#!/bin/sh trap InstallationInterrupted 2 #This function checks which pipelines have an available Reflex workflow #and stores in file "${download_dir}"/available_pipelines the following info: #Pipeline Version Data Pipeline-kit Demodataset GetAvailablePipelines() { cd "${tempdir}" if [ $offline -eq 0 ] ; then $httpcommand https://ftp.eso.org/pub/dfs/pipelines/repositories/${release_channel}/kit/reflex_cfg/reflex_${release_channel}.txt > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not retrieve available pipelines. echo ERROR: Please make sure you have access to ESO webpages echo ERROR: Also, try with the latest version of install_esoreflex echo ERROR: from https://www.eso.org/sci/software/pipelines/install_esoreflex echo ERROR: If problem persists, contact usd-help@eso.org Cleanup exit 1 fi sort -k 1 reflex_${release_channel}.txt | uniq > available_pipelines_sorted \mv -f available_pipelines_sorted available_pipelines if [ ! -s available_pipelines ] then echo echo ERROR: No pipelines are available in this release channel Cleanup exit 1 fi \rm -f "${tempdir}/index.html" \cp available_pipelines "${download_dir}" else if [ ! -f "${download_dir}"/available_pipelines ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: ${download_dir}/available_pipelines Cleanup exit 1 fi fi } GetInstalledPipelines() { if [ -f "${installation_dir}/etc/vltpipe_reflex_install/installed_pipelines" ] then echo ================================================================== echo The following pipelines and associated demo dataset echo are already installed in your system: echo 'Instrument Version' awk '{printf("%-16s %-22s\n",$1,$2)}' "${installation_dir}/etc/vltpipe_reflex_install/installed_pipelines" echo echo The current procedure will first delete all the installed pipelines echo \(but not the datasets\) and then install the requested ones echo \(unless all currently installed pipelines are exactly echo the same as the all requested pipelines\) printf "Do you want to continue [Y/n]? " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ "x$proceed" = "xn" ] ; then echo Aborting Cleanup exit 1 fi fi } GetInstalledReflex() { if [ -f "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" ] then echo ================================================================== echo The following Reflex version is already installed in you system: cat "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" | sed 's%.*://ftp.eso.org/pub/dfs/reflex/%%g' | sed 's%.tar.gz%%g' fi } #This function will show the available pipelines and their versions and #will prompt for the desired pipelines to be installed GetPipelinesToInstall() { cd "${tempdir}" echo ================================================================== echo The following list contains the latest available versions of echo pipelines with workflows published by the VLT pipelines team echo Please specify ALL the pipelines you want to install. echo WARNING: It is not possible to add, upgrade or delete individual echo pipelines to an existing installation. Any change in the choice of echo pipelines at a later time or any upgrade of a pipeline will require a echo complete re-installation of ALL pipelines. echo echo Please specify \'A\' to install all available pipelines \(recommended\), or a echo selection of pipelines by writing a space-separated list of the PipeIDs. echo 'PipeID Instrument Version ' awk '{printf("%-9d %-16s %-22s %-s\n",NR,$1,$2,$5)}' "${download_dir}"/available_pipelines echo while : do printf "Input PipeIDs for pipelines to install [A]: " read -r pipeline_numbers_to_install if [ -z "$pipeline_numbers_to_install" ] ; then pipeline_numbers_to_install="A" fi \rm -f pipelines_to_install number_pipes=`wc -l < ${download_dir}/available_pipelines` cat -n "${download_dir}"/available_pipelines | while read pipeid pipename pipever somethings do echo ${pipeid} ${pipename} ${pipever} ${pipeline_numbers_to_install} | awk -v number_pipes="$number_pipes" '{for(i=4; i<=NF; i++){if( $i != "A" && ( ( $i != $i + 0 ) || ( ( $i == $i + 0 ) && ( ( $i < 1 ) || ( $i > number_pipes ) ) ) ) ) {print "WARNING: Invalid input. Enter numbers in the valid range or A."}; if( $i == $1 || $i == "A" ){printf("%s %s\n", $2, $3)}}}' >> pipelines_to_install done grep WARNING pipelines_to_install | head -1 if grep WARNING pipelines_to_install > /dev/null then echo else if [ -s pipelines_to_install ] then break else echo echo WARNING: No pipeline has been specified. Please try again echo fi fi done sort -k 1 pipelines_to_install | uniq > pipelines_to_install_sorted \mv -f pipelines_to_install_sorted pipelines_to_install if [ -f "${installation_dir}/etc/vltpipe_reflex_install/installed_pipelines" ] then sort -k 1 "${installation_dir}/etc/vltpipe_reflex_install/installed_pipelines" > installed_pipelines_sorted join -j 1 -v 2 pipelines_to_install installed_pipelines_sorted > pipelines_to_remove local lines_pipe_remove=`wc -l < pipelines_to_remove` if [ $lines_pipe_remove -eq 0 ] then \rm -f pipelines_to_remove fi diff pipelines_to_install installed_pipelines_sorted > difference_installed_pipelines local lines_diff_inst=`wc -l < difference_installed_pipelines` if [ $lines_diff_inst -eq 0 ] then \rm -f pipelines_to_install fi fi echo } #This function will select the desired demo data to be installed