Mercurial > hg > orthanc
view OrthancServer/ServerJobs/ArchiveJob.cpp @ 3716:ae0e3fd609df
sample for "Manufacturer" option in "DicomModalities" config
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 04 Mar 2020 10:00:42 +0100 |
parents | 2a170a8f1faf |
children | 56f2397f027a |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2020 Osimis S.A., Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "../PrecompiledHeadersServer.h" #include "ArchiveJob.h" #include "../../Core/Cache/SharedArchive.h" #include "../../Core/Compression/HierarchicalZipWriter.h" #include "../../Core/DicomParsing/DicomDirWriter.h" #include "../../Core/Logging.h" #include "../../Core/OrthancException.h" #include "../OrthancConfiguration.h" #include "../ServerContext.h" #include <stdio.h> #if defined(_MSC_VER) #define snprintf _snprintf #endif static const uint64_t MEGA_BYTES = 1024 * 1024; static const uint64_t GIGA_BYTES = 1024 * 1024 * 1024; static const char* const MEDIA_IMAGES_FOLDER = "IMAGES"; static const char* const KEY_DESCRIPTION = "Description"; static const char* const KEY_INSTANCES_COUNT = "InstancesCount"; static const char* const KEY_UNCOMPRESSED_SIZE_MB = "UncompressedSizeMB"; namespace Orthanc { static bool IsZip64Required(uint64_t uncompressedSize, unsigned int countInstances) { static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; // Should be large enough to hold DICOMDIR static const unsigned int FILES_MARGIN = 10; /** * Determine whether ZIP64 is required. Original ZIP format can * store up to 2GB of data (some implementation supporting up to * 4GB of data), and up to 65535 files. * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64 **/ const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES - SAFETY_MARGIN || countInstances >= 65535 - FILES_MARGIN); LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " << (uncompressedSize / MEGA_BYTES) << "MB using the " << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; return isZip64; } class ArchiveJob::ResourceIdentifiers : public boost::noncopyable { private: ResourceType level_; std::string patient_; std::string study_; std::string series_; std::string instance_; static void GoToParent(ServerIndex& index, std::string& current) { std::string tmp; if (index.LookupParent(tmp, current)) { current = tmp; } else { throw OrthancException(ErrorCode_UnknownResource); } } public: ResourceIdentifiers(ServerIndex& index, const std::string& publicId) { if (!index.LookupResourceType(level_, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } std::string current = publicId;; switch (level_) // Do not add "break" below! { case ResourceType_Instance: instance_ = current; GoToParent(index, current); case ResourceType_Series: series_ = current; GoToParent(index, current); case ResourceType_Study: study_ = current; GoToParent(index, current); case ResourceType_Patient: patient_ = current; break; default: throw OrthancException(ErrorCode_InternalError); } } ResourceType GetLevel() const { return level_; } const std::string& GetIdentifier(ResourceType level) const { // Some sanity check to ensure enumerations are not altered assert(ResourceType_Patient < ResourceType_Study); assert(ResourceType_Study < ResourceType_Series); assert(ResourceType_Series < ResourceType_Instance); if (level > level_) { throw OrthancException(ErrorCode_InternalError); } switch (level) { case ResourceType_Patient: return patient_; case ResourceType_Study: return study_; case ResourceType_Series: return series_; case ResourceType_Instance: return instance_; default: throw OrthancException(ErrorCode_InternalError); } } }; class ArchiveJob::IArchiveVisitor : public boost::noncopyable { public: virtual ~IArchiveVisitor() { } virtual void Open(ResourceType level, const std::string& publicId) = 