Mercurial > hg > orthanc
changeset 5758:ca06dde85358 large-queries
merged find-refactoring -> large-queries
| author | Alain Mazy <am@orthanc.team> |
|---|---|
| date | Thu, 05 Sep 2024 18:52:27 +0200 |
| parents | 5463c3ae3235 (current diff) fc591f166d53 (diff) |
| children | 868e3df40d5e 29af9fc796d2 |
| files | NEWS OrthancFramework/Sources/SQLite/Connection.h OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.cpp OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h OrthancServer/Plugins/Include/orthanc/OrthancDatabasePlugin.proto OrthancServer/Sources/Database/BaseDatabaseWrapper.cpp OrthancServer/Sources/Database/BaseDatabaseWrapper.h OrthancServer/Sources/Database/IDatabaseWrapper.h OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp OrthancServer/Sources/Database/SQLiteDatabaseWrapper.h OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp OrthancServer/Sources/Database/StatelessDatabaseOperations.h OrthancServer/Sources/OrthancRestApi/OrthancRestChanges.cpp OrthancServer/Sources/ServerEnumerations.h |
| diffstat | 70 files changed, 7239 insertions(+), 804 deletions(-) [+] |
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--- a/NEWS Thu Sep 05 18:21:56 2024 +0200 +++ b/NEWS Thu Sep 05 18:52:27 2024 +0200 @@ -1,8 +1,12 @@ Pending changes in the mainline =============================== +* TODO-FIND: complete the list of updated routes: + - /studies?expand and sibbling routes now also return "Metadata" (if the DB implements 'extended-api-v1') + - /studies?since=x&limit=0 and sibbling routes: limit=0 now means "no limit" instead of "no results" + REST API ------------ +-------- * Improved parsing of multiple numerical values in DICOM tags. https://discourse.orthanc-server.org/t/qido-includefield-with-sequences/4746/6 @@ -14,7 +18,6 @@ - 'to' to potentially cycle through changes in reverse order. example: /changes?type=StableStudy&to=7584&limit=100 - Maintenance ----------- @@ -24,6 +27,17 @@ DB plugins that are implementing the UpdateAndGetStatistics function (currently only PostgreSQL). This avoids very long update times in case you don't call /statistics for a long period. +* Fix C-Find queries not returning computed tags like ModalitiesInStudy, NumberOfStudyRelatedSeries, ... + in very specific use-cases. +* Fix extremely rare error when 2 threads are trying to create the same folder in the File Storage + at the same time. +* Upgraded dependencies for static builds: + - curl 8.9.0 +* Added a new fallback when trying to decode a frame: transcode the file using the plugin + before decoding the frame. This solves some issues with JP2K Lossy compression: + https://discourse.orthanc-server.org/t/decoding-displaying-jpeg2000-lossy-images/5117 +* Added a new warning that can be disabled in the configuration: W003_DecoderFailure + Version 1.12.4 (2024-06-05)
--- a/OrthancFramework/Resources/CMake/Compiler.cmake Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Resources/CMake/Compiler.cmake Thu Sep 05 18:52:27 2024 +0200 @@ -232,6 +232,10 @@ endif() elseif (${CMAKE_SYSTEM_NAME} STREQUAL "Darwin") + + # fix this error that appears with recent compilers on MacOS: boost/mpl/aux_/integral_wrapper.hpp:73:31: error: integer value -1 is outside the valid range of values [0, 3] for this enumeration type [-Wenum-constexpr-conversion] + SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-enum-constexpr-conversion") + add_definitions( -D_XOPEN_SOURCE=1 )
--- a/OrthancFramework/Resources/CMake/LibCurlConfiguration.cmake Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Resources/CMake/LibCurlConfiguration.cmake Thu Sep 05 18:52:27 2024 +0200 @@ -21,9 +21,9 @@ if (STATIC_BUILD OR NOT USE_SYSTEM_CURL) - SET(CURL_SOURCES_DIR ${CMAKE_BINARY_DIR}/curl-8.5.0) - SET(CURL_URL "https://orthanc.uclouvain.be/downloads/third-party-downloads/curl-8.5.0.tar.gz") - SET(CURL_MD5 "0bc69288b20ae165ff4b7d6d7bbe70d2") + SET(CURL_SOURCES_DIR ${CMAKE_BINARY_DIR}/curl-8.9.0) + SET(CURL_URL "https://orthanc.uclouvain.be/downloads/third-party-downloads/curl-8.9.0.tar.gz") + SET(CURL_MD5 "f9bca5d4d5bac1f04e6c5eb4d0418618") if (IS_DIRECTORY "${CURL_SOURCES_DIR}") set(FirstRun OFF) @@ -36,7 +36,7 @@ if (FirstRun) execute_process( COMMAND ${PATCH_EXECUTABLE} -p0 -N -i - ${CMAKE_CURRENT_LIST_DIR}/../Patches/curl-8.5.0.patch + ${CMAKE_CURRENT_LIST_DIR}/../Patches/curl-8.9.0.patch WORKING_DIRECTORY ${CMAKE_BINARY_DIR} RESULT_VARIABLE Failure )
--- a/OrthancFramework/Resources/Patches/curl-8.5.0.patch Thu Sep 05 18:21:56 2024 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -diff -urEb curl-8.5.0.orig/CMake/Macros.cmake curl-8.5.0/CMake/Macros.cmake ---- curl-8.5.0.orig/CMake/Macros.cmake 2024-01-24 17:21:21.387965189 +0100 -+++ curl-8.5.0/CMake/Macros.cmake 2024-01-24 17:21:48.523719072 +0100 -@@ -48,7 +48,7 @@ - message(STATUS "Performing Curl Test ${CURL_TEST}") - try_compile(${CURL_TEST} - ${CMAKE_BINARY_DIR} -- ${CMAKE_CURRENT_SOURCE_DIR}/CMake/CurlTests.c -+ ${CURL_SOURCES_DIR}/CMake/CurlTests.c - CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS} - "${CURL_TEST_ADD_LIBRARIES}" - OUTPUT_VARIABLE OUTPUT)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancFramework/Resources/Patches/curl-8.9.0.patch Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,12 @@ +diff -urEb curl-8.9.0.orig/CMake/Macros.cmake curl-8.9.0/CMake/Macros.cmake +--- curl-8.9.0.orig/CMake/Macros.cmake 2024-07-26 18:47:52.920588300 +0200 ++++ curl-8.9.0/CMake/Macros.cmake 2024-07-26 18:48:08.345522100 +0200 +@@ -48,7 +48,7 @@ + message(STATUS "Performing Test ${CURL_TEST}") + try_compile(${CURL_TEST} + ${CMAKE_BINARY_DIR} +- ${CMAKE_CURRENT_SOURCE_DIR}/CMake/CurlTests.c ++ ${CURL_SOURCES_DIR}/CMake/CurlTests.c + CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS} + "${CURL_TEST_ADD_LIBRARIES}" + OUTPUT_VARIABLE OUTPUT)
--- a/OrthancFramework/Resources/Patches/protobuf-3.5.1.patch Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Resources/Patches/protobuf-3.5.1.patch Thu Sep 05 18:52:27 2024 +0200 @@ -2,7 +2,7 @@ --- protobuf-3.5.1.orig/src/google/protobuf/stubs/io_win32.cc 2023-03-26 20:13:45.095021011 +0200 +++ protobuf-3.5.1/src/google/protobuf/stubs/io_win32.cc 2023-03-26 20:19:19.932920102 +0200 @@ -91,7 +91,12 @@ - + template <typename char_type> bool null_or_empty(const char_type* s) { - return s == nullptr || *s == 0; @@ -13,5 +13,18 @@ + **/ + return s == NULL || *s == 0; } - + // Returns true if the path starts with a drive letter, e.g. "c:". +diff -urEb protobuf-3.5.1.orig/src/google/protobuf/stubs/hash.h protobuf-3.5.1/src/google/protobuf/stubs/hash.h +--- protobuf-3.5.1.orig/src/google/protobuf/stubs/hash.h 2023-03-26 20:13:45.095021011 +0200 ++++ protobuf-3.5.1/src/google/protobuf/stubs/hash.h 2023-03-26 20:19:19.932920102 +0200 +@@ -1,3 +1,9 @@ ++#if _MSC_VER >= 1930 // Since Visual Studio 2022 ++#define _SILENCE_STDEXT_HASH_DEPRECATION_WARNINGS ++#include <unordered_map> ++#include <hash_map> ++#endif ++ + // Protocol Buffers - Google's data interchange format + // Copyright 2008 Google Inc. All rights reserved. + // https://developers.google.com/protocol-buffers/ \ No newline at end of file
--- a/OrthancFramework/Sources/DicomFormat/DicomArray.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Sources/DicomFormat/DicomArray.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -95,7 +95,8 @@ } else if (v.IsSequence()) { - s = "(sequence)"; + //s = "(sequence)"; + s = "(sequence) " + v.GetSequenceContent().toStyledString(); } else {
--- a/OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -949,12 +949,12 @@ { throw OrthancException(ErrorCode_NotImplemented, "The built-in DCMTK decoder cannot decode some DICOM instance " - "whose transfer syntax is: " + std::string(GetTransferSyntaxUid(s))); + "whose transfer syntax is: " + std::string(GetTransferSyntaxUid(s)), false /* don't log here*/); } else { throw OrthancException(ErrorCode_NotImplemented, - "The built-in DCMTK decoder cannot decode some DICOM instance"); + "The built-in DCMTK decoder cannot decode some DICOM instance", false /* don't log here*/); } }
--- a/OrthancFramework/Sources/FileStorage/FilesystemStorage.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Sources/FileStorage/FilesystemStorage.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -24,6 +24,7 @@ #include "../PrecompiledHeaders.h" #include "FilesystemStorage.h" +#include <boost/thread.hpp> // http://stackoverflow.com/questions/1576272/storing-large-number-of-files-in-file-system // http://stackoverflow.com/questions/446358/storing-a-large-number-of-images @@ -135,26 +136,54 @@ { // Extremely unlikely case: This Uuid has already been created // in the past. - throw OrthancException(ErrorCode_InternalError); + throw OrthancException(ErrorCode_InternalError, "This file UUID already exists"); } - if (boost::filesystem::exists(path.parent_path())) + // In very unlikely cases, a thread could be deleting a + // directory while another thread needs it -> introduce 3 retries at 1 ms interval + int retryCount = 0; + const int maxRetryCount = 3; + + while (retryCount < maxRetryCount) { - if (!boost::filesystem::is_directory(path.parent_path())) + retryCount++; + if (retryCount > 1) + { + boost::this_thread::sleep(boost::posix_time::milliseconds(2 * retryCount + (rand() % 10))); + LOG(INFO) << "Retrying to create attachment \"" << uuid << "\" of \"" << GetDescriptionInternal(type) + << "\" type"; + } + + try + { + boost::filesystem::create_directories(path.parent_path()); // the function ensures that the directory exists or throws + } + catch (boost::filesystem::filesystem_error& er) { - throw OrthancException(ErrorCode_DirectoryOverFile); + if (er.code() == boost::system::errc::file_exists // the last element of the parent_path is a file + || er.code() == boost::system::errc::not_a_directory) // one of the element of the parent_path is not a directory + { + throw OrthancException(ErrorCode_DirectoryOverFile, "One of the element of the path is a file"); // no need to retry this error + } + + // ignore other errors and retry + } + + try + { + SystemToolbox::WriteFile(content, size, path.string(), fsyncOnWrite_); + + LOG(INFO) << "Created attachment \"" << uuid << "\" (" << timer.GetHumanTransferSpeed(true, size) << ")"; + return; + } + catch (OrthancException& ex) + { + if (retryCount >= maxRetryCount) + { + throw ex; + } } } - else - { - if (!boost::filesystem::create_directories(path.parent_path())) - { - throw OrthancException(ErrorCode_FileStorageCannotWrite); - } - } - - SystemToolbox::WriteFile(content, size, path.string(), fsyncOnWrite_); - LOG(INFO) << "Created attachment \"" << uuid << "\" (" << timer.GetHumanTransferSpeed(true, size) << ")"; }
--- a/OrthancFramework/Sources/SQLite/Connection.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/Sources/SQLite/Connection.h Thu Sep 05 18:52:27 2024 +0200 @@ -59,7 +59,6 @@ #define SQLITE_FROM_HERE ::Orthanc::SQLite::StatementId(__ORTHANC_FILE__, __LINE__) #define SQLITE_FROM_HERE_DYNAMIC(sql) ::Orthanc::SQLite::StatementId(__ORTHANC_FILE__, __LINE__, sql) - namespace Orthanc { namespace SQLite
--- a/OrthancFramework/UnitTestsSources/FileStorageTests.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancFramework/UnitTestsSources/FileStorageTests.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -37,6 +37,7 @@ #include "../Sources/Logging.h" #include "../Sources/OrthancException.h" #include "../Sources/Toolbox.h" +#include "../Sources/SystemToolbox.h" #include <ctype.h> @@ -88,6 +89,48 @@ ASSERT_EQ(s.GetSize(uid), data.size()); } +TEST(FilesystemStorage, FileWithSameNameAsTopDirectory) +{ + FilesystemStorage s("UnitTestsStorageTop"); + s.Clear(); + + std::vector<uint8_t> data; + StringToVector(data, Toolbox::GenerateUuid()); + + SystemToolbox::WriteFile("toto", "UnitTestsStorageTop/12"); + ASSERT_THROW(s.Create("12345678-1234-1234-1234-1234567890ab", &data[0], data.size(), FileContentType_Unknown), OrthancException); + s.Clear(); +} + +TEST(FilesystemStorage, FileWithSameNameAsChildDirectory) +{ + FilesystemStorage s("UnitTestsStorageChild"); + s.Clear(); + + std::vector<uint8_t> data; + StringToVector(data, Toolbox::GenerateUuid()); + + SystemToolbox::MakeDirectory("UnitTestsStorageChild/12"); + SystemToolbox::WriteFile("toto", "UnitTestsStorageChild/12/34"); + ASSERT_THROW(s.Create("12345678-1234-1234-1234-1234567890ab", &data[0], data.size(), FileContentType_Unknown), OrthancException); + s.Clear(); +} + +TEST(FilesystemStorage, FileAlreadyExists) +{ + FilesystemStorage s("UnitTestsStorageFileAlreadyExists"); + s.Clear(); + + std::vector<uint8_t> data; + StringToVector(data, Toolbox::GenerateUuid()); + + SystemToolbox::MakeDirectory("UnitTestsStorageFileAlreadyExists/12/34"); + SystemToolbox::WriteFile("toto", "UnitTestsStorageFileAlreadyExists/12/34/12345678-1234-1234-1234-1234567890ab"); + ASSERT_THROW(s.Create("12345678-1234-1234-1234-1234567890ab", &data[0], data.size(), FileContentType_Unknown), OrthancException); + s.Clear(); +} + + TEST(FilesystemStorage, EndToEnd) { FilesystemStorage s("UnitTestsStorage");
--- a/OrthancServer/CMakeLists.txt Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/CMakeLists.txt Thu Sep 05 18:52:27 2024 +0200 @@ -90,11 +90,16 @@ set(ORTHANC_SERVER_SOURCES ${CMAKE_SOURCE_DIR}/Sources/Database/BaseDatabaseWrapper.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/DatabaseLookup.cpp + ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/GenericFind.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/ICreateInstance.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/IGetChildrenMetadata.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/ILookupResourceAndParent.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/ILookupResources.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/Compatibility/SetOfResources.cpp + ${CMAKE_SOURCE_DIR}/Sources/Database/FindRequest.cpp + ${CMAKE_SOURCE_DIR}/Sources/Database/FindResponse.cpp + ${CMAKE_SOURCE_DIR}/Sources/Database/MainDicomTagsRegistry.cpp + ${CMAKE_SOURCE_DIR}/Sources/Database/OrthancIdentifiers.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/ResourcesContent.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/SQLiteDatabaseWrapper.cpp ${CMAKE_SOURCE_DIR}/Sources/Database/StatelessDatabaseOperations.cpp @@ -119,6 +124,7 @@ ${CMAKE_SOURCE_DIR}/Sources/OrthancRestApi/OrthancRestSystem.cpp ${CMAKE_SOURCE_DIR}/Sources/OrthancWebDav.cpp ${CMAKE_SOURCE_DIR}/Sources/QueryRetrieveHandler.cpp + ${CMAKE_SOURCE_DIR}/Sources/ResourceFinder.cpp ${CMAKE_SOURCE_DIR}/Sources/Search/DatabaseConstraint.cpp ${CMAKE_SOURCE_DIR}/Sources/Search/DatabaseLookup.cpp ${CMAKE_SOURCE_DIR}/Sources/Search/DicomTagConstraint.cpp
--- a/OrthancServer/OrthancExplorer/explorer.js Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/OrthancExplorer/explorer.js Thu Sep 05 18:52:27 2024 +0200 @@ -715,7 +715,7 @@ $('.' + liClass).remove(); for (var key in attachments) { if (attachments[key] >= 1024) { - target.append('<li data-icon="gear" class="' + liClass + '"><a href="#" id="' + attachments[key] + '">Download ' + key + '</a></li>') + target.append('<li data-icon="gear" class="' + liClass + '"><a href="#" id="' + attachments[key] + '">Download attachment "' + key + '"</a></li>') } } target.listview('refresh');
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -564,7 +564,7 @@ virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -586,20 +586,20 @@ std::vector<OrthancPluginDatabaseConstraint> constraints; std::vector< std::vector<const char*> > constraintsValues; - constraints.resize(lookup.size()); - constraintsValues.resize(lookup.size()); + constraints.resize(lookup.GetSize()); + constraintsValues.resize(lookup.GetSize()); - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - lookup[i].EncodeForPlugins(constraints[i], constraintsValues[i]); + lookup.GetConstraint(i).EncodeForPlugins(constraints[i], constraintsValues[i]); } ResetAnswers(); answerMatchingResources_ = &resourcesId; answerMatchingInstances_ = instancesId; - CheckSuccess(that_.extensions_.lookupResources(that_.GetContext(), that_.payload_, lookup.size(), - (lookup.empty() ? NULL : &constraints[0]), + CheckSuccess(that_.extensions_.lookupResources(that_.GetContext(), that_.payload_, lookup.GetSize(), + (lookup.IsEmpty() ? NULL : &constraints[0]), Plugins::Convert(queryLevel), limit, (instancesId == NULL ? 0 : 1))); }
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV3.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -798,7 +798,7 @@ virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, // Can be NULL if not needed - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -812,16 +812,16 @@ std::vector<OrthancPluginDatabaseConstraint> constraints; std::vector< std::vector<const char*> > constraintsValues; - constraints.resize(lookup.size()); - constraintsValues.resize(lookup.size()); + constraints.resize(lookup.GetSize()); + constraintsValues.resize(lookup.GetSize()); - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - lookup[i].EncodeForPlugins(constraints[i], constraintsValues[i]); + lookup.GetConstraint(i).EncodeForPlugins(constraints[i], constraintsValues[i]); } - CheckSuccess(that_.backend_.lookupResources(transaction_, lookup.size(), - (lookup.empty() ? NULL : &constraints[0]), + CheckSuccess(that_.backend_.lookupResources(transaction_, lookup.GetSize(), + (lookup.IsEmpty() ? NULL : &constraints[0]), Plugins::Convert(queryLevel), limit, (instancesId == NULL ? 0 : 1))); CheckNoEvent();
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -31,6 +31,7 @@ #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" #include "../../../OrthancFramework/Sources/Logging.h" #include "../../../OrthancFramework/Sources/OrthancException.h" +#include "../../Sources/Database/Compatibility/GenericFind.h" #include "../../Sources/Database/ResourcesContent.h" #include "../../Sources/Database/VoidDatabaseListener.h" #include "../../Sources/ServerToolbox.h" @@ -134,6 +135,136 @@ } + static void Convert(DatabasePluginMessages::DatabaseConstraint& target, + const DatabaseConstraint& source) + { + target.set_level(Convert(source.GetLevel())); + target.set_tag_group(source.GetTag().GetGroup()); + target.set_tag_element(source.GetTag().GetElement()); + target.set_is_identifier_tag(source.IsIdentifier()); + target.set_is_case_sensitive(source.IsCaseSensitive()); + target.set_is_mandatory(source.IsMandatory()); + + target.mutable_values()->Reserve(source.GetValuesCount()); + for (size_t j = 0; j < source.GetValuesCount(); j++) + { + target.add_values(source.GetValue(j)); + } + + switch (source.GetConstraintType()) + { + case ConstraintType_Equal: + target.set_type(DatabasePluginMessages::CONSTRAINT_EQUAL); + break; + + case ConstraintType_SmallerOrEqual: + target.set_type(DatabasePluginMessages::CONSTRAINT_SMALLER_OR_EQUAL); + break; + + case ConstraintType_GreaterOrEqual: + target.set_type(DatabasePluginMessages::CONSTRAINT_GREATER_OR_EQUAL); + break; + + case ConstraintType_Wildcard: + target.set_type(DatabasePluginMessages::CONSTRAINT_WILDCARD); + break; + + case ConstraintType_List: + target.set_type(DatabasePluginMessages::CONSTRAINT_LIST); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + static DatabasePluginMessages::LabelsConstraintType Convert(LabelsConstraint constraint) + { + switch (constraint) + { + case LabelsConstraint_All: + return DatabasePluginMessages::LABELS_CONSTRAINT_ALL; + + case LabelsConstraint_Any: + return DatabasePluginMessages::LABELS_CONSTRAINT_ANY; + + case LabelsConstraint_None: + return DatabasePluginMessages::LABELS_CONSTRAINT_NONE; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + static void Convert(DatabasePluginMessages::Find_Request_ChildrenSpecification& target, + const FindRequest::ChildrenSpecification& source) + { + target.set_retrieve_identifiers(source.IsRetrieveIdentifiers()); + + for (std::set<MetadataType>::const_iterator it = source.GetMetadata().begin(); it != source.GetMetadata().end(); ++it) + { + target.add_retrieve_metadata(*it); + } + + for (std::set<DicomTag>::const_iterator it = source.GetMainDicomTags().begin(); it != source.GetMainDicomTags().end(); ++it) + { + DatabasePluginMessages::Find_Request_Tag* tag = target.add_retrieve_main_dicom_tags(); + tag->set_group(it->GetGroup()); + tag->set_element(it->GetElement()); + } + } + + + static void Convert(FindResponse::Resource& target, + ResourceType level, + const DatabasePluginMessages::Find_Response_ResourceContent& source) + { + for (int i = 0; i < source.main_dicom_tags().size(); i++) + { + target.AddStringDicomTag(level, source.main_dicom_tags(i).group(), + source.main_dicom_tags(i).element(), source.main_dicom_tags(i).value()); + } + + for (int i = 0; i < source.metadata().size(); i++) + { + target.AddMetadata(level, static_cast<MetadataType>(source.metadata(i).key()), source.metadata(i).value()); + } + } + + + static void Convert(FindResponse::Resource& target, + ResourceType level, + const DatabasePluginMessages::Find_Response_ChildrenContent& source) + { + for (int i = 0; i < source.identifiers().size(); i++) + { + target.AddChildIdentifier(level, source.identifiers(i)); + } + + for (int i = 0; i < source.main_dicom_tags().size(); i++) + { + const DicomTag tag(source.main_dicom_tags(i).group(), source.main_dicom_tags(i).element()); + + for (int j = 0; j < source.main_dicom_tags(i).values().size(); j++) + { + target.AddChildrenMainDicomTagValue(level, tag, source.main_dicom_tags(i).values(j)); + } + } + + for (int i = 0; i < source.metadata().size(); i++) + { + MetadataType key = static_cast<MetadataType>(source.metadata(i).key()); + + for (int j = 0; j < source.metadata(i).values().size(); j++) + { + target.AddChildrenMetadataValue(level, key, source.metadata(i).values(j)); + } + } + } + + static void Execute(DatabasePluginMessages::Response& response, const OrthancPluginDatabaseV4& database, const DatabasePluginMessages::Request& request) @@ -999,10 +1130,10 @@ return response.is_disk_size_above().result(); } - + virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, // Can be NULL if not needed - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -1019,49 +1150,11 @@ request.mutable_lookup_resources()->set_limit(limit); request.mutable_lookup_resources()->set_retrieve_instances_ids(instancesId != NULL); - request.mutable_lookup_resources()->mutable_lookup()->Reserve(lookup.size()); + request.mutable_lookup_resources()->mutable_lookup()->Reserve(lookup.GetSize()); - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - DatabasePluginMessages::DatabaseConstraint* constraint = request.mutable_lookup_resources()->add_lookup(); - constraint->set_level(Convert(lookup[i].GetLevel())); - constraint->set_tag_group(lookup[i].GetTag().GetGroup()); - constraint->set_tag_element(lookup[i].GetTag().GetElement()); - constraint->set_is_identifier_tag(lookup[i].IsIdentifier()); - constraint->set_is_case_sensitive(lookup[i].IsCaseSensitive()); - constraint->set_is_mandatory(lookup[i].IsMandatory()); - - constraint->mutable_values()->Reserve(lookup[i].GetValuesCount()); - for (size_t j = 0; j < lookup[i].GetValuesCount(); j++) - { - constraint->add_values(lookup[i].GetValue(j)); - } - - switch (lookup[i].GetConstraintType()) - { - case ConstraintType_Equal: - constraint->set_type(DatabasePluginMessages::CONSTRAINT_EQUAL); - break; - - case ConstraintType_SmallerOrEqual: - constraint->set_type(DatabasePluginMessages::CONSTRAINT_SMALLER_OR_EQUAL); - break; - - case ConstraintType_GreaterOrEqual: - constraint->set_type(DatabasePluginMessages::CONSTRAINT_GREATER_OR_EQUAL); - break; - - case ConstraintType_Wildcard: - constraint->set_type(DatabasePluginMessages::CONSTRAINT_WILDCARD); - break; - - case ConstraintType_List: - constraint->set_type(DatabasePluginMessages::CONSTRAINT_LIST); - break; - - default: - throw OrthancException(ErrorCode_ParameterOutOfRange); - } + Convert(*request.mutable_lookup_resources()->add_lookup(), lookup.GetConstraint(i)); } for (std::set<std::string>::const_iterator it = labels.begin(); it != labels.end(); ++it) @@ -1069,23 +1162,7 @@ request.mutable_lookup_resources()->add_labels(*it); } - switch (labelsConstraint) - { - case LabelsConstraint_All: - request.mutable_lookup_resources()->set_labels_constraint(DatabasePluginMessages::LABELS_CONSTRAINT_ALL); - break; - - case LabelsConstraint_Any: - request.mutable_lookup_resources()->set_labels_constraint(DatabasePluginMessages::LABELS_CONSTRAINT_ANY); - break; - - case LabelsConstraint_None: - request.mutable_lookup_resources()->set_labels_constraint(DatabasePluginMessages::LABELS_CONSTRAINT_NONE); - break; - - default: - throw OrthancException(ErrorCode_ParameterOutOfRange); - } + request.mutable_lookup_resources()->set_labels_constraint(Convert(labelsConstraint)); DatabasePluginMessages::TransactionResponse response; ExecuteTransaction(response, DatabasePluginMessages::OPERATION_LOOKUP_RESOURCES, request); @@ -1303,6 +1380,212 @@ { ListLabelsInternal(target, false, -1); } + + + virtual void ExecuteFind(FindResponse& response, + const FindRequest& request, + const Capabilities& capabilities) ORTHANC_OVERRIDE + { + if (capabilities.HasFindSupport()) + { + DatabasePluginMessages::TransactionRequest dbRequest; + dbRequest.mutable_find()->set_level(Convert(request.GetLevel())); + + if (request.GetOrthancIdentifiers().HasPatientId()) + { + dbRequest.mutable_find()->set_orthanc_id_patient(request.GetOrthancIdentifiers().GetPatientId()); + } + + if (request.GetOrthancIdentifiers().HasStudyId()) + { + dbRequest.mutable_find()->set_orthanc_id_study(request.GetOrthancIdentifiers().GetStudyId()); + } + + if (request.GetOrthancIdentifiers().HasSeriesId()) + { + dbRequest.mutable_find()->set_orthanc_id_series(request.GetOrthancIdentifiers().GetSeriesId()); + } + + if (request.GetOrthancIdentifiers().HasInstanceId()) + { + dbRequest.mutable_find()->set_orthanc_id_instance(request.GetOrthancIdentifiers().GetInstanceId()); + } + + for (size_t i = 0; i < request.GetDicomTagConstraints().GetSize(); i++) + { + Convert(*dbRequest.mutable_find()->add_dicom_tag_constraints(), request.GetDicomTagConstraints().GetConstraint(i)); + } + + if (request.HasLimits()) + { + dbRequest.mutable_find()->mutable_limits()->set_since(request.GetLimitsSince()); + dbRequest.mutable_find()->mutable_limits()->set_count(request.GetLimitsCount()); + } + + for (std::set<std::string>::const_iterator it = request.GetLabels().begin(); it != request.GetLabels().end(); ++it) + { + dbRequest.mutable_find()->add_labels(*it); + } + + dbRequest.mutable_find()->set_labels_constraint(Convert(request.GetLabelsConstraint())); + + // TODO-FIND: ordering_ + // TODO-FIND: metadataConstraints__ + + dbRequest.mutable_find()->set_retrieve_main_dicom_tags(request.IsRetrieveMainDicomTags()); + dbRequest.mutable_find()->set_retrieve_metadata(request.IsRetrieveMetadata()); + dbRequest.mutable_find()->set_retrieve_labels(request.IsRetrieveLabels()); + dbRequest.mutable_find()->set_retrieve_attachments(request.IsRetrieveAttachments()); + dbRequest.mutable_find()->set_retrieve_parent_identifier(request.IsRetrieveParentIdentifier()); + dbRequest.mutable_find()->set_retrieve_at_least_one_instance(request.IsRetrieveOneInstanceIdentifier()); + + if (request.GetLevel() == ResourceType_Study || + request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) + { + dbRequest.mutable_find()->mutable_parent_patient()->set_retrieve_main_dicom_tags(request.GetParentSpecification(ResourceType_Patient).IsRetrieveMainDicomTags()); + dbRequest.mutable_find()->mutable_parent_patient()->set_retrieve_metadata(request.GetParentSpecification(ResourceType_Patient).IsRetrieveMetadata()); + } + + if (request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) + { + dbRequest.mutable_find()->mutable_parent_study()->set_retrieve_main_dicom_tags(request.GetParentSpecification(ResourceType_Study).IsRetrieveMainDicomTags()); + dbRequest.mutable_find()->mutable_parent_study()->set_retrieve_metadata(request.GetParentSpecification(ResourceType_Study).IsRetrieveMetadata()); + } + + if (request.GetLevel() == ResourceType_Instance) + { + dbRequest.mutable_find()->mutable_parent_series()->set_retrieve_main_dicom_tags(request.GetParentSpecification(ResourceType_Series).IsRetrieveMainDicomTags()); + dbRequest.mutable_find()->mutable_parent_series()->set_retrieve_metadata(request.GetParentSpecification(ResourceType_Series).IsRetrieveMetadata()); + } + + if (request.GetLevel() == ResourceType_Patient) + { + Convert(*dbRequest.mutable_find()->mutable_children_studies(), request.GetChildrenSpecification(ResourceType_Study)); + } + + if (request.GetLevel() == ResourceType_Patient || + request.GetLevel() == ResourceType_Study) + { + Convert(*dbRequest.mutable_find()->mutable_children_series(), request.GetChildrenSpecification(ResourceType_Series)); + } + + if (request.GetLevel() == ResourceType_Patient || + request.GetLevel() == ResourceType_Study || + request.GetLevel() == ResourceType_Series) + { + Convert(*dbRequest.mutable_find()->mutable_children_instances(), request.GetChildrenSpecification(ResourceType_Instance)); + } + + DatabasePluginMessages::TransactionResponse dbResponse; + ExecuteTransaction(dbResponse, DatabasePluginMessages::OPERATION_FIND, dbRequest); + + for (int i = 0; i < dbResponse.find().size(); i++) + { + const DatabasePluginMessages::Find_Response& source = dbResponse.find(i); + + std::unique_ptr<FindResponse::Resource> target( + new FindResponse::Resource(request.GetLevel(), source.internal_id(), source.public_id())); + + if (request.IsRetrieveParentIdentifier()) + { + target->SetParentIdentifier(source.parent_public_id()); + } + + for (int i = 0; i < source.labels().size(); i++) + { + target->AddLabel(source.labels(i)); + } + + for (int i = 0; i < source.attachments().size(); i++) + { + target->AddAttachment(Convert(source.attachments(i))); + } + + Convert(*target, ResourceType_Patient, source.patient_content()); + + if (request.GetLevel() == ResourceType_Study || + request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) + { + Convert(*target, ResourceType_Study, source.study_content()); + } + + if (request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) + { + Convert(*target, ResourceType_Series, source.series_content()); + } + + if (request.GetLevel() == ResourceType_Instance) + { + Convert(*target, ResourceType_Instance, source.instance_content()); + } + + if (request.GetLevel() == ResourceType_Patient) + { + Convert(*target, ResourceType_Patient, source.children_studies_content()); + } + + if (request.GetLevel() == ResourceType_Patient || + request.GetLevel() == ResourceType_Study) + { + Convert(*target, ResourceType_Study, source.children_series_content()); + } + + if (request.GetLevel() == ResourceType_Patient || + request.GetLevel() == ResourceType_Study || + request.GetLevel() == ResourceType_Series) + { + Convert(*target, ResourceType_Series, source.children_instances_content()); + } + + response.Add(target.release()); + } + + throw OrthancException(ErrorCode_NotImplemented); + } + else + { + throw OrthancException(ErrorCode_NotImplemented); + } + } + + + virtual void ExecuteFind(std::list<std::string>& identifiers, + const Capabilities& capabilities, + const FindRequest& request) ORTHANC_OVERRIDE + { + if (capabilities.HasFindSupport()) + { + // The integrated version of "ExecuteFind()" should have been called + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + Compatibility::GenericFind find(*this); + find.ExecuteFind(identifiers, capabilities, request); + } + } + + + virtual void ExecuteExpand(FindResponse& response, + const Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) ORTHANC_OVERRIDE + { + if (capabilities.HasFindSupport()) + { + // The integrated version of "ExecuteFind()" should have been called + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + Compatibility::GenericFind find(*this); + find.ExecuteExpand(response, capabilities, request, identifier); + } + } }; @@ -1392,6 +1675,7 @@ dbCapabilities_.SetUpdateAndGetStatistics(systemInfo.has_update_and_get_statistics()); dbCapabilities_.SetMeasureLatency(systemInfo.has_measure_latency()); dbCapabilities_.SetHasExtendedChanges(systemInfo.has_extended_changes()); + dbCapabilities_.SetHasFindSupport(systemInfo.supports_find()); } open_ = true; @@ -1518,4 +1802,10 @@ return dbCapabilities_; } } + + + bool OrthancPluginDatabaseV4::HasIntegratedFind() const + { + return dbCapabilities_.HasFindSupport(); + } }