GetPipelineDemoDataToInstall() { cd "${tempdir}" if [ ! -f pipelines_to_install ] ; then return fi echo ================================================================== echo Pipeline workflows are distributed with demo data that allows echo to run the workflow right away. echo Please specify \'A\' to install all available demo data \(recommended\), echo \'None\' to not install any demo data, or a echo selection of demo data by writing a space-separated list of the PipeIDs. echo 'PipeID Instrument Version' awk '{printf("%-9d %-16s %-22s\n",NR,$1,$2)}' pipelines_to_install echo while : do printf "Input PipeIDs for demo data to install [A]: " read -r pipedata_numbers_to_install if [ -z "$pipedata_numbers_to_install" ] ; then pipedata_numbers_to_install="A" fi \rm -f pipedata_to_install number_pipe_data=`wc -l < pipelines_to_install` cat -n pipelines_to_install | while read pipeid pipename pipever somethings do echo ${pipeid} ${pipename} ${pipever} ${pipedata_numbers_to_install} | awk -v number_pipe_data="$number_pipe_data" '{for(i=4; i<=NF; i++){if( $i != "None" && $i != "A" && ( ( $i != $i + 0 ) || ( ( $i == $i + 0 ) && ( ( $i < 1 ) || ( $i > number_pipe_data ) ) ) ) ) {print "WARNING: Invalid input. Enter numbers in the valid range, None or A."}; if( $i == $1 || $i == "A" ){printf("%s %s\n", $2, $3)}}}' >> pipedata_to_install done grep WARNING pipedata_to_install | head -1 if grep WARNING pipedata_to_install > /dev/null then echo else break fi done echo } GetReflexToInstall() { cd "$tempdir" echo ================================================================== echo The following Reflex version is the latest one available: cat "${download_dir}"/reflex_version cp "${download_dir}"/reflex_version reflex_to_install if [ -f "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" ] then diff "${tempdir}/reflex_to_install" "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" > difference_installed_reflex local lines_diff_inst=`wc -l < difference_installed_reflex` if [ $lines_diff_inst -eq 0 ] then \rm -f "${tempdir}/reflex_to_install" else \cp "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" "${tempdir}/reflex_to_remove" \cp "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex_path" "${tempdir}/reflex_path_to_remove" fi fi } GetAvailableReflexVersion() { cd "${tempdir}" if [ $offline -eq 0 ] ; then ${httpcommand} http://www.eso.org/sci/software/esoreflex/releases/${release_channel}/index.html > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not retrieve available Reflex versions. echo ERROR: Please make sure you have access to ESO webpages echo ERROR: If problem persists, contact usd-help@eso.org Cleanup exit 1 fi awk '/tar.gz/' index.html | awk -F "<|>" '{gsub(/a href=/,"",$2); gsub(/"/,"",$2); print $2}' > reflex_package cat reflex_package | sed 's%https://ftp.eso.org/pub/dfs/reflex/%%g' | sed 's%.tar.gz%%g' > reflex_version # echo The available version of Reflex is: # cat reflex_version echo \rm -f "${tempdir}/index.html" \cp reflex_version "${download_dir}" else if [ ! -f "${download_dir}"/reflex_version ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: ${download_dir}/reflex_version Cleanup exit 1 fi fi } WriteInstalledPackagesConfiguration() { CreateDirectory "${installation_dir}/etc/vltpipe_reflex_install" if [ -f "${tempdir}/pipelines_to_install" ] ; then \cp "${tempdir}/pipelines_to_install" "${installation_dir}/etc/vltpipe_reflex_install/installed_pipelines" fi if [ -f "${tempdir}/reflex_to_install" ] ; then \cp "${download_dir}/reflex_version" "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex" \cp "${tempdir}/reflex_base_path" "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex_path" fi } AskOffline() { echo ================================================================== echo This install script requires an internet connection to check for echo the latest versions of the software and download them if necessary. echo It can work without an internet connection if the download directory echo \($download_dir\) contains already the needed files, echo either from a previous run of the script or copied from some media. printf "Do you want to use your internet connection [Y/n]? " read -r offline offline=`echo $offline | tr '[:upper:]' '[:lower:]'` if [ "x$offline" = "xn" ] ; then offline=1 else offline=0 fi } #Present a summary of the steps to be done and will exit if not confirmed ConfirmInstallation() { cd "${tempdir}" echo ================================================================== if [ -f pipelines_to_install ] ; then echo The following pipelines will be installed/reinstalled: cat pipelines_to_install echo echo The following demo data sets will be installed: cat pipedata_to_install else echo No pipelines or associated demo dataset will be installed. echo Current installed pipelines and associated demo dataset are kept. fi echo if [ -f reflex_to_install ] ; then echo The following Reflex version will be installed: cat reflex_to_install else echo The current Reflex version will be kept. fi echo echo ================================================================== if [ ! -f reflex_to_install ] && [ ! -f pipelines_to_install ] ; then echo Current Reflex and pipeline installations will be kept. echo There is nothing to be done. Exiting Cleanup exit 1 fi echo "The following directories will