resolve merge conflict

JeffersonLab · Nov 19, 2024 · 75926d3 · 75926d3
2 parents eb393b7 + d1f48d3
commit 75926d3
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diff --git a/.containers/coatjava.Dockerfile b/.containers/coatjava.Dockerfile
@@ -0,0 +1,25 @@
+#syntax=docker/dockerfile:1
+
+FROM ubuntu:noble
+
+LABEL name="coatjava"
+LABEL maintainer="Whitney Armstrong <[email protected]>"
+LABEL architecture="amd64"
+
+USER root
+
+
+RUN apt update && apt upgrade -y
+RUN apt install cmake vim maven groovy git ca-certificates wget curl python-is-python3 \
+                openjdk-17-jdk openjdk-17-jre openjdk-17-jdk-headless openjdk-17-jre-headless \
+                python3-sqlalchemy -y && update-ca-certificates
+
+# CA certificates
+ADD https://pki.jlab.org/JLabCA.crt /etc/ssl/certs/JLabCA.crt 
+#RUN trust anchor --store /image/JLabCA.crt
+
+ARG REF_NAME=development 
+# build coatjava 
+RUN java --version && cd /opt && \
+    git clone https://code.jlab.org/hallb/alert/coatjava.git && cd coatjava && \
+    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --nomaps
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,31 @@
+workflow:
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+    - if: '$CI_PIPELINE_SOURCE == "web"'
+    - if: '$CI_PIPELINE_SOURCE == "webide"'
+    - if: '$CI_COMMIT_BRANCH == "master"'
+    - if: '$CI_COMMIT_BRANCH == "development"'
+    - if: '$CI_COMMIT_TAG'
+
+default:
+  image: ubuntu:noble
+  retry: 2
+
+coatjava_build:
+  image: gcr.io/kaniko-project/executor:debug
+  script:
+    - echo "${CI_COMMIT_REF_NAME}"
+    - >-
+      /kaniko/executor
+      --context     $CI_PROJECT_DIR/docker
+      --dockerfile  $CI_PROJECT_DIR/.containers/coatjava.Dockerfile
+      --destination $CI_REGISTRY_IMAGE/coatjava:${CI_COMMIT_REF_NAME}
+      --build-arg REF_NAME=${CI_COMMIT_REF_NAME}
+    
+alert_testing:
+  needs: ["coatjava_build"]
+  variables:
+    REF_NAME: "$CI_COMMIT_REF_NAME"
+  trigger:
+    project: hallb/alert/c12
+    strategy: depend
diff --git a/bin/run-clara b/bin/run-clara
@@ -34,7 +34,7 @@ do
         p) prefix=$OPTARG ;;
         c) CLARA_HOME=$OPTARG ;;
         t) threads=$OPTARG && echo $threads | grep -q -E '^[0-9]+$' || error "-t must be an integer, threads" ;;
-        n) nevents="-e $OPTARG" && echo $nevents | grep -q -E '^-e [0-9]+$' || error "-n must be an integer, events" ;;
+        n) nevents="-e $OPTARG" && echo "$nevents" | grep -q -E '^-e [0-9]+$' || error "-n must be an integer, events" ;;
         m) merge=1 ;;
         h) echo -e "\n$usage" && echo -e $info && exit 0 ;;
     esac

diff --git a/common-tools/clara-io/pom.xml b/common-tools/clara-io/pom.xml
@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clara-io</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>

diff --git a/common-tools/clas-analysis/pom.xml b/common-tools/clas-analysis/pom.xml
@@ -3,63 +3,63 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-analysis</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-physics</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-jcsg</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>swim-tools</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-reco</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

diff --git a/common-tools/clas-detector/pom.xml b/common-tools/clas-detector/pom.xml
@@ -3,21 +3,21 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-detector</artifactId>
-  <version>11.0.3-SNAPSHOT</version>
+  <version>11.0.5-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.0.3-SNAPSHOT</version>
+    <version>11.0.5-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -29,13 +29,13 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.0.3-SNAPSHOT</version>
+      <version>11.0.5-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java b/common-tools/clas-detector/src/main/java/org/jlab/detector/base/DetectorType.java
@@ -29,6 +29,8 @@ public enum DetectorType {
     BAND      (21, "BAND"),
     RASTER    (22, "RASTER"),
     URWELL    (23, "URWELL"),
+    AHDC      (24, "AHDC"),
+    ATOF      (25, "ATOF"),
     TARGET    (100, "TARGET"),
     MAGNETS   (101, "MAGNETS"),
     ECIN      (110, "ECIN"),

diff --git a/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java b/common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java
@@ -181,6 +181,7 @@ public List<DetectorDataDgtz>  getEntriesADC(DetectorType type,
     public List<DetectorDataDgtz>  getEntriesTDC(DetectorType type){
         return getEntriesTDC(type,dataList);
     }
+
     /**
      * returns TDC entries from decoded data for given detector type
      * @param type detector type
@@ -290,6 +291,31 @@ public Bank getDataBankTDC(String name, DetectorType type){
         return tdcBANK;
     }
 