--- a/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Engine/OrthancPluginDatabaseV4.h Thu Sep 05 18:52:27 2024 +0200 @@ -93,6 +93,8 @@ virtual uint64_t MeasureLatency() ORTHANC_OVERRIDE; virtual const Capabilities GetDatabaseCapabilities() const ORTHANC_OVERRIDE; + + virtual bool HasIntegratedFind() const ORTHANC_OVERRIDE; }; }
--- a/OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Include/orthanc/OrthancCPlugin.h Thu Sep 05 18:52:27 2024 +0200 @@ -120,8 +120,8 @@ #endif #define ORTHANC_PLUGINS_MINIMAL_MAJOR_NUMBER 1 -#define ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER 13 -#define ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER 0 +#define ORTHANC_PLUGINS_MINIMAL_MINOR_NUMBER 12 +#define ORTHANC_PLUGINS_MINIMAL_REVISION_NUMBER 5 #if !defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE)
--- a/OrthancServer/Plugins/Include/orthanc/OrthancDatabasePlugin.proto Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Plugins/Include/orthanc/OrthancDatabasePlugin.proto Thu Sep 05 18:52:27 2024 +0200 @@ -141,7 +141,8 @@ bool supports_increment_global_property = 5; bool has_update_and_get_statistics = 6; bool has_measure_latency = 7; - bool has_extended_changes = 8; + bool supports_find = 8; // New in Orthanc 1.12.5 + bool has_extended_changes = 9; // New in Orthanc 1.12.5 } } @@ -289,12 +290,13 @@ OPERATION_GET_CHILDREN_METADATA = 42; OPERATION_GET_LAST_CHANGE_INDEX = 43; OPERATION_LOOKUP_RESOURCE_AND_PARENT = 44; - OPERATION_ADD_LABEL = 45; // New in Orthanc 1.12.0 - OPERATION_REMOVE_LABEL = 46; // New in Orthanc 1.12.0 - OPERATION_LIST_LABELS = 47; // New in Orthanc 1.12.0 - OPERATION_INCREMENT_GLOBAL_PROPERTY = 48; // New in Orthanc 1.12.3 - OPERATION_UPDATE_AND_GET_STATISTICS = 49; // New in Orthanc 1.12.3 - OPERATION_GET_CHANGES_2 = 50; // New in Orthanc 1.13.0 + OPERATION_ADD_LABEL = 45; // New in Orthanc 1.12.0 + OPERATION_REMOVE_LABEL = 46; // New in Orthanc 1.12.0 + OPERATION_LIST_LABELS = 47; // New in Orthanc 1.12.0 + OPERATION_INCREMENT_GLOBAL_PROPERTY = 48; // New in Orthanc 1.12.3 + OPERATION_UPDATE_AND_GET_STATISTICS = 49; // New in Orthanc 1.12.3 + OPERATION_FIND = 50; // New in Orthanc 1.12.5 + OPERATION_GET_CHANGES_2 = 51; // New in Orthanc 1.12.5 } message Rollback { @@ -839,6 +841,99 @@ } } +message Find { // New in Orthanc 1.12.5 + message Request { // This corresponds to "FindRequest" in C++ + message Tag { + uint32 group = 1; + uint32 element = 2; + } + message Limits { + uint64 since = 1; + uint64 count = 2; + } + message ParentSpecification { + bool retrieve_main_dicom_tags = 1; + bool retrieve_metadata = 2; + } + message ChildrenSpecification { + bool retrieve_identifiers = 1; + repeated int32 retrieve_metadata = 2; + repeated Tag retrieve_main_dicom_tags = 3; + } + + // Part 1 of the request: Constraints + ResourceType level = 1; + string orthanc_id_patient = 2; // optional - GetOrthancIdentifiers().GetPatientId(); + string orthanc_id_study = 3; // optional - GetOrthancIdentifiers().GetStudyId(); + string orthanc_id_series = 4; // optional - GetOrthancIdentifiers().GetSeriesId(); + string orthanc_id_instance = 5; // optional - GetOrthancIdentifiers().GetInstanceId(); + repeated DatabaseConstraint dicom_tag_constraints = 6; + Limits limits = 7; // optional + repeated string labels = 8; + LabelsConstraintType labels_constraint = 9; + + // TODO-FIND: ordering_ + // TODO-FIND: metadataConstraints_ + + // Part 2 of the request: What is to be retrieved + bool retrieve_main_dicom_tags = 100; + bool retrieve_metadata = 101; + bool retrieve_labels = 102; + bool retrieve_attachments = 103; + bool retrieve_parent_identifier = 104; + bool retrieve_at_least_one_instance = 105; + ParentSpecification parent_patient = 106; + ParentSpecification parent_study = 107; + ParentSpecification parent_series = 108; + ChildrenSpecification children_studies = 109; + ChildrenSpecification children_series = 110; + ChildrenSpecification children_instances = 111; + } + + message Response { // This corresponds to "FindResponse" in C++ + message Tag { + uint32 group = 1; + uint32 element = 2; + string value = 3; + } + message Metadata { + int32 key = 1; + string value = 2; + } + message MultipleTags { + uint32 group = 1; + uint32 element = 2; + repeated string values = 3; + } + message MultipleMetadata { + int32 key = 1; + repeated string values = 2; + } + message ResourceContent { + repeated Tag main_dicom_tags = 1; + repeated Metadata metadata = 2; + } + message ChildrenContent { + repeated string identifiers = 1; + repeated MultipleTags main_dicom_tags = 2; + repeated MultipleMetadata metadata = 3; + } + + int64 internal_id = 1; + string public_id = 2; + string parent_public_id = 3; // optional + repeated string labels = 4; + repeated FileInfo attachments = 5; + ResourceContent patient_content = 6; + ResourceContent study_content = 7; + ResourceContent series_content = 8; + ResourceContent instance_content = 9; + ChildrenContent children_studies_content = 10; + ChildrenContent children_series_content = 11; + ChildrenContent children_instances_content = 12; + } +} + message TransactionRequest { sfixed64 transaction = 1; TransactionOperation operation = 2; @@ -893,7 +988,8 @@ ListLabels.Request list_labels = 147; IncrementGlobalProperty.Request increment_global_property = 148; UpdateAndGetStatistics.Request update_and_get_statistics = 149; - GetChangesExtended.Request get_changes_extended = 150; + Find.Request find = 150; + GetChangesExtended.Request get_changes_extended = 151; } message TransactionResponse { @@ -947,7 +1043,8 @@ ListLabels.Response list_labels = 147; IncrementGlobalProperty.Response increment_global_property = 148; UpdateAndGetStatistics.Response update_and_get_statistics = 149; - GetChangesExtended.Response get_changes_extended = 150; + repeated Find.Response find = 150; // One message per found resources + GetChangesExtended.Response get_changes_extended = 151; } enum RequestType {
--- a/OrthancServer/Resources/Configuration.json Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Resources/Configuration.json Thu Sep 05 18:52:27 2024 +0200 @@ -205,6 +205,7 @@ // Set the timeout (in seconds) after which the DICOM associations // are closed by the Orthanc SCP (server) if no further DIMSE // command is received from the SCU (client). + // A value of 0 means "no timeout". "DicomScpTimeout" : 30, @@ -491,6 +492,7 @@ // The timeout (in seconds) after which the DICOM associations are // considered as closed by the Orthanc SCU (client) if the remote // DICOM SCP (server) does not answer. + // A value of 0 means "no timeout". "DicomScuTimeout" : 10, // During a C-STORE SCU request initiated by Orthanc, if the remote @@ -984,7 +986,11 @@ // your response might be incomplete/inconsistent. // You should call patients|studies|series|instances/../reconstruct to rebuild // the DB. You may also check for the "Housekeeper" plugin - "W002_InconsistentDicomTagsInDb": true + "W002_InconsistentDicomTagsInDb": true, + + // Display a warning message when Orthanc and its plugins are unable + // to decode a frame (new in Orthanc 1.12.5). + "W003_DecoderFailure": true } }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Resources/Graveyard/FindRefactoringForSQLite.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,167 @@ +#if 0 + // TODO-FIND: Remove this implementation, as it should be done by + // the compatibility mode implemented by "GenericFind" + + virtual void ExecuteFind(FindResponse& response, + const FindRequest& request, + const std::vector<DatabaseConstraint>& normalized) ORTHANC_OVERRIDE + { +#if 0 + Compatibility::GenericFind find(*this); + find.Execute(response, request); +#else + { + SQLite::Statement s(db_, SQLITE_FROM_HERE, "DROP TABLE IF EXISTS FilteredResourcesIds"); + s.Run(); + } + + { + + LookupFormatter formatter; + + std::string sqlLookup; + LookupFormatter::Apply(sqlLookup, + formatter, + normalized, + request.GetLevel(), + request.GetLabels(), + request.GetLabelsConstraint(), + (request.HasLimits() ? request.GetLimitsCount() : 0)); // TODO: handles since and count + + { + // first create a temporary table that with the filtered and ordered results + sqlLookup = "CREATE TEMPORARY TABLE FilteredResourcesIds AS " + sqlLookup; + + SQLite::Statement statement(db_, SQLITE_FROM_HERE_DYNAMIC(sqlLookup), sqlLookup); + formatter.Bind(statement); + statement.Run(); + } + + { + // create the response item with the public ids only + SQLite::Statement statement(db_, SQLITE_FROM_HERE, "SELECT publicId FROM FilteredResourcesIds"); + formatter.Bind(statement); + + while (statement.Step()) + { + const std::string resourceId = statement.ColumnString(0); + response.Add(new FindResponse::Resource(request.GetLevel(), resourceId)); + } + } + + // request Each response content through INNER JOIN with the temporary table + if (request.IsRetrieveMainDicomTags()) + { + // TODO-FIND: handle the case where we request tags from multiple levels + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT publicId, tagGroup, tagElement, value FROM MainDicomTags AS tags " + " INNER JOIN FilteredResourcesIds ON tags.id = FilteredResourcesIds.internalId"); + formatter.Bind(statement); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).AddStringDicomTag(statement.ColumnInt(1), + statement.ColumnInt(2), + statement.ColumnString(3)); + } + } + + if (request.IsRetrieveChildrenIdentifiers()) + { + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT filtered.publicId, childLevel.publicId AS childPublicId " + "FROM Resources as currentLevel " + " INNER JOIN FilteredResourcesIds filtered ON filtered.internalId = currentLevel.internalId " + " INNER JOIN Resources childLevel ON childLevel.parentId = currentLevel.internalId"); + formatter.Bind(statement); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).AddChildIdentifier(GetChildResourceType(request.GetLevel()), statement.ColumnString(1)); + } + } + + if (request.IsRetrieveParentIdentifier()) + { + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT filtered.publicId, parentLevel.publicId AS parentPublicId " + "FROM Resources as currentLevel " + " INNER JOIN FilteredResourcesIds filtered ON filtered.internalId = currentLevel.internalId " + " INNER JOIN Resources parentLevel ON currentLevel.parentId = parentLevel.internalId"); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + const std::string& parentId = statement.ColumnString(1); + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).SetParentIdentifier(parentId); + } + } + + if (request.IsRetrieveMetadata()) + { + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT filtered.publicId, metadata.type, metadata.value " + "FROM Metadata " + " INNER JOIN FilteredResourcesIds filtered ON filtered.internalId = Metadata.id"); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).AddMetadata(static_cast<MetadataType>(statement.ColumnInt(1)), + statement.ColumnString(2)); + } + } + + if (request.IsRetrieveLabels()) + { + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT filtered.publicId, label " + "FROM Labels " + " INNER JOIN FilteredResourcesIds filtered ON filtered.internalId = Labels.id"); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).AddLabel(statement.ColumnString(1)); + } + } + + if (request.IsRetrieveAttachments()) + { + SQLite::Statement statement(db_, SQLITE_FROM_HERE, + "SELECT filtered.publicId, uuid, fileType, uncompressedSize, compressionType, compressedSize, " + " uncompressedMD5, compressedMD5 " + "FROM AttachedFiles " + " INNER JOIN FilteredResourcesIds filtered ON filtered.internalId = AttachedFiles.id"); + + while (statement.Step()) + { + const std::string& resourceId = statement.ColumnString(0); + FileInfo attachment = FileInfo(statement.ColumnString(1), + static_cast<FileContentType>(statement.ColumnInt(2)), + statement.ColumnInt64(3), + statement.ColumnString(6), + static_cast<CompressionType>(statement.ColumnInt(4)), + statement.ColumnInt64(5), + statement.ColumnString(7)); + + assert(response.HasResource(resourceId)); + response.GetResource(resourceId).AddAttachment(attachment); + }; + } + + // TODO-FIND: implement other responseContent: ResponseContent_ChildInstanceId, ResponseContent_ChildrenMetadata (later: ResponseContent_IsStable) + + } + +#endif + } +#endif +
--- a/OrthancServer/Resources/Orthanc.doxygen Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Resources/Orthanc.doxygen Thu Sep 05 18:52:27 2024 +0200 @@ -755,6 +755,7 @@ # Note: If this tag is empty the current directory is searched. INPUT = @CMAKE_SOURCE_DIR@/../OrthancFramework/Sources \ + @CMAKE_SOURCE_DIR@/Plugins/Engine \ @CMAKE_SOURCE_DIR@/Sources # This tag can be used to specify the character encoding of the source files
--- a/OrthancServer/Resources/RunCppCheck.sh Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Resources/RunCppCheck.sh Thu Sep 05 18:52:27 2024 +0200 @@ -16,8 +16,8 @@ stlFindInsert:../../OrthancFramework/Sources/DicomFormat/DicomMap.cpp:1477 stlFindInsert:../../OrthancFramework/Sources/RestApi/RestApiCallDocumentation.cpp:166 stlFindInsert:../../OrthancFramework/Sources/RestApi/RestApiCallDocumentation.cpp:74 -stlFindInsert:../../OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp:374 -stlFindInsert:../../OrthancServer/Sources/OrthancWebDav.cpp:378 +stlFindInsert:../../OrthancServer/Sources/Database/MainDicomTagsRegistry.cpp:65 +stlFindInsert:../../OrthancServer/Sources/OrthancWebDav.cpp:480 stlFindInsert:../../OrthancServer/Sources/ServerJobs/MergeStudyJob.cpp:41 stlFindInsert:../../OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp:191 stlFindInsert:../../OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp:361 @@ -34,9 +34,9 @@ useInitializationList:../../OrthancServer/Sources/ServerJobs/DicomModalityStoreJob.cpp:275 assertWithSideEffect:../../OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp:277 assertWithSideEffect:../../OrthancServer/Plugins/Engine/OrthancPluginDatabase.cpp:1026 -assertWithSideEffect:../../OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp:290 -assertWithSideEffect:../../OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp:389 -assertWithSideEffect:../../OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp:3663 +assertWithSideEffect:../../OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp:292 +assertWithSideEffect:../../OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp:391 +assertWithSideEffect:../../OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp:3527 assertWithSideEffect:../../OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp:286 assertWithSideEffect:../../OrthancFramework/Sources/DicomNetworking/Internals/CommandDispatcher.cpp:454 EOF
--- a/OrthancServer/Sources/Database/BaseDatabaseWrapper.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/BaseDatabaseWrapper.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -24,6 +24,7 @@ #include "BaseDatabaseWrapper.h" #include "../../../OrthancFramework/Sources/OrthancException.h" +#include "Compatibility/GenericFind.h" namespace Orthanc { @@ -57,6 +58,33 @@ + void BaseDatabaseWrapper::BaseTransaction::ExecuteFind(FindResponse& response, + const FindRequest& request, + const Capabilities& capabilities) + { + throw OrthancException(ErrorCode_NotImplemented); // Not supported + } + + + void BaseDatabaseWrapper::BaseTransaction::ExecuteFind(std::list<std::string>& identifiers, + const Capabilities& capabilities, + const FindRequest& request) + { + Compatibility::GenericFind find(*this); + find.ExecuteFind(identifiers, capabilities, request); + } + + + void BaseDatabaseWrapper::BaseTransaction::ExecuteExpand(FindResponse& response, + const Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) + { + Compatibility::GenericFind find(*this); + find.ExecuteExpand(response, capabilities, request, identifier); + } + + uint64_t BaseDatabaseWrapper::MeasureLatency() { throw OrthancException(ErrorCode_NotImplemented); // only implemented in V4
--- a/OrthancServer/Sources/Database/BaseDatabaseWrapper.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/BaseDatabaseWrapper.h Thu Sep 05 18:52:27 2024 +0200 @@ -48,15 +48,32 @@ int64_t& compressedSize, int64_t& uncompressedSize) ORTHANC_OVERRIDE; + virtual void ExecuteFind(FindResponse& response, + const FindRequest& request, + const Capabilities& capabilities) ORTHANC_OVERRIDE; + + virtual void ExecuteFind(std::list<std::string>& identifiers, + const Capabilities& capabilities, + const FindRequest& request) ORTHANC_OVERRIDE; + + virtual void ExecuteExpand(FindResponse& response, + const Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) ORTHANC_OVERRIDE; + virtual void GetChangesExtended(std::list<ServerIndexChange>& target /*out*/, bool& done /*out*/, int64_t since, int64_t to, uint32_t limit, ChangeType filterType) ORTHANC_OVERRIDE; - }; virtual uint64_t MeasureLatency() ORTHANC_OVERRIDE; + + virtual bool HasIntegratedFind() const ORTHANC_OVERRIDE + { + return false; + } }; }
--- a/OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/Compatibility/DatabaseLookup.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -153,7 +153,7 @@ static void ApplyLevel(SetOfResources& candidates, IDatabaseWrapper::ITransaction& transaction, ILookupResources& compatibility, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType level) { typedef std::set<const DatabaseConstraint*> SetOfConstraints; @@ -166,17 +166,19 @@ Identifiers identifiers; SetOfConstraints mainTags; - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - if (lookup[i].GetLevel() == level) + const DatabaseConstraint& constraint = lookup.GetConstraint(i); + + if (constraint.GetLevel() == level) { - if (lookup[i].IsIdentifier()) + if (constraint.IsIdentifier()) { - identifiers[lookup[i].GetTag()].insert(&lookup[i]); + identifiers[constraint.GetTag()].insert(&constraint); } else { - mainTags.insert(&lookup[i]); + mainTags.insert(&constraint); } } } @@ -306,7 +308,7 @@ void DatabaseLookup::ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, size_t limit) { @@ -320,9 +322,9 @@ ResourceType upperLevel = queryLevel; ResourceType lowerLevel = queryLevel; - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - ResourceType level = lookup[i].GetLevel(); + ResourceType level = lookup.GetConstraint(i).GetLevel(); if (level < upperLevel) {
--- a/OrthancServer/Sources/Database/Compatibility/DatabaseLookup.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/Compatibility/DatabaseLookup.h Thu Sep 05 18:52:27 2024 +0200 @@ -46,7 +46,7 @@ void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, size_t limit); };
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/Compatibility/GenericFind.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,596 @@ +/** + * 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 "GenericFind.h" + +#include "../../../../OrthancFramework/Sources/DicomFormat/DicomArray.h" +#include "../../../../OrthancFramework/Sources/OrthancException.h" + +#include <stack> + + +namespace Orthanc +{ + namespace Compatibility + { + static bool IsRequestWithoutContraint(const FindRequest& request) + { + return (request.GetDicomTagConstraints().IsEmpty() && + request.GetMetadataConstraintsCount() == 0 && + request.GetLabels().empty() && + request.GetOrdering().empty()); + } + + static void GetChildren(std::list<int64_t>& target, + IDatabaseWrapper::ITransaction& transaction, + const std::list<int64_t>& resources) + { + target.clear(); + + for (std::list<int64_t>::const_iterator it = resources.begin(); it != resources.end(); ++it) + { + std::list<int64_t> tmp; + transaction.GetChildrenInternalId(tmp, *it); + target.splice(target.begin(), tmp); + } + } + + static void GetChildren(std::list<std::string>& target, + IDatabaseWrapper::ITransaction& transaction, + const std::list<int64_t>& resources) + { + target.clear(); + + for (std::list<int64_t>::const_iterator it = resources.begin(); it != resources.end(); ++it) + { + std::list<std::string> tmp; + transaction.GetChildrenPublicId(tmp, *it); + target.splice(target.begin(), tmp); + } + } + + static void GetChildrenIdentifiers(std::list<std::string>& children, + IDatabaseWrapper::ITransaction& transaction, + const OrthancIdentifiers& identifiers, + ResourceType topLevel, + ResourceType bottomLevel) + { + if (!IsResourceLevelAboveOrEqual(topLevel, bottomLevel) || + topLevel == bottomLevel) + { + throw OrthancException(ErrorCode_InternalError); + } + + std::list<int64_t> currentResources; + ResourceType currentLevel; + + { + int64_t id; + if (!transaction.LookupResource(id, currentLevel, identifiers.GetLevel(topLevel)) || + currentLevel != topLevel) + { + throw OrthancException(ErrorCode_InexistentItem); + } + + currentResources.push_back(id); + } + + while (currentLevel != bottomLevel) + { + ResourceType nextLevel = GetChildResourceType(currentLevel); + if (nextLevel == bottomLevel) + { + GetChildren(children, transaction, currentResources); + } + else + { + std::list<int64_t> nextResources; + GetChildren(nextResources, transaction, currentResources); + currentResources.swap(nextResources); + } + + currentLevel = nextLevel; + } + } + + void GenericFind::ExecuteFind(std::list<std::string>& identifiers, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request) + { + if (!request.GetLabels().empty() && + !capabilities.HasLabelsSupport()) + { + throw OrthancException(ErrorCode_NotImplemented, "The database backend doesn't support labels"); + } + + if (IsRequestWithoutContraint(request) && + !request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + if (request.HasLimits()) + { + transaction_.GetAllPublicIds(identifiers, request.GetLevel(), request.GetLimitsSince(), request.GetLimitsCount()); + } + else + { + transaction_.GetAllPublicIds(identifiers, request.GetLevel()); + } + } + else if (IsRequestWithoutContraint(request) && + request.GetLevel() == ResourceType_Patient && + request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + // TODO-FIND: This is a trivial case for which no transaction is needed + identifiers.push_back(request.GetOrthancIdentifiers().GetPatientId()); + } + else if (IsRequestWithoutContraint(request) && + request.GetLevel() == ResourceType_Study && + !request.GetOrthancIdentifiers().HasPatientId() && + request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + // TODO-FIND: This is a trivial case for which no transaction is needed + identifiers.push_back(request.GetOrthancIdentifiers().GetStudyId()); + } + else if (IsRequestWithoutContraint(request) && + request.GetLevel() == ResourceType_Series && + !request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + // TODO-FIND: This is a trivial case for which no transaction is needed + identifiers.push_back(request.GetOrthancIdentifiers().GetSeriesId()); + } + else if (IsRequestWithoutContraint(request) && + request.GetLevel() == ResourceType_Instance && + !request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + request.GetOrthancIdentifiers().HasInstanceId()) + { + // TODO-FIND: This is a trivial case for which no transaction is needed + identifiers.push_back(request.GetOrthancIdentifiers().GetInstanceId()); + } + else if (IsRequestWithoutContraint(request) && + (request.GetLevel() == ResourceType_Study || + request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) && + request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + GetChildrenIdentifiers(identifiers, transaction_, request.GetOrthancIdentifiers(), ResourceType_Patient, request.GetLevel()); + } + else if (IsRequestWithoutContraint(request) && + (request.GetLevel() == ResourceType_Series || + request.GetLevel() == ResourceType_Instance) && + !request.GetOrthancIdentifiers().HasPatientId() && + request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + GetChildrenIdentifiers(identifiers, transaction_, request.GetOrthancIdentifiers(), ResourceType_Study, request.GetLevel()); + } + else if (IsRequestWithoutContraint(request) && + request.GetLevel() == ResourceType_Instance && + !request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + GetChildrenIdentifiers(identifiers, transaction_, request.GetOrthancIdentifiers(), ResourceType_Series, request.GetLevel()); + } + else if (request.GetMetadataConstraintsCount() == 0 && + request.GetOrdering().empty() && + !request.GetOrthancIdentifiers().HasPatientId() && + !request.GetOrthancIdentifiers().HasStudyId() && + !request.GetOrthancIdentifiers().HasSeriesId() && + !request.GetOrthancIdentifiers().HasInstanceId()) + { + transaction_.ApplyLookupResources(identifiers, NULL /* TODO-FIND: Could the "instancesId" information be exploited? */, + request.GetDicomTagConstraints(), request.GetLevel(), request.GetLabels(), + request.GetLabelsConstraint(), request.HasLimits() ? request.GetLimitsCount() : 0); + } + else + { + throw OrthancException(ErrorCode_NotImplemented); + } + } + + + void GenericFind::RetrieveMainDicomTags(FindResponse::Resource& target, + ResourceType level, + int64_t internalId) + { + DicomMap m; + transaction_.GetMainDicomTags(m, internalId); + + DicomArray a(m); + for (size_t i = 0; i < a.GetSize(); i++) + { + const DicomElement& element = a.GetElement(i); + if (element.GetValue().IsString()) + { + target.AddStringDicomTag(level, element.GetTag().GetGroup(), + element.GetTag().GetElement(), element.GetValue().GetContent()); + } + else + { + throw OrthancException(ErrorCode_BadParameterType); + } + } + } + + + static ResourceType GetTopLevelOfInterest(const FindRequest& request) + { + switch (request.GetLevel()) + { + case ResourceType_Patient: + return ResourceType_Patient; + + case ResourceType_Study: + if (request.GetParentSpecification(ResourceType_Patient).IsOfInterest()) + { + return ResourceType_Patient; + } + else + { + return ResourceType_Study; + } + + case ResourceType_Series: + if (request.GetParentSpecification(ResourceType_Patient).IsOfInterest()) + { + return ResourceType_Patient; + } + else if (request.GetParentSpecification(ResourceType_Study).IsOfInterest()) + { + return ResourceType_Study; + } + else + { + return ResourceType_Series; + } + + case ResourceType_Instance: + if (request.GetParentSpecification(ResourceType_Patient).IsOfInterest()) + { + return ResourceType_Patient; + } + else if (request.GetParentSpecification(ResourceType_Study).IsOfInterest()) + { + return ResourceType_Study; + } + else if (request.GetParentSpecification(ResourceType_Series).IsOfInterest()) + { + return ResourceType_Series; + } + else + { + return ResourceType_Instance; + } + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + static ResourceType GetBottomLevelOfInterest(const FindRequest& request) + { + switch (request.GetLevel()) + { + case ResourceType_Patient: + if (request.GetChildrenSpecification(ResourceType_Instance).IsOfInterest()) + { + return ResourceType_Instance; + } + else if (request.GetChildrenSpecification(ResourceType_Series).IsOfInterest()) + { + return ResourceType_Series; + } + else if (request.GetChildrenSpecification(ResourceType_Study).IsOfInterest()) + { + return ResourceType_Study; + } + else + { + return ResourceType_Patient; + } + + case ResourceType_Study: + if (request.GetChildrenSpecification(ResourceType_Instance).IsOfInterest()) + { + return ResourceType_Instance; + } + else if (request.GetChildrenSpecification(ResourceType_Series).IsOfInterest()) + { + return ResourceType_Series; + } + else + { + return ResourceType_Study; + } + + case ResourceType_Series: + if (request.GetChildrenSpecification(ResourceType_Instance).IsOfInterest()) + { + return ResourceType_Instance; + } + else + { + return ResourceType_Series; + } + + case ResourceType_Instance: + return ResourceType_Instance; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + void GenericFind::ExecuteExpand(FindResponse& response, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) + { + int64_t internalId; + ResourceType level; + std::string parent; + + if (request.IsRetrieveParentIdentifier()) + { + if (!transaction_.LookupResourceAndParent(internalId, level, parent, identifier)) + { + return; // The resource is not available anymore + } + + if (level == ResourceType_Patient) + { + if (!parent.empty()) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + } + else + { + if (parent.empty()) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + } + } + else + { + if (!transaction_.LookupResource(internalId, level, identifier)) + { + return; // The resource is not available anymore + } + } + + if (level != request.GetLevel()) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + + std::unique_ptr<FindResponse::Resource> resource(new FindResponse::Resource(request.GetLevel(), internalId, identifier)); + + if (request.IsRetrieveParentIdentifier()) + { + assert(!parent.empty()); + resource->SetParentIdentifier(parent); + } + + if (request.IsRetrieveMainDicomTags()) + { + RetrieveMainDicomTags(*resource, level, internalId); + } + + if (request.IsRetrieveMetadata()) + { + transaction_.GetAllMetadata(resource->GetMetadata(level), internalId); + } + + { + const ResourceType topLevel = GetTopLevelOfInterest(request); + + int64_t currentId = internalId; + ResourceType currentLevel = level; + + while (currentLevel != topLevel) + { + int64_t parentId; + if (transaction_.LookupParent(parentId, currentId)) + { + currentId = parentId; + currentLevel = GetParentResourceType(currentLevel); + } + else + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + + if (request.GetParentSpecification(currentLevel).IsRetrieveMainDicomTags()) + { + RetrieveMainDicomTags(*resource, currentLevel, currentId); + } + + if (request.GetParentSpecification(currentLevel).IsRetrieveMetadata()) + { + transaction_.GetAllMetadata(resource->GetMetadata(currentLevel), currentId); + } + } + } + + if (capabilities.HasLabelsSupport() && + request.IsRetrieveLabels()) + { + transaction_.ListLabels(resource->GetLabels(), internalId); + } + + if (request.IsRetrieveAttachments()) + { + std::set<FileContentType> attachments; + transaction_.ListAvailableAttachments(attachments, internalId); + + for (std::set<FileContentType>::const_iterator it = attachments.begin(); it != attachments.end(); ++it) + { + FileInfo info; + int64_t revision; + if (transaction_.LookupAttachment(info, revision, internalId, *it) && + info.GetContentType() == *it) + { + resource->AddAttachment(info); + } + else + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + } + } + + { + const ResourceType bottomLevel = GetBottomLevelOfInterest(request); + + std::list<int64_t> currentIds; + currentIds.push_back(internalId); + + ResourceType currentLevel = level; + + while (currentLevel != bottomLevel) + { + ResourceType childrenLevel = GetChildResourceType(currentLevel); + + if (request.GetChildrenSpecification(childrenLevel).IsRetrieveIdentifiers()) + { + for (std::list<int64_t>::const_iterator it = currentIds.begin(); it != currentIds.end(); ++it) + { + std::list<std::string> ids; + transaction_.GetChildrenPublicId(ids, *it); + + for (std::list<std::string>::const_iterator it2 = ids.begin(); it2 != ids.end(); ++it2) + { + resource->AddChildIdentifier(childrenLevel, *it2); + } + } + } + + const std::set<MetadataType>& metadata = request.GetChildrenSpecification(childrenLevel).GetMetadata(); + + for (std::set<MetadataType>::const_iterator it = metadata.begin(); it != metadata.end(); ++it) + { + for (std::list<int64_t>::const_iterator it2 = currentIds.begin(); it2 != currentIds.end(); ++it2) + { + std::list<std::string> values; + transaction_.GetChildrenMetadata(values, *it2, *it); + + for (std::list<std::string>::const_iterator it3 = values.begin(); it3 != values.end(); ++it3) + { + resource->AddChildrenMetadataValue(childrenLevel, *it, *it3); + } + } + } + + const std::set<DicomTag>& mainDicomTags = request.GetChildrenSpecification(childrenLevel).GetMainDicomTags(); + + if (childrenLevel != bottomLevel || + !mainDicomTags.empty()) + { + std::list<int64_t> childrenIds; + + for (std::list<int64_t>::const_iterator it = currentIds.begin(); it != currentIds.end(); ++it) + { + std::list<int64_t> tmp; + transaction_.GetChildrenInternalId(tmp, *it); + + childrenIds.splice(childrenIds.end(), tmp); + } + + if (!mainDicomTags.empty()) + { + for (std::list<int64_t>::const_iterator it = childrenIds.begin(); it != childrenIds.end(); ++it) + { + DicomMap m; + transaction_.GetMainDicomTags(m, *it); + + for (std::set<DicomTag>::const_iterator it2 = mainDicomTags.begin(); it2 != mainDicomTags.end(); ++it2) + { + std::string value; + if (m.LookupStringValue(value, *it2, false /* no binary allowed */)) + { + resource->AddChildrenMainDicomTagValue(childrenLevel, *it2, value); + } + } + } + } + + currentIds = childrenIds; + } + else + { + currentIds.clear(); + } + + currentLevel = childrenLevel; + } + } + + if (request.IsRetrieveOneInstanceIdentifier() && + !request.GetChildrenSpecification(ResourceType_Instance).IsRetrieveIdentifiers()) + { + int64_t currentId = internalId; + ResourceType currentLevel = level; + + while (currentLevel != ResourceType_Instance) + { + std::list<int64_t> children; + transaction_.GetChildrenInternalId(children, currentId); + if (children.empty()) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + else + { + currentId = children.front(); + currentLevel = GetChildResourceType(currentLevel); + } + } + + resource->AddChildIdentifier(ResourceType_Instance, transaction_.GetPublicId(currentId)); + } + + response.Add(resource.release()); + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/Compatibility/GenericFind.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,57 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "../IDatabaseWrapper.h" + +namespace Orthanc +{ + namespace Compatibility + { + class GenericFind : public boost::noncopyable + { + private: + IDatabaseWrapper::ITransaction& transaction_; + + void RetrieveMainDicomTags(FindResponse::Resource& target, + ResourceType level, + int64_t internalId); + + public: + explicit GenericFind(IDatabaseWrapper::ITransaction& transaction) : + transaction_(transaction) + { + } + + void ExecuteFind(std::list<std::string>& identifiers, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request); + + void ExecuteExpand(FindResponse& response, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier); + }; + } +}
