JeffersonLab · c-dilks · Apr 16, 2025 · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,6 +4,9 @@ registries:
   clas12maven:
     type: maven-repository
     url: https://clasweb.jlab.org/clas12maven
+  groovy_jfrog:
+    type: maven-repository
+    url: https://groovy.jfrog.io/artifactory/plugins-release
 
 updates:
   - package-ecosystem: "maven"
@@ -12,6 +15,7 @@ updates:
       interval: "weekly"
     registries:
       - clas12maven
+      - groovy_jfrog
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,11 +12,9 @@ defaults:
 
 env:
   dataset: ci_test
-  rcdb_connection: mysql://rcdb@clasdb.jlab.org/rcdb # RCDB server available to runners
   # NOTE: if any of these versions are changed, update the POM files too
   java_version: 21
   java_distribution: zulu
-  groovy_version: 4.x
 
 
 concurrency:
@@ -38,42 +36,16 @@ jobs:
         java-version: ${{ env.java_version }}
         distribution: ${{ env.java_distribution }}
     - name: build
-      run: mvn package
+      run: ./install.sh
     - name: tar # to preserve any permissions
       run: |
-        tar cavf build_detectors.tar.zst detectors/target
-        tar cavf build_monitoring.tar.zst monitoring/target
+        tar cavf build_timeline.tar.zst target
     - uses: actions/upload-artifact@v4
       with:
         name: build_timelines
         retention-days: 1
         path: build*.tar.zst
 
-  build_coatjava:
-    runs-on: ubuntu-latest
-    steps:
-    - name: setup java
-      uses: actions/setup-java@v4
-      with:
-        java-version: ${{ env.java_version }}
-        distribution: ${{ env.java_distribution }}
-    - name: checkout coatjava
-      uses: actions/checkout@v4
-      with:
-        repository: JeffersonLab/coatjava
-        ref: development
-    - name: build coatjava
-      run: ./build-coatjava.sh
-    - name: tree
-      run: tree
-    - name: tar
-      run: tar cavf build_coatjava.tar.zst coatjava
-    - uses: actions/upload-artifact@v4
-      with:
-        name: build_coatjava
-        retention-days: 1
-        path: build*.tar.zst
-
   # download test data
   #############################################################################
 
@@ -112,7 +84,6 @@ jobs:
   run_monitoring:
     needs:
       - build_timelines
-      - build_coatjava
       - download_test_data
     runs-on: ubuntu-latest
     strategy:
@@ -125,12 +96,6 @@ jobs:
       with:
         java-version: ${{ env.java_version }}
         distribution: ${{ env.java_distribution }}
-    - name: setup groovy
-      uses: wtfjoke/setup-groovy@v2
-      with:
-        groovy-version: ${{ env.groovy_version }}
-    - name: groovy version
-      run: groovy --version
     - uses: actions/checkout@v4
     - uses: actions/cache/restore@v4
       with:
@@ -144,8 +109,6 @@ jobs:
       run: ls *.tar.zst | xargs -I{} tar xavf {}
     - name: tree
       run: tree
-    - name: set RCDB connection # to one that's available to the runner
-      run: echo RCDB_CONNECTION=${{env.rcdb_connection}} | tee -a $GITHUB_ENV
     - name: run monitoring
       run: bin/run-monitoring.sh -d ${{env.dataset}} --findhipo --series --focus-${{matrix.type}} validation_files
     - name: tree slurm
@@ -166,7 +129,6 @@ jobs:
   test_swifjob:
     needs:
       - build_timelines
-      - build_coatjava
       - download_test_data
     runs-on: ubuntu-latest
     strategy:
@@ -179,12 +141,6 @@ jobs:
       with:
         java-version: ${{ env.java_version }}
         distribution: ${{ env.java_distribution }}
-    - name: setup groovy
-      uses: wtfjoke/setup-groovy@v2
-      with:
-        groovy-version: ${{ env.groovy_version }}
-    - name: groovy version
-      run: groovy --version
     - uses: actions/checkout@v4
     - uses: actions/cache/restore@v4
       with:
@@ -198,8 +154,6 @@ jobs:
       run: ls *.tar.zst | xargs -I{} tar xavf {}
     - name: tree
       run: tree
-    - name: set RCDB connection # to one that's available to the runner
-      run: echo RCDB_CONNECTION=${{env.rcdb_connection}} | tee -a $GITHUB_ENV
     - name: test monitoring swifjob
       run: |
         single_rundir=$(find validation_files -mindepth 1 -maxdepth 1 -type d | head -n1)
@@ -227,12 +181,6 @@ jobs:
       with:
         java-version: ${{ env.java_version }}
         distribution: ${{ env.java_distribution }}
-    - name: setup groovy
-      uses: wtfjoke/setup-groovy@v2
-      with:
-        groovy-version: ${{ env.groovy_version }}
-    - name: groovy version
-      run: groovy --version
     - uses: actions/checkout@v4
     - uses: actions/download-artifact@v4
       with:
@@ -266,12 +214,6 @@ jobs:
       - run_timelines
     runs-on: ubuntu-latest
     steps:
-    - name: setup groovy
-      uses: wtfjoke/setup-groovy@v2
-      with:
-        groovy-version: ${{ env.groovy_version }}
-    - name: groovy version
-      run: groovy --version
     - uses: actions/checkout@v4
     - uses: actions/download-artifact@v4
       with:

