |
| 366 class Command : public boost::noncopyable | |
| 367 { | |
| 368 private: | |
| 369 Type type_; | |
| 370 std::string filename_; | |
| 371 std::string instanceId_; | |
| 372 FileInfo info_; | |
| 373 | |
| 374 public: | |
| 375 explicit Command(Type type) : | |
| 376 type_(type) | |
| 377 { | |
| 378 assert(type_ == Type_CloseDirectory); | |
| 379 } | |
| 380 | |
| 381 Command(Type type, | |
| 382 const std::string& filename) : | |
| 383 type_(type), | |
| 384 filename_(filename) | |
| 385 { | |
| 386 assert(type_ == Type_OpenDirectory); | |
| 387 } | |
| 388 | |
| 389 Command(Type type, | |
| 390 const std::string& filename, | |
| 391 const std::string& instanceId, | |
| 392 const FileInfo& info) : | |
| 393 type_(type), | |
| 394 filename_(filename), | |
| 395 instanceId_(instanceId), | |
| 396 info_(info) | |
| 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 { | |
| 424 context.ReadAttachment(content, info_); | |
| 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, | |
| 579 const FileInfo& info) | |
| 580 { | |
| 581 commands_.push_back(new Command(Type_WriteInstance, filename, instanceId, info)); | |
| 582 instancesCount_ ++; | |
| 583 uncompressedSize_ += info.GetUncompressedSize(); | |
| 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, | |
| 634 const std::string& publicId) | |
| 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 | |
| 691 virtual void Close() | |
| 692 { | |
| 693 commands_.AddCloseDirectory(); | |
| 694 } | |
| 695 | |
| 696 virtual void AddInstance(const std::string& instanceId, | |
| 697 const FileInfo& dicom) | |
| 698 { | |
| 699 char filename[24]; | |
| 700 snprintf(filename, sizeof(filename) - 1, instanceFormat_, counter_); | |
| 701 counter_ ++; | |
| 702 | |
| 703 commands_.AddWriteInstance(filename, instanceId, dicom); | |
| 704 } | |
| 705 }; | |
| 706 | |
| 707 | |
| 708 class ArchiveJob::MediaIndexVisitor : public IArchiveVisitor | |
| 709 { | |
| 710 private: | |
| 711 ZipCommands& commands_; | |
| 712 ServerContext& context_; | |
| 713 unsigned int counter_; | |
| 714 | |
| 715 public: | |
| 716 MediaIndexVisitor(ZipCommands& commands, | |
| 717 ServerContext& context) : | |
| 718 commands_(commands), | |
| 719 context_(context), | |
| 720 counter_(0) | |
| 721 { | |
| 722 } | |
| 723 | |
| 724 virtual void Open(ResourceType level, | |
| 725 const std::string& publicId) | |
| 726 { | |
| 727 } | |
| 728 | |
| 729 virtual void Close() | |
| 730 { | |
| 731 } | |
| 732 | |
| 733 virtual void AddInstance(const std::string& instanceId, | |
| 734 const FileInfo& dicom) | |
| 735 { | |
| 736 // "DICOM restricts the filenames on DICOM media to 8 | |
| 737 // characters (some systems wrongly use 8.3, but this does not | |
| 738 // conform to the standard)." | |
| 739 std::string filename = "IM" + boost::lexical_cast<std::string>(counter_); | |
| 740 commands_.AddWriteInstance(filename, instanceId, dicom); | |
| 741 | |
| 742 counter_ ++; | |
| 743 } | |
| 744 }; | |
| 745 | |
| 746 | |
| 747 class ArchiveJob::ZipWriterIterator : public boost::noncopyable | |
| 748 { | |
| 749 private: | |
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750 TemporaryFile& target_; |
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751 ServerContext& context_; |
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752 ZipCommands commands_; |
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753 std::unique_ptr<HierarchicalZipWriter> zip_; |
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754 std::unique_ptr<DicomDirWriter> dicomDir_; |
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755 bool isMedia_; |
| 2632 | 756 |
| 757 public: | |
| 758 ZipWriterIterator(TemporaryFile& target, | |
| 759 ServerContext& context, | |
| 760 ArchiveIndex& archive, | |
| 761 bool isMedia, | |
| 762 bool enableExtendedSopClass) : | |
| 763 target_(target), | |
| 764 context_(context), | |
| 765 isMedia_(isMedia) | |
| 766 { | |
| 767 if (isMedia) | |
| 768 { | |
| 769 MediaIndexVisitor visitor(commands_, context); | |
| 770 archive.Expand(context.GetIndex()); | |
| 771 | |
| 772 commands_.AddOpenDirectory(MEDIA_IMAGES_FOLDER); | |
| 773 archive.Apply(visitor); | |
| 774 commands_.AddCloseDirectory(); | |
| 775 | |
| 776 dicomDir_.reset(new DicomDirWriter); | |
| 777 dicomDir_->EnableExtendedSopClass(enableExtendedSopClass); | |
| 778 } | |
| 779 else | |
| 780 { | |
| 781 ArchiveIndexVisitor visitor(commands_, context); | |
| 782 archive.Expand(context.GetIndex()); | |
| 783 archive.Apply(visitor); | |
| 784 } | |
| 785 | |
| 786 zip_.reset(new HierarchicalZipWriter(target.GetPath().c_str())); | |
| 787 zip_->SetZip64(commands_.IsZip64()); | |
| 788 } | |
| 789 | |
| 790 size_t GetStepsCount() const | |
| 791 { | |
| 792 return commands_.GetSize() + 1; | |
| 793 } | |
| 794 | |
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795 void RunStep(size_t index, |
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796 bool transcode, |
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797 DicomTransferSyntax transferSyntax) |
| 2632 | 798 { |
| 799 if (index > commands_.GetSize()) | |
| 800 { | |
| 801 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 802 } | |
| 803 else if (index == commands_.GetSize()) | |
