Mercurial > hg > orthanc
view OrthancServer/Sources/ServerToolbox.cpp @ 5141:023569e7155b
moved DicomModification thread safety into ResourceModificationJob (trying to avoid mutex in OrthancFramework as much as possible)
author | Alain Mazy <am@osimis.io> |
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date | Fri, 20 Jan 2023 18:10:42 +0100 |
parents | 22966345eaba |
children | dd085f7e7e71 |
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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) 2017-2022 Osimis S.A., Belgium * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, 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. * * 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 "ServerToolbox.h" #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h" #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h" #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h" #include "../../OrthancFramework/Sources/Logging.h" #include "../../OrthancFramework/Sources/OrthancException.h" #include "Database/IDatabaseWrapper.h" #include "Database/ResourcesContent.h" #include "OrthancConfiguration.h" #include "ServerContext.h" #include <cassert> namespace Orthanc { static const DicomTag PATIENT_IDENTIFIERS[] = { DICOM_TAG_PATIENT_ID, DICOM_TAG_PATIENT_NAME, DICOM_TAG_PATIENT_BIRTH_DATE }; static const DicomTag STUDY_IDENTIFIERS[] = { DICOM_TAG_PATIENT_ID, DICOM_TAG_PATIENT_NAME, DICOM_TAG_PATIENT_BIRTH_DATE, DICOM_TAG_STUDY_INSTANCE_UID, DICOM_TAG_ACCESSION_NUMBER, DICOM_TAG_STUDY_DESCRIPTION, DICOM_TAG_STUDY_DATE }; static const DicomTag SERIES_IDENTIFIERS[] = { DICOM_TAG_SERIES_INSTANCE_UID }; static const DicomTag INSTANCE_IDENTIFIERS[] = { DICOM_TAG_SOP_INSTANCE_UID }; namespace ServerToolbox { bool FindOneChildInstance(int64_t& result, IDatabaseWrapper::ITransaction& transaction, int64_t resource, ResourceType type) { for (;;) { if (type == ResourceType_Instance) { result = resource; return true; } std::list<int64_t> children; transaction.GetChildrenInternalId(children, resource); if (children.empty()) { return false; } resource = children.front(); type = GetChildResourceType(type); } } void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction, IStorageArea& storageArea, ResourceType level) { // WARNING: The database should be locked with a transaction! // TODO: This function might consume much memory if level == // ResourceType_Instance. To improve this, first download the // list of studies, then remove the instances for each single // study (check out OrthancRestApi::InvalidateTags for an // example). Take this improvement into consideration for the // next upgrade of the database schema. const char* plural = Orthanc::GetResourceTypeText(level, true, true); LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; std::list<std::string> resources; transaction.GetAllPublicIds(resources, level); for (std::list<std::string>::const_iterator it = resources.begin(); it != resources.end(); ++it) { // Locate the resource and one of its child instances int64_t resource, instance; ResourceType tmp; if (!transaction.LookupResource(resource, tmp, *it) || tmp != level || !FindOneChildInstance(instance, transaction, resource, level)) { throw OrthancException(ErrorCode_InternalError, "Cannot find an instance for " + std::string(EnumerationToString(level)) + " with identifier " + *it); } // Get the DICOM file attached to some instances in the resource FileInfo attachment; int64_t revision; if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom)) { throw OrthancException(ErrorCode_InternalError, "Cannot retrieve the DICOM file associated with instance " + transaction.GetPublicId(instance)); } try { // Read and parse the content of the DICOM file StorageAccessor accessor(storageArea, NULL); // no cache std::string content; accessor.Read(content, attachment); ParsedDicomFile dicom(content); // Update the tags of this resource DicomMap dicomSummary; OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom); transaction.ClearMainDicomTags(resource); ResourcesContent tags(false /* prevent the setting of metadata */); tags.AddResource(resource, level, dicomSummary); transaction.SetResourcesContent(tags); transaction.DeleteMetadata(resource, MetadataType_MainDicomTagsSignature); transaction.SetMetadata(resource, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(level), 0); } catch (OrthancException&) { LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() << " associated with instance " << transaction.GetPublicId(instance); throw; } } } void LoadIdentifiers(const DicomTag*& tags, size_t& size, ResourceType level) { switch (level) { case ResourceType_Patient: tags = PATIENT_IDENTIFIERS; size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); break; case ResourceType_Study: tags = STUDY_IDENTIFIERS; size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); break; case ResourceType_Series: tags = SERIES_IDENTIFIERS; size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); break; case ResourceType_Instance: tags = INSTANCE_IDENTIFIERS; size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } std::string NormalizeIdentifier(const std::string& value) { std::string t; t.reserve(value.size()); for (size_t i = 0; i < value.size(); i++) { if (value[i] == '%' || value[i] == '_') { t.push_back(' '); // These characters might break wildcard queries in SQL } else if (isascii(value[i]) && !iscntrl(value[i]) && (!isspace(value[i]) || value[i] == ' ')) { t.push_back(value[i]); } } Toolbox::ToUpperCase(t); return Toolbox::StripSpaces(t); } bool IsIdentifier(const DicomTag& tag, ResourceType level) { const DicomTag* tags; size_t size; LoadIdentifiers(tags, size, level); for (size_t i = 0; i < size; i++) { if (tag == tags[i]) { return true; } } return false; } void ReconstructResource(ServerContext& context, const std::string& resource, bool reconstructFiles) { LOG(WARNING) << "Reconstructing resource " << resource; std::list<std::string> instances; context.GetIndex().GetChildInstances(instances, resource); for (std::list<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { ServerContext::DicomCacheLocker locker(context, *it); // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext" context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */, -1 /* dummy revision */, "" /* dummy MD5 */); context.GetIndex().ReconstructInstance(locker.GetDicom()); if (reconstructFiles) { // preserve metadata from old resource typedef std::map<MetadataType, std::string> InstanceMetadata; InstanceMetadata instanceMetadata; std::string resultPublicId; // ignored std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom())); context.GetIndex().GetAllMetadata(instanceMetadata, *it, ResourceType_Instance); for (InstanceMetadata::const_iterator itm = instanceMetadata.begin(); itm != instanceMetadata.end(); ++itm) { dicomInstancetoStore->AddMetadata(ResourceType_Instance, itm->first, itm->second); } context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true); } } } } }