+    public Bank getDataBankTDCPetiroc(String name, DetectorType type){
+
+        List<DetectorDataDgtz> tdcDGTZ = this.getEntriesTDC(type);
+        if(schemaFactory.hasSchema(name)==false){
+          System.out.println("WARNING: No schema for TDC type : "  + type);
+          return null;
+        }
+        Bank tdcBANK = new Bank(schemaFactory.getSchema(name), tdcDGTZ.size());
+
+        if(tdcBANK==null) return null;
+
+        // Not sure why  the schemea information isn't used here. 
+        for(int i = 0; i < tdcDGTZ.size(); i++){
+            tdcBANK.putByte("sector", i, (byte) tdcDGTZ.get(i).getDescriptor().getSector());
+            tdcBANK.putByte("layer", i, (byte) tdcDGTZ.get(i).getDescriptor().getLayer());
+            tdcBANK.putShort("component", i, (short) tdcDGTZ.get(i).getDescriptor().getComponent());
+            tdcBANK.putByte("order", i, (byte) tdcDGTZ.get(i).getDescriptor().getOrder());
+            tdcBANK.putInt("TDC", i, tdcDGTZ.get(i).getTDCData(0).getTime());
+            tdcBANK.putInt("ToT", i, tdcDGTZ.get(i).getTDCData(0).getToT());
+            //System.err.println("event: " + tdcDGTZ.get(i).toString());
+        }
+        return tdcBANK;
+    }
+
+
     public Bank getDataBankTimeStamp(String name, DetectorType type) {
 
         List<DetectorDataDgtz> tdcDGTZ = this.getEntriesTDC(type);
@@ -300,7 +326,8 @@ public Bank getDataBankTimeStamp(String name, DetectorType type) {
             int hash = ((desc.getCrate()<<8)&0xFF00) | (desc.getSlot()&0x00FF);
             if(tsMap.containsKey(hash)) {
                 if(tsMap.get(hash).getTimeStamp() != tdc.getTimeStamp()) 
-                    System.out.println("WARNING: inconsistent timestamp for DCRB crate/slot " + desc.getCrate() + "/" + desc.getSlot());
+                    System.out.println("WARNING: inconsistent timestamp for DCRB crate/slot " 
+                                       + desc.getCrate() + "/" + desc.getSlot());
             }
             else {
                 tsMap.put(hash, tdc);
@@ -393,16 +420,29 @@ public Event getDataEvent(){
 
         Event event = new Event();
 
