Mercurial > hg > orthanc
changeset 5226:49e906a8fea2 db-protobuf
integration mainline->db-protobuf
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 04 Apr 2023 07:09:22 +0200 |
| parents | 3a61fd50f804 (diff) 5874e5dd9a38 (current diff) |
| children | 988dab8deb1c |
| files | NEWS OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp |
| diffstat | 24 files changed, 743 insertions(+), 122 deletions(-) [+] |
line wrap: on
line diff
--- a/NEWS Mon Apr 03 22:31:32 2023 +0200 +++ b/NEWS Tue Apr 04 07:09:22 2023 +0200 @@ -1,11 +1,19 @@ Pending changes in the mainline =============================== +General +------- + +* Support for labels associated with patients, studies, series, and instances + REST API -------- * API version upgraded to 20 -* /system: added "UserMetadata" +* New URIs "/.../{id}/labels/{label}" to test/set/remove labels +* The "/patients/{id}", "/studies/{id}", "/series/{id}" and "/instances/{id}" + contain the "Labels" field +* "/system": added "UserMetadata" Plugins ------- @@ -18,7 +26,7 @@ * Enforce the existence of the patient/study/instance while creating its archive * Security: New configuration option "RestApiWriteToFileSystemEnabled" - to allow "/instances/../export" that is now disabled by default + to allow "/instances/../export" (the latter is now disabled by default) * Fix issue 214: VOILUTSequence is not returned in Wado-RS * Fix /tools/reset crashing when ExtraMainDicomTags were defined * Fix Housekeeper plugin infinite loop if Orthanc is empty. @@ -37,7 +45,7 @@ AcceptedTransferSyntaxes. * Made the default SQLite DB more robust wrt future updates like adding new columns in DB. -* Made the HTTP Client errors more verbose by including the url in the logs. +* Made the HTTP Client errors more verbose by including the URL in the logs. * Optimization: now using multiple threads to transcode files for asynchronous download of studies archive. * New configuration "KeepAliveTimeout" with a default value of 1 second. @@ -148,7 +156,7 @@ * Housekeeper plugin: Fix resume of previous processing * Added missing MOVEPatientRootQueryRetrieveInformationModel in DicomControlUserConnection::SetupPresentationContexts() -* Improved HttpClient error logging (add method + url) +* Improved HttpClient error logging (add method + URL) REST API --------
--- a/OrthancServer/CMakeLists.txt Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/CMakeLists.txt Tue Apr 04 07:09:22 2023 +0200 @@ -228,16 +228,15 @@ ##################################################################### set(ORTHANC_EMBEDDED_FILES - CONFIGURATION_SAMPLE ${CMAKE_SOURCE_DIR}/Resources/Configuration.json - DICOM_CONFORMANCE_STATEMENT ${CMAKE_SOURCE_DIR}/Resources/DicomConformanceStatement.txt - FONT_UBUNTU_MONO_BOLD_16 ${CMAKE_SOURCE_DIR}/Resources/Fonts/UbuntuMonoBold-16.json - LUA_TOOLBOX ${CMAKE_SOURCE_DIR}/Resources/Toolbox.lua - PREPARE_DATABASE ${CMAKE_SOURCE_DIR}/Sources/Database/PrepareDatabase.sql - UPGRADE_DATABASE_3_TO_4 ${CMAKE_SOURCE_DIR}/Sources/Database/Upgrade3To4.sql - UPGRADE_DATABASE_4_TO_5 ${CMAKE_SOURCE_DIR}/Sources/Database/Upgrade4To5.sql - - INSTALL_TRACK_ATTACHMENTS_SIZE - ${CMAKE_SOURCE_DIR}/Sources/Database/InstallTrackAttachmentsSize.sql + CONFIGURATION_SAMPLE ${CMAKE_SOURCE_DIR}/Resources/Configuration.json + DICOM_CONFORMANCE_STATEMENT ${CMAKE_SOURCE_DIR}/Resources/DicomConformanceStatement.txt + FONT_UBUNTU_MONO_BOLD_16 ${CMAKE_SOURCE_DIR}/Resources/Fonts/UbuntuMonoBold-16.json + LUA_TOOLBOX ${CMAKE_SOURCE_DIR}/Resources/Toolbox.lua + PREPARE_DATABASE ${CMAKE_SOURCE_DIR}/Sources/Database/PrepareDatabase.sql + UPGRADE_DATABASE_3_TO_4 ${CMAKE_SOURCE_DIR}/Sources/Database/Upgrade3To4.sql + UPGRADE_DATABASE_4_TO_5 ${CMAKE_SOURCE_DIR}/Sources/Database/Upgrade4To5.sql + INSTALL_TRACK_ATTACHMENTS_SIZE ${CMAKE_SOURCE_DIR}/Sources/Database/InstallTrackAttachmentsSize.sql + INSTALL_LABELS_TABLE ${CMAKE_SOURCE_DIR}/Sources/Database/InstallLabelsTable.sql ) if (STANDALONE_BUILD)
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -565,8 +565,16 @@ std::list<std::string>* instancesId, const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, uint32_t limit) ORTHANC_OVERRIDE { + if (!withLabels.empty() || + !withoutLabels.empty()) + { + throw OrthancException(ErrorCode_InternalError); // "HasLabelsSupport()" has returned "false" + } + if (that_.extensions_.lookupResources == NULL) { // Fallback to compatibility mode @@ -1413,6 +1421,27 @@ CheckSuccess(that_.extensions_.tagMostRecentPatient(that_.payload_, patient)); } } + + + virtual void AddLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } + + + virtual void RemoveLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } + + + virtual void ListLabels(std::set<std::string>& target, + int64_t resource) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } };
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabase.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabase.h Tue Apr 04 07:09:22 2023 +0200 @@ -113,6 +113,11 @@ return false; // No support for revisions in old API } + virtual bool HasLabelsSupport() const ORTHANC_OVERRIDE + { + return false; + } + void AnswerReceived(const _OrthancPluginDatabaseAnswer& answer); }; }
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -800,8 +800,16 @@ std::list<std::string>* instancesId, // Can be NULL if not needed const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, uint32_t limit) ORTHANC_OVERRIDE { + if (!withLabels.empty() || + !withoutLabels.empty()) + { + throw OrthancException(ErrorCode_InternalError); // "HasLabelsSupport()" has returned "false" + } + std::vector<OrthancPluginDatabaseConstraint> constraints; std::vector< std::vector<const char*> > constraintsValues; @@ -1027,6 +1035,27 @@ return false; } } + + + virtual void AddLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } + + + virtual void RemoveLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } + + + virtual void ListLabels(std::set<std::string>& target, + int64_t resource) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_InternalError); // Not supported + } };
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.h Tue Apr 04 07:09:22 2023 +0200 @@ -82,6 +82,11 @@ IStorageArea& storageArea) ORTHANC_OVERRIDE; virtual bool HasRevisionsSupport() const ORTHANC_OVERRIDE; + + virtual bool HasLabelsSupport() const ORTHANC_OVERRIDE + { + return false; + } }; }
