v0.1.0, get (JSON string) and save ThermoDataSet to file (#1)

* v0.1.0, get (JSON string) and save ThermoDataSet to file

.gitignore

@@ -27,6 +27,14 @@
 *.lib
 
 # Executables
-*.exe
+#*.exe
 *.out
 *.app
+
+.vscode
+
+# Build
+build/
+
+*.ipynb*
+environment.yml

.travis.yml

@@ -0,0 +1,18 @@
+language: cpp
+
+os:
+  - linux
+  - osx
+
+cache:
+  directories:
+    - $HOME/miniconda
+
+install:
+  - bash ci/travis/install.sh
+
+script:
+  - bash ci/travis/test.sh
+
+before_cache:
+  - rm -f $HOME/miniconda/envs/thermofun/conda-meta/history*  # Delete these history files to prevent a new cache upload step.

CMakeLists.txt

@@ -0,0 +1,82 @@
+# Require a certain version of cmake
+cmake_minimum_required(VERSION 3.0)
+
+# Set the name of the project
+project(ThermoHubClient VERSION 0.1.0 LANGUAGES CXX)
+
+# Set the cmake module path of the project
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
+
+# Use ccache to speed up repeated compilations
+include(CCache)
+
+# Define variables with the GNU standard installation directories
+include(GNUInstallDirs)
+
+# Ensure proper configuration if in a conda environment
+include(CondaAware)
+
+# Define which types of libraries to build
+option(THERMOHUBCLIENT_BUILD_SHARED_LIBS "Build shared libraries." ON)
+option(THERMOHUBCLIENT_BUILD_SHARED_LIBS "Build static libraries." ON)
+option(THERMOHUBCLIENT_BUILD_PYTHON "Build the python wrappers and python package thermohubclient." ON)
+#option(REFRESH_THIRDPARTY "Refresh thirdparty libraries." OFF)
+
+# Modify the HUBCLIENT_BUILD_* variables accordingly to BUILD_ALL
+if(THERMOHUBCLIENT_BUILD_ALL MATCHES ON)
+    set(THERMOHUBCLIENT_BUILD_SHARED_LIBS          ON)
+    set(THERMOHUBCLIENT_BUILD_STATIC_LIBS          ON)
+    set(THERMOHUBCLIENT_BUILD_PYTHON               ON)
+endif()
+
+# Set the default build type to Release
+if(NOT CMAKE_BUILD_TYPE)
+    # The build type selection for the project
+    set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the build type for ${PROJECT_NAME}." FORCE)
+    # The build type options for the project
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS Debug Release MinSizeRel RelWithDebInfo)
+endif()
+
+# Define if shared library should be build instead of static.
+option(BUILD_SHARED_LIBS "Build shared libraries." ON)
+
+# Set libraries to be compiled with position independent code mode (i.e., fPIC option in GNU compilers)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# Set the C++ standard
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Set the list of compiler flags for MSVC compiler
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
+    add_compile_options(
+        /D_SCL_SECURE_NO_WARNINGS
+        /D_CRT_SECURE_NO_WARNINGS=1
+        /MP4
+        /EHsc
+        /D_SILENCE_TR1_NAMESPACE_DEPRECATION_WARNING
+        /DNOMINMAX
+    )
+endif()
+
+# Set the ThermoHubClient source directory path
+set(THERMOHUBCLIENT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/ThermoHubClient)
+
+# Set the include directories
+include_directories(${THERMOHUBCLIENT_SOURCE_DIR})
+
+# Find all ThermoHubClient dependencies
+include(ThermoHubClientFindDeps)
+
+# Build ThermoHubClient library
+add_subdirectory(ThermoHubClient)
+
+# Build python wraper
+if(THERMOHUBCLIENT_BUILD_PYTHON)
+    add_subdirectory(python)
+else()
+#    add_subdirectory(python EXCLUDE_FROM_ALL)
+endif()
+
+# Install the cmake config files that permit users to use find_package(ThermoHubClient)
+include(ThermoHubClientInstallCMakeConfigFiles)