--- a/OrthancServer/Sources/Database/Compatibility/ILookupResources.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/Compatibility/ILookupResources.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -35,7 +35,7 @@ ILookupResources& compatibility, std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, size_t limit) {
--- a/OrthancServer/Sources/Database/Compatibility/ILookupResources.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/Compatibility/ILookupResources.h Thu Sep 05 18:52:27 2024 +0200 @@ -60,7 +60,7 @@ ILookupResources& compatibility, std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, size_t limit); };
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/FindRequest.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,260 @@ +/** + * 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 "FindRequest.h" + +#include "../../../OrthancFramework/Sources/OrthancException.h" + +#include "MainDicomTagsRegistry.h" + +#include <cassert> + + +namespace Orthanc +{ + FindRequest::ParentSpecification& FindRequest::GetParentSpecification(ResourceType level) + { + if (!IsResourceLevelAboveOrEqual(level, level_) || + level == level_) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + switch (level) + { + case ResourceType_Patient: + return retrieveParentPatient_; + + case ResourceType_Study: + return retrieveParentStudy_; + + case ResourceType_Series: + return retrieveParentSeries_; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + FindRequest::ChildrenSpecification& FindRequest::GetChildrenSpecification(ResourceType level) + { + if (!IsResourceLevelAboveOrEqual(level_, level) || + level == level_) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + switch (level) + { + case ResourceType_Study: + return retrieveChildrenStudies_; + + case ResourceType_Series: + return retrieveChildrenSeries_; + + case ResourceType_Instance: + return retrieveChildrenInstances_; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + FindRequest::FindRequest(ResourceType level) : + level_(level), + hasLimits_(false), + limitsSince_(0), + limitsCount_(0), + labelsConstraint_(LabelsConstraint_All), + retrieveMainDicomTags_(false), + retrieveMetadata_(false), + retrieveLabels_(false), + retrieveAttachments_(false), + retrieveParentIdentifier_(false), + retrieveOneInstanceIdentifier_(false) + { + } + + + FindRequest::~FindRequest() + { + + for (std::deque<Ordering*>::iterator it = ordering_.begin(); it != ordering_.end(); ++it) + { + assert(*it != NULL); + delete *it; + } + } + + + void FindRequest::SetOrthancId(ResourceType level, + const std::string& id) + { + switch (level) + { + case ResourceType_Patient: + SetOrthancPatientId(id); + break; + + case ResourceType_Study: + SetOrthancStudyId(id); + break; + + case ResourceType_Series: + SetOrthancSeriesId(id); + break; + + case ResourceType_Instance: + SetOrthancInstanceId(id); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + void FindRequest::SetOrthancPatientId(const std::string& id) + { + orthancIdentifiers_.SetPatientId(id); + } + + + void FindRequest::SetOrthancStudyId(const std::string& id) + { + if (level_ == ResourceType_Patient) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + orthancIdentifiers_.SetStudyId(id); + } + } + + + void FindRequest::SetOrthancSeriesId(const std::string& id) + { + if (level_ == ResourceType_Patient || + level_ == ResourceType_Study) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + orthancIdentifiers_.SetSeriesId(id); + } + } + + + void FindRequest::SetOrthancInstanceId(const std::string& id) + { + if (level_ == ResourceType_Patient || + level_ == ResourceType_Study || + level_ == ResourceType_Series) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + orthancIdentifiers_.SetInstanceId(id); + } + } + + + void FindRequest::SetLimits(uint64_t since, + uint64_t count) + { + hasLimits_ = true; + limitsSince_ = since; + limitsCount_ = count; + } + + + uint64_t FindRequest::GetLimitsSince() const + { + if (hasLimits_) + { + return limitsSince_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + uint64_t FindRequest::GetLimitsCount() const + { + if (hasLimits_) + { + return limitsCount_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void FindRequest::AddOrdering(const DicomTag& tag, + OrderingDirection direction) + { + ordering_.push_back(new Ordering(Key(tag), direction)); + } + + + void FindRequest::AddOrdering(MetadataType metadataType, + OrderingDirection direction) + { + ordering_.push_back(new Ordering(Key(metadataType), direction)); + } + + + void FindRequest::SetRetrieveParentIdentifier(bool retrieve) + { + if (level_ == ResourceType_Patient) + { + throw OrthancException(ErrorCode_BadParameterType); + } + else + { + retrieveParentIdentifier_ = retrieve; + } + } + + + void FindRequest::SetRetrieveOneInstanceIdentifier(bool retrieve) + { + if (level_ == ResourceType_Instance) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + retrieveOneInstanceIdentifier_ = retrieve; + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/FindRequest.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,425 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "../../../OrthancFramework/Sources/DicomFormat/DicomTag.h" +#include "../Search/DatabaseConstraint.h" +#include "../Search/DicomTagConstraint.h" +#include "../Search/ISqlLookupFormatter.h" +#include "../ServerEnumerations.h" +#include "OrthancIdentifiers.h" + +#include <deque> +#include <map> +#include <set> +#include <cassert> +#include <boost/shared_ptr.hpp> + +namespace Orthanc +{ + class MainDicomTagsRegistry; + + class FindRequest : public boost::noncopyable + { + public: + enum KeyType // used for ordering and filters + { + KeyType_DicomTag, + KeyType_Metadata + }; + + + enum OrderingDirection + { + OrderingDirection_Ascending, + OrderingDirection_Descending + }; + + + class Key + { + private: + KeyType type_; + DicomTag dicomTag_; + MetadataType metadata_; + + // TODO-FIND: to execute the query, we actually need: + // ResourceType level_; + // DicomTagType dicomTagType_; + // these are however only populated in StatelessDatabaseOperations -> we had to add the normalized lookup arg to ExecuteFind + + public: + explicit Key(const DicomTag& dicomTag) : + type_(KeyType_DicomTag), + dicomTag_(dicomTag), + metadata_(MetadataType_EndUser) + { + } + + explicit Key(MetadataType metadata) : + type_(KeyType_Metadata), + dicomTag_(0, 0), + metadata_(metadata) + { + } + + KeyType GetType() const + { + return type_; + } + + const DicomTag& GetDicomTag() const + { + assert(GetType() == KeyType_DicomTag); + return dicomTag_; + } + + MetadataType GetMetadataType() const + { + assert(GetType() == KeyType_Metadata); + return metadata_; + } + }; + + class Ordering : public boost::noncopyable + { + private: + OrderingDirection direction_; + Key key_; + + public: + Ordering(const Key& key, + OrderingDirection direction) : + direction_(direction), + key_(key) + { + } + + KeyType GetKeyType() const + { + return key_.GetType(); + } + + OrderingDirection GetDirection() const + { + return direction_; + } + + MetadataType GetMetadataType() const + { + return key_.GetMetadataType(); + } + + DicomTag GetDicomTag() const + { + return key_.GetDicomTag(); + } + }; + + + class ParentSpecification : public boost::noncopyable + { + private: + bool mainDicomTags_; + bool metadata_; + + public: + ParentSpecification() : + mainDicomTags_(false), + metadata_(false) + { + } + + void SetRetrieveMainDicomTags(bool retrieve) + { + mainDicomTags_ = retrieve; + } + + bool IsRetrieveMainDicomTags() const + { + return mainDicomTags_; + } + + void SetRetrieveMetadata(bool retrieve) + { + metadata_ = retrieve; + } + + bool IsRetrieveMetadata() const + { + return metadata_; + } + + bool IsOfInterest() const + { + return (mainDicomTags_ || metadata_); + } + }; + + + class ChildrenSpecification : public boost::noncopyable + { + private: + bool identifiers_; + std::set<MetadataType> metadata_; + std::set<DicomTag> mainDicomTags_; + + public: + ChildrenSpecification() : + identifiers_(false) + { + } + + void SetRetrieveIdentifiers(bool retrieve) + { + identifiers_ = retrieve; + } + + bool IsRetrieveIdentifiers() const + { + return identifiers_; + } + + void AddMetadata(MetadataType metadata) + { + metadata_.insert(metadata); + } + + const std::set<MetadataType>& GetMetadata() const + { + return metadata_; + } + + void AddMainDicomTag(const DicomTag& tag) + { + mainDicomTags_.insert(tag); + } + + const std::set<DicomTag>& GetMainDicomTags() const + { + return mainDicomTags_; + } + + bool IsOfInterest() const + { + return (identifiers_ || !metadata_.empty() || !mainDicomTags_.empty()); + } + }; + + + private: + // filter & ordering fields + ResourceType level_; // The level of the response (the filtering on tags, labels and metadata also happens at this level) + OrthancIdentifiers orthancIdentifiers_; // The response must belong to this Orthanc resources hierarchy + DatabaseConstraints dicomTagConstraints_; // All tags filters (note: the order is not important) + bool hasLimits_; + uint64_t limitsSince_; + uint64_t limitsCount_; + std::set<std::string> labels_; + LabelsConstraint labelsConstraint_; + + // TODO-FIND + std::deque<Ordering*> ordering_; // The ordering criteria (note: the order is important !) + std::deque<void*> /* TODO-FIND */ metadataConstraints_; // All metadata filters (note: the order is not important) + + bool retrieveMainDicomTags_; + bool retrieveMetadata_; + bool retrieveLabels_; + bool retrieveAttachments_; + bool retrieveParentIdentifier_; + ParentSpecification retrieveParentPatient_; + ParentSpecification retrieveParentStudy_; + ParentSpecification retrieveParentSeries_; + ChildrenSpecification retrieveChildrenStudies_; + ChildrenSpecification retrieveChildrenSeries_; + ChildrenSpecification retrieveChildrenInstances_; + bool retrieveOneInstanceIdentifier_; + + std::unique_ptr<MainDicomTagsRegistry> mainDicomTagsRegistry_; + + public: + explicit FindRequest(ResourceType level); + + ~FindRequest(); + + ResourceType GetLevel() const + { + return level_; + } + + void SetOrthancId(ResourceType level, + const std::string& id); + + void SetOrthancPatientId(const std::string& id); + + void SetOrthancStudyId(const std::string& id); + + void SetOrthancSeriesId(const std::string& id); + + void SetOrthancInstanceId(const std::string& id); + + const OrthancIdentifiers& GetOrthancIdentifiers() const + { + return orthancIdentifiers_; + } + + DatabaseConstraints& GetDicomTagConstraints() + { + return dicomTagConstraints_; + } + + const DatabaseConstraints& GetDicomTagConstraints() const + { + return dicomTagConstraints_; + } + + size_t GetMetadataConstraintsCount() const + { + return metadataConstraints_.size(); + } + + void ClearLimits() + { + hasLimits_ = false; + } + + void SetLimits(uint64_t since, + uint64_t count); + + bool HasLimits() const + { + return hasLimits_; + } + + uint64_t GetLimitsSince() const; + + uint64_t GetLimitsCount() const; + + void AddOrdering(const DicomTag& tag, + OrderingDirection direction); + + void AddOrdering(MetadataType metadataType, + OrderingDirection direction); + + const std::deque<Ordering*>& GetOrdering() const + { + return ordering_; + } + + void SetLabels(const std::set<std::string>& labels) + { + labels_ = labels; + } + + void AddLabel(const std::string& label) + { + labels_.insert(label); + } + + const std::set<std::string>& GetLabels() const + { + return labels_; + } + + LabelsConstraint GetLabelsConstraint() const + { + return labelsConstraint_; + } + + void SetLabelsConstraint(LabelsConstraint constraint) + { + labelsConstraint_ = constraint; + } + + void SetRetrieveMainDicomTags(bool retrieve) + { + retrieveMainDicomTags_ = retrieve; + } + + bool IsRetrieveMainDicomTags() const + { + return retrieveMainDicomTags_; + } + + void SetRetrieveMetadata(bool retrieve) + { + retrieveMetadata_ = retrieve; + } + + bool IsRetrieveMetadata() const + { + return retrieveMetadata_; + } + + void SetRetrieveLabels(bool retrieve) + { + retrieveLabels_ = retrieve; + } + + bool IsRetrieveLabels() const + { + return retrieveLabels_; + } + + void SetRetrieveAttachments(bool retrieve) + { + retrieveAttachments_ = retrieve; + } + + bool IsRetrieveAttachments() const + { + return retrieveAttachments_; + } + + void SetRetrieveParentIdentifier(bool retrieve); + + bool IsRetrieveParentIdentifier() const + { + return retrieveParentIdentifier_; + } + + ParentSpecification& GetParentSpecification(ResourceType level); + + const ParentSpecification& GetParentSpecification(ResourceType level) const + { + return const_cast<FindRequest&>(*this).GetParentSpecification(level); + } + + ChildrenSpecification& GetChildrenSpecification(ResourceType level); + + const ChildrenSpecification& GetChildrenSpecification(ResourceType level) const + { + return const_cast<FindRequest&>(*this).GetChildrenSpecification(level); + } + + void SetRetrieveOneInstanceIdentifier(bool retrieve); + + bool IsRetrieveOneInstanceIdentifier() const + { + return (retrieveOneInstanceIdentifier_ || + (level_ != ResourceType_Instance && + GetChildrenSpecification(ResourceType_Instance).IsRetrieveIdentifiers())); + } + }; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/FindResponse.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,745 @@ +/** + * 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 "FindResponse.h" + +#include "../../../OrthancFramework/Sources/DicomFormat/DicomArray.h" +#include "../../../OrthancFramework/Sources/OrthancException.h" +#include "../../../OrthancFramework/Sources/SerializationToolbox.h" + +#include <boost/lexical_cast.hpp> +#include <cassert> + + +namespace Orthanc +{ + class FindResponse::MainDicomTagsAtLevel::DicomValue : public boost::noncopyable + { + public: + enum ValueType + { + ValueType_String, + ValueType_Null + }; + + private: + ValueType type_; + std::string value_; + + public: + DicomValue(ValueType type, + const std::string& value) : + type_(type), + value_(value) + { + } + + ValueType GetType() const + { + return type_; + } + + const std::string& GetValue() const + { + switch (type_) + { + case ValueType_Null: + throw OrthancException(ErrorCode_BadSequenceOfCalls); + + case ValueType_String: + return value_; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + }; + + + FindResponse::MainDicomTagsAtLevel::~MainDicomTagsAtLevel() + { + for (MainDicomTags::iterator it = mainDicomTags_.begin(); it != mainDicomTags_.end(); ++it) + { + assert(it->second != NULL); + delete it->second; + } + } + + + void FindResponse::MainDicomTagsAtLevel::AddNullDicomTag(uint16_t group, + uint16_t element) + { + const DicomTag tag(group, element); + + if (mainDicomTags_.find(tag) == mainDicomTags_.end()) + { + mainDicomTags_[tag] = new DicomValue(DicomValue::ValueType_Null, ""); + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void FindResponse::MainDicomTagsAtLevel::AddStringDicomTag(uint16_t group, + uint16_t element, + const std::string& value) + { + const DicomTag tag(group, element); + + if (mainDicomTags_.find(tag) == mainDicomTags_.end()) + { + mainDicomTags_[tag] = new DicomValue(DicomValue::ValueType_String, value); + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void FindResponse::MainDicomTagsAtLevel::Export(DicomMap& target) const + { + for (MainDicomTags::const_iterator it = mainDicomTags_.begin(); it != mainDicomTags_.end(); ++it) + { + assert(it->second != NULL); + + switch (it->second->GetType()) + { + case DicomValue::ValueType_String: + target.SetValue(it->first, it->second->GetValue(), false /* not binary */); + break; + + case DicomValue::ValueType_Null: + target.SetNullValue(it->first); + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + } + } + + + FindResponse::ChildrenInformation::~ChildrenInformation() + { + for (MetadataValues::iterator it = metadataValues_.begin(); it != metadataValues_.end(); ++it) + { + assert(it->second != NULL); + delete it->second; + } + + for (MainDicomTagValues::iterator it = mainDicomTagValues_.begin(); it != mainDicomTagValues_.end(); ++it) + { + assert(it->second != NULL); + delete it->second; + } + } + + + void FindResponse::ChildrenInformation::AddIdentifier(const std::string& identifier) + { + // The same identifier can be added through AddChildIdentifier and through AddOneInstanceIdentifier + identifiers_.insert(identifier); + } + + + void FindResponse::ChildrenInformation::AddMetadataValue(MetadataType metadata, + const std::string& value) + { + MetadataValues::iterator found = metadataValues_.find(metadata); + + if (found == metadataValues_.end()) + { + std::set<std::string> s; + s.insert(value); + metadataValues_[metadata] = new std::set<std::string>(s); + } + else + { + assert(found->second != NULL); + found->second->insert(value); + } + } + + + void FindResponse::ChildrenInformation::GetMetadataValues(std::set<std::string>& values, + MetadataType metadata) const + { + MetadataValues::const_iterator found = metadataValues_.find(metadata); + + if (found == metadataValues_.end()) + { + values.clear(); + } + else + { + assert(found->second != NULL); + values = *found->second; + } + } + + + void FindResponse::ChildrenInformation::AddMainDicomTagValue(const DicomTag& tag, + const std::string& value) + { + MainDicomTagValues::iterator found = mainDicomTagValues_.find(tag); + + if (found == mainDicomTagValues_.end()) + { + std::set<std::string> s; + s.insert(value); + mainDicomTagValues_[tag] = new std::set<std::string>(s); + } + else + { + assert(found->second != NULL); + found->second->insert(value); + } + } + + + void FindResponse::ChildrenInformation::GetMainDicomTagValues(std::set<std::string>& values, + const DicomTag& tag) const + { + MainDicomTagValues::const_iterator found = mainDicomTagValues_.find(tag); + + if (found == mainDicomTagValues_.end()) + { + values.clear(); + } + else + { + assert(found->second != NULL); + values = *found->second; + } + } + + + FindResponse::ChildrenInformation& FindResponse::Resource::GetChildrenInformation(ResourceType level) + { + switch (level) + { + case ResourceType_Study: + if (level_ == ResourceType_Patient) + { + return childrenStudiesInformation_; + } + else + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + case ResourceType_Series: + if (level_ == ResourceType_Patient || + level_ == ResourceType_Study) + { + return childrenSeriesInformation_; + } + else + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + case ResourceType_Instance: + if (level_ == ResourceType_Patient || + level_ == ResourceType_Study || + level_ == ResourceType_Series) + { + return childrenInstancesInformation_; + } + else + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + FindResponse::MainDicomTagsAtLevel& FindResponse::Resource::GetMainDicomTagsAtLevel(ResourceType level) + { + if (!IsResourceLevelAboveOrEqual(level, level_)) + { + throw OrthancException(ErrorCode_BadParameterType); + } + + switch (level) + { + case ResourceType_Patient: + return mainDicomTagsPatient_; + + case ResourceType_Study: + return mainDicomTagsStudy_; + + case ResourceType_Series: + return mainDicomTagsSeries_; + + case ResourceType_Instance: + return mainDicomTagsInstance_; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + void FindResponse::Resource::GetAllMainDicomTags(DicomMap& target) const + { + switch (level_) + { + // Don't reorder or add "break" below + case ResourceType_Instance: + mainDicomTagsInstance_.Export(target); + + case ResourceType_Series: + mainDicomTagsSeries_.Export(target); + + case ResourceType_Study: + mainDicomTagsStudy_.Export(target); + + case ResourceType_Patient: + mainDicomTagsPatient_.Export(target); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + void FindResponse::Resource::AddMetadata(ResourceType level, + MetadataType metadata, + const std::string& value) + { + std::map<MetadataType, std::string>& m = GetMetadata(level); + + if (m.find(metadata) != m.end()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); // Metadata already present + } + else + { + m[metadata] = value; + } + } + + + std::map<MetadataType, std::string>& FindResponse::Resource::GetMetadata(ResourceType level) + { + if (!IsResourceLevelAboveOrEqual(level, level_)) + { + throw OrthancException(ErrorCode_BadParameterType); + } + + switch (level) + { + case ResourceType_Patient: + return metadataPatient_; + + case ResourceType_Study: + return metadataStudy_; + + case ResourceType_Series: + return metadataSeries_; + + case ResourceType_Instance: + return metadataInstance_; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + bool FindResponse::Resource::LookupMetadata(std::string& value, + ResourceType level, + MetadataType metadata) const + { + const std::map<MetadataType, std::string>& m = GetMetadata(level); + + std::map<MetadataType, std::string>::const_iterator found = m.find(metadata); + + if (found == m.end()) + { + return false; + } + else + { + value = found->second; + return true; + } + } + + + void FindResponse::Resource::SetParentIdentifier(const std::string& id) + { + if (level_ == ResourceType_Patient) + { + throw OrthancException(ErrorCode_BadParameterType); + } + else if (HasParentIdentifier()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + parentIdentifier_.reset(new std::string(id)); + } + } + + + const std::string& FindResponse::Resource::GetParentIdentifier() const + { + if (level_ == ResourceType_Patient) + { + throw OrthancException(ErrorCode_BadParameterType); + } + else if (HasParentIdentifier()) + { + return *parentIdentifier_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + bool FindResponse::Resource::HasParentIdentifier() const + { + if (level_ == ResourceType_Patient) + { + throw OrthancException(ErrorCode_BadParameterType); + } + else + { + return parentIdentifier_.get() != NULL; + } + } + + + void FindResponse::Resource::AddLabel(const std::string& label) + { + if (labels_.find(label) == labels_.end()) + { + labels_.insert(label); + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void FindResponse::Resource::AddAttachment(const FileInfo& attachment) + { + if (attachments_.find(attachment.GetContentType()) == attachments_.end()) + { + attachments_[attachment.GetContentType()] = attachment; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + bool FindResponse::Resource::LookupAttachment(FileInfo& target, FileContentType type) const + { + std::map<FileContentType, FileInfo>::const_iterator it = attachments_.find(type); + if (it != attachments_.end()) + { + target = it->second; + return true; + } + else + { + return false; + } + } + + + const std::string& FindResponse::Resource::GetOneInstanceIdentifier() const + { + const std::set<std::string>& instances = GetChildrenInformation(ResourceType_Instance).GetIdentifiers(); + + if (instances.size() == 0) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); // HasOneInstanceIdentifier() should have been called + } + else + { + return *instances.begin(); + } + } + + + static void DebugDicomMap(Json::Value& target, + const DicomMap& m) + { + DicomArray a(m); + for (size_t i = 0; i < a.GetSize(); i++) + { + if (a.GetElement(i).GetValue().IsNull()) + { + target[a.GetElement(i).GetTag().Format()] = Json::nullValue; + } + else if (a.GetElement(i).GetValue().IsString()) + { + target[a.GetElement(i).GetTag().Format()] = a.GetElement(i).GetValue().GetContent(); + } + else + { + throw OrthancException(ErrorCode_InternalError); + } + } + } + + + static void DebugMetadata(Json::Value& target, + const std::map<MetadataType, std::string>& m) + { + target = Json::objectValue; + + for (std::map<MetadataType, std::string>::const_iterator it = m.begin(); it != m.end(); ++it) + { + target[EnumerationToString(it->first)] = it->second; + } + } + + + static void DebugAddAttachment(Json::Value& target, + const FileInfo& info) + { + Json::Value u = Json::arrayValue; + u.append(info.GetUuid()); + u.append(static_cast<Json::UInt64>(info.GetUncompressedSize())); + target[EnumerationToString(info.GetContentType())] = u; + } + + + static void DebugSetOfStrings(Json::Value& target, + const std::set<std::string>& values) + { + target = Json::arrayValue; + for (std::set<std::string>::const_iterator it = values.begin(); it != values.end(); ++it) + { + target.append(*it); + } + } + + + void FindResponse::Resource::DebugExport(Json::Value& target, + const FindRequest& request) const + { + target = Json::objectValue; + + target["Level"] = EnumerationToString(GetLevel()); + target["ID"] = GetIdentifier(); + + if (request.IsRetrieveParentIdentifier()) + { + target["ParentID"] = GetParentIdentifier(); + } + + if (request.IsRetrieveMainDicomTags()) + { + DicomMap m; + GetMainDicomTags(m, request.GetLevel()); + DebugDicomMap(target[EnumerationToString(GetLevel())]["MainDicomTags"], m); + } + + if (request.IsRetrieveMetadata()) + { + DebugMetadata(target[EnumerationToString(GetLevel())]["Metadata"], GetMetadata(request.GetLevel())); + } + + static const ResourceType levels[4] = { ResourceType_Patient, ResourceType_Study, ResourceType_Series, ResourceType_Instance }; + + for (size_t i = 0; i < 4; i++) + { + const char* level = EnumerationToString(levels[i]); + + if (levels[i] != request.GetLevel() && + IsResourceLevelAboveOrEqual(levels[i], request.GetLevel())) + { + if (request.GetParentSpecification(levels[i]).IsRetrieveMainDicomTags()) + { + DicomMap m; + GetMainDicomTags(m, levels[i]); + DebugDicomMap(target[level]["MainDicomTags"], m); + } + + if (request.GetParentSpecification(levels[i]).IsRetrieveMetadata()) + { + DebugMetadata(target[level]["Metadata"], GetMetadata(levels[i])); + } + } + + if (levels[i] != request.GetLevel() && + IsResourceLevelAboveOrEqual(request.GetLevel(), levels[i])) + { + if (request.GetChildrenSpecification(levels[i]).IsRetrieveIdentifiers()) + { + DebugSetOfStrings(target[level]["Identifiers"], GetChildrenInformation(levels[i]).GetIdentifiers()); + } + + const std::set<MetadataType>& metadata = request.GetChildrenSpecification(levels[i]).GetMetadata(); + for (std::set<MetadataType>::const_iterator it = metadata.begin(); it != metadata.end(); ++it) + { + std::set<std::string> values; + GetChildrenInformation(levels[i]).GetMetadataValues(values, *it); + DebugSetOfStrings(target[level]["Metadata"][EnumerationToString(*it)], values); + } + + const std::set<DicomTag>& tags = request.GetChildrenSpecification(levels[i]).GetMainDicomTags(); + for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) + { + std::set<std::string> values; + GetChildrenInformation(levels[i]).GetMainDicomTagValues(values, *it); + DebugSetOfStrings(target[level]["MainDicomTags"][it->Format()], values); + } + } + } + + if (request.IsRetrieveLabels()) + { + DebugSetOfStrings(target["Labels"], labels_); + } + + if (request.IsRetrieveAttachments()) + { + Json::Value v = Json::objectValue; + for (std::map<FileContentType, FileInfo>::const_iterator it = attachments_.begin(); + it != attachments_.end(); ++it) + { + if (it->first != it->second.GetContentType()) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + else + { + DebugAddAttachment(v, it->second); + } + } + target["Attachments"] = v; + } + + if (request.IsRetrieveOneInstanceIdentifier()) + { + target["OneInstance"] = GetOneInstanceIdentifier(); + } + } + + + FindResponse::~FindResponse() + { + for (size_t i = 0; i < items_.size(); i++) + { + assert(items_[i] != NULL); + delete items_[i]; + } + } + + + void FindResponse::Add(Resource* item /* takes ownership */) + { + std::unique_ptr<Resource> protection(item); + + if (item == NULL) + { + throw OrthancException(ErrorCode_NullPointer); + } + else if (!items_.empty() && + items_[0]->GetLevel() != item->GetLevel()) + { + throw OrthancException(ErrorCode_BadParameterType, "A find response must only contain resources of the same type"); + } + else + { + const std::string& id = item->GetIdentifier(); + int64_t internalId = item->GetInternalId(); + + if (identifierIndex_.find(id) == identifierIndex_.end() && internalIdIndex_.find(internalId) == internalIdIndex_.end()) + { + items_.push_back(protection.release()); + identifierIndex_[id] = item; + internalIdIndex_[internalId] = item; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls, "This resource has already been added: " + id + "/" + boost::lexical_cast<std::string>(internalId)); + } + } + } + + + const FindResponse::Resource& FindResponse::GetResourceByIndex(size_t index) const + { + if (index >= items_.size()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + assert(items_[index] != NULL); + return *items_[index]; + } + } + + + FindResponse::Resource& FindResponse::GetResourceByIdentifier(const std::string& id) + { + IdentifierIndex::const_iterator found = identifierIndex_.find(id); + + if (found == identifierIndex_.end()) + { + throw OrthancException(ErrorCode_InexistentItem); + } + else + { + assert(found->second != NULL); + return *found->second; + } + } + + + FindResponse::Resource& FindResponse::GetResourceByInternalId(int64_t internalId) + { + InternalIdIndex::const_iterator found = internalIdIndex_.find(internalId); + + if (found == internalIdIndex_.end()) + { + throw OrthancException(ErrorCode_InexistentItem); + } + else + { + assert(found->second != NULL); + return *found->second; + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/FindResponse.