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -915,8 +915,17 @@ std::list<std::string>* instancesId, // Can be NULL if not needed const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, uint32_t limit) ORTHANC_OVERRIDE { + if (!database_.HasLabelsSupport() && + (!withLabels.empty() || + !withoutLabels.empty())) + { + throw OrthancException(ErrorCode_InternalError); + } + DatabasePluginMessages::TransactionRequest request; request.mutable_lookup_resources()->set_query_level(Convert(queryLevel)); request.mutable_lookup_resources()->set_limit(limit); @@ -966,6 +975,12 @@ throw OrthancException(ErrorCode_ParameterOutOfRange); } } + + if (!withLabels.empty() || + !withoutLabels.empty()) + { + throw OrthancException(ErrorCode_NotImplemented); // TODO + } DatabasePluginMessages::TransactionResponse response; ExecuteTransaction(response, DatabasePluginMessages::OPERATION_LOOKUP_RESOURCES, request); @@ -1132,6 +1147,27 @@ return false; } } + + + virtual void AddLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_NotImplemented); + } + + + virtual void RemoveLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_NotImplemented); + } + + + virtual void ListLabels(std::set<std::string>& target, + int64_t resource) ORTHANC_OVERRIDE + { + throw OrthancException(ErrorCode_NotImplemented); + } }; @@ -1146,7 +1182,8 @@ open_(false), databaseVersion_(0), hasFlushToDisk_(false), - hasRevisionsSupport_(false) + hasRevisionsSupport_(false), + hasLabelsSupport_(false) { CLOG(INFO, PLUGINS) << "Identifier of this Orthanc server for the global properties " << "of the custom database: \"" << serverIdentifier << "\""; @@ -1186,6 +1223,7 @@ databaseVersion_ = response.get_system_information().database_version(); hasFlushToDisk_ = response.get_system_information().supports_flush_to_disk(); hasRevisionsSupport_ = response.get_system_information().supports_revisions(); + hasLabelsSupport_ = response.get_system_information().supports_labels(); } open_ = true; @@ -1307,4 +1345,17 @@ return hasRevisionsSupport_; } } + + + bool OrthancPluginDatabaseV4::HasLabelsSupport() const + { + if (!open_) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + return hasLabelsSupport_; + } + } }
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.h Tue Apr 04 07:09:22 2023 +0200 @@ -44,6 +44,7 @@ unsigned int databaseVersion_; bool hasFlushToDisk_; bool hasRevisionsSupport_; + bool hasLabelsSupport_; void CheckSuccess(OrthancPluginErrorCode code) const; @@ -93,6 +94,8 @@ IStorageArea& storageArea) ORTHANC_OVERRIDE; virtual bool HasRevisionsSupport() const ORTHANC_OVERRIDE; + + virtual bool HasLabelsSupport() const ORTHANC_OVERRIDE; }; }
--- a/OrthancServer/Plugins/Include/orthanc/OrthancDatabasePlugin.proto Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Plugins/Include/orthanc/OrthancDatabasePlugin.proto Tue Apr 04 07:09:22 2023 +0200 @@ -129,6 +129,7 @@ uint32 database_version = 1; bool supports_flush_to_disk = 2; bool supports_revisions = 3; + bool supports_labels = 4; } }
--- a/OrthancServer/Sources/Database/IDatabaseWrapper.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/IDatabaseWrapper.h Tue Apr 04 07:09:22 2023 +0200 @@ -200,6 +200,8 @@ std::list<std::string>* instancesId, // Can be NULL if not needed const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, uint32_t limit) = 0; // Returns "true" iff. the instance is new and has been inserted @@ -236,6 +238,20 @@ ResourceType& type, std::string& parentPublicId, const std::string& publicId) = 0; + + + /** + * Primitives introduced in Orthanc 1.12.0 + **/ + + virtual void AddLabel(int64_t resource, + const std::string& label) = 0; + + virtual void RemoveLabel(int64_t resource, + const std::string& label) = 0; + + virtual void ListLabels(std::set<std::string>& target, + int64_t resource) = 0; }; @@ -260,5 +276,7 @@ IStorageArea& storageArea) = 0; virtual bool HasRevisionsSupport() const = 0; + + virtual bool HasLabelsSupport() const = 0; }; }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/InstallLabelsTable.sql Tue Apr 04 07:09:22 2023 +0200 @@ -0,0 +1,24 @@ +-- 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) 2021-2023 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/>. + + +CREATE TABLE Labels( + internalId INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE, + label TEXT + );
--- a/OrthancServer/Sources/Database/PrepareDatabase.sql Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/PrepareDatabase.sql Tue Apr 04 07:09:22 2023 +0200 @@ -91,6 +91,12 @@ patientId INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE ); +-- New in Orthanc 1.12.0 +CREATE TABLE Labels( + internalId INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE, + label TEXT + ); + CREATE INDEX ChildrenIndex ON Resources(parentId); CREATE INDEX PublicIndex ON Resources(publicId); CREATE INDEX ResourceTypeIndex ON Resources(resourceType);
--- a/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -341,8 +341,16 @@ std::list<std::string>* instancesId, const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, uint32_t limit) ORTHANC_OVERRIDE { + if (!withLabels.empty() || + !withoutLabels.empty()) + { + throw OrthancException(ErrorCode_NotImplemented); + } + LookupFormatter formatter; std::string sql; @@ -1071,6 +1079,56 @@ s.Run(); } } + + + virtual void AddLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + if (label.empty()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Labels (internalId, label) VALUES(?, ?)"); + s.BindInt64(0, resource); + s.BindString(1, label); + s.Run(); + } + } + + + virtual void RemoveLabel(int64_t resource, + const std::string& label) ORTHANC_OVERRIDE + { + if (label.empty()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Labels WHERE internalId=? AND label=?"); + s.BindInt64(0, resource); + s.BindString(1, label); + s.Run(); + } + } + + + virtual void ListLabels(std::set<std::string>& target, + int64_t resource) ORTHANC_OVERRIDE + { + target.clear(); + + SQLite::Statement s(db_, SQLITE_FROM_HERE, + "SELECT label FROM Labels WHERE internalId=?"); + s.BindInt64(0, resource); + + while (s.Step()) + { + target.insert(s.ColumnString(0)); + } + } }; @@ -1344,9 +1402,9 @@ "Incompatible version of the Orthanc database: " + tmp); } - // New in Orthanc 1.5.1 if (version_ == 6) { + // New in Orthanc 1.5.1 if (!transaction->LookupGlobalProperty(tmp, GlobalProperty_GetTotalSizeIsFast, true /* unused in SQLite */) || tmp != "1") { @@ -1355,6 +1413,15 @@ ServerResources::GetFileResource(query, ServerResources::INSTALL_TRACK_ATTACHMENTS_SIZE); db_.Execute(query); } + + // New in Orthanc 1.12.0 + if (!db_.DoesTableExist("Labels")) + { + LOG(INFO) << "Installing the \"Labels\" table"; + std::string query; + ServerResources::GetFileResource(query, ServerResources::INSTALL_LABELS_TABLE); + db_.Execute(query); + } } transaction->Commit(0);