be used:" echo "Directory for temporary downloaded files: " $download_dir echo "Directory for installation of all software: " $installation_dir echo "Directory for demo datasets: " $dataset_dir echo printf "Please confirm to proceed [Y/n]: " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ "x$proceed" = "xn" ] ; then echo Aborting Cleanup exit 1 fi echo WARNING: Please, do not interrupt the installation from this point on echo WARNING: Otherwise you might get a broken installation } #Do the installation of the pipelines InstallPipelines() { if [ -f "${tempdir}/pipelines_to_install" ] ; then cd "${download_dir}" local all_pipeline_kits= local all_pipeline_data= while read pipename pipeversion do echo Downloading ${pipename} pipeline local pipekit=`grep "^${pipename} " "${download_dir}/available_pipelines" | awk '{print $3}' ` local pipe_kit_name=`echo $pipekit | awk -F'/' '{print $(NF)}'` if [ $offline -eq 0 ] ; then ${httpcommand} $pipekit > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not retrieve pipeline kit. Check disk space or permissions echo ERROR: You might also want to delete old downloads from ${download_dir} Cleanup exit 1 fi ${httpcommand} $pipekit.cksum > /dev/null 2>&1 else if [ ! -f $pipe_kit_name ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: "${download_dir}"/$pipe_kit_name Cleanup exit 1 fi fi all_pipeline_kits=`echo $all_pipeline_kits "${download_dir}/$pipe_kit_name"` cut -f 1,2 -d' ' $pipe_kit_name.cksum > "${tempdir}/$pipe_kit_name.cksum.orig" cat $pipe_kit_name | cksum > "${tempdir}/$pipe_kit_name.cksum.computed" diff "${tempdir}/$pipe_kit_name.cksum.computed" "${tempdir}/$pipe_kit_name.cksum.orig" > /dev/null if [ ! $? -eq 0 ] then echo ERROR: The pipeline kit contains errors in the checksum. echo Remove ${download_dir} and start over. Cleanup exit 1 fi done < "${tempdir}/pipelines_to_install" echo Downloading pipeline installation script if [ $offline -eq 0 ] ; then \rm -f install_pipelinekit ${httpcommand} https://ftp.eso.org/pub/dfs/pipelines/repositories/${release_channel}/kit/reflex_cfg/install_pipelinekit_${release_channel} > /dev/null 2>&1 mv install_pipelinekit_${release_channel} install_pipelinekit chmod u+x install_pipelinekit else if [ ! -f install_pipelinekit ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: "${download_dir}"/install_pipelinekit Cleanup exit 1 fi fi echo echo Executing pipeline installation script starting at `date`. echo This might take a while, around 10 minutes per pipeline. echo Inspect the following file if you want to check progress: echo ${download_dir}/install.log echo ./install_pipelinekit -ignore_esorex_rc -ignore_gasgano "${installation_dir}" "${installation_dir}" $all_pipeline_kits > "${tempdir}/install_pipelinekit.log" 2>&1 if [ $? -ne 0 ]; then if [ ! -f "${download_dir}/install.log" ] ; then # In case the command completely failed even to generate a log, # copy piped output to the log file. \cp "${tempdir}/install_pipelinekit.log" "${download_dir}/install.log" fi echo ERROR: Could not install pipelines. echo ERROR: Check "${download_dir}"/install.log to verify what went wrong echo ERROR: If error persists, send a report to usd-help@eso.org echo ERROR: including the following files: echo "${download_dir}/install.log" find "${download_dir}" -name config.log # Do not call Cleanup since it will remove the pipeline-kit-*.tmp directory. # Cleanup only the install_esoreflex_temp.* directory. RemoveTempDir exit 1 fi echo Installation of pipelines successful. echo Installing pipeline demo data while read pipename pipeversion do if grep "^$pipename " "${tempdir}/pipedata_to_install" > /dev/null 2>&1 ; then echo Downloading ${pipename} data local pipedata=`grep "^${pipename} " "${download_dir}"/available_pipelines | awk '{print $4}' ` local pipe_data_name=`echo $pipedata | awk -F'/' '{print $(NF)}' ` local pipe_name=`echo $pipe_data_name | awk -F'-' '{print $1}' ` if [ $offline -eq 0 ] ; then ${httpcommand} $pipedata > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not retrieve pipeline data $pipedata. echo ERROR: Check disk space or permissions Cleanup exit 1 fi else if [ ! -f $pipe_data_name ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: "${download_dir}"/$pipe_data_name Cleanup exit 1 fi fi echo Installing ${pipename} data file $pipe_data_name > "${tempdir}/file_tmp" 2>&1 grep gzip "${tempdir}/file_tmp" > /dev/null 2>&1 if [ $? -eq 0 ]; then compress_opt=z fi grep bzip2 "${tempdir}/file_tmp" > /dev/null 2>&1 if [ $? -eq 0 ]; then compress_opt=j fi # Both lower and upper case needs to be handled since the output string # is declared differently with the 'file' command on Mac OSX and Linux. grep xz "${tempdir}/file_tmp" > /dev/null 2>&1 if [ $? -eq 0 ]; then compress_opt=J fi grep XZ "${tempdir}/file_tmp" > /dev/null 2>&1 if [ $? -eq 0 ]; then compress_opt=J fi if [ ! -d "${dataset_dir}/reflex_input/${pipe_name}" ] ; then CreateDirectory "${dataset_dir}/reflex_input/${pipe_name}" fi tar -${compress_opt} -xf $pipe_data_name -C "${dataset_dir}/reflex_input/${pipe_name}" > /dev/null 2>&1 if [ $? -ne 0 ]; then echo WARNING: Could not install pipeline data. Check disk space or permissions echo WARNING: Installation will continue without this data being installed fi \rm -rf "${tempdir}/file_tmp" fi done < "${tempdir}/pipelines_to_install" echo