Mercurial > hg > orthanc
annotate OrthancServer/Sources/OrthancWebDav.cpp @ 4934:94a7b681b340 more-tags
added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Thu, 10 Mar 2022 09:03:24 +0100 |
| parents | 6eff25f70121 |
| children | acd3f72e2a21 |
| rev | line source |
|---|---|
| 4240 | 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) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 4240 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
| 9 * modify it under the terms of the GNU General Public License as | |
| 10 * published by the Free Software Foundation, either version 3 of the | |
| 11 * License, or (at your option) any later version. | |
| 12 * | |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 16 * General Public License for more details. | |
| 17 * | |
| 18 * You should have received a copy of the GNU General Public License | |
| 19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 20 **/ | |
| 21 | |
| 22 | |
| 23 #include "OrthancWebDav.h" | |
| 24 | |
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25 #include "../../OrthancFramework/Sources/Compression/ZipReader.h" |
| 4240 | 26 #include "../../OrthancFramework/Sources/DicomFormat/DicomArray.h" |
| 27 #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" | |
| 28 #include "../../OrthancFramework/Sources/HttpServer/WebDavStorage.h" | |
| 4304 | 29 #include "../../OrthancFramework/Sources/Logging.h" |
| 4240 | 30 #include "Search/DatabaseLookup.h" |
| 31 #include "ServerContext.h" | |
| 32 | |
| 33 #include <boost/regex.hpp> | |
| 34 #include <boost/algorithm/string/predicate.hpp> | |
| 35 | |
| 36 | |
| 37 static const char* const BY_PATIENTS = "by-patients"; | |
| 38 static const char* const BY_STUDIES = "by-studies"; | |
| 4241 | 39 static const char* const BY_DATES = "by-dates"; |
| 4240 | 40 static const char* const BY_UIDS = "by-uids"; |
| 41 static const char* const UPLOADS = "uploads"; | |
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42 static const char* const STUDY_INFO = "study.json"; |
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43 static const char* const SERIES_INFO = "series.json"; |
| 4240 | 44 |
| 45 | |
| 46 namespace Orthanc | |
| 47 { | |
| 48 static boost::posix_time::ptime GetNow() | |
| 49 { | |
| 50 return boost::posix_time::second_clock::universal_time(); | |
| 51 } | |
| 52 | |
| 53 | |
| 54 static void LookupTime(boost::posix_time::ptime& target, | |
| 55 ServerContext& context, | |
| 56 const std::string& publicId, | |
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57 ResourceType level, |
| 4240 | 58 MetadataType metadata) |
| 59 { | |
| 60 std::string value; | |
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61 int64_t revision; // Ignored |
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62 if (context.GetIndex().LookupMetadata(value, revision, publicId, level, metadata)) |
| 4240 | 63 { |
| 64 try | |
| 65 { | |
| 66 target = boost::posix_time::from_iso_string(value); | |
| 67 return; | |
| 68 } | |
| 69 catch (std::exception& e) | |
| 70 { | |
| 71 } | |
| 72 } | |
| 73 | |
| 74 target = GetNow(); | |
| 75 } | |
| 76 | |
| 77 | |
| 78 class OrthancWebDav::DicomIdentifiersVisitor : public ServerContext::ILookupVisitor | |
| 79 { | |
| 80 private: | |
| 81 ServerContext& context_; | |
| 82 bool isComplete_; | |
| 83 Collection& target_; | |
| 84 ResourceType level_; | |
| 85 | |
| 86 public: | |
| 87 DicomIdentifiersVisitor(ServerContext& context, | |
| 88 Collection& target, | |
| 89 ResourceType level) : | |
| 90 context_(context), | |
| 91 isComplete_(false), | |
| 92 target_(target), | |
| 93 level_(level) | |
| 94 { | |
| 95 } | |
| 96 | |
| 97 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE | |
| 98 { | |
| 99 return false; // (*) | |
| 100 } | |
| 101 | |
| 102 virtual void MarkAsComplete() ORTHANC_OVERRIDE | |
| 103 { | |
| 104 isComplete_ = true; // TODO | |
| 105 } | |
| 106 | |
| 107 virtual void Visit(const std::string& publicId, | |
| 108 const std::string& instanceId /* unused */, | |
| 109 const DicomMap& mainDicomTags, | |
| 110 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE | |
| 111 { | |
| 112 DicomTag tag(0, 0); | |
| 113 MetadataType timeMetadata; | |
| 114 | |
| 115 switch (level_) | |
| 116 { | |
| 117 case ResourceType_Study: | |
| 118 tag = DICOM_TAG_STUDY_INSTANCE_UID; | |
| 119 timeMetadata = MetadataType_LastUpdate; | |
| 120 break; | |
| 121 | |
| 122 case ResourceType_Series: | |
| 123 tag = DICOM_TAG_SERIES_INSTANCE_UID; | |
| 124 timeMetadata = MetadataType_LastUpdate; | |
| 125 break; | |
| 126 | |
| 127 case ResourceType_Instance: | |
| 128 tag = DICOM_TAG_SOP_INSTANCE_UID; | |
| 129 timeMetadata = MetadataType_Instance_ReceptionDate; | |
| 130 break; | |
| 131 | |
| 132 default: | |
| 133 throw OrthancException(ErrorCode_InternalError); | |
| 134 } | |
| 135 | |
| 136 std::string s; | |
| 137 if (mainDicomTags.LookupStringValue(s, tag, false) && | |
| 138 !s.empty()) | |
| 139 { | |
| 140 std::unique_ptr<Resource> resource; | |
| 141 | |
| 142 if (level_ == ResourceType_Instance) | |
| 143 { | |
| 144 FileInfo info; | |
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145 int64_t revision; // Ignored |
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146 if (context_.GetIndex().LookupAttachment(info, revision, publicId, FileContentType_Dicom)) |
| 4240 | 147 { |
| 148 std::unique_ptr<File> f(new File(s + ".dcm")); | |
| 149 f->SetMimeType(MimeType_Dicom); | |
| 150 f->SetContentLength(info.GetUncompressedSize()); | |
| 151 resource.reset(f.release()); | |
| 152 } | |
| 153 } | |
| 154 else | |
| 155 { | |
| 156 resource.reset(new Folder(s)); | |
| 157 } | |
| 158 | |
| 159 if (resource.get() != NULL) | |
| 160 { | |
| 161 boost::posix_time::ptime t; | |
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162 LookupTime(t, context_, publicId, level_, timeMetadata); |
| 4240 | 163 resource->SetCreationTime(t); |
| 164 target_.AddResource(resource.release()); | |
| 165 } | |
| 166 } | |
| 167 } | |
| 168 }; | |
| 169 | |
| 170 | |
| 171 class OrthancWebDav::DicomFileVisitor : public ServerContext::ILookupVisitor | |
| 172 { | |
| 173 private: | |
| 174 ServerContext& context_; | |
| 175 bool success_; | |
| 176 std::string& target_; | |
| 177 boost::posix_time::ptime& time_; | |
| 178 | |
| 179 public: | |
| 180 DicomFileVisitor(ServerContext& context, | |
| 181 std::string& target, | |
| 182 boost::posix_time::ptime& time) : | |
| 183 context_(context), | |
| 184 success_(false), | |
| 185 target_(target), | |
| 186 time_(time) | |
| 187 { | |
| 188 } | |
| 189 | |
| 190 bool IsSuccess() const | |
| 191 { | |
| 192 return success_; | |
| 193 } | |
| 194 | |
| 195 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE | |
| 196 { | |
| 197 return false; // (*) | |
| 198 } | |
| 199 | |
| 200 virtual void MarkAsComplete() ORTHANC_OVERRIDE | |
| 201 { | |
| 202 } | |
| 203 | |
| 204 virtual void Visit(const std::string& publicId, | |
| 205 const std::string& instanceId /* unused */, | |
| 206 const DicomMap& mainDicomTags, | |
| 207 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE | |
| 208 { | |
| 209 if (success_) | |
| 210 { | |
| 211 success_ = false; // Two matches => Error | |
| 212 } | |
| 213 else | |
| 214 { | |
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215 LookupTime(time_, context_, publicId, ResourceType_Instance, MetadataType_Instance_ReceptionDate); |
| 4240 | 216 context_.ReadDicom(target_, publicId); |
| 217 success_ = true; | |
| 218 } | |
| 219 } | |
| 220 }; | |
| 221 | |
| 222 | |
| 223 class OrthancWebDav::OrthancJsonVisitor : public ServerContext::ILookupVisitor | |
| 224 { | |
| 225 private: | |
| 226 ServerContext& context_; | |
| 227 bool success_; | |
| 228 std::string& target_; | |
| 229 ResourceType level_; | |
| 230 | |
| 231 public: | |
| 232 OrthancJsonVisitor(ServerContext& context, | |
| 233 std::string& target, | |
| 234 ResourceType level) : | |
| 235 context_(context), | |
| 236 success_(false), | |
| 237 target_(target), | |
| 238 level_(level) | |
| 239 { | |
| 240 } | |
| 241 | |
| 242 bool IsSuccess() const | |
| 243 { | |
| 244 return success_; | |
| 245 } | |
| 246 | |
| 247 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE | |
| 248 { | |
| 249 return false; // (*) | |
| 250 } | |
| 251 | |
| 252 virtual void MarkAsComplete() ORTHANC_OVERRIDE | |
| 253 { | |
| 254 } | |
| 255 | |
| 256 virtual void Visit(const std::string& publicId, | |
| 257 const std::string& instanceId /* unused */, | |
| 258 const DicomMap& mainDicomTags, | |
| 259 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE | |
| 260 { | |
| 4554 | 261 Json::Value resource; |
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262 if (context_.GetIndex().ExpandResource(resource, publicId, level_, DicomToJsonFormat_Human)) |
| 4240 | 263 { |
| 264 if (success_) | |
| 265 { | |
| 266 success_ = false; // Two matches => Error | |
| 267 } | |
| 268 else | |
| 269 { | |
| 4554 | 270 target_ = resource.toStyledString(); |
| 4240 | 271 |