--- a/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.h Tue Apr 04 07:09:22 2023 +0200 @@ -97,6 +97,11 @@ return false; // TODO - REVISIONS } + virtual bool HasLabelsSupport() const ORTHANC_OVERRIDE + { + return true; + } + /** * The "StartTransaction()" method is guaranteed to return a class
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -715,10 +715,10 @@ const std::string& publicId, ResourceType level, const std::set<DicomTag>& requestedTags, - ExpandResourceDbFlags expandFlags) + ExpandResourceFlags expandFlags) { class Operations : public ReadOnlyOperationsT6< - bool&, ExpandedResource&, const std::string&, ResourceType, const std::set<DicomTag>&, ExpandResourceDbFlags> + bool&, ExpandedResource&, const std::string&, ResourceType, const std::set<DicomTag>&, ExpandResourceFlags> { private: @@ -778,7 +778,7 @@ else { ExpandedResource& target = tuple.get<1>(); - ExpandResourceDbFlags expandFlags = tuple.get<5>(); + ExpandResourceFlags expandFlags = tuple.get<5>(); // Set information about the parent resource (if it exists) if (type == ResourceType_Patient) @@ -798,16 +798,15 @@ target.parentId_ = parent; } - target.type_ = type; - target.id_ = tuple.get<2>(); - - if (expandFlags & ExpandResourceDbFlags_IncludeChildren) + target.SetResource(type, tuple.get<2>()); + + if (expandFlags & ExpandResourceFlags_IncludeChildren) { // List the children resources transaction.GetChildrenPublicId(target.childrenIds_, internalId); } - if (expandFlags & ExpandResourceDbFlags_IncludeMetadata) + if (expandFlags & ExpandResourceFlags_IncludeMetadata) { // Extract the metadata transaction.GetAllMetadata(target.metadata_, internalId); @@ -869,10 +868,10 @@ LookupStringMetadata(target.mainDicomTagsSignature_, target.metadata_, MetadataType_MainDicomTagsSignature); } - if (expandFlags & ExpandResourceDbFlags_IncludeMainDicomTags) + if (expandFlags & ExpandResourceFlags_IncludeMainDicomTags) { // read all tags from DB - transaction.GetMainDicomTags(target.tags_, internalId); + transaction.GetMainDicomTags(target.GetMainDicomTags(), internalId); // read all main sequences from DB std::string serializedSequences; @@ -882,7 +881,7 @@ Toolbox::ReadJson(jsonMetadata, serializedSequences); assert(jsonMetadata["Version"].asInt() == 1); - target.tags_.FromDicomAsJson(jsonMetadata["Sequences"], true /* append */, true /* parseSequences */); + target.GetMainDicomTags().FromDicomAsJson(jsonMetadata["Sequences"], true /* append */, true /* parseSequences */); } // check if we have access to all requestedTags or if we must get tags from parents @@ -895,7 +894,7 @@ FromDcmtkBridge::ParseListOfTags(savedMainDicomTags, target.mainDicomTagsSignature_); // read parent main dicom tags as long as we have not gathered all requested tags - ResourceType currentLevel = target.type_; + ResourceType currentLevel = target.GetLevel(); int64_t currentInternalId = internalId; Toolbox::GetMissingsFromSet(target.missingRequestedTags_, requestedTags, savedMainDicomTags); @@ -931,7 +930,7 @@ DicomMap parentTags; transaction.GetMainDicomTags(parentTags, currentParentId); - target.tags_.Merge(parentTags); + target.GetMainDicomTags().Merge(parentTags); } currentInternalId = currentParentId; @@ -939,6 +938,11 @@ } } + if (expandFlags & ExpandResourceFlags_IncludeLabels) + { + transaction.ListLabels(target.labels_, internalId); + } + std::string tmp; if (LookupStringMetadata(tmp, target.metadata_, MetadataType_AnonymizedFrom)) @@ -1066,7 +1070,7 @@ void StatelessDatabaseOperations::GetAllUuids(std::list<std::string>& target, ResourceType resourceType, size_t since, - size_t limit) + uint32_t limit) { if (limit == 0) { @@ -1646,7 +1650,9 @@ { // TODO - CANDIDATE FOR "TransactionType_Implicit" std::list<std::string> tmp; - transaction.ApplyLookupResources(tmp, NULL, query_, level_, 0); + std::set<std::string> withLabels; + std::set<std::string> withoutLabels; + transaction.ApplyLookupResources(tmp, NULL, query_, level_, withLabels, withoutLabels, 0); CopyListToVector(result_, tmp); } }; @@ -1915,9 +1921,12 @@ std::vector<std::string>* instancesId, const DatabaseLookup& lookup, ResourceType queryLevel, - size_t limit) + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, + uint32_t limit) { - class Operations : public ReadOnlyOperationsT4<bool, const std::vector<DatabaseConstraint>&, ResourceType, size_t> + class Operations : public ReadOnlyOperationsT6<bool, const std::vector<DatabaseConstraint>&, ResourceType, + const std::set<std::string>&, const std::set<std::string>&, size_t> { private: std::list<std::string> resourcesList_; @@ -1940,11 +1949,13 @@ // TODO - CANDIDATE FOR "TransactionType_Implicit" if (tuple.get<0>()) { - transaction.ApplyLookupResources(resourcesList_, &instancesList_, tuple.get<1>(), tuple.get<2>(), tuple.get<3>()); + transaction.ApplyLookupResources( + resourcesList_, &instancesList_, tuple.get<1>(), tuple.get<2>(), tuple.get<3>(), tuple.get<4>(), tuple.get<5>()); } else { - transaction.ApplyLookupResources(resourcesList_, NULL, tuple.get<1>(), tuple.get<2>(), tuple.get<3>()); + transaction.ApplyLookupResources( + resourcesList_, NULL, tuple.get<1>(), tuple.get<2>(), tuple.get<3>(), tuple.get<4>(), tuple.get<5>()); } } }; @@ -1954,7 +1965,7 @@ NormalizeLookup(normalized, lookup, queryLevel); Operations operations; - operations.Apply(*this, (instancesId != NULL), normalized, queryLevel, limit); + operations.Apply(*this, (instancesId != NULL), normalized, queryLevel, withLabels, withoutLabels, limit); CopyListToVector(resourcesId, operations.GetResourcesList()); @@ -3530,4 +3541,96 @@ Apply(operations); return operations.GetStatus(); } + + + void StatelessDatabaseOperations::ListLabels(std::set<std::string>& target, + const std::string& publicId, + ResourceType level) + { + class Operations : public ReadOnlyOperationsT3<std::set<std::string>&, const std::string&, ResourceType> + { + public: + virtual void