diff --git a/.gitignore b/.gitignore
@@ -1,10 +1,13 @@
 # text editor tmp files
 .*.sw*
 .sw*
+.settings
+.project
+.classpath
+.factorypath
 
 # builds
-detectors/target
-monitoring/target
+/target
 
 # transient files
 *.hipo

diff --git a/bin/deploy-timelines.sh b/bin/deploy-timelines.sh
@@ -169,7 +169,7 @@ mkdir -pv $targetDir
 cp -rv $inputDir/* $targetDir/
 [ -n "$metadataFile" ] && cp -v $metadataFile $targetDir/metadata.json
 [ -n "$readmeNote" ] && echo "$readmeNote" > $targetDir/README
-run-groovy $TIMELINE_GROOVY_OPTS $TIMELINESRC/bin/index-webpage.groovy $targetDir
+$TIMELINESRC/bin/run-groovy-timeline.sh $TIMELINESRC/bin/index-webpage.groovy $targetDir
 echo "DONE."
 
 # print URL

diff --git a/bin/dump-timelines.groovy b/bin/dump-timelines.groovy
@@ -4,7 +4,7 @@ import org.jlab.groot.data.TDirectory
 def outFilePrefix = "out"
 if(args.length<1) {
   System.err.println """
-  USAGE: run-groovy ${this.class.getSimpleName()}.groovy [TIMELINE] [OUTPUT FILE PREFIX]
+  USAGE: groovy ${this.class.getSimpleName()}.groovy [TIMELINE] [OUTPUT FILE PREFIX]
   - [TIMELINE] may either be a timeline URL or a timeline HIPO file
   - [OUTPUT FILE PREFIX] for the dumped timelines (default = $outFilePrefix)
   """

diff --git a/bin/environ.sh b/bin/environ.sh
@@ -7,63 +7,24 @@ printWarning() { echo -e "\e[1;35m[WARNING]: $* \e[0m" >&2; }
 # enable/disable verbose logger
 log_config=logging # set to 'logging' for quiet, or to 'debug' for verbose
 
-# get the working directory
-[ -z "${BASH_SOURCE[0]}" ] && thisEnv=$0 || thisEnv=${BASH_SOURCE[0]}
-export TIMELINESRC=$(realpath $(dirname $thisEnv)/..)
+# get the source code directory
+[ -z "${BASH_SOURCE[0]}" ] && this_env=$0 || this_env=${BASH_SOURCE[0]}
+export TIMELINESRC=$(realpath $(dirname $this_env)/..)
 
 # RCDB
-[ -z "${RCDB_CONNECTION-}" ] && RCDB_CONNECTION=mysql://rcdb@clasdb-farm.jlab.org/rcdb
-export RCDB_CONNECTION
+[ -z "${RCDB_CONNECTION-}" ] && export RCDB_CONNECTION=mysql://rcdb@clasdb.jlab.org/rcdb
 