Installation of pipeline data succeed. fi } # Sets the version file if it is missing in the installed path. # PatchReflexVersionFile() { local reflex_version=`cat "${download_dir}/reflex_version"` local reflex_base_path=`cat "${tempdir}/reflex_base_path"` if [ ! -f "${reflex_base_path}/esoreflex/version" -a -d "${reflex_base_path}/esoreflex" ] ; then if echo "${reflex_version}" | \grep '^reflex-' > /dev/null ; then # Update to new naming scheme with the 'eso' prefix. echo "eso${reflex_version}" > "${reflex_base_path}/esoreflex/version" else echo "${reflex_version}" > "${reflex_base_path}/esoreflex/version" fi if [ $? -ne 0 ]; then echo ERROR: Could not create the Reflex version file. Cleanup exit 1 fi fi } # Download and copy the launch script if dealing with an older Reflex package. # Also remove old launch scripts to prevent confusion or problems. # PatchLaunchScripts() { local reflex_base_path=`cat "${tempdir}/reflex_base_path"` local reflex_sub_path="esoreflex" for script in esoreflex esoreflex_set_memory ; do if [ ! -f "${reflex_base_path}/${reflex_sub_path}/bin/${script}" ] ; then if [ ! -f "${download_dir}/${script}" ] ; then if [ $offline -eq 0 ] ; then cd "${download_dir}" ${httpcommand} "https://ftp.eso.org/pub/dfs/reflex/${script}" > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not download the "${script}" script. Check disk space or permissions. echo ERROR: You might also want to delete old downloads from "${download_dir}" Cleanup exit 1 fi else echo ERROR: The following file needed in offline mode is missing: echo ERROR: "$script" Cleanup exit 1 fi fi \cp "${download_dir}/${script}" "${reflex_base_path}/${reflex_sub_path}/bin/${script}" if [ $? -ne 0 ]; then echo ERROR: Failed to copy the "${script}" script to the installation directory. Cleanup exit 1 fi fi done # Remove old launch scripts so they cannot be picked up via the PATH variable. for script in "${reflex_base_path}/${reflex_sub_path}/bin/reflex" \ "${reflex_base_path}/${reflex_sub_path}/bin/esoreflex.old" ; do if [ -f "${script}" ] ; then \rm -f "${script}" fi done } # This will move the Reflex folder to follow the naming scheme: esoreflex-* # The installed folder is in addition identified by creation time in case there # are multiple directories with the same name. # Finally the new Reflex base path is written to ${tempdir}/reflex_base_path for # later use. # UpdateReflexBasePath() { local reflex_name=`cat "${tempdir}/reflex_to_install"` local untarred_reflex_dir=$(\ls -t "${installation_dir}" | \grep "${reflex_name}" | \head -n 1) if [ -z "${untarred_reflex_dir}" ] ; then echo ERROR: Could not find untarred Reflex package directory. Cleanup exit 1 fi reflex_base_path="${installation_dir}/${untarred_reflex_dir}" echo "${reflex_base_path}" > "${tempdir}/reflex_base_path" } # Prints the full path to the ESO module subdirectory in the Reflex base path. # GetEsoSubDir() { local reflex_base_path="" if [ -f "${tempdir}/reflex_base_path" ] ; then reflex_base_path=`cat "${tempdir}/reflex_base_path"` else reflex_base_path=`cat "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex_path"` fi printf %s "${reflex_base_path}/esoreflex" } # Prints the full correct path to a script name in the Reflex bin directory, # taking into account older Reflex package layouts. # $1 - The name of the script. # GetBinScriptPath() { printf %s "`GetEsoSubDir`/bin/$1" } # Writes modifications to the esoreflex launch script to setup the various # installation and workflow paths. Will also make sure the script is executable. # UpdateReflexCommand() { local reflex_base_path=`cat "${tempdir}/reflex_base_path"` local script_path=`GetBinScriptPath esoreflex` \sed "s|^ESOREFLEX_BASE=.*$|ESOREFLEX_BASE=\"${reflex_base_path}\"|g" "${script_path}" | \ \sed "s|^ESOREFLEX_WORKFLOW_PATH=.*$|ESOREFLEX_WORKFLOW_PATH=\"${installation_dir}/share/reflex/workflows\":~/KeplerData/workflows/MyWorkflows|g" | \ \sed "s|^LOAD_ESOREX_CONFIG=.*$|LOAD_ESOREX_CONFIG=\"${installation_dir}/etc/esorex.rc\"|g" | \ \sed "s|^LOAD_ESOREX_RECIPE_CONFIG=.*$|LOAD_ESOREX_RECIPE_CONFIG=\"${installation_dir}/etc/esoreflex_default_recipe_config.rc\"|g" | \ \sed "s|^ESOREFLEX_SYSTEM_RC=.*$|ESOREFLEX_SYSTEM_RC=\"${installation_dir}/etc/esoreflex.rc\"|g" \ > "${script_path}.tmp" if [ $? -ne 0 ]; then echo ERROR: Failed to update the esoreflex script. Cleanup exit 1 fi \mv "${script_path}.tmp" "${script_path}" if [ $? -ne 0 ]; then echo ERROR: Failed to update the esoreflex script. Cleanup exit 1 fi \chmod 755 "${script_path}" if [ $? -ne 0 ]; then echo ERROR: Failed to update file mode bits for the esoreflex script. Cleanup exit 1 fi } # Writes modifications to the esoreflex_set_memory script to setup the base path # where Reflex was installed. Will also make sure the script is executable. # UpdateSetMemoryCommand() { local reflex_base_path=`cat "${tempdir}/reflex_base_path"` local script_path=`GetBinScriptPath esoreflex_set_memory` \sed "s|^ESOREFLEX_BASE=.