ApplyTuple(ReadOnlyTransaction& transaction, + const Tuple& tuple) ORTHANC_OVERRIDE + { + ResourceType type; + int64_t id; + if (!transaction.LookupResource(id, type, tuple.get<1>()) || + tuple.get<2>() != type) + { + throw OrthancException(ErrorCode_UnknownResource); + } + else + { + transaction.ListLabels(tuple.get<0>(), id); + } + } + }; + + Operations operations; + operations.Apply(*this, target, publicId, level); + } + + + void StatelessDatabaseOperations::ModifyLabel(const std::string& publicId, + ResourceType level, + const std::string& label, + LabelOperation operation) + { + class Operations : public IReadWriteOperations + { + private: + const std::string& publicId_; + ResourceType level_; + const std::string& label_; + LabelOperation operation_; + + public: + Operations(const std::string& publicId, + ResourceType level, + const std::string& label, + LabelOperation operation) : + publicId_(publicId), + level_(level), + label_(label), + operation_(operation) + { + } + + virtual void Apply(ReadWriteTransaction& transaction) ORTHANC_OVERRIDE + { + ResourceType type; + int64_t id; + if (!transaction.LookupResource(id, type, publicId_) || + level_ != type) + { + throw OrthancException(ErrorCode_UnknownResource); + } + else + { + switch (operation_) + { + case LabelOperation_Add: + transaction.AddLabel(id, label_); + break; + + case LabelOperation_Remove: + transaction.RemoveLabel(id, label_); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + } + }; + + if (!Toolbox::IsAsciiString(label)) + { + throw OrthancException(ErrorCode_ParameterOutOfRange, "A label must only contain ASCII characters"); + } + + Operations operations(publicId, level, label, operation); + Apply(operations); + } }
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Tue Apr 04 07:09:22 2023 +0200 @@ -37,15 +37,18 @@ class ParsedDicomFile; struct ServerIndexChange; - struct ExpandedResource : public boost::noncopyable + class ExpandedResource : public boost::noncopyable { + private: std::string id_; - DicomMap tags_; // all main tags and main sequences from DB + ResourceType level_; + DicomMap tags_; // all main tags and main sequences from DB + + public: std::string mainDicomTagsSignature_; std::string parentId_; std::list<std::string> childrenIds_; std::map<MetadataType, std::string> metadata_; - ResourceType type_; std::string anonymizedFrom_; std::string modifiedFrom_; std::string lastUpdate_; @@ -62,18 +65,51 @@ size_t fileSize_; std::string fileUuid_; int indexInSeries_; + + // New in Orthanc 1.12.0 + std::set<std::string> labels_; + + public: + void SetResource(ResourceType level, + const std::string& id) + { + level_ = level; + id_ = id; + } + + const std::string& GetPublicId() const + { + return id_; + } + + ResourceType GetLevel() const + { + return level_; + } + + DicomMap& GetMainDicomTags() + { + return tags_; + } + + const DicomMap& GetMainDicomTags() const + { + return tags_; + } }; - enum ExpandResourceDbFlags + enum ExpandResourceFlags { - ExpandResourceDbFlags_None = 0, - ExpandResourceDbFlags_IncludeMetadata = (1 << 0), - ExpandResourceDbFlags_IncludeChildren = (1 << 1), - ExpandResourceDbFlags_IncludeMainDicomTags = (1 << 2), + ExpandResourceFlags_None = 0, + ExpandResourceFlags_IncludeMetadata = (1 << 0), + ExpandResourceFlags_IncludeChildren = (1 << 1), + ExpandResourceFlags_IncludeMainDicomTags = (1 << 2), + ExpandResourceFlags_IncludeLabels = (1 << 3), - ExpandResourceDbFlags_Default = (ExpandResourceDbFlags_IncludeMetadata | - ExpandResourceDbFlags_IncludeChildren | - ExpandResourceDbFlags_IncludeMainDicomTags) + ExpandResourceFlags_Default = (ExpandResourceFlags_IncludeMetadata | + ExpandResourceFlags_IncludeChildren | + ExpandResourceFlags_IncludeMainDicomTags | + ExpandResourceFlags_IncludeLabels) }; class StatelessDatabaseOperations : public boost::noncopyable @@ -82,6 +118,12 @@ typedef std::list<FileInfo> Attachments; typedef std::map<std::pair<ResourceType, MetadataType>, std::string> MetadataMap; + enum LabelOperation + { + LabelOperation_Add, + LabelOperation_Remove + }; + class ITransactionContext : public IDatabaseListener { public: @@ -157,9 +199,11 @@ std::list<std::string>* instancesId, // Can be NULL if not needed const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, - size_t limit) + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, + uint32_t limit) { - return transaction_.ApplyLookupResources(resourcesId, instancesId, lookup, queryLevel, limit); + return transaction_.ApplyLookupResources(resourcesId, instancesId, lookup, queryLevel, withLabels, withoutLabels, limit); } void GetAllMetadata(std::map<MetadataType, std::string>& target, @@ -177,7 +221,7 @@ void GetAllPublicIds(std::list<std::string>& target, ResourceType resourceType, size_t since, - size_t limit) + uint32_t limit) { return transaction_.GetAllPublicIds(target, resourceType, since, limit); } @@ -185,9 +229,9 @@ void GetChanges(std::list<ServerIndexChange>& target /*out*/, bool& done /*out*/, int64_t since, - uint32_t maxResults) + uint32_t limit) { - transaction_.GetChanges(target, done, since, maxResults); + transaction_.GetChanges(target, done, since, limit); } void GetChildrenInternalId(std::list<int64_t>& target, @@ -205,9 +249,9 @@ void GetExportedResources(std::list<ExportedResource>& target /*out*/, bool& done /*out*/, int64_t since, - uint32_t maxResults) + uint32_t limit) { - return transaction_.GetExportedResources(target, done, since, maxResults); + return transaction_.GetExportedResources(target, done, since, limit); } void GetLastChange(std::list<ServerIndexChange>& target /*out*/) @@ -310,6 +354,12 @@ { return transaction_.LookupResourceAndParent(id, type, parentPublicId, publicId); } + + void ListLabels(std::set<std::string>& target, + int64_t id) + { + transaction_.ListLabels(target, id); + } }; @@ -422,6 +472,18 @@ unsigned int maximumPatients, uint64_t addedInstanceSize, const std::string& newPatientId); + + void AddLabel(int64_t id, + const std::string& label) + { + transaction_.AddLabel(id, label); + } + + void RemoveLabel(int64_t id, + const std::string& label) + { + transaction_.RemoveLabel(id, label); + } }; @@ -503,7 +565,7 @@ const std::string& publicId, ResourceType level, const std::set<DicomTag>& requestedTags, - ExpandResourceDbFlags expandFlags); + ExpandResourceFlags expandFlags); void GetAllMetadata(std::map<MetadataType, std::string>& target, const