Mercurial > hg > orthanc-dicomweb
view Plugin/WadoRs.cpp @ 368:979776c2f75b
simplification in wado-rs retrieve metadata
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 27 Sep 2019 16:24:38 +0200 |
parents | 96dc376e4679 |
children | 331c30ae41c3 |
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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 "Configuration.h" #include "DicomWebFormatter.h" #include <Core/ChunkedBuffer.h> #include <Core/Toolbox.h> #include <Plugins/Samples/Common/OrthancPluginCppWrapper.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 + ")"); } } static const char* const TRANSFER_SYNTAX = "transfer-syntax"; /** * The "*" case below is related to Google Healthcare API: * https://groups.google.com/d/msg/orthanc-users/w1Ekrsc6-U8/T2a_DoQ5CwAJ **/ if (attributes.find(TRANSFER_SYNTAX) != attributes.end() && attributes[TRANSFER_SYNTAX] != "*") { 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); std::vector<std::string> applicationTokens; Orthanc::Toolbox::TokenizeString(applicationTokens, application, ','); for (size_t i = 0; i < applicationTokens.size(); i++) { std::string token = Orthanc::Toolbox::StripSpaces(applicationTokens[i]); if (token == "application/json" || token == "application/dicom+json" || token == "*/*") { 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); } } } static void WriteInstanceMetadata(OrthancPlugins::DicomWebFormatter::HttpWriter& writer, const std::string& orthancId, const std::string& studyInstanceUid, const std::string& seriesInstanceUid, const std::string& sopInstanceUid, const std::string& wadoBase) { assert(!orthancId.empty() && !studyInstanceUid.empty() && !seriesInstanceUid.empty() && !sopInstanceUid.empty() && !wadoBase.empty()); const std::string bulkRoot = (wadoBase + "studies/" + studyInstanceUid + "/series/" + seriesInstanceUid + "/instances/" + sopInstanceUid + "/bulk"); #if 0 // On a SSD drive, this version is twice slower than if using // cache (see below) OrthancPlugins::MemoryBuffer dicom; if (dicom.RestApiGet("/instances/" + orthancId + "/file", false)) { writer.AddDicom(dicom.GetData(), dicom.GetSize(), bulkRoot); } #else // TODO - Have a global setting to enable/disable caching of DICOMweb // TODO - Have a way to clear the "4444" attachments if Orthanc // version changes => Store Orthanc core version in a prefix or in // another attachment? OrthancPlugins::MemoryBuffer buffer; if (writer.IsXml()) { // DICOMweb XML is not cached if (buffer.RestApiGet("/instances/" + orthancId + "/file", false)) { writer.AddDicom(buffer.GetData(), buffer.GetSize(), bulkRoot); } } else { if (buffer.RestApiGet("/instances/" + orthancId + "/attachments/4444/data", false)) { writer.AddDicomWebSerializedJson(buffer.GetData(), buffer.GetSize()); } else if (buffer.RestApiGet("/instances/" + orthancId + "/file", false)) { // "Ignore binary mode" in DICOMweb conversion if caching is // enabled, as the bulk root can change across executions std::string dicomweb; { // TODO - Avoid a global mutex => Need to change Orthanc SDK OrthancPlugins::DicomWebFormatter::Locker locker(OrthancPluginDicomWebBinaryMode_Ignore, ""); locker.Apply(dicomweb, OrthancPlugins::GetGlobalContext(), buffer.GetData(), buffer.GetSize(), false /* JSON */); } buffer.RestApiPut("/instances/" + orthancId + "/attachments/4444", dicomweb, false); writer.AddDicomWebSerializedJson(dicomweb.c_str(), dicomweb.size()); } } #endif } static bool LocateStudy(OrthancPluginRestOutput* output, std::string& orthancId, std::string& studyInstanceUid, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } studyInstanceUid = request->groups[0]; try { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupStudy(context, studyInstanceUid.c_str())); if (tmp.GetContent() != NULL) { tmp.ToString(orthancId); return true; } } catch (Orthanc::OrthancException&) { } throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent study with WADO-RS: " + studyInstanceUid); } bool LocateSeries(OrthancPluginRestOutput* output, std::string& orthancId, std::string& studyInstanceUid, std::string& seriesInstanceUid, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } studyInstanceUid = request->groups[0]; seriesInstanceUid = request->groups[1]; bool found = false; try { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupSeries(context, seriesInstanceUid.c_str())); if (tmp.GetContent() != NULL) { tmp.ToString(orthancId); found = true; } } catch (Orthanc::OrthancException&) { } if (!found) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent series with WADO-RS: " + seriesInstanceUid); } Json::Value study; if (!OrthancPlugins::RestApiGet(study, "/series/" + orthancId + "/study", false)) { OrthancPluginSendHttpStatusCode(context, output, 