*$|ESOREFLEX_BASE=\"${reflex_base_path}\"|g" "${script_path}" > "${script_path}.tmp" if [ $? -ne 0 ]; then echo ERROR: Failed to update the esoreflex_set_memory script. Cleanup exit 1 fi \mv "${script_path}.tmp" "${script_path}" if [ $? -ne 0 ]; then echo ERROR: Failed to update the esoreflex_set_memory script. Cleanup exit 1 fi \chmod 755 "${script_path}" if [ $? -ne 0 ]; then echo ERROR: Failed to update file mode bits for the esoreflex_set_memory script. Cleanup exit 1 fi } # Configure the default directory that is used when the open file dialog pops up. # This is done by uncommenting and setting the _alternateDefaultOpenDirectory # property in the Kepler configuration.xml file. # UpdateDefaultOpenDirectory() { local reflex_version=`cat "${download_dir}/reflex_version" | \ sed 's|^reflex-||' | sed 's|^esoreflex-||' | \ sed 's|-linux$||' | sed 's|-osx$||' | sed 's|-||g'` local major_version=`echo "${reflex_version}" | cut -d . -f 1` local minor_version=`echo "${reflex_version}" | cut -d . -f 2` if [ "${major_version}" -lt 2 -o \( "${major_version}" -eq 2 -a "${minor_version}" -lt 9 \) ] ; then local kepler_version="-2.4" elif [ "${major_version}" -eq 2 -a "${minor_version}" -lt 10 ] ; then local kepler_version="-2.5" else local kepler_version="" fi local config_file=`cat "${tempdir}/reflex_base_path"`"/common${kepler_version}/configs/ptolemy/configs/kepler/configuration.xml" local workflow_path="${installation_dir}/share/reflex/workflows" \sed "s|<\!--[[:space:]]*\(property[[:space:]][[:space:]]*name=\"_alternateDefaultOpenDirectory\"\).*|<\1 value=\"${workflow_path}\"|" "${config_file}" | \ \sed "s|\(class[[:space:]]*=[[:space:]]*\"ptolemy[.]kernel[.]util[.]StringAttribute\"[[:space:]]*\)/[[:space:]]*-->|\1 />|" > "${config_file}.tmp" if [ $? -ne 0 ]; then echo ERROR: Failed to update default open file directory in configuration.xml. Cleanup exit 1 fi \mv "${config_file}.tmp" "${config_file}" if [ $? -ne 0 ]; then echo ERROR: Failed to update default open file directory in configuration.xml. Cleanup exit 1 fi } # Creates a link to the Reflex demo workflows path in share/reflex/workflows # AddLinkToDemoWorkflows() { CreateDirectory "${installation_dir}/share/reflex/workflows" local reflex_base_path=`cat "${tempdir}/reflex_base_path"` local targetname=`basename "${reflex_base_path}"` \rm -f "${installation_dir}/share/reflex/workflows/${targetname}-demos" \ln -s "`GetEsoSubDir`/eso-demo-workflows" "${installation_dir}/share/reflex/workflows/${targetname}-demos" if [ $? -ne 0 ]; then echo ERROR: Failed to set link to demo Reflex workflows. Cleanup exit 1 fi } InstallReflex() { if [ -f "${tempdir}/reflex_to_install" ] ; then cd "${download_dir}" echo Installing Reflex... local reflex_local_file="${download_dir}"/`cat "${tempdir}/reflex_to_install"`.tar.gz if [ $offline -eq 0 ] ; then ${httpcommand} `cat "${tempdir}/reflex_package"` > /dev/null 2>&1 if [ $? -ne 0 ]; then echo ERROR: Could not get Reflex package. Check disk space or permissions Cleanup exit 1 fi else if [ ! -f $reflex_local_file ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: $reflex_local_file Cleanup exit 1 fi fi cd "${installation_dir}" tar xzf $reflex_local_file -C "${installation_dir}" if [ $? -ne 0 ]; then echo ERROR: Could not install Reflex package. Check disk space or permissions Cleanup exit 1 fi UpdateReflexBasePath PatchReflexVersionFile PatchLaunchScripts UpdateReflexCommand UpdateSetMemoryCommand UpdateDefaultOpenDirectory AddLinkToDemoWorkflows fi } InstallInstallationScript() { CreateDirectory "${installation_dir}/bin" cd "$tempdir" if [ $offline -eq 0 ] ; then ${httpcommand} https://www.eso.org/sci/software/pipelines/install_esoreflex > /dev/null 2>&1 cp install_esoreflex "${installation_dir}/bin" chmod u+x "${installation_dir}/bin/install_esoreflex" cp install_esoreflex "${download_dir}" else if [ ! -f "${download_dir}"/install_esoreflex ] ; then echo ERROR: The following file needed in offline mode is missing: echo ERROR: "{$download_dir}"/install_esoreflex Cleanup exit 1 fi fi } RemoveCurrentPipelines() { if [ -f pipelines_to_install ] ; then echo Purging installed pipelines # Careful not to delete vltpipe_reflex_install path under etc/ since it # keeps a register of the installed pipelines and Reflex. for path_to_delete in "${installation_dir}"/etc/* ; do if [ "${path_to_delete}" != "${installation_dir}/etc/vltpipe_reflex_install" ] ; then rm -rf "${path_to_delete}" fi done \rm -rf "${installation_dir}/bin" "${installation_dir}/lib" "${installation_dir}/share" "${installation_dir}/calib" "${installation_dir}/include" "${installation_dir}/man" fi } RemoveCurrentReflex() { if [ -f "${tempdir}/reflex_to_remove" ] ; then echo Purging installed Reflex `cat "${tempdir}/reflex_to_remove"` \rm -rf `cat "${tempdir}/reflex_path_to_remove"` fi } WriteDummyRecipeConfig() { echo '# No default parameters should be specified for recipes under Reflex.' \ > ${installation_dir}/etc/esoreflex_default_recipe_config.rc } WriteReflexCommand() { local script_path=`GetBinScriptPath esoreflex` \rm -f "${installation_dir}/bin/esoreflex" \ln -s "${script_path}" "${installation_dir}/bin/esoreflex" if [ $? -ne 0 ]; then echo ERROR: Failed to install the esoreflex command. Cleanup exit 1 fi } WriteSetMemoryCommand() { local script_path=`GetBinScriptPath esoreflex_set_memory` \rm -f "${installation_dir}/bin/esoreflex_set_memory" \ln -s "${script_path}" "${installation_dir}/bin/esoreflex_set_memory" if [ $? -ne 0 ]; then echo ERROR: Failed to install the esoreflex_set_memory command. Cleanup exit 1 fi } # This function checks to see if a path exists in a colon separated path list. # 0 is returned