std::string& publicId, @@ -515,7 +577,7 @@ void GetAllUuids(std::list<std::string>& target, ResourceType resourceType, size_t since, - size_t limit); + uint32_t limit); void GetGlobalStatistics(/* out */ uint64_t& diskSize, /* out */ uint64_t& uncompressedSize, @@ -531,13 +593,13 @@ void GetChanges(Json::Value& target, int64_t since, - unsigned int maxResults); + uint32_t limit); void GetLastChange(Json::Value& target); void GetExportedResources(Json::Value& target, int64_t since, - unsigned int maxResults); + uint32_t limit); void GetLastExportedResource(Json::Value& target); @@ -605,7 +667,9 @@ std::vector<std::string>* instancesId, // Can be NULL if not needed const DatabaseLookup& lookup, ResourceType queryLevel, - size_t limit); + const std::set<std::string>& withLabels, + const std::set<std::string>& withoutLabels, + uint32_t limit); bool DeleteResource(Json::Value& remainingAncestor /* out */, const std::string& uuid, @@ -683,5 +747,14 @@ bool hasOldRevision, int64_t oldRevision, const std::string& oldMd5); + + void ListLabels(std::set<std::string>& target, + const std::string& publicId, + ResourceType level); + + void ModifyLabel(const std::string& publicId, + ResourceType level, + const std::string& label, + LabelOperation operation); }; }
--- a/OrthancServer/Sources/OrthancFindRequestHandler.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/OrthancFindRequestHandler.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -59,7 +59,8 @@ requestedTags.erase(DICOM_TAG_QUERY_RETRIEVE_LEVEL); // this is not part of the answer // reuse ExpandResource to get missing tags and computed tags (ModalitiesInStudy ...). This code is therefore shared between C-Find, tools/find, list-resources and QIDO-RS - context.ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, level, requestedTags, ExpandResourceDbFlags_IncludeMainDicomTags, allowStorageAccess); + context.ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, + level, requestedTags, ExpandResourceFlags_IncludeMainDicomTags, allowStorageAccess); DicomMap result; @@ -84,7 +85,7 @@ else { const DicomTag& tag = query.GetElement(i).GetTag(); - const DicomValue* value = resource.tags_.TestAndGetValue(tag); + const DicomValue* value = resource.GetMainDicomTags().TestAndGetValue(tag); if (value != NULL && !value->IsNull() &&
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -1971,6 +1971,129 @@ + // Handling of labels ------------------------------------------------------- + + static void ListLabels(RestApiGetCall& call) + { + if (call.IsDocumentation()) + { + ResourceType t = StringToResourceType(call.GetFullUri()[0].c_str()); + std::string r = GetResourceTypeText(t, false /* plural */, false /* upper case */); + call.GetDocumentation() + .SetTag(GetResourceTypeText(t, true /* plural */, true /* upper case */)) + .SetSummary("List labels (new in Orthanc 1.12.0)") + .SetDescription("Get the labels that are associated with the given " + r) + .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest") + .AddAnswerType(MimeType_Json, "JSON array containing the names of the labels") + .SetHttpGetSample(GetDocumentationSampleResource(t) + "/labels", true); + return; + } + + assert(!call.GetFullUri().empty()); + const std::string publicId = call.GetUriComponent("id", ""); + ResourceType level = StringToResourceType(call.GetFullUri() [0].c_str()); + + std::set<std::string> labels; + OrthancRestApi::GetIndex(call).ListLabels(labels, publicId, level); + + Json::Value result = Json::arrayValue; + + for (std::set<std::string>::const_iterator it = labels.begin(); it != labels.end(); ++it) + { + result.append(*it); + } + + call.GetOutput().AnswerJson(result); + } + + + static void GetLabel(RestApiGetCall& call) + { + if (call.IsDocumentation()) + { + ResourceType t = StringToResourceType(call.GetFullUri()[0].c_str()); + std::string r = GetResourceTypeText(t, false /* plural */, false /* upper case */); + call.GetDocumentation() + .SetTag(GetResourceTypeText(t, true /* plural */, true /* upper case */)) + .SetSummary("Test label") + .SetDescription("Test whether the " + r + " is associated with the given label") + .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest") + .SetUriArgument("label", "The label of interest") + .AddAnswerType(MimeType_PlainText, "Empty string is returned in the case of presence, error 404 in the case of absence"); + return; + } + + CheckValidResourceType(call); + + assert(!call.GetFullUri().empty()); + const std::string publicId = call.GetUriComponent("id", ""); + const ResourceType level = StringToResourceType(call.GetFullUri() [0].c_str()); + + std::string label = call.GetUriComponent("label", ""); + + std::set<std::string> labels; + OrthancRestApi::GetIndex(call).ListLabels(labels, publicId, level); + + if (labels.find(label) != labels.end()) + { + call.GetOutput().AnswerBuffer("", MimeType_PlainText); + } + } + + + static void AddLabel(RestApiPutCall& call) + { + if (call.IsDocumentation()) + { + ResourceType t = StringToResourceType(call.GetFullUri()[0].c_str()); + std::string r = GetResourceTypeText(t, false /* plural */, false /* upper case */); + call.GetDocumentation() + .SetTag(GetResourceTypeText(t, true /* plural */, true /* upper case */)) + .SetSummary("Add label") + .SetDescription("Associate a label with a " + r) + .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest") + .SetUriArgument("label", "The label to be added"); + return; + } + + CheckValidResourceType(call); + + std::string publicId = call.GetUriComponent("id", ""); + const ResourceType level = StringToResourceType(call.GetFullUri() [0].c_str()); + + std::string label = call.GetUriComponent("label", ""); + OrthancRestApi::GetIndex(call).ModifyLabel(publicId, level, label, StatelessDatabaseOperations::LabelOperation_Add); + + call.GetOutput().AnswerBuffer("", MimeType_PlainText); + } + + + static void RemoveLabel(RestApiDeleteCall& call) + { + if (call.IsDocumentation()) + { + ResourceType t = StringToResourceType(call.GetFullUri()[0].c_str()); + std::string r = GetResourceTypeText(t, false /* plural */, false /* upper case */); + call.GetDocumentation() + .SetTag(GetResourceTypeText(t, true /* plural */, true /* upper case */)) + .SetSummary("Remove label") + .SetDescription("Remove a label associated with a " + r) + .SetUriArgument("id", "Orthanc identifier of the " + r + " of