Mercurial > hg > orthanc
view OrthancServer/OrthancRestApi/OrthancRestArchive.cpp @ 2544:d5ca5a5abe12
merge
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 17 Apr 2018 20:42:07 +0200 |
parents | 878b59270859 |
children | 00b6a7f935fc |
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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) 2017-2018 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 "OrthancRestApi.h" #include "../../Core/DicomParsing/DicomDirWriter.h" #include "../../Core/FileStorage/StorageAccessor.h" #include "../../Core/Compression/HierarchicalZipWriter.h" #include "../../Core/HttpServer/FilesystemHttpSender.h" #include "../../Core/Logging.h" #include "../../Core/TemporaryFile.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; namespace Orthanc { // Download of ZIP files ---------------------------------------------------- static bool IsZip64Required(uint64_t uncompressedSize, unsigned int countInstances) { static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; /** * 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); LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " << (uncompressedSize / MEGA_BYTES) << "MB using the " << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; return isZip64; } namespace { class ResourceIdentifiers { 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 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 ArchiveIndex { 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::auto_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::auto_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 StatisticsVisitor : public IArchiveVisitor { private: uint64_t size_; unsigned int instances_; public: StatisticsVisitor() : size_(0), instances_(0) { } uint64_t GetUncompressedSize() const { return size_; } unsigned int GetInstancesCount() const { return instances_; } virtual void Open(ResourceType level, const std::string& publicId) { } virtual void Close() { } virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) { instances_ ++; size_ += dicom.GetUncompressedSize(); } }; class PrintVisitor : public IArchiveVisitor { private: std::ostream& out_; std::string indent_; public: PrintVisitor(std::ostream& out) : out_(out) { } virtual void Open(ResourceType level, const std::string& publicId) { switch (level) { case ResourceType_Patient: indent_ = ""; break; case ResourceType_Study: indent_ = " "; break; case ResourceType_Series: indent_ = " "; break; default: throw OrthancException(ErrorCode_InternalError); } out_ << indent_ << publicId << std::endl; } virtual void Close() { } virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) { out_ << " " << instanceId << std::endl; } }; class ArchiveWriterVisitor : public IArchiveVisitor { private: HierarchicalZipWriter& writer_; ServerContext& context_; char instanceFormat_[24]; unsigned int countInstances_; 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: ArchiveWriterVisitor(HierarchicalZipWriter& writer, ServerContext& context) : writer_(writer), context_(context), countInstances_(0) { 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])); } countInstances_ = 0; break; } default: throw OrthancException(ErrorCode_InternalError); } } path = Toolbox::StripSpaces(Toolbox::ConvertToAscii(path)); if (path.empty()) { path = std::string("Unknown ") + EnumerationToString(level); } writer_.OpenDirectory(path.c_str()); } virtual void Close() { writer_.CloseDirectory(); } virtual void AddInstance(const std::string& instanceId, const FileInfo& dicom) { std::string content; context_.ReadAttachment(content, dicom); char filename[24]; snprintf(filename, sizeof(filename) - 1, instanceFormat_, countInstances_); countInstances_ ++; writer_.OpenFile(filename); writer_.Write(content); } static void Apply(RestApiOutput& output, ServerContext& context, ArchiveIndex& archive, const std::string& filename) { archive.Expand(context.GetIndex()); StatisticsVisitor stats; archive.Apply(stats); const bool isZip64 = IsZip64Required(stats.GetUncompressedSize(), stats.GetInstancesCount()); // Create a RAII for the temporary file to manage the ZIP file TemporaryFile tmp; { // Create a ZIP writer HierarchicalZipWriter writer(tmp.GetPath().c_str()); writer.SetZip64(isZip64); ArchiveWriterVisitor v(writer, context); archive.Apply(v); } // Prepare the sending of the ZIP file FilesystemHttpSender