Release 1.4.0

qcscine · Aug 26, 2024 · 22e9dc8 · 22e9dc8
1 parent 3cb70af
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,17 @@
 Changelog
 =========
 
+Release 1.4.0
+-------------
+
+Changes (DB schema changing)
+ - Remove `MODEL_TRANSFORMATION` elementary step type
+
+Additions (backwards compatible):
+ - Exact type of stored integers in the database is checked before retrieval in case fields have been manipulated with other MongoDB applications
+ - Projection options are added to almost all internal database queries to reduce the bandwidth requirements.
+ - Added support for list-of-lists of integers as elements in value collections (calculation settings etc.).
+
 Release 1.3.0
 -------------
 
@@ -13,8 +24,12 @@ Changes (DB schema changing):
 
 Additions (backwards compatible):
  - Python package now includes pure Python code for more complex query utilities. This code is added in the modules
- `queries`, `energy_query_functions`, `compound_and_flask_creation`, `concentration_query_functions`, and `insert_concentration`.
- All of them are top level modules (`import scine_database.energy_query_functions`)
+    - `queries`
+    - `energy_query_functions`
+    - `compound_and_flask_creation`
+    - `concentration_query_functions`
+    - `insert_concentration`.
+   All of them are top level modules (`import scine_database.energy_query_functions`)
  - Added the possibility to configure the connection based on a custom URI instead of credentials.
 
 Release 1.2.0

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.9)
 
 project(Database
-  VERSION 1.3.0
+  VERSION 1.4.0
   DESCRIPTION "The SCINE database interface."
 )
 

diff --git a/README.rst b/README.rst
@@ -66,6 +66,13 @@ J. P. Unsleber, S. A. Grimmel, M. Reiher,
 "Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks",
 *J. Chem. Theory Comput.*, **2022**, *18*, 5393.
 
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
+
 Support and Contact
 -------------------
 

diff --git a/conanfile.py b/conanfile.py
@@ -10,7 +10,7 @@
 
 class ScineDatabaseConan(ScineConan):
     name = "scine_database"
-    version = "1.3.0"
+    version = "1.4.0"
     url = "https://github.com/qcscine/database"
     description = """
 The SCINE Database is a database wrapper for a MongoDB encoding reaction
@@ -48,7 +48,7 @@ class ScineDatabaseConan(ScineConan):
     requires = [
         "mongo-cxx-driver/3.6.0",
         "eigen/[~=3.3.7]",
-        "scine_utilities/9.0.0"
+        "scine_utilities/10.0.0"
     ]
     cmake_name = "Database"
     cmake_definitions = {

diff --git a/dev b/dev
diff --git a/src/Database/Database/Exceptions.h b/src/Database/Database/Exceptions.h
@@ -25,6 +25,17 @@ class DuplicateIDException : public std::exception {
   }
 };
 
+/**
+ * @class SelfDuplicateException
+ * @brief An exception to throw if a given structure is a duplicate of itself.
+ */
+class SelfDuplicateException : public std::exception {
+ public:
+  const char* what() const throw() {
+    return "The given structure is a duplicate of itself. This cannot be.";
+  }
+};
+
 /**
  * @class MissingCredentialsException
  * @brief An exception to throw if no credentials are present to establish a connection to a database.

diff --git a/src/Database/Database/Layout.cpp b/src/Database/Database/Layout.cpp
@@ -45,13 +45,11 @@ const std::map<CalculationStatus, std::string> EnumMaps::status2str = {
 // clang-format off
 const std::map<std::string, ElementaryStepType> EnumMaps::str2estype = {
   {"regular", ElementaryStepType::REGULAR},
-  {"barrierless", ElementaryStepType::BARRIERLESS},
-  {"model_transformation", ElementaryStepType::MODEL_TRANSFORMATION}
+  {"barrierless", ElementaryStepType::BARRIERLESS}
 };
 const std::map<ElementaryStepType, std::string> EnumMaps::estype2str = {
   {ElementaryStepType::REGULAR, "regular"},
-  {ElementaryStepType::BARRIERLESS, "barrierless"},
-  {ElementaryStepType::MODEL_TRANSFORMATION, "model_transformation"}
+  {ElementaryStepType::BARRIERLESS, "barrierless"}
 };
 // clang-format on
 

diff --git a/src/Database/Database/Layout.h b/src/Database/Database/Layout.h
@@ -57,7 +57,7 @@ enum class StructureLabel : unsigned {
   SCAN_OBSERVER = 107,
 };
 