| 272 // Replace UNIX newlines with DOS newlines | |
| 273 boost::replace_all(target_, "\n", "\r\n"); | |
| 274 | |
| 275 success_ = true; | |
| 276 } | |
| 277 } | |
| 278 } | |
| 279 }; | |
| 280 | |
| 281 | |
| 282 class OrthancWebDav::ResourcesIndex : public boost::noncopyable | |
| 283 { | |
| 284 public: | |
| 285 typedef std::map<std::string, std::string> Map; | |
| 286 | |
| 287 private: | |
| 288 ServerContext& context_; | |
| 289 ResourceType level_; | |
| 290 std::string template_; | |
| 291 Map pathToResource_; | |
| 292 Map resourceToPath_; | |
| 293 | |
| 294 void CheckInvariants() | |
| 295 { | |
| 296 #ifndef NDEBUG | |
| 297 assert(pathToResource_.size() == resourceToPath_.size()); | |
| 298 | |
| 299 for (Map::const_iterator it = pathToResource_.begin(); it != pathToResource_.end(); ++it) | |
| 300 { | |
| 301 assert(resourceToPath_[it->second] == it->first); | |
| 302 } | |
| 303 | |
| 304 for (Map::const_iterator it = resourceToPath_.begin(); it != resourceToPath_.end(); ++it) | |
| 305 { | |
| 306 assert(pathToResource_[it->second] == it->first); | |
| 307 } | |
| 308 #endif | |
| 309 } | |
| 310 | |
| 311 void AddTags(DicomMap& target, | |
| 312 const std::string& resourceId, | |
| 313 ResourceType tagsFromLevel) | |
| 314 { | |
| 315 DicomMap tags; | |
| 316 if (context_.GetIndex().GetMainDicomTags(tags, resourceId, level_, tagsFromLevel)) | |
| 317 { | |
| 318 target.Merge(tags); | |
| 319 } | |
| 320 } | |
| 321 | |
| 322 void Register(const std::string& resourceId) | |
| 323 { | |
| 324 // Don't register twice the same resource | |
| 325 if (resourceToPath_.find(resourceId) == resourceToPath_.end()) | |
| 326 { | |
| 327 std::string name = template_; | |
| 328 | |
| 329 DicomMap tags; | |
| 330 | |
| 331 AddTags(tags, resourceId, level_); | |
| 332 | |
| 333 if (level_ == ResourceType_Study) | |
| 334 { | |
| 335 AddTags(tags, resourceId, ResourceType_Patient); | |
| 336 } | |
| 337 | |
| 338 DicomArray arr(tags); | |
| 339 for (size_t i = 0; i < arr.GetSize(); i++) | |
| 340 { | |
| 341 const DicomElement& element = arr.GetElement(i); | |
| 342 if (!element.GetValue().IsNull() && | |
| 343 !element.GetValue().IsBinary()) | |
| 344 { | |
| 345 const std::string tag = FromDcmtkBridge::GetTagName(element.GetTag(), ""); | |
| 346 boost::replace_all(name, "{{" + tag + "}}", element.GetValue().GetContent()); | |
| 347 } | |
| 348 } | |
| 349 | |
| 350 // Blank the tags that were not matched | |
| 351 static const boost::regex REGEX_BLANK_TAGS("{{.*?}}"); // non-greedy match | |
| 352 name = boost::regex_replace(name, REGEX_BLANK_TAGS, ""); | |
| 353 | |
| 354 // UTF-8 characters cannot be used on Windows XP | |
| 355 name = Toolbox::ConvertToAscii(name); | |
| 356 boost::replace_all(name, "/", ""); | |
| 357 boost::replace_all(name, "\\", ""); | |
| 358 | |
| 359 // Trim sequences of spaces as one single space | |
| 360 static const boost::regex REGEX_TRIM_SPACES("{{.*?}}"); | |
| 361 name = boost::regex_replace(name, REGEX_TRIM_SPACES, " "); | |
| 362 name = Toolbox::StripSpaces(name); | |
| 363 | |
| 364 size_t count = 0; | |
| 365 for (;;) | |
| 366 { | |
| 367 std::string path = name; | |
| 368 if (count > 0) | |
| 369 { | |
| 370 path += " (" + boost::lexical_cast<std::string>(count) + ")"; | |
| 371 } | |
| 372 | |
| 373 if (pathToResource_.find(path) == pathToResource_.end()) | |
| 374 { | |
| 375 pathToResource_[path] = resourceId; | |
| 376 resourceToPath_[resourceId] = path; | |
| 377 return; | |
| 378 } | |
| 379 | |
| 380 count++; | |
| 381 } | |
| 382 | |
| 383 throw OrthancException(ErrorCode_InternalError); | |
| 384 } | |
| 385 } | |
| 386 | |
| 387 public: | |
| 388 ResourcesIndex(ServerContext& context, | |
| 389 ResourceType level, | |
| 390 const std::string& templateString) : | |
| 391 context_(context), | |
| 392 level_(level), | |
| 393 template_(templateString) | |
| 394 { | |
| 395 } | |
| 396 | |
| 397 ResourceType GetLevel() const | |
| 398 { | |
| 399 return level_; | |
| 400 } | |
| 401 | |
| 402 void Refresh(std::set<std::string>& removedPaths /* out */, | |
| 403 const std::set<std::string>& resources) | |
| 404 { | |
| 405 CheckInvariants(); | |
| 406 | |
| 407 // Detect the resources that have been removed since last refresh | |
| 408 removedPaths.clear(); | |
| 409 std::set<std::string> removedResources; | |
| 410 | |
| 411 for (Map::iterator it = resourceToPath_.begin(); it != resourceToPath_.end(); ++it) | |
| 412 { | |
| 413 if (resources.find(it->first) == resources.end()) | |
| 414 { | |
| 415 const std::string& path = it->second; | |
| 416 | |
| 417 assert(pathToResource_.find(path) != pathToResource_.end()); | |
| 418 pathToResource_.erase(path); | |
| 419 removedPaths.insert(path); | |
| 420 | |
| 421 removedResources.insert(it->first); // Delay the removal to avoid disturbing the iterator | |
| 422 } | |
| 423 } | |
| 424 | |
| 425 // Remove the missing resources | |
| 426 for (std::set<std::string>::const_iterator it = removedResources.begin(); it != removedResources.end(); ++it) | |
| 427 { | |
| 428 assert(resourceToPath_.find(*it) != resourceToPath_.end()); | |
| 429 resourceToPath_.erase(*it); | |
| 430 } | |
| 431 | |
| 432 CheckInvariants(); | |
| 433 | |
| 434 for (std::set<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) | |
| 435 { | |
| 436 Register(*it); | |
| 437 } | |
| 438 | |
| 439 CheckInvariants(); | |
| 440 } | |
| 441 | |
| 442 const Map& GetPathToResource() const | |
| 443 { | |
| 444 return pathToResource_; | |
| 445 } | |
| 446 }; | |
| 447 | |
| 448 | |
| 449 class OrthancWebDav::InstancesOfSeries : public INode | |
| 450 { | |
| 451 private: | |
| 452 ServerContext& context_; | |
| 453 std::string parentSeries_; | |
| 454 | |
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455 static bool LookupInstanceId(std::string& instanceId, |
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456 const UriComponents& path) |
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457 { |
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458 if (path.size() == 1 && |
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459 boost::ends_with(path[0], ".dcm")) |
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460 { |
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461 instanceId = path[0].substr(0, path[0].size() - 4); |
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462 return true; |
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463 } |
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464 else |
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465 { |
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466 return false; |
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467 } |
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468 } |
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469 |
| 4240 | 470 public: |
| 471 InstancesOfSeries(ServerContext& context, | |
| 472 const std::string& parentSeries) : | |
| 473 context_(context), | |
| 474 parentSeries_(parentSeries) | |
| 475 { | |
| 476 } | |
| 477 | |
| 478 virtual bool ListCollection(IWebDavBucket::Collection& target, | |
| 479 const UriComponents& path) ORTHANC_OVERRIDE | |
| 480 { | |
| 481 if (path.empty()) | |
| 482 { | |
| 483 std::list<std::string> resources; | |
| 484 try | |
| 485 { | |
| 486 context_.GetIndex().GetChildren(resources, parentSeries_); | |
| 487 } | |
| 488 catch (OrthancException&) | |
| 489 { | |
| 490 // Unknown (or deleted) parent series | |
| 491 return false; | |
| 492 } | |
| 493 | |
| 494 for (std::list<std::string>::const_iterator | |
| 495 it = resources.begin(); it != resources.end(); ++it) | |
| 496 { | |
| 497 boost::posix_time::ptime time; | |
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498 LookupTime(time, context_, *it, ResourceType_Instance, MetadataType_Instance_ReceptionDate); |
| 4240 | 499 |
| 500 FileInfo info; | |
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501 int64_t revision; // Ignored |
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502 if (context_.GetIndex().LookupAttachment(info, revision, *it, FileContentType_Dicom)) |
| 4240 | 503 { |
| 504 std::unique_ptr<File> resource(new File(*it + ".dcm")); | |
| 505 resource->SetMimeType(MimeType_Dicom); | |
| 506 resource->SetContentLength(info.GetUncompressedSize()); | |
| 507 resource->SetCreationTime(time); | |
| 508 target.AddResource(resource.release()); | |
| 509 } | |
| 510 } | |
| 511 | |
| 512 return true; | |
| 513 } | |
| 514 else | |
| 515 { | |
| 516 return false; | |
| 517 } | |
| 518 } | |
| 519 | |
| 520 virtual bool GetFileContent(MimeType& mime, | |
| 521 std::string& content, | |
| 522 boost::posix_time::ptime& time, | |
| 523 const UriComponents& path) ORTHANC_OVERRIDE | |
| 524 { | |
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525 std::string instanceId; |
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526 if (LookupInstanceId(instanceId, path)) |
| 4240 | 527 { |
| 528 try | |
| 529 { | |
| 530 mime = MimeType_Dicom; | |