0; virtual void Close() = 0; virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) = 0; }; class ArchiveJob::ArchiveIndex : public boost::noncopyable { private: struct Instance { std::string id_; FileInfo dicom_; Instance(const std::string& id, const FileInfo& dicom) : id_(id), dicom_(dicom) { } }; // A "NULL" value for ArchiveIndex indicates a non-expanded node typedef std::map<std::string, ArchiveIndex*> Resources; ResourceType level_; Resources resources_; // Only at patient/study/series level std::list<Instance> instances_; // Only at instance level void AddResourceToExpand(ServerIndex& index, const std::string& id) { if (level_ == ResourceType_Instance) { FileInfo tmp; if (index.LookupAttachment(tmp, id, FileContentType_Dicom)) { instances_.push_back(Instance(id, tmp)); } } else { resources_[id] = NULL; } } public: ArchiveIndex(ResourceType level) : level_(level) { } ~ArchiveIndex() { for (Resources::iterator it = resources_.begin(); it != resources_.end(); ++it) { delete it->second; } } void Add(ServerIndex& index, const ResourceIdentifiers& resource) { const std::string& id = resource.GetIdentifier(level_); Resources::iterator previous = resources_.find(id); if (level_ == ResourceType_Instance) { AddResourceToExpand(index, id); } else if (resource.GetLevel() == level_) { // Mark this resource for further expansion if (previous != resources_.end()) { delete previous->second; } resources_[id] = NULL; } else if (previous == resources_.end()) { // This is the first time we meet this resource std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); child->Add(index, resource); resources_[id] = child.release(); } else if (previous->second != NULL) { previous->second->Add(index, resource); } else { // Nothing to do: This item is marked for further expansion } } void Expand(ServerIndex& index) { if (level_ == ResourceType_Instance) { // Expanding an instance node makes no sense return; } for (Resources::iterator it = resources_.begin(); it != resources_.end(); ++it) { if (it->second == NULL) { // This is resource is marked for expansion std::list<std::string> children; index.GetChildren(children, it->first); std::unique_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); for (std::list<std::string>::const_iterator it2 = children.begin(); it2 != children.end(); ++it2) { child->AddResourceToExpand(index, *it2); } it->second = child.release(); } assert(it->second != NULL); it->second->Expand(index); } } void Apply(IArchiveVisitor& visitor) const { if (level_ == ResourceType_Instance) { for (std::list<Instance>::const_iterator it = instances_.begin(); it != instances_.end(); ++it) { visitor.AddInstance(it->id_, it->dicom_); } } else { for (Resources::const_iterator it = resources_.begin(); it != resources_.end(); ++it) { assert(it->second != NULL); // There must have been a call to "Expand()" visitor.Open(level_, it->first); it->second->Apply(visitor); visitor.Close(); } } } }; class ArchiveJob::ZipCommands : public boost::noncopyable { private: enum Type { Type_OpenDirectory, Type_CloseDirectory, Type_WriteInstance }; class Command : public boost::noncopyable { private: Type type_; std::string filename_; std::string instanceId_; FileInfo info_; public: explicit Command(Type type) : type_(type) { assert(type_ == Type_CloseDirectory); } Command(Type type, const std::string& filename) : type_(type), filename_(filename) { assert(type_ == Type_OpenDirectory); } Command(Type type, const std::string& filename, const std::string& instanceId, const FileInfo& info) : type_(type), filename_(filename), instanceId_(instanceId), info_(info) { assert(type_ == Type_WriteInstance); } void Apply(HierarchicalZipWriter& writer, ServerContext& context, DicomDirWriter* dicomDir, const std::string& dicomDirFolder) const { switch (type_) { case Type_OpenDirectory: writer.OpenDirectory(filename_.c_str()); break; case Type_CloseDirectory: writer.CloseDirectory(); break; case Type_WriteInstance: { std::string content; try { context.ReadAttachment(content, info_); } catch (OrthancException& e) { LOG(WARNING) << "An instance was removed after the job was issued: " << instanceId_; return; } //boost::this_thread::sleep(boost::posix_time::milliseconds(300)); writer.OpenFile(filename_.c_str()); writer.Write(content); if (dicomDir != NULL) { ParsedDicomFile parsed(content); dicomDir->Add(dicomDirFolder, filename_, parsed); } break; } default: throw OrthancException(ErrorCode_InternalError); } } }; std::deque<Command*> commands_; uint64_t uncompressedSize_; unsigned int instancesCount_; void ApplyInternal(HierarchicalZipWriter& writer, ServerContext& context, size_t index, DicomDirWriter* dicomDir, const std::string& dicomDirFolder) const { if (index >= commands_.size()) { throw OrthancException(ErrorCode_ParameterOutOfRange); } commands_[index]->Apply(writer, context, dicomDir, dicomDirFolder); } public: ZipCommands() : uncompressedSize_(0), instancesCount_(0) { } ~ZipCommands() { for (std::deque<Command*>::iterator it = commands_.begin(); it != commands_.end(); ++it) { assert(*it != NULL); delete *it; } } size_t GetSize() const { return commands_.size(); } unsigned int GetInstancesCount() const { return instancesCount_; } uint64_t GetUncompressedSize() const { return uncompressedSize_; } void Apply(HierarchicalZipWriter& writer, ServerContext& context, size_t index, DicomDirWriter& dicomDir, const std::string& dicomDirFolder) const { ApplyInternal(writer, context, index, &dicomDir, dicomDirFolder); } void Apply(HierarchicalZipWriter& writer, ServerContext& context, size_t index) const { ApplyInternal(writer, context, index, NULL, ""); } void AddOpenDirectory(const std::string& filename) { commands_.push_back(new Command(Type_OpenDirectory, filename)); } void AddCloseDirectory() { commands_.push_back(new Command(Type_CloseDirectory)); } void AddWriteInstance(const std::string& filename, const std::string& instanceId, const FileInfo& info) { commands_.push_back(new Command(Type_WriteInstance, filename, instanceId, info)); instancesCount_ ++; uncompressedSize_ += info.GetUncompressedSize(); } bool IsZip64() const { return IsZip64Required(GetUncompressedSize(), GetInstancesCount()); } }; class ArchiveJob::ArchiveIndexVisitor : public IArchiveVisitor { private: ZipCommands& commands_; ServerContext& context_; char instanceFormat_[24]; unsigned int counter_; static std::string GetTag(const DicomMap& tags, const DicomTag& tag) { const DicomValue* v = tags.TestAndGetValue(tag); if (v != NULL && !v->IsBinary() && !v->IsNull()) { return v->GetContent(); } else { return ""; } } public: ArchiveIndexVisitor(ZipCommands& commands, ServerContext& context) : commands_(commands), context_(context), counter_(0) { if (commands.GetSize() != 0) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); } virtual void Open(ResourceType level, const std::string& publicId) { std::string path; DicomMap tags; if (context_.GetIndex().GetMainDicomTags(tags, publicId, level, level)) { switch (level) { case ResourceType_Patient: path = GetTag(tags, DICOM_TAG_PATIENT_ID) + " " + GetTag(tags, DICOM_TAG_PATIENT_NAME); break; case ResourceType_Study: path = GetTag(tags, DICOM_TAG_ACCESSION_NUMBER) + " " + GetTag(tags, DICOM_TAG_STUDY_DESCRIPTION); break; case ResourceType_Series: { std::string modality = GetTag(tags, DICOM_TAG_MODALITY); path = modality + " " + GetTag(tags, DICOM_TAG_SERIES_DESCRIPTION); if (modality.size() == 0) { snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); } else if (modality.size() == 1) { snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%%07d.dcm", toupper(modality[0])); } else