Mercurial > hg > orthanc-dicomweb
view Plugin/WadoRs.cpp @ 247:09dcb4cd574f
starting the refactoring to use improved Orthanc SDK
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 26 Feb 2019 12:56:05 +0100 |
parents | d73e463dd5bc |
children | 8bcb07e58817 |
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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) 2017-2019 Osimis S.A., Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Affero General Public License * as published by the Free Software Foundation, either version 3 of * the License, or (at your option) any later version. * * 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 * Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "Plugin.h" #include "Configuration.h" #include "Dicom.h" #include "DicomResults.h" #include <Core/Toolbox.h> #include <memory> static std::string GetResourceUri(Orthanc::ResourceType level, const std::string& publicId) { switch (level) { case Orthanc::ResourceType_Study: return "/studies/" + publicId; case Orthanc::ResourceType_Series: return "/series/" + publicId; case Orthanc::ResourceType_Instance: return "/instances/" + publicId; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } static bool AcceptMultipartDicom(const OrthancPluginHttpRequest* request) { std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { return true; // By default, return "multipart/related; type=application/dicom;" } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application != "multipart/related" && application != "*/*") { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin cannot generate the following content type: " + accept); } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s != "application/dicom") { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin only supports application/dicom " "return type for DICOM retrieval (" + accept + ")"); } } if (attributes.find("transfer-syntax") != attributes.end()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin cannot change the transfer syntax to " + attributes["transfer-syntax"]); } return true; } static bool AcceptMetadata(const OrthancPluginHttpRequest* request, bool& isXml) { isXml = false; // By default, return application/dicom+json std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { return true; } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application == "application/json" || application == "application/dicom+json" || application == "*/*") { return true; } if (application != "multipart/related") { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin cannot generate the following content type: " + accept); } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s == "application/dicom+xml") { isXml = true; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin only supports application/dicom+xml " "type for multipart/related accept (" + accept + ")"); } } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Missing \"type\" in multipart/related accept type (" + accept + ")"); } if (attributes.find("transfer-syntax") != attributes.end()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin cannot change the transfer syntax to " + attributes["transfer-syntax"]); } return true; } static bool AcceptBulkData(const OrthancPluginHttpRequest* request) { std::string accept; if (!OrthancPlugins::LookupHttpHeader(accept, request, "accept")) { return true; // By default, return "multipart/related; type=application/octet-stream;" } std::string application; std::map<std::string, std::string> attributes; OrthancPlugins::ParseContentType(application, attributes, accept); if (application != "multipart/related" && application != "*/*") { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin cannot generate the following " "bulk data type: " + accept); } if (attributes.find("type") != attributes.end()) { std::string s = attributes["type"]; Orthanc::Toolbox::ToLowerCase(s); if (s != "application/octet-stream") { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin only supports application/octet-stream " "return type for bulk data retrieval (" + accept + ")"); } } if (attributes.find("ra,ge") != attributes.end()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "This WADO-RS plugin does not support Range