/
knime_package_support.cmake
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/
knime_package_support.cmake
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# --------------------------------------------------------------------------
# OpenMS -- Open-Source Mass Spectrometry
# --------------------------------------------------------------------------
# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
# ETH Zurich, and Freie Universitaet Berlin 2002-2018.
#
# 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.
#
# --------------------------------------------------------------------------
# $Maintainer: Julianus Pfeuffer$
# $Authors: Stephan Aiche, Julianus Pfeuffer$
# --------------------------------------------------------------------------
# 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 where the executables can be found
if(CMAKE_CONFIGURATION_TYPES)
set(TOPP_BIN_PATH ${OPENMS_BINARY_DIR}/${CMAKE_CFG_INTDIR})
else()
set(TOPP_BIN_PATH ${OPENMS_BINARY_DIR})
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)
# Find Qt5 includes for KNIME packaging
find_package(Qt5 COMPONENTS ${OpenMS_QT_COMPONENTS} REQUIRED)
get_target_property(QT_QMAKE_EXECUTABLE Qt5::qmake IMPORTED_LOCATION)
exec_program(${QT_QMAKE_EXECUTABLE} ARGS "-query QT_INSTALL_LIBS" OUTPUT_VARIABLE QT_INSTALL_LIBS)
exec_program(${QT_QMAKE_EXECUTABLE} ARGS "-query QT_INSTALL_BINS" OUTPUT_VARIABLE QT_INSTALL_BINS)
# script directory
set(SCRIPT_DIRECTORY ${PROJECT_SOURCE_DIR}/cmake/knime/)
# variables for the scripts
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()
# 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 (at configure time??)
file(COPY ${PROJECT_SOURCE_DIR}/cmake/knime/icons
DESTINATION ${KNIME_PLUGIN_DIRECTORY}
PATTERN ".git" EXCLUDE)
# list of all tools that can generate CTDs and do not include GUI libraries
set(CTD_executables ${TOPP_TOOLS} ${UTILS_TOOLS})
# remove tools that do not produce CTDs or should not be shipped (because of dependencies or specifics that can not be resolved in KNIME)
list(REMOVE_ITEM CTD_executables OpenMSInfo ExecutePipeline INIUpdater ImageCreator GenericWrapper InspectAdapter MascotAdapter 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 to write ctds
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 or do not want to model in KNIME
# e.g. paths to executables that we ship and whose directories are in path environment
add_custom_target(
final_ctds
# MaRaClusterAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=MaRaClusterAdapter -DPARAM=maracluster_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# 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
# CruxAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=CruxAdapter -DPARAM=crux_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
# 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
# MSGFPlusAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=MSGFPlusAdapter -DPARAM=executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# LuciPhorAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=LuciphorAdapter -DPARAM=executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# CometAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=CometAdapter -DPARAM=comet_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# PercolatorAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=PercolatorAdapter -DPARAM=percolator_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# SiriusAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=SiriusAdapter -DPARAM=executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
# FidoAdapter
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=FidoAdapter -DPARAM=fido_executable -D CTD_PATH=${CTD_PATH} -P ${SCRIPT_DIRECTORY}remove_parameter_from_ctd.cmake
COMMAND ${CMAKE_COMMAND} -D SCRIPT_DIR=${SCRIPT_DIRECTORY} -DTOOLNAME=FidoAdapter -DPARAM=fidocp_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}${CMAKE_EXECUTABLE_SUFFIX})
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
if (APPLE) ## On APPLE use our script because the executables need to be relinked
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 common required libraries for win and lnx
