PWGPP/QA/scripts/runQA.sh

   1 #!/bin/bash
   2 # process QA output into plots and trending
   3 # run without arguments for examples
   4 # origin: Mikolaj Krzewicki, mkrzewic@cern.ch
   5 #
   6 if [ ${BASH_VERSINFO} -lt 4 ]; then
   7   echo "bash version >= 4 needed, you have ${BASH_VERSION}, exiting..."
   8   exit 1
   9 fi
  10
  11 main()
  12 {
  13   if [[ -z $1 ]]; then
  14     echo "Usage: "
  15     echo "  ${0##*/} option=value [option=value]"
  16     echo "  at least inputList should be specified, or configFile containing it:"
  17     echo "  ${0##*/} inputList=file.list"
  18     echo "  options override config file (if any), e.g.:"
  19     echo "  ${0##*/} configFile=runQA.config inputList=file.list outputDirectory=%det"
  20     echo "some expert options"
  21     echo "  inputListHighPtTrees=file.list - external list of filtered trees, requires inputList to be set"
  22     echo "  includeDetectors=TPC,V0,MU - only process those"
  23     echo "  excludeDetectors=EVS,TPC - skip processing of those"
  24     echo "  - see example config file for more"
  25     return 1
  26   fi
  27
  28   if ! parseConfig "$@"; then
  29     ${0}
  30     return 1
  31   fi
  32
  33   [[ -z $ALICE_ROOT ]] && echo "ALICE_ROOT not defined" && return 1
  34
  35   ocdbregex='raw://'
  36   if [[ ${ocdbStorage} =~ ${ocdbregex} ]]; then
  37     alien-token-init ${alienUserName}
  38     #this is a hack! alien-token init seems not enough
  39     #but the gclient_env script messes up the LD_LIBRARY_PATH
  40     while read x; do
  41       eval ${x};
  42     done < <(grep -v "LD_LIBRARY_PATH" /tmp/gclient_env_${UID})
  43   fi
  44
  45   updateQA "$@"
  46   return 0
  47 }
  48
  49 updateQA()
  50 {
  51   umask 0002
  52   parseConfig "$@"
  53
  54   #be paranoid and make some full paths
  55   [[ ! -f ${inputList} ]] && echo "no input list: ${inputList}" && return 1
  56   inputList=$(get_realpath ${inputList})
  57   mkdir -p ${workingDirectory}
  58   #this is a trick to get the full path of workingDirectory
  59   #(on a mac 'readlink -f' does not work...)
  60   workingDirectory=$(workingDirectory=${workingDirectory%/}; cd ${workingDirectory%/*}; echo "${PWD}/${workingDirectory##*/}")
  61   if [[ ! -d ${workingDirectory} ]]; then
  62     echo "working dir $workingDirectory does not exist and cannot be created"
  63     return 1
  64   fi
  65   cd ${workingDirectory}
  66
  67   echo JOB config:
  68   echo inputList=$inputList
  69   echo outputDirectory=$outputDirectory
  70   echo
  71
  72   dateString=$(date +%Y-%m-%d-%H-%M-%S-%N)
  73   echo "Start time QA process: $dateString"
  74
  75   #logging
  76   mkdir -p $logDirectory
  77   [[ ! -d $logDirectory ]] && echo "no log dir $logDirectory" && return 1
  78   logFile="$logDirectory/${0##*/}.${dateString}.log"
  79   touch ${logFile}
  80   [[ ! -f ${logFile} ]] && echo "cannot write logfile $logfile" && return 1
  81   echo "logFile = $logFile"
  82
  83   #check lock
  84   lockFile=${workingDirectory}/runQA.lock
  85   [[ -f ${lockFile} ]] && echo "lock ${lockFile} exists!" | tee ${logFile} && return 1
  86   touch ${lockFile}
  87   [[ ! -f ${lockFile} ]] && echo "cannot lock $lockFile" | tee ${logFile} && return 1
  88
  89   exec &>${logFile}
  90
  91   ################################################################
  92   #ze detector loop
  93   for detectorScript in $ALICE_ROOT/PWGPP/QA/detectorQAscripts/*; do
  94     echo
  95     echo "##############################################"
  96     echo $(date)
  97     unset planB
  98     [[ ! ${detectorScript} =~ .*\.sh$ ]] && continue
  99     detector=${detectorScript%.sh}
 100     detector=${detector##*/}
 101     #by default we expect the container in the QA root file to de named like
 102     #the detector
 103     detectorQAcontainerName=${detector}
 104
 105     #skip if excluded
 106     if [[ "${excludeDetectors}" =~ ${detector} ]]; then
 107       echo "${detector} is excluded in config, skipping..."