| 531 context_.ReadDicom(content, instanceId); | |
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532 LookupTime(time, context_, instanceId, ResourceType_Instance, MetadataType_Instance_ReceptionDate); |
| 4240 | 533 return true; |
| 534 } | |
| 535 catch (OrthancException&) | |
| 536 { | |
| 537 // File was removed | |
| 538 return false; | |
| 539 } | |
| 540 } | |
| 541 else | |
| 542 { | |
| 543 return false; | |
| 544 } | |
| 545 } | |
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546 |
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547 virtual bool DeleteItem(const UriComponents& path) ORTHANC_OVERRIDE |
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548 { |
| 4252 | 549 if (path.empty()) |
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550 { |
| 4252 | 551 // Delete all |
| 552 std::list<std::string> resources; | |
| 553 try | |
| 554 { | |
| 555 context_.GetIndex().GetChildren(resources, parentSeries_); | |
| 556 } | |
| 557 catch (OrthancException&) | |
| 558 { | |
| 559 // Unknown (or deleted) parent series | |
| 560 return true; | |
| 561 } | |
| 562 | |
| 563 for (std::list<std::string>::const_iterator it = resources.begin(); | |
| 564 it != resources.end(); ++it) | |
| 565 { | |
| 566 Json::Value info; | |
| 567 context_.DeleteResource(info, *it, ResourceType_Instance); | |
| 568 } | |
| 569 | |
| 570 return true; | |
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571 } |
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572 else |
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573 { |
| 4252 | 574 std::string instanceId; |
| 575 if (LookupInstanceId(instanceId, path)) | |
| 576 { | |
| 577 Json::Value info; | |
| 578 return context_.DeleteResource(info, instanceId, ResourceType_Instance); | |
| 579 } | |
| 580 else | |
| 581 { | |
| 582 return false; | |
| 583 } | |
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584 } |
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585 } |
| 4240 | 586 }; |
| 587 | |
| 588 | |
| 589 | |
| 590 /** | |
| 591 * The "InternalNode" class corresponds to a non-leaf node in the | |
| 592 * WebDAV tree, that only contains subfolders (no file). | |
| 593 * | |
| 594 * TODO: Implement a LRU index to dynamically remove the oldest | |
| 595 * children on high RAM usage. | |
| 596 **/ | |
| 597 class OrthancWebDav::InternalNode : public INode | |
| 598 { | |
| 599 private: | |
| 600 typedef std::map<std::string, INode*> Children; | |
| 601 | |
| 602 Children children_; | |
| 603 | |
| 604 INode* GetChild(const std::string& path) // Don't delete the result pointer! | |
| 605 { | |
| 606 Children::const_iterator child = children_.find(path); | |
| 607 if (child == children_.end()) | |
| 608 { | |
| 4253 | 609 INode* node = CreateSubfolder(path); |
| 4240 | 610 |
| 4253 | 611 if (node == NULL) |
| 4240 | 612 { |
| 613 return NULL; | |
| 614 } | |
| 615 else | |
| 616 { | |
| 4253 | 617 children_[path] = node; |
| 618 return node; | |
| 4240 | 619 } |
| 620 } | |
| 621 else | |
| 622 { | |
| 623 assert(child->second != NULL); | |
| 624 return child->second; | |
| 625 } | |
| 626 } | |
| 627 | |
| 628 protected: | |
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629 void InvalidateSubfolder(const std::string& path) |
| 4240 | 630 { |
| 631 Children::iterator child = children_.find(path); | |
| 632 if (child != children_.end()) | |
| 633 { | |
| 634 assert(child->second != NULL); | |
| 635 delete child->second; | |
| 636 children_.erase(child); | |
| 637 } | |
| 638 } | |
| 639 | |
| 640 virtual void Refresh() = 0; | |
| 641 | |
| 642 virtual bool ListSubfolders(IWebDavBucket::Collection& target) = 0; | |
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643 |
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644 virtual INode* CreateSubfolder(const std::string& path) = 0; |
| 4240 | 645 |
| 646 public: | |
| 647 virtual ~InternalNode() | |
| 648 { | |
| 649 for (Children::iterator it = children_.begin(); it != children_.end(); ++it) | |
| 650 { | |
| 651 assert(it->second != NULL); | |
| 652 delete it->second; | |
| 653 } | |
| 654 } | |
| 655 | |
| 656 virtual bool ListCollection(IWebDavBucket::Collection& target, | |
| 657 const UriComponents& path) | |
| 658 ORTHANC_OVERRIDE ORTHANC_FINAL | |
| 659 { | |
| 660 Refresh(); | |
| 661 | |
| 662 if (path.empty()) | |
| 663 { | |
| 664 return ListSubfolders(target); | |
| 665 } | |
| 666 else | |
| 667 { | |
| 668 // Recursivity | |
| 669 INode* child = GetChild(path[0]); | |
| 670 if (child == NULL) | |
| 671 { | |
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672 // Must be "true" to allow DELETE on folders that are |
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673 // automatically removed through recursive deletion |
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674 return true; |
| 4240 | 675 } |
| 676 else | |
| 677 { | |
| 678 UriComponents subpath(path.begin() + 1, path.end()); | |
| 679 return child->ListCollection(target, subpath); | |
| 680 } | |
| 681 } | |
| 682 } | |
| 683 | |
| 684 virtual bool GetFileContent(MimeType& mime, | |
| 685 std::string& content, | |
| 686 boost::posix_time::ptime& time, | |
| 687 const UriComponents& path) | |
| 688 ORTHANC_OVERRIDE ORTHANC_FINAL | |
| 689 { | |
| 690 if (path.empty()) | |
| 691 { | |
| 692 return false; // An internal node doesn't correspond to a file | |
| 693 } | |
| 694 else | |
| 695 { | |
| 696 // Recursivity | |
| 697 Refresh(); | |
| 698 | |
| 699 INode* child = GetChild(path[0]); | |
| 700 if (child == NULL) | |
| 701 { | |
| 702 return false; | |
| 703 } | |
| 704 else | |
| 705 { | |
| 706 UriComponents subpath(path.begin() + 1, path.end()); | |
| 707 return child->GetFileContent(mime, content, time, subpath); | |
| 708 } | |
| 709 } | |
| 710 } | |
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711 |
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712 |
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713 virtual bool DeleteItem(const UriComponents& path) ORTHANC_OVERRIDE ORTHANC_FINAL |
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714 { |
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715 Refresh(); |
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716 |
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717 if (path.empty()) |
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718 { |
| 4252 | 719 IWebDavBucket::Collection collection; |
| 720 if (ListSubfolders(collection)) | |
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721 { |
| 4252 | 722 std::set<std::string> content; |
| 723 collection.ListDisplayNames(content); | |
| 724 | |
| 725 for (std::set<std::string>::const_iterator | |
| 726 it = content.begin(); it != content.end(); ++it) | |
| 727 { | |
| 728 INode* node = GetChild(*it); | |
| 729 if (node) | |
| 730 { | |
| 731 node->DeleteItem(path); | |
| 732 } | |
| 733 } | |
| 734 | |
| 735 return true; | |
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736 } |
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737 else |
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738 { |
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739 return false; |
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740 } |
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741 } |
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742 else |
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743 { |
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744 INode* child = GetChild(path[0]); |
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745 if (child == NULL) |
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746 { |
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747 return true; |
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748 } |
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749 else |
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750 { |
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751 // Recursivity |
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752 UriComponents subpath(path.begin() + 1, path.end()); |
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753 return child->DeleteItem(subpath); |
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754 } |
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755 } |
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756 } |
| 4240 | 757 }; |
| 758 | |
| 759 | |
| 760 class OrthancWebDav::ListOfResources : public InternalNode | |
| 761 { | |
| 762 private: | |
| 763 ServerContext& context_; | |
| 764 const Templates& templates_; | |
| 765 std::unique_ptr<ResourcesIndex> index_; | |
| 766 MetadataType timeMetadata_; | |
| 767 | |
| 768 protected: | |
| 769 virtual void Refresh() ORTHANC_OVERRIDE ORTHANC_FINAL | |
| 770 { | |
| 771 std::list<std::string> resources; | |
| 772 GetCurrentResources(resources); | |
| 773 | |
| 774 std::set<std::string> removedPaths; | |
| 775 index_->Refresh(removedPaths, std::set<std::string>(resources.begin(), resources.end())); | |
| 776 | |