## Note that we do not need the QT plugins or QTGui libraries since we do not include GUI tools here.
foreach (KNIME_TOOLS_DEPENDENCY OpenMS OpenSwathAlgo SuperHirn)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:${KNIME_TOOLS_DEPENDENCY}> ${PAYLOAD_LIB_PATH}
)
endforeach()
foreach (KNIME_TOOLS_QT5_DEPENDENCY ${OpenMS_QT_COMPONENTS})
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:Qt5::${KNIME_TOOLS_QT5_DEPENDENCY}> ${PAYLOAD_LIB_PATH}
)
endforeach()
else()
foreach (KNIME_DEPENDENCY OpenMS OpenSwathAlgo SuperHirn)
add_custom_command(
TARGET prepare_knime_payload_libs POST_BUILD
COMMAND ${CMAKE_COMMAND} -V -DDEPS="$<TARGET_FILE:${KNIME_DEPENDENCY}>" -DTARGET="${PAYLOAD_LIB_PATH}" -DLOOKUP_DIRS="${OPENMS_CONTRIB_LIBS}/lib\;${QT_INSTALL_BINS}\;${QT_INSTALL_LIBS}" -P ${SCRIPT_DIRECTORY}knime_copy_deps.cmake
)
endforeach()
endif()
if(WIN32) ## Add dynamic libraries if you linked to them.
## TODO Check how we can auto-determine which are static and dynamic and only install dynamic ones here.
## For now we got rid of dynamic libs on Win (except for QT above).
## TODO if we update our modules we can use properties of the imported targets.
#add_custom_command(
# TARGET prepare_knime_payload_libs POST_BUILD
# COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:XercesC::XercesC> ${PAYLOAD_LIB_PATH}
# COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:SQLite::sqlite_shared> ${PAYLOAD_LIB_PATH}
# )
## If you need to install dynamic libs use the following snippets:
# Caution: The ..._LIBRARY variables from the find packages might point to the *.lib files
# instead of the *.dlls
# xerces-c
# get_filename_component(xerces_path "${XercesC_LIBRARY_RELEASE}" PATH)
# file(TO_NATIVE_PATH "${xerces_path}/xerces-c_3_1.dll" target_native_xerces)
# add_custom_command(
# TARGET prepare_knime_payload_libs POST_BUILD
# COMMAND ${CMAKE_COMMAND} -E copy "${target_native_xerces}" "${PAYLOAD_LIB_PATH}"
# )
# sqlite3
# get_filename_component(sqlite_path "${SQLite_LIBRARY}" PATH)
# file(TO_NATIVE_PATH "${sqlite_path}/sqlite3.dll" target_native_sqlite)
# add_custom_command(
# TARGET prepare_knime_payload_libs POST_BUILD
# COMMAND ${CMAKE_COMMAND} -E copy "${target_native_sqlite}" "${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
)
set(FOLDER_STRUCTURE_MESSAGE "You can clone all Thirdparty binaries from our OpenMS/THIRDPARTY Git repository but you have to flatten the folder structure such that it is only one level deep with the versions specific for your platform. Do not change the folder names.")
# check if we have valid search engines
## TODO check if we still need this. Maintenance. Maybe check for non-empty and otherwise just copy everything.
## Would also allow custom packages.
if(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY})
message(FATAL_ERROR "Please specify the path to the search engines to build the KNIME packages. ${FOLDER_STRUCTURE_MESSAGE} Then call cmake again with cmake -D SEARCH_ENGINES_DIRECTORY=<Path-To-Checkedout-SE>.")
elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/OMSSA OR NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/XTandem OR NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/MSGFPlus)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout. ${FOLDER_STRUCTURE_MESSAGE}")
elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/Fido)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (Fido is missing). ${FOLDER_STRUCTURE_MESSAGE}")
elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/LuciPHOr2)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (LuciPHOr2 is missing). ${FOLDER_STRUCTURE_MESSAGE}")
elseif(NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/Percolator)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (Percolator is missing). ${FOLDER_STRUCTURE_MESSAGE}")
elseif(NOT APPLE AND NOT EXISTS ${SEARCH_ENGINES_DIRECTORY}/MyriMatch)
message(FATAL_ERROR "The given search engine directory seems to have an invalid layout (MyriMatch is missing). ${FOLDER_STRUCTURE_MESSAGE}")
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
)