ThermoHubClient/AqlQueries.h

@@ -0,0 +1,128 @@
+// Copyright (C) 2019 G. Dan Miron
+// 
+// thermohubclient is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+// 
+// thermohubclient 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 Lesser General Public License for more details.
+// 
+// You should have received a copy of the GNU Lesser General Public License
+// along with thermohubclient. If not, see <http://www.gnu.org/licenses/>.
+
+#include <string>
+
+namespace ThermoHubClient
+{
+const std::string aql_thermofun_database_from_thermodataset =   
+"/* clean the result with vs code \n "
+"replace ^.*null.*,$\n with empty \n "
+" \n "
+"replace ,\n^.*null.*$\n with \n \n "
+" \n "
+"*/ \n "
+" \n "
+"// Query works only for GEM and GEM-LMA ThermoDataSet traversing on edge pulls \n "
+" \n "
+"/* Get Elements */ \n "
+"LET elements_ = ( \n "
+"   FOR v,e IN 1..1 INBOUND @idThermoDataSet basis \n "
+"        FILTER v._label == 'element' \n "
+"        LET references_ = ( \n "
+"            FOR rf IN 1..1 OUTBOUND v citing \n "
+"            RETURN rf.properties.shortname // substances_[*][*].id \n "
+"        )  \n "
+"        RETURN { \n "
+"            symbol: v.properties.symbol, \n "
+"            class_:   v.properties.class_, \n "
+"            entropy : v.properties.entropy, \n "
+"            atomic_mass : v.properties.atomic_mass, \n "
+"            datasources : v.properties.datasources \n "
+"//            _label : 'element' \n "
+"        } \n "
+") \n "
+"/* Get Substances */ \n "
+"LET substances_ = ( \n "
+"   FOR s,e IN 1..1 INBOUND @idThermoDataSet pulls \n "
+"        FILTER s._label == 'substance' \n "
+"        LET reaction_symbol = ( \n "
+"            FOR r IN 1..1 INBOUND s defines \n "
+"            RETURN r.properties.symbol \n "
+"        ) \n "
+"        LET references_ = ( \n "
+"            FOR rf IN 1..1 OUTBOUND s citing \n "
+"            RETURN rf.properties.shortname // substances_[*][*].id \n "
+"        ) \n "
+"        RETURN { \n "
+"            name:   s.properties.name, \n "
+"            symbol: s.properties.symbol, \n "
+"            formula:    s.properties.formula, \n "
+"            formula_charge: s.properties.formula_charge, \n "
+"            reaction : reaction_symbol[0], \n "
+"//            mass_per_mole:  s.properties.mass_per_mole, \n "
+"            aggregate_state:    s.properties.aggregate_state, \n "
+"            class_:    s.properties.class_, \n "
+"            limitsTP:   s.properties.limitsTP, \n "
+"            Tst:    s.properties.Tst, \n "
+"            Pst:    s.properties.Pst, \n "
+"            TPMethods:  s.properties.TPMethods, \n "
+"            sm_heat_capacity_p: s.properties.sm_heat_capacity_p, \n "
+"            sm_gibbs_energy:    s.properties.sm_gibbs_energy, \n "
+"            sm_enthalpy:    s.properties.sm_enthalpy, \n "
+"            sm_entropy_abs: s.properties.sm_entropy_abs, \n "
+"            sm_volume:  s.properties.sm_volume, \n "
+"            m_compressibility: s.properties.m_compressibility, \n "
+"            m_expansivity: s.properties.m_expansivity, \n "
+"            datasources : s.properties.datasources \n "
+"//            _label : 'substance' \n "
+"//            id: s._id \n "
+"        } \n "
+") \n "
+"/* Get Reactions */ \n "
+"LET reactions_ = ( \n "
+"   FOR s,e IN 1..1 INBOUND @idThermoDataSet pulls \n "
+"        FILTER s._label == 'substance' \n "
+"        FOR r IN 1..1 INBOUND s defines \n "
+"        LET reactants_ = ( \n "
+"            FOR ss, t IN 1..1 INBOUND r takes \n "
+"/*            LET ids_2 = PUSH(ids_, ss._id, true) /* add substance id to idlist */ \n "
+"            RETURN { \n "
+"                symbol: ss.properties.symbol, \n "
+"                coefficient: t.properties.stoi_coeff \n "
+"//                id: ss._id \n "
+"            } \n "
+"        ) \n "
+"        LET references_ = ( \n "
+"            FOR rf IN 1..1 OUTBOUND r citing \n "
+"            RETURN rf.properties.shortname // substances_[*][*].id \n "
+"        ) \n "
+"        RETURN { \n "
+"//            name:   r.properties.name, \n "
+"            symbol: r.properties.symbol, \n "
+"//            substance : s.properties.symbol, \n "
+"            equation:    r.properties.equation, \n "
+"            reactants: reactants_, \n "
+"            limitsTP:   r.properties.limitsTP, \n "
+"            Tst:    r.properties.Tst, \n "
+"            Pst:    r.properties.Pst, \n "
+"            TPMethods:  r.properties.TPMethods, \n "
+"            logKr : r.properties.logKr, \n "
+"            drsm_heat_capacity_p : r.properties.drsm_heat_capacity_p, \n "
+"            drsm_gibbs_energy : r.properties.drsm_gibbs_energy, \n "
+"            drsm_enthalpy : r.properties.drsm_enthalpy, \n "
+"            drsm_entropy : r.properties.drsm_entropy, \n "
+"            drsm_volume : r.properties.drsm_volume, \n "
+"            datasources : r.properties.datasources \n "
+"//            _label : 'reaction' \n "
+"//            id: r._id \n "
+"        } \n "
+") \n "
+"//LET data_ = (APPEND(SORTED_UNIQUE(FLATTEN(substances_,1)), SORTED_UNIQUE(FLATTEN(reactions_,1)), true) ) \n "
+"//RETURN {result : APPEND(data_, SORTED_UNIQUE(FLATTEN(elements_,1)), true) } \n "
+"RETURN { thermodataset : 'cemdata18', datasources : ['db.thermohub.org','[2014THO/HUM]', '[2019LOT/KUL]', 'https://www.empa.ch/web/s308/thermodynamic-data'], date : DATE_FORMAT(DATE_NOW(), '%dd.%mm.%yyyy %hh:%ii:%ss'),  \n "
+"          substances : SORTED_UNIQUE(FLATTEN(substances_,1)), reactions : SORTED_UNIQUE(FLATTEN(reactions_,1)), elements : SORTED_UNIQUE(FLATTEN(elements_,1))} \n ";
+
+}