if it does and 1 otherwise. # $1 - The path to find. # $2 - The list of paths to search. # PathExistsInPathList() { # Save the field splitting characters and set it to a colon to split the # paths in $1. OLDIFS="$IFS" IFS=":" for N in $2 ; do if [ "$N" = "$1" ] ; then IFS="$OLDIFS" # Restore field splitting character. return 0 fi done IFS="$OLDIFS" # Restore field splitting character. return 1 } # Writes the default etc/esoreflex.rc file for the esoreflex launch command. # WriteEsoreflexConfig() { local reflex_base_path="" if [ -f "${tempdir}/reflex_base_path" ] ; then reflex_base_path=`cat "${tempdir}/reflex_base_path"` else reflex_base_path=`cat "${installation_dir}/etc/vltpipe_reflex_install/installed_reflex_path"` fi esoreflex_python_path="${reflex_base_path}/esoreflex/python" if [ -n "$PYTHONPATH" ] ; then esoreflex_python_path="$esoreflex_python_path:$PYTHONPATH" fi local java_command=`command -v java` if [ $? -ne 0 ]; then echo ERROR: Could not find the location of the Java binary. Cleanup exit 1 fi # Try find the directory to the python command and add it to the field # esoreflex.path in the configuration file if necessary, i.e. if it is # not already in the path list returned by getconf. if PathExistsInPathList `dirname ${python_command}` `getconf PATH` ; then local python_command_dir="" else local python_command_dir=:`dirname ${python_command}` fi local reflex_version=`cat "${download_dir}/reflex_version" | \ sed 's|^reflex-||' | sed 's|^esoreflex-||' | \ sed 's|-linux$||' | sed 's|-osx$||' | sed 's|-||g'` cat > "${installation_dir}/etc/esoreflex.rc" < ${installation_dir}/etc/esoreflex-esorex.rc } HowToRunMessages() { echo ================================================================== echo Run the following command to execute Reflex echo ${installation_dir}/bin/esoreflex echo You might want to define an alias for this command, e.g. echo For sh / bash / zsh: echo alias esoreflex=${installation_dir}/bin/esoreflex echo For csh / tcsh: echo alias esoreflex ${installation_dir}/bin/esoreflex echo To customize the memory Reflex will use, please run: echo ${installation_dir}/bin/esoreflex_set_memory echo ================================================================== } #Creates a temporary unique directory and stores its name in the #variable name passed as first argument MakeTempDir() { local _tempdir=$1 mytempdir=$(mktemp -d "$download_dir"/install_esoreflex_temp.XXXXXXXXXXXX) || { echo "ERROR creating a temporary directory" >&2; Cleanup; exit 1; } eval $_tempdir="'$mytempdir'" } #Remove completely the temporary directory. RemoveTempDir() { test -n "$tempdir" && \rm -rf "$tempdir" } #Remove the directories left by the install_pipelinekit script RemoveInstallPipelineKitTempDir() { test -n "${download_dir}" && \rm -rf "${download_dir}"/pipeline-kit-*tmp } #Check that the superset of python modules are available #It tries both the python3 (prefered) and python2 stacks CheckPythonCommandAndModules() { cd "$tempdir" cat > python_check </dev/null python3_modules_found=$? fi if [ "$python3_found" -ne 0 ] || [ "$python3_modules_found" -ne 0 ] ; then echo WARNING: Your python3 environment does not seem to have all needed Python modules. echo WARNING: Trying python2 environment... python_command=`command -v python2` python2_found=$? if [ "$python2_found" -ne 0 ] && [ "$python3_found" -ne 0 ]; then echo WARNING: No python2 or python3 commands found. echo WARNING: Some pipeline workflows might require them. echo printf "Do you want to continue anyway? [y/N] " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ ! "x$proceed" = "xy" ] ; then echo Aborting Cleanup exit 1 fi else $python_command ./python_check 2>/dev/null if [ ! $? -eq 0 ] ; then echo WARNING: Some Python modules are not installed in your system echo WARNING: The following script has been used to test for those modules: echo ============= cat ./python_check echo ============= echo WARNING: Some pipeline workflows might require them those modules. if [ $python3_found -eq 0 ] ; then echo WARNING: The python3 environment used was `command -v python3` else echo WARNING: No python3 environment has been found fi if [ $python2_found -eq 0 ] ; then echo WARNING: The python2 environment used was `command -v python2` else echo WARNING: No python2 environment has been found fi echo printf "Do you want to continue anyway? [y/N] " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ ! "x$proceed" = "xy" ] ; then echo Aborting Cleanup exit 1 fi fi fi fi } #Check that java is installed CheckJava() { CheckCommandExist java echo echo "Please make sure you have a compatible Java JRE installed." echo "Versions 8 to 11 are supported by Reflex." echo } GetScriptOptions() { #Default release channel release_channel=stable while getopts "d:i:s:r:h" option_name; do case "$option_name" in d) download_dir="$OPTARG";; i) installation_dir="$OPTARG";; s) dataset_dir="$OPTARG";; r) release_channel="$OPTARG";; h) PrintUsageAndExit;; [?]) PrintUsageAndExit ;; esac done } PrintUsageAndExit() { version=`echo \$Revision: 280466 $ | cut -f 2 -d' '` echo This is the $0 script to install Reflex. Version $version echo This script allows to install Reflex together with pipelines echo with Reflex workflows support. It retrieves the latest versions echo of the pipelines from the ESO servers. An offline