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,326 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "../../../OrthancFramework/Sources/DicomFormat/DicomMap.h" +#include "../../../OrthancFramework/Sources/Enumerations.h" +#include "../../../OrthancFramework/Sources/FileStorage/FileInfo.h" +#include "../ServerEnumerations.h" +#include "OrthancIdentifiers.h" +#include "FindRequest.h" + +#include <boost/noncopyable.hpp> +#include <deque> +#include <map> +#include <set> +#include <list> + + +namespace Orthanc +{ + class FindResponse : public boost::noncopyable + { + private: + class MainDicomTagsAtLevel : public boost::noncopyable + { + private: + class DicomValue; + + typedef std::map<DicomTag, DicomValue*> MainDicomTags; + + MainDicomTags mainDicomTags_; + + public: + ~MainDicomTagsAtLevel(); + + void AddStringDicomTag(uint16_t group, + uint16_t element, + const std::string& value); + + // The "Null" value could be used in the future to indicate a + // value that is not available, typically a new "ExtraMainDicomTag" + void AddNullDicomTag(uint16_t group, + uint16_t element); + + void Export(DicomMap& target) const; + }; + + class ChildrenInformation : public boost::noncopyable + { + private: + typedef std::map<MetadataType, std::set<std::string>* > MetadataValues; + typedef std::map<DicomTag, std::set<std::string>* > MainDicomTagValues; + + std::set<std::string> identifiers_; + MetadataValues metadataValues_; + MainDicomTagValues mainDicomTagValues_; + + public: + ~ChildrenInformation(); + + void AddIdentifier(const std::string& identifier); + + const std::set<std::string>& GetIdentifiers() const + { + return identifiers_; + } + + void AddMetadataValue(MetadataType metadata, + const std::string& value); + + void GetMetadataValues(std::set<std::string>& values, + MetadataType metadata) const; + + void AddMainDicomTagValue(const DicomTag& tag, + const std::string& value); + + void GetMainDicomTagValues(std::set<std::string>& values, + const DicomTag& tag) const; + }; + + + public: + class Resource : public boost::noncopyable + { + private: + typedef std::map<MetadataType, std::list<std::string>*> ChildrenMetadata; + + ResourceType level_; + int64_t internalId_; // Internal ID of the resource in the database + std::string identifier_; + std::unique_ptr<std::string> parentIdentifier_; + MainDicomTagsAtLevel mainDicomTagsPatient_; + MainDicomTagsAtLevel mainDicomTagsStudy_; + MainDicomTagsAtLevel mainDicomTagsSeries_; + MainDicomTagsAtLevel mainDicomTagsInstance_; + std::map<MetadataType, std::string> metadataPatient_; + std::map<MetadataType, std::string> metadataStudy_; + std::map<MetadataType, std::string> metadataSeries_; + std::map<MetadataType, std::string> metadataInstance_; + ChildrenInformation childrenStudiesInformation_; + ChildrenInformation childrenSeriesInformation_; + ChildrenInformation childrenInstancesInformation_; + std::set<std::string> labels_; + std::map<FileContentType, FileInfo> attachments_; + + MainDicomTagsAtLevel& GetMainDicomTagsAtLevel(ResourceType level); + + const MainDicomTagsAtLevel& GetMainDicomTagsAtLevel(ResourceType level) const + { + return const_cast<Resource&>(*this).GetMainDicomTagsAtLevel(level); + } + + ChildrenInformation& GetChildrenInformation(ResourceType level); + + const ChildrenInformation& GetChildrenInformation(ResourceType level) const + { + return const_cast<Resource&>(*this).GetChildrenInformation(level); + } + + public: + Resource(ResourceType level, + int64_t internalId, + const std::string& identifier) : + level_(level), + internalId_(internalId), + identifier_(identifier) + { + } + + ResourceType GetLevel() const + { + return level_; + } + + int64_t GetInternalId() const + { + return internalId_; + } + + const std::string& GetIdentifier() const + { + return identifier_; + } + + void SetParentIdentifier(const std::string& id); + + const std::string& GetParentIdentifier() const; + + bool HasParentIdentifier() const; + + void AddStringDicomTag(ResourceType level, + uint16_t group, + uint16_t element, + const std::string& value) + { + GetMainDicomTagsAtLevel(level).AddStringDicomTag(group, element, value); + } + + void AddNullDicomTag(ResourceType level, + uint16_t group, + uint16_t element) + { + GetMainDicomTagsAtLevel(level).AddNullDicomTag(group, element); + } + + void GetMainDicomTags(DicomMap& target, + ResourceType level) const + { + GetMainDicomTagsAtLevel(level).Export(target); + } + + void GetAllMainDicomTags(DicomMap& target) const; + + void AddMetadata(ResourceType level, + MetadataType metadata, + const std::string& value); + + std::map<MetadataType, std::string>& GetMetadata(ResourceType level); + + const std::map<MetadataType, std::string>& GetMetadata(ResourceType level) const + { + return const_cast<Resource&>(*this).GetMetadata(level); + } + + bool LookupMetadata(std::string& value, + ResourceType level, + MetadataType metadata) const; + + void AddChildIdentifier(ResourceType level, + const std::string& childId) + { + GetChildrenInformation(level).AddIdentifier(childId); + } + + const std::set<std::string>& GetChildrenIdentifiers(ResourceType level) const + { + return GetChildrenInformation(level).GetIdentifiers(); + } + + void AddChildrenMetadataValue(ResourceType level, + MetadataType metadata, + const std::string& value) + { + GetChildrenInformation(level).AddMetadataValue(metadata, value); + } + + void GetChildrenMetadataValues(std::set<std::string>& values, + ResourceType level, + MetadataType metadata) const + { + GetChildrenInformation(level).GetMetadataValues(values, metadata); + } + + void AddChildrenMainDicomTagValue(ResourceType level, + const DicomTag& tag, + const std::string& value) + { + GetChildrenInformation(level).AddMainDicomTagValue(tag, value); + } + + void GetChildrenMainDicomTagValues(std::set<std::string>& values, + ResourceType level, + const DicomTag& tag) const + { + GetChildrenInformation(level).GetMainDicomTagValues(values, tag); + } + + void AddLabel(const std::string& label); + + std::set<std::string>& GetLabels() + { + return labels_; + } + + const std::set<std::string>& GetLabels() const + { + return labels_; + } + + void AddAttachment(const FileInfo& attachment); + + bool LookupAttachment(FileInfo& target, + FileContentType type) const; + + const std::map<FileContentType, FileInfo>& GetAttachments() const + { + return attachments_; + } + + const std::string& GetOneInstanceIdentifier() const; + + bool HasOneInstanceIdentifier() const + { + return !GetChildrenIdentifiers(ResourceType_Instance).empty(); + } + + void DebugExport(Json::Value& target, + const FindRequest& request) const; + }; + + private: + typedef std::map<std::string, Resource*> IdentifierIndex; + typedef std::map<int64_t, Resource*> InternalIdIndex; + + std::deque<Resource*> items_; + IdentifierIndex identifierIndex_; + InternalIdIndex internalIdIndex_; + + public: + ~FindResponse(); + + void Add(Resource* item /* takes ownership */); + + size_t GetSize() const + { + return items_.size(); + } + + const Resource& GetResourceByIndex(size_t index) const; + + Resource& GetResourceByIdentifier(const std::string& id); + + Resource& GetResourceByInternalId(int64_t internalId); + + const Resource& GetResourceByIdentifier(const std::string& id) const + { + return const_cast<FindResponse&>(*this).GetResourceByIdentifier(id); + } + + const Resource& GetResourceByInternalId(int64_t internalId) const + { + return const_cast<FindResponse&>(*this).GetResourceByInternalId(internalId); + } + + bool HasResource(const std::string& id) const + { + return (identifierIndex_.find(id) != identifierIndex_.end()); + } + + bool HasResource(int64_t& internalId) const + { + return (internalIdIndex_.find(internalId) != internalIdIndex_.end()); + } + }; +}
--- a/OrthancServer/Sources/Database/IDatabaseWrapper.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/IDatabaseWrapper.h Thu Sep 05 18:52:27 2024 +0200 @@ -29,6 +29,8 @@ #include "../ExportedResource.h" #include "../Search/ISqlLookupFormatter.h" #include "../ServerIndexChange.h" +#include "FindRequest.h" +#include "FindResponse.h" #include "IDatabaseListener.h" #include <list> @@ -37,7 +39,7 @@ namespace Orthanc { - class DatabaseConstraint; + class DatabaseConstraints; class ResourcesContent; class IDatabaseWrapper : public boost::noncopyable @@ -52,6 +54,7 @@ bool hasAtomicIncrementGlobalProperty_; bool hasUpdateAndGetStatistics_; bool hasMeasureLatency_; + bool hasFindSupport_; bool hasExtendedChanges_; public: @@ -62,6 +65,7 @@ hasAtomicIncrementGlobalProperty_(false), hasUpdateAndGetStatistics_(false), hasMeasureLatency_(false), + hasFindSupport_(false), hasExtendedChanges_(false) { } @@ -135,6 +139,16 @@ { return hasMeasureLatency_; } + + void SetHasFindSupport(bool value) + { + hasFindSupport_ = value; + } + + bool HasFindSupport() const + { + return hasFindSupport_; + } }; @@ -294,7 +308,7 @@ virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, // Can be NULL if not needed - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -365,14 +379,41 @@ int64_t& compressedSize, int64_t& uncompressedSize) = 0; - // New in Orthanc 1.13.0 + /** + * Primitives introduced in Orthanc 1.12.4 + **/ + + // This is only implemented if "HasIntegratedFind()" is "true" + virtual void ExecuteFind(FindResponse& response, + const FindRequest& request, + const Capabilities& capabilities) = 0; + + // This is only implemented if "HasIntegratedFind()" is "false" + virtual void ExecuteFind(std::list<std::string>& identifiers, + const Capabilities& capabilities, + const FindRequest& request) = 0; + + /** + * This is only implemented if "HasIntegratedFind()" is + * "false". In this flavor, the resource of interest might have + * been deleted, as the expansion is not done in the same + * transaction as the "ExecuteFind()". In such cases, the + * wrapper should not throw an exception, but simply ignore the + * request to expand the resource (i.e., "response" must not be + * modified). + **/ + virtual void ExecuteExpand(FindResponse& response, + const Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) = 0; + + // New in Orthanc 1.12.5 virtual void GetChangesExtended(std::list<ServerIndexChange>& target /*out*/, bool& done /*out*/, int64_t since, int64_t to, uint32_t limit, ChangeType filterType) = 0; - }; @@ -397,5 +438,9 @@ virtual const Capabilities GetDatabaseCapabilities() const = 0; virtual uint64_t MeasureLatency() = 0; + + // Returns "true" iff. the database engine supports the + // simultaneous find and expansion of resources. + virtual bool HasIntegratedFind() const = 0; }; }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/MainDicomTagsRegistry.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,142 @@ +/** + * 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 "MainDicomTagsRegistry.h" + +#include "../ServerToolbox.h" + +namespace Orthanc +{ + void MainDicomTagsRegistry::LoadTags(ResourceType level) + { + { + const DicomTag* tags = NULL; + size_t size; + + ServerToolbox::LoadIdentifiers(tags, size, level); + + for (size_t i = 0; i < size; i++) + { + if (registry_.find(tags[i]) == registry_.end()) + { + registry_[tags[i]] = TagInfo(level, DicomTagType_Identifier); + } + else + { + // These patient-level tags are copied in the study level + assert(level == ResourceType_Study && + (tags[i] == DICOM_TAG_PATIENT_ID || + tags[i] == DICOM_TAG_PATIENT_NAME || + tags[i] == DICOM_TAG_PATIENT_BIRTH_DATE)); + } + } + } + + { + std::set<DicomTag> tags; + DicomMap::GetMainDicomTags(tags, level); + + for (std::set<DicomTag>::const_iterator + tag = tags.begin(); tag != tags.end(); ++tag) + { + if (registry_.find(*tag) == registry_.end()) + { + registry_[*tag] = TagInfo(level, DicomTagType_Main); + } + } + } + } + + + MainDicomTagsRegistry::MainDicomTagsRegistry() + { + LoadTags(ResourceType_Patient); + LoadTags(ResourceType_Study); + LoadTags(ResourceType_Series); + LoadTags(ResourceType_Instance); + } + + + void MainDicomTagsRegistry::LookupTag(ResourceType& level, + DicomTagType& type, + const DicomTag& tag) const + { + Registry::const_iterator it = registry_.find(tag); + + if (it == registry_.end()) + { + // Default values + level = ResourceType_Instance; + type = DicomTagType_Generic; + } + else + { + level = it->second.GetLevel(); + type = it->second.GetType(); + } + } + + + bool MainDicomTagsRegistry::NormalizeLookup(DatabaseConstraints& target, + const DatabaseLookup& source, + ResourceType queryLevel) const + { + bool isEquivalentLookup = true; + + target.Clear(); + + for (size_t i = 0; i < source.GetConstraintsCount(); i++) + { + ResourceType level; + DicomTagType type; + + LookupTag(level, type, source.GetConstraint(i).GetTag()); + + if (type == DicomTagType_Identifier || + type == DicomTagType_Main) + { + // Use the fact that patient-level tags are copied at the study level + if (level == ResourceType_Patient && + queryLevel != ResourceType_Patient) + { + level = ResourceType_Study; + } + + bool isEquivalentConstraint; + target.AddConstraint(source.GetConstraint(i).ConvertToDatabaseConstraint(isEquivalentConstraint, level, type)); + + if (!isEquivalentConstraint) + { + isEquivalentLookup = false; + } + } + else + { + isEquivalentLookup = false; + } + } + + return isEquivalentLookup; + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/MainDicomTagsRegistry.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,88 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "../Search/DatabaseLookup.h" + +#include <boost/noncopyable.hpp> + + +namespace Orthanc +{ + class MainDicomTagsRegistry : public boost::noncopyable + { + private: + class TagInfo + { + private: + ResourceType level_; + DicomTagType type_; + + public: + TagInfo() + { + } + + TagInfo(ResourceType level, + DicomTagType type) : + level_(level), + type_(type) + { + } + + ResourceType GetLevel() const + { + return level_; + } + + DicomTagType GetType() const + { + return type_; + } + }; + + typedef std::map<DicomTag, TagInfo> Registry; + + Registry registry_; + + void LoadTags(ResourceType level); + + public: + MainDicomTagsRegistry(); + + void LookupTag(ResourceType& level, + DicomTagType& type, + const DicomTag& tag) const; + + /** + * Returns "true" iff. the normalized lookup is the same as the + * original DatabaseLookup. If "false" is returned, the target + * constraints are less strict than the original DatabaseLookup, + * so more resources will match them. + **/ + bool NormalizeLookup(DatabaseConstraints& target, + const DatabaseLookup& source, + ResourceType queryLevel) const; + }; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/OrthancIdentifiers.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,248 @@ +/** + * 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 "FindRequest.h" + +#include "../../../OrthancFramework/Sources/OrthancException.h" + + +namespace Orthanc +{ + OrthancIdentifiers::OrthancIdentifiers(const OrthancIdentifiers& other) + { + if (other.HasPatientId()) + { + SetPatientId(other.GetPatientId()); + } + + if (other.HasStudyId()) + { + SetStudyId(other.GetStudyId()); + } + + if (other.HasSeriesId()) + { + SetSeriesId(other.GetSeriesId()); + } + + if (other.HasInstanceId()) + { + SetInstanceId(other.GetInstanceId()); + } + } + + + void OrthancIdentifiers::SetPatientId(const std::string& id) + { + if (HasPatientId()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + patientId_.reset(new std::string(id)); + } + } + + + const std::string& OrthancIdentifiers::GetPatientId() const + { + if (HasPatientId()) + { + return *patientId_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void OrthancIdentifiers::SetStudyId(const std::string& id) + { + if (HasStudyId()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + studyId_.reset(new std::string(id)); + } + } + + + const std::string& OrthancIdentifiers::GetStudyId() const + { + if (HasStudyId()) + { + return *studyId_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void OrthancIdentifiers::SetSeriesId(const std::string& id) + { + if (HasSeriesId()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + seriesId_.reset(new std::string(id)); + } + } + + + const std::string& OrthancIdentifiers::GetSeriesId() const + { + if (HasSeriesId()) + { + return *seriesId_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + void OrthancIdentifiers::SetInstanceId(const std::string& id) + { + if (HasInstanceId()) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + instanceId_.reset(new std::string(id)); + } + } + + + const std::string& OrthancIdentifiers::GetInstanceId() const + { + if (HasInstanceId()) + { + return *instanceId_; + } + else + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + } + + + ResourceType OrthancIdentifiers::DetectLevel() const + { + if (HasPatientId() && + !HasStudyId() && + !HasSeriesId() && + !HasInstanceId()) + { + return ResourceType_Patient; + } + else if (// HasPatientId() && + HasStudyId() && + !HasSeriesId() && + !HasInstanceId()) + { + return ResourceType_Study; + } + else if (// HasPatientId() && + // HasStudyId() && + HasSeriesId() && + !HasInstanceId()) + { + return ResourceType_Series; + } + else if (// HasPatientId() && + // HasStudyId() && + // HasSeriesId() && + HasInstanceId()) + { + return ResourceType_Instance; + } + else + { + throw OrthancException(ErrorCode_InexistentItem); + } + } + + + void OrthancIdentifiers::SetLevel(ResourceType level, + const std::string& id) + { + switch (level) + { + case ResourceType_Patient: + SetPatientId(id); + break; + + case ResourceType_Study: + SetStudyId(id); + break; + + case ResourceType_Series: + SetSeriesId(id); + break; + + case ResourceType_Instance: + SetInstanceId(id); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + + std::string OrthancIdentifiers::GetLevel(ResourceType level) const + { + switch (level) + { + case ResourceType_Patient: + return GetPatientId(); + + case ResourceType_Study: + return GetStudyId(); + + case ResourceType_Series: + return GetSeriesId(); + + case ResourceType_Instance: + return GetInstanceId(); + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + bool OrthancIdentifiers::IsDefined() const + { + return HasPatientId() || HasStudyId() || HasSeriesId() || HasInstanceId(); + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/Database/OrthancIdentifiers.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,95 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "../../../OrthancFramework/Sources/Compatibility.h" +#include "../../../OrthancFramework/Sources/Enumerations.h" + +#include <boost/noncopyable.hpp> +#include <string> + + +namespace Orthanc +{ + class OrthancIdentifiers : public boost::noncopyable + { + private: + std::unique_ptr<std::string> patientId_; + std::unique_ptr<std::string> studyId_; + std::unique_ptr<std::string> seriesId_; + std::unique_ptr<std::string> instanceId_; + + public: + OrthancIdentifiers() + { + } + + OrthancIdentifiers(const OrthancIdentifiers& other); + + void SetPatientId(const std::string& id); + + bool HasPatientId() const + { + return patientId_.get() != NULL; + } + + const std::string& GetPatientId() const; + + void SetStudyId(const std::string& id); + + bool HasStudyId() const + { + return studyId_.get() != NULL; + } + + const std::string& GetStudyId() const; + + void SetSeriesId(const std::string& id); + + bool HasSeriesId() const + { + return seriesId_.get() != NULL; + } + + const std::string& GetSeriesId() const; + + void SetInstanceId(const std::string& id); + + bool HasInstanceId() const + { + return instanceId_.get() != NULL; + } + + const std::string& GetInstanceId() const; + + ResourceType DetectLevel() const; + + void SetLevel(ResourceType level, + const std::string& id); + + std::string GetLevel(ResourceType level) const; + + bool IsDefined() const; + }; +}
--- a/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -29,6 +29,7 @@ #include "../../../OrthancFramework/Sources/SQLite/Transaction.h" #include "../Search/ISqlLookupFormatter.h" #include "../ServerToolbox.h" +#include "Compatibility/GenericFind.h" #include "Compatibility/ICreateInstance.h" #include "Compatibility/IGetChildrenMetadata.h" #include "Compatibility/ILookupResourceAndParent.h" @@ -356,7 +357,7 @@ virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -397,6 +398,324 @@ } } + virtual void ExecuteFind(FindResponse& response, + const FindRequest& request, + const Capabilities& capabilities) ORTHANC_OVERRIDE + { + const ResourceType requestLevel = request.GetLevel(); + std::string sql; + + { + // clean previous lookup table + SQLite::Statement s(db_, SQLITE_FROM_HERE, "DROP TABLE IF EXISTS Lookup"); + s.Run(); + } + + { + // extract the resource id of interest by executing the lookup + LookupFormatter formatter; + LookupFormatter::Apply(sql, formatter, request); + + sql = "CREATE TEMPORARY TABLE Lookup AS " + sql; + + SQLite::Statement statement(db_, sql); + formatter.Bind(statement); + statement.Run(); + + SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId, internalId FROM Lookup"); + while (s.Step()) + { + response.Add(new FindResponse::Resource(requestLevel, s.ColumnInt64(1), s.ColumnString(0))); + } + } + + // need MainDicomTags from resource ? + if (request.IsRetrieveMainDicomTags()) + { + sql = "SELECT id, tagGroup, tagElement, value " + "FROM MainDicomTags " + "INNER JOIN Lookup ON MainDicomTags.id = Lookup.internalId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddStringDicomTag(requestLevel, + static_cast<uint16_t>(s.ColumnInt(1)), + static_cast<uint16_t>(s.ColumnInt(2)), + s.ColumnString(3)); + } + } + + // need MainDicomTags from parent ? + if (requestLevel > ResourceType_Patient && request.GetParentSpecification(static_cast<ResourceType>(requestLevel - 1)).IsRetrieveMainDicomTags()) + { + sql = "SELECT currentLevel.internalId, tagGroup, tagElement, value " + "FROM MainDicomTags " + "INNER JOIN Resources currentLevel ON Lookup.internalId = currentLevel.internalId " + "INNER JOIN Lookup ON MainDicomTags.id = currentLevel.parentId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddStringDicomTag(static_cast<ResourceType>(requestLevel - 1), + static_cast<uint16_t>(s.ColumnInt(1)), + static_cast<uint16_t>(s.ColumnInt(2)), + s.ColumnString(3)); + } + } + + // need MainDicomTags from grandparent ? + if (requestLevel > ResourceType_Study && request.GetParentSpecification(static_cast<ResourceType>(requestLevel - 2)).IsRetrieveMainDicomTags()) + { + sql = "SELECT currentLevel.internalId, tagGroup, tagElement, value " + "FROM MainDicomTags " + "INNER JOIN Resources currentLevel ON Lookup.internalId = currentLevel.internalId " + "INNER JOIN Resources parentLevel ON currentLevel.parentId = parentLevel.internalId " + "INNER JOIN Lookup ON MainDicomTags.id = parentLevel.parentId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddStringDicomTag(static_cast<ResourceType>(requestLevel - 2), + static_cast<uint16_t>(s.ColumnInt(1)), + static_cast<uint16_t>(s.ColumnInt(2)), + s.ColumnString(3)); + } + } + + // need MainDicomTags from children ? + if (requestLevel <= ResourceType_Series && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 1)).GetMainDicomTags().size() > 0) + { + sql = "SELECT Lookup.internalId, tagGroup, tagElement, value " + "FROM MainDicomTags " + "INNER JOIN Resources childLevel ON childLevel.parentId = Lookup.internalId " + "INNER JOIN Lookup ON MainDicomTags.id = childLevel.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildrenMainDicomTagValue(static_cast<ResourceType>(requestLevel + 1), + DicomTag(static_cast<uint16_t>(s.ColumnInt(1)), + static_cast<uint16_t>(s.ColumnInt(2))), + s.ColumnString(3)); + } + } + + // need MainDicomTags from grandchildren ? + if (requestLevel <= ResourceType_Study && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 2)).GetMainDicomTags().size() > 0) + { + sql = "SELECT Lookup.internalId, tagGroup, tagElement, value " + "FROM MainDicomTags " + "INNER JOIN Resources childLevel ON childLevel.parentId = Lookup.internalId " + "INNER JOIN Resources grandChildLevel ON childLevel.parentId = Lookup.internalId " + "INNER JOIN Lookup ON MainDicomTags.id = grandChildLevel.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildrenMainDicomTagValue(static_cast<ResourceType>(requestLevel + 2), + DicomTag(static_cast<uint16_t>(s.ColumnInt(1)), + static_cast<uint16_t>(s.ColumnInt(2))), + s.ColumnString(3)); + } + } + + // need parent identifier ? + if (request.IsRetrieveParentIdentifier()) + { + sql = "SELECT currentLevel.internalId, parentLevel.publicId " + "FROM Resources AS currentLevel " + "INNER JOIN Lookup ON currentLevel.internalId = Lookup.internalId " + "INNER JOIN Resources parentLevel ON currentLevel.parentId = parentLevel.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.SetParentIdentifier(s.ColumnString(1)); + } + } + + // need resource metadata ? + if (request.IsRetrieveMetadata()) + { + sql = "SELECT id, type, value " + "FROM Metadata " + "INNER JOIN Lookup ON Metadata.id = Lookup.internalId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddMetadata(requestLevel, + static_cast<MetadataType>(s.ColumnInt(1)), + s.ColumnString(2)); + } + } + + // need resource labels ? + if (request.IsRetrieveLabels()) + { + sql = "SELECT Lookup.internalId, label " + "FROM Labels " + "INNER JOIN Lookup ON Labels.id = Lookup.internalId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddLabel(s.ColumnString(1)); + } + } + + // need one instance identifier ? TODO: it might be actually more interesting to retrieve directly the attachment ids .... + if (request.IsRetrieveOneInstanceIdentifier()) + { + if (requestLevel == ResourceType_Series) + { + sql = "SELECT Lookup.internalId, childLevel.publicId " + "FROM Resources AS childLevel " + "INNER JOIN Lookup ON childLevel.parentId = Lookup.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildIdentifier(ResourceType_Instance, s.ColumnString(1)); + } + } + else if (requestLevel == ResourceType_Study) + { + sql = "SELECT Lookup.internalId, grandChildLevel.publicId " + "FROM Resources AS grandChildLevel " + "INNER JOIN Resources childLevel ON grandChildLevel.parentId = childLevel.internalId " + "INNER JOIN Lookup ON childLevel.parentId = Lookup.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildIdentifier(ResourceType_Instance, s.ColumnString(1)); + } + } + else if (requestLevel == ResourceType_Patient) + { + sql = "SELECT Lookup.internalId, grandGrandChildLevel.publicId " + "FROM Resources AS grandGrandChildLevel " + "INNER JOIN Resources grandChildLevel ON grandGrandChildLevel.parentId = grandChildLevel.internalId " + "INNER JOIN Resources childLevel ON grandChildLevel.parentId = childLevel.internalId " + "INNER JOIN Lookup ON childLevel.parentId = Lookup.internalId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildIdentifier(ResourceType_Instance, s.ColumnString(1)); + } + } + else + { + throw OrthancException(ErrorCode_InternalError); + } + } + + // need children metadata ? + if (requestLevel <= ResourceType_Series && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 1)).GetMetadata().size() > 0) + { + sql = "SELECT Lookup.internalId, type, value " + "FROM Metadata " + "INNER JOIN Lookup ON Lookup.internalId = childLevel.parentId " + "INNER JOIN Resources childLevel ON childLevel.internalId = Metadata.id"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildrenMetadataValue(static_cast<ResourceType>(requestLevel + 1), + static_cast<MetadataType>(s.ColumnInt(1)), + s.ColumnString(2)); + } + } + + // need grandchildren metadata ? + if (requestLevel <= ResourceType_Study && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 2)).GetMetadata().size() > 0) + { + sql = "SELECT Lookup.internalId, type, value " + "FROM Metadata " + "INNER JOIN Lookup ON Lookup.internalId = childLevel.parentId " + "INNER JOIN Resources childLevel ON childLevel.internalId = grandChildLevel.parentId " + "INNER JOIN Resources grandChildLevel ON grandChildLevel.internalId = Metadata.id"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildrenMetadataValue(static_cast<ResourceType>(requestLevel + 2), + static_cast<MetadataType>(s.ColumnInt(1)), + s.ColumnString(2)); + } + } + + // need children identifiers ? + if (requestLevel <= ResourceType_Series && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 1)).IsRetrieveIdentifiers()) + { + sql = "SELECT Lookup.internalId, childLevel.publicId " + "FROM Resources AS currentLevel " + "INNER JOIN Lookup ON currentLevel.internalId = Lookup.internalId " + "INNER JOIN Resources childLevel ON currentLevel.internalId = childLevel.parentId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildIdentifier(static_cast<ResourceType>(requestLevel + 1), s.ColumnString(1)); + } + } + + // need grandchildren identifiers ? + if (requestLevel <= ResourceType_Study && request.GetChildrenSpecification(static_cast<ResourceType>(requestLevel + 2)).IsRetrieveIdentifiers()) + { + sql = "SELECT Lookup.internalId, grandChildLevel.publicId " + "FROM Resources AS currentLevel " + "INNER JOIN Lookup ON currentLevel.internalId = Lookup.internalId " + "INNER JOIN Resources childLevel ON currentLevel.internalId = childLevel.parentId " + "INNER JOIN Resources grandChildLevel ON childLevel.internalId = grandChildLevel.parentId "; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + res.AddChildIdentifier(static_cast<ResourceType>(requestLevel + 2), s.ColumnString(1)); + } + } + + // need resource attachments ? + if (request.IsRetrieveAttachments()) + { + sql = "SELECT Lookup.internalId, fileType, uuid, uncompressedSize, compressedSize, compressionType, uncompressedMD5, compressedMD5 " + "FROM AttachedFiles " + "INNER JOIN Lookup ON AttachedFiles.id = Lookup.internalId"; + + SQLite::Statement s(db_, SQLITE_FROM_HERE, sql); + while (s.Step()) + { + FindResponse::Resource& res = response.GetResourceByInternalId(s.ColumnInt64(0)); + FileInfo file(s.ColumnString(2), static_cast<FileContentType>(s.ColumnInt(1)), + s.ColumnInt64(3), s.ColumnString(6), + static_cast<CompressionType>(s.ColumnInt(5)), + s.ColumnInt64(4), s.ColumnString(7)); + res.AddAttachment(file); + } + + } + } + + // From the "ICreateInstance" interface virtual void AttachChild(int64_t parent,
--- a/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/SQLiteDatabaseWrapper.h Thu Sep 05 18:52:27 2024 +0200 @@ -100,6 +100,11 @@ throw OrthancException(ErrorCode_NotImplemented); } + virtual bool HasIntegratedFind() const ORTHANC_OVERRIDE + { + return true; + } + /** * The "StartTransaction()" method is guaranteed to return a class * derived from "UnitTestsTransaction". The methods of