ThermoHubClient/CMakeLists.txt

@@ -0,0 +1,81 @@
+# Recursively collect all header files from the current directory
+file(GLOB_RECURSE HEADER_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.hpp *.h)
+
+# Recursively collect all source files from the current directory
+file(GLOB_RECURSE SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
+
+# The name of the shared and static libraries
+set(THERMOHUBCLIENT_SHARED_LIB ${PROJECT_NAME}${SUFFIX_SHARED_LIBS})
+set(THERMOHUBCLIENT_STATIC_LIB ${PROJECT_NAME}${SUFFIX_STATIC_LIBS})
+
+# Set the list of names of the third-party targets and libraries
+# set(THIRDPARTY_LIBS jsonio boost_regex boost_filesystem curl velocypack)
+
+# Enable automatic creation of a module definition (.def) file for a SHARED library on Windows.
+set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+
+# Build a ThermoHubClient C++ library
+add_library(ThermoHubClient ${HEADER_FILES} ${SOURCE_FILES})
+
+# Add an alias ThermoHubClient::ThermoHubClient to the target library ThermoHubClient
+add_library(ThermoHubClient::ThermoHubClient ALIAS ThermoHubClient)
+
+# Add the include paths to the ThermoHubClient target
+target_include_directories(ThermoHubClient
+    PUBLIC
+        $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}>
+        $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+
+# Link ThermoHubClient library against external dependencies
+target_link_libraries(ThermoHubClient
+    PRIVATE ${THIRDPARTY_LIBS}
+#    PUBLIC ThermoFun::ThermoFun
+    PUBLIC jsonarango
+    PUBLIC velocypack
+    PUBLIC Boost::regex
+    )
+
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
+# Link ThermoHubClient library against external (linked in static jsonarango) dependencies
+target_link_libraries(ThermoHubClient
+    PUBLIC libcurl
+    )
+else()
+target_link_libraries(ThermoHubClient
+    PUBLIC curl
+    )
+endif()
+
+# Set compilation features to be propagated to dependent codes.
+# target_compile_features(ThermoHubClient PUBLIC cxx_std_17)
+
+# Set some target properties
+set_target_properties(ThermoHubClient PROPERTIES
+    POSITION_INDEPENDENT_CODE ON
+    CXX_EXTENSIONS OFF)
+
+# Install ThermoHubClient C++ library
+install(TARGETS ThermoHubClient
+    EXPORT ThermoHubClientTargets
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT libraries)
+
+# Install debug symbols
+ if(MSVC)
+     install(
+         FILES $<TARGET_PDB_FILE:ThermoHubClient>
+         DESTINATION ${CMAKE_INSTALL_BINDIR}
+         COMPONENT libraries
+         OPTIONAL
+     )
+ endif()
+
+# Install ThermoHubClient header files
+install(DIRECTORY ${PROJECT_SOURCE_DIR}/ThermoHubClient
+    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT headers
+    FILES_MATCHING PATTERN "*.hpp" PATTERN "*.h")
+
+# Install deps header files
+#install(DIRECTORY ${PROJECT_SOURCE_DIR}/ThermoHubClient/deps
+#    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/ThermoHubClient COMPONENT headers)