| 777 // Remove the children whose associated resource doesn't exist anymore | |
| 778 for (std::set<std::string>::const_iterator | |
| 779 it = removedPaths.begin(); it != removedPaths.end(); ++it) | |
| 780 { | |
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781 InvalidateSubfolder(*it); |
| 4240 | 782 } |
| 783 } | |
| 784 | |
| 785 virtual bool ListSubfolders(IWebDavBucket::Collection& target) ORTHANC_OVERRIDE ORTHANC_FINAL | |
| 786 { | |
| 787 if (index_->GetLevel() == ResourceType_Instance) | |
| 788 { | |
| 789 // Not a collection, no subfolders | |
| 790 return false; | |
| 791 } | |
| 792 else | |
| 793 { | |
| 794 const ResourcesIndex::Map& paths = index_->GetPathToResource(); | |
| 795 | |
| 796 for (ResourcesIndex::Map::const_iterator it = paths.begin(); it != paths.end(); ++it) | |
| 797 { | |
| 798 boost::posix_time::ptime time; | |
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799 LookupTime(time, context_, it->second, index_->GetLevel(), timeMetadata_); |
| 4240 | 800 |
| 801 std::unique_ptr<IWebDavBucket::Resource> resource(new IWebDavBucket::Folder(it->first)); | |
| 802 resource->SetCreationTime(time); | |
| 803 target.AddResource(resource.release()); | |
| 804 } | |
| 805 | |
| 806 return true; | |
| 807 } | |
| 808 } | |
| 809 | |
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810 virtual INode* CreateSubfolder(const std::string& path) ORTHANC_OVERRIDE ORTHANC_FINAL |
| 4240 | 811 { |
| 812 ResourcesIndex::Map::const_iterator resource = index_->GetPathToResource().find(path); | |
| 813 if (resource == index_->GetPathToResource().end()) | |
| 814 { | |
| 815 return NULL; | |
| 816 } | |
| 817 else | |
| 818 { | |
| 819 return CreateResourceNode(resource->second); | |
| 820 } | |
| 821 } | |
| 822 | |
| 823 ServerContext& GetContext() const | |
| 824 { | |
| 825 return context_; | |
| 826 } | |
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827 |
| 4240 | 828 virtual void GetCurrentResources(std::list<std::string>& resources) = 0; |
| 829 | |
| 830 virtual INode* CreateResourceNode(const std::string& resource) = 0; | |
| 831 | |
| 832 public: | |
| 833 ListOfResources(ServerContext& context, | |
| 834 ResourceType level, | |
| 835 const Templates& templates) : | |
| 836 context_(context), | |
| 837 templates_(templates) | |
| 838 { | |
| 839 Templates::const_iterator t = templates.find(level); | |
| 840 if (t == templates.end()) | |
| 841 { | |
| 842 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 843 } | |
| 844 | |
| 845 index_.reset(new ResourcesIndex(context, level, t->second)); | |
| 846 | |
| 847 if (level == ResourceType_Instance) | |
| 848 { | |
| 849 timeMetadata_ = MetadataType_Instance_ReceptionDate; | |
| 850 } | |
| 851 else | |
| 852 { | |
| 853 timeMetadata_ = MetadataType_LastUpdate; | |
| 854 } | |
| 855 } | |
| 856 | |
| 857 ResourceType GetLevel() const | |
| 858 { | |
| 859 return index_->GetLevel(); | |
| 860 } | |
| 861 | |
| 862 const Templates& GetTemplates() const | |
| 863 { | |
| 864 return templates_; | |
| 865 } | |
| 866 }; | |
| 867 | |
| 868 | |
| 869 | |
| 870 class OrthancWebDav::SingleDicomResource : public ListOfResources | |
| 871 { | |
| 872 private: | |
| 873 std::string parentId_; | |
| 874 | |
| 875 protected: | |
| 876 virtual void GetCurrentResources(std::list<std::string>& resources) ORTHANC_OVERRIDE | |
| 877 { | |
| 878 try | |
| 879 { | |
| 880 GetContext().GetIndex().GetChildren(resources, parentId_); | |
| 881 } | |
| 882 catch (OrthancException&) | |
| 883 { | |
| 884 // Unknown parent resource | |
| 885 resources.clear(); | |
| 886 } | |
| 887 } | |
| 888 | |
| 889 virtual INode* CreateResourceNode(const std::string& resource) ORTHANC_OVERRIDE | |
| 890 { | |
| 891 if (GetLevel() == ResourceType_Instance) | |
| 892 { | |
| 893 return NULL; | |
| 894 } | |
| 895 else if (GetLevel() == ResourceType_Series) | |
| 896 { | |
| 897 return new InstancesOfSeries(GetContext(), resource); | |
| 898 } | |
| 899 else | |
| 900 { | |
| 901 ResourceType l = GetChildResourceType(GetLevel()); | |
| 902 return new SingleDicomResource(GetContext(), l, resource, GetTemplates()); | |
| 903 } | |
| 904 } | |
| 905 | |
| 906 public: | |
| 907 SingleDicomResource(ServerContext& context, | |
| 908 ResourceType level, | |
| 909 const std::string& parentId, | |
| 910 const Templates& templates) : | |
| 911 ListOfResources(context, level, templates), | |
| 912 parentId_(parentId) | |
| 913 { | |
| 914 } | |
| 915 }; | |
| 916 | |
| 917 | |
| 918 class OrthancWebDav::RootNode : public ListOfResources | |
| 919 { | |
| 920 protected: | |
| 921 virtual void GetCurrentResources(std::list<std::string>& resources) ORTHANC_OVERRIDE | |
| 922 { | |
| 923 GetContext().GetIndex().GetAllUuids(resources, GetLevel()); | |
| 924 } | |
| 925 | |
| 926 virtual INode* CreateResourceNode(const std::string& resource) ORTHANC_OVERRIDE | |
| 927 { | |
| 928 if (GetLevel() == ResourceType_Series) | |
| 929 { | |
| 930 return new InstancesOfSeries(GetContext(), resource); | |
| 931 } | |
| 932 else | |
| 933 { | |
| 934 ResourceType l = GetChildResourceType(GetLevel()); | |
| 935 return new SingleDicomResource(GetContext(), l, resource, GetTemplates()); | |
| 936 } | |
| 937 } | |
| 938 | |
| 939 public: | |
| 940 RootNode(ServerContext& context, | |
| 941 ResourceType level, | |
| 942 const Templates& templates) : | |
| 943 ListOfResources(context, level, templates) | |
| 944 { | |
| 945 } | |
| 946 }; | |
| 947 | |
| 948 | |
| 949 class OrthancWebDav::ListOfStudiesByDate : public ListOfResources | |
| 950 { | |
| 951 private: | |
| 952 std::string year_; | |
| 953 std::string month_; | |
| 954 | |
| 955 class Visitor : public ServerContext::ILookupVisitor | |
| 956 { | |
| 957 private: | |
| 958 std::list<std::string>& resources_; | |
| 959 | |
| 960 public: | |
| 4253 | 961 explicit Visitor(std::list<std::string>& resources) : |
| 4240 | 962 resources_(resources) |
| 963 { | |
| 964 } | |
| 965 | |
| 966 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE | |
| 967 { | |
| 968 return false; // (*) | |
| 969 } | |
| 970 | |
| 971 virtual void MarkAsComplete() ORTHANC_OVERRIDE | |
| 972 { | |
| 973 } | |
| 974 | |
| 975 virtual void Visit(const std::string& publicId, | |
| 976 const std::string& instanceId /* unused */, | |
| 977 const DicomMap& mainDicomTags, | |
| 978 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE | |
| 979 { | |
| 980 resources_.push_back(publicId); | |
| 981 } | |
| 982 }; | |
| 983 | |
| 984 protected: | |
| 985 virtual void GetCurrentResources(std::list<std::string>& resources) ORTHANC_OVERRIDE | |
| 986 { | |
| 987 DatabaseLookup query; | |
| 988 query.AddRestConstraint(DICOM_TAG_STUDY_DATE, year_ + month_ + "01-" + year_ + month_ + "31", | |
| 989 true /* case sensitive */, true /* mandatory tag */); | |
| 990 | |
| 991 Visitor visitor(resources); | |
| 992 GetContext().Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); | |
| 993 } | |
| 994 | |
| 995 virtual INode* CreateResourceNode(const std::string& resource) ORTHANC_OVERRIDE | |
| 996 { | |
| 997 return new SingleDicomResource(GetContext(), ResourceType_Series, resource, GetTemplates()); | |
| 998 } | |
| 999 | |
| 1000 public: | |
| 1001 ListOfStudiesByDate(ServerContext& context, | |
| 1002 const std::string& year, | |
| 1003 const std::string& month, | |
| 1004 const Templates& templates) : | |
| 1005 ListOfResources(context, ResourceType_Study, templates), | |
| 1006 year_(year), | |
| 1007 month_(month) | |
| 1008 { | |
| 1009 if (year.size() != 4 || | |
| 1010 month.size() != 2) | |
| 1011 { | |
| 1012 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 1013 } | |
| 1014 } | |
| 1015 }; | |
| 1016 | |
| 1017 | |
| 1018 class OrthancWebDav::ListOfStudiesByMonth : public InternalNode | |
| 1019 { | |
| 1020 private: | |
| 1021 ServerContext& context_; | |
| 1022 std::string year_; | |
| 1023 const Templates& templates_; | |
| 1024 | |
| 1025 class Visitor : public ServerContext::ILookupVisitor | |
| 1026 { | |
| 1027 private: | |
| 1028 std::set<std::string> months_; | |
| 1029 | |
| 1030 public: | |
| 1031 const std::set<std::string>& GetMonths() const | |
| 1032 { | |
| 1033 return months_; | |
| 1034 } | |
| 1035 | |
| 1036 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE | |
| 1037 { | |
| 1038 return false; // (*) | |
| 1039 } | |
| 1040 | |
| 1041 virtual void MarkAsComplete() ORTHANC_OVERRIDE | |
| 1042 { | |
| 1043 } | |
| 1044 | |
| 1045 virtual void Visit(const std::string& publicId, | |
| 1046 const std::string& instanceId /* unused */, | |
| 1047 const DicomMap& mainDicomTags, | |
| 1048 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE | |
| 1049 { | |
| 1050 std::string s; | |
| 1051 if (mainDicomTags.LookupStringValue(s, DICOM_TAG_STUDY_DATE, false) && | |
| 1052 s.size() == 8) | |
| 1053 { | |
| 1054 months_.insert(s.substr(4, 2)); // Get the month from "YYYYMMDD" | |
| 1055 } | |
| 1056 } | |
| 1057 }; | |
| 1058 | |
| 1059 protected: | |
| 1060 virtual void Refresh() ORTHANC_OVERRIDE | |
| 1061 { | |
