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# --------------------------------------------------------------------------
# OpenMS -- Open-Source Mass Spectrometry
# --------------------------------------------------------------------------
# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
# ETH Zurich, and Freie Universitaet Berlin 2002-2012.
#
# This software is released under a three-clause BSD license:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of any author or any participating institution
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
# For a full list of authors, refer to the file AUTHORS.
# --------------------------------------------------------------------------
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# --------------------------------------------------------------------------
# $Maintainer: Stephan Aiche $
# $Authors: Stephan Aiche $
# --------------------------------------------------------------------------
# path were the CTDs will be stored
set(KNIME_PLUGIN_DIRECTORY ${PROJECT_BINARY_DIR}/ctds CACHE PATH "Directory containing the generated plugin-sources for the OpenMS KNIME package")
set(CTD_PATH ${KNIME_PLUGIN_DIRECTORY}/descriptors)
# path were the executables can be found
set(TOPP_BIN_PATH ${OPENMS_BINARY_DIR})
if(WIN32)
set(TOPP_BIN_PATH ${OPENMS_BINARY_DIR}/$(ConfigurationName))
endif()
# payload paths
set(PAYLOAD_PATH ${KNIME_PLUGIN_DIRECTORY}/payload)
set(PAYLOAD_BIN_PATH ${PAYLOAD_PATH}/bin)
set(PAYLOAD_LIB_PATH ${PAYLOAD_PATH}/lib)
set(PAYLOAD_SHARE_PATH ${PAYLOAD_PATH}/share)
# script directory
set(SCRIPT_DIRECTORY ${PROJECT_SOURCE_DIR}/cmake/knime/)
set(ARCH "")
if(OPENMS_64BIT_ARCHITECTURE)
set(ARCH "64")
else()
set(ARCH "32")
endif()
set(PLATFORM "")
if (APPLE)
set(PLATFORM "mac")
elseif(WIN32)
set(PLATFORM "win")
else()
set(PLATFORM "lnx")
endif()
##
function(remove_parameter_from_ctd toolname param)
set(FILE_CONTENT "")
file(READ ${CTD_PATH}/${toolname}.ctd FILE_CONTENT)
foreach(LINE ${FILE_CONTENT})
message(STATUS ${FILE})
endforeach()
endfunction()
# create the target directory
file(MAKE_DIRECTORY ${KNIME_PLUGIN_DIRECTORY})
add_custom_target(
configure_plugin_properties
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -D SOURCE_PATH=${PROJECT_SOURCE_DIR} -D TARGET_PATH=${KNIME_PLUGIN_DIRECTORY} -D OPENMS_VERSION=${CF_OPENMS_PACKAGE_VERSION} -P ${SCRIPT_DIRECTORY}configure_plugin_properties.cmake
)
# copy the icons
file(COPY ${PROJECT_SOURCE_DIR}/cmake/knime/icons
DESTINATION ${KNIME_PLUGIN_DIRECTORY}
PATTERN ".svn" EXCLUDE)
# list of all tools that can generate CTDs
set(CTD_executables ${TOPP_executables} ${UTILS_executables})
# remove tools that do not produce CTDs
list(REMOVE_ITEM CTD_executables PhosphoScoring OpenMSInfo FuzzyDiff GenericWrapper InspectAdapter MascotAdapter PILISIdentification PILISModelCV PILISModelTrainer PILISSpectraGenerator SvmTheoreticalSpectrumGeneratorTrainer OpenSwathMzMLFileCacher PepNovoAdapter)
# pseudo-ctd target
add_custom_target(
create_ctds
# we first create the directory to make sure that the remove command does not fail
COMMAND ${CMAKE_COMMAND} -E make_directory ${CTD_PATH}
COMMAND ${CMAKE_COMMAND} -E remove_directory ${CTD_PATH}
COMMAND ${CMAKE_COMMAND} -E make_directory ${CTD_PATH}
DEPENDS TOPP UTILS
)
# call the tools
foreach(TOOL ${CTD_executables})
add_custom_command(
TARGET create_ctds POST_BUILD
COMMAND ${TOPP_BIN_PATH}/${TOOL} -write_ctd ${CTD_PATH}
)
endforeach()
# remove those parts of the CTDs we cannot model in KNIME
add_custom_target(
final_ctds
# OMSSAAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=OMSSAAdapter -DPARAM=omssa_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# XTandemAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=XTandemAdapter -DPARAM=xtandem_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=XTandemAdapter -DPARAM=default_input_file -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# IDPosteriorErrorProbability
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=IDPosteriorErrorProbability -DPARAM=output_name -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# MyriMatchAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=MyriMatchAdapter -DPARAM=myrimatch_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
DEPENDS create_ctds
)
# create final target that collects all sub-calls
add_custom_target(
prepare_knime_descriptors
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/cmake/knime/mimetypes.xml ${CTD_PATH}
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/cmake/knime/mime.types ${CTD_PATH}
DEPENDS final_ctds
)
add_custom_target(
prepare_knime_payload_binaries
# 1st create the directory to make sure that the remove_directory does not fail
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_PATH}
COMMAND ${CMAKE_COMMAND} -E remove_directory ${PAYLOAD_PATH}
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_PATH}
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_BIN_PATH}
DEPENDS TOPP UTILS
)
add_custom_target(
create_payload_share
# 1st create the directory to make sure that the remove_directory does not fail
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_SHARE_PATH}
# remove old directory
COMMAND ${CMAKE_COMMAND} -E remove_directory ${PAYLOAD_SHARE_PATH}
# create new one and fill with the appropriate content
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_SHARE_PATH}
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -D SOURCE_PATH=${PROJECT_SOURCE_DIR} -D TARGET_DIRECTORY=${PAYLOAD_SHARE_PATH} -P ${SCRIPT_DIRECTORY}copy_share.cmake
DEPENDS prepare_knime_payload_binaries
)
# copy the binaries
foreach(TOOL ${CTD_executables})
set(tool_path ${TOPP_BIN_PATH}/${TOOL})
if(WIN32)
set(tool_path "${tool_path}.exe")
endif()
add_custom_command(
TARGET prepare_knime_payload_binaries POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy ${tool_path} "${PAYLOAD_BIN_PATH}/"
)
endforeach()
add_custom_target(
prepare_knime_payload_libs
# 1st create the directory to make sure that the remove_directory does not fail
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E remove_directory ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E make_directory ${PAYLOAD_LIB_PATH}
# we need the binaries to determine what libraries we need
DEPENDS prepare_knime_payload_binaries
)
# assemble the libraries, this differs drastically between the different platforms
if (APPLE)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${PROJECT_SOURCE_DIR}/cmake/MacOSX/fix_dependencies.rb -l ${PAYLOAD_LIB_PATH} -b ${PAYLOAD_BIN_PATH}
)
elseif(WIN32)
# assemble required libraries for win32
# OpenMS, OpenMS_GUI, OpenSWATHAlgo, Qt, xerces
get_target_property(WIN32_DLLLOCATION OpenMS LOCATION)
get_filename_component(WIN32_DLLPATH ${WIN32_DLLLOCATION} PATH)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy ${WIN32_DLLPATH}/OpenMS.dll ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E copy ${WIN32_DLLPATH}/OpenMS_GUI.dll ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E copy ${WIN32_DLLPATH}/OpenSwathAlgo.dll ${PAYLOAD_LIB_PATH}
)
function(copy_library lib target_path)
string(REGEX REPLACE "lib$" "dll" target_dll "${lib}")
