fix: do not require any of coatjava's environment

Author: c-dilks

.github/workflows/ci.yml

@@ -15,7 +15,6 @@ env:
   # NOTE: if any of these versions are changed, update the POM files too
   java_version: 21
   java_distribution: zulu
-  groovy_version: 4.x
 
 
 concurrency:
@@ -47,31 +46,6 @@ jobs:
         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
   #############################################################################
 
@@ -110,7 +84,6 @@ jobs:
   run_monitoring:
     needs:
       - build_timelines
-      - build_coatjava
       - download_test_data
     runs-on: ubuntu-latest
     strategy:
@@ -123,12 +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:
@@ -162,7 +129,6 @@ jobs:
   test_swifjob:
     needs:
       - build_timelines
-      - build_coatjava
       - download_test_data
     runs-on: ubuntu-latest
     strategy:
@@ -175,12 +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:
@@ -221,12 +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:
@@ -260,12 +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:

bin/environ.sh

@@ -7,51 +7,33 @@ 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
+# get the source code directory
 [ -z "${BASH_SOURCE[0]}" ] && thisEnv=$0 || thisEnv=${BASH_SOURCE[0]}
 export TIMELINESRC=$(realpath $(dirname $thisEnv)/..)
 
 # RCDB
-[ -z "${RCDB_CONNECTION-}" ] && RCDB_CONNECTION=mysql://rcdb@clasdb.jlab.org/rcdb
-export RCDB_CONNECTION
-
-# check coatjava environment
-if [ -z "${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
-target_classpath=(
-  "$TIMELINESRC/target/*"
-  "$TIMELINESRC/target/dependency/*"
-)
+[ -z "${RCDB_CONNECTION-}" ] && export RCDB_CONNECTION=mysql://rcdb@clasdb.jlab.org/rcdb
 
-# 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
 )
 
-# run java with more resources, to mitigate large memory residence for long run periods
-timeline_java_opts_highmem=$(echo ${timeline_java_opts[*]} | sed 's;Xmx1024m;Xmx2048m;')
+# groovy options
+timeline_groovy_opts=(
+  -cp "$TIMELINESRC/target/*:$TIMELINESRC/target/dependency/*"
+  -Djava.awt.headless=true
+)
 
 # exports
-export CLASSPATH="$(echo "${target_classpath[*]}" | sed 's; ;:;g')${CLASSPATH:+:${CLASSPATH}}"
 export TIMELINE_JAVA_OPTS="${timeline_java_opts[*]}"
-export TIMELINE_JAVA_OPTS_HIGHMEM=$timeline_java_opts_highmem
+export TIMELINE_GROOVY_OPTS="${timeline_groovy_opts[*]}"
 
 # cleanup vars
 unset thisEnv
 unset log_config
-unset target_classpath
 unset timeline_java_opts
-unset timeline_java_opts_highmem
+unset timeline_groovy_opts

bin/hipo-check.sh

@@ -43,7 +43,7 @@ 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

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 \

bin/run-groovy-timeline.sh

@@ -2,5 +2,10 @@
 # run the timeline's version of `groovy`, to ensure the correct dependencies are used
 # FIXME: this script should only exist until ALL timeline groovy code is compiled;
 #        at the moment, the physics QA code needs this
-# NOTE: this assumes $CLASSPATH has already been set, by sourcing `environ.sh`
-exec java groovy.ui.GroovyMain -Djava.awt.headless=true "$@"
+
+if [ -z "$TIMELINE_GROOVY_OPTS" ]; then
+  echo "ERROR: please source environ.sh first" >&2
+  exit 100
+fi
+
+exec java $TIMELINE_GROOVY_OPTS groovy.ui.GroovyMain "$@"

data/logging/README.md

@@ -0,0 +1,3 @@
+# Logging Configuration
+
+Shamefully copied from [`coatjava`](https://github.com/JeffersonLab/coatjava/tree/development/etc/logging), to avoid relying on `$COATJAVA` environment variable.