 108       continue
 109     fi
 110
 111     #if includeDetectors set, only process thoe detectors specified there
 112     if [[ -n ${includeDetectors} && ! "${includeDetectors}" =~ ${detector} ]]; then
 113       echo "${detector} not included in includeDetectors, skipping..."
 114       continue
 115     fi
 116
 117     logSummary=${logDirectory}/summary-${detector}-${dateString}.log
 118     hostInfo >> ${logSummary}
 119     outputDir=$(substituteDetectorName ${detector} ${outputDirectory})
 120     tmpDetectorRunDir=${workingDirectory}/tmpQAtmpRunDir${detector}-${dateString}
 121     if ! mkdir -p ${tmpDetectorRunDir}; then
 122       echo "cannot create the temp dir $tmpDetectorRunDir"
 123       continue
 124     fi
 125     cd ${tmpDetectorRunDir}
 126
 127     tmpPrefix=${tmpDetectorRunDir}/${outputDir}
 128     echo "running QA for ${detector}"
 129     echo "  outputDir=$outputDir"
 130     echo "  tmpPrefix=$tmpPrefix"
 131
 132     #source the detector script
 133     #unset the detector functions from previous iterations (detectors)
 134     unset -f runLevelQA
 135     unset -f runLevelQAouter
 136     unset -f periodLevelQA
 137     unset -f runLevelEventStatQA
 138     unset -f runLevelHighPtTreeQA
 139     unset -f periodLevelHighPtTreeQA
 140     source ${detectorScript}
 141
 142     #################################################################
 143     #produce the QA and trending tree for each file (run)
 144     unset arrOfTouchedProductions
 145     declare -A arrOfTouchedProductions
 146     while read inputFile; do
 147       echo
 148       echo $(date)
 149
 150       #first check if input file exists
 151       [[ ! -f ${inputFile%\#*} ]] && echo "file ${inputFile%\#*} not accessible" && continue
 152
 153       if ! guessRunData ${inputFile}; then
 154         echo "could not guess run data from ${inputFile}"
 155         continue
 156       fi
 157       echo "anchorYear for ${originalPeriod} is: ${anchorYear}"
 158
 159       tmpProductionDir=${tmpPrefix}/${dataType}/${year}/${period}/${pass}
 160       tmpRunDir=${tmpProductionDir}/000${runNumber}
 161       mkdir -p ${tmpRunDir}
 162       cd ${tmpRunDir}
 163
 164       #check what kind of input file we have, default is a zip archive
 165       #set the inputs accordingly
 166       qaFile=""
 167       qaFileOuter=""
 168       highPtTree=""
 169       eventStatFile=""
 170       eventStatFileOuter=""
 171       #it is possible we get the highPt trees from somewhere else
 172       #search the list of high pt trees for the proper run number
 173       if [[ -n ${inputListHighPtTrees} ]]; then
 174         highPtTree=$(egrep -m1 ${runNumber} ${inputListHighPtTrees})
 175         echo "loaded the highPtTree ${highPtTree} from external file ${inputListHighPtTrees}"
 176       fi
 177       #if we are explicit about the input file this takes precedence
 178       #over earlier additions
 179       [[ "${inputFile}" =~ QAresults.root$ ]] && qaFile=${inputFile}
 180       [[ "${inputFile}" =~ QAresults_outer.root$ ]] && qaFileOuter=${inputFile}
 181       [[ "${inputFile}" =~ FilterEvents_Trees.root$ ]] && highPtTree=${inputFile}
 182       [[ "${inputFile}" =~ event_stat.root$ ]] && eventStatFile=${inputFile}
 183       [[ "${inputFile}" =~ event_stat_outer.root$ ]] && eventStatFileOuter=${inputFile}
 184       if [[ "${inputFile}" =~ \.zip$ ]]; then
 185         [[ -z ${qaFile} ]] && qaFile=${inputFile}