404); return false; } else if (study["MainDicomTags"]["StudyInstanceUID"].asString() != studyInstanceUid) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "No series " + seriesInstanceUid + " in study " + studyInstanceUid); } else { return true; } } bool LocateInstance(OrthancPluginRestOutput* output, std::string& orthancId, std::string& studyInstanceUid, std::string& seriesInstanceUid, std::string& sopInstanceUid, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); if (request->method != OrthancPluginHttpMethod_Get) { OrthancPluginSendMethodNotAllowed(context, output, "GET"); return false; } studyInstanceUid = request->groups[0]; seriesInstanceUid = request->groups[1]; sopInstanceUid = request->groups[2]; { OrthancPlugins::OrthancString tmp; tmp.Assign(OrthancPluginLookupInstance(context, sopInstanceUid.c_str())); if (tmp.GetContent() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Accessing an inexistent instance with WADO-RS: " + sopInstanceUid); } tmp.ToString(orthancId); } Json::Value study, series; if (!OrthancPlugins::RestApiGet(series, "/instances/" + orthancId + "/series", false) || !OrthancPlugins::RestApiGet(study, "/instances/" + orthancId + "/study", false)) { OrthancPluginSendHttpStatusCode(context, output, 404); return false; } else if (study["MainDicomTags"]["StudyInstanceUID"].asString() != studyInstanceUid || series["MainDicomTags"]["SeriesInstanceUID"].asString() != seriesInstanceUid) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem, "Instance " + sopInstanceUid + " is not both in study " + studyInstanceUid + " and in series " + seriesInstanceUid); } 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 orthancId, studyInstanceUid; if (LocateStudy(output, orthancId, studyInstanceUid, request)) { AnswerListOfDicomInstances(output, Orthanc::ResourceType_Study, orthancId); } } } void RetrieveDicomSeries(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { if (!AcceptMultipartDicom(request)) { OrthancPluginSendHttpStatusCode(OrthancPlugins::GetGlobalContext(), output, 400 /* Bad request */); } else { std::string orthancId, studyInstanceUid, seriesInstanceUid; if (LocateSeries(output, orthancId, studyInstanceUid, seriesInstanceUid, request)) { AnswerListOfDicomInstances(output, Orthanc::ResourceType_Series, orthancId); } } } 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 orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid; if (LocateInstance(output, orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, request)) { if (OrthancPluginStartMultipartAnswer(context, output, "related", "application/dicom")) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } OrthancPlugins::MemoryBuffer dicom; if (dicom.RestApiGet("/instances/" + orthancId + "/file", false) && OrthancPluginSendMultipartItem(context, output, dicom.GetData(), dicom.GetSize()) != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } } } } namespace { class Identifier { private: std::string orthancId_; std::string dicomUid_; public: Identifier(const std::string& orthancId, const std::string& dicomUid) : orthancId_(orthancId), dicomUid_(dicomUid) { } const std::string& GetOrthancId() const { return orthancId_; } const std::string& GetDicomUid() const { return dicomUid_; } }; } static void GetChildrenIdentifiers(std::list<Identifier>& target, Orthanc::ResourceType level, const std::string& orthancId) { static const char* const ID = "ID"; static const char* const MAIN_DICOM_TAGS = "MainDicomTags"; static const char* const SERIES_INSTANCE_UID = "SeriesInstanceUID"; static const char* const SOP_INSTANCE_UID = "SOPInstanceUID"; target.clear(); const char* tag = NULL; std::string uri; switch (level) { case Orthanc::ResourceType_Study: uri = "/studies/" + orthancId + "/series"; tag = SERIES_INSTANCE_UID; break; case Orthanc::ResourceType_Series: uri = "/series/" + orthancId + "/instances"; tag = SOP_INSTANCE_UID; break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } assert(tag != NULL); Json::Value children; if (OrthancPlugins::RestApiGet(children, uri, false)) { if (children.type() != Json::arrayValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } for (Json::Value::ArrayIndex i = 0; i < children.size(); i++) { if (children[i].type() != Json::objectValue || !children[i].isMember(ID) || !children[i].isMember(MAIN_DICOM_TAGS) || children[i][ID].type() != Json::stringValue || children[i][MAIN_DICOM_TAGS].type() != Json::objectValue || !children[i][MAIN_DICOM_TAGS].isMember(tag) || children[i][MAIN_DICOM_TAGS][tag].type() != Json::stringValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } else { target.push_back(Identifier(children[i][ID].asString(), children[i][MAIN_DICOM_TAGS][tag].asString())); } } } } 