| 1062 } | |
| 1063 | |
| 1064 virtual bool ListSubfolders(IWebDavBucket::Collection& target) ORTHANC_OVERRIDE | |
| 1065 { | |
| 1066 DatabaseLookup query; | |
| 1067 query.AddRestConstraint(DICOM_TAG_STUDY_DATE, year_ + "0101-" + year_ + "1231", | |
| 1068 true /* case sensitive */, true /* mandatory tag */); | |
| 1069 | |
| 1070 Visitor visitor; | |
| 1071 context_.Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); | |
| 1072 | |
| 1073 for (std::set<std::string>::const_iterator it = visitor.GetMonths().begin(); | |
| 1074 it != visitor.GetMonths().end(); ++it) | |
| 1075 { | |
| 1076 target.AddResource(new IWebDavBucket::Folder(year_ + "-" + *it)); | |
| 1077 } | |
| 1078 | |
| 1079 return true; | |
| 1080 } | |
| 1081 | |
|
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1082 virtual INode* CreateSubfolder(const std::string& path) ORTHANC_OVERRIDE |
| 4240 | 1083 { |
| 1084 if (path.size() != 7) // Format: "YYYY-MM" | |
| 1085 { | |
| 1086 throw OrthancException(ErrorCode_InternalError); | |
| 1087 } | |
| 1088 else | |
| 1089 { | |
| 1090 const std::string year = path.substr(0, 4); | |
| 1091 const std::string month = path.substr(5, 2); | |
| 1092 return new ListOfStudiesByDate(context_, year, month, templates_); | |
| 1093 } | |
| 1094 } | |
| 1095 | |
| 1096 public: | |
| 1097 ListOfStudiesByMonth(ServerContext& context, | |
| 1098 const std::string& year, | |
| 1099 const Templates& templates) : | |
| 1100 context_(context), | |
| 1101 year_(year), | |
| 1102 templates_(templates) | |
| 1103 { | |
| 1104 if (year_.size() != 4) | |
| 1105 { | |
| 1106 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
| 1107 } | |
| 1108 } | |
| 1109 }; | |
| 1110 | |
| 1111 | |
| 1112 class OrthancWebDav::ListOfStudiesByYear : public InternalNode | |
| 1113 { | |
| 1114 private: | |
| 1115 ServerContext& context_; | |
| 1116 const Templates& templates_; | |
| 1117 | |
| 1118 protected: | |
| 1119 virtual void Refresh() ORTHANC_OVERRIDE | |
| 1120 { | |
| 1121 } | |
| 1122 | |
| 1123 virtual bool ListSubfolders(IWebDavBucket::Collection& target) ORTHANC_OVERRIDE | |
| 1124 { | |
| 1125 std::list<std::string> resources; | |
| 1126 context_.GetIndex().GetAllUuids(resources, ResourceType_Study); | |
| 1127 | |
| 1128 std::set<std::string> years; | |
| 1129 | |
| 1130 for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) | |
| 1131 { | |
| 1132 DicomMap tags; | |
| 1133 std::string studyDate; | |
| 1134 if (context_.GetIndex().GetMainDicomTags(tags, *it, ResourceType_Study, ResourceType_Study) && | |
| 1135 tags.LookupStringValue(studyDate, DICOM_TAG_STUDY_DATE, false) && | |
| 1136 studyDate.size() == 8) | |
| 1137 { | |
| 1138 years.insert(studyDate.substr(0, 4)); // Get the year from "YYYYMMDD" | |
| 1139 } | |
| 1140 } | |
| 1141 | |
| 1142 for (std::set<std::string>::const_iterator it = years.begin(); it != years.end(); ++it) | |
| 1143 { | |
| 1144 target.AddResource(new IWebDavBucket::Folder(*it)); | |
| 1145 } | |
| 1146 | |
| 1147 return true; | |
| 1148 } | |
| 1149 | |
|
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1150 virtual INode* CreateSubfolder(const std::string& path) ORTHANC_OVERRIDE |
| 4240 | 1151 { |
| 1152 return new ListOfStudiesByMonth(context_, path, templates_); | |
| 1153 } | |
| 1154 | |
| 1155 public: | |
| 1156 ListOfStudiesByYear(ServerContext& context, | |
| 1157 const Templates& templates) : | |
| 1158 context_(context), | |
| 1159 templates_(templates) | |
| 1160 { | |
| 1161 } | |
| 1162 }; | |
| 1163 | |
| 1164 | |
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1165 class OrthancWebDav::DicomDeleteVisitor : public ServerContext::ILookupVisitor |
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1166 { |
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1167 private: |
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1168 ServerContext& context_; |
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1169 ResourceType level_; |
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1170 |
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1171 public: |
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1172 DicomDeleteVisitor(ServerContext& context, |
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1173 ResourceType level) : |
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1174 context_(context), |
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1175 level_(level) |
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1176 { |
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1177 } |
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1178 |
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1179 virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE |
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1180 { |
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1181 return false; // (*) |
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1182 } |
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1183 |
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1184 virtual void MarkAsComplete() ORTHANC_OVERRIDE |
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1185 { |
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1186 } |
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1187 |
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1188 virtual void Visit(const std::string& publicId, |
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1189 const std::string& instanceId /* unused */, |
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1190 const DicomMap& mainDicomTags /* unused */, |
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1191 const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE |
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1192 { |
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1193 Json::Value info; |
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1194 context_.DeleteResource(info, publicId, level_); |
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1195 } |
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1196 }; |
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1197 |
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1198 |
| 4240 | 1199 void OrthancWebDav::AddVirtualFile(Collection& collection, |
| 1200 const UriComponents& path, | |
| 1201 const std::string& filename) | |
| 1202 { | |
| 1203 MimeType mime; | |
| 1204 std::string content; | |
| 4246 | 1205 boost::posix_time::ptime modification; // Unused, let the date be set to "GetNow()" |
| 4240 | 1206 |
| 1207 UriComponents p = path; | |
| 1208 p.push_back(filename); | |
| 1209 | |
| 1210 if (GetFileContent(mime, content, modification, p)) | |
| 1211 { | |
| 1212 std::unique_ptr<File> f(new File(filename)); | |
| 1213 f->SetMimeType(mime); | |
| 1214 f->SetContentLength(content.size()); | |
| 1215 collection.AddResource(f.release()); | |
| 1216 } | |
| 1217 } | |
| 1218 | |
| 1219 | |
| 1220 void OrthancWebDav::UploadWorker(OrthancWebDav* that) | |
| 1221 { | |
| 1222 assert(that != NULL); | |
| 1223 | |
| 1224 boost::posix_time::ptime lastModification = GetNow(); | |
| 1225 | |
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1226 while (that->uploadRunning_) |
| 4240 | 1227 { |
| 1228 std::unique_ptr<IDynamicObject> obj(that->uploadQueue_.Dequeue(100)); | |
| 1229 if (obj.get() != NULL) | |
| 1230 { | |
| 1231 that->Upload(reinterpret_cast<const SingleValueObject<std::string>&>(*obj).GetValue()); | |
| 1232 lastModification = GetNow(); | |
| 1233 } | |
|
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1234 else if (GetNow() - lastModification > boost::posix_time::seconds(30)) |
| 4240 | 1235 { |
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1236 /** |
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1237 * After every 30 seconds of inactivity, remove the empty |
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1238 * folders. This delay is needed to avoid removing |
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1239 * just-created folders before the remote WebDAV has time to |
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1240 * write files into it. |
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1241 **/ |
|
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1242 LOG(TRACE) << "Cleaning up the empty WebDAV upload folders"; |
| 4240 | 1243 that->uploads_.RemoveEmptyFolders(); |
| 1244 lastModification = GetNow(); | |
| 1245 } | |
| 1246 } | |
| 1247 } | |
| 1248 | |
| 1249 | |
| 1250 void OrthancWebDav::Upload(const std::string& path) | |
| 1251 { | |
| 1252 UriComponents uri; | |
| 1253 Toolbox::SplitUriComponents(uri, path); | |
| 1254 | |
| 1255 LOG(INFO) << "Upload from WebDAV: " << path; | |
| 1256 | |
| 1257 MimeType mime; | |
| 1258 std::string content; | |
| 1259 boost::posix_time::ptime time; | |
| 1260 if (uploads_.GetFileContent(mime, content, time, uri)) | |
| 1261 { | |
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1262 bool success = false; |
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1263 |