 186         [[ -z ${qaFileOuter} ]] && qaFileOuter=${inputFile}
 187         [[ -z ${highPtTree} ]] && highPtTree=${inputFile}
 188         [[ -z ${eventStatFile} ]] && eventStatFile=${inputFile}
 189         [[ -z ${eventStatFileOuter} ]] && eventStatFileOuter=${inputFile}
 190       fi
 191
 192       #if we have zip archives in the input, extract the proper file name
 193       #from the archive and append in a root-like fashion
 194       if [[ "$qaFile" =~ .*.zip$ ]]; then
 195         if unzip -l ${qaFile} | egrep "QAresults.root" &>/dev/null; then
 196           qaFile+="#QAresults.root"
 197         elif unzip -l ${qaFile} | egrep "QAresults_barrel.root" &>/dev/null; then
 198           qaFile+="#QAresults_barrel.root"
 199         else
 200           qaFile=""
 201         fi
 202       fi
 203       if [[ "$qaFileOuter" =~ .*.zip$ ]]; then
 204         if unzip -l ${qaFileOuter} | egrep "QAresults_outer.root" &>/dev/null; then
 205           qaFileOuter+="#QAresults_outer.root"
 206         else
 207           qaFileOuter=""
 208         fi
 209       fi
 210       if [[ "$highPtTree" =~ .*.zip$ ]]; then
 211         if unzip -l ${highPtTree} | egrep "FilterEvents_Trees.root" &>/dev/null; then
 212           highPtTree+="#FilterEvents_Trees.root"
 213         else
 214           highPtTree=""
 215         fi
 216       fi
 217       if [[ "${eventStatFile}" =~ .*.zip$ ]]; then
 218         if unzip -l ${eventStatFile} | egrep "event_stat.root" &>/dev/null; then
 219           eventStatFile+="#event_stat.root"
 220         elif unzip -l ${eventStatFile} | egrep "event_stat_barrel.root" &>/dev/null; then
 221           eventStatFile+="#event_stat_barrel.root"
 222         else
 223           eventStatFile=""
 224         fi
 225       fi
 226       if [[ "${eventStatFileOuter}" =~ .*.zip$ ]]; then
 227         if unzip -l ${eventStatFileOuter} | egrep "event_stat_outer.root" &>/dev/null; then
 228           eventStatFileOuter+="#event_stat.root"
 229         else
 230           eventStatFileOuter=""
 231         fi
 232       fi
 233
 234       echo qaFile=$qaFile
 235       echo qaFileOuter=$qaFileOuter
 236       echo highPtTree=$highPtTree
 237       echo eventStatFile=$eventStatFile
 238       echo eventStatFileOuter=$eventStatFileOuter
 239       echo ocdbStorage=${ocdbStorage}
 240       echo
 241
 242       #standard QA based on QAresults.root file (and variants)
 243       if [[ -n ${qaFile} && $(type -t runLevelQA) =~ "function" ]]; then
 244         echo running ${detector} runLevelQA for run ${runNumber} from ${qaFile}
 245         ( runLevelQA "${qaFile}" ) &>> runLevelQA.log
 246         #cache the touched production + an example file to guarantee consistent run data parsing
 247         arrOfTouchedProductions[${tmpProductionDir}]="${inputFile%\#*}"
 248       fi
 249       #standard QA based on QAresults_outer.root file (there in cpass, with different triggers)
 250       if [[ -n ${qaFileOuter} && $(type -t runLevelQAouter) =~ "function" ]]; then
 251         echo running ${detector} runLevelQAouter for run ${runNumber} from ${qaFileOuter}
 252         ( runLevelQAouter "${qaFileOuter}" ) &>> runLevelQA.log
 253         #cache the touched production + an example file to guarantee consistent run data parsing
 254         arrOfTouchedProductions[${tmpProductionDir}]="${inputFile%\#*}"
 255       fi
 256       #expert QA based on high pt trees
