Mercurial > hg > orthanc
view OrthancServer/Sources/ServerToolbox.cpp @ 5656:a3c244090f67 find-refactoring
integration mainline->find-refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 06 Jun 2024 13:24:04 +0200 |
parents | f7adfb22e20e |
children |
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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) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium * Copyright (C) 2021-2024 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); // 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()); #if 0 // This version solves some indexing issue (https://discourse.orthanc-server.org/t/postgress-index-effectively-disabled-when-searching-for-greek-names/3371) // and seems functional: I could run the integration tests with both SQLite and PG + the DicomWeb tests with PG. // However, it can not go into production because NormalizeIdentifier is used both at ingest time and at search time; // therefore, if we change it while we have an already populated DB, the searches won't work anymore and, on very large // systems, running the Housekeeper to rebuild the indexes might take months ... // We keep it here because it might be handy once we refactor the DicomIdentifier searches in the future. 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); t = Toolbox::ToUpperCaseWithAccents(t); #else 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); #endif 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, bool limitToThisLevelDicomTags, ResourceType limitToLevel) { LOG(WARNING) << "Reconstructing resource " << resource; std::list<std::string> instances; context.GetIndex().GetChildInstances(instances, resource); if (limitToThisLevelDicomTags && instances.size() > 0) // in this case, we only need to rebuild one instance ! { ServerContext::DicomCacheLocker locker(context, instances.front()); context.GetIndex().ReconstructInstance(locker.GetDicom(), true, limitToLevel); } else { 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(), false, ResourceType_Instance /* dummy */); if (reconstructFiles) { std::string resultPublicId; // ignored std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom())); // TODO: TranscodeAndStore and specifically ServerIndex::Store have been "poluted" by the isReconstruct parameter // we should very likely refactor it context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true); } } } } bool IsValidLabel(const std::string& label) { if (label.empty()) { return false; } if (label.size() > 64) { // This limitation is for MySQL, which cannot use a TEXT // column of undefined length as a primary key return false; } for (size_t i = 0; i < label.size(); i++) { if (!(label[i] == '_' || label[i] == '-' || (label[i] >= 'a' && label[i] <= 'z') || (label[i] >= 'A' && label[i] <= 'Z') || (label[i] >= '0' && label[i] <= '9'))) { return false; } } return true; } void CheckValidLabel(const std::string& label) { if (!IsValidLabel(label)) { throw OrthancException(ErrorCode_ParameterOutOfRange, "A label must be a non-empty, alphanumeric string, " "possibly with '_' or '-' characters, " "with maximum 64 characters, but got: " + label); } } } }