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -304,113 +304,6 @@ } - class StatelessDatabaseOperations::MainDicomTagsRegistry : public boost::noncopyable - { - private: - class TagInfo - { - private: - ResourceType level_; - DicomTagType type_; - - public: - TagInfo() - { - } - - TagInfo(ResourceType level, - DicomTagType type) : - level_(level), - type_(type) - { - } - - ResourceType GetLevel() const - { - return level_; - } - - DicomTagType GetType() const - { - return type_; - } - }; - - typedef std::map<DicomTag, TagInfo> Registry; - - - Registry registry_; - - void LoadTags(ResourceType level) - { - { - const DicomTag* tags = NULL; - size_t size; - - ServerToolbox::LoadIdentifiers(tags, size, level); - - for (size_t i = 0; i < size; i++) - { - if (registry_.find(tags[i]) == registry_.end()) - { - registry_[tags[i]] = TagInfo(level, DicomTagType_Identifier); - } - else - { - // These patient-level tags are copied in the study level - assert(level == ResourceType_Study && - (tags[i] == DICOM_TAG_PATIENT_ID || - tags[i] == DICOM_TAG_PATIENT_NAME || - tags[i] == DICOM_TAG_PATIENT_BIRTH_DATE)); - } - } - } - - { - std::set<DicomTag> tags; - DicomMap::GetMainDicomTags(tags, level); - - for (std::set<DicomTag>::const_iterator - tag = tags.begin(); tag != tags.end(); ++tag) - { - if (registry_.find(*tag) == registry_.end()) - { - registry_[*tag] = TagInfo(level, DicomTagType_Main); - } - } - } - } - - public: - MainDicomTagsRegistry() - { - LoadTags(ResourceType_Patient); - LoadTags(ResourceType_Study); - LoadTags(ResourceType_Series); - LoadTags(ResourceType_Instance); - } - - void LookupTag(ResourceType& level, - DicomTagType& type, - const DicomTag& tag) const - { - Registry::const_iterator it = registry_.find(tag); - - if (it == registry_.end()) - { - // Default values - level = ResourceType_Instance; - type = DicomTagType_Generic; - } - else - { - level = it->second.GetLevel(); - type = it->second.GetType(); - } - } - }; - - void StatelessDatabaseOperations::ReadWriteTransaction::LogChange(int64_t internalId, ChangeType changeType, ResourceType resourceType, @@ -475,38 +368,6 @@ } - void StatelessDatabaseOperations::NormalizeLookup(std::vector<DatabaseConstraint>& target, - const DatabaseLookup& source, - ResourceType queryLevel) const - { - assert(mainDicomTagsRegistry_.get() != NULL); - - target.clear(); - target.reserve(source.GetConstraintsCount()); - - for (size_t i = 0; i < source.GetConstraintsCount(); i++) - { - ResourceType level; - DicomTagType type; - - mainDicomTagsRegistry_->LookupTag(level, type, source.GetConstraint(i).GetTag()); - - if (type == DicomTagType_Identifier || - type == DicomTagType_Main) - { - // Use the fact that patient-level tags are copied at the study level - if (level == ResourceType_Patient && - queryLevel != ResourceType_Patient) - { - level = ResourceType_Study; - } - - target.push_back(source.GetConstraint(i).ConvertToDatabaseConstraint(level, type)); - } - } - } - - class StatelessDatabaseOperations::Transaction : public boost::noncopyable { private: @@ -910,7 +771,7 @@ Toolbox::GetMissingsFromSet(target.missingRequestedTags_, requestedTags, savedMainDicomTags); while ((target.missingRequestedTags_.size() > 0) - && currentLevel != ResourceType_Patient) + && currentLevel != ResourceType_Patient) { currentLevel = GetParentResourceType(currentLevel); @@ -1727,20 +1588,21 @@ DicomTagConstraint c(tag, ConstraintType_Equal, value, true, true); - std::vector<DatabaseConstraint> query; - query.push_back(c.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); + DatabaseConstraints query; + bool isIdentical; // unused + query.AddConstraint(c.ConvertToDatabaseConstraint(isIdentical, level, DicomTagType_Identifier)); class Operations : public IReadOnlyOperations { private: - std::vector<std::string>& result_; - const std::vector<DatabaseConstraint>& query_; - ResourceType level_; + std::vector<std::string>& result_; + const DatabaseConstraints& query_; + ResourceType level_; public: Operations(std::vector<std::string>& result, - const std::vector<DatabaseConstraint>& query, + const DatabaseConstraints& query, ResourceType level) : result_(result), query_(query), @@ -2026,7 +1888,7 @@ LabelsConstraint labelsConstraint, uint32_t limit) { - class Operations : public ReadOnlyOperationsT6<bool, const std::vector<DatabaseConstraint>&, ResourceType, + class Operations : public ReadOnlyOperationsT6<bool, const DatabaseConstraints&, ResourceType, const std::set<std::string>&, LabelsConstraint, size_t> { private: @@ -2072,8 +1934,10 @@ ServerToolbox::CheckValidLabel(*it); } - std::vector<DatabaseConstraint> normalized; - NormalizeLookup(normalized, lookup, queryLevel); + DatabaseConstraints normalized; + + assert(mainDicomTagsRegistry_.get() != NULL); + mainDicomTagsRegistry_->NormalizeLookup(normalized, lookup, queryLevel); Operations operations; operations.Apply(*this, (instancesId != NULL), normalized, queryLevel, labels, labelsConstraint, limit); @@ -2554,7 +2418,7 @@ catch (boost::bad_lexical_cast&) { LOG(ERROR) << "Cannot read the global sequence " - << boost::lexical_cast<std::string>(sequence_) << ", resetting it"; + << boost::lexical_cast<std::string>(sequence_) << ", resetting it"; oldValue = 0; } @@ -2853,8 +2717,8 @@ public: explicit Operations(const ParsedDicomFile& dicom, bool limitToThisLevelDicomTags, ResourceType limitToLevel) - : limitToThisLevelDicomTags_(limitToThisLevelDicomTags), - limitToLevel_(limitToLevel) + : limitToThisLevelDicomTags_(limitToThisLevelDicomTags), + limitToLevel_(limitToLevel) { OrthancConfiguration::DefaultExtractDicomSummary(summary_, dicom); hasher_.reset(new DicomInstanceHasher(summary_)); @@ -2979,7 +2843,7 @@ } bool StatelessDatabaseOperations::ReadWriteTransaction::HasReachedMaxPatientCount(unsigned int maximumPatientCount, - const std::string& patientId) + const std::string& patientId) { if (maximumPatientCount != 0) { @@ -3081,7 +2945,7 @@ }; if (maximumStorageMode == MaxStorageMode_Recycle - && (maximumStorageSize != 0 || maximumPatientCount != 0)) + && (maximumStorageSize != 0 || maximumPatientCount != 0)) { Operations operations(maximumStorageSize, maximumPatientCount); Apply(operations); @@ -3145,9 +3009,9 @@ } static void SetMainDicomSequenceMetadata(ResourcesContent& content, - int64_t resource, - const DicomMap& dicomSummary, - ResourceType level) + int64_t resource, + const DicomMap& dicomSummary, + ResourceType level) { std::string serialized; GetMainDicomSequenceMetadataContent(serialized, dicomSummary, level); @@ -3340,7 +3204,7 @@ // Ensure there is enough room in the storage for the new instance uint64_t instanceSize = 0; for (Attachments::const_iterator it = attachments_.begin(); - it != attachments_.end(); ++it) + it != attachments_.end(); ++it) { instanceSize += it->GetCompressedSize(); } @@ -3369,7 +3233,7 @@ // Attach the files to the newly created instance for (Attachments::const_iterator it = attachments_.begin(); - it != attachments_.end(); ++it) + it != attachments_.end(); ++it) { if (isReconstruct_) { @@ -3851,4 +3715,75 @@ boost::shared_lock<boost::shared_mutex> lock(mutex_); return db_.GetDatabaseCapabilities().HasExtendedChanges(); } + + void StatelessDatabaseOperations::ExecuteFind(FindResponse& response, + const FindRequest& request) + { + class IntegratedFind : public ReadOnlyOperationsT3<FindResponse&, const FindRequest&, + const IDatabaseWrapper::Capabilities&> + { + public: + virtual void ApplyTuple(ReadOnlyTransaction& transaction, + const Tuple& tuple) ORTHANC_OVERRIDE + { + transaction.ExecuteFind(tuple.get<0>(), tuple.get<1>(), tuple.get<2>()); + } + }; + + class FindStage : public ReadOnlyOperationsT3<std::list<std::string>&, const IDatabaseWrapper::Capabilities&, const FindRequest& > + { + public: + virtual void ApplyTuple(ReadOnlyTransaction& transaction, + const Tuple& tuple) ORTHANC_OVERRIDE + { + transaction.ExecuteFind(tuple.get<0>(), tuple.get<1>(), tuple.get<2>()); + } + }; + + class ExpandStage : public ReadOnlyOperationsT4<FindResponse&, const IDatabaseWrapper::Capabilities&, const FindRequest&, const std::string&> + { + public: + virtual void ApplyTuple(ReadOnlyTransaction& transaction, + const Tuple& tuple) ORTHANC_OVERRIDE + { + transaction.ExecuteExpand(tuple.get<0>(), tuple.get<1>(), tuple.get<2>(), tuple.get<3>()); + } + }; + + IDatabaseWrapper::Capabilities capabilities = db_.GetDatabaseCapabilities(); + + if (db_.HasIntegratedFind()) + { + /** + * In this flavor, the "find" and the "expand" phases are + * executed in one single transaction. + **/ + IntegratedFind operations; + operations.Apply(*this, response, request, capabilities); + } + else + { + /** + * In this flavor, the "find" and the "expand" phases for each + * found resource are executed in distinct transactions. This is + * the compatibility mode equivalent to Orthanc <= 1.12.3. + **/ + std::list<std::string> identifiers; + + FindStage find; + find.Apply(*this, identifiers, capabilities, request); + + ExpandStage expand; + + for (std::list<std::string>::const_iterator it = identifiers.begin(); it != identifiers.end(); ++it) + { + /** + * Not that the resource might have been deleted (as we are in + * another transaction). The database engine must ignore such + * error cases. + **/ + expand.Apply(*this, response, capabilities, request, *it); + } + } + } }
--- a/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Database/StatelessDatabaseOperations.h Thu Sep 05 18:52:27 2024 +0200 @@ -25,8 +25,9 @@ #include "../../../OrthancFramework/Sources/DicomFormat/DicomMap.h" +#include "../DicomInstanceOrigin.h" #include "IDatabaseWrapper.h" -#include "../DicomInstanceOrigin.h" +#include "MainDicomTagsRegistry.h" #include <boost/shared_ptr.hpp> #include <boost/thread/shared_mutex.hpp> @@ -80,7 +81,7 @@ indexInSeries_(0) { } - + void SetResource(ResourceType level, const std::string& id) { @@ -112,15 +113,26 @@ enum ExpandResourceFlags { ExpandResourceFlags_None = 0, + // used to fetch from DB and for output ExpandResourceFlags_IncludeMetadata = (1 << 0), ExpandResourceFlags_IncludeChildren = (1 << 1), ExpandResourceFlags_IncludeMainDicomTags = (1 << 2), ExpandResourceFlags_IncludeLabels = (1 << 3), - ExpandResourceFlags_Default = (ExpandResourceFlags_IncludeMetadata | - ExpandResourceFlags_IncludeChildren | - ExpandResourceFlags_IncludeMainDicomTags | - ExpandResourceFlags_IncludeLabels) + // only used for output + ExpandResourceFlags_IncludeAllMetadata = (1 << 4), // new in Orthanc 1.12.4 + ExpandResourceFlags_IncludeIsStable = (1 << 5), // new in Orthanc 1.12.4 + + ExpandResourceFlags_DefaultExtract = (ExpandResourceFlags_IncludeMetadata | + ExpandResourceFlags_IncludeChildren | + ExpandResourceFlags_IncludeMainDicomTags | + ExpandResourceFlags_IncludeLabels), + + ExpandResourceFlags_DefaultOutput = (ExpandResourceFlags_IncludeMetadata | + ExpandResourceFlags_IncludeChildren | + ExpandResourceFlags_IncludeMainDicomTags | + ExpandResourceFlags_IncludeLabels | + ExpandResourceFlags_IncludeIsStable) }; class StatelessDatabaseOperations : public boost::noncopyable @@ -209,7 +221,7 @@ void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, // Can be NULL if not needed - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, // New in Orthanc 1.12.0 LabelsConstraint labelsConstraint, // New in Orthanc 1.12.0 @@ -388,6 +400,28 @@ { transaction_.ListAllLabels(target); } + + void ExecuteFind(FindResponse& response, + const FindRequest& request, + const IDatabaseWrapper::Capabilities& capabilities) + { + transaction_.ExecuteFind(response, request, capabilities); + } + + void ExecuteFind(std::list<std::string>& identifiers, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request) + { + transaction_.ExecuteFind(identifiers, capabilities, request); + } + + void ExecuteExpand(FindResponse& response, + const IDatabaseWrapper::Capabilities& capabilities, + const FindRequest& request, + const std::string& identifier) + { + transaction_.ExecuteExpand(response, capabilities, request, identifier); + } }; @@ -555,7 +589,6 @@ private: - class MainDicomTagsRegistry; class Transaction; IDatabaseWrapper& db_; @@ -566,10 +599,6 @@ std::unique_ptr<ITransactionContextFactory> factory_; unsigned int maxRetries_; - void NormalizeLookup(std::vector<DatabaseConstraint>& target, - const DatabaseLookup& source, - ResourceType level) const; - void ApplyInternal(IReadOnlyOperations* readOperations, IReadWriteOperations* writeOperations); @@ -820,5 +849,8 @@ const std::set<std::string>& labels); bool HasLabelsSupport(); + + void ExecuteFind(FindResponse& response, + const FindRequest& request); }; }
--- a/OrthancServer/Sources/OrthancConfiguration.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancConfiguration.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -1157,6 +1157,10 @@ { warning = Warnings_002_InconsistentDicomTagsInDb; } + else if (name == "W003_DecoderFailure") + { + warning = Warnings_003_DecoderFailure; + } else { throw OrthancException(ErrorCode_BadFileFormat, name + " is not recognized as a valid warning name");
--- a/OrthancServer/Sources/OrthancFindRequestHandler.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancFindRequestHandler.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -30,6 +30,7 @@ #include "../../OrthancFramework/Sources/Lua/LuaFunctionCall.h" #include "../../OrthancFramework/Sources/MetricsRegistry.h" #include "OrthancConfiguration.h" +#include "ResourceFinder.cpp" #include "Search/DatabaseLookup.h" #include "ServerContext.h" #include "ServerToolbox.h" @@ -39,6 +40,48 @@ namespace Orthanc { + static void CopySequence(ParsedDicomFile& dicom, + const DicomTag& tag, + const Json::Value& source, + const std::string& defaultPrivateCreator, + const std::map<uint16_t, std::string>& privateCreators) + { + if (source.type() == Json::objectValue && + source.isMember("Type") && + source.isMember("Value") && + source["Type"].asString() == "Sequence" && + source["Value"].type() == Json::arrayValue) + { + Json::Value content = Json::arrayValue; + + for (Json::Value::ArrayIndex i = 0; i < source["Value"].size(); i++) + { + Json::Value item; + Toolbox::SimplifyDicomAsJson(item, source["Value"][i], DicomToJsonFormat_Short); + content.append(item); + } + + if (tag.IsPrivate()) + { + std::map<uint16_t, std::string>::const_iterator found = privateCreators.find(tag.GetGroup()); + + if (found != privateCreators.end()) + { + dicom.Replace(tag, content, false, DicomReplaceMode_InsertIfAbsent, found->second.c_str()); + } + else + { + dicom.Replace(tag, content, false, DicomReplaceMode_InsertIfAbsent, defaultPrivateCreator); + } + } + else + { + dicom.Replace(tag, content, false, DicomReplaceMode_InsertIfAbsent, "" /* no private creator */); + } + } + } + + static void AddAnswer(DicomFindAnswers& answers, ServerContext& context, const std::string& publicId, @@ -126,39 +169,7 @@ assert(dicomAsJson != NULL); const Json::Value& source = (*dicomAsJson) [tag->Format()]; - if (source.type() == Json::objectValue && - source.isMember("Type") && - source.isMember("Value") && - source["Type"].asString() == "Sequence" && - source["Value"].type() == Json::arrayValue) - { - Json::Value content = Json::arrayValue; - - for (Json::Value::ArrayIndex i = 0; i < source["Value"].size(); i++) - { - Json::Value item; - Toolbox::SimplifyDicomAsJson(item, source["Value"][i], DicomToJsonFormat_Short); - content.append(item); - } - - if (tag->IsPrivate()) - { - std::map<uint16_t, std::string>::const_iterator found = privateCreators.find(tag->GetGroup()); - - if (found != privateCreators.end()) - { - dicom.Replace(*tag, content, false, DicomReplaceMode_InsertIfAbsent, found->second.c_str()); - } - else - { - dicom.Replace(*tag, content, false, DicomReplaceMode_InsertIfAbsent, defaultPrivateCreator); - } - } - else - { - dicom.Replace(*tag, content, false, DicomReplaceMode_InsertIfAbsent, "" /* no private creator */); - } - } + CopySequence(dicom, *tag, source, defaultPrivateCreator, privateCreators); } answers.Add(dicom); @@ -319,6 +330,124 @@ }; + namespace + { + class LookupVisitorV2 : public ResourceFinder::IVisitor + { + private: + DicomFindAnswers& answers_; + DicomArray queryAsArray_; + const std::list<DicomTag>& sequencesToReturn_; + std::string defaultPrivateCreator_; // the private creator to use if the group is not defined in the query itself + const std::map<uint16_t, std::string>& privateCreators_; // the private creators defined in the query itself + std::string retrieveAet_; + + public: + LookupVisitorV2(DicomFindAnswers& answers, + const DicomMap& query, + const std::list<DicomTag>& sequencesToReturn, + const std::map<uint16_t, std::string>& privateCreators) : + answers_(answers), + queryAsArray_(query), + sequencesToReturn_(sequencesToReturn), + privateCreators_(privateCreators) + { + answers_.SetComplete(false); + + { + OrthancConfiguration::ReaderLock lock; + defaultPrivateCreator_ = lock.GetConfiguration().GetDefaultPrivateCreator(); + retrieveAet_ = lock.GetConfiguration().GetOrthancAET(); + } + } + + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE + { + DicomMap resourceTags; + resource.GetAllMainDicomTags(resourceTags); + resourceTags.Merge(requestedTags); + + DicomMap result; + + /** + * Add the mandatory "Retrieve AE Title (0008,0054)" tag, which was missing in Orthanc <= 1.7.2. + * http://dicom.nema.org/medical/dicom/current/output/html/part04.html#sect_C.4.1.1.3.2 + * https://groups.google.com/g/orthanc-users/c/-7zNTKR_PMU/m/kfjwzEVNAgAJ + **/ + result.SetValue(DICOM_TAG_RETRIEVE_AE_TITLE, retrieveAet_, false /* not binary */); + + for (size_t i = 0; i < queryAsArray_.GetSize(); i++) + { + const DicomTag tag = queryAsArray_.GetElement(i).GetTag(); + + if (tag == DICOM_TAG_QUERY_RETRIEVE_LEVEL) + { + // Fix issue 30 on Google Code (QR response missing "Query/Retrieve Level" (008,0052)) + result.SetValue(tag, queryAsArray_.GetElement(i).GetValue()); + } + else if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET) + { + // Do not include the encoding, this is handled by class ParsedDicomFile + } + else + { + const DicomValue* value = resourceTags.TestAndGetValue(tag); + + if (value == NULL || + value->IsNull() || + value->IsBinary()) + { + result.SetValue(tag, "", false); + } + else + { + result.SetValue(tag, value->GetContent(), false); + } + } + } + + if (result.GetSize() == 0 && + sequencesToReturn_.empty()) + { + CLOG(WARNING, DICOM) << "The C-FIND request does not return any DICOM tag"; + } + else if (sequencesToReturn_.empty()) + { + answers_.Add(result); + } + else + { + ParsedDicomFile dicom(result, GetDefaultDicomEncoding(), + true /* be permissive, cf. issue #136 */, defaultPrivateCreator_, privateCreators_); + + for (std::list<DicomTag>::const_iterator tag = sequencesToReturn_.begin(); + tag != sequencesToReturn_.end(); ++tag) + { + const DicomValue* value = resourceTags.TestAndGetValue(*tag); + if (value != NULL && + value->IsSequence()) + { + CopySequence(dicom, *tag, value->GetSequenceContent(), defaultPrivateCreator_, privateCreators_); + } + else + { + dicom.Replace(*tag, std::string(""), false, DicomReplaceMode_InsertIfAbsent, defaultPrivateCreator_); + } + } + + answers_.Add(dicom); + } + } + + virtual void MarkAsComplete() ORTHANC_OVERRIDE + { + answers_.SetComplete(true); + } + }; + } + + void OrthancFindRequestHandler::Handle(DicomFindAnswers& answers, const DicomMap& input, const std::list<DicomTag>& sequencesToReturn, @@ -396,7 +525,6 @@ throw OrthancException(ErrorCode_NotImplemented); } - DicomArray query(*filteredInput); CLOG(INFO, DICOM) << "DICOM C-Find request at level: " << EnumerationToString(level); @@ -410,9 +538,12 @@ } } + std::set<DicomTag> requestedTags; + for (std::list<DicomTag>::const_iterator it = sequencesToReturn.begin(); it != sequencesToReturn.end(); ++it) { + requestedTags.insert(*it); CLOG(INFO, DICOM) << " (" << it->Format() << ") " << FromDcmtkBridge::GetTagName(*it, "") << " : sequence tag whose content will be copied"; @@ -441,18 +572,26 @@ const DicomTag tag = element.GetTag(); // remove tags that are not used for matching - if (element.GetValue().IsNull() || - tag == DICOM_TAG_QUERY_RETRIEVE_LEVEL || + if (tag == DICOM_TAG_QUERY_RETRIEVE_LEVEL || tag == DICOM_TAG_SPECIFIC_CHARACTER_SET || tag == DICOM_TAG_TIMEZONE_OFFSET_FROM_UTC) // time zone is not directly used for matching. Once we support "Timezone query adjustment", we may use it to adjust date-time filters but for now, just ignore it { continue; } + requestedTags.insert(tag); + + if (element.GetValue().IsNull()) + { + // There is no constraint on this tag + continue; + } + std::string value = element.GetValue().GetContent(); if (value.size() == 0) { // An empty string corresponds to an universal constraint, so we ignore it + requestedTags.insert(tag); continue; } @@ -486,8 +625,28 @@ size_t limit = (level == ResourceType_Instance) ? maxInstances_ : maxResults_; - LookupVisitor visitor(answers, context_, level, *filteredInput, sequencesToReturn, privateCreators, context_.GetFindStorageAccessMode()); - context_.Apply(visitor, lookup, level, 0 /* "since" is not relevant to C-FIND */, limit); + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + + ResourceFinder finder(level, false /* don't expand */); + finder.SetDatabaseLookup(lookup); + finder.AddRequestedTags(requestedTags); + + LookupVisitorV2 visitor(answers, *filteredInput, sequencesToReturn, privateCreators); + finder.Execute(visitor, context_); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + + LookupVisitor visitor(answers, context_, level, *filteredInput, sequencesToReturn, privateCreators, context_.GetFindStorageAccessMode()); + context_.Apply(visitor, lookup, level, 0 /* "since" is not relevant to C-FIND */, limit); + } }
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestApi.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestApi.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -472,7 +472,7 @@ "If `true`, run the job in asynchronous mode, which means that the REST API call will immediately " "return, reporting the identifier of a job. Prefer this flavor wherever possible.", false) .SetRequestField(KEY_PRIORITY, RestApiCallDocumentation::Type_Number, - "In asynchronous mode, the priority of the job. The lower the value, the higher the priority.", false) + "In asynchronous mode, the priority of the job. The higher the value, the higher the priority.", false) .SetAnswerField("ID", RestApiCallDocumentation::Type_String, "In asynchronous mode, identifier of the job") .SetAnswerField("Path", RestApiCallDocumentation::Type_String, "In asynchronous mode, path to access the job in the REST API"); }
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestArchive.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestArchive.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -509,7 +509,7 @@ "If present, the DICOM files in the archive will be transcoded to the provided " "transfer syntax: https://orthanc.uclouvain.be/book/faq/transcoding.html", false) .SetRequestField("Priority", RestApiCallDocumentation::Type_Number, - "In asynchronous mode, the priority of the job. The lower the value, the higher the priority.", false) + "In asynchronous mode, the priority of the job. The higher the value, the higher the priority.", false) .AddAnswerType(MimeType_Zip, "In synchronous mode, the ZIP file containing the archive") .AddAnswerType(MimeType_Json, "In asynchronous mode, information about the job that has been submitted to " "generate the archive: https://orthanc.uclouvain.be/book/users/advanced-rest.html#jobs")
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestChanges.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestChanges.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -68,7 +68,7 @@ call.GetDocumentation() .SetTag("Tracking changes") .SetSummary("List changes") - .SetDescription("Whenever Orthanc receives a new DICOM instance, this event is recorded in the so-called _Changes Log_. This enables remote scripts to react to the arrival of new DICOM resources. A typical application is auto-routing, where an external script waits for a new DICOM instance to arrive into Orthanc, then forward this instance to another modality.") + .SetDescription("Whenever Orthanc receives a new DICOM instance, this event is recorded in the so-called _Changes Log_. This enables remote scripts to react to the arrival of new DICOM resources. A typical application is auto-routing, where an external script waits for a new DICOM instance to arrive into Orthanc, then forward this instance to another modality. Please note that, when resources are deleted, their corresponding change entries are also removed from the Changes Log, which helps ensuring that this log does not grow indefinitely.") .SetHttpGetArgument("last", RestApiCallDocumentation::Type_Number, "Request only the last change id (this argument must be used alone)", false) .SetHttpGetArgument("limit", RestApiCallDocumentation::Type_Number, "Limit the number of results", false) .SetHttpGetArgument("since", RestApiCallDocumentation::Type_Number, "Show only the resources since the provided index excluded", false)
--- a/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -22,6 +22,8 @@ #include "../PrecompiledHeadersServer.h" +#include "../ResourceFinder.h" + #include "OrthancRestApi.h" #include "../../../OrthancFramework/Sources/Compression/GzipCompressor.h" @@ -127,9 +129,24 @@ } + static bool ExpandResource(Json::Value& target, + ServerContext& context, + ResourceType level, + const std::string& identifier, + DicomToJsonFormat format, + bool retrieveMetadata) + { + ResourceFinder finder(level, true /* expand */); + finder.SetOrthancId(level, identifier); + finder.SetRetrieveMetadata(retrieveMetadata); + + return finder.ExecuteOneResource(target, context, format, retrieveMetadata); + } + + // List all the patients, studies, series or instances ---------------------- - static void AnswerListOfResources(RestApiOutput& output, + static void AnswerListOfResources1(RestApiOutput& output, ServerContext& context, const std::list<std::string>& resources, const std::map<std::string, std::string>& instancesIds, // optional: the id of an instance for each found resource. @@ -183,7 +200,7 @@ } - static void AnswerListOfResources(RestApiOutput& output, + static void AnswerListOfResources2(RestApiOutput& output, ServerContext& context, const std::list<std::string>& resources, ResourceType level, @@ -196,7 +213,7 @@ std::map<std::string, boost::shared_ptr<DicomMap> > unusedResourcesMainDicomTags; std::map<std::string, boost::shared_ptr<Json::Value> > unusedResourcesDicomAsJson; - AnswerListOfResources(output, context, resources, unusedInstancesIds, unusedResourcesMainDicomTags, unusedResourcesDicomAsJson, level, expand, format, requestedTags, allowStorageAccess); + AnswerListOfResources1(output, context, resources, unusedInstancesIds, unusedResourcesMainDicomTags, unusedResourcesDicomAsJson, level, expand, format, requestedTags, allowStorageAccess); } @@ -226,41 +243,92 @@ ServerIndex& index = OrthancRestApi::GetIndex(call); ServerContext& context = OrthancRestApi::GetContext(call); - std::list<std::string> result; - - std::set<DicomTag> requestedTags; - OrthancRestApi::GetRequestedTags(requestedTags, call); - - if (call.HasArgument("limit") || - call.HasArgument("since")) + if (true) { - if (!call.HasArgument("limit")) + /** + * EXPERIMENTAL VERSION + **/ + + // TODO-FIND: include the FindRequest options parsing in a method (parse from get-arguments and from post payload) + // TODO-FIND: support other values for expand like expand=MainDicomTags,Labels,Parent,SeriesStatus + const bool expand = (call.HasArgument("expand") && + call.GetBooleanArgument("expand", true)); + + std::set<DicomTag> requestedTags; + OrthancRestApi::GetRequestedTags(requestedTags, call); + + ResourceFinder finder(resourceType, expand); + finder.AddRequestedTags(requestedTags); + + if (call.HasArgument("limit") || + call.HasArgument("since")) { - throw OrthancException(ErrorCode_BadRequest, - "Missing \"limit\" argument for GET request against: " + - call.FlattenUri()); + if (!call.HasArgument("limit")) + { + throw OrthancException(ErrorCode_BadRequest, + "Missing \"limit\" argument for GET request against: " + + call.FlattenUri()); + } + + if (!call.HasArgument("since")) + { + throw OrthancException(ErrorCode_BadRequest, + "Missing \"since\" argument for GET request against: " + + call.FlattenUri()); + } + + uint64_t since = boost::lexical_cast<uint64_t>(call.GetArgument("since", "")); + uint64_t limit = boost::lexical_cast<uint64_t>(call.GetArgument("limit", "")); + finder.SetLimitsSince(since); + finder.SetLimitsCount(limit); } - if (!call.HasArgument("since")) - { - throw OrthancException(ErrorCode_BadRequest, - "Missing \"since\" argument for GET request against: " + - call.FlattenUri()); - } - - size_t since = boost::lexical_cast<size_t>(call.GetArgument("since", "")); - size_t limit = boost::lexical_cast<size_t>(call.GetArgument("limit", "")); - index.GetAllUuids(result, resourceType, since, limit); + Json::Value answer; + finder.Execute(answer, context, OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human), false /* no "Metadata" field */); + call.GetOutput().AnswerJson(answer); } else { - index.GetAllUuids(result, resourceType); + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + + std::list<std::string> result; + + std::set<DicomTag> requestedTags; + OrthancRestApi::GetRequestedTags(requestedTags, call); + + if (call.HasArgument("limit") || + call.HasArgument("since")) + { + if (!call.HasArgument("limit")) + { + throw OrthancException(ErrorCode_BadRequest, + "Missing \"limit\" argument for GET request against: " + + call.FlattenUri()); + } + + if (!call.HasArgument("since")) + { + throw OrthancException(ErrorCode_BadRequest, + "Missing \"since\" argument for GET request against: " + + call.FlattenUri()); + } + + size_t since = boost::lexical_cast<size_t>(call.GetArgument("since", "")); + size_t limit = boost::lexical_cast<size_t>(call.GetArgument("limit", "")); + index.GetAllUuids(result, resourceType, since, limit); + } + else + { + index.GetAllUuids(result, resourceType); + } + + AnswerListOfResources2(call.GetOutput(), context, result, resourceType, call.HasArgument("expand") && call.GetBooleanArgument("expand", true), + OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human), + requestedTags, + true /* allowStorageAccess */); } - - AnswerListOfResources(call.GetOutput(), context, result, resourceType, call.HasArgument("expand") && call.GetBooleanArgument("expand", true), - OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human), - requestedTags, - true /* allowStorageAccess */); } @@ -289,11 +357,34 @@ std::set<DicomTag> requestedTags; OrthancRestApi::GetRequestedTags(requestedTags, call); - Json::Value json; - if (OrthancRestApi::GetContext(call).ExpandResource( - json, call.GetUriComponent("id", ""), resourceType, format, requestedTags, true /* allowStorageAccess */)) + if (true) { - call.GetOutput().AnswerJson(json); + /** + * EXPERIMENTAL VERSION + **/ + + ResourceFinder finder(resourceType, true /* expand */); + finder.AddRequestedTags(requestedTags); + finder.SetOrthancId(resourceType, call.GetUriComponent("id", "")); + + Json::Value json; + if (finder.ExecuteOneResource(json, OrthancRestApi::GetContext(call), format, false /* no "Metadata" field */)) + { + call.GetOutput().AnswerJson(json); + } + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + + Json::Value json; + if (OrthancRestApi::GetContext(call).ExpandResource( + json, call.GetUriComponent("id", ""), resourceType, format, requestedTags, true /* allowStorageAccess */)) + { + call.GetOutput().AnswerJson(json); + } } } @@ -3140,7 +3231,7 @@ bool expand, const std::set<DicomTag>& requestedTags) const { - AnswerListOfResources(output, context, resources_, instancesIds_, resourcesMainDicomTags_, resourcesDicomAsJson_, level, expand, format_, requestedTags, IsStorageAccessAllowedForAnswers(findStorageAccessMode_)); + AnswerListOfResources1(output, context, resources_, instancesIds_, resourcesMainDicomTags_, resourcesDicomAsJson_, level, expand, format_, requestedTags, IsStorageAccessAllowedForAnswers(findStorageAccessMode_)); } }; } @@ -3252,8 +3343,140 @@ throw OrthancException(ErrorCode_BadRequest, "Field \"" + std::string(KEY_LABELS_CONSTRAINT) + "\" must be an array of strings"); } + else if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + + bool expand = false; + if (request.isMember(KEY_EXPAND)) + { + expand = request[KEY_EXPAND].asBool(); + } + + const ResourceType level = StringToResourceType(request[KEY_LEVEL].asCString()); + + ResourceFinder finder(level, expand); + finder.SetDatabaseLimits(context.GetDatabaseLimits(level)); + + const DicomToJsonFormat format = OrthancRestApi::GetDicomFormat(request, DicomToJsonFormat_Human); + + if (request.isMember(KEY_LIMIT)) + { + int64_t tmp = request[KEY_LIMIT].asInt64(); + if (tmp < 0) + { + throw OrthancException(ErrorCode_ParameterOutOfRange, + "Field \"" + std::string(KEY_LIMIT) + "\" must be a positive integer"); + } + else if (tmp != 0) // This is for compatibility with Orthanc 1.12.4 + { + finder.SetLimitsCount(static_cast<uint64_t>(tmp)); + } + } + + if (request.isMember(KEY_SINCE)) + { + int64_t tmp = request[KEY_SINCE].asInt64(); + if (tmp < 0) + { + throw OrthancException(ErrorCode_ParameterOutOfRange, + "Field \"" + std::string(KEY_SINCE) + "\" must be a positive integer"); + } + else + { + finder.SetLimitsSince(static_cast<uint64_t>(tmp)); + } + } + + { + bool caseSensitive = false; + if (request.isMember(KEY_CASE_SENSITIVE)) + { + caseSensitive = request[KEY_CASE_SENSITIVE].asBool(); + } + + DatabaseLookup query; + + Json::Value::Members members = request[KEY_QUERY].getMemberNames(); + for (size_t i = 0; i < members.size(); i++) + { + if (request[KEY_QUERY][members[i]].type() != Json::stringValue) + { + throw OrthancException(ErrorCode_BadRequest, + "Tag \"" + members[i] + "\" must be associated with a string"); + } + + const std::string value = request[KEY_QUERY][members[i]].asString(); + + if (!value.empty()) + { + // An empty string corresponds to an universal constraint, + // so we ignore it. This mimics the behavior of class + // "OrthancFindRequestHandler" + query.AddRestConstraint(FromDcmtkBridge::ParseTag(members[i]), + value, caseSensitive, true); + } + } + + finder.SetDatabaseLookup(query); + } + + if (request.isMember(KEY_REQUESTED_TAGS)) + { + std::set<DicomTag> requestedTags; + FromDcmtkBridge::ParseListOfTags(requestedTags, request[KEY_REQUESTED_TAGS]); + finder.AddRequestedTags(requestedTags); + } + + if (request.isMember(KEY_LABELS)) // New in Orthanc 1.12.0 + { + for (Json::Value::ArrayIndex i = 0; i < request[KEY_LABELS].size(); i++) + { + if (request[KEY_LABELS][i].type() != Json::stringValue) + { + throw OrthancException(ErrorCode_BadRequest, "Field \"" + std::string(KEY_LABELS) + "\" must contain strings"); + } + else + { + finder.AddLabel(request[KEY_LABELS][i].asString()); + } + } + } + + finder.SetLabelsConstraint(LabelsConstraint_All); + + if (request.isMember(KEY_LABELS_CONSTRAINT)) + { + const std::string& s = request[KEY_LABELS_CONSTRAINT].asString(); + if (s == "All") + { + finder.SetLabelsConstraint(LabelsConstraint_All); + } + else if (s == "Any") + { + finder.SetLabelsConstraint(LabelsConstraint_Any); + } + else if (s == "None") + { + finder.SetLabelsConstraint(LabelsConstraint_None); + } + else + { + throw OrthancException(ErrorCode_BadRequest, "Field \"" + std::string(KEY_LABELS_CONSTRAINT) + "\" must be \"All\", \"Any\", or \"None\""); + } + } + + Json::Value answer; + finder.Execute(answer, context, format, false /* no "Metadata" field */); + call.GetOutput().AnswerJson(answer); + } else { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ bool expand = false; if (request.isMember(KEY_EXPAND)) { @@ -3324,6 +3547,8 @@ } } + std::set<std::string> labels; + if (request.isMember(KEY_LABELS)) // New in Orthanc 1.12.0 { for (Json::Value::ArrayIndex i = 0; i < request[KEY_LABELS].size(); i++) @@ -3334,27 +3559,27 @@ } else { - query.AddLabel(request[KEY_LABELS][i].asString()); + labels.insert(request[KEY_LABELS][i].asString()); } } } - query.SetLabelsConstraint(LabelsConstraint_All); + LabelsConstraint labelsConstraint = LabelsConstraint_All; if (request.isMember(KEY_LABELS_CONSTRAINT)) { const std::string& s = request[KEY_LABELS_CONSTRAINT].asString(); if (s == "All") { - query.SetLabelsConstraint(LabelsConstraint_All); + labelsConstraint = LabelsConstraint_All; } else if (s == "Any") { - query.SetLabelsConstraint(LabelsConstraint_Any); + labelsConstraint = LabelsConstraint_Any; } else if (s == "None") { - query.SetLabelsConstraint(LabelsConstraint_None); + labelsConstraint = LabelsConstraint_None; } else { @@ -3363,7 +3588,7 @@ } FindVisitor visitor(OrthancRestApi::GetDicomFormat(request, DicomToJsonFormat_Human), context.GetFindStorageAccessMode()); - context.Apply(visitor, query, level, since, limit); + context.Apply(visitor, query, level, labels, labelsConstraint, since, limit); visitor.Answer(call.GetOutput(), context, level, expand, requestedTags); } } @@ -3396,34 +3621,56 @@ ServerIndex& index = OrthancRestApi::GetIndex(call); ServerContext& context = OrthancRestApi::GetContext(call); + const bool expand = (!call.HasArgument("expand") || + // this "expand" is the only one to have a false default value to keep backward compatibility + call.GetBooleanArgument("expand", false)); + const DicomToJsonFormat format = OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human); + std::set<DicomTag> requestedTags; OrthancRestApi::GetRequestedTags(requestedTags, call); - std::list<std::string> a, b, c; - a.push_back(call.GetUriComponent("id", "")); - - ResourceType type = start; - while (type != end) + if (true) { - b.clear(); - - for (std::list<std::string>::const_iterator - it = a.begin(); it != a.end(); ++it) + /** + * EXPERIMENTAL VERSION + **/ + + ResourceFinder finder(end, expand); + finder.SetOrthancId(start, call.GetUriComponent("id", "")); + finder.AddRequestedTags(requestedTags); + + Json::Value answer; + finder.Execute(answer, context, format, false /* no "Metadata" field */); + call.GetOutput().AnswerJson(answer); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + std::list<std::string> a, b, c; + a.push_back(call.GetUriComponent("id", "")); + + ResourceType type = start; + while (type != end) { - index.GetChildren(c, *it); - b.splice(b.begin(), c); + b.clear(); + + for (std::list<std::string>::const_iterator + it = a.begin(); it != a.end(); ++it) + { + index.GetChildren(c, *it); + b.splice(b.begin(), c); + } + + type = GetChildResourceType(type); + + a.clear(); + a.splice(a.begin(), b); } - type = GetChildResourceType(type); - - a.clear(); - a.splice(a.begin(), b); + AnswerListOfResources2(call.GetOutput(), context, a, type, expand, format, requestedTags, true /* allowStorageAccess */); } - - AnswerListOfResources(call.GetOutput(), context, a, type, !call.HasArgument("expand") || call.GetBooleanArgument("expand", false), // this "expand" is the only one to have a false default value to keep backward compatibility - OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human), - requestedTags, - true /* allowStorageAccess */); } @@ -3536,9 +3783,26 @@ const DicomToJsonFormat format = OrthancRestApi::GetDicomFormat(call, DicomToJsonFormat_Human); Json::Value resource; - if (OrthancRestApi::GetContext(call).ExpandResource(resource, current, end, format, requestedTags, true /* allowStorageAccess */)) + + if (true) { - call.GetOutput().AnswerJson(resource); + /** + * EXPERIMENTAL VERSION + **/ + if (ExpandResource(resource, OrthancRestApi::GetContext(call), currentType, current, format, false)) + { + call.GetOutput().AnswerJson(resource); + } + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + if (OrthancRestApi::GetContext(call).ExpandResource(resource, current, end, format, requestedTags, true /* allowStorageAccess */)) + { + call.GetOutput().AnswerJson(resource); + } } } @@ -3969,17 +4233,34 @@ for (std::set<std::string>::const_iterator it = interest.begin(); it != interest.end(); ++it) { - Json::Value item; - std::set<DicomTag> emptyRequestedTags; // not supported for bulk content - - if (OrthancRestApi::GetContext(call).ExpandResource(item, *it, level, format, emptyRequestedTags, true /* allowStorageAccess */)) + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + Json::Value item; + if (ExpandResource(item, OrthancRestApi::GetContext(call), level, *it, format, metadata)) + { + answer.append(item); + } + } + else { - if (metadata) + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + Json::Value item; + std::set<DicomTag> emptyRequestedTags; // not supported for bulk content + + if (OrthancRestApi::GetContext(call).ExpandResource(item, *it, level, format, emptyRequestedTags, true /* allowStorageAccess */)) { - AddMetadata(item[METADATA], index, *it, level); + if (metadata) + { + AddMetadata(item[METADATA], index, *it, level); + } + + answer.append(item); } - - answer.append(item); } } } @@ -3996,19 +4277,36 @@ Json::Value item; std::set<DicomTag> emptyRequestedTags; // not supported for bulk content - if (index.LookupResourceType(level, *it) && - OrthancRestApi::GetContext(call).ExpandResource(item, *it, level, format, emptyRequestedTags, true /* allowStorageAccess */)) + if (true) { - if (metadata) + /** + * EXPERIMENTAL VERSION + **/ + if (index.LookupResourceType(level, *it) && + ExpandResource(item, OrthancRestApi::GetContext(call), level, *it, format, metadata)) { - AddMetadata(item[METADATA], index, *it, level); + answer.append(item); } - - answer.append(item); } else { - CLOG(INFO, HTTP) << "Unknown resource during a bulk content retrieval: " << *it; + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + if (index.LookupResourceType(level, *it) && + OrthancRestApi::GetContext(call).ExpandResource(item, *it, level, format, emptyRequestedTags, true /* allowStorageAccess */)) + { + if (metadata) + { + AddMetadata(item[METADATA], index, *it, level); + } + + answer.append(item); + } + else + { + CLOG(INFO, HTTP) << "Unknown resource during a bulk content retrieval: " << *it; + } } } }
--- a/OrthancServer/Sources/OrthancWebDav.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancWebDav.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -28,6 +28,7 @@ #include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" #include "../../OrthancFramework/Sources/HttpServer/WebDavStorage.h" #include "../../OrthancFramework/Sources/Logging.h" +#include "ResourceFinder.h" #include "Search/DatabaseLookup.h" #include "ServerContext.h" @@ -50,6 +51,20 @@ { return boost::posix_time::second_clock::universal_time(); } + + + static void ParseTime(boost::posix_time::ptime& target, + const std::string& value) + { + try + { + target = boost::posix_time::from_iso_string(value); + } + catch (std::exception& e) + { + target = GetNow(); + } + } static void LookupTime(boost::posix_time::ptime& target, @@ -62,17 +77,12 @@ int64_t revision; // Ignored if (context.GetIndex().LookupMetadata(value, revision, publicId, level, metadata)) { - try - { - target = boost::posix_time::from_iso_string(value); - return; - } - catch (std::exception& e) - { - } + ParseTime(target, value); } - - target = GetNow(); + else + { + target = GetNow(); + } } @@ -169,6 +179,98 @@ }; + class OrthancWebDav::DicomIdentifiersVisitorV2 : public ResourceFinder::IVisitor + { + private: + bool isComplete_; + Collection& target_; + + public: + explicit DicomIdentifiersVisitorV2(Collection& target) : + isComplete_(false), + target_(target) + { + } + + virtual void MarkAsComplete() ORTHANC_OVERRIDE + { + isComplete_ = true; // TODO + } + + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE + { + DicomMap resourceTags; + resource.GetMainDicomTags(resourceTags, resource.GetLevel()); + + std::string uid; + bool hasUid; + + std::string time; + bool hasTime; + + switch (resource.GetLevel()) + { + case ResourceType_Study: + hasUid = resourceTags.LookupStringValue(uid, DICOM_TAG_STUDY_INSTANCE_UID, false); + hasTime = resource.LookupMetadata(time, resource.GetLevel(), MetadataType_LastUpdate); + break; + + case ResourceType_Series: + hasUid = resourceTags.LookupStringValue(uid, DICOM_TAG_SERIES_INSTANCE_UID, false); + hasTime = resource.LookupMetadata(time, resource.GetLevel(), MetadataType_LastUpdate); + break; + + case ResourceType_Instance: + hasUid = resourceTags.LookupStringValue(uid, DICOM_TAG_SOP_INSTANCE_UID, false); + hasTime = resource.LookupMetadata(time, resource.GetLevel(), MetadataType_Instance_ReceptionDate); + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + + if (hasUid && + !uid.empty()) + { + std::unique_ptr<Resource> item; + + if (resource.GetLevel() == ResourceType_Instance) + { + FileInfo info; + if (resource.LookupAttachment(info, FileContentType_Dicom)) + { + std::unique_ptr<File> f(new File(uid + ".dcm")); + f->SetMimeType(MimeType_Dicom); + f->SetContentLength(info.GetUncompressedSize()); + item.reset(f.release()); + } + } + else + { + item.reset(new Folder(uid)); + } + + if (item.get() != NULL) + { + if (hasTime) + { + boost::posix_time::ptime t; + ParseTime(t, time); + item->SetCreationTime(t); + } + else + { + item->SetCreationTime(GetNow()); + } + + target_.AddResource(item.release()); + } + } + } + }; + + class OrthancWebDav::DicomFileVisitor : public ServerContext::ILookupVisitor { private: @@ -221,6 +323,60 @@ }; + class OrthancWebDav::DicomFileVisitorV2 : public ResourceFinder::IVisitor + { + private: + ServerContext& context_; + bool success_; + std::string& target_; + boost::posix_time::ptime& time_; + + public: + DicomFileVisitorV2(ServerContext& context, + std::string& target, + boost::posix_time::ptime& time) : + context_(context), + success_(false), + target_(target), + time_(time) + { + } + + bool IsSuccess() const + { + return success_; + } + + virtual void MarkAsComplete() ORTHANC_OVERRIDE + { + } + + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE + { + if (success_) + { + success_ = false; // Two matches => Error + } + else + { + std::string s; + if (resource.LookupMetadata(s, ResourceType_Instance, MetadataType_Instance_ReceptionDate)) + { + ParseTime(time_, s); + } + else + { + time_ = GetNow(); + } + + context_.ReadDicom(target_, resource.GetIdentifier()); + success_ = true; + } + } + }; + + class OrthancWebDav::OrthancJsonVisitor : public ServerContext::ILookupVisitor { private: @@ -955,7 +1111,7 @@ std::string year_; std::string month_; - class Visitor : public ServerContext::ILookupVisitor + class Visitor : public ResourceFinder::IVisitor { private: std::list<std::string>& resources_; @@ -966,21 +1122,14 @@ { } - virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE - { - return false; // (*) - } - virtual void MarkAsComplete() ORTHANC_OVERRIDE { } - virtual void Visit(const std::string& publicId, - const std::string& instanceId /* unused */, - const DicomMap& mainDicomTags, - const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE { - resources_.push_back(publicId); + resources_.push_back(resource.GetIdentifier()); } }; @@ -992,7 +1141,10 @@ true /* case sensitive */, true /* mandatory tag */); Visitor visitor(resources); - GetContext().Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); + + ResourceFinder finder(ResourceType_Study, false /* no expand */); + finder.SetDatabaseLookup(query); + finder.Execute(visitor, GetContext()); } virtual INode* CreateResourceNode(const std::string& resource) ORTHANC_OVERRIDE @@ -1025,7 +1177,7 @@ std::string year_; const Templates& templates_; - class Visitor : public ServerContext::ILookupVisitor + class Visitor : public ResourceFinder::IVisitor { private: std::set<std::string> months_; @@ -1036,20 +1188,16 @@ return months_; } - virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE - { - return false; // (*) - } - virtual void MarkAsComplete() ORTHANC_OVERRIDE { } - virtual void Visit(const std::string& publicId, - const std::string& instanceId /* unused */, - const DicomMap& mainDicomTags, - const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE { + DicomMap mainDicomTags; + resource.GetMainDicomTags(mainDicomTags, ResourceType_Study); + std::string s; if (mainDicomTags.LookupStringValue(s, DICOM_TAG_STUDY_DATE, false) && s.size() == 8) @@ -1071,7 +1219,10 @@ true /* case sensitive */, true /* mandatory tag */); Visitor visitor; - context_.Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); + + ResourceFinder finder(ResourceType_Study, false /* no expand */); + finder.SetDatabaseLookup(query); + finder.Execute(visitor, context_); for (std::set<std::string>::const_iterator it = visitor.GetMonths().begin(); it != visitor.GetMonths().end(); ++it) @@ -1165,7 +1316,7 @@ }; - class OrthancWebDav::DicomDeleteVisitor : public ServerContext::ILookupVisitor + class OrthancWebDav::DicomDeleteVisitor : public ResourceFinder::IVisitor { private: ServerContext& context_; @@ -1179,22 +1330,15 @@ { } - virtual bool IsDicomAsJsonNeeded() const ORTHANC_OVERRIDE - { - return false; // (*) - } - virtual void MarkAsComplete() ORTHANC_OVERRIDE { } - virtual void Visit(const std::string& publicId, - const std::string& instanceId /* unused */, - const DicomMap& mainDicomTags /* unused */, - const Json::Value* dicomAsJson /* unused (*) */) ORTHANC_OVERRIDE + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE { Json::Value info; - context_.DeleteResource(info, publicId, level_); + context_.DeleteResource(info, resource.GetIdentifier(), level_); } }; @@ -1455,9 +1599,48 @@ return false; } - DicomIdentifiersVisitor visitor(context_, collection, level); - context_.Apply(visitor, query, level, 0 /* since */, limit); - + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + + ResourceFinder finder(level, false /* don't expand */); + finder.SetDatabaseLookup(query); + finder.SetRetrieveMetadata(true); + + switch (level) + { + case ResourceType_Study: + finder.AddRequestedTag(DICOM_TAG_STUDY_INSTANCE_UID); + break; + + case ResourceType_Series: + finder.AddRequestedTag(DICOM_TAG_SERIES_INSTANCE_UID); + break; + + case ResourceType_Instance: + finder.AddRequestedTag(DICOM_TAG_SOP_INSTANCE_UID); + finder.SetRetrieveAttachments(true); + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + + DicomIdentifiersVisitorV2 visitor(collection); + finder.Execute(visitor, context_); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + + DicomIdentifiersVisitor visitor(context_, collection, level); + context_.Apply(visitor, query, level, 0 /* since */, limit); + } + return true; } else if (path[0] == BY_PATIENTS || @@ -1478,6 +1661,33 @@ } + static bool GetOrthancJson(std::string& target, + ServerContext& context, + ResourceType level, + const DatabaseLookup& query) + { + ResourceFinder finder(level, true /* expand */); + finder.SetDatabaseLookup(query); + + Json::Value expanded; + finder.Execute(expanded, context, DicomToJsonFormat_Human, false /* don't add "Metadata" */); + + if (expanded.size() != 1) + { + return false; + } + else + { + target = expanded[0].toStyledString(); + + // Replace UNIX newlines with DOS newlines + boost::replace_all(target, "\n", "\r\n"); + + return true; + } + } + + bool OrthancWebDav::GetFileContent(MimeType& mime, std::string& content, boost::posix_time::ptime& modificationTime, @@ -1495,12 +1705,25 @@ DatabaseLookup query; query.AddRestConstraint(DICOM_TAG_STUDY_INSTANCE_UID, path[1], true /* case sensitive */, true /* mandatory tag */); - - OrthancJsonVisitor visitor(context_, content, ResourceType_Study); - context_.Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); mime = MimeType_Json; - return visitor.IsSuccess(); + + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + return GetOrthancJson(content, context_, ResourceType_Study, query); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + OrthancJsonVisitor visitor(context_, content, ResourceType_Study); + context_.Apply(visitor, query, ResourceType_Study, 0 /* since */, 0 /* no limit */); + return visitor.IsSuccess(); + } } else if (path.size() == 4 && path[3] == SERIES_INFO) @@ -1511,11 +1734,24 @@ query.AddRestConstraint(DICOM_TAG_SERIES_INSTANCE_UID, path[2], true /* case sensitive */, true /* mandatory tag */); - OrthancJsonVisitor visitor(context_, content, ResourceType_Series); - context_.Apply(visitor, query, ResourceType_Series, 0 /* since */, 0 /* no limit */); + mime = MimeType_Json; - mime = MimeType_Json; - return visitor.IsSuccess(); + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + return GetOrthancJson(content, context_, ResourceType_Series, query); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + OrthancJsonVisitor visitor(context_, content, ResourceType_Series); + context_.Apply(visitor, query, ResourceType_Series, 0 /* since */, 0 /* no limit */); + return visitor.IsSuccess(); + } } else if (path.size() == 4 && boost::ends_with(path[3], ".dcm")) @@ -1530,11 +1766,32 @@ query.AddRestConstraint(DICOM_TAG_SOP_INSTANCE_UID, sopInstanceUid, true /* case sensitive */, true /* mandatory tag */); - DicomFileVisitor visitor(context_, content, modificationTime); - context_.Apply(visitor, query, ResourceType_Instance, 0 /* since */, 0 /* no limit */); - mime = MimeType_Dicom; - return visitor.IsSuccess(); + + if (true) + { + /** + * EXPERIMENTAL VERSION + **/ + ResourceFinder finder(ResourceType_Instance, false /* no expand */); + finder.SetDatabaseLookup(query); + finder.SetRetrieveMetadata(true); + finder.SetRetrieveAttachments(true); + + DicomFileVisitorV2 visitor(context_, content, modificationTime); + finder.Execute(visitor, context_); + + return visitor.IsSuccess(); + } + else + { + /** + * VERSION IN ORTHANC <= 1.12.4 + **/ + DicomFileVisitor visitor(context_, content, modificationTime); + context_.Apply(visitor, query, ResourceType_Instance, 0 /* since */, 0 /* no limit */); + return visitor.IsSuccess(); + } } else { @@ -1655,7 +1912,10 @@ } DicomDeleteVisitor visitor(context_, level); - context_.Apply(visitor, query, level, 0 /* since */, 0 /* no limit */); + + ResourceFinder finder(level, false /* no expand */); + finder.SetDatabaseLookup(query); + finder.Execute(visitor, context_); return true; } else
--- a/OrthancServer/Sources/OrthancWebDav.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/OrthancWebDav.h Thu Sep 05 18:52:27 2024 +0200 @@ -39,7 +39,9 @@ class DicomDeleteVisitor; class DicomFileVisitor; + class DicomFileVisitorV2; class DicomIdentifiersVisitor; + class DicomIdentifiersVisitorV2; class InstancesOfSeries; class InternalNode; class ListOfResources; @@ -47,6 +49,7 @@ class ListOfStudiesByMonth; class ListOfStudiesByYear; class OrthancJsonVisitor; + class OrthancJsonVisitorV2; class ResourcesIndex; class RootNode; class SingleDicomResource;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/ResourceFinder.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,1102 @@ +/** + * 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 "ResourceFinder.h" + +#include "../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" +#include "../../OrthancFramework/Sources/Logging.h" +#include "../../OrthancFramework/Sources/OrthancException.h" +#include "../../OrthancFramework/Sources/SerializationToolbox.h" +#include "OrthancConfiguration.h" +#include "Search/DatabaseLookup.h" +#include "ServerContext.h" +#include "ServerIndex.h" + + +namespace Orthanc +{ + static bool IsComputedTag(const DicomTag& tag) + { + return (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES || + tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES || + tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES || + tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES || + tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES || + tag == DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES || + tag == DICOM_TAG_SOP_CLASSES_IN_STUDY || + tag == DICOM_TAG_MODALITIES_IN_STUDY || + tag == DICOM_TAG_INSTANCE_AVAILABILITY); + } + + void ResourceFinder::ConfigureChildrenCountComputedTag(DicomTag tag, + ResourceType parentLevel, + ResourceType childLevel) + { + if (request_.GetLevel() == parentLevel) + { + requestedComputedTags_.insert(tag); + hasRequestedTags_ = true; + request_.GetChildrenSpecification(childLevel).SetRetrieveIdentifiers(true); + } + } + + + void ResourceFinder::InjectChildrenCountComputedTag(DicomMap& requestedTags, + DicomTag tag, + const FindResponse::Resource& resource, + ResourceType level) const + { + if (IsRequestedComputedTag(tag)) + { + const std::set<std::string>& children = resource.GetChildrenIdentifiers(level); + requestedTags.SetValue(tag, boost::lexical_cast<std::string>(children.size()), false); + } + } + + + void ResourceFinder::InjectComputedTags(DicomMap& requestedTags, + const FindResponse::Resource& resource) const + { + switch (resource.GetLevel()) + { + case ResourceType_Patient: + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES, resource, ResourceType_Study); + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES, resource, ResourceType_Series); + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES, resource, ResourceType_Instance); + break; + + case ResourceType_Study: + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES, resource, ResourceType_Series); + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES, resource, ResourceType_Instance); + + if (IsRequestedComputedTag(DICOM_TAG_MODALITIES_IN_STUDY)) + { + std::set<std::string> modalities; + resource.GetChildrenMainDicomTagValues(modalities, ResourceType_Series, DICOM_TAG_MODALITY); + + std::string s; + Toolbox::JoinStrings(s, modalities, "\\"); + + requestedTags.SetValue(DICOM_TAG_MODALITIES_IN_STUDY, s, false); + } + + if (IsRequestedComputedTag(DICOM_TAG_SOP_CLASSES_IN_STUDY)) + { + std::set<std::string> classes; + resource.GetChildrenMetadataValues(classes, ResourceType_Instance, MetadataType_Instance_SopClassUid); + + std::string s; + Toolbox::JoinStrings(s, classes, "\\"); + + requestedTags.SetValue(DICOM_TAG_SOP_CLASSES_IN_STUDY, s, false); + } + + break; + + case ResourceType_Series: + InjectChildrenCountComputedTag(requestedTags, DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES, resource, ResourceType_Instance); + break; + + case ResourceType_Instance: + if (IsRequestedComputedTag(DICOM_TAG_INSTANCE_AVAILABILITY)) + { + requestedTags.SetValue(DICOM_TAG_INSTANCE_AVAILABILITY, "ONLINE", false); + } + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + } + + + SeriesStatus ResourceFinder::GetSeriesStatus(uint32_t& expectedNumberOfInstances, + const FindResponse::Resource& resource) + { + if (resource.GetLevel() != ResourceType_Series) + { + throw OrthancException(ErrorCode_BadParameterType); + } + + std::string s; + if (!resource.LookupMetadata(s, ResourceType_Series, MetadataType_Series_ExpectedNumberOfInstances) || + !SerializationToolbox::ParseUnsignedInteger32(expectedNumberOfInstances, s)) + { + return SeriesStatus_Unknown; + } + + std::set<std::string> values; + resource.GetChildrenMetadataValues(values, ResourceType_Instance, MetadataType_Instance_IndexInSeries); + + std::set<int64_t> instances; + + for (std::set<std::string>::const_iterator + it = values.begin(); it != values.end(); ++it) + { + int64_t index; + + if (!SerializationToolbox::ParseInteger64(index, *it)) + { + return SeriesStatus_Unknown; + } + + if (index <= 0 || + index > static_cast<int64_t>(expectedNumberOfInstances)) + { + // Out-of-range instance index + return SeriesStatus_Inconsistent; + } + + if (instances.find(index) != instances.end()) + { + // Twice the same instance index + return SeriesStatus_Inconsistent; + } + + instances.insert(index); + } + + if (instances.size() == static_cast<size_t>(expectedNumberOfInstances)) + { + return SeriesStatus_Complete; + } + else + { + return SeriesStatus_Missing; + } + } + + + void ResourceFinder::Expand(Json::Value& target, + const FindResponse::Resource& resource, + ServerIndex& index, + DicomToJsonFormat format, + bool includeAllMetadata) const + { + /** + * This method closely follows "SerializeExpandedResource()" in + * "ServerContext.cpp" from Orthanc 1.12.4. + **/ + + if (!expand_) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + + if (resource.GetLevel() != request_.GetLevel()) + { + throw OrthancException(ErrorCode_InternalError); + } + + target = Json::objectValue; + + target["Type"] = GetResourceTypeText(resource.GetLevel(), false, true); + target["ID"] = resource.GetIdentifier(); + + switch (resource.GetLevel()) + { + case ResourceType_Patient: + break; + + case ResourceType_Study: + target["ParentPatient"] = resource.GetParentIdentifier(); + break; + + case ResourceType_Series: + target["ParentStudy"] = resource.GetParentIdentifier(); + break; + + case ResourceType_Instance: + target["ParentSeries"] = resource.GetParentIdentifier(); + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + + if (resource.GetLevel() != ResourceType_Instance) + { + const std::set<std::string>& children = resource.GetChildrenIdentifiers(GetChildResourceType(resource.GetLevel())); + + Json::Value c = Json::arrayValue; + for (std::set<std::string>::const_iterator + it = children.begin(); it != children.end(); ++it) + { + c.append(*it); + } + + switch (resource.GetLevel()) + { + case ResourceType_Patient: + target["Studies"] = c; + break; + + case ResourceType_Study: + target["Series"] = c; + break; + + case ResourceType_Series: + target["Instances"] = c; + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + } + + switch (resource.GetLevel()) + { + case ResourceType_Patient: + case ResourceType_Study: + break; + + case ResourceType_Series: + { + uint32_t expectedNumberOfInstances; + SeriesStatus status = GetSeriesStatus(expectedNumberOfInstances, resource); + + target["Status"] = EnumerationToString(status); + + static const char* const EXPECTED_NUMBER_OF_INSTANCES = "ExpectedNumberOfInstances"; + + if (status == SeriesStatus_Unknown) + { + target[EXPECTED_NUMBER_OF_INSTANCES] = Json::nullValue; + } + else + { + target[EXPECTED_NUMBER_OF_INSTANCES] = expectedNumberOfInstances; + } + + break; + } + + case ResourceType_Instance: + { + FileInfo info; + if (resource.LookupAttachment(info, FileContentType_Dicom)) + { + target["FileSize"] = static_cast<Json::UInt64>(info.GetUncompressedSize()); + target["FileUuid"] = info.GetUuid(); + } + else + { + throw OrthancException(ErrorCode_InternalError); + } + + static const char* const INDEX_IN_SERIES = "IndexInSeries"; + + std::string s; + uint32_t indexInSeries; + if (resource.LookupMetadata(s, ResourceType_Instance, MetadataType_Instance_IndexInSeries) && + SerializationToolbox::ParseUnsignedInteger32(indexInSeries, s)) + { + target[INDEX_IN_SERIES] = indexInSeries; + } + else + { + target[INDEX_IN_SERIES] = Json::nullValue; + } + + break; + } + + default: + throw OrthancException(ErrorCode_InternalError); + } + + std::string s; + if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_AnonymizedFrom)) + { + target["AnonymizedFrom"] = s; + } + + if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_ModifiedFrom)) + { + target["ModifiedFrom"] = s; + } + + if (resource.GetLevel() == ResourceType_Patient || + resource.GetLevel() == ResourceType_Study || + resource.GetLevel() == ResourceType_Series) + { + target["IsStable"] = !index.IsUnstableResource(resource.GetLevel(), resource.GetInternalId()); + + if (resource.LookupMetadata(s, resource.GetLevel(), MetadataType_LastUpdate)) + { + target["LastUpdate"] = s; + } + } + + { + DicomMap allMainDicomTags; + resource.GetMainDicomTags(allMainDicomTags, resource.GetLevel()); + + /** + * This section was part of "StatelessDatabaseOperations::ExpandResource()" + * in Orthanc <= 1.12.3 + **/ + + // read all main sequences from DB + std::string serializedSequences; + if (resource.LookupMetadata(serializedSequences, resource.GetLevel(), MetadataType_MainDicomSequences)) + { + Json::Value jsonMetadata; + Toolbox::ReadJson(jsonMetadata, serializedSequences); + + if (jsonMetadata["Version"].asInt() == 1) + { + allMainDicomTags.FromDicomAsJson(jsonMetadata["Sequences"], true /* append */, true /* parseSequences */); + } + else + { + throw OrthancException(ErrorCode_NotImplemented); + } + } + + /** + * End of section from StatelessDatabaseOperations + **/ + + + static const char* const MAIN_DICOM_TAGS = "MainDicomTags"; + static const char* const PATIENT_MAIN_DICOM_TAGS = "PatientMainDicomTags"; + + // TODO-FIND : Ignore "null" values + + DicomMap levelMainDicomTags; + allMainDicomTags.ExtractResourceInformation(levelMainDicomTags, resource.GetLevel()); + + target[MAIN_DICOM_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], levelMainDicomTags, format); + + if (resource.GetLevel() == ResourceType_Study) + { + DicomMap