 257       if [[ -n ${highPtTree} && $(type -t runLevelHighPtTreeQA) =~ "function" ]]; then
 258         echo running ${detector} runLevelHighPtTreeQA for run ${runNumber} from ${highPtTree}
 259         ( runLevelHighPtTreeQA "${highPtTree}" ) &>> runLevelQA.log
 260         #cache the touched production + an example file to guarantee consistent run data parsing
 261         arrOfTouchedProductions[${tmpProductionDir}]="${inputFile%\#*}"
 262       fi
 263       #event stat QA based on event_stat.root file
 264       if [[ -n ${eventStatFile} && $(type -t runLevelEventStatQA) =~ "function" ]]; then
 265         echo running ${detector} runLevelEventStatQA for run ${runNumber} from ${eventStatFile}
 266         ( runLevelEventStatQA "${eventStatFile}" ) &>> runLevelQA.log
 267         #cache the touched production + an example file to guarantee consistent run data parsing
 268         arrOfTouchedProductions[${tmpProductionDir}]="${inputFile%\#*}"
 269       fi
 270       #event stat QA based on event_stat_outer.root file
 271       if [[ -n ${eventStatFileOuter} && $(type -t runLevelEventStatQAouter) =~ "function" ]]; then
 272         echo running ${detector} runLevelEventStatQAouter for run ${runNumber} from ${eventStatFileOuter}
 273         ( runLevelEventStatQAouter "${eventStatFileOuter}" ) &>> runLevelQA.log
 274         #cache the touched production + an example file to guarantee consistent run data parsing
 275         arrOfTouchedProductions[${tmpProductionDir}]="${inputFile%\#*}"
 276       fi
 277
 278       #perform some default actions:
 279       #if trending.root not created, create a default one
 280       if [[ ! -f trending.root ]]; then
 281         aliroot -b -q -l "$ALICE_ROOT/PWGPP/macros/simpleTrending.C(\"${qaFile}\",${runNumber},\"${detectorQAcontainerName}\",\"trending.root\",\"trending\",\"recreate\")" 2>&1 | tee -a runLevelQA.log
 282       fi
 283       if [[ ! -f trending.root ]]; then
 284         echo "trending.root not created"
 285       fi
 286
 287       cd ${tmpDetectorRunDir}
 288
 289     done < ${inputList}
 290
 291     #################################################################
 292     #cache which productions were (re)done
 293     echo "list of processed productions:"
 294     echo "    ${!arrOfTouchedProductions[@]}"
 295     echo
 296
 297     #################################################################
 298     #(re)do the merging/trending
 299     for tmpProductionDir in ${!arrOfTouchedProductions[@]}; do
 300       cd ${tmpProductionDir}
 301       echo
 302       echo "running period level stuff in ${tmpProductionDir}"
 303       echo $(date)
 304
 305       productionDir=${outputDir}/${tmpProductionDir#${tmpPrefix}}
 306       echo productionDir=${outputDir}/${tmpProductionDir#${tmpPrefix}}
 307
 308       mkdir -p ${productionDir}
 309       if [[ ! -d ${productionDir} ]]; then
 310         echo "cannot make productionDir $productionDir" && continue
 311       fi
 312
 313       #move runs to final destination
 314       for dir in ${tmpProductionDir}/000*; do
 315         echo
 316         oldRunDir=${outputDir}/${dir#${tmpPrefix}}
 317         if ! guessRunData "${arrOfTouchedProductions[${tmpProductionDir}]}"; then
 318           echo "could not guess run data from ${arrOfTouchedProductions[${tmpProductionDir}]}"
 319           continue
 320         fi
 321
 322         #before moving - VALIDATE!!!