| 804 { | |
| 805 // Last step: Add the DICOMDIR | |
| 806 if (isMedia_) | |
| 807 { | |
| 808 assert(dicomDir_.get() != NULL); | |
| 809 std::string s; | |
| 810 dicomDir_->Encode(s); | |
| 811 | |
| 812 zip_->OpenFile("DICOMDIR"); | |
| 813 zip_->Write(s); | |
| 814 } | |
| 815 } | |
| 816 else | |
| 817 { | |
| 818 if (isMedia_) | |
| 819 { | |
| 820 assert(dicomDir_.get() != NULL); | |
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821 commands_.Apply(*zip_, context_, index, *dicomDir_, |
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822 MEDIA_IMAGES_FOLDER, transcode, transferSyntax); |
| 2632 | 823 } |
| 824 else | |
| 825 { | |
| 826 assert(dicomDir_.get() == NULL); | |
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827 commands_.Apply(*zip_, context_, index, transcode, transferSyntax); |
| 2632 | 828 } |
| 829 } | |
| 830 } | |
| 831 | |
| 832 unsigned int GetInstancesCount() const | |
| 833 { | |
| 834 return commands_.GetInstancesCount(); | |
| 835 } | |
| 836 | |
| 837 uint64_t GetUncompressedSize() const | |
| 838 { | |
| 839 return commands_.GetUncompressedSize(); | |
| 840 } | |
| 841 }; | |
| 842 | |
| 843 | |
| 2966 | 844 ArchiveJob::ArchiveJob(ServerContext& context, |
| 2632 | 845 bool isMedia, |
| 846 bool enableExtendedSopClass) : | |
| 847 context_(context), | |
| 848 archive_(new ArchiveIndex(ResourceType_Patient)), // root | |
| 849 isMedia_(isMedia), | |
| 850 enableExtendedSopClass_(enableExtendedSopClass), | |
| 851 currentStep_(0), | |
| 852 instancesCount_(0), | |
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853 uncompressedSize_(0), |
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854 transcode_(false), |
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855 transferSyntax_(DicomTransferSyntax_LittleEndianImplicit) |
| 2632 | 856 { |
| 2966 | 857 } |
| 858 | |
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859 |
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860 ArchiveJob::~ArchiveJob() |
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861 { |
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|
862 if (!mediaArchiveId_.empty()) |
|
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|
863 { |
|
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diff
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|
864 context_.GetMediaArchive().Remove(mediaArchiveId_); |
|
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diff
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|
865 } |
|
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Asynchronous generation of ZIP archives and DICOM medias
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diff
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|
866 } |
|
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diff
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|
867 |
| 2966 | 868 |
| 869 void ArchiveJob::SetSynchronousTarget(boost::shared_ptr<TemporaryFile>& target) | |
| 870 { | |
| 871 if (target.get() == NULL) | |
| 2632 | 872 { |
| 873 throw OrthancException(ErrorCode_NullPointer); | |
| 874 } | |
|
2976
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diff
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|
875 else if (writer_.get() != NULL || // Already started |
|
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diff
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|
876 synchronousTarget_.get() != NULL || |
|
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diff
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|
877 asynchronousTarget_.get() != NULL) |
| 2966 | 878 { |
| 879 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 880 } | |
| 881 else | |
| 882 { | |
| 883 synchronousTarget_ = target; | |
| 884 } | |
| 2632 | 885 } |
| 886 | |
| 887 | |
|
2976
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|
888 void ArchiveJob::SetDescription(const std::string& description) |
|
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|
889 { |
|
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Asynchronous generation of ZIP archives and DICOM medias
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|
890 if (writer_.get() != NULL) // Already started |
|
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diff
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|
891 { |
|
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diff
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|
892 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
|
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|
893 } |
|
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diff
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|
894 else |
|
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diff
changeset
|
895 { |
|
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|
896 description_ = description; |
|
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diff
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|
897 } |
|
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Asynchronous generation of ZIP archives and DICOM medias
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diff
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|
898 } |
|