sender(tmp.GetPath()); sender.SetContentType("application/zip"); sender.SetContentFilename(filename); // Send the ZIP output.AnswerStream(sender); // The temporary file is automatically removed thanks to the RAII } }; class MediaWriterVisitor : public IArchiveVisitor { private: HierarchicalZipWriter& writer_; DicomDirWriter dicomDir_; ServerContext& context_; unsigned int countInstances_; public: MediaWriterVisitor(HierarchicalZipWriter& writer, ServerContext& context) : writer_(writer), context_(context), countInstances_(0) { } void EncodeDicomDir(std::string& result) { dicomDir_.Encode(result); } 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>(countInstances_); writer_.OpenFile(filename.c_str()); std::string content; context_.ReadAttachment(content, dicom); writer_.Write(content); ParsedDicomFile parsed(content); dicomDir_.Add("IMAGES", filename, parsed); countInstances_ ++; } static void Apply(RestApiOutput& output, ServerContext& context, ArchiveIndex& archive, const std::string& filename, bool enableExtendedSopClass) { archive.Expand(context.GetIndex()); StatisticsVisitor stats; archive.Apply(stats); const bool isZip64 = IsZip64Required(stats.GetUncompressedSize(), stats.GetInstancesCount()); // Create a RAII for the temporary file to manage the ZIP file TemporaryFile tmp; { // Create a ZIP writer HierarchicalZipWriter writer(tmp.GetPath().c_str()); writer.SetZip64(isZip64); writer.OpenDirectory("IMAGES"); // Create a DICOMDIR writer MediaWriterVisitor v(writer, context); // Request type-3 arguments to be added to the DICOMDIR v.dicomDir_.EnableExtendedSopClass(enableExtendedSopClass); archive.Apply(v); // Add the DICOMDIR writer.CloseDirectory(); writer.OpenFile("DICOMDIR"); std::string s; v.EncodeDicomDir(s); writer.Write(s); } // Prepare the sending of the ZIP file FilesystemHttpSender sender(tmp.GetPath()); sender.SetContentType("application/zip"); sender.SetContentFilename(filename); // Send the ZIP output.AnswerStream(sender); // The temporary file is automatically removed thanks to the RAII } }; } static bool AddResourcesOfInterest(ArchiveIndex& archive, RestApiPostCall& call) { ServerIndex& index = OrthancRestApi::GetIndex(call); Json::Value resources; if (call.ParseJsonRequest(resources) && resources.type() == Json::arrayValue) { for (Json::Value::ArrayIndex i = 0; i < resources.size(); i++) { if (resources[i].type() != Json::stringValue) { return false; // Bad request } ResourceIdentifiers resource(index, resources[i].asString()); archive.Add(index, resource); } return true; } else { return false; } } static void CreateBatchArchive(RestApiPostCall& call) { ArchiveIndex archive(ResourceType_Patient); // root if (AddResourcesOfInterest(archive, call)) { ArchiveWriterVisitor::Apply(call.GetOutput(), OrthancRestApi::GetContext(call), archive, "Archive.zip"); } } template <bool Extended> static void CreateBatchMedia(RestApiPostCall& call) { ArchiveIndex archive(ResourceType_Patient); // root if (AddResourcesOfInterest(archive, call)) { MediaWriterVisitor::Apply(call.GetOutput(), OrthancRestApi::GetContext(call), archive, "Archive.zip", Extended); } } static void CreateArchive(RestApiGetCall& call) { ServerIndex& index = OrthancRestApi::GetIndex(call); std::string id = call.GetUriComponent("id", ""); ResourceIdentifiers resource(index, id); ArchiveIndex archive(ResourceType_Patient); // root archive.Add(OrthancRestApi::GetIndex(call), resource); ArchiveWriterVisitor::Apply(call.GetOutput(), OrthancRestApi::GetContext(call), archive, id + ".zip"); } static void CreateMedia(RestApiGetCall& call) { ServerIndex& index = OrthancRestApi::GetIndex(call); std::string id = call.GetUriComponent("id", ""); ResourceIdentifiers resource(index, id); ArchiveIndex archive(ResourceType_Patient); // root archive.Add(OrthancRestApi::GetIndex(call), resource); MediaWriterVisitor::Apply(call.GetOutput(), OrthancRestApi::GetContext(call), archive, id + ".zip", call.HasArgument("extended")); } void OrthancRestApi::RegisterArchive() { Register("/patients/{id}/archive", CreateArchive); Register("/studies/{id}/archive", CreateArchive); Register("/series/{id}/archive", CreateArchive); Register("/patients/{id}/media", CreateMedia); Register("/studies/{id}/media", CreateMedia); Register("/series/{id}/media", CreateMedia); Register("/tools/create-archive", CreateBatchArchive); Register("/tools/create-media", CreateBatchMedia<false>); Register("/tools/create-media-extended", CreateBatchMedia<true>); } }