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1264 if (ZipReader::IsZipMemoryBuffer(content)) |
| 4240 | 1265 { |
|
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1266 // New in Orthanc 1.8.2 |
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1267 std::unique_ptr<ZipReader> reader(ZipReader::CreateFromMemory(content)); |
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1268 |
| 4386 | 1269 std::string filename, uncompressedFile; |
| 1270 while (reader->ReadNextFile(filename, uncompressedFile)) | |
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robustness against non-dicom files
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diff
changeset
|
1271 { |
| 4386 | 1272 if (!uncompressedFile.empty()) |
|
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diff
changeset
|
1273 { |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1274 LOG(INFO) << "Uploading DICOM file extracted from a ZIP archive in WebDAV: " << filename; |
|
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diff
changeset
|
1275 |
|
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Optimization in C-STORE SCP by avoiding an unnecessary DICOM parsing
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1276 std::unique_ptr<DicomInstanceToStore> instance(DicomInstanceToStore::CreateFromBuffer(uncompressedFile)); |
|
8f9090b137f1
Optimization in C-STORE SCP by avoiding an unnecessary DICOM parsing
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1277 instance->SetOrigin(DicomInstanceOrigin::FromWebDav()); |
|
4358
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diff
changeset
|
1278 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1279 std::string publicId; |
|
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diff
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|
1280 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1281 try |
|
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diff
changeset
|
1282 { |
|
4508
8f9090b137f1
Optimization in C-STORE SCP by avoiding an unnecessary DICOM parsing
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1283 context_.Store(publicId, *instance, StoreInstanceMode_Default); |
|
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diff
changeset
|
1284 } |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1285 catch (OrthancException& e) |
|
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diff
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|
1286 { |
|
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ZIP archives containing DICOM files can be uploaded using WebDAV
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1287 if (e.GetErrorCode() == ErrorCode_BadFileFormat) |
|
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diff
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|
1288 { |
|
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ZIP archives containing DICOM files can be uploaded using WebDAV
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1289 LOG(ERROR) << "Cannot import non-DICOM file from ZIP archive: " << filename; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1290 } |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1291 } |
|
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diff
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|
1292 } |
|
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diff
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|
1293 } |
|
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diff
changeset
|
1294 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1295 success = true; |
| 4240 | 1296 } |
|
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diff
changeset
|
1297 else |
| 4240 | 1298 { |
|
4508
8f9090b137f1
Optimization in C-STORE SCP by avoiding an unnecessary DICOM parsing
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1299 std::unique_ptr<DicomInstanceToStore> instance(DicomInstanceToStore::CreateFromBuffer(content)); |
|
8f9090b137f1
Optimization in C-STORE SCP by avoiding an unnecessary DICOM parsing
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1300 instance->SetOrigin(DicomInstanceOrigin::FromWebDav()); |
|
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diff
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|
1301 |
|
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diff
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|
1302 try |
|
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diff
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|
1303 { |
|
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diff
changeset
|
1304 std::string publicId; |
|
4796
94616af363ec
added ReceivedCStoreInstanceFilter lua callback + OrthancPluginRegisterIncomingCStoreInstanceFilter in sdk
Alain Mazy <am@osimis.io>
parents:
4697
diff
changeset
|
1305 ServerContext::StoreResult result = context_.Store(publicId, *instance, StoreInstanceMode_Default); |
|
94616af363ec
added ReceivedCStoreInstanceFilter lua callback + OrthancPluginRegisterIncomingCStoreInstanceFilter in sdk
Alain Mazy <am@osimis.io>
parents:
4697
diff
changeset
|
1306 if (result.GetStatus() == StoreStatus_Success || |
|
94616af363ec
added ReceivedCStoreInstanceFilter lua callback + OrthancPluginRegisterIncomingCStoreInstanceFilter in sdk
Alain Mazy <am@osimis.io>
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4697
diff
changeset
|
1307 result.GetStatus() == StoreStatus_AlreadyStored) |
|
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|
1308 { |
|
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|
1309 LOG(INFO) << "Successfully imported DICOM instance from WebDAV: " |
|
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|
1310 << path << " (Orthanc ID: " << publicId << ")"; |
|
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|
1311 success = true; |
|
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|
1312 } |
|
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|
1313 } |
|
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|
1314 catch (OrthancException& e) |
|
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|
1315 { |
|
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|
1316 } |
|
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|
1317 } |
|
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|
1318 |
|
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|
1319 uploads_.DeleteItem(uri); |
|
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|
1320 |
|
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|
1321 if (!success) |
|
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|
1322 { |
|
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|
1323 LOG(WARNING) << "Cannot import DICOM instance from WebWAV (maybe not a DICOM file): " << path; |
| 4240 | 1324 } |
| 1325 } | |
| 1326 } | |
| 1327 | |
| 1328 | |
|
4242
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deleting resources from Orthanc WebDAV
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diff
changeset
|
1329 OrthancWebDav::INode& OrthancWebDav::GetRootNode(const std::string& rootPath) |
|
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|
1330 { |
|
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|
1331 if (rootPath == BY_PATIENTS) |
|
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|
1332 { |
|
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diff
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|
1333 return *patients_; |
|
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|
1334 } |
|
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|
1335 else if (rootPath == BY_STUDIES) |
|
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|
1336 { |
|
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diff
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|
1337 return *studies_; |
|
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|
1338 } |
|
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|
1339 else if (rootPath == BY_DATES) |
|
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|
1340 { |
|
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|
1341 return *dates_; |
|
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|
1342 } |
|
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|
1343 else |
|
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diff
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|
1344 { |
|
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|
1345 throw OrthancException(ErrorCode_InternalError); |
|
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|
1346 } |
|
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|
1347 } |
|
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|
1348 |
|
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|
1349 |
|
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diff
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|
1350 OrthancWebDav::OrthancWebDav(ServerContext& context, |
|
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|
1351 bool allowDicomDelete, |