-enum class ElementaryStepType : unsigned { REGULAR = 0, BARRIERLESS = 1, MODEL_TRANSFORMATION = 2 };
+enum class ElementaryStepType : unsigned { REGULAR = 0, BARRIERLESS = 1 };
 
 namespace Layout {
 

diff --git a/src/Database/Database/Manager.cpp b/src/Database/Database/Manager.cpp
@@ -13,14 +13,14 @@
 #include "Database/Objects/Calculation.h"
 #include "Database/Objects/Compound.h"
 #include "Database/Objects/ElementaryStep.h"
+#include "Database/Objects/Impl/Fields.h"
 #include "Database/Objects/Property.h"
 #include "Database/Objects/Reaction.h"
 #include "Database/Objects/Structure.h"
 #include "Database/Version.h"
 /* External Includes */
 #include <bsoncxx/builder/stream/document.hpp>
 #include <cassert>
-#include <iostream>
 #include <mongocxx/client.hpp>
 #include <mongocxx/collection.hpp>
 #include <mongocxx/database.hpp>
@@ -200,9 +200,10 @@ std::tuple<int, int, int> Manager::getDBVersion() {
   if (!optional)
     return {0, 0, 0};
   auto view = optional.value().view();
-  int major = view["version"]["major"].get_int32();
-  int minor = view["version"]["minor"].get_int32();
-  int patch = view["version"]["patch"].get_int32();
+  auto versionView = view["version"];
+  const int major = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["major"]);
+  const int minor = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["minor"]);
+  const int patch = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["patch"]);
   return {major, minor, patch};
 }
 void Manager::init(bool moreIndices) {

diff --git a/src/Database/Database/Objects/Calculation.cpp b/src/Database/Database/Objects/Calculation.cpp
@@ -144,7 +144,7 @@ Calculation::Job Calculation::getJob() const {
   Calculation::Job job("dummy");
   job.order = jobDoc["order"].get_utf8().value.to_string();
   job.memory = jobDoc["memory"].get_double();
-  job.cores = jobDoc["cores"].get_int32();
+  job.cores = Fields::getInteger<int>(jobDoc, "cores");
   job.disk = jobDoc["disk"].get_double();
   return job;
 }
@@ -167,7 +167,9 @@ void Calculation::setJob(const Calculation::Job& job) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*=========*
@@ -201,7 +203,9 @@ void Calculation::addStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::removeStructure(const ID& id) const {
@@ -219,7 +223,9 @@ void Calculation::removeStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 bool Calculation::hasStructure(const ID& id) const {
@@ -275,7 +281,9 @@ void Calculation::setSetting(const std::string& key, const Utils::UniversalSetti
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Utils::UniversalSettings::GenericValue Calculation::getSetting(const std::string& key) const {
@@ -319,7 +327,9 @@ void Calculation::removeSetting(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearSettings() const {
@@ -337,7 +347,9 @@ void Calculation::clearSettings() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Utils::UniversalSettings::ValueCollection Calculation::getSettings() const {
@@ -372,7 +384,9 @@ void Calculation::setSettings(const Utils::UniversalSettings::ValueCollection& s
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*===========*
@@ -410,7 +424,9 @@ void Calculation::setResults(Calculation::Results& results) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearResults() const {
@@ -435,7 +451,9 @@ void Calculation::clearResults() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Calculation::Results Calculation::getResults() const {
@@ -487,7 +505,9 @@ void Calculation::setAuxiliary(std::string key, const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 ID Calculation::getAuxiliary(std::string key) const {
@@ -531,7 +551,9 @@ void Calculation::removeAuxiliary(std::string key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::setAuxiliaries(std::map<std::string, ID> auxiliaries) const {
@@ -553,7 +575,9 @@ void Calculation::setAuxiliaries(std::map<std::string, ID> auxiliaries) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearAuxiliaries() const {
@@ -571,7 +595,9 @@ void Calculation::clearAuxiliaries() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, ID> Calculation::getAuxiliaries() const {
@@ -615,7 +641,9 @@ void Calculation::setRestartInformation(const std::string& key, const ID& id) co
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 ID Calculation::getRestartInformation(const std::string& key) const {
@@ -659,7 +687,9 @@ void Calculation::removeRestartInformation(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::setRestartInformation(const std::map<std::string, ID>& restart_information) const {
@@ -681,7 +711,9 @@ void Calculation::setRestartInformation(const std::map<std::string, ID>& restart
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearRestartInformation() const {
@@ -699,7 +731,9 @@ void Calculation::clearRestartInformation() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, ID> Calculation::getRestartInformation() const {