 323         if ! validate ${dir}; then
 324           continue
 325         fi
 326
 327         #moving a dir is an atomic operation, no locking necessary
 328         if [[ -d ${oldRunDir} ]]; then
 329           echo "removing old ${oldRunDir}"
 330           rm -rf ${oldRunDir}
 331         fi
 332         echo "moving new ${runNumber} to ${productionDir}"
 333         mv -f ${dir} ${productionDir}
 334       done
 335
 336       #go to a temp dir to do the period level stuff in a completely clean dir
 337       tmpPeriodLevelQAdir="${tmpProductionDir}/periodLevelQA"
 338       echo
 339       echo tmpPeriodLevelQAdir="${tmpPeriodLevelQAdir}"
 340       if ! mkdir -p ${tmpPeriodLevelQAdir}; then continue; fi
 341       cd ${tmpPeriodLevelQAdir}
 342
 343       #link the final list of per-run dirs here, just the dirs
 344       #to have a clean working directory
 345       unset linkedStuff
 346       declare -a linkedStuff
 347       for x in ${productionDir}/000*; do [[ -d $x ]] && ln -s $x && linkedStuff+=(${x##*/}); done
 348
 349       #merge trending files if any
 350       if /bin/ls 000*/trending.root &>/dev/null; then
 351         hadd trending.root 000*/trending.root &> periodLevelQA.log
 352       fi
 353
 354       #run the period level trending/QA
 355       if [[ -f "trending.root" && $(type -t periodLevelQA) =~ "function" ]]; then
 356         echo running ${detector} periodLevelQA for production ${period}/${pass}
 357         ( periodLevelQA trending.root ) &>> periodLevelQA.log
 358       else
 359         echo "WARNING: not running ${detector} periodLevelQA for production ${period}/${pass}, no trending.root"
 360       fi
 361
 362       if ! validate ${PWD}; then continue; fi
 363
 364       #here we are validated so move the produced QA to the final place
 365       #clean up linked stuff first
 366       [[ -n ${linkedStuff[@]} ]] && rm ${linkedStuff[@]}
 367       periodLevelLock=${productionDir}/runQA.lock
 368       if [[ ! -f ${periodLevelLock} ]]; then
 369         #some of the output could be a directory, so handle that
 370         #TODO: maybe use rsync?
 371         #lock to avoid conflicts:
 372         echo "${HOSTNAME} ${dateString}" > ${periodLevelLock}
 373         for x in ${tmpPeriodLevelQAdir}/*; do
 374           if [[ -d ${x} ]]; then
 375             echo "removing ${productionDir}/${x##*/}"
 376             rm -rf ${productionDir}/${x##*/}
 377             echo "moving ${x} to ${productionDir}"
 378             mv ${x} ${productionDir}
 379           fi
 380           if [[ -f ${x} ]]; then
 381             echo "moving ${x} to ${productionDir}"
 382             mv -f ${x} ${productionDir}
 383           fi
 384         done
 385         rm -f ${periodLevelLock}
 386         #remove the temp dir
 387         rm -rf ${tmpPeriodLevelQAdir}
 388       else
 389         echo "ERROR: cannot move to destination"                     >> ${logSummary}
 390         echo "production dir ${productionDir} locked!"               >> ${logSummary}
 391         echo "check and maybe manually do:"                          >> ${logSummary}
 392         echo " rm ${periodLevelLock}"                                >> ${logSummary}
 393         echo " rsync -av ${tmpPeriodLevelQAdir}/ ${productionDir}/"  >> ${logSummary}
 394         planB=1
 395       fi
 396
 397     done
 398
 399     cd ${workingDirectory}
 400
 401     if [[ -z ${planB} ]]; then
 402       echo
 403       echo removing ${tmpDetectorRunDir}
 404       rm -rf ${tmpDetectorRunDir}
 405     else
 406       executePlanB
 407     fi
 408   done #end of detector loop
 409
 410   #remove lock
 411   rm -f ${lockFile}
 412   return 0
 413 }
 414
 415 executePlanB()
 416 {
 417   #in case of emergency
 418   #first check if we have the email of the detector expert defined,
 419   #if yes, append to the mailing list
 420   local mailTo=${MAILTO}
 421   local detExpertEmailVar="MAILTO_${detector}"
 422   [[ -n "${!detExpertEmailVar}" ]] && mailTo+=" ${!detExpertEmailVar}"
 423   if [[ -n ${mailTo} ]]; then
 424     echo
 425     echo "trouble detected, sending email to ${mailTo}"
 426     cat ${logSummary} | mail -s "${detector} QA in need of assistance" ${mailTo}
 427   fi
 428   return 0
 429 }
 430
 431 validate()
 432 {
 433   summarizeLogs ${1} >> ${logSummary}
 434   logStatus=$?