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|
899 |
|
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diff
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|
900 |
| 2632 | 901 void ArchiveJob::AddResource(const std::string& publicId) |
| 902 { | |
| 903 if (writer_.get() != NULL) // Already started | |
| 904 { | |
| 905 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 906 } | |
|
2976
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diff
changeset
|
907 else |
|
cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
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diff
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|
908 { |
|
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diff
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|
909 ResourceIdentifiers resource(context_.GetIndex(), publicId); |
|
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|
910 archive_->Add(context_.GetIndex(), resource); |
|
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|
911 } |
| 2632 | 912 } |
| 913 | |
|
3913
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|
914 |
|
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|
915 void ArchiveJob::SetTranscode(DicomTransferSyntax transferSyntax) |
|
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|
916 { |
|
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|
917 if (writer_.get() != NULL) // Already started |
|
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transcoding ZIP archive and media
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|
918 { |
|
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diff
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|
919 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
|
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diff
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|
920 } |
|
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transcoding ZIP archive and media
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|
921 else |
|
6ddad3e0b569
transcoding ZIP archive and media
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diff
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|
922 { |
|
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transcoding ZIP archive and media
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diff
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|
923 transcode_ = true; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
924 transferSyntax_ = transferSyntax; |
|
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parents:
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diff
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|
925 } |
|
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transcoding ZIP archive and media
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diff
changeset
|
926 } |
|
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diff
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|
927 |
| 2632 | 928 |
|
2812
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improved naming of methods in IJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
929 void ArchiveJob::Reset() |
| 2632 | 930 { |
| 2955 | 931 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
| 932 "Cannot resubmit the creation of an archive"); | |
| 2632 | 933 } |
| 934 | |
| 935 | |
| 936 void ArchiveJob::Start() | |
| 937 { | |
|
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changeset
|
938 TemporaryFile* target = NULL; |
|
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changeset
|
939 |
| 2966 | 940 if (synchronousTarget_.get() == NULL) |
| 941 { | |
|
3181
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Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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diff
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|
942 { |
|
6fd38327e777
Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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parents:
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diff
changeset
|
943 OrthancConfiguration::ReaderLock lock; |
|
6fd38327e777
Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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parents:
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diff
changeset
|
944 asynchronousTarget_.reset(lock.GetConfiguration().CreateTemporaryFile()); |
|
6fd38327e777
Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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diff
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|
945 } |
|
6fd38327e777
Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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parents:
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diff
changeset
|
946 |
|
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diff
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|
947 target = asynchronousTarget_.get(); |
|
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diff
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|
948 } |
|
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Asynchronous generation of ZIP archives and DICOM medias
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diff