interest") + .SetUriArgument("label", "The label to be removed"); + return; + } + + CheckValidResourceType(call); + + std::string publicId = call.GetUriComponent("id", ""); + const ResourceType level = StringToResourceType(call.GetFullUri() [0].c_str()); + + std::string label = call.GetUriComponent("label", ""); + OrthancRestApi::GetIndex(call).ModifyLabel(publicId, level, label, StatelessDatabaseOperations::LabelOperation_Remove); + + call.GetOutput().AnswerBuffer("", MimeType_PlainText); + } + // Handling of attached files ----------------------------------------------- @@ -3854,6 +3977,12 @@ Register("/" + resourceTypes[i] + "/{id}/metadata/{name}", GetMetadata); Register("/" + resourceTypes[i] + "/{id}/metadata/{name}", SetMetadata); + // New in Orthanc 1.12.0 + Register("/" + resourceTypes[i] + "/{id}/labels", ListLabels); + Register("/" + resourceTypes[i] + "/{id}/labels/{label}", GetLabel); + Register("/" + resourceTypes[i] + "/{id}/labels/{label}", RemoveLabel); + Register("/" + resourceTypes[i] + "/{id}/labels/{label}", AddLabel); + Register("/" + resourceTypes[i] + "/{id}/attachments", ListAttachments); Register("/" + resourceTypes[i] + "/{id}/attachments/{name}", DeleteAttachment); Register("/" + resourceTypes[i] + "/{id}/attachments/{name}", GetAttachmentOperations);
--- a/OrthancServer/Sources/Search/DatabaseLookup.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Search/DatabaseLookup.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -368,4 +368,30 @@ return clone.release(); } + + + void DatabaseLookup::AddWithLabel(const std::string& label) + { + if (label.empty()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + withLabels_.insert(label); + } + } + + + void DatabaseLookup::AddWithoutLabel(const std::string& label) + { + if (label.empty()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + withoutLabels_.insert(label); + } + } }
--- a/OrthancServer/Sources/Search/DatabaseLookup.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/Search/DatabaseLookup.h Tue Apr 04 07:09:22 2023 +0200 @@ -32,6 +32,8 @@ { private: std::vector<DicomTagConstraint*> constraints_; + std::set<std::string> withLabels_; + std::set<std::string> withoutLabels_; void AddDicomConstraintInternal(const DicomTag& tag, ValueRepresentation vr, @@ -92,5 +94,19 @@ bool HasTag(const DicomTag& tag) const; void RemoveConstraint(const DicomTag& tag); + + void AddWithLabel(const std::string& label); + + void AddWithoutLabel(const std::string& label); + + const std::set<std::string>& GetWithLabels() const + { + return withLabels_; + } + + const std::set<std::string>& GetWithoutLabels() const + { + return withoutLabels_; + } }; }
--- a/OrthancServer/Sources/ServerContext.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/ServerContext.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -1448,8 +1448,9 @@ } { - const size_t lookupLimit = (databaseLimit == 0 ? 0 : databaseLimit + 1); - GetIndex().ApplyLookupResources(resources, &instances, *fastLookup, queryLevel, lookupLimit); + const size_t lookupLimit = (databaseLimit == 0 ? 0 : databaseLimit + 1); + GetIndex().ApplyLookupResources(resources, &instances, *fastLookup, queryLevel, + lookup.GetWithLabels(), lookup.GetWithoutLabels(), lookupLimit); } bool complete = (databaseLimit == 0 || @@ -1542,7 +1543,7 @@ ComputeStudyTags(resource, *this, resources[i], requestedTags); std::vector<std::string> modalities; - Toolbox::TokenizeString(modalities, resource.tags_.GetValue(DICOM_TAG_MODALITIES_IN_STUDY).GetContent(), '\\'); + Toolbox::TokenizeString(modalities, resource.GetMainDicomTags().GetValue(DICOM_TAG_MODALITIES_IN_STUDY).GetContent(), '\\'); bool hasAtLeastOneModalityMatching = false; for (size_t m = 0; m < modalities.size(); m++) { @@ -1551,7 +1552,7 @@ isMatch = isMatch && hasAtLeastOneModalityMatching; // copy the value of ModalitiesInStudy such that it can be reused to build the answer - allMainDicomTagsFromDB.SetValue(DICOM_TAG_MODALITIES_IN_STUDY, resource.tags_.GetValue(DICOM_TAG_MODALITIES_IN_STUDY)); + allMainDicomTagsFromDB.SetValue(DICOM_TAG_MODALITIES_IN_STUDY, resource.GetMainDicomTags().GetValue(DICOM_TAG_MODALITIES_IN_STUDY)); } if (isMatch) @@ -1990,10 +1991,10 @@ { target = Json::objectValue; - target["Type"] = GetResourceTypeText(resource.type_, false, true); - target["ID"] = resource.id_; + target["Type"] = GetResourceTypeText(resource.GetLevel(), false, true); + target["ID"] = resource.GetPublicId(); - switch (resource.type_) + switch (resource.GetLevel()) { case ResourceType_Patient: break; @@ -2014,7 +2015,7 @@ throw OrthancException(ErrorCode_InternalError); } - switch (resource.type_) + switch (resource.GetLevel()) { case ResourceType_Patient: case ResourceType_Study: @@ -2028,11 +2029,11 @@ c.append(*it); } - if (resource.type_ == ResourceType_Patient) + if (resource.GetLevel() == ResourceType_Patient) { target["Studies"] = c; } - else if (resource.type_ == ResourceType_Study) + else if (resource.GetLevel() == ResourceType_Study) { target["Series"] = c; } @@ -2050,7 +2051,7 @@ throw OrthancException(ErrorCode_InternalError); } - switch (resource.type_) + switch (resource.GetLevel()) { case ResourceType_Patient: case ResourceType_Study: @@ -2099,9 +2100,9 @@ target["ModifiedFrom"] = resource.modifiedFrom_; } - if (resource.type_ == ResourceType_Patient || - resource.type_ == ResourceType_Study || - resource.type_ == ResourceType_Series) + if (resource.GetLevel() == ResourceType_Patient || + resource.GetLevel() == ResourceType_Study || + resource.GetLevel() == ResourceType_Series) { target["IsStable"] = resource.isStable_; @@ -2117,15 +2118,15 @@ static const char* const PATIENT_MAIN_DICOM_TAGS = "PatientMainDicomTags"; DicomMap mainDicomTags; - resource.tags_.ExtractResourceInformation(mainDicomTags, resource.type_); + resource.GetMainDicomTags().ExtractResourceInformation(mainDicomTags, resource.GetLevel()); target[MAIN_DICOM_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format); - if (resource.type_ == ResourceType_Study) + if (resource.GetLevel() == ResourceType_Study) { DicomMap patientMainDicomTags; - resource.tags_.ExtractPatientInformation(patientMainDicomTags); + resource.GetMainDicomTags().ExtractPatientInformation(patientMainDicomTags); target[PATIENT_MAIN_DICOM_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[PATIENT_MAIN_DICOM_TAGS], patientMainDicomTags, format); @@ -2136,13 +2137,23 @@ static const char* const REQUESTED_TAGS = "RequestedTags"; DicomMap tags; - resource.tags_.ExtractTags(tags, requestedTags); + resource.GetMainDicomTags().ExtractTags(tags, requestedTags); target[REQUESTED_TAGS] = Json::objectValue; FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format); } + { + Json::Value labels = Json::arrayValue; + + for (std::set<std::string>::const_iterator it = resource.labels_.begin(); it != resource.labels_.end(); ++it) + { + labels.append(*it); + } + + target["Labels"] = labels; + } } @@ -2153,7 +2164,7 @@ { if (requestedTags.count(DICOM_TAG_INSTANCE_AVAILABILITY) > 0) { - resource.tags_.SetValue(DICOM_TAG_INSTANCE_AVAILABILITY, "ONLINE", false); + resource.GetMainDicomTags().SetValue(DICOM_TAG_INSTANCE_AVAILABILITY, "ONLINE", false); resource.missingRequestedTags_.erase(DICOM_TAG_INSTANCE_AVAILABILITY); } } @@ -2171,7 +2182,7 @@ index.GetChildren(instances, seriesPublicId); - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES); } @@ -2216,13 +2227,13 @@ std::string modalities; Toolbox::JoinStrings(modalities, values, "\\"); - resource.tags_.SetValue(DICOM_TAG_MODALITIES_IN_STUDY, modalities, false); + resource.GetMainDicomTags().SetValue(DICOM_TAG_MODALITIES_IN_STUDY, modalities, false); resource.missingRequestedTags_.erase(DICOM_TAG_MODALITIES_IN_STUDY); } if (hasNbRelatedSeries) { - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES, boost::lexical_cast<std::string>(series.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES); } @@ -2240,7 +2251,7 @@ if (hasNbRelatedInstances) { - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES); } @@ -2264,7 +2275,7 @@ { std::string sopClassUids; Toolbox::JoinStrings(sopClassUids, values, "\\"); - resource.tags_.SetValue(DICOM_TAG_SOP_CLASSES_IN_STUDY, sopClassUids, false); + resource.GetMainDicomTags().SetValue(DICOM_TAG_SOP_CLASSES_IN_STUDY, sopClassUids, false); } resource.missingRequestedTags_.erase(DICOM_TAG_SOP_CLASSES_IN_STUDY); @@ -2291,7 +2302,7 @@ if (hasNbRelatedStudies) { - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES, boost::lexical_cast<std::string>(studies.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES); } @@ -2308,7 +2319,7 @@ if (hasNbRelatedSeries) { - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES, boost::lexical_cast<std::string>(series.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES); } @@ -2324,7 +2335,7 @@ instances.splice(instances.end(), thisInstancesIds); } - resource.tags_.SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES, + resource.GetMainDicomTags().SetValue(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES, boost::lexical_cast<std::string>(instances.size()), false); resource.missingRequestedTags_.erase(DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES); } @@ -2388,7 +2399,7 @@ { ExpandedResource resource; - if (ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, level, requestedTags, ExpandResourceDbFlags_Default, allowStorageAccess)) + if (ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, level, requestedTags, ExpandResourceFlags_Default, allowStorageAccess)) { SerializeExpandedResource(target, resource, format, requestedTags); return true; @@ -2404,57 +2415,63 @@ const Json::Value* dicomAsJson, // optional: the dicom-as-json for the resource (if already available) ResourceType level, const std::set<DicomTag>& requestedTags, - ExpandResourceDbFlags expandFlags, + ExpandResourceFlags expandFlags, bool allowStorageAccess) { // first try to get the tags from what is already available - if ((expandFlags & ExpandResourceDbFlags_IncludeMainDicomTags) - && (mainDicomTags.GetSize() > 0) - && (dicomAsJson != NULL)) + if ((expandFlags & ExpandResourceFlags_IncludeMainDicomTags) && + mainDicomTags.GetSize() > 0 && + dicomAsJson != NULL) { - resource.tags_.Merge(mainDicomTags); + resource.GetMainDicomTags().Merge(mainDicomTags); if (dicomAsJson->isObject()) { - resource.tags_.FromDicomAsJson(*dicomAsJson); + resource.GetMainDicomTags().FromDicomAsJson(*dicomAsJson); } std::set<DicomTag> retrievedTags; std::set<DicomTag> missingTags; - resource.tags_.GetTags(retrievedTags); + resource.GetMainDicomTags().GetTags(retrievedTags); Toolbox::GetMissingsFromSet(missingTags, requestedTags, retrievedTags); // if all possible tags have been read, no need to get them from DB anymore if (missingTags.size() == 0 || DicomMap::HasOnlyComputedTags(missingTags)) { - expandFlags = static_cast<ExpandResourceDbFlags>(expandFlags & ~ExpandResourceDbFlags_IncludeMainDicomTags); + expandFlags = static_cast<ExpandResourceFlags>(expandFlags & ~ExpandResourceFlags_IncludeMainDicomTags); } - if (missingTags.size() == 0 && expandFlags == ExpandResourceDbFlags_None) // we have already retrieved anything we need + if (missingTags.size() == 0 && expandFlags == ExpandResourceFlags_None) // we have already retrieved anything we need { return true; } } - if (expandFlags != ExpandResourceDbFlags_None - && GetIndex().ExpandResource(resource, publicId, level, requestedTags, static_cast<ExpandResourceDbFlags>(expandFlags | ExpandResourceDbFlags_IncludeMetadata))) // we always need the metadata to get the mainDicomTagsSignature + if (expandFlags != ExpandResourceFlags_None && + GetIndex().ExpandResource(resource, publicId, level, requestedTags, + static_cast<ExpandResourceFlags>(expandFlags | ExpandResourceFlags_IncludeMetadata))) // we always need the metadata to get the mainDicomTagsSignature { // check the main dicom tags list has not changed since the resource was stored - if (resource.mainDicomTagsSignature_ != DicomMap::GetMainDicomTagsSignature(resource.type_)) + if (resource.mainDicomTagsSignature_ != DicomMap::GetMainDicomTagsSignature(resource.GetLevel())) { OrthancConfiguration::ReaderLock lock; if (lock.GetConfiguration().IsWarningEnabled(Warnings_002_InconsistentDicomTagsInDb)) { - LOG(WARNING) << "W002: " << Orthanc::GetResourceTypeText(resource.type_, false , false) << " has been stored with another version of Main Dicom Tags list, you should POST to /" << Orthanc::GetResourceTypeText(resource.type_, true, false) << "/" << resource.id_ << "/reconstruct to update the list of tags saved in DB. Some MainDicomTags might be missing from this answer."; + LOG(WARNING) << "W002: " << Orthanc::GetResourceTypeText(resource.GetLevel(), false , false) + << " has been stored with another version of Main