 435   if [[ ${logStatus} -ne 0 ]]; then
 436     echo "WARNING not validated: ${1}"
 437     planB=1
 438     return 1
 439   fi
 440   return 0
 441 }
 442
 443 summarizeLogs()
 444 {
 445   local dir=$1
 446   [[ ! -d ${dir} ]] && dir=${PWD}
 447
 448   #print a summary of logs
 449   logFiles=(
 450       "*.log"
 451       "stdout"
 452       "stderr"
 453   )
 454
 455   #check logs
 456   local logstatus=0
 457   for log in ${dir}/${logFiles[*]}; do
 458     [[ ! -f ${log} ]] && continue
 459     errorSummary=$(validateLog ${log})
 460     validationStatus=$?
 461     [[ validationStatus -ne 0 ]] && logstatus=1
 462     if [[ ${validationStatus} -eq 0 ]]; then
 463       #in pretend mode randomly report an error in rec.log some cases
 464       if [[ -n ${pretend} && "${log}" == "rec.log" ]]; then
 465         [[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${log} BAD random error" || echo "${log} OK"
 466       else
 467         echo "${log} OK"
 468       fi
 469     elif [[ ${validationStatus} -eq 1 ]]; then
 470       echo "${log} BAD ${errorSummary}"
 471     elif [[ ${validationStatus} -eq 2 ]]; then
 472       echo "${log} OK MWAH ${errorSummary}"
 473     fi
 474   done
 475
 476   #report core files
 477   while read x; do
 478     echo ${x}
 479     chmod 644 ${x}
 480     gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
 481   done < <(/bin/ls ${PWD}/*/core 2>/dev/null; /bin/ls ${PWD}/core 2>/dev/null)
 482
 483   return ${logstatus}
 484 }
 485
 486 validateLog()
 487 {
 488   log=${1}
 489   errorConditions=(
 490             'There was a crash'
 491             'floating'
 492             'error while loading shared libraries'
 493             'std::bad_alloc'
 494             's_err_syswatch_'
 495             'Thread [0-9]* (Thread'
 496             'AliFatal'
 497             'core dumped'
 498             '\.C.*error:.*\.h: No such file'
 499             'segmentation'
 500             'Interpreter error recovered'
 501   )
 502
 503   warningConditions=(
 504             'This is serious'
 505   )
 506
 507   local logstatus=0
 508   local errorSummary=""
 509   local warningSummary=""
 510
 511   for ((i=0; i<${#errorConditions[@]};i++)); do
 512     local tmp=$(grep -m1 -e "${errorConditions[${i}]}" ${log})
 513     [[ -n ${tmp} ]] && tmp+=" : "
 514     errorSummary+=${tmp}
 515   done
 516
 517   for ((i=0; i<${#warningConditions[@]};i++)); do
 518     local tmp=$(grep -m1 -e "${warningConditions[${i}]}" ${log})
 519     [[ -n ${tmp} ]] && tmp+=" : "
 520     warningSummary+=${tmp}
 521   done
 522
 523   if [[ -n ${errorSummary} ]]; then
 524     echo "${errorSummary}"
 525     return 1
 526   fi
 527
 528   if [[ -n ${warningSummary} ]]; then
 529     echo "${warningSummary}"
 530     return 2
 531   fi
 532
 533   return 0
 534 }
 535
 536 parseConfig()
 537 {
 538   args=("$@")
 539
 540   #config file
 541   configFile=""
 542   #where to search for qa files
 543   inputList=file.list
 544   #working directory
 545   workingDirectory="${PWD}"
 546   #where to place the final qa plots
 547   #outputDirectory="/afs/cern.ch/work/a/aliqa%det/www/"
 548   outputDirectory="${workingDirectory}/%DET"
 549   #filter out detector option
 550   excludeDetectors="EXAMPLE"
 551   #logs
 552   logDirectory=${workingDirectory}/logs
 553   #OCDB storage
 554   ocdbStorage="raw://"
 555   #email to
 556   #MAILTO="fbellini@cern.ch"
 557   runMap="
 558   2010 108350 139517
 559   2011 140441 170593
 560   2012 171590 193766
 561   2013 194482 197692
 562   "
 563
 564   #first, check if the config file is configured
 565   #is yes - source it so that other options can override it
 566   #if any
 567   for opt in "${args[@]}"; do
 568     if [[ ${opt} =~ configFile=.* ]]; then
 569       eval "${opt}"
 570       [[ ! -f ${configFile} ]] && echo "configFile ${configFile} not found, exiting..." && return 1
 571       echo "using config file: ${configFile}"
 572       source "${configFile}"
 573       break
 574     fi
 575   done
 576
 577   #then, parse the options as they override the options from file
 578   for opt in "${args[@]}"; do
 579     if [[ ! "${opt}" =~ .*=.* ]]; then
 580       echo "badly formatted option ${var}, should be: option=value, stopping..."