mode also exists. echo Please follow the instructions that appear in the screen. echo echo "Usage: $0 [-d DOWNLOAD_DIR] [-i INSTALL_DIR] [-s DATA_DIR] [-h]" echo echo " -d DOWNLOAD_DIR The directory where to download all the data." echo " If not given, the script will ask" echo " -i INSTALL_DIR The directory where to install the software," echo " including Reflex and the pipelines." echo " If not given, the script will ask" echo " -s DATA_DIR The directory where to download all the data." echo " The products of the pipeline, logs and" echo " bookkeeping will also be stored here." echo " If not given, the script will ask" echo " If not given, the script will ask" echo echo " Example: install_esoreflex -d d_dir -i i_dir -s d_dir" Cleanup exit 1 } #Get the name of the directories GetConfigDirectories() { if [ -z "$download_dir" ] ; then printf "Input directory for temporary downloaded files (> 500 Mb) [download_reflex]: " read -r download_dir if [ -z "$download_dir" ] ; then download_dir="download_reflex" fi fi test `pwd` -ef $download_dir if [ $? -eq 0 ] ; then echo "ERROR: The download dir is the same as current one. Choose other" Cleanup exit 1 fi if [ -z "$installation_dir" ] ; then printf "Input directory for installation of all software (> 500 Mb) [install]: " read -r installation_dir if [ -z "$installation_dir" ] ; then installation_dir="install" fi fi echo NOTE: The default ROOT_DATA_DIR for installed workflows is set to \$HOME/reflex_data if [ -z "$dataset_dir" ] ; then printf "Input directory for installation of demo datasets (variable size) [data_wkf]: " read -r dataset_dir if [ -z "$dataset_dir" ] ; then dataset_dir="data_wkf" fi fi if [ ! -d "${download_dir}" ] ; then CreateDirectory "${download_dir}" fi if [ ! -d "${installation_dir}" ] ; then CreateDirectory "${installation_dir}" fi if [ ! -d "${dataset_dir}" ] ; then CreateDirectory "${dataset_dir}" fi local base_dir=$PWD cd "${base_dir}" cd "${download_dir}" download_dir=${PWD} cd "${base_dir}" cd "${installation_dir}" installation_dir=${PWD} cd "${base_dir}" cd "${dataset_dir}" dataset_dir=${PWD} if [ "${download_dir}" = "${installation_dir}" ] ; then # If the download dir is the same as the installation directory this will # not work. Therefore we create a subdirectory within the installation path # instead for this case (PIPE-6954). download_dir="${installation_dir}/download" CreateDirectory "${download_dir}" fi echo Using the following directory configuration echo Download directory: ${download_dir} echo Installation directory: ${installation_dir} echo Demo dataset directory: ${dataset_dir} echo } GetReleaseChannel() { if [ "$release_channel" != "stable" ] && [ "$release_channel" != "testing" ] && [ "$release_channel" != "devel" ] && [ "$release_channel" != "legacy" ] ; then echo Unknown release channel $release_channel Cleanup exit 1 fi if [ "$release_channel" != "stable" ] ; then echo Using release channel $release_channel fi } CreateDirectory() { echo "Creating dir '$1'" mkdir -p "$1" > /dev/null 2> /dev/null retval=$? if [ $retval -ne 0 ]; then echo ERROR: Could not create dir $1. Verify path or permissions Cleanup exit 1 fi } #Check if a command is in the path CheckCommandExist() { exec_com=$1 command -v $exec_com > /dev/null 2> /dev/null local retval=$? if [ $retval -ne 0 ]; then echo ERROR: $exec_com is not installed in your system. Cleanup exit 1 fi } #Check that the needed programas are in the path CheckTextUtils() { CheckCommandExist awk CheckCommandExist tr CheckCommandExist cat CheckCommandExist sed CheckCommandExist grep CheckCommandExist mkdir CheckCommandExist rm CheckCommandExist cksum CheckCommandExist basename CheckCommandExist touch CheckCommandExist perl } #Get the command used to retrieve web pages. It can be wget or curl GetHttpCommand() { local _httpcommand=$1 command -v wget > /dev/null 2> /dev/null retval=$? if [ $retval -ne 0 ]; then command -v curl > /dev/null 2> /dev/null retval=$? if [ $retval -ne 0 ]; then echo ERROR: Neither wget or curl are installed. Please install them. Cleanup exit 1 else local myhttpcommand='curl -O -L -C -' fi else local myhttpcommand='wget -c' fi eval $_httpcommand="'$myhttpcommand'" } # This has to be calculated here, before and change of directory to get the # correct path of the script in case $0 is a relative path. current_revision=`grep '\$Revision' "$0" 2> /dev/null | sed -e 's|^.*\$Revision: \([[:digit:]]*\).*$|\1|' 2> /dev/null` # Check if there is a newer version of this script and alert the user. CheckForNewerScriptVersion() { if [ $offline -eq 0 ] ; then local topdir=`pwd` cd "${tempdir}" ${httpcommand} https://www.eso.org/sci/software/pipelines/install_esoreflex > /dev/null 2>&1 if [ $? -eq 0 ]; then local new_revision=`grep '\$Revision' install_esoreflex 2> /dev/null | sed -e 's|^.*\$Revision: \([[:digit:]]*\).