Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/ArchiveJob.cpp @ 4032:058b5ade8acd
renaming embedded resources
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 09 Jun 2020 21:43:42 +0200 |
parents | 5fe8c6d3212e |
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rev | line source |
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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 | |
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37 #include "../../Core/Cache/SharedArchive.h" |
2632 | 38 #include "../../Core/Compression/HierarchicalZipWriter.h" |
39 #include "../../Core/DicomParsing/DicomDirWriter.h" | |
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40 #include "../../Core/DicomParsing/FromDcmtkBridge.h" |
2632 | 41 #include "../../Core/Logging.h" |
42 #include "../../Core/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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864 context_.GetMediaArchive().Remove(mediaArchiveId_); |
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865 } |
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866 } |
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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 } | |
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875 else if (writer_.get() != NULL || // Already started |
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876 synchronousTarget_.get() != NULL || |
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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 | |
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888 void ArchiveJob::SetDescription(const std::string& description) |
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889 { |
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890 if (writer_.get() != NULL) // Already started |
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|
891 { |
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|
892 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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|
893 } |
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Asynchronous generation of ZIP archives and DICOM medias
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diff
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|
894 else |
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diff
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|
895 { |
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diff
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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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diff
changeset
|
899 |
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2966
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 |
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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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diff
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|
910 archive_->Add(context_.GetIndex(), resource); |
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diff
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|
911 } |
2632 | 912 } |
913 | |
3913
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transcoding ZIP archive and media
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diff
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|
914 |
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changeset
|
915 void ArchiveJob::SetTranscode(DicomTransferSyntax transferSyntax) |
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transcoding ZIP archive and media
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|
916 { |
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|
917 if (writer_.get() != NULL) // Already started |
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|
918 { |
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|
919 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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transcoding ZIP archive and media
Sebastien Jodogne <s.jodogne@gmail.com>
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|
920 } |
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diff
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|
921 else |
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transcoding ZIP archive and media
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|
922 { |
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|
923 transcode_ = true; |
6ddad3e0b569
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|
924 transferSyntax_ = transferSyntax; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
925 } |
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|
926 } |
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|
927 |
2632 | 928 |
2812
ea7aea6f6a95
improved naming of methods in IJob
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
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 { | |
2976
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|
938 TemporaryFile* target = NULL; |
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|
939 |
2966 | 940 if (synchronousTarget_.get() == NULL) |
941 { | |
3181
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|
942 { |
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diff
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|
943 OrthancConfiguration::ReaderLock lock; |
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Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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|
944 asynchronousTarget_.reset(lock.GetConfiguration().CreateTemporaryFile()); |
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|
945 } |
6fd38327e777
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diff
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|
946 |
2976
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|
947 target = asynchronousTarget_.get(); |
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|
948 } |
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diff
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|
949 else |
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diff
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|
950 { |
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diff
changeset
|
951 target = synchronousTarget_.get(); |
2966 | 952 } |
3181
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diff
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|
953 |
6fd38327e777
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diff
changeset
|
954 assert(target != NULL); |
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Fix issue #130 (Orthanc failed to start when /tmp partition was full)
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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 | |
2976
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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 | |
2976
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diff
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|
969 |
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diff
changeset
|
970 |
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diff
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|
971 namespace |
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diff
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|
972 { |
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diff
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|
973 class DynamicTemporaryFile : public IDynamicObject |
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diff
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|
974 { |
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diff
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|
975 private: |
3712
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replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
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3640
diff
changeset
|
976 std::unique_ptr<TemporaryFile> file_; |
2976
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diff
changeset
|
977 |
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diff
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|
978 public: |
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diff
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|
979 DynamicTemporaryFile(TemporaryFile* f) : file_(f) |
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diff
changeset
|
980 { |
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diff
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|
981 if (f == NULL) |
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|
982 { |
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|
983 throw OrthancException(ErrorCode_NullPointer); |
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|
984 } |
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|
985 } |
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diff
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|
986 |
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diff
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|
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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diff
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|
991 } |
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diff
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|
992 }; |
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diff
changeset
|
993 } |
2632 | 994 |
2976
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diff
changeset
|
995 |
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diff
changeset
|
996 void ArchiveJob::FinalizeTarget() |
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|
997 { |
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|
998 writer_.reset(); // Flush all the results |
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diff
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|
999 |
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diff
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|
1000 if (asynchronousTarget_.get() != NULL) |
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|
1001 { |
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diff
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|
1002 // Asynchronous behavior: Move the resulting file into the media archive |
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diff
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|
1003 mediaArchiveId_ = context_.GetMediaArchive().Add( |
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diff
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|
1004 new DynamicTemporaryFile(asynchronousTarget_.release())); |
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diff
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|
1005 } |
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|
1006 } |
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|
1007 |
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diff
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|
1008 |
3658
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providing job ID to the IJob::Step() methods
Sebastien Jodogne <s.jodogne@gmail.com>
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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"; | |
3240
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Fix issue #134 (/patient/modify gives 500, should really be 400)
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|
1017 return JobStepResult::Failure(ErrorCode_NetworkProtocol, |
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Fix issue #134 (/patient/modify gives 500, should really be 400)
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|
1018 "A client has disconnected while creating an archive"); |
2632 | 1019 } |
1020 | |
1021 if (writer_->GetStepsCount() == 0) | |
1022 { | |
2976
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|
1023 FinalizeTarget(); |
2632 | 1024 return JobStepResult::Success(); |
1025 } | |
1026 else | |
1027 { | |
3913
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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 { | |
2976
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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); |
3913
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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 } |
2976
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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 } |