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|
## @file CMakeLists.txt
## @brief CMake build script for example programs
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
## Copyright (C) 2013-2018 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
## 3. University of Heidelberg, Heidelberg, Germany
##
## Copyright (C) 2009-2013 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
##
## Copyright (C) 2006-2008 by the California Institute of Technology,
## Pasadena, CA, USA
##
## Copyright (C) 2002-2005 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. Japan Science and Technology Agency, Japan
##
## This library 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. A copy of the license agreement is provided
## in the file named "LICENSE.txt" included with this software distribution
## and also available online as http://sbml.org/software/libsbml/license.html
## ------------------------------------------------------------------------ -->
find_package(Java COMPONENTS Development REQUIRED)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_BINARY_DIR} CURRENT_BIN)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_BINARY_DIR}/../../src/bindings/java/libsbmlj.jar CURRENT_JAR )
file(TO_NATIVE_PATH $<TARGET_FILE_DIR:binding_java_lib> LIBRARY_PATH)
if (JAVA_COMPATIBILITY)
SET(COMPAT_ARGS "-source ${JAVA_COMPATIBILITY} -target ${JAVA_COMPATIBILITY}")
endif()
foreach(file
addCustomValidator
addCVTerms
addingEvidenceCodes_1
addingEvidenceCodes_2
addModelHistory
appendAnnotation
callExternalValidator
convertSBML
createExampleSBML
echoSBML
evaluateMath
getAllElementsWithNotes
printAnnotation
printMath
printNotes
printRegisteredPackages
printSBML
printsupported
printUnits
promoteParameters
readSBML
stripPackage
setIdFromNames
translateMath
unsetAnnotation
unsetNotes
validateSBML
evaluateCustomMath
inlineInitialAssignments
replaceOneFD
)
file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/${file}.java CURRENT_FILE)
add_custom_command(
OUTPUT ${file}.class
COMMAND "${Java_JAVAC_EXECUTABLE}"
ARGS -cp ".${FILE_SEP}\"${CURRENT_JAR}\"${FILE_SEP}${CMAKE_CURRENT_SOURCE_DIR}"
${CURRENT_FILE}
${COMPAT_ARGS}
-d ${CMAKE_CURRENT_BINARY_DIR}
MAIN_DEPENDENCY "${CMAKE_CURRENT_SOURCE_DIR}/../../src/bindings/java/local.i"
WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${file}.java
COMMENT "Build java example ${file}"
)
add_custom_target(example_java_${file} ALL
DEPENDS
${CMAKE_CURRENT_BINARY_DIR}/${file}.class
SOURCES
${CMAKE_CURRENT_SOURCE_DIR}/${file}.java
)
add_dependencies(example_java_${file} binding_java_jar)
endforeach()
# run examples as test
add_test(NAME test_java_addCVTerms
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
addCVTerms
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
addCVTerms.out.xml
)
add_test(NAME test_java_addingEvidenceCodes_1
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
addingEvidenceCodes_1
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
addingEvidenceCodes_1.out.xml
)
add_test(NAME test_java_addingEvidenceCodes_2
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
addingEvidenceCodes_2
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
addingEvidenceCodes_2.out.xml
)
add_test(NAME test_java_addModelHistory
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
addModelHistory
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
addModelHistory.out.xml
)
add_test(NAME test_java_appendAnnotation
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
appendAnnotation
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
appendAnnotation.out.xml
)
add_test(NAME test_java_createExampleSBML
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
createExampleSBML
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
createExampleSBML.out.xml
)
add_test(NAME test_java_echoSBML
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
echoSBML
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
echoSBML.out.xml
)
add_test(NAME test_java_evaluateCustomMath
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
evaluateCustomMath
2*3+4
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_getAllElementsWithNotes
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
getAllElementsWithNotes
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_inlineInitialAssignments
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
inlineInitialAssignments
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
inlineInitialAssignments.out.xml
)
add_test(NAME test_java_printAnnotation
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printAnnotation
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_printMath
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printMath
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_printNotes
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printNotes
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_printRegisteredPackages
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printRegisteredPackages
)
add_test(NAME test_java_printSBML
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printSBML
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_printsupported
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printsupported
)
add_test(NAME test_java_printUnits
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
printUnits
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_promoteParameters
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
promoteParameters
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
promoteParameters.out.xml
)
add_test(NAME test_java_readSBML
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
readSBML
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
)
add_test(NAME test_java_replaceOneFD
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
replaceOneFD
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/functiondef.xml
f
reaction_1
replaceOneFD.out.xml
)
add_test(NAME test_java_setIdFromNames
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
setIdFromNames
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
setIdFromNames.out.xml
)
if(ENABLE_FBC)
add_test(NAME test_java_stripPackage
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
stripPackage
${CMAKE_SOURCE_DIR}/examples/sample-models/fbc/fbc_example1.xml
fbc
stripPackage.out.xml
)
endif(ENABLE_FBC)
add_test(NAME test_java_unsetAnnotation
COMMAND ${Java_JAVA_EXECUTABLE}
-cp ".${FILE_SEP}${CURRENT_JAR}${FILE_SEP}"
-Djava.library.path=$<TARGET_FILE_DIR:binding_java_lib>
unsetAnnotation
${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
unsetAnnotation.out.xml
)
|