*$|\1|' 2> /dev/null` if [ "$new_revision" -gt "$current_revision" ] 2> /dev/null; then echo echo "A newer version of the current script is available on the FTP server." echo "It is recommended to use the newer version. It can be downloaded from:" echo " https://www.eso.org/sci/software/pipelines/install_esoreflex" printf "Do you want to continue using the older script [y/N]? " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ "x$proceed" != "xy" ] ; then Cleanup exit 0 fi fi fi cd "${topdir}" fi } PrintWelcome() { echo ====================================================================== echo " Welcome to the installation script for Reflex and pipeline workflows" echo ====================================================================== } ReplaceWorkflowDataPath() { #Do this only if pipelines have been installed if [ -f "${tempdir}/pipelines_to_install" ] ; then # replace data dir in the workflows # Note that we are performing the replacement to be more consistent with how # RPM and MacPorts installations work (PIPE-8250). find "${installation_dir}/share/reflex/workflows" -name "*.xml" -exec sh -c 'file="{}" ; sed "s%ROOT_DATA_PATH_TO_REPLACE%\$HOME/reflex_data%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; find "${installation_dir}/share/esopipes" -name "*.xml" -exec sh -c 'file="{}" ; sed "s%ROOT_DATA_PATH_TO_REPLACE%\$HOME/reflex_data%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; find "${installation_dir}/share/reflex/workflows" -name "*.xml" -exec sh -c 'file="{}" ; pipename=$(echo $file | sed "s%.*/share/reflex/workflows/\([^-]*\).*%\1%") ; sed "s%\(%\1'${dataset_dir}'/reflex_input/$pipename\">%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; find "${installation_dir}/share/esopipes" -name "*.xml" -exec sh -c 'file="{}" ; pipename=$(echo $file | sed "s%.*/share/esopipes/\([^-]*\).*%\1%") ; sed "s%\(%\1'${dataset_dir}'/reflex_input/$pipename\">%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; # The following is for workflows that did not move to the new RAW_DATA_DIR standard. find "${installation_dir}/share/reflex/workflows" -name "*.xml" -exec sh -c 'file="{}" ; pipename=$(echo $file | sed "s%.*/share/reflex/workflows/\([^-]*\).*%\1%") ; sed "s%\(%\1'${dataset_dir}'/reflex_input/$pipename\">%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; find "${installation_dir}/share/esopipes" -name "*.xml" -exec sh -c 'file="{}" ; pipename=$(echo $file | sed "s%.*/share/esopipes/\([^-]*\).*%\1%") ; sed "s%\(%\1'${dataset_dir}'/reflex_input/$pipename\">%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; # replace calib dir in the workflows find "${installation_dir}/share/reflex/workflows" -name "*.xml" -exec sh -c 'file="{}" ; sed "s%CALIB_DATA_PATH_TO_REPLACE%'${installation_dir}/share/esopipes/datastatic'%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; find "${installation_dir}/share/esopipes" -name "*.xml" -exec sh -c 'file="{}" ; sed "s%CALIB_DATA_PATH_TO_REPLACE%'${installation_dir}/share/esopipes/datastatic'%g" "$file" > "$file.edit" ; mv "$file.edit" "$file" ' \; fi } RemoveKeplerDataESO() { if [ -d $HOME/KeplerData/modules/esoreflex ] ; then echo WARNING: The installation has detected the following directory: echo WARNING: $HOME/KeplerData/modules/esoreflex echo WARNING: This means that a previous installation of Reflex echo WARNING: existed, which is known to gives problems in some cases. echo WARNING: Additionally, the $HOME/.kepler, echo WARNING: $HOME/KeplerData/kepler.modules and $HOME/KeplerData/MyData echo WARNING: directories should also be removed. printf "Do you want to delete these directories [Y/n]? " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ "x$proceed" = "xn" ] ; then echo $HOME/KeplerData has been kept else \rm -rf $HOME/KeplerData/modules \rm -rf $HOME/KeplerData/kepler.modules \rm -rf $HOME/KeplerData/MyData \rm -rf $HOME/.kepler echo $HOME/KeplerData and $HOME/.kepler have been removed fi fi } # Offer to move existing ~/.esoreflex/esoreflex.rc file to a backup copy if it # exists so that the config installed with this script takes precedence. # RemoveEsoreflexrcFromHome() { if [ -f ~/.esoreflex/esoreflex.rc ] ; then echo WARNING: The configuration file "~/.esoreflex/esoreflex.rc" already exists. echo WARNING: This will take precedence over the Reflex configuration file shipped echo WARNING: with this installation. printf "Do you want to move this file so that it does not get used [Y/n]? " read -r proceed proceed=`echo $proceed | tr '[:upper:]' '[:lower:]'` if [ "x$proceed" = "xn" ] ; then echo "~/.esoreflex/esoreflex.rc" will be used for the Reflex configuration. else suffix="" while [ -f ~/.esoreflex/esoreflex.rc.backup"${suffix}" ] ; do if [ -z "${suffix}" ] ; then suffix=1 else suffix=$(($suffix+1)) fi done \mv ~/.esoreflex/esoreflex.rc ~/.esoreflex/esoreflex.rc.backup"${suffix}" echo "~/.esoreflex/esoreflex.rc" moved to "~/.esoreflex/esoreflex.rc.backup${suffix}" fi fi } Cleanup() { RemoveTempDir RemoveInstallPipelineKitTempDir } InstallationInterrupted() { echo echo Installation interrupted Cleanup exit 1 } PrintWelcome GetScriptOptions $@ GetConfigDirectories AskOffline GetReleaseChannel MakeTempDir tempdir GetHttpCommand httpcommand CheckForNewerScriptVersion CheckJava CheckTextUtils CheckPythonCommandAndModules GetAvailableReflexVersion GetAvailablePipelines GetInstalledReflex GetInstalledPipelines GetReflexToInstall GetPipelinesToInstall GetPipelineDemoDataToInstall ConfirmInstallation RemoveCurrentPipelines RemoveCurrentReflex InstallPipelines InstallReflex InstallInstallationScript WriteDummyRecipeConfig WriteEsoreflexConfig WriteReflexCommand ReplaceWorkflowDataPath WriteInstalledPackagesConfiguration RemoveKeplerDataESO RemoveEsoreflexrcFromHome WriteSetMemoryCommand HowToRunMessages Cleanup exit