-# check coatjava environment
-if [ -z "${COATJAVA-}" ]; then
-  # if on a CI runner, use CI coatjava build artifacts; otherwise print error
-  coatjava_ci=$TIMELINESRC/coatjava
-  [ -d $coatjava_ci ] &&
-    export COATJAVA=$coatjava_ci ||
-    printError "cannot find coatjava; please make sure environment variable COATJAVA is set to your coatjava installation"
-fi
-
-# ensure coatjava executables are found
-[ -n "${COATJAVA-}" ] && export PATH="$COATJAVA/bin${PATH:+:${PATH}}"
-
-# class paths
-java_classpath=(
-  "$COATJAVA/lib/clas/*"
-  "$COATJAVA/lib/utils/*"
-  "$TIMELINESRC/monitoring/target/*"
-)
-groovy_classpath=(
-  "$TIMELINESRC/detectors/target/*"
-  "$(dirname $(dirname $(which groovy)))/lib/*"
-)
-
-# java and groovy options
+# java options
 timeline_java_opts=(
-  -DCLAS12DIR=$COATJAVA/
-  -Djava.util.logging.config.file=$COATJAVA/etc/logging/$log_config.properties
+  -cp "$TIMELINESRC/target/*:$TIMELINESRC/target/dependency/*"
+  -Djava.util.logging.config.file=$TIMELINESRC/data/logging/$log_config.properties
   -Xmx1536m
   -XX:+UseSerialGC
-)
-timeline_groovy_opts=(
   -Djava.awt.headless=true
 )
-
-# run java with more resources, to mitigate large memory residence for long run periods
-timeline_java_opts_highmem=$(echo ${timeline_java_opts[*]} | sed 's;Xmx1024m;Xmx2048m;')
-
-# exports
-export CLASSPATH="$(echo "${java_classpath[*]}" | sed 's; ;:;g')${CLASSPATH:+:${CLASSPATH}}"
-export JYPATH="$(echo "${groovy_classpath[*]}" | sed 's; ;:;g')${JYPATH:+:${JYPATH}}"
 export TIMELINE_JAVA_OPTS="${timeline_java_opts[*]}"
-export TIMELINE_GROOVY_OPTS="${timeline_groovy_opts[*]}"
-export TIMELINE_JAVA_OPTS_HIGHMEM=$timeline_java_opts_highmem
 
 # cleanup vars
-unset thisEnv
+unset this_env
 unset log_config
-unset java_classpath
-unset groovy_classpath
 unset timeline_java_opts
-unset timeline_groovy_opts
-unset timeline_java_opts_highmem
diff --git a/bin/get-beam-energy.sh b/bin/get-beam-energy.sh
@@ -4,7 +4,4 @@ set -e
 set -u
 source $(dirname $0)/environ.sh
 
-# set class path to include groovy's classpath, for `java` calls
-export CLASSPATH="$JYPATH${CLASSPATH:+:${CLASSPATH}}"
-
-java org.jlab.clas.timeline.get_beam_energy $*
+java $TIMELINE_JAVA_OPTS org.jlab.clas.timeline.get_beam_energy $*
diff --git a/bin/get-run-number.groovy b/bin/get-run-number.groovy
@@ -4,7 +4,7 @@ Tools T = new Tools()
 
 if(args.length<1) {
   System.err.println """
-  USAGE: run-groovy ${this.class.getSimpleName()}.groovy [HIPO file]
+  USAGE: groovy ${this.class.getSimpleName()}.groovy [HIPO file]
   Returns run number for a given file
   """
   System.exit(101)

diff --git a/bin/hipo-check.sh b/bin/hipo-check.sh
@@ -59,7 +59,7 @@ for hipoFile in ${hipoFiles[@]}; do
 
   # run `hipo-utils -test`
   set +e
-  hipo-utils -test $hipoFile
+  java $TIMELINE_JAVA_OPTS org.jlab.jnp.hipo4.utils.HipoUtilities -test $hipoFile
   testCode=$?
   set -e
   [ $testCode -ne 0 ] && markBad $hipoFile "\`hipo-utils -test\` failed" && continue

diff --git a/bin/hipo-trim.sh b/bin/hipo-trim.sh
@@ -54,7 +54,7 @@ for inputDir in $inputDirs; do
       outputSubDir: $outputSubDir
     """
 
-    # if the output file exists, `hipo-utils -filter` will fail
+    # if the output file exists, `HipoUtilities -filter` will fail
     if [ -f $outputFile ]; then
       echo """
       ERROR: this output file already exists...
@@ -69,7 +69,7 @@ for inputDir in $inputDirs; do
     mkdir -pv $outputSubDir
 