changeset
|
949 else |
|
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Asynchronous generation of ZIP archives and DICOM medias
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diff
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|
950 { |
|
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Asynchronous generation of ZIP archives and DICOM medias
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diff
changeset
|
951 target = synchronousTarget_.get(); |
| 2966 | 952 } |
|
3181
6fd38327e777
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
953 |
|
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
|
954 assert(target != NULL); |
|
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
|
955 target->Touch(); // Make sure we can write to the temporary file |
| 2966 | 956 |
| 2632 | 957 if (writer_.get() != NULL) |
| 958 { | |
| 959 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 960 } | |
| 961 | |
|
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diff
changeset
|
962 writer_.reset(new ZipWriterIterator(*target, context_, *archive_, |
| 2632 | 963 isMedia_, enableExtendedSopClass_)); |
| 964 | |
| 965 instancesCount_ = writer_->GetInstancesCount(); | |
| 966 uncompressedSize_ = writer_->GetUncompressedSize(); | |
| 967 } | |
| 968 | |
|
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diff
changeset
|
969 |
|
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diff
changeset
|
970 |
|
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diff
changeset
|
971 namespace |
|
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diff
changeset
|
972 { |
|
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2966
diff
changeset
|
973 class DynamicTemporaryFile : public IDynamicObject |
|
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diff
changeset
|
974 { |
|
cb5d75143da0
Asynchronous generation of ZIP archives and DICOM medias
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2966
diff
changeset
|
975 private: |
|
3712
2a170a8f1faf
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
976 std::unique_ptr<TemporaryFile> file_; |
|
2976
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diff
changeset
|
977 |
|
cb5d75143da0
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diff
changeset
|
978 public: |
|
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diff
changeset
|
979 DynamicTemporaryFile(TemporaryFile* f) : file_(f) |
|
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diff
changeset
|
980 { |
|
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diff
changeset
|
981 if (f == NULL) |
|
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diff
changeset
|
982 { |
|
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diff
changeset
|
983 throw OrthancException(ErrorCode_NullPointer); |
|
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diff
changeset
|
984 } |
|
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diff
changeset
|
985 } |
|
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diff
changeset
|
986 |
|
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diff
changeset
|
987 const TemporaryFile& GetFile() const |
|
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|
988 { |
|
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diff
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|
989 assert(file_.get() != NULL); |
|
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diff
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|
990 return *file_; |
|
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|
991 } |
|
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diff
changeset
|
992 }; |
|
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diff
changeset
|
993 } |
| 2632 | 994 |
|
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diff
changeset
|
995 |
|
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diff
changeset
|
996 void ArchiveJob::FinalizeTarget() |
|
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diff
changeset
|
997 { |
|
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diff
changeset
|
998 writer_.reset(); // Flush all the results |
|
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changeset
|
999 |
|
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diff
changeset
|
1000 if (asynchronousTarget_.get() != NULL) |
|
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changeset
|
1001 { |
|
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diff
changeset
|
1002 // Asynchronous behavior: Move the resulting file into the media archive |
|
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diff
changeset
|
1003 mediaArchiveId_ = context_.GetMediaArchive().Add( |
|
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diff
changeset
|
1004 new DynamicTemporaryFile(asynchronousTarget_.release())); |
|
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changeset
|
1005 } |
|
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changeset
|
1006 } |
|
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diff
changeset
|
1007 |
|
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diff
changeset
|
1008 |
|
3658
2d90dd30858c
providing job ID to the IJob::Step() methods
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