 581       return 1
 582     fi
 583     local var="${opt%%=*}"
 584     local value="${opt#*=}"
 585     echo "${var}=${value}"
 586     export ${var}="${value}"
 587   done
 588   return 0
 589 }
 590
 591 guessRunData()
 592 {
 593   #guess the period from the path, pick the rightmost one
 594   period=""
 595   runNumber=""
 596   year=""
 597   pass=""
 598   legoTrainRunNumber=""
 599   dataType=""
 600   originalPass=""
 601   originalPeriod=""
 602   anchorYear=""
 603
 604   shortRunNumber=""
 605   oldIFS=${IFS}
 606   local IFS="/"
 607   declare -a path=( $1 )
 608   IFS="${oldIFS}"
 609   local dirDepth=$(( ${#path[*]}-1 ))
 610   i=0
 611   for ((x=${dirDepth};x>=0;x--)); do
 612
 613     [[ $((x-1)) -ge 0 ]] && local fieldPrev=${path[$((x-1))]}
 614     local field=${path[${x}]}
 615     local fieldNext=${path[$((x+1))]}
 616
 617     [[ ${field} =~ ^[0-9]*$ && ${fieldNext} =~ (.*\.zip$|.*\.root$) ]] && legoTrainRunNumber=${field}
 618     [[ -n ${legoTrainRunNumber} && -z ${pass} ]] && pass=${fieldPrev}
 619     [[ ${field} =~ ^LHC[0-9][0-9][a-z].*$ ]] && period=${field%_*} && originalPeriod=${field}
 620     [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000}
 621     [[ ${field} =~ ^[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && shortRunNumber=${field}
 622     [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
 623     [[ ${field} =~ ^(^sim$|^data$) ]] && dataType=${field}
 624     (( i++ ))
 625   done
 626   originalPass=${pass}
 627   [[ -n ${shortRunNumber} && "${legoTrainRunNumber}" =~ ${shortRunNumber} ]] && legoTrainRunNumber=""
 628   [[ -z ${legoTrainRunNumber} ]] && pass=${path[$((dirDepth-1))]}
 629   [[ "${dataType}" =~ ^sim$ ]] && pass="passMC" && runNumber=${shortRunNumber} && originalPass="" #for MC not from lego, the runnumber is identified as lego train number, thus needs to be nulled
 630   [[ -n ${legoTrainRunNumber} ]] && pass+="_lego${legoTrainRunNumber}"
 631
 632   #modify the OCDB: set the year
 633   if [[ ${dataType} =~ sim ]]; then
 634     anchorYear=$(run2year $runNumber)
 635     if [[ -z "${anchorYear}" ]]; then
 636       echo "WARNING: anchorYear not available for this production: ${originalPeriod}, runNumber: ${runNumber}. Cannot set the OCDB."
 637       return 1
 638     fi
 639     ocdbStorage=$(setYear ${anchorYear} ${ocdbStorage})
 640   else
 641     ocdbStorage=$(setYear ${year} ${ocdbStorage})
 642   fi
 643
 644   #if [[ -z ${dataType} || -z ${year} || -z ${period} || -z ${runNumber}} || -z ${pass} ]];
 645   if [[ -z ${runNumber} ]]
 646   then
 647     #error condition
 648     return 1
 649   fi
 650
 651   #ALL OK
 652   return 0
 653 }
 654
 655 run2year()
 656 {
 657   #for a given run print the year.