|
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|
1352 bool allowUpload) : |
| 4240 | 1353 context_(context), |
|
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|
1354 allowDicomDelete_(allowDicomDelete), |
|
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|
1355 allowUpload_(allowUpload), |
| 4240 | 1356 uploads_(false /* store uploads as temporary files */), |
|
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|
1357 uploadRunning_(false) |
| 4240 | 1358 { |
| 1359 patientsTemplates_[ResourceType_Patient] = "{{PatientID}} - {{PatientName}}"; | |
| 1360 patientsTemplates_[ResourceType_Study] = "{{StudyDate}} - {{StudyDescription}}"; | |
| 1361 patientsTemplates_[ResourceType_Series] = "{{Modality}} - {{SeriesDescription}}"; | |
| 1362 | |
| 1363 studiesTemplates_[ResourceType_Study] = "{{PatientID}} - {{PatientName}} - {{StudyDescription}}"; | |
| 1364 studiesTemplates_[ResourceType_Series] = patientsTemplates_[ResourceType_Series]; | |
| 1365 | |
| 1366 patients_.reset(new RootNode(context, ResourceType_Patient, patientsTemplates_)); | |
| 1367 studies_.reset(new RootNode(context, ResourceType_Study, studiesTemplates_)); | |
| 1368 dates_.reset(new ListOfStudiesByYear(context, studiesTemplates_)); | |
| 1369 } | |
| 1370 | |
| 1371 | |
| 1372 bool OrthancWebDav::IsExistingFolder(const UriComponents& path) | |
| 1373 { | |
| 1374 if (path.empty()) | |
| 1375 { | |
| 1376 return true; | |
| 1377 } | |
| 1378 else if (path[0] == BY_UIDS) | |
| 1379 { | |
| 1380 return (path.size() <= 3 && | |
|
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|
1381 (path.size() != 3 || path[2] != STUDY_INFO)); |
| 4240 | 1382 } |
|
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|
1383 else if (path[0] == BY_PATIENTS || |
|
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|
1384 path[0] == BY_STUDIES || |
|
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|
1385 path[0] == BY_DATES) |
| 4240 | 1386 { |
| 4252 | 1387 IWebDavBucket::Collection collection; |
| 1388 return GetRootNode(path[0]).ListCollection(collection, UriComponents(path.begin() + 1, path.end())); | |
| 4240 | 1389 } |
|
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|
1390 else if (allowUpload_ && |
|
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|
1391 path[0] == UPLOADS) |
| 4240 | 1392 { |
| 1393 return uploads_.IsExistingFolder(UriComponents(path.begin() + 1, path.end())); | |
| 1394 } | |
| 1395 else | |
| 1396 { | |
| 1397 return false; | |
| 1398 } | |
| 1399 } | |
| 1400 | |
| 1401 | |
| 1402 bool OrthancWebDav::ListCollection(Collection& collection, | |
| 1403 const UriComponents& path) | |
| 1404 { | |
| 1405 if (path.empty()) | |
| 1406 { | |
| 4241 | 1407 collection.AddResource(new Folder(BY_DATES)); |
| 4240 | 1408 collection.AddResource(new Folder(BY_PATIENTS)); |
| 1409 collection.AddResource(new Folder(BY_STUDIES)); | |
| 1410 collection.AddResource(new Folder(BY_UIDS)); | |
|
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|
1411 |
|
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|
1412 if (allowUpload_) |
|
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|
1413 { |
|
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|
1414 collection.AddResource(new Folder(UPLOADS)); |
|
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|
1415 } |
|
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|
1416 |
| 4240 | 1417 return true; |
| 1418 } | |
| 1419 else if (path[0] == BY_UIDS) | |
| 1420 { | |
| 1421 DatabaseLookup query; | |
| 1422 ResourceType level; | |
| 1423 size_t limit = 0; // By default, no limits | |
| 1424 | |
| 1425 if (path.size() == 1) | |
| 1426 { | |
| 1427 level = ResourceType_Study; | |
|
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|
1428 limit = 0; // TODO - Should we limit here? |
| 4240 | 1429 } |
| 1430 else if (path.size() == 2) | |
| 1431 { | |
|
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changeset
|
1432 AddVirtualFile(collection, path, STUDY_INFO); |
| 4240 | 1433 |
| 1434 level = ResourceType_Series; | |
| 1435 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], | |
| 1436 true /* case sensitive */, true /* mandatory tag */); | |
| 1437 } | |
| 1438 else if (path.size() == 3) | |
| 1439 { | |
|
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1440 AddVirtualFile(collection, path, SERIES_INFO); |
| 4240 | 1441 |
| 1442 level = ResourceType_Instance; | |
| 1443 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], | |
| 1444 true /* case sensitive */, true /* mandatory tag */); | |
| 1445 query.AddRestConstraint(DICOM_TAG_SERIES_INSTANCE_UID, path[2], | |
| 1446 true /* case sensitive */, true /* mandatory tag */); | |
| 1447 } | |
| 1448 else | |
| 1449 { | |
| 1450 return false; | |
| 1451 } | |
| 1452 | |
| 1453 DicomIdentifiersVisitor visitor(context_, collection, level); | |
| 1454 context_.Apply(visitor, query, level, 0 /* since */, limit); | |
| 1455 | |
| 1456 return true; | |
| 1457 } | |
|
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1458 else if (path[0] == BY_PATIENTS || |
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1459 path[0] == BY_STUDIES || |
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1460 path[0] == BY_DATES) |
| 4240 | 1461 { |
|
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1462 return GetRootNode(path[0]).ListCollection(collection, UriComponents(path.begin() + 1, path.end())); |
| 4240 | 1463 } |
|
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1464 else if (allowUpload_ && |
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1465 path[0] == UPLOADS) |
| 4240 | 1466 { |
| 1467 return uploads_.ListCollection(collection, UriComponents(path.begin() + 1, path.end())); | |
| 1468 } | |
| 1469 else | |
| 1470 { | |
| 1471 return false; | |
| 1472 } | |
| 1473 } | |
| 1474 | |
| 1475 | |
| 1476 bool OrthancWebDav::GetFileContent(MimeType& mime, | |
| 1477 std::string& content, | |
| 1478 boost::posix_time::ptime& modificationTime, | |
| 1479 const UriComponents& path) | |
| 1480 { | |
| 1481 if (path.empty()) | |
| 1482 { | |
| 1483 return false; | |
| 1484 } | |
| 1485 else if (path[0] == BY_UIDS) | |
| 1486 { | |
| 1487 if (path.size() == 3 && | |
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1488 path[2] == STUDY_INFO) |
| 4240 | 1489 { |
| 1490 DatabaseLookup query; | |
| 1491 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], | |
| 1492 true /* case sensitive */, true /* mandatory tag */); | |
| 1493 | |
| 1494 OrthancJsonVisitor visitor(context_, content, ResourceType_Study); | |
| 1495 context_.Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); | |
| 1496 | |
| 1497 mime = MimeType_Json; | |
| 1498 return visitor.IsSuccess(); | |
| 1499 } | |
| 1500 else if (path.size() == 4 && | |
|
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1501 path[3] == SERIES_INFO) |
| 4240 | 1502 { |
| 1503 DatabaseLookup query; | |
| 1504 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], | |
| 1505 true /* case sensitive */, true /* mandatory tag */); | |
| 1506 query.AddRestConstraint(DICOM_TAG_SERIES_INSTANCE_UID, path[2], | |
| 1507 true /* case sensitive */, true /* mandatory tag */); | |
| 1508 | |
| 1509 OrthancJsonVisitor visitor(context_, content, ResourceType_Series); | |
| 1510 context_.Apply(visitor, query, ResourceType_Series, 0 /* since */, 0 /* no limit */); | |
| 1511 | |
| 1512 mime = MimeType_Json; | |
| 1513 return visitor.IsSuccess(); | |
| 1514 } | |
| 1515 else if (path.size() == 4 && | |
| 1516 boost::ends_with(path[3], ".dcm")) | |
| 1517 { | |
|
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1518 const std::string sopInstanceUid = path[3].substr(0, path[3].size() - 4); |
| 4240 | 1519 |
| 1520 DatabaseLookup query; | |
| 1521 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], | |
| 1522 true /* case sensitive */, true /* mandatory tag */); | |
| 1523 query.AddRestConstraint(DICOM_TAG_SERIES_INSTANCE_UID, path[2], | |
| 1524 true /* case sensitive */, true /* mandatory tag */); | |
| 1525 query.AddRestConstraint(DICOM_TAG_SOP_INSTANCE_UID, sopInstanceUid, | |
| 1526 true /* case sensitive */, true /* mandatory tag */); | |
| 1527 | |
| 1528 DicomFileVisitor visitor(context_, content, modificationTime); | |
| 1529 context_.Apply(visitor, query, ResourceType_Instance, 0 /* since */, 0 /* no limit */); | |
| 1530 | |
| 1531 mime = MimeType_Dicom; | |
| 1532 return visitor.IsSuccess(); | |
| 1533 } | |
| 1534 else | |
| 1535 { | |
| 1536 return false; | |
| 1537 } | |
| 1538 } | |
|
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1539 else if (path[0] == BY_PATIENTS || |
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|
1540 path[0] == BY_STUDIES || |
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1541 path[0] == BY_DATES) |
| 4240 | 1542 { |
|
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|
1543 return GetRootNode(path[0]).GetFileContent(mime, content, modificationTime, UriComponents(path.begin() + 1, path.end())); |
| 4241 | 1544 } |
|