-        String[]        adcBankNames = new String[]{"FTOF::adc","ECAL::adc","FTCAL::adc","FTHODO::adc","FTTRK::adc",
-                                                    "HTCC::adc","BST::adc","CTOF::adc","CND::adc","LTCC::adc","BMT::adc",
-                                                    "FMT::adc","HEL::adc","RF::adc","BAND::adc","RASTER::adc"};
-        DetectorType[]  adcBankTypes = new DetectorType[]{DetectorType.FTOF,DetectorType.ECAL,DetectorType.FTCAL,DetectorType.FTHODO,DetectorType.FTTRK,
-                                                          DetectorType.HTCC,DetectorType.BST,DetectorType.CTOF,DetectorType.CND,DetectorType.LTCC,DetectorType.BMT,
-                                                          DetectorType.FMT,DetectorType.HEL,DetectorType.RF,DetectorType.BAND, DetectorType.RASTER};
-
-        String[]        tdcBankNames = new String[]{"FTOF::tdc","ECAL::tdc","DC::tdc","HTCC::tdc","LTCC::tdc","CTOF::tdc","CND::tdc","RF::tdc","RICH::tdc","BAND::tdc"};
-        DetectorType[]  tdcBankTypes = new DetectorType[]{DetectorType.FTOF,DetectorType.ECAL,
-            DetectorType.DC,DetectorType.HTCC,DetectorType.LTCC,DetectorType.CTOF,DetectorType.CND,DetectorType.RF,DetectorType.RICH,DetectorType.BAND};
+        String[]        adcBankNames = new String[]{"FTOF::adc","ECAL::adc","FTCAL::adc",
+                                                    "FTHODO::adc", "FTTRK::adc",
+                                                    "HTCC::adc","BST::adc","CTOF::adc",
+                                                    "CND::adc","LTCC::adc","BMT::adc",
+                                                    "FMT::adc","HEL::adc","RF::adc",
+                                                    "BAND::adc","RASTER::adc", 
+                                                    "AHDC::adc"};
+        DetectorType[]  adcBankTypes = new DetectorType[]{DetectorType.FTOF,DetectorType.ECAL,DetectorType.FTCAL,
+                                                          DetectorType.FTHODO,DetectorType.FTTRK,
+                                                          DetectorType.HTCC,DetectorType.BST,DetectorType.CTOF,
+                                                          DetectorType.CND,DetectorType.LTCC,DetectorType.BMT,
+                                                          DetectorType.FMT,DetectorType.HEL,DetectorType.RF,
+                                                          DetectorType.BAND, DetectorType.RASTER, 
+                                                          DetectorType.AHDC};
+
+        String[] tdcBankNames = new String[]{"FTOF::tdc","ECAL::tdc","DC::tdc",
+                                             "HTCC::tdc","LTCC::tdc","CTOF::tdc",
+                                             "CND::tdc","RF::tdc","RICH::tdc",
+                                             "BAND::tdc"};
+        DetectorType[] tdcBankTypes = new DetectorType[]{DetectorType.FTOF,DetectorType.ECAL,
+                                                         DetectorType.DC,DetectorType.HTCC,DetectorType.LTCC,
+                                                         DetectorType.CTOF,DetectorType.CND,DetectorType.RF,
+                                                         DetectorType.RICH,DetectorType.BAND};
 
         for(int i = 0; i < adcBankTypes.length; i++){
             Bank adcBank = getDataBankADC(adcBankNames[i],adcBankTypes[i]);
@@ -421,6 +461,18 @@ public Event getDataEvent(){
                 }
             }
         }
+        try {
+            // Do ATOF 
+            Bank tdcBank = getDataBankTDCPetiroc("ATOF::tdc",DetectorType.ATOF);
+            if(tdcBank!=null){
+                if(tdcBank.getRows()>0){
+                    event.write(tdcBank);
+                }
+            }
+        } catch(Exception e) {
+            e.printStackTrace();
+        }
+
 
         try {
             Bank tsBank = getDataBankTimeStamp("DC::jitter", DetectorType.DC);
@@ -432,10 +484,10 @@ public Event getDataEvent(){
         } catch(Exception e) {
             e.printStackTrace();
         }
+
         /**
          * Adding un-decoded banks to the event
          */
-
         try {
             Bank adcBankUD = this.getDataBankUndecodedADC("RAW::adc", DetectorType.UNDEFINED);
             if(adcBankUD!=null){
@@ -671,6 +723,8 @@ public Bank createHelicityDecoderBank(EvioDataEvent event) {
     public static void main(String[] args){
 
         OptionParser parser = new OptionParser("decoder");
+
+        parser.setDescription("CLAS12 Data Decoder");
         parser.addOption("-n", "-1", "maximum number of events to process");
         parser.addOption("-c", "2", "compression type (0-NONE, 1-LZ4 Fast, 2-LZ4 Best, 3-GZIP)");
         parser.addOption("-d", "0","debug mode, set >0 for more verbose output");
@@ -721,8 +775,8 @@ public static void main(String[] args){
         writer.setCompressionType(compression);
         writer.getSchemaFactory().initFromDirectory(ClasUtilsFile.getResourceDir("CLAS12DIR", "etc/bankdefs/hipo4"));
 
-        Bank   rawScaler = new Bank(writer.getSchemaFactory().getSchema("RAW::scaler"));
-        Bank  rawRunConf = new Bank(writer.getSchemaFactory().getSchema("RUN::config"));
+        Bank  rawScaler   = new Bank(writer.getSchemaFactory().getSchema("RAW::scaler"));
+        Bank  rawRunConf  = new Bank(writer.getSchemaFactory().getSchema("RUN::config"));
         Bank  helicityAdc = new Bank(writer.getSchemaFactory().getSchema("HEL::adc"));
         Event scalerEvent = new Event();