retrieval, " "it can only return entire bulk data object"); } return true; } static void AnswerListOfDicomInstances(OrthancPluginRestOutput* output, Orthanc::ResourceType level, const std::string& publicId) { if (level != Orthanc::ResourceType_Study && level != Orthanc::ResourceType_Series) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); Json::Value instances; if (!OrthancPlugins::RestApiGet(instances, GetResourceUri(level, publicId) + "/instances", false)) { // Internal error OrthancPluginSendHttpStatusCode(context, output, 400); return; } if (OrthancPluginStartMultipartAnswer(context, output, "related", "application/dicom")) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) { std::string uri = "/instances/" + instances[i]["ID"].asString() + "/file"; OrthancPlugins::MemoryBuffer dicom; if (dicom.RestApiGet(uri, false) && OrthancPluginSendMultipartItem(context, output, dicom.GetData(), dicom.GetSize()) != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } } #if 0 #include <boost/thread/mutex.hpp> class DicomWebFormatter : public boost::noncopyable { private: boost::mutex mutex_; std::string wadoBase_; static DicomWebFormatter& GetSingleton() { static DicomWebFormatter formatter; return formatter; } static std::string FormatTag(uint16_t group, uint16_t element) { char buf[16]; sprintf(buf, "%04x%04x", group, element); return std::string(buf); } static void Callback(OrthancPluginDicomWebNode *node, OrthancPluginDicomWebSetBinaryNode setter, uint32_t levelDepth, const uint16_t *levelTagGroup, const uint16_t *levelTagElement, const uint32_t *levelIndex, uint16_t tagGroup, uint16_t tagElement, OrthancPluginValueRepresentation vr) { std::string uri = GetSingleton().wadoBase_; for (size_t i = 0; i < levelDepth; i++) { uri += ("/" + FormatTag(levelTagGroup[i], levelTagElement[i]) + "/" + boost::lexical_cast<std::string>(levelIndex[i])); } uri += "/" + FormatTag(tagGroup, tagElement); setter(node, OrthancPluginDicomWebBinaryMode_BulkDataUri, uri.c_str()); } public: class Locker : public boost::noncopyable { private: DicomWebFormatter& that_; boost::mutex::scoped_lock lock_; public: Locker(const std::string& wadoBase) : that_(GetSingleton()), lock_(that_.mutex_) { that_.wadoBase_ = wadoBase; } void Apply(std::string& target, OrthancPluginContext* context, const void* data, size_t size, bool xml) { OrthancPlugins::OrthancString s; if (xml) { s.Assign(OrthancPluginEncodeDicomWebXml(context, data, size, Callback)); } else { s.Assign(OrthancPluginEncodeDicomWebJson(context, data, size, Callback)); } s.ToString(target); } }; }; static bool GetDicomIdentifiers(std::string& studyInstanceUid, std::string& seriesInstanceUid, std::string& sopInstanceUid, const std::string& orthancId) { // TODO - Any way of speeding this up? static const char* const STUDY_INSTANCE_UID = "0020,000d"; static const char* const SERIES_INSTANCE_UID = "0020,000e"; static const char* const SOP_INSTANCE_UID = "0008,0018"; Json::Value dicom; if (OrthancPlugins::RestApiGet(dicom, "/instances/" + orthancId + "/tags", false) && dicom.isMember(STUDY_INSTANCE_UID) && dicom.isMember(SERIES_INSTANCE_UID) && dicom.isMember(SOP_INSTANCE_UID) && dicom[STUDY_INSTANCE_UID].type() == Json::objectValue && dicom[SERIES_INSTANCE_UID].type() == Json::objectValue && dicom[SOP_INSTANCE_UID].type() == Json::objectValue && dicom[STUDY_INSTANCE_UID].isMember("Value") && dicom[SERIES_INSTANCE_UID].isMember("Value") && dicom[SOP_INSTANCE_UID].isMember("Value") && dicom[STUDY_INSTANCE_UID]["Value"].isString() && dicom[SERIES_INSTANCE_UID]["Value"].isString() && dicom[SOP_INSTANCE_UID]["Value"].isString()) { studyInstanceUid = dicom[STUDY_INSTANCE_UID]["Value"].asString(); seriesInstanceUid = dicom[SERIES_INSTANCE_UID]["Value"].asString(); sopInstanceUid = dicom[SOP_INSTANCE_UID]["Value"].asString(); return true; } else { return false; } } #endif static void AnswerMetadata(OrthancPluginRestOutput* output, const OrthancPluginHttpRequest* request, Orthanc::ResourceType level, const std::string& resource, bool isInstance, bool isXml) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); #if 1 std::string tmp = GetResourceUri(level, resource); std::list<std::string> files; if (isInstance) { files.push_back(tmp + "/file"); } else { Json::Value instances; if (!OrthancPlugins::RestApiGet(instances, tmp + "/instances", false)) { // Internal error OrthancPluginSendHttpStatusCode(context, output, 400); return; } for (Json::Value::ArrayIndex i = 0; i < instances.size(); i++) { files.push_back("/instances/" + instances[i]["ID"].asString() + "/file"); } } const std::string wadoBase = OrthancPlugins::Configuration::GetBaseUrl(request); OrthancPlugins::DicomResults results(output, wadoBase, *dictionary_, isXml, true); for (std::list<std::string>::const_iterator it = files.begin(); it != files.end(); ++it) { OrthancPlugins::MemoryBuffer content; if (content.RestApiGet(*it, false)) { OrthancPlugins::ParsedDicomFile dicom(content); results.Add(dicom.GetFile()); } } results.Answer(); #else std::list<std::string> instances; if (isInstance) { instances.push_back(resource); } else { Json::Value children; if (!OrthancPlugins::RestApiGet(children, GetResourceUri(level, resource) + "/instances", false)) { // Internal error OrthancPluginSendHttpStatusCode(context, output, 400); return; } for (Json::Value::ArrayIndex i = 0; i < children.size(); i++) { instances.push_back(children[i]["ID"].asString()); } } const std::string wadoBase = OrthancPlugins::Configuration::GetBaseUrl(request); // For JSON Orthanc::ChunkedBuffer buffer; buffer.AddChunk("["); bool first = true; if (isXml) { OrthancPluginStartMultipartAnswer(context, output, "related", "application/dicom+xml"); } for (std::list<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { std::string studyInstanceUid, seriesInstanceUid, sopInstanceUid; if (GetDicomIdentifiers(studyInstanceUid, seriesInstanceUid, sopInstanceUid, *it)) { OrthancPlugins::MemoryBuffer dicom; if (dicom.RestApiGet("/instances/" + *it + "/file", false)) { std::string item; { // TODO - Avoid a global mutex DicomWebFormatter::Locker locker(wadoBase + "studies/" + studyInstanceUid + "/series/" + seriesInstanceUid + "/instances/" + sopInstanceUid + "/bulk"); locker.Apply(item, context, dicom.GetData(), dicom.GetSize(), isXml); } if (isXml) { OrthancPluginSendMultipartItem(context, output, item.c_str(), item.size()); } else { if (!first) { buffer.AddChunk(","); first = false; } buffer.AddChunk(item); } } } } if (!isXml) { buffer.AddChunk("]"); std::string answer; buffer.Flatten(answer); OrthancPluginAnswerBuffer(context, output, answer.c_str(), answer.size(), "application/dicom+json"); } #endif } static bool LocateStudy(OrthancPluginRestOutput* output, std::string& publicId, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } try { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupStudy(context, request->groups[0])); tmp.ToString(publicId); } catch (Orthanc::OrthancException&) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent study with WADO-RS: " + std::string(request->groups[0])); } return true; } static bool LocateSeries(OrthancPluginRestOutput* output, std::string& publicId, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } try { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupSeries(context, request->groups[1])); tmp.ToString(publicId); } catch (Orthanc::OrthancException&) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent series with WADO-RS: " + std::string(request->groups[1])); } Json::Value study; if (!OrthancPlugins::RestApiGet(study, "/series/" + publicId + "/study", false)) { OrthancPluginSendHttpStatusCode(context, output, 404); return false; } else if (study["MainDicomTags"]["StudyInstanceUID"].asString() != std::string(request->groups[0])) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "No series " + std::string(request->groups[1]) + " in study " + std::string(request->groups[0])); } else { return true; } } bool LocateInstance(OrthancPluginRestOutput* output, std::string& publicId, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupInstance(context, request->groups[2])); if (tmp.GetContent() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent instance with WADO-RS: " + std::string(request->groups[2])); } tmp.ToString(publicId); } Json::Value study, series; if (!OrthancPlugins::RestApiGet(series, "/instances/" + publicId + "/series", false) || !OrthancPlugins::RestApiGet(study, "/instances/" + publicId + "/study", false)) { OrthancPluginSendHttpStatusCode(context, output, 404); return false; } else if (study["MainDicomTags"]["StudyInstanceUID"].asString() != std::string(request->groups[0]) || series["MainDicomTags"]["SeriesInstanceUID"].asString() != std::string(request->groups[1])) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "No instance " + std::string(request->groups[2]) + " in study " + std::string(request->groups[0]) + " or " + " in series " + std::string(request->groups[1])); } else { return true; } } void RetrieveDicomStudy(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string publicId; if (LocateStudy(output, publicId, request)) { AnswerListOfDicomInstances(output, Orthanc::ResourceType_Study, publicId); } } } void RetrieveDicomSeries(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string publicId; if (LocateSeries(output, publicId, request)) { AnswerListOfDicomInstances(output, Orthanc::ResourceType_Series, publicId); } } } void RetrieveDicomInstance(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(context, output, 400 /* Bad request */); } else { std::string publicId; if (LocateInstance(output, publicId, request)) { if (OrthancPluginStartMultipartAnswer(context, output, "related", "application/dicom")) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } OrthancPlugins::MemoryBuffer dicom; if (dicom.RestApiGet("/instances/" + publicId + "/file", false) && OrthancPluginSendMultipartItem(context, output, dicom.GetData(), dicom.GetSize()) != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } } } } void RetrieveStudyMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string publicId; if (LocateStudy(output, publicId, request)) { AnswerMetadata(output, request, Orthanc::ResourceType_Study, publicId, false, isXml); } } } void RetrieveSeriesMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string publicId; if (LocateSeries(output, publicId, request)) { AnswerMetadata(output, request, Orthanc::ResourceType_Series, publicId, false, isXml); } } } void RetrieveInstanceMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string publicId; if (LocateInstance(output, publicId, request)) { AnswerMetadata(output, request, Orthanc::ResourceType_Instance, publicId, true, isXml); } } } static uint32_t Hex2Dec(char c) { return (c >= '0' && c <= '9') ? c - '0' : c - 'a' + 10; } static bool ParseBulkTag(gdcm::Tag& tag, const std::string& s) { if (s.size() != 8) { return false; } for (size_t i = 0; i < 8; i++) { if ((s[i] < '0' || s[i] > '9') && (s[i] < 'a' || s[i] > 'f')) { return false; } } uint32_t g = ((Hex2Dec(s[0]) << 12) + (Hex2Dec(s[1]) << 8) + (Hex2Dec(s[2]) << 4) + Hex2Dec(s[3])); uint32_t e = ((Hex2Dec(s[4]) << 12) + (Hex2Dec(s[5]) << 8) + (Hex2Dec(s[6]) << 4) + Hex2Dec(s[7])); tag = gdcm::Tag(g, e); return true; } static bool ExploreBulkData(std::string& content, const std::vector<std::string>& path, size_t position, const gdcm::DataSet& dataset) { gdcm::Tag tag; if (!ParseBulkTag(tag, path[position]) || !dataset.FindDataElement(tag)) { return false; } const gdcm::DataElement& element = dataset.GetDataElement(tag); if (position + 1 == path.size()) { const gdcm::ByteValue* data = element.GetByteValue(); if (!data) { content.clear(); } else { content.assign(data->GetPointer(), data->GetLength()); } return true; } return false; } void RetrieveBulkData(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (!AcceptBulkData(request)) { OrthancPluginSendHttpStatusCode(context, output, 400 /* Bad request */); return; } std::string uri; OrthancPlugins::MemoryBuffer content; if (LocateInstance(output, uri, request) && content.RestApiGet(uri + "/file", false)) { OrthancPlugins::ParsedDicomFile dicom(content); std::vector<std::string> path; Orthanc::Toolbox::TokenizeString(path, request->groups[3], '/'); std::string result; if (path.size() % 2 == 1 && ExploreBulkData(result, path, 0, dicom.GetDataSet())) { if (OrthancPluginStartMultipartAnswer(context, output, "related", "application/octet-stream") != 0 || OrthancPluginSendMultipartItem(context, output, result.c_str(), result.size()) != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); } } else { OrthancPluginSendHttpStatusCode(context, output, 400 /* Bad request */); } } }