     # trim the input file
-    hipo-utils -filter \
+    java $TIMELINE_JAVA_OPTS org.jlab.jnp.hipo4.utils.HipoUtilities -filter \
       -b "*::*"      \
       -n $nEvents    \
       -o $outputFile \

diff --git a/bin/index-webpage.groovy b/bin/index-webpage.groovy
@@ -5,7 +5,7 @@ import groovy.json.JsonOutput
 
 if(args.length!=1) {
   System.err.println """
-  USAGE: run-groovy ${this.class.getSimpleName()}.groovy [WEBSERVER_DIRECTORY]
+  USAGE: groovy ${this.class.getSimpleName()}.groovy [WEBSERVER_DIRECTORY]
   """
   System.exit(101)
 }

diff --git a/bin/run-detectors-timelines.sh b/bin/run-detectors-timelines.sh
@@ -12,7 +12,7 @@ outputDir=""
 numThreads=8
 singleTimeline=""
 declare -A modes
-for key in list build skip-mya focus-timelines focus-qa debug help; do
+for key in list skip-mya focus-timelines focus-qa debug help; do
   modes[$key]=false
 done
 
@@ -48,8 +48,6 @@ usage() {
 
     --list              dump the list of timelines and exit
 
-    --build             cleanly-rebuild the timeline code, then run
-
     --skip-mya          skip timelines which require MYA (needed if running offsite or on CI)
 
     --focus-timelines   only produce the detector timelines, do not run detector QA code
@@ -92,17 +90,14 @@ if ${modes['help']}; then
   exit 101
 fi
 
-# set class path to include groovy's classpath, for `java` calls
-export CLASSPATH="$JYPATH${CLASSPATH:+:${CLASSPATH}}"
-
 # get main executable for detector timelines
-run_detectors_script="org.jlab.clas.timeline.run_detectors"
+run_analysis_script="org.jlab.clas.timeline.analysis.run_analysis"
 
 # build list of timelines
 if ${modes['skip-mya']}; then
-  timelineList=$(java $run_detectors_script --timelines | grep -vE '^epics_' | sort | grep $match)
+  timelineList=$(java $TIMELINE_JAVA_OPTS $run_analysis_script --timelines | grep -vE '^epics_' | sort | grep $match)
 else
-  timelineList=$(java $run_detectors_script --timelines | sort | grep $match)
+  timelineList=$(java $TIMELINE_JAVA_OPTS $run_analysis_script --timelines | sort | grep $match)
 fi
 
 # list detector timelines, if requested
@@ -145,15 +140,6 @@ OPTIONS = {"""
 for key in "${!modes[@]}"; do printf "%20s => %s,\n" $key ${modes[$key]}; done
 echo "}"
 
-# rebuild, if desired
-if ${modes['build']}; then
-  echo "building detector timeline"
-  pushd $TIMELINESRC/detectors
-  mvn clean package
-  [ $? -ne 0 ] && exit 100
-  popd
-fi
-
 # output detector subdirectories
 detDirs=(
   band
@@ -238,11 +224,11 @@ if ${modes['focus-all']} || ${modes['focus-timelines']}; then
     [ -n "$singleTimeline" -a "$timelineObj" != "$singleTimeline" ] && continue
     echo ">>> producing timeline '$timelineObj' ..."
     if ${modes['debug']}; then
-      java $TIMELINE_JAVA_OPTS $run_detectors_script $timelineObj $inputDir
+      java $TIMELINE_JAVA_OPTS $run_analysis_script $timelineObj $inputDir
       echo "PREMATURE EXIT, since --debug option was used"
       exit
     else
-      java $TIMELINE_JAVA_OPTS $run_detectors_script $timelineObj $inputDir > $logFile.out 2> $logFile.err || touch $logFile.fail &
+      java $TIMELINE_JAVA_OPTS $run_analysis_script  $timelineObj $inputDir > $logFile.out 2> $logFile.err || touch $logFile.fail &
       job_ids+=($!)
       job_names+=($timelineObj)
     fi
@@ -308,7 +294,7 @@ cp -rL $finalDirPreQA/* $finalDir/
 if ${modes['focus-all']} || ${modes['focus-qa']}; then
   echo ">>> add QA lines..."
   logFile=$logDir/qa
-  run-groovy $TIMELINE_GROOVY_OPTS $TIMELINESRC/qa-detectors/util/applyBounds.groovy $finalDirPreQA $finalDir > $logFile.out 2> $logFile.err || touch $logFile.fail
+  $TIMELINESRC/bin/run-groovy-timeline.sh $TIMELINESRC/qa-detectors/util/applyBounds.groovy $finalDirPreQA $finalDir > $logFile.out 2> $logFile.err || touch $logFile.fail
   outputFiles=$(find $finalDir -name "*_QA.hipo")
   [ -n "$outputFiles" ] && $TIMELINESRC/bin/hipo-check.sh $outputFiles
 fi