if (modality.size() >= 2) { snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%c%%06d.dcm", toupper(modality[0]), toupper(modality[1])); } counter_ = 0; break; } default: throw OrthancException(ErrorCode_InternalError); } } path = Toolbox::StripSpaces(Toolbox::ConvertToAscii(path)); if (path.empty()) { path = std::string("Unknown ") + EnumerationToString(level); } commands_.AddOpenDirectory(path.c_str()); } virtual void Close() { commands_.AddCloseDirectory(); } virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) { char filename[24]; snprintf(filename, sizeof(filename) - 1, instanceFormat_, counter_); counter_ ++; commands_.AddWriteInstance(filename, instanceId, dicom); } }; class ArchiveJob::MediaIndexVisitor : public IArchiveVisitor { private: ZipCommands& commands_; ServerContext& context_; unsigned int counter_; public: MediaIndexVisitor(ZipCommands& commands, ServerContext& context) : commands_(commands), context_(context), counter_(0) { } virtual void Open(ResourceType level, const std::string& publicId) { } virtual void Close() { } virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) { // "DICOM restricts the filenames on DICOM media to 8 // characters (some systems wrongly use 8.3, but this does not // conform to the standard)." std::string filename = "IM" + boost::lexical_cast<std::string>(counter_); commands_.AddWriteInstance(filename, instanceId, dicom); counter_ ++; } }; class ArchiveJob::ZipWriterIterator : public boost::noncopyable { private: TemporaryFile& target_; ServerContext& context_; ZipCommands commands_; std::unique_ptr<HierarchicalZipWriter> zip_; std::unique_ptr<DicomDirWriter> dicomDir_; bool isMedia_; public: ZipWriterIterator(TemporaryFile& target, ServerContext& context, ArchiveIndex& archive, bool isMedia, bool enableExtendedSopClass) : target_(target), context_(context), isMedia_(isMedia) { if (isMedia) { MediaIndexVisitor visitor(commands_, context); archive.Expand(context.GetIndex()); commands_.AddOpenDirectory(MEDIA_IMAGES_FOLDER); archive.Apply(visitor); commands_.AddCloseDirectory(); dicomDir_.reset(new DicomDirWriter); dicomDir_->EnableExtendedSopClass(enableExtendedSopClass); } else { ArchiveIndexVisitor visitor(commands_, context); archive.Expand(context.GetIndex()); archive.Apply(visitor); } zip_.reset(new HierarchicalZipWriter(target.GetPath().c_str())); zip_->SetZip64(commands_.IsZip64()); } size_t GetStepsCount() const { return commands_.GetSize() + 1; } void RunStep(size_t index) { if (index > commands_.GetSize()) { throw OrthancException(ErrorCode_ParameterOutOfRange); } else if (index == commands_.GetSize()) { // Last step: Add the DICOMDIR if (isMedia_) { assert(dicomDir_.get() != NULL); std::string s; dicomDir_->Encode(s); zip_->OpenFile("DICOMDIR"); zip_->Write(s); } } else { if (isMedia_) { assert(dicomDir_.get() != NULL); commands_.Apply(*zip_, context_, index, *dicomDir_, MEDIA_IMAGES_FOLDER); } else { assert(dicomDir_.get() == NULL); commands_.Apply(*zip_, context_, index); } } } unsigned int GetInstancesCount() const { return commands_.GetInstancesCount(); } uint64_t GetUncompressedSize() const { return commands_.GetUncompressedSize(); } }; ArchiveJob::ArchiveJob(ServerContext& context, bool isMedia, bool enableExtendedSopClass) : context_(context), archive_(new ArchiveIndex(ResourceType_Patient)), // root isMedia_(isMedia), enableExtendedSopClass_(enableExtendedSopClass), currentStep_(0), instancesCount_(0), uncompressedSize_(0) { } ArchiveJob::~ArchiveJob() { if (!mediaArchiveId_.empty()) { context_.GetMediaArchive().Remove(mediaArchiveId_); } } void ArchiveJob::SetSynchronousTarget(boost::shared_ptr<TemporaryFile>& target) { if (target.get() == NULL) { throw OrthancException(ErrorCode_NullPointer); } else if (writer_.get() != NULL || // Already started synchronousTarget_.get() != NULL || asynchronousTarget_.get() != NULL) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { synchronousTarget_ = target; } } void ArchiveJob::SetDescription(const std::string& description) { if (writer_.get() != NULL) // Already started { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { description_ = description; } } void ArchiveJob::AddResource(const std::string& publicId) { if (writer_.get() != NULL) // Already started { throw OrthancException(ErrorCode_BadSequenceOfCalls); } else { ResourceIdentifiers resource(context_.GetIndex(), publicId); archive_->Add(context_.GetIndex(), resource); } } void ArchiveJob::Reset() { throw OrthancException(ErrorCode_BadSequenceOfCalls, "Cannot resubmit the creation of an archive"); } void ArchiveJob::Start() { TemporaryFile* target = NULL; if (synchronousTarget_.get() == NULL) { { OrthancConfiguration::ReaderLock lock; asynchronousTarget_.reset(lock.GetConfiguration().CreateTemporaryFile()); } target = asynchronousTarget_.get(); } else { target = synchronousTarget_.get(); } assert(target != NULL); target->Touch(); // Make sure we can write to the temporary file if (writer_.get() != NULL) { throw OrthancException(ErrorCode_BadSequenceOfCalls); } writer_.reset(new ZipWriterIterator(*target, context_, *archive_, isMedia_, enableExtendedSopClass_)); instancesCount_ = writer_->GetInstancesCount(); uncompressedSize_ = writer_->GetUncompressedSize(); } namespace { class DynamicTemporaryFile : public IDynamicObject { private: std::unique_ptr<TemporaryFile> file_; public: DynamicTemporaryFile(TemporaryFile* f) : file_(f) { if (f == NULL) { throw OrthancException(ErrorCode_NullPointer); } } const TemporaryFile& GetFile() const { assert(file_.get() != NULL); return *file_; } }; } void ArchiveJob::FinalizeTarget() { writer_.reset(); // Flush all the results if (asynchronousTarget_.get() != NULL) { // Asynchronous behavior: Move the resulting file into the media archive mediaArchiveId_ = context_.GetMediaArchive().Add( new DynamicTemporaryFile(asynchronousTarget_.release())); } } JobStepResult ArchiveJob::Step() { assert(writer_.get() != NULL); if (synchronousTarget_.get() != NULL && synchronousTarget_.unique()) { LOG(WARNING) << "A client has disconnected while creating an archive"; return JobStepResult::Failure(ErrorCode_NetworkProtocol, "A client has disconnected while creating an archive"); } if (writer_->GetStepsCount() == 0) { FinalizeTarget(); return JobStepResult::Success(); } else { writer_->RunStep(currentStep_); currentStep_ ++; if (currentStep_ == writer_->GetStepsCount()) { FinalizeTarget(); return JobStepResult::Success(); } else { return JobStepResult::Continue(); } } } float ArchiveJob::GetProgress() { if (writer_.get() == NULL || writer_->GetStepsCount() == 0) { return 1; } else { return (static_cast<float>(currentStep_) / static_cast<float>(writer_->GetStepsCount() - 1)); } } void ArchiveJob::GetJobType(std::string& target) { if (isMedia_) { target = "Media"; } else { target = "Archive"; } } void ArchiveJob::GetPublicContent(Json::Value& value) { value = Json::objectValue; value[KEY_DESCRIPTION] = description_; value[KEY_INSTANCES_COUNT] = instancesCount_; value[KEY_UNCOMPRESSED_SIZE_MB] = static_cast<unsigned int>(uncompressedSize_ / MEGA_BYTES); } bool ArchiveJob::GetOutput(std::string& output, MimeType& mime, const std::string& key) { if (key == "archive" && !mediaArchiveId_.empty()) { SharedArchive::Accessor accessor(context_.GetMediaArchive(), mediaArchiveId_); if (accessor.IsValid()) { const DynamicTemporaryFile& f = dynamic_cast<DynamicTemporaryFile&>(accessor.GetItem()); f.GetFile().Read(output); mime = MimeType_Zip; return true; } else { return false; } } else { return false; } } }