Dicom Tags list, you should POST to /" + << Orthanc::GetResourceTypeText(resource.GetLevel(), true, false) + << "/" << resource.GetPublicId() + << "/reconstruct to update the list of tags saved in DB. Some MainDicomTags might be missing from this answer."; } } // possibly merge missing requested tags from dicom-as-json - if (allowStorageAccess - && !resource.missingRequestedTags_.empty() && !DicomMap::HasOnlyComputedTags(resource.missingRequestedTags_)) + if (allowStorageAccess && + !resource.missingRequestedTags_.empty() && + !DicomMap::HasOnlyComputedTags(resource.missingRequestedTags_)) { OrthancConfiguration::ReaderLock lock; if (lock.GetConfiguration().IsWarningEnabled(Warnings_001_TagsBeingReadFromStorage)) @@ -2472,7 +2489,9 @@ std::string missings; FromDcmtkBridge::FormatListOfTags(missings, missingTags); - LOG(WARNING) << "W001: Accessing Dicom tags from storage when accessing " << Orthanc::GetResourceTypeText(resource.type_, false , false) << " : " << missings; + LOG(WARNING) << "W001: Accessing Dicom tags from storage when accessing " + << Orthanc::GetResourceTypeText(resource.GetLevel(), false, false) + << " : " << missings; } @@ -2508,7 +2527,7 @@ tagsFromJson.FromDicomAsJson(*dicomAsJson, false /* append */, true /* parseSequences*/); } - resource.tags_.Merge(tagsFromJson); + resource.GetMainDicomTags().Merge(tagsFromJson); } // compute the requested tags
--- a/OrthancServer/Sources/ServerContext.h Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/ServerContext.h Tue Apr 04 07:09:22 2023 +0200 @@ -585,7 +585,7 @@ const Json::Value* dicomAsJson, // optional: the dicom-as-json for the resource ResourceType level, const std::set<DicomTag>& requestedTags, - ExpandResourceDbFlags expandFlags, + ExpandResourceFlags expandFlags, bool allowStorageAccess); FindStorageAccessMode GetFindStorageAccessMode() const
--- a/OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -675,9 +675,12 @@ replacePatientMainDicomTags |= DicomMap::IsMainDicomTag(*it, ResourceType_Patient); } - if ((modificationLevel == ResourceType_Study || modificationLevel == ResourceType_Patient) - && !modification_->IsReplaced(DICOM_TAG_PATIENT_ID) - && modification_->IsKept(DICOM_TAG_STUDY_INSTANCE_UID) && modification_->IsKept(DICOM_TAG_SERIES_INSTANCE_UID) && modification_->IsKept(DICOM_TAG_SOP_INSTANCE_UID)) + if ((modificationLevel == ResourceType_Study || + modificationLevel == ResourceType_Patient) && + !modification_->IsReplaced(DICOM_TAG_PATIENT_ID) && + modification_->IsKept(DICOM_TAG_STUDY_INSTANCE_UID) && + modification_->IsKept(DICOM_TAG_SERIES_INSTANCE_UID) && + modification_->IsKept(DICOM_TAG_SOP_INSTANCE_UID)) { // if we keep the SOPInstanceUID, it very likely means that we are modifying existing resources 'in place' @@ -715,9 +718,9 @@ else { ExpandedResource originalStudy; - if (GetContext().GetIndex().ExpandResource(originalStudy, *studyId, ResourceType_Study, emptyRequestedTags, ExpandResourceDbFlags_IncludeMainDicomTags)) + if (GetContext().GetIndex().ExpandResource(originalStudy, *studyId, ResourceType_Study, emptyRequestedTags, ExpandResourceFlags_IncludeMainDicomTags)) { - targetPatientId = originalStudy.tags_.GetStringValue(DICOM_TAG_PATIENT_ID, "", false); + targetPatientId = originalStudy.GetMainDicomTags().GetStringValue(DICOM_TAG_PATIENT_ID, "", false); } else { @@ -734,7 +737,7 @@ { ExpandedResource targetPatient; - if (GetContext().GetIndex().ExpandResource(targetPatient, lookupPatientResult[0], ResourceType_Patient, emptyRequestedTags, static_cast<ExpandResourceDbFlags>(ExpandResourceDbFlags_IncludeMainDicomTags | ExpandResourceDbFlags_IncludeChildren))) + if (GetContext().GetIndex().ExpandResource(targetPatient, lookupPatientResult[0], ResourceType_Patient, emptyRequestedTags, static_cast<ExpandResourceFlags>(ExpandResourceFlags_IncludeMainDicomTags | ExpandResourceFlags_IncludeChildren))) { const std::list<std::string> childrenIds = targetPatient.childrenIds_; bool targetPatientHasOtherStudies = childrenIds.size() > 1; @@ -747,7 +750,7 @@ { // this is allowed if all patient replacedTags do match the target patient tags DicomMap targetPatientTags; - targetPatient.tags_.ExtractPatientInformation(targetPatientTags); + targetPatient.GetMainDicomTags().ExtractPatientInformation(targetPatientTags); std::set<DicomTag> mainPatientTags; DicomMap::GetMainDicomTags(mainPatientTags, ResourceType_Patient); @@ -755,9 +758,9 @@ for (std::set<DicomTag>::const_iterator mainPatientTag = mainPatientTags.begin(); mainPatientTag != mainPatientTags.end(); ++mainPatientTag) { - if (targetPatientTags.HasTag(*mainPatientTag) - && (!modification_->IsReplaced(*mainPatientTag) - || modification_->GetReplacementAsString(*mainPatientTag) != targetPatientTags.GetStringValue(*mainPatientTag, "", false))) + if (targetPatientTags.HasTag(*mainPatientTag) && + (!modification_->IsReplaced(*mainPatientTag) || + modification_->GetReplacementAsString(*mainPatientTag) != targetPatientTags.GetStringValue(*mainPatientTag, "", false))) { throw OrthancException(ErrorCode_BadRequest, std::string("Trying to change patient tags in a study. The Patient already exists and has other studies. All the 'Replace' tags should match the existing patient main dicom tags. Try using /patients/../modify instead to modify the patient. Failing tag: ") + mainPatientTag->Format()); } @@ -769,8 +772,7 @@ } } } - } - + } } } }
--- a/OrthancServer/UnitTestsSources/ServerIndexTests.cpp Mon Apr 03 22:31:32 2023 +0200 +++ b/OrthancServer/UnitTestsSources/ServerIndexTests.cpp Tue Apr 04 07:09:22 2023 +0200 @@ -167,8 +167,9 @@ std::vector<DatabaseConstraint> lookup; lookup.push_back(c.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); - - transaction_->ApplyLookupResources(result, NULL, lookup, level, 0 /* no limit */); + + std::set<std::string> noLabel; + transaction_->ApplyLookupResources(result, NULL, lookup, level, noLabel, noLabel, 0 /* no limit */); } void DoLookupIdentifier2(std::list<std::string>& result, @@ -188,7 +189,8 @@ lookup.push_back(c1.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); lookup.push_back(c2.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); - transaction_->ApplyLookupResources(result, NULL, lookup, level, 0 /* no limit */); + std::set<std::string> noLabel; + transaction_->ApplyLookupResources(result, NULL, lookup, level, noLabel, noLabel, 0 /* no limit */); } }; }