patientMainDicomTags; + allMainDicomTags.ExtractPatientInformation(patientMainDicomTags); + + target[PATIENT_MAIN_DICOM_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(target[PATIENT_MAIN_DICOM_TAGS], patientMainDicomTags, format); + } + } + + { + Json::Value labels = Json::arrayValue; + + for (std::set<std::string>::const_iterator + it = resource.GetLabels().begin(); it != resource.GetLabels().end(); ++it) + { + labels.append(*it); + } + + target["Labels"] = labels; + } + + if (includeAllMetadata) // new in Orthanc 1.12.4 + { + const std::map<MetadataType, std::string>& m = resource.GetMetadata(resource.GetLevel()); + + Json::Value metadata = Json::objectValue; + + for (std::map<MetadataType, std::string>::const_iterator it = m.begin(); it != m.end(); ++it) + { + metadata[EnumerationToString(it->first)] = it->second; + } + + target["Metadata"] = metadata; + } + } + + + void ResourceFinder::UpdateRequestLimits() + { + // By default, use manual paging + pagingMode_ = PagingMode_FullManual; + + if (databaseLimits_ != 0) + { + request_.SetLimits(0, databaseLimits_ + 1); + } + else + { + request_.ClearLimits(); + } + + if (lookup_.get() == NULL && + (hasLimitsSince_ || hasLimitsCount_)) + { + pagingMode_ = PagingMode_FullDatabase; + request_.SetLimits(limitsSince_, limitsCount_); + } + + if (lookup_.get() != NULL && + isSimpleLookup_ && + (hasLimitsSince_ || hasLimitsCount_)) + { + /** + * TODO-FIND: "IDatabaseWrapper::ApplyLookupResources()" only + * accept the "limit" argument. The "since" must be implemented + * manually. + **/ + + if (hasLimitsSince_ && + limitsSince_ != 0) + { + pagingMode_ = PagingMode_ManualSkip; + request_.SetLimits(0, limitsCount_ + limitsSince_); + } + else + { + pagingMode_ = PagingMode_FullDatabase; + request_.SetLimits(0, limitsCount_); + } + } + + // TODO-FIND: More cases could be added, depending on "GetDatabaseCapabilities()" + } + + + ResourceFinder::ResourceFinder(ResourceType level, + bool expand) : + request_(level), + databaseLimits_(0), + isSimpleLookup_(true), + pagingMode_(PagingMode_FullManual), + hasLimitsSince_(false), + hasLimitsCount_(false), + limitsSince_(0), + limitsCount_(0), + expand_(expand), + allowStorageAccess_(true), + hasRequestedTags_(false) + { + UpdateRequestLimits(); + + if (expand) + { + request_.SetRetrieveMainDicomTags(true); + request_.SetRetrieveMetadata(true); + request_.SetRetrieveLabels(true); + + switch (level) + { + case ResourceType_Patient: + request_.GetChildrenSpecification(ResourceType_Study).SetRetrieveIdentifiers(true); + break; + + case ResourceType_Study: + request_.GetChildrenSpecification(ResourceType_Series).SetRetrieveIdentifiers(true); + request_.SetRetrieveParentIdentifier(true); + break; + + case ResourceType_Series: + request_.GetChildrenSpecification(ResourceType_Instance).AddMetadata(MetadataType_Instance_IndexInSeries); // required for the SeriesStatus + request_.GetChildrenSpecification(ResourceType_Instance).SetRetrieveIdentifiers(true); + request_.SetRetrieveParentIdentifier(true); + break; + + case ResourceType_Instance: + request_.SetRetrieveAttachments(true); // for FileSize & FileUuid + request_.SetRetrieveParentIdentifier(true); + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + } + + + void ResourceFinder::SetDatabaseLimits(uint64_t limits) + { + databaseLimits_ = limits; + UpdateRequestLimits(); + } + + + void ResourceFinder::SetLimitsSince(uint64_t since) + { + if (hasLimitsSince_) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + hasLimitsSince_ = true; + limitsSince_ = since; + UpdateRequestLimits(); + } + } + + + void ResourceFinder::SetLimitsCount(uint64_t count) + { + if (hasLimitsCount_) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls); + } + else + { + hasLimitsCount_ = true; + limitsCount_ = count; + UpdateRequestLimits(); + } + } + + + void ResourceFinder::SetDatabaseLookup(const DatabaseLookup& lookup) + { + MainDicomTagsRegistry registry; + + lookup_.reset(lookup.Clone()); + + for (size_t i = 0; i < lookup.GetConstraintsCount(); i++) + { + DicomTag tag = lookup.GetConstraint(i).GetTag(); + if (IsComputedTag(tag)) + { + AddRequestedTag(tag); + } + else + { + ResourceType level; + DicomTagType tagType; + registry.LookupTag(level, tagType, tag); + if (tagType == DicomTagType_Generic) + { + AddRequestedTag(tag); + } + } + } + + isSimpleLookup_ = registry.NormalizeLookup(request_.GetDicomTagConstraints(), lookup, request_.GetLevel()); + + // "request_.GetDicomTagConstraints()" only contains constraints on main DICOM tags + + for (size_t i = 0; i < request_.GetDicomTagConstraints().GetSize(); i++) + { + const DatabaseConstraint& constraint = request_.GetDicomTagConstraints().GetConstraint(i); + if (constraint.GetLevel() == request_.GetLevel()) + { + request_.SetRetrieveMainDicomTags(true); + } + else if (IsResourceLevelAboveOrEqual(constraint.GetLevel(), request_.GetLevel())) + { + request_.GetParentSpecification(constraint.GetLevel()).SetRetrieveMainDicomTags(true); + } + else + { + LOG(WARNING) << "Executing a database lookup at level " << EnumerationToString(request_.GetLevel()) + << " on main DICOM tag " << constraint.GetTag().Format() << " from an inferior level (" + << EnumerationToString(constraint.GetLevel()) << "), this will return no result"; + } + + if (IsComputedTag(constraint.GetTag())) + { + // Sanity check + throw OrthancException(ErrorCode_InternalError); + } + } + + UpdateRequestLimits(); + } + + + void ResourceFinder::AddRequestedTag(const DicomTag& tag) + { + if (DicomMap::IsMainDicomTag(tag, ResourceType_Patient)) + { + if (request_.GetLevel() == ResourceType_Patient) + { + request_.SetRetrieveMainDicomTags(true); + requestedPatientTags_.insert(tag); + } + else + { + /** + * This comes from the fact that patient-level tags are copied + * at the study level, as implemented by "ResourcesContent::AddResource()". + **/ + requestedStudyTags_.insert(tag); + + if (request_.GetLevel() == ResourceType_Study) + { + request_.SetRetrieveMainDicomTags(true); + } + else + { + request_.GetParentSpecification(ResourceType_Study).SetRetrieveMainDicomTags(true); + } + + requestedStudyTags_.insert(tag); + } + + hasRequestedTags_ = true; + } + else if (DicomMap::IsMainDicomTag(tag, ResourceType_Study)) + { + if (request_.GetLevel() == ResourceType_Patient) + { + LOG(WARNING) << "Requested tag " << tag.Format() + << " should only be read at the study, series, or instance level"; + requestedTagsFromFileStorage_.insert(tag); + request_.SetRetrieveOneInstanceIdentifier(true); + } + else + { + if (request_.GetLevel() == ResourceType_Study) + { + request_.SetRetrieveMainDicomTags(true); + } + else + { + request_.GetParentSpecification(ResourceType_Study).SetRetrieveMainDicomTags(true); + } + + requestedStudyTags_.insert(tag); + } + + hasRequestedTags_ = true; + } + else if (DicomMap::IsMainDicomTag(tag, ResourceType_Series)) + { + if (request_.GetLevel() == ResourceType_Patient || + request_.GetLevel() == ResourceType_Study) + { + LOG(WARNING) << "Requested tag " << tag.Format() + << " should only be read at the series or instance level"; + requestedTagsFromFileStorage_.insert(tag); + request_.SetRetrieveOneInstanceIdentifier(true); + } + else + { + if (request_.GetLevel() == ResourceType_Series) + { + request_.SetRetrieveMainDicomTags(true); + } + else + { + request_.GetParentSpecification(ResourceType_Series).SetRetrieveMainDicomTags(true); + } + + requestedSeriesTags_.insert(tag); + } + + hasRequestedTags_ = true; + } + else if (DicomMap::IsMainDicomTag(tag, ResourceType_Instance)) + { + if (request_.GetLevel() == ResourceType_Patient || + request_.GetLevel() == ResourceType_Study || + request_.GetLevel() == ResourceType_Series) + { + LOG(WARNING) << "Requested tag " << tag.Format() + << " should only be read at the instance level"; + requestedTagsFromFileStorage_.insert(tag); + request_.SetRetrieveOneInstanceIdentifier(true); + } + else + { + request_.SetRetrieveMainDicomTags(true); + requestedInstanceTags_.insert(tag); + } + + hasRequestedTags_ = true; + } + else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_STUDIES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Study); + } + else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_SERIES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Series); + } + else if (tag == DICOM_TAG_NUMBER_OF_PATIENT_RELATED_INSTANCES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Patient, ResourceType_Instance); + } + else if (tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_SERIES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Study, ResourceType_Series); + } + else if (tag == DICOM_TAG_NUMBER_OF_STUDY_RELATED_INSTANCES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Study, ResourceType_Instance); + } + else if (tag == DICOM_TAG_NUMBER_OF_SERIES_RELATED_INSTANCES) + { + ConfigureChildrenCountComputedTag(tag, ResourceType_Series, ResourceType_Instance); + } + else if (tag == DICOM_TAG_SOP_CLASSES_IN_STUDY) + { + requestedComputedTags_.insert(tag); + hasRequestedTags_ = true; + request_.GetChildrenSpecification(ResourceType_Instance).AddMetadata(MetadataType_Instance_SopClassUid); + } + else if (tag == DICOM_TAG_MODALITIES_IN_STUDY) + { + requestedComputedTags_.insert(tag); + hasRequestedTags_ = true; + if (request_.GetLevel() < ResourceType_Series) + { + request_.GetChildrenSpecification(ResourceType_Series).AddMainDicomTag(DICOM_TAG_MODALITY); + } + else if (request_.GetLevel() == ResourceType_Instance) // this happens in QIDO-RS when searching for instances without specifying a StudyInstanceUID -> all Study level tags must be included in the response + { + request_.GetParentSpecification(ResourceType_Series).SetRetrieveMainDicomTags(true); + } + } + else if (tag == DICOM_TAG_INSTANCE_AVAILABILITY) + { + requestedComputedTags_.insert(tag); + hasRequestedTags_ = true; + } + else + { + // This is neither a main DICOM tag, nor a computed DICOM tag: + // We will be forced to access the DICOM file anyway + requestedTagsFromFileStorage_.insert(tag); + + if (request_.GetLevel() != ResourceType_Instance) + { + request_.SetRetrieveOneInstanceIdentifier(true); + } + + hasRequestedTags_ = true; + } + } + + + void ResourceFinder::AddRequestedTags(const std::set<DicomTag>& tags) + { + for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) + { + AddRequestedTag(*it); + } + } + + + static void InjectRequestedTags(DicomMap& requestedTags, + std::set<DicomTag>& missingTags /* out */, + const FindResponse::Resource& resource, + ResourceType level, + const std::set<DicomTag>& tags) + { + if (!tags.empty()) + { + DicomMap m; + resource.GetMainDicomTags(m, level); + + for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) + { + std::string value; + if (m.LookupStringValue(value, *it, false /* not binary */)) + { + requestedTags.SetValue(*it, value, false /* not binary */); + } + else + { + // This is the case where the Housekeeper should be run + missingTags.insert(*it); + } + } + } + } + + + static void ReadMissingTagsFromStorageArea(DicomMap& requestedTags, + ServerContext& context, + const FindRequest& request, + const FindResponse::Resource& resource, + const std::set<DicomTag>& missingTags) + { + OrthancConfiguration::ReaderLock lock; + if (lock.GetConfiguration().IsWarningEnabled(Warnings_001_TagsBeingReadFromStorage)) + { + std::string missings; + FromDcmtkBridge::FormatListOfTags(missings, missingTags); + + LOG(WARNING) << "W001: Accessing DICOM tags from storage when accessing " + << Orthanc::GetResourceTypeText(resource.GetLevel(), false, false) + << ": " << missings; + } + + std::string instancePublicId; + + if (request.IsRetrieveOneInstanceIdentifier()) + { + instancePublicId = resource.GetOneInstanceIdentifier(); + } + else if (request.GetLevel() == ResourceType_Instance) + { + instancePublicId = resource.GetIdentifier(); + } + else + { + FindRequest requestDicomAttachment(request.GetLevel()); + requestDicomAttachment.SetOrthancId(request.GetLevel(), resource.GetIdentifier()); + requestDicomAttachment.SetRetrieveOneInstanceIdentifier(true); + + FindResponse responseDicomAttachment; + context.GetIndex().ExecuteFind(responseDicomAttachment, requestDicomAttachment); + + if (responseDicomAttachment.GetSize() != 1 || + !responseDicomAttachment.GetResourceByIndex(0).HasOneInstanceIdentifier()) + { + throw OrthancException(ErrorCode_InexistentFile); + } + else + { + instancePublicId = responseDicomAttachment.GetResourceByIndex(0).GetOneInstanceIdentifier(); + } + } + + LOG(INFO) << "Will retrieve missing DICOM tags from instance: " << instancePublicId; + + // TODO-FIND: What do we do if the DICOM has been removed since the request? + // Do we fail, or do we skip the resource? + + Json::Value tmpDicomAsJson; + context.ReadDicomAsJson(tmpDicomAsJson, instancePublicId, missingTags /* ignoreTagLength */); + + DicomMap tmpDicomMap; + tmpDicomMap.FromDicomAsJson(tmpDicomAsJson, false /* append */, true /* parseSequences*/); + + for (std::set<DicomTag>::const_iterator it = missingTags.begin(); it != missingTags.end(); ++it) + { + assert(!requestedTags.HasTag(*it)); + if (tmpDicomMap.HasTag(*it)) + { + requestedTags.SetValue(*it, tmpDicomMap.GetValue(*it)); + } + else + { + requestedTags.SetNullValue(*it); // TODO-FIND: Is this compatible with Orthanc <= 1.12.3? + } + } + } + + + void ResourceFinder::Execute(IVisitor& visitor, + ServerContext& context) const + { + FindResponse response; + context.GetIndex().ExecuteFind(response, request_); + + bool complete; + + switch (pagingMode_) + { + case PagingMode_FullDatabase: + case PagingMode_ManualSkip: + complete = true; + break; + + case PagingMode_FullManual: + complete = (databaseLimits_ == 0 || + response.GetSize() <= databaseLimits_); + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + + if (lookup_.get() != NULL) + { + LOG(INFO) << "Number of candidate resources after fast DB filtering on main DICOM tags: " << response.GetSize(); + } + + size_t countResults = 0; + size_t skipped = 0; + + for (size_t i = 0; i < response.GetSize(); i++) + { + const FindResponse::Resource& resource = response.GetResourceByIndex(i); + + DicomMap requestedTags; + + if (hasRequestedTags_) + { + InjectComputedTags(requestedTags, resource); + + std::set<DicomTag> missingTags = requestedTagsFromFileStorage_; + InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Patient, requestedPatientTags_); + InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Study, requestedStudyTags_); + InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Series, requestedSeriesTags_); + InjectRequestedTags(requestedTags, missingTags, resource, ResourceType_Instance, requestedInstanceTags_); + + if (!missingTags.empty()) + { + if (!allowStorageAccess_) + { + throw OrthancException(ErrorCode_BadSequenceOfCalls, + "Cannot add missing requested tags, as access to file storage is disallowed"); + } + else + { + ReadMissingTagsFromStorageArea(requestedTags, context, request_, resource, missingTags); + } + } + } + + bool match = true; + + if (lookup_.get() != NULL) + { + DicomMap tags; + resource.GetAllMainDicomTags(tags); + tags.Merge(requestedTags); + match = lookup_->IsMatch(tags); + } + + if (match) + { + if (pagingMode_ == PagingMode_FullDatabase) + { + visitor.Apply(resource, requestedTags); + } + else + { + if (hasLimitsSince_ && + skipped < limitsSince_) + { + skipped++; + } + else if (hasLimitsCount_ && + countResults >= limitsCount_) + { + // Too many results, don't mark as complete + complete = false; + break; + } + else + { + visitor.Apply(resource, requestedTags); + countResults++; + } + } + } + } + + if (complete) + { + visitor.MarkAsComplete(); + } + } + + + void ResourceFinder::Execute(Json::Value& target, + ServerContext& context, + DicomToJsonFormat format, + bool includeAllMetadata) const + { + class Visitor : public IVisitor + { + private: + const ResourceFinder& that_; + ServerIndex& index_; + Json::Value& target_; + DicomToJsonFormat format_; + bool hasRequestedTags_; + bool includeAllMetadata_; + + public: + Visitor(const ResourceFinder& that, + ServerIndex& index, + Json::Value& target, + DicomToJsonFormat format, + bool hasRequestedTags, + bool includeAllMetadata) : + that_(that), + index_(index), + target_(target), + format_(format), + hasRequestedTags_(hasRequestedTags), + includeAllMetadata_(includeAllMetadata) + { + } + + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) ORTHANC_OVERRIDE + { + if (that_.expand_) + { + Json::Value item; + that_.Expand(item, resource, index_, format_, includeAllMetadata_); + + if (hasRequestedTags_) + { + static const char* const REQUESTED_TAGS = "RequestedTags"; + item[REQUESTED_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(item[REQUESTED_TAGS], requestedTags, format_); + } + + target_.append(item); + } + else + { + target_.append(resource.GetIdentifier()); + } + } + + virtual void MarkAsComplete() ORTHANC_OVERRIDE + { + } + }; + + target = Json::arrayValue; + + Visitor visitor(*this, context.GetIndex(), target, format, hasRequestedTags_, includeAllMetadata); + Execute(visitor, context); + } + + + bool ResourceFinder::ExecuteOneResource(Json::Value& target, + ServerContext& context, + DicomToJsonFormat format, + bool includeAllMetadata) const + { + Json::Value answer; + Execute(answer, context, format, includeAllMetadata); + + if (answer.type() != Json::arrayValue) + { + throw OrthancException(ErrorCode_InternalError); + } + else if (answer.size() > 1) + { + throw OrthancException(ErrorCode_DatabasePlugin); + } + else if (answer.empty()) + { + // Inexistent resource (or was deleted between the first and second phases) + return false; + } + else + { + target = answer[0]; + return true; + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/Sources/ResourceFinder.h Thu Sep 05 18:52:27 2024 +0200 @@ -0,0 +1,182 @@ +/** + * 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/>. + **/ + + +#pragma once + +#include "Database/FindRequest.h" +#include "Database/FindResponse.h" + +namespace Orthanc +{ + class DatabaseLookup; + class ServerContext; + class ServerIndex; + + class ResourceFinder : public boost::noncopyable + { + public: + class IVisitor : public boost::noncopyable + { + public: + virtual ~IVisitor() + { + } + + virtual void Apply(const FindResponse::Resource& resource, + const DicomMap& requestedTags) = 0; + + virtual void MarkAsComplete() = 0; + }; + + private: + enum PagingMode + { + PagingMode_FullDatabase, + PagingMode_FullManual, + PagingMode_ManualSkip + }; + + FindRequest request_; + uint64_t databaseLimits_; + std::unique_ptr<DatabaseLookup> lookup_; + bool isSimpleLookup_; + PagingMode pagingMode_; + bool hasLimitsSince_; + bool hasLimitsCount_; + uint64_t limitsSince_; + uint64_t limitsCount_; + bool expand_; + bool allowStorageAccess_; + bool hasRequestedTags_; + std::set<DicomTag> requestedPatientTags_; + std::set<DicomTag> requestedStudyTags_; + std::set<DicomTag> requestedSeriesTags_; + std::set<DicomTag> requestedInstanceTags_; + std::set<DicomTag> requestedTagsFromFileStorage_; + std::set<DicomTag> requestedComputedTags_; + + bool IsRequestedComputedTag(const DicomTag& tag) const + { + return requestedComputedTags_.find(tag) != requestedComputedTags_.end(); + } + + void ConfigureChildrenCountComputedTag(DicomTag tag, + ResourceType parentLevel, + ResourceType childLevel); + + void InjectChildrenCountComputedTag(DicomMap& requestedTags, + DicomTag tag, + const FindResponse::Resource& resource, + ResourceType level) const; + + static SeriesStatus GetSeriesStatus(uint32_t& expectedNumberOfInstances, + const FindResponse::Resource& resource); + + void InjectComputedTags(DicomMap& requestedTags, + const FindResponse::Resource& resource) const; + + void UpdateRequestLimits(); + + public: + ResourceFinder(ResourceType level, + bool expand); + + void SetDatabaseLimits(uint64_t limits); + + bool IsAllowStorageAccess() const + { + return allowStorageAccess_; + } + + void SetAllowStorageAccess(bool allow) + { + allowStorageAccess_ = allow; + } + + void SetOrthancId(ResourceType level, + const std::string& id) + { + request_.SetOrthancId(level, id); + } + + void SetLimitsSince(uint64_t since); + + void SetLimitsCount(uint64_t count); + + void SetDatabaseLookup(const DatabaseLookup& lookup); + + void AddRequestedTag(const DicomTag& tag); + + void AddRequestedTags(const std::set<DicomTag>& tags); + + void SetLabels(const std::set<std::string>& labels) + { + request_.SetLabels(labels); + } + + void AddLabel(const std::string& label) + { + request_.AddLabel(label); + } + + void SetLabelsConstraint(LabelsConstraint constraint) + { + request_.SetLabelsConstraint(constraint); + } + + void SetRetrieveOneInstanceIdentifier(bool retrieve) + { + request_.SetRetrieveOneInstanceIdentifier(retrieve); + } + + void SetRetrieveMetadata(bool retrieve) + { + request_.SetRetrieveMetadata(retrieve); + } + + void SetRetrieveAttachments(bool retrieve) + { + request_.SetRetrieveAttachments(retrieve); + } + + // NB: "index" is only used in this method to fill the "IsStable" information + void Expand(Json::Value& target, + const FindResponse::Resource& resource, + ServerIndex& index, + DicomToJsonFormat format, + bool includeAllMetadata /* Same as: ExpandResourceFlags_IncludeAllMetadata */) const; + + void Execute(IVisitor& visitor, + ServerContext& context) const; + + void Execute(Json::Value& target, + ServerContext& context, + DicomToJsonFormat format, + bool includeAllMetadata) const; + + bool ExecuteOneResource(Json::Value& target, + ServerContext& context, + DicomToJsonFormat format, + bool includeAllMetadata) const; + }; +}
--- a/OrthancServer/Sources/Search/DatabaseConstraint.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DatabaseConstraint.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -37,6 +37,7 @@ # include <OrthancException.h> #endif +#include <boost/lexical_cast.hpp> #include <cassert> @@ -245,4 +246,103 @@ constraint.values = (tmpValues.empty() ? NULL : &tmpValues[0]); } #endif + + + void DatabaseConstraints::Clear() + { + for (size_t i = 0; i < constraints_.size(); i++) + { + assert(constraints_[i] != NULL); + delete constraints_[i]; + } + + constraints_.clear(); + } + + + void DatabaseConstraints::AddConstraint(DatabaseConstraint* constraint) + { + if (constraint == NULL) + { + throw OrthancException(ErrorCode_NullPointer); + } + else + { + constraints_.push_back(constraint); + } + } + + + const DatabaseConstraint& DatabaseConstraints::GetConstraint(size_t index) const + { + if (index >= constraints_.size()) + { + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + else + { + assert(constraints_[index] != NULL); + return *constraints_[index]; + } + } + + + std::string DatabaseConstraints::Format() const + { + std::string s; + + for (size_t i = 0; i < constraints_.size(); i++) + { + assert(constraints_[i] != NULL); + const DatabaseConstraint& constraint = *constraints_[i]; + s += "Constraint " + boost::lexical_cast<std::string>(i) + " at " + EnumerationToString(constraint.GetLevel()) + + ": " + constraint.GetTag().Format(); + + switch (constraint.GetConstraintType()) + { + case ConstraintType_Equal: + s += " == " + constraint.GetSingleValue(); + break; + + case ConstraintType_SmallerOrEqual: + s += " <= " + constraint.GetSingleValue(); + break; + + case ConstraintType_GreaterOrEqual: + s += " >= " + constraint.GetSingleValue(); + break; + + case ConstraintType_Wildcard: + s += " ~~ " + constraint.GetSingleValue(); + break; + + case ConstraintType_List: + { + s += " in [ "; + bool first = true; + for (size_t j = 0; j < constraint.GetValuesCount(); j++) + { + if (first) + { + first = false; + } + else + { + s += ", "; + } + s += constraint.GetValue(j); + } + s += "]"; + break; + } + + default: + throw OrthancException(ErrorCode_InternalError); + } + + s += "\n"; + } + + return s; + } }
--- a/OrthancServer/Sources/Search/DatabaseConstraint.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DatabaseConstraint.h Thu Sep 05 18:52:27 2024 +0200 @@ -46,6 +46,8 @@ # endif #endif +#include <deque> + namespace Orthanc { enum ConstraintType @@ -78,7 +80,7 @@ // This class is also used by the "orthanc-databases" project - class DatabaseConstraint + class DatabaseConstraint : public boost::noncopyable { private: ResourceType level_; @@ -148,4 +150,35 @@ std::vector<const char*>& tmpValues) const; #endif }; + + + class DatabaseConstraints : public boost::noncopyable + { + private: + std::deque<DatabaseConstraint*> constraints_; + + public: + ~DatabaseConstraints() + { + Clear(); + } + + void Clear(); + + void AddConstraint(DatabaseConstraint* constraint); // Takes ownership + + bool IsEmpty() const + { + return constraints_.empty(); + } + + size_t GetSize() const + { + return constraints_.size(); + } + + const DatabaseConstraint& GetConstraint(size_t index) const; + + std::string Format() const; + }; }
--- a/OrthancServer/Sources/Search/DatabaseLookup.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DatabaseLookup.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -369,14 +369,4 @@ return clone.release(); } - - - void DatabaseLookup::AddLabel(const std::string& label) - { - if (!label.empty()) - { - ServerToolbox::CheckValidLabel(label); - labels_.insert(label); - } - } }
--- a/OrthancServer/Sources/Search/DatabaseLookup.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DatabaseLookup.h Thu Sep 05 18:52:27 2024 +0200 @@ -23,7 +23,6 @@ #pragma once -#include "../Search/ISqlLookupFormatter.h" #include "DicomTagConstraint.h" class DcmItem; @@ -34,8 +33,6 @@ { private: std::vector<DicomTagConstraint*> constraints_; - std::set<std::string> labels_; - LabelsConstraint labelsConstraint_; void AddDicomConstraintInternal(const DicomTag& tag, ValueRepresentation vr, @@ -46,11 +43,6 @@ void AddConstraintInternal(DicomTagConstraint* constraint); // Takes ownership public: - DatabaseLookup() : - labelsConstraint_(LabelsConstraint_All) - { - } - ~DatabaseLookup(); DatabaseLookup* Clone() const; @@ -97,22 +89,5 @@ bool HasTag(const DicomTag& tag) const; void RemoveConstraint(const DicomTag& tag); - - void AddLabel(const std::string& label); - - void SetLabelsConstraint(LabelsConstraint constraint) - { - labelsConstraint_ = constraint; - } - - const std::set<std::string>& GetLabels() const - { - return labels_; - } - - LabelsConstraint GetLabelsConstraint() const - { - return labelsConstraint_; - } }; }
--- a/OrthancServer/Sources/Search/DicomTagConstraint.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DicomTagConstraint.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -215,6 +215,24 @@ } + static bool HasIntersection(const std::set<std::string>& expected, + const std::string& values) + { + std::vector<std::string> tokens; + Toolbox::TokenizeString(tokens, values, '\\'); + + for (size_t i = 0; i < tokens.size(); i++) + { + if (expected.find(tokens[i]) != expected.end()) + { + return true; + } + } + + return false; + } + + bool DicomTagConstraint::IsMatch(const std::string& value) const { NormalizedString source(value, caseSensitive_); @@ -224,7 +242,17 @@ case ConstraintType_Equal: { NormalizedString reference(GetValue(), caseSensitive_); - return source.GetValue() == reference.GetValue(); + + if (GetTag() == DICOM_TAG_MODALITIES_IN_STUDY) + { + std::set<std::string> expected; + expected.insert(reference.GetValue()); + return HasIntersection(expected, source.GetValue()); + } + else + { + return source.GetValue() == reference.GetValue(); + } } case ConstraintType_SmallerOrEqual: @@ -251,17 +279,16 @@ case ConstraintType_List: { + std::set<std::string> references; + for (std::set<std::string>::const_iterator it = values_.begin(); it != values_.end(); ++it) { NormalizedString reference(*it, caseSensitive_); - if (source.GetValue() == reference.GetValue()) - { - return true; - } + references.insert(reference.GetValue()); } - return false; + return HasIntersection(references, source.GetValue()); } default: @@ -342,8 +369,9 @@ } - DatabaseConstraint DicomTagConstraint::ConvertToDatabaseConstraint(ResourceType level, - DicomTagType tagType) const + DatabaseConstraint* DicomTagConstraint::ConvertToDatabaseConstraint(bool& isIdentical, + ResourceType level, + DicomTagType tagType) const { bool isIdentifier, caseSensitive; @@ -365,13 +393,21 @@ std::vector<std::string> values; values.reserve(values_.size()); - + + isIdentical = true; + for (std::set<std::string>::const_iterator it = values_.begin(); it != values_.end(); ++it) { if (isIdentifier) { - values.push_back(ServerToolbox::NormalizeIdentifier(*it)); + std::string normalized = ServerToolbox::NormalizeIdentifier(*it); + values.push_back(normalized); + + if (normalized != *it) + { + isIdentical = false; + } } else { @@ -379,7 +415,7 @@ } } - return DatabaseConstraint(level, tag_, isIdentifier, constraintType_, - values, caseSensitive, mandatory_); + return new DatabaseConstraint(level, tag_, isIdentifier, constraintType_, + values, caseSensitive, mandatory_); } }
--- a/OrthancServer/Sources/Search/DicomTagConstraint.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/DicomTagConstraint.h Thu Sep 05 18:52:27 2024 +0200 @@ -109,7 +109,8 @@ std::string Format() const; - DatabaseConstraint ConvertToDatabaseConstraint(ResourceType level, - DicomTagType tagType) const; + DatabaseConstraint* ConvertToDatabaseConstraint(bool& isIdentical /* out */, + ResourceType level, + DicomTagType tagType) const; }; }