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 studyOrthancId, studyInstanceUid; if (LocateStudy(output, studyOrthancId, studyInstanceUid, request)) { OrthancPlugins::DicomWebFormatter::HttpWriter writer(output, isXml); const std::string& wadoBase = OrthancPlugins::Configuration::GetBaseUrl(request); std::list<Identifier> series; GetChildrenIdentifiers(series, Orthanc::ResourceType_Study, studyOrthancId); for (std::list<Identifier>::const_iterator a = series.begin(); a != series.end(); ++a) { std::list<Identifier> instances; GetChildrenIdentifiers(instances, Orthanc::ResourceType_Series, a->GetOrthancId()); for (std::list<Identifier>::const_iterator b = instances.begin(); b != instances.end(); ++b) { WriteInstanceMetadata(writer, b->GetOrthancId(), studyInstanceUid, a->GetDicomUid(), b->GetDicomUid(), OrthancPlugins::Configuration::GetBaseUrl(request)); } } writer.Send(); } } } void RetrieveSeriesMetadata(OrthancPluginRestOutput* output, const char* url, const OrthancPluginHttpRequest* request) { OrthancPluginContext* context = OrthancPlugins::GetGlobalContext(); bool isXml; if (!AcceptMetadata(request, isXml)) { OrthancPluginSendHttpStatusCode(context, output, 400 /* Bad request */); } else { std::string seriesOrthancId, studyInstanceUid, seriesInstanceUid; if (LocateSeries(output, seriesOrthancId, studyInstanceUid, seriesInstanceUid, request)) { OrthancPlugins::DicomWebFormatter::HttpWriter writer(output, isXml); const std::string& wadoBase = OrthancPlugins::Configuration::GetBaseUrl(request); std::list<Identifier> instances; GetChildrenIdentifiers(instances, Orthanc::ResourceType_Series, seriesOrthancId); for (std::list<Identifier>::const_iterator a = instances.begin(); a != instances.end(); ++a) { WriteInstanceMetadata(writer, a->GetOrthancId(), studyInstanceUid, seriesOrthancId, a->GetDicomUid(), OrthancPlugins::Configuration::GetBaseUrl(request)); } writer.Send(); } } } 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 orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid; if (LocateInstance(output, orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, request)) { OrthancPlugins::DicomWebFormatter::HttpWriter writer(output, isXml); WriteInstanceMetadata(writer, orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, OrthancPlugins::Configuration::GetBaseUrl(request)); writer.Send(); } } } 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 orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid; OrthancPlugins::MemoryBuffer content; if (LocateInstance(output, orthancId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, request) && content.RestApiGet("/instances/" + orthancId + "/file", false)) { std::string bulk(request->groups[3]); std::vector<std::string> path; Orthanc::Toolbox::TokenizeString(path, bulk, '/'); // Map the bulk data URI to the Orthanc "/instances/.../content/..." built-in URI std::string orthanc = "/instances/" + orthancId + "/content"; Orthanc::DicomTag tmp(0, 0); if (path.size() == 1 && Orthanc::DicomTag::ParseHexadecimal(tmp, path[0].c_str()) && tmp == Orthanc::DICOM_TAG_PIXEL_DATA) { // Accessing pixel data: Return the raw content of the fragments in a multipart stream. // TODO - Is this how DICOMweb should work? orthanc += "/" + Orthanc::DICOM_TAG_PIXEL_DATA.Format(); Json::Value frames; if (OrthancPlugins::RestApiGet(frames, orthanc, false)) { if (frames.type() != Json::arrayValue || OrthancPluginStartMultipartAnswer(context, output, "related", "application/octet-stream") != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); } for (Json::Value::ArrayIndex i = 0; i < frames.size(); i++) { std::string frame; if (frames[i].type() != Json::stringValue || !OrthancPlugins::RestApiGetString(frame, orthanc + "/" + frames[i].asString(), false) || OrthancPluginSendMultipartItem(context, output, frame.c_str(), frame.size()) != 0) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); } } } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem); } } else { if (path.size() % 2 != 1) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Bulk data URI in WADO-RS should have an odd number of items: " + bulk); } for (size_t i = 0; i < path.size() / 2; i++) { int index; try { index = boost::lexical_cast<int>(path[2 * i + 1]); } catch (boost::bad_lexical_cast&) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "Bad sequence index in bulk data URI: " + bulk); } orthanc += "/" + path[2 * i] + "/" + boost::lexical_cast<std::string>(index - 1); } orthanc += "/" + path.back(); std::string result; if (OrthancPlugins::RestApiGetString(result, orthanc, false)) { 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 { throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentItem); } } } }