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1545 else if (allowUpload_ && |
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|
1546 path[0] == UPLOADS) |
| 4240 | 1547 { |
| 1548 return uploads_.GetFileContent(mime, content, modificationTime, UriComponents(path.begin() + 1, path.end())); | |
| 1549 } | |
| 1550 else | |
| 1551 { | |
| 1552 return false; | |
| 1553 } | |
| 1554 } | |
| 1555 | |
| 1556 | |
| 1557 bool OrthancWebDav::StoreFile(const std::string& content, | |
| 1558 const UriComponents& path) | |
| 1559 { | |
|
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1560 if (allowUpload_ && |
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|
1561 path.size() >= 1 && |
| 4240 | 1562 path[0] == UPLOADS) |
| 1563 { | |
| 1564 UriComponents subpath(UriComponents(path.begin() + 1, path.end())); | |
| 1565 | |
| 1566 if (uploads_.StoreFile(content, subpath)) | |
| 1567 { | |
| 1568 if (!content.empty()) | |
| 1569 { | |
| 1570 uploadQueue_.Enqueue(new SingleValueObject<std::string>(Toolbox::FlattenUri(subpath))); | |
| 1571 } | |
| 1572 return true; | |
| 1573 } | |
| 1574 else | |
| 1575 { | |
| 1576 return false; | |
| 1577 } | |
| 1578 } | |
| 1579 else | |
| 1580 { | |
| 1581 return false; | |
| 1582 } | |
| 1583 } | |
| 1584 | |
| 1585 | |
| 1586 bool OrthancWebDav::CreateFolder(const UriComponents& path) | |
| 1587 { | |
|
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1588 if (allowUpload_ && |
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|
1589 path.size() >= 1 && |
| 4240 | 1590 path[0] == UPLOADS) |
| 1591 { | |
| 1592 return uploads_.CreateFolder(UriComponents(path.begin() + 1, path.end())); | |
| 1593 } | |
| 1594 else | |
| 1595 { | |
| 1596 return false; | |
| 1597 } | |
| 1598 } | |
| 1599 | |
| 1600 | |
| 1601 bool OrthancWebDav::DeleteItem(const std::vector<std::string>& path) | |
| 1602 { | |
|
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1603 if (path.empty()) |
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|
1604 { |
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|
1605 return false; |
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|
1606 } |
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|
1607 else if (path[0] == BY_UIDS && |
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|
1608 path.size() >= 2 && |
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|
1609 path.size() <= 4) |
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|
1610 { |
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|
1611 if (allowDicomDelete_) |
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|
1612 { |
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|
1613 ResourceType level; |
|
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|
1614 DatabaseLookup query; |
|
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|
1615 |
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|
1616 query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], |
|
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|
1617 true /* case sensitive */, true /* mandatory tag */); |
|
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|
1618 level = ResourceType_Study; |
|
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|
1619 |
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|
1620 if (path.size() >= 3) |
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|
1621 { |
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|
1622 if (path[2] == STUDY_INFO) |
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|
1623 { |
| 4252 | 1624 return true; // Allow deletion of virtual files (to avoid blocking recursive DELETE) |
|
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|
1625 } |
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|
1626 |
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|
1627 query.AddRestConstraint(DICOM_TAG_SERIES_INSTANCE_UID, path[2], |
|
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|
1628 true /* case sensitive */, true /* mandatory tag */); |
|
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|
1629 level = ResourceType_Series; |
|
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|
1630 } |
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|
1631 |
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1632 if (path.size() == 4) |
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|
1633 { |
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|
1634 if (path[3] == SERIES_INFO) |
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|
1635 { |
| 4252 | 1636 return true; // Allow deletion of virtual files (to avoid blocking recursive DELETE) |
|
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1637 } |
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1638 else if (boost::ends_with(path[3], ".dcm")) |
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|
1639 { |
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|
1640 const std::string sopInstanceUid = path[3].substr(0, path[3].size() - 4); |
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1641 |
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|
1642 query.AddRestConstraint(DICOM_TAG_SOP_INSTANCE_UID, sopInstanceUid, |
|
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|
1643 true /* case sensitive */, true /* mandatory tag */); |
|
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|
1644 level = ResourceType_Instance; |
|
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1645 } |
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1646 else |
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|
1647 { |
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|
1648 return false; |
|
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|
1649 } |
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|
1650 } |
|
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|
1651 |
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|
1652 DicomDeleteVisitor visitor(context_, level); |
| 4252 | 1653 context_.Apply(visitor, query, level, 0 /* since */, 0 /* no limit */); |
|
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1654 return true; |
|
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|
1655 } |
|
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|
1656 else |
|
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|
1657 { |
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|
1658 return false; // read-only |
|
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|
1659 } |
|
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|
1660 } |
|
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|
1661 else if (path[0] == BY_PATIENTS || |
|
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|
1662 path[0] == BY_STUDIES || |
|
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1663 path[0] == BY_DATES) |
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1664 { |
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1665 if (allowDicomDelete_) |
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1666 { |
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1667 return GetRootNode(path[0]).DeleteItem(UriComponents(path.begin() + 1, path.end())); |
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1668 } |
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1669 else |
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1670 { |
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1671 return false; // read-only |
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1672 } |
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1673 } |
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1674 else if (allowUpload_ && |
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1675 path[0] == UPLOADS) |
| 4240 | 1676 { |
| 1677 return uploads_.DeleteItem(UriComponents(path.begin() + 1, path.end())); | |
| 1678 } | |
| 1679 else | |
| 1680 { | |
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1681 return false; |
| 4240 | 1682 } |
| 1683 } | |
| 1684 | |
| 1685 | |
| 1686 void OrthancWebDav::Start() | |
| 1687 { | |
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1688 if (uploadRunning_) |
| 4240 | 1689 { |
| 1690 throw OrthancException(ErrorCode_BadSequenceOfCalls); | |
| 1691 } | |
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1692 else if (allowUpload_) |
| 4240 | 1693 { |
| 1694 LOG(INFO) << "Starting the WebDAV upload thread"; | |
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1695 uploadRunning_ = true; |
| 4240 | 1696 uploadThread_ = boost::thread(UploadWorker, this); |
| 1697 } | |
| 1698 } | |
| 1699 | |
| 1700 | |
| 1701 void OrthancWebDav::Stop() | |
| 1702 { | |
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1703 if (uploadRunning_) |
| 4240 | 1704 { |
| 1705 LOG(INFO) << "Stopping the WebDAV upload thread"; | |
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1706 uploadRunning_ = false; |
| 4240 | 1707 if (uploadThread_.joinable()) |
| 1708 { | |
| 1709 uploadThread_.join(); | |
| 1710 } | |
| 1711 } | |
| 1712 } | |
| 1713 } |