--- a/OrthancServer/Sources/Search/ISqlLookupFormatter.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/ISqlLookupFormatter.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -34,6 +34,7 @@ #if ORTHANC_BUILDING_SERVER_LIBRARY == 1 # include "../../../OrthancFramework/Sources/OrthancException.h" # include "../../../OrthancFramework/Sources/Toolbox.h" +# include "../Database/FindRequest.h" #else # include <OrthancException.h> # include <Toolbox.h> @@ -475,7 +476,10 @@ } - void ISqlLookupFormatter::GetLookupLevels(ResourceType& lowerLevel, ResourceType& upperLevel, const ResourceType& queryLevel, const std::vector<DatabaseConstraint>& lookup) + void ISqlLookupFormatter::GetLookupLevels(ResourceType& lowerLevel, + ResourceType& upperLevel, + const ResourceType& queryLevel, + const DatabaseConstraints& lookup) { assert(ResourceType_Patient < ResourceType_Study && ResourceType_Study < ResourceType_Series && @@ -484,9 +488,9 @@ lowerLevel = queryLevel; upperLevel = queryLevel; - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { - ResourceType level = lookup[i].GetLevel(); + ResourceType level = lookup.GetConstraint(i).GetLevel(); if (level < upperLevel) { @@ -503,7 +507,7 @@ void ISqlLookupFormatter::Apply(std::string& sql, ISqlLookupFormatter& formatter, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -521,14 +525,16 @@ size_t count = 0; - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { + const DatabaseConstraint& constraint = lookup.GetConstraint(i); + std::string comparison; - if (FormatComparison(comparison, formatter, lookup[i], count, escapeBrackets)) + if (FormatComparison(comparison, formatter, constraint, count, escapeBrackets)) { std::string join; - FormatJoin(join, lookup[i], count); + FormatJoin(join, constraint, count); joins += join; if (!comparison.empty()) @@ -611,10 +617,158 @@ } } +#if ORTHANC_BUILDING_SERVER_LIBRARY == 1 + void ISqlLookupFormatter::Apply(std::string& sql, + ISqlLookupFormatter& formatter, + const FindRequest& request) + { + const bool escapeBrackets = formatter.IsEscapeBrackets(); + ResourceType queryLevel = request.GetLevel(); + const std::string& strQueryLevel = FormatLevel(queryLevel); + + ResourceType lowerLevel, upperLevel; + GetLookupLevels(lowerLevel, upperLevel, queryLevel, request.GetDicomTagConstraints()); + + assert(upperLevel <= queryLevel && + queryLevel <= lowerLevel); + + + sql = ("SELECT " + + strQueryLevel + ".publicId, " + + strQueryLevel + ".internalId" + + " FROM Resources AS " + strQueryLevel); + + + std::string joins, comparisons; + + if (request.GetOrthancIdentifiers().IsDefined() && request.GetOrthancIdentifiers().DetectLevel() <= queryLevel) + { + // single child resource matching, there should not be other constraints (at least for now) + assert(request.GetDicomTagConstraints().GetSize() == 0); + assert(request.GetLabels().size() == 0); + assert(request.HasLimits() == false); + + ResourceType topParentLevel = request.GetOrthancIdentifiers().DetectLevel(); + const std::string& strTopParentLevel = FormatLevel(topParentLevel); + + comparisons = " AND " + strTopParentLevel + ".publicId = " + formatter.GenerateParameter(request.GetOrthancIdentifiers().GetLevel(topParentLevel)); + + for (int level = queryLevel; level > topParentLevel; level--) + { + sql += (" INNER JOIN Resources " + + FormatLevel(static_cast<ResourceType>(level - 1)) + " ON " + + FormatLevel(static_cast<ResourceType>(level - 1)) + ".internalId=" + + FormatLevel(static_cast<ResourceType>(level)) + ".parentId"); + } + } + else + { + size_t count = 0; + + const DatabaseConstraints& dicomTagsConstraints = request.GetDicomTagConstraints(); + for (size_t i = 0; i < dicomTagsConstraints.GetSize(); i++) + { + const DatabaseConstraint& constraint = dicomTagsConstraints.GetConstraint(i); + + std::string comparison; + + if (FormatComparison(comparison, formatter, constraint, count, escapeBrackets)) + { + std::string join; + FormatJoin(join, constraint, count); + joins += join; + + if (!comparison.empty()) + { + comparisons += " AND " + comparison; + } + + count ++; + } + } + } + + for (int level = queryLevel - 1; level >= upperLevel; level--) + { + sql += (" INNER JOIN Resources " + + FormatLevel(static_cast<ResourceType>(level)) + " ON " + + FormatLevel(static_cast<ResourceType>(level)) + ".internalId=" + + FormatLevel(static_cast<ResourceType>(level + 1)) + ".parentId"); + } + + for (int level = queryLevel + 1; level <= lowerLevel; level++) + { + sql += (" INNER JOIN Resources " + + FormatLevel(static_cast<ResourceType>(level)) + " ON " + + FormatLevel(static_cast<ResourceType>(level - 1)) + ".internalId=" + + FormatLevel(static_cast<ResourceType>(level)) + ".parentId"); + } + + std::list<std::string> where; + where.push_back(strQueryLevel + ".resourceType = " + + formatter.FormatResourceType(queryLevel) + comparisons); + + + if (!request.GetLabels().empty()) + { + /** + * "In SQL Server, NOT EXISTS and NOT IN predicates are the best + * way to search for missing values, as long as both columns in + * question are NOT NULL." + * https://explainextended.com/2009/09/15/not-in-vs-not-exists-vs-left-join-is-null-sql-server/ + **/ + + const std::set<std::string>& labels = request.GetLabels(); + std::list<std::string> formattedLabels; + for (std::set<std::string>::const_iterator it = labels.begin(); it != labels.end(); ++it) + { + formattedLabels.push_back(formatter.GenerateParameter(*it)); + } + + std::string condition; + switch (request.GetLabelsConstraint()) + { + case LabelsConstraint_Any: + condition = "> 0"; + break; + + case LabelsConstraint_All: + condition = "= " + boost::lexical_cast<std::string>(labels.size()); + break; + + case LabelsConstraint_None: + condition = "= 0"; + break; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + + where.push_back("(SELECT COUNT(1) FROM Labels AS selectedLabels WHERE selectedLabels.id = " + strQueryLevel + + ".internalId AND selectedLabels.label IN (" + Join(formattedLabels, "", ", ") + ")) " + condition); + } + + sql += joins + Join(where, " WHERE ", " AND "); + + if (request.HasLimits()) + { + if (request.GetLimitsCount() > 0) + { + sql += " LIMIT " + boost::lexical_cast<std::string>(request.GetLimitsCount()); + } + if (request.GetLimitsSince() > 0) + { + sql += " OFFSET " + boost::lexical_cast<std::string>(request.GetLimitsSince()); + } + } + + } +#endif + void ISqlLookupFormatter::ApplySingleLevel(std::string& sql, ISqlLookupFormatter& formatter, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, LabelsConstraint labelsConstraint, @@ -631,15 +785,17 @@ std::vector<std::string> mainDicomTagsComparisons, dicomIdentifiersComparisons; - for (size_t i = 0; i < lookup.size(); i++) + for (size_t i = 0; i < lookup.GetSize(); i++) { + const DatabaseConstraint& constraint = lookup.GetConstraint(i); + std::string comparison; - if (FormatComparison2(comparison, formatter, lookup[i], escapeBrackets)) + if (FormatComparison2(comparison, formatter, constraint, escapeBrackets)) { if (!comparison.empty()) { - if (lookup[i].IsIdentifier()) + if (constraint.IsIdentifier()) { dicomIdentifiersComparisons.push_back(comparison); }
--- a/OrthancServer/Sources/Search/ISqlLookupFormatter.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/Search/ISqlLookupFormatter.h Thu Sep 05 18:52:27 2024 +0200 @@ -34,8 +34,9 @@ namespace Orthanc { - class DatabaseConstraint; - + class DatabaseConstraints; + class FindRequest; + enum LabelsConstraint { LabelsConstraint_All, @@ -64,11 +65,14 @@ **/ virtual bool IsEscapeBrackets() const = 0; - static void GetLookupLevels(ResourceType& lowerLevel, ResourceType& upperLevel, const ResourceType& queryLevel, const std::vector<DatabaseConstraint>& lookup); + static void GetLookupLevels(ResourceType& lowerLevel, + ResourceType& upperLevel, + const ResourceType& queryLevel, + const DatabaseConstraints& lookup); static void Apply(std::string& sql, ISqlLookupFormatter& formatter, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, // New in Orthanc 1.12.0 LabelsConstraint labelsConstraint, // New in Orthanc 1.12.0 @@ -76,10 +80,16 @@ static void ApplySingleLevel(std::string& sql, ISqlLookupFormatter& formatter, - const std::vector<DatabaseConstraint>& lookup, + const DatabaseConstraints& lookup, ResourceType queryLevel, const std::set<std::string>& labels, // New in Orthanc 1.12.0 LabelsConstraint labelsConstraint, // New in Orthanc 1.12.0 size_t limit); + +#if ORTHANC_BUILDING_SERVER_LIBRARY == 1 + static void Apply(std::string& sql, + ISqlLookupFormatter& formatter, + const FindRequest& request); +#endif }; }
--- a/OrthancServer/Sources/ServerContext.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/ServerContext.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -42,6 +42,7 @@ #include "OrthancConfiguration.h" #include "OrthancRestApi/OrthancRestApi.h" +#include "ResourceFinder.h" #include "Search/DatabaseLookup.h" #include "ServerJobs/OrthancJobUnserializer.h" #include "ServerToolbox.h" @@ -1346,18 +1347,17 @@ // Throttle to avoid loading several large DICOM files simultaneously largeDicomLocker_.reset(new Semaphore::Locker(context.largeDicomThrottler_)); - std::string content; - context_.ReadDicom(content, instancePublicId); + context_.ReadDicom(buffer_, instancePublicId_); // Release the throttle if loading "small" DICOM files (under // 50MB, which is an arbitrary value) - if (content.size() < 50 * 1024 * 1024) + if (buffer_.size() < 50 * 1024 * 1024) { largeDicomLocker_.reset(NULL); } - dicom_.reset(new ParsedDicomFile(content)); - dicomSize_ = content.size(); + dicom_.reset(new ParsedDicomFile(buffer_)); + dicomSize_ = buffer_.size(); } assert(accessor_.get() != NULL || @@ -1393,6 +1393,18 @@ } } + const std::string& ServerContext::DicomCacheLocker::GetBuffer() + { + if (buffer_.size() > 0) + { + return buffer_; + } + else + { + context_.ReadDicom(buffer_, instancePublicId_); + return buffer_; + } + } void ServerContext::SetStoreMD5ForAttachments(bool storeMD5) { @@ -1533,11 +1545,12 @@ void ServerContext::Apply(ILookupVisitor& visitor, const DatabaseLookup& lookup, ResourceType queryLevel, + const std::set<std::string>& labels, + LabelsConstraint labelsConstraint, size_t since, size_t limit) { - unsigned int databaseLimit = (queryLevel == ResourceType_Instance ? - limitFindInstances_ : limitFindResults_); + const uint64_t databaseLimit = GetDatabaseLimits(queryLevel); std::vector<std::string> resources, instances; const DicomTagConstraint* dicomModalitiesConstraint = NULL; @@ -1554,11 +1567,8 @@ fastLookup->RemoveConstraint(DICOM_TAG_MODALITIES_IN_STUDY); } - { - const size_t lookupLimit = (databaseLimit == 0 ? 0 : databaseLimit + 1); - GetIndex().ApplyLookupResources(resources, &instances, *fastLookup, queryLevel, - lookup.GetLabels(), lookup.GetLabelsConstraint(), lookupLimit); - } + const size_t lookupLimit = (databaseLimit == 0 ? 0 : databaseLimit + 1); + GetIndex().ApplyLookupResources(resources, &instances, *fastLookup, queryLevel, labels, labelsConstraint, lookupLimit); bool complete = (databaseLimit == 0 || resources.size() <= databaseLimit); @@ -1846,27 +1856,50 @@ } + + + ImageAccessor* ServerContext::DecodeDicomFrame(const std::string& publicId, unsigned int frameIndex) { + ServerContext::DicomCacheLocker locker(*this, publicId); + std::unique_ptr<ImageAccessor> decoded(DecodeDicomFrame(locker.GetDicom(), locker.GetBuffer().c_str(), locker.GetBuffer().size(), frameIndex)); + + if (decoded.get() == NULL) + { + OrthancConfiguration::ReaderLock configLock; + if (configLock.GetConfiguration().IsWarningEnabled(Warnings_003_DecoderFailure)) + { + LOG(WARNING) << "W003: Unable to decode frame " << frameIndex << " from instance " << publicId; + } + return NULL; + } + + return decoded.release(); + } + + + ImageAccessor* ServerContext::DecodeDicomFrame(const ParsedDicomFile& parsedDicom, + const void* buffer, // actually the buffer that is the source of the ParsedDicomFile + size_t size, + unsigned int frameIndex) + { + std::unique_ptr<ImageAccessor> decoded; + if (builtinDecoderTranscoderOrder_ == BuiltinDecoderTranscoderOrder_Before) { - // Use Orthanc's built-in decoder, using the cache to speed-up - // things on multi-frame images - - std::unique_ptr<ImageAccessor> decoded; + // Use Orthanc's built-in decoder + try { - ServerContext::DicomCacheLocker locker(*this, publicId); - decoded.reset(locker.GetDicom().DecodeFrame(frameIndex)); + decoded.reset(parsedDicom.DecodeFrame(frameIndex)); + if (decoded.get() != NULL) + { + return decoded.release(); + } } catch (OrthancException& e) - { - } - - if (decoded.get() != NULL) - { - return decoded.release(); + { // ignore, we'll try other alternatives } } @@ -1874,14 +1907,9 @@ if (HasPlugins() && GetPlugins().HasCustomImageDecoder()) { - // TODO: Store the raw buffer in the DicomCacheLocker - std::string dicomContent; - ReadDicom(dicomContent, publicId); - - std::unique_ptr<ImageAccessor> decoded; try { - decoded.reset(GetPlugins().Decode(dicomContent.c_str(), dicomContent.size(), frameIndex)); + decoded.reset(GetPlugins().Decode(buffer, size, frameIndex)); } catch (OrthancException& e) { @@ -1901,69 +1929,50 @@ if (builtinDecoderTranscoderOrder_ == BuiltinDecoderTranscoderOrder_After) { - ServerContext::DicomCacheLocker locker(*this, publicId); - return locker.GetDicom().DecodeFrame(frameIndex); + try + { + decoded.reset(parsedDicom.DecodeFrame(frameIndex)); + if (decoded.get() != NULL) + { + return decoded.release(); + } + } + catch (OrthancException& e) + { + LOG(INFO) << e.GetDetails(); + } } - else + + if (HasPlugins() && GetPlugins().HasCustomTranscoder()) { - return NULL; // Built-in decoder is disabled + LOG(INFO) << "The plugins and built-in image decoders failed to decode a frame, " + << "trying to transcode the file to LittleEndianExplicit using the plugins."; + DicomImage explicitTemporaryImage; + DicomImage source; + std::set<DicomTransferSyntax> allowedSyntaxes; + + source.SetExternalBuffer(buffer, size); + allowedSyntaxes.insert(DicomTransferSyntax_LittleEndianExplicit); + + if (Transcode(explicitTemporaryImage, source, allowedSyntaxes, true)) + { + std::unique_ptr<ParsedDicomFile> file(explicitTemporaryImage.ReleaseAsParsedDicomFile()); + return file->DecodeFrame(frameIndex); + } } + + return NULL; } ImageAccessor* ServerContext::DecodeDicomFrame(const DicomInstanceToStore& dicom, unsigned int frameIndex) { - if (builtinDecoderTranscoderOrder_ == BuiltinDecoderTranscoderOrder_Before) - { - std::unique_ptr<ImageAccessor> decoded; - try - { - decoded.reset(dicom.DecodeFrame(frameIndex)); - } - catch (OrthancException& e) - { - } - - if (decoded.get() != NULL) - { - return decoded.release(); - } - } - -#if ORTHANC_ENABLE_PLUGINS == 1 - if (HasPlugins() && - GetPlugins().HasCustomImageDecoder()) - { - std::unique_ptr<ImageAccessor> decoded; - try - { - decoded.reset(GetPlugins().Decode(dicom.GetBufferData(), dicom.GetBufferSize(), frameIndex)); - } - catch (OrthancException& e) - { - } - - if (decoded.get() != NULL) - { - return decoded.release(); - } - else if (builtinDecoderTranscoderOrder_ == BuiltinDecoderTranscoderOrder_After) - { - LOG(INFO) << "The installed image decoding plugins cannot handle an image, " - << "fallback to the built-in DCMTK decoder"; - } - } -#endif - - if (builtinDecoderTranscoderOrder_ == BuiltinDecoderTranscoderOrder_After) - { - return dicom.DecodeFrame(frameIndex); - } - else - { - return NULL; - } + return DecodeDicomFrame(dicom.GetParsedDicomFile(), + dicom.GetBufferData(), + dicom.GetBufferSize(), + frameIndex); + } @@ -1971,8 +1980,8 @@ size_t size, unsigned int frameIndex) { - std::unique_ptr<DicomInstanceToStore> instance(DicomInstanceToStore::CreateFromBuffer(dicom, size)); - return DecodeDicomFrame(*instance, frameIndex); + std::unique_ptr<ParsedDicomFile> instance(new ParsedDicomFile(dicom, size)); + return DecodeDicomFrame(*instance, dicom, size, frameIndex); } @@ -2126,124 +2135,137 @@ static void SerializeExpandedResource(Json::Value& target, const ExpandedResource& resource, DicomToJsonFormat format, - const std::set<DicomTag>& requestedTags) + const std::set<DicomTag>& requestedTags, + ExpandResourceFlags expandFlags) { target = Json::objectValue; target["Type"] = GetResourceTypeText(resource.GetLevel(), false, true); target["ID"] = resource.GetPublicId(); - switch (resource.GetLevel()) - { - case ResourceType_Patient: - break; - - case ResourceType_Study: - target["ParentPatient"] = resource.parentId_; - break; - - case ResourceType_Series: - target["ParentStudy"] = resource.parentId_; - break; - - case ResourceType_Instance: - target["ParentSeries"] = resource.parentId_; - break; - - default: - throw OrthancException(ErrorCode_InternalError); - } - - switch (resource.GetLevel()) + if (!resource.parentId_.empty()) { - case ResourceType_Patient: - case ResourceType_Study: - case ResourceType_Series: + switch (resource.GetLevel()) { - Json::Value c = Json::arrayValue; - - for (std::list<std::string>::const_iterator - it = resource.childrenIds_.begin(); it != resource.childrenIds_.end(); ++it) - { - c.append(*it); - } - - if (resource.GetLevel() == ResourceType_Patient) - { - target["Studies"] = c; - } - else if (resource.GetLevel() == ResourceType_Study) - { - target["Series"] = c; - } - else - { - target["Instances"] = c; - } - break; + case ResourceType_Patient: + break; + + case ResourceType_Study: + target["ParentPatient"] = resource.parentId_; + break; + + case ResourceType_Series: + target["ParentStudy"] = resource.parentId_; + break; + + case ResourceType_Instance: + target["ParentSeries"] = resource.parentId_; + break; + + default: + throw OrthancException(ErrorCode_InternalError); } - - case ResourceType_Instance: - break; - - default: - throw OrthancException(ErrorCode_InternalError); } - switch (resource.GetLevel()) + if ((expandFlags & ExpandResourceFlags_IncludeChildren) != 0) { - case ResourceType_Patient: - case ResourceType_Study: - break; - - case ResourceType_Series: - if (resource.expectedNumberOfInstances_ < 0) + switch (resource.GetLevel()) + { + case ResourceType_Patient: + case ResourceType_Study: + case ResourceType_Series: { - target["ExpectedNumberOfInstances"] = Json::nullValue; + Json::Value c = Json::arrayValue; + + for (std::list<std::string>::const_iterator + it = resource.childrenIds_.begin(); it != resource.childrenIds_.end(); ++it) + { + c.append(*it); + } + + if (resource.GetLevel() == ResourceType_Patient) + { + target["Studies"] = c; + } + else if (resource.GetLevel() == ResourceType_Study) + { + target["Series"] = c; + } + else + { + target["Instances"] = c; + } + break; } - else - { - target["ExpectedNumberOfInstances"] = resource.expectedNumberOfInstances_; - } - target["Status"] = resource.status_; - break; - - case ResourceType_Instance: + + case ResourceType_Instance: + break; + + default: + throw OrthancException(ErrorCode_InternalError); + } + } + + if ((expandFlags & ExpandResourceFlags_IncludeMetadata) != 0) + { + switch (resource.GetLevel()) { - target["FileSize"] = static_cast<unsigned int>(resource.fileSize_); - target["FileUuid"] = resource.fileUuid_; - - if (resource.indexInSeries_ < 0) + case ResourceType_Patient: + case ResourceType_Study: + break; + + case ResourceType_Series: + if (resource.expectedNumberOfInstances_ < 0) + { + target["ExpectedNumberOfInstances"] = Json::nullValue; + } + else + { + target["ExpectedNumberOfInstances"] = resource.expectedNumberOfInstances_; + } + target["Status"] = resource.status_; + break; + + case ResourceType_Instance: { - target["IndexInSeries"] = Json::nullValue; + target["FileSize"] = static_cast<unsigned int>(resource.fileSize_); + target["FileUuid"] = resource.fileUuid_; + + if (resource.indexInSeries_ < 0) + { + target["IndexInSeries"] = Json::nullValue; + } + else + { + target["IndexInSeries"] = resource.indexInSeries_; + } + + break; } - else - { - target["IndexInSeries"] = resource.indexInSeries_; - } - - break; + + default: + throw OrthancException(ErrorCode_InternalError); } - - default: - throw OrthancException(ErrorCode_InternalError); - } - - if (!resource.anonymizedFrom_.empty()) - { - target["AnonymizedFrom"] = resource.anonymizedFrom_; - } - if (!resource.modifiedFrom_.empty()) - { - target["ModifiedFrom"] = resource.modifiedFrom_; + if (!resource.anonymizedFrom_.empty()) + { + target["AnonymizedFrom"] = resource.anonymizedFrom_; + } + + if (!resource.modifiedFrom_.empty()) + { + target["ModifiedFrom"] = resource.modifiedFrom_; + } } if (resource.GetLevel() == ResourceType_Patient || resource.GetLevel() == ResourceType_Study || resource.GetLevel() == ResourceType_Series) { - target["IsStable"] = resource.isStable_; + if ((expandFlags & ExpandResourceFlags_IncludeIsStable) != 0) + { + target["IsStable"] = resource.isStable_; + } if (!resource.lastUpdate_.empty()) { @@ -2251,38 +2273,42 @@ } } - // serialize tags - - static const char* const MAIN_DICOM_TAGS = "MainDicomTags"; - static const char* const PATIENT_MAIN_DICOM_TAGS = "PatientMainDicomTags"; - - DicomMap mainDicomTags; - resource.GetMainDicomTags().ExtractResourceInformation(mainDicomTags, resource.GetLevel()); - - target[MAIN_DICOM_TAGS] = Json::objectValue; - FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format); - - if (resource.GetLevel() == ResourceType_Study) + if ((expandFlags & ExpandResourceFlags_IncludeMainDicomTags) != 0) { - DicomMap patientMainDicomTags; - resource.GetMainDicomTags().ExtractPatientInformation(patientMainDicomTags); - - target[PATIENT_MAIN_DICOM_TAGS] = Json::objectValue; - FromDcmtkBridge::ToJson(target[PATIENT_MAIN_DICOM_TAGS], patientMainDicomTags, format); + // serialize tags + + static const char* const MAIN_DICOM_TAGS = "MainDicomTags"; + static const char* const PATIENT_MAIN_DICOM_TAGS = "PatientMainDicomTags"; + + DicomMap mainDicomTags; + resource.GetMainDicomTags().ExtractResourceInformation(mainDicomTags, resource.GetLevel()); + + target[MAIN_DICOM_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(target[MAIN_DICOM_TAGS], mainDicomTags, format); + + if (resource.GetLevel() == ResourceType_Study) + { + DicomMap patientMainDicomTags; + resource.GetMainDicomTags().ExtractPatientInformation(patientMainDicomTags); + + target[PATIENT_MAIN_DICOM_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(target[PATIENT_MAIN_DICOM_TAGS], patientMainDicomTags, format); + } + + if (requestedTags.size() > 0) + { + static const char* const REQUESTED_TAGS = "RequestedTags"; + + DicomMap tags; + resource.GetMainDicomTags().ExtractTags(tags, requestedTags); + + target[REQUESTED_TAGS] = Json::objectValue; + FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format); + + } } - if (requestedTags.size() > 0) - { - static const char* const REQUESTED_TAGS = "RequestedTags"; - - DicomMap tags; - resource.GetMainDicomTags().ExtractTags(tags, requestedTags); - - target[REQUESTED_TAGS] = Json::objectValue; - FromDcmtkBridge::ToJson(target[REQUESTED_TAGS], tags, format); - - } - + if ((expandFlags & ExpandResourceFlags_IncludeLabels) != 0) { Json::Value labels = Json::arrayValue; @@ -2293,6 +2319,19 @@ target["Labels"] = labels; } + + // new in Orthanc 1.12.4 + if ((expandFlags & ExpandResourceFlags_IncludeAllMetadata) != 0) + { + Json::Value metadata = Json::objectValue; + + for (std::map<MetadataType, std::string>::const_iterator it = resource.metadata_.begin(); it != resource.metadata_.end(); ++it) + { + metadata[EnumerationToString(it->first)] = it->second; + } + + target["Metadata"] = metadata; + } } @@ -2538,9 +2577,9 @@ { ExpandedResource resource; - if (ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, level, requestedTags, ExpandResourceFlags_Default, allowStorageAccess)) + if (ExpandResource(resource, publicId, mainDicomTags, instanceId, dicomAsJson, level, requestedTags, ExpandResourceFlags_DefaultExtract, allowStorageAccess)) { - SerializeExpandedResource(target, resource, format, requestedTags); + SerializeExpandedResource(target, resource, format, requestedTags, ExpandResourceFlags_DefaultOutput); return true; } @@ -2578,7 +2617,13 @@ 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)) + if (missingTags.size() > 0 && DicomMap::HasOnlyComputedTags(missingTags)) + { + resource.missingRequestedTags_ = missingTags; + ComputeTags(resource, *this, publicId, level, requestedTags); + return true; + } + else if (missingTags.size() == 0) { expandFlags = static_cast<ExpandResourceFlags>(expandFlags & ~ExpandResourceFlags_IncludeMainDicomTags); } @@ -2687,5 +2732,4 @@ return elapsed.total_seconds(); } - }
--- a/OrthancServer/Sources/ServerContext.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/ServerContext.h Thu Sep 05 18:52:27 2024 +0200 @@ -305,6 +305,7 @@ std::unique_ptr<ParsedDicomFile> dicom_; size_t dicomSize_; std::unique_ptr<Semaphore::Locker> largeDicomLocker_; + std::string buffer_; public: DicomCacheLocker(ServerContext& context, @@ -313,6 +314,8 @@ ~DicomCacheLocker(); ParsedDicomFile& GetDicom() const; + + const std::string& GetBuffer(); }; ServerContext(IDatabaseWrapper& database, @@ -442,11 +445,27 @@ void Stop(); + uint64_t GetDatabaseLimits(ResourceType level) const + { + return (level == ResourceType_Instance ? limitFindInstances_ : limitFindResults_); + } + + void Apply(ILookupVisitor& visitor, + const DatabaseLookup& lookup, + ResourceType queryLevel, + const std::set<std::string>& labels, + LabelsConstraint labelsConstraint, + size_t since, + size_t limit); + void Apply(ILookupVisitor& visitor, const DatabaseLookup& lookup, ResourceType queryLevel, size_t since, - size_t limit); + size_t limit) + { + Apply(visitor, lookup, queryLevel, std::set<std::string>(), LabelsConstraint_All, since, limit); + } bool LookupOrReconstructMetadata(std::string& target, const std::string& publicId, @@ -544,7 +563,12 @@ ImageAccessor* DecodeDicomFrame(const void* dicom, size_t size, unsigned int frameIndex); - + + ImageAccessor* DecodeDicomFrame(const ParsedDicomFile& parsedDicom, + const void* buffer, // actually the buffer that is the source of the ParsedDicomFile + size_t size, + unsigned int frameIndex); + void StoreWithTranscoding(std::string& sopClassUid, std::string& sopInstanceUid, DicomStoreUserConnection& connection,
--- a/OrthancServer/Sources/ServerEnumerations.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/ServerEnumerations.h Thu Sep 05 18:52:27 2024 +0200 @@ -208,6 +208,7 @@ Warnings_None, Warnings_001_TagsBeingReadFromStorage, Warnings_002_InconsistentDicomTagsInDb, + Warnings_003_DecoderFailure, // new in Orthanc 1.12.5 };
--- a/OrthancServer/Sources/ServerIndex.h Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/ServerIndex.h Thu Sep 05 18:52:27 2024 +0200 @@ -64,9 +64,6 @@ int64_t id, const std::string& publicId); - bool IsUnstableResource(ResourceType type, - int64_t id); - public: ServerIndex(ServerContext& context, IDatabaseWrapper& database, @@ -103,5 +100,8 @@ bool hasOldRevision, int64_t oldRevision, const std::string& oldMD5); + + bool IsUnstableResource(ResourceType type, + int64_t id); }; }
--- a/OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -744,10 +744,18 @@ } else { - ExpandedResource originalStudy; - if (GetContext().GetIndex().ExpandResource(originalStudy, *studyId, ResourceType_Study, emptyRequestedTags, ExpandResourceFlags_IncludeMainDicomTags)) + FindRequest request(ResourceType_Study); + request.SetOrthancStudyId(*studyId); + request.SetRetrieveMainDicomTags(true); + + FindResponse response; + GetContext().GetIndex().ExecuteFind(response, request); + + if (response.GetSize() == 1) { - targetPatientId = originalStudy.GetMainDicomTags().GetStringValue(DICOM_TAG_PATIENT_ID, "", false); + DicomMap tags; + response.GetResourceByIndex(0).GetMainDicomTags(tags, ResourceType_Study); + targetPatientId = tags.GetStringValue(DICOM_TAG_PATIENT_ID, "", false); } else { @@ -762,22 +770,34 @@ // if the patient exists, check how many child studies it has. if (lookupPatientResult.size() >= 1) { - ExpandedResource targetPatient; - - if (GetContext().GetIndex().ExpandResource(targetPatient, lookupPatientResult[0], ResourceType_Patient, emptyRequestedTags, static_cast<ExpandResourceFlags>(ExpandResourceFlags_IncludeMainDicomTags | ExpandResourceFlags_IncludeChildren))) + FindRequest request(ResourceType_Patient); + request.SetOrthancPatientId(lookupPatientResult[0]); + request.SetRetrieveMainDicomTags(true); + request.GetChildrenSpecification(ResourceType_Study).SetRetrieveIdentifiers(true); + + FindResponse response; + GetContext().GetIndex().ExecuteFind(response, request); + + if (response.GetSize() == 1) { - const std::list<std::string> childrenIds = targetPatient.childrenIds_; + const FindResponse::Resource& targetPatient = response.GetResourceByIndex(0); + + const std::set<std::string>& childrenIds = targetPatient.GetChildrenIdentifiers(ResourceType_Study); + bool targetPatientHasOtherStudies = childrenIds.size() > 1; if (childrenIds.size() == 1) { - targetPatientHasOtherStudies = std::find(childrenIds.begin(), childrenIds.end(), *studyId) == childrenIds.end(); // if the patient has one study that is not the one being modified + targetPatientHasOtherStudies = (childrenIds.find(*studyId) == childrenIds.end()); // if the patient has one study that is not the one being modified } if (targetPatientHasOtherStudies) { + DicomMap mainDicomTags; + targetPatient.GetMainDicomTags(mainDicomTags, ResourceType_Patient); + // this is allowed if all patient replacedTags do match the target patient tags DicomMap targetPatientTags; - targetPatient.GetMainDicomTags().ExtractPatientInformation(targetPatientTags); + mainDicomTags.ExtractPatientInformation(targetPatientTags); std::set<DicomTag> mainPatientTags; DicomMap::GetMainDicomTags(mainPatientTags, ResourceType_Patient);
--- a/OrthancServer/UnitTestsSources/ServerIndexTests.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/UnitTestsSources/ServerIndexTests.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -166,8 +166,9 @@ DicomTagConstraint c(tag, type, value, true, true); - std::vector<DatabaseConstraint> lookup; - lookup.push_back(c.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); + DatabaseConstraints lookup; + bool isEquivalent; // unused + lookup.AddConstraint(c.ConvertToDatabaseConstraint(isEquivalent, level, DicomTagType_Identifier)); std::set<std::string> noLabel; transaction_->ApplyLookupResources(result, NULL, lookup, level, noLabel, LabelsConstraint_All, 0 /* no limit */); @@ -185,10 +186,11 @@ DicomTagConstraint c1(tag, type1, value1, true, true); DicomTagConstraint c2(tag, type2, value2, true, true); - - std::vector<DatabaseConstraint> lookup; - lookup.push_back(c1.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); - lookup.push_back(c2.ConvertToDatabaseConstraint(level, DicomTagType_Identifier)); + + DatabaseConstraints lookup; + bool isEquivalent; // unused + lookup.AddConstraint(c1.ConvertToDatabaseConstraint(isEquivalent, level, DicomTagType_Identifier)); + lookup.AddConstraint(c2.ConvertToDatabaseConstraint(isEquivalent, level, DicomTagType_Identifier)); std::set<std::string> noLabel; transaction_->ApplyLookupResources(result, NULL, lookup, level, noLabel, LabelsConstraint_All, 0 /* no limit */);
--- a/OrthancServer/UnitTestsSources/VersionsTests.cpp Thu Sep 05 18:21:56 2024 +0200 +++ b/OrthancServer/UnitTestsSources/VersionsTests.cpp Thu Sep 05 18:52:27 2024 +0200 @@ -120,7 +120,7 @@ TEST(Versions, CurlStatic) { curl_version_info_data* v = curl_version_info(CURLVERSION_NOW); - ASSERT_STREQ("8.5.0", v->version); + ASSERT_STREQ("8.9.0", v->version); } TEST(Versions, PngStatic)
--- a/TODO Thu Sep 05 18:21:56 2024 +0200 +++ b/TODO Thu Sep 05 18:52:27 2024 +0200 @@ -29,11 +29,6 @@ * (1) Accept extra DICOM tags dictionaries in the DCMTK format '.dic' (easier to use than declare them in the Orthanc configuration file). Even the standard dictionaries could be overriden by these custom dictionaries. -* Provide more flexibility wrt Dicom TLS ciphers and TLS version: - https://groups.google.com/g/orthanc-users/c/X4IhmXCSr7I/m/EirawAFcBwAJ - Can maybe be achieved by adding a configuration to select the TLS Security Profile: - https://github.com/DCMTK/dcmtk/blob/master/dcmtls/include/dcmtk/dcmtls/tlsciphr.h#L83 - (e.g: TSP_Profile_BCP195_ND instead of TSP_Profile_BCP195) * Add configurations to enable/disable warnings: - Modifying an instance while keeping its original SOPInstanceUID: This should be avoided! - Modifying a study while keeping its original StudyInstanceUID: This should be avoided! @@ -41,6 +36,7 @@ https://discourse.orthanc-server.org/t/performance-issue-when-adding-a-lot-of-jobs-in-the-queue/3915/2 Note: that might also be the right time to have a central jobs registry when working with multiple Orthanc instances on the same DB. + Note: the json serialization of a job "content" can be very large -> compress it before saving it to DB ? * Right now, some Stable events never occurs (e.g. when Orthanc is restarted before the event is triggered). Since these events are used to e.g. generate dicom-web cache (or update it !), we should try to make sure these events always happen. @@ -71,7 +67,7 @@ * Write a getting started guide (step by step) for each platform to replace https://orthanc.uclouvain.be/book/users/cookbook.html : - Ubuntu/Debian - - Windows + - Windows (done) - OSX - Docker on Linux Each step by step guide should contain: @@ -153,7 +149,7 @@ https://groups.google.com/g/orthanc-users/c/hsZ1jng5rIg/m/8xZL2C1VBgAJ * add an "AutoDeleteIfSuccessful": false option when creating jobs https://discourse.orthanc-server.org/t/job-history-combined-with-auto-forwarding/3729/10 -* Allow skiping automatic conversion of color-space in transcoding/decoding. +* Allow skipping automatic conversion of color-space in transcoding/decoding. The patch that was initialy provided was breaking the IngestTranscoding. This might require a DCMTK decoding plugin ? https://discourse.orthanc-server.org/t/orthanc-convert-ybr-to-rgb-but-does-not-change-metadata/3533/9 @@ -191,6 +187,8 @@ progress callbacks available in DIMSE_moveUser https://groups.google.com/g/orthanc-users/c/c8cGnA7FzsE/m/BSs66D8wBwAJ * Log outgoing C-Find queries +* Support other Transfer Syntaxes in the Worklist plugin: + https://discourse.orthanc-server.org/t/could-you-please-create-an-option-to-set-the-transfer-syntax-in-the-worklist-plugin-currently-little-endian-explicit-is-fixed/4871 --------- Long-term