 658   #the run-year table is ${runMap} (a string)
 659   #defined in the config file
 660   #one line per year, format: year runMin runMax
 661   local run=$1
 662   [[ -z ${run} ]] && return 1
 663   local year=""
 664   local runMin=""
 665   local runMax=""
 666   while read year runMin runMax; do
 667     [[ -z ${year} || -z ${runMin} || -z ${runMax} ]] && continue
 668     [[ ${run} -ge ${runMin} && ${run} -le ${runMax} ]] && echo ${year} && break
 669   done < <(echo "${runMap}")
 670   return 0
 671 }
 672
 673 substituteDetectorName()
 674 {
 675   local det=$1
 676   local dir=$2
 677   [[ ${dir} =~ \%det ]] && det=${det,,} && echo ${dir/\%det/${det}}
 678   [[ ${dir} =~ \%DET ]] && det=${det} && echo ${dir/\%DET/${det}}
 679   return 0
 680 }
 681
 682 get_realpath()
 683 {
 684   if [[ -f "$1" ]]
 685   then
 686     # file *must* exist
 687     if cd "$(echo "${1%/*}")" &>/dev/null
 688     then
 689       # file *may* not be local
 690       # exception is ./file.ext
 691       # try 'cd .; cd -;' *works!*
 692       local tmppwd="$PWD"
 693       cd - &>/dev/null
 694     else
 695       # file *must* be local
 696       local tmppwd="$PWD"
 697     fi
 698   else
 699     # file *cannot* exist
 700     return 1 # failure
 701   fi
 702   # reassemble realpath
 703   echo "$tmppwd"/"${1##*/}"
 704   return 0 # success
 705 }
 706
 707 setYear()
 708 {
 709   #set the year
 710   #  ${1} - year to be set
 711   #  ${2} - where to set the year
 712   local year1=$(guessYear ${1})
 713   local year2=$(guessYear ${2})
 714   local path=${2}
 715   [[ ${year1} -ne ${year2} && -n ${year2} && -n ${year1} ]] && path=${2/\/${year2}\//\/${year1}\/}
 716   echo ${path}
 717   return 0
 718 }
 719
 720 guessYear()
 721 {
 722   #guess the year from the path, pick the rightmost one
 723   local IFS="/"
 724   declare -a pathArray=( ${1} )
 725   local field
 726   local year
 727   for field in ${pathArray[@]}; do
 728     [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
 729   done
 730   echo ${year}
 731   return 0
 732 }
 733
 734 hostInfo(){
 735 #
 736 # Hallo world -  Print AliRoot/Root/Alien system info
 737 #
 738
 739 #
 740 # HOST info
 741 #
 742     echo --------------------------------------
 743         echo
 744         echo HOSTINFO
 745         echo
 746         echo HOSTINFO HOSTNAME"      "$HOSTNAME
 747         echo HOSTINFO DATE"          "`date`
 748         echo HOSTINFO gccpath"       "`which gcc`
 749         echo HOSTINFO gcc version"   "`gcc --version | grep gcc`
 750         echo --------------------------------------
 751
 752 #
 753 # ROOT info
 754 #
 755         echo --------------------------------------
 756         echo
 757         echo ROOTINFO
 758         echo
 759         echo ROOTINFO ROOT"           "`which root`
 760         echo ROOTINFO VERSION"        "`root-config --version`
 761         echo
 762         echo --------------------------------------
 763
 764
 765 #
 766 # ALIROOT info
 767 #
 768         echo --------------------------------------
 769         echo
 770         echo ALIROOTINFO
 771         echo
 772         echo ALIROOTINFO ALIROOT"        "`which aliroot`
 773         echo ALIROOTINFO VERSION"        "`echo $ALICE_LEVEL`
 774         echo ALIROOTINFO TARGET"         "`echo $ALICE_TARGET`
 775         echo
 776         echo --------------------------------------
 777
 778 #
 779 # Alien info
 780 #
 781 #echo --------------------------------------
 782 #echo
 783 #echo ALIENINFO
 784 #for a in `alien --printenv`; do echo ALIENINFO $a; done
 785 #echo
 786 #echo --------------------------------------
 787
 788 #
 789 # Local Info
 790 #
 791         echo PWD `pwd`
 792         echo Dir
 793         ls -al
 794         echo
 795         echo
 796         echo
 797
 798   return 0
 799 }
 800
 801 main "$@"