file(TO_NATIVE_PATH "${target_dll}" target_native)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy "${target_native}" "${target_path}"
)
endfunction()
set(QT_PAYLOAD_LIBS "QTCORE;QTGUI;QTNETWORK;QTOPENGL;QTSQL;QTSVG;QTWEBKIT;PHONON")
foreach(QT_PAYLOAD_LIB ${QT_PAYLOAD_LIBS})
set(target_lib "${QT_${QT_PAYLOAD_LIB}_LIBRARY_RELEASE}")
copy_library(${target_lib} ${PAYLOAD_LIB_PATH})
endforeach()
# xerces
set(target_lib)
get_filename_component(xerces_path ${CONTRIB_XERCESC_OPT} PATH)
file(TO_NATIVE_PATH "${xerces_path}/xerces-c_3_1.dll" target_native)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy "${target_native}" "${PAYLOAD_LIB_PATH}"
)
else()
# assemble required libraries for lnx
set(QT_PAYLOAD_LIBS "QTCORE;QTGUI;QTNETWORK;QTOPENGL;QTSQL;QTSVG;QTWEBKIT;PHONON")
foreach(QT_PAYLOAD_LIB ${QT_PAYLOAD_LIBS})
if(NOT "${QT_${QT_PAYLOAD_LIB}_LIBRARY_RELEASE}" STREQUAL "QT_${QT_PAYLOAD_LIB}_LIBRARY_RELEASE-NOTFOUND")
set(target_lib "${QT_${QT_PAYLOAD_LIB}_LIBRARY_RELEASE}")
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy "${target_lib}" "${PAYLOAD_LIB_PATH}"
)
endif()
endforeach()
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_BINARY_DIR}/lib/libOpenMS.so ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_BINARY_DIR}/lib/libOpenMS_GUI.so ${PAYLOAD_LIB_PATH}
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_BINARY_DIR}/lib/libOpenSwathAlgo.so ${PAYLOAD_LIB_PATH}
)
endif()
# handle the binaries.ini
add_custom_target(
prepare_knime_payload_ini
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -D ARCH=${ARCH} -D PLATFORM=${PLATFORM} -D TARGET_DIR=${PAYLOAD_PATH} -D TEMPLATE_FOLDER=${SCRIPT_DIRECTORY} -P ${SCRIPT_DIRECTORY}copy_binaries_ini.cmake
DEPENDS prepare_knime_payload_binaries
)
# check if we have valid search engines
if(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY})
message(FATAL_ERROR "Please specify the path to the search engines to build the KNIME packages. Call cmake -D SEARCH_ENGINES_DIRECTORY=<Path-To-Checkedout-SE> .")
elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/OMSSA OR NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/OMSSA)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout. Please check use the one from the SVN.")
elseif(NOT APPLE AND NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/MyriMatch)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout. Please check use the one from the SVN.")
endif()
add_custom_target(
prepare_knime_payload_searchengines
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -D SE_PATH=${SEARCH_ENGINES_DIRECTORY} -D TARGET_DIRECTORY=${PAYLOAD_BIN_PATH} -P ${SCRIPT_DIRECTORY}copy_searchengines.cmake
# We need the folder layout from the bin target
DEPENDS prepare_knime_payload_binaries
)
# the complete payload target
add_custom_target(
prepare_knime_payload
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -D ARCH=${ARCH} -D PLATFORM=${PLATFORM} -D PAYLOAD_FOLDER=${PAYLOAD_PATH} -P ${SCRIPT_DIRECTORY}compress_payload.cmake
DEPENDS prepare_knime_payload_binaries prepare_knime_payload_libs create_payload_share prepare_knime_payload_ini prepare_knime_payload_searchengines
)
add_custom_target(
prepare_meta_information
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/cmake/knime/LICENSE ${KNIME_PLUGIN_DIRECTORY}/
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/cmake/knime/COPYRIGHT ${KNIME_PLUGIN_DIRECTORY}/
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/cmake/knime/DESCRIPTION ${KNIME_PLUGIN_DIRECTORY}/
)
add_custom_target(
prepare_knime_package
DEPENDS prepare_meta_information configure_plugin_properties prepare_knime_descriptors prepare_knime_payload
)
|