3640
diff
changeset
|
1009 JobStepResult ArchiveJob::Step(const std::string& jobId) |
| 2632 | 1010 { |
| 1011 assert(writer_.get() != NULL); | |
| 1012 | |
|
2976
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1013 if (synchronousTarget_.get() != NULL && |
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1014 synchronousTarget_.unique()) |
| 2632 | 1015 { |
| 1016 LOG(WARNING) << "A client has disconnected while creating an archive"; | |
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1017 return JobStepResult::Failure(ErrorCode_NetworkProtocol, |
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1018 "A client has disconnected while creating an archive"); |
| 2632 | 1019 } |
| 1020 | |
| 1021 if (writer_->GetStepsCount() == 0) | |
| 1022 { | |
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1023 FinalizeTarget(); |
| 2632 | 1024 return JobStepResult::Success(); |
| 1025 } | |
| 1026 else | |
| 1027 { | |
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1028 writer_->RunStep(currentStep_, transcode_, transferSyntax_); |
| 2632 | 1029 |
| 1030 currentStep_ ++; | |
| 1031 | |
| 1032 if (currentStep_ == writer_->GetStepsCount()) | |
| 1033 { | |
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1034 FinalizeTarget(); |
| 2632 | 1035 return JobStepResult::Success(); |
| 1036 } | |
| 1037 else | |
| 1038 { | |
| 1039 return JobStepResult::Continue(); | |
| 1040 } | |
| 1041 } | |
| 1042 } | |
| 1043 | |
| 1044 | |
| 1045 float ArchiveJob::GetProgress() | |
| 1046 { | |
| 1047 if (writer_.get() == NULL || | |
| 1048 writer_->GetStepsCount() == 0) | |
| 1049 { | |
| 1050 return 1; | |
| 1051 } | |
| 1052 else | |
| 1053 { | |
| 1054 return (static_cast<float>(currentStep_) / | |
| 1055 static_cast<float>(writer_->GetStepsCount() - 1)); | |
| 1056 } | |
| 1057 } | |
| 1058 | |
| 1059 | |
| 1060 void ArchiveJob::GetJobType(std::string& target) | |
| 1061 { | |
| 1062 if (isMedia_) | |
| 1063 { | |
| 1064 target = "Media"; | |
| 1065 } | |
| 1066 else | |
| 1067 { | |
| 1068 target = "Archive"; | |
| 1069 } | |
| 1070 } | |
| 1071 | |
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1072 |
| 2632 | 1073 void ArchiveJob::GetPublicContent(Json::Value& value) |
| 1074 { | |
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1075 value = Json::objectValue; |
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1076 value[KEY_DESCRIPTION] = description_; |
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1077 value[KEY_INSTANCES_COUNT] = instancesCount_; |
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1078 value[KEY_UNCOMPRESSED_SIZE_MB] = |
| 2643 | 1079 static_cast<unsigned int>(uncompressedSize_ / MEGA_BYTES); |
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1080 |
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1081 if (transcode_) |
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1082 { |
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1083 value[KEY_TRANSCODE] = GetTransferSyntaxUid(transferSyntax_); |
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1084 } |
| 2632 | 1085 } |
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1086 |
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1087 |
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1088 bool ArchiveJob::GetOutput(std::string& output, |
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1089 MimeType& mime, |
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1090 const std::string& key) |
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1091 { |
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1092 if (key == "archive" && |
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1093 !mediaArchiveId_.empty()) |
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1094 { |
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1095 SharedArchive::Accessor accessor(context_.GetMediaArchive(), mediaArchiveId_); |
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1096 |
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1097 if (accessor.IsValid()) |
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1098 { |
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1099 const DynamicTemporaryFile& f = dynamic_cast<DynamicTemporaryFile&>(accessor.GetItem()); |
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1100 f.GetFile().Read(output); |
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1101 mime = MimeType_Zip; |
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1102 return true; |
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1103 } |
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1104 else |
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1105 { |
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1106 return false; |
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1107 } |
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1108 } |
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1109 else |
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1110 { |
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1111 return false; |
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1112 } |
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1113 } |
| 2632 | 1114 } |