data/logging/debug.properties

@@ -0,0 +1,29 @@
+#
+# Global logging configuration for clas
+# Nick Tyler, UofSC
+#
+# Modified from hps-java logging
+# Jeremy McCormick, SLAC
+#
+
+# default global level
+.level = INFO
+
+# default handler which prints to console
+handlers = java.util.logging.ConsoleHandler
+
+# Old detailed format
+# prints timestamp (1$), level (4$), source ($2), message (5$), and (optionally) an exception (6$).
+#java.util.logging.SimpleFormatter.format = %1$tY-%1$tm-%1$td %1$tT [%4$s] %2$s :: %5$s%6$s%n
+
+# New simplified format
+# MESSAGE
+java.util.logging.SimpleFormatter.format = %5$s%6$s%n
+
+# configure the console handler
+java.util.logging.ConsoleHandler.level = ALL
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+
+
+

data/logging/logging.properties

@@ -0,0 +1,51 @@
+#
+# Global logging configuration for clas
+# Nick Tyler, UofSC
+#
+# Modified from hps-java logging
+# Jeremy McCormick, SLAC
+#
+
+# default global level
+.level = WARNING
+
+# default handler which prints to console
+handlers = java.util.logging.ConsoleHandler
+
+# Old detailed format
+# prints timestamp (1$), level (4$), source ($2), message (5$), and (optionally) an exception (6$).
+#java.util.logging.SimpleFormatter.format = %1$tY-%1$tm-%1$td %1$tT [%4$s] %2$s :: %5$s%6$s%n
+
+# New simplified format
+# [LEVEL][LOGGER] MESSAGE
+java.util.logging.SimpleFormatter.format = %1$tT [%4$s] %5$s%6$s%n
+
+# configure the console handler
+java.util.logging.ConsoleHandler.level = ALL
+java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+# turn minuit logging off
+org.freehep.math.minuit.level = OFF
+
+# calibration logging
+org.jlab.detector.calib.level = OFF
+
+# Reconstruction level
+org.jlab.clas.reco.level = OFF
+
+# Hipo io level
+org.jlab.io.hipo = OFF
+
+# Magnetic Field level
+cnuphys.magfield.level = OFF
+
+# Log level for each service
+org.jlab.service.ec.level = OFF
+org.jlab.service.eb.level = OFF
+org.jlab.rec.cvt.services.level = OFF
+org.jlab.service.htcc.level = OFF
+org.jlab.rec.dc.level = OFF
+
+
+
+

qa-physics/README.md

@@ -23,15 +23,6 @@ Physics QA features:
 > [!IMPORTANT]
 > See the [QADB Ground rules](https://github.com/JeffersonLab/clas12-qadb), which must be strictly followed for the QA procedure.
 
-# Setup
-
-It is recommended to use `bash` or `zsh` as your shell; `tcsh` is not supported.
-
-1. Set `COATJAVA` environment (follow CLAS12 software documentation)
-2. Note for developers: set local environment variables with `source ../bin/environ.sh`.
-   Wrapper scripts in `../bin/` do this automatically, but if you intend to run
-   individual scripts here (namely during manual QA), you may need to call this `source` command.
-
 # Notes
 
 For run-group specific notes, including the commands used to perform the QA, see

src/main/java/org/jlab/clas/timeline/run_histograms.java

@@ -31,7 +31,7 @@ public static void main(String[] args) {
     if(args.length>5)if(Integer.parseInt(args[5])==0)useTB=false;
     System.out.println("will process run number "+runNum+" from list "+filelist+" looking for up to "+maxevents+" events, beam energy setting "+EB);
 
-    //// instantiate monitors
+    //// instantiate histogramming classes
     monitor2p2GeV ana_mon     = new monitor2p2GeV(runNum,outputDir,EB,useTB);
     FTOFandDC     ana_ftof_dc = new FTOFandDC(runNum,outputDir,useTB);
     CTOF          ana_ctof    = new CTOF(runNum,outputDir,useTB);
@@ -79,7 +79,7 @@ public static void main(String[] args) {
       while(reader.hasEvent()&& count<maxevents ) {
         DataEvent event = reader.getNextEvent();
 
-        //// call each monitor's `processEvent`
+        //// call each histogramming class instance's `processEvent`
         ana_mon.processEvent(event);
         ana_ctof.processEvent(event);
         ana_ftof_dc.processEvent(event);
@@ -108,7 +108,7 @@ public static void main(String[] args) {
     }
     System.out.println("Total : " + count + " events");
 
-    //// call each monitor's `write`
+    //// call each histogramming class instance's `write`
     ana_mon.write();
     ana_ctof.write();
     ana_ftof_dc.write();