fix: don't attempt to analyze empty ALERT timelines

- if before RG-L, don't even run the timeline engine
- if during RG-L, run the engine, but if data are empty, don't attempt
  to produce the final timeline and instead complain to `stderr` so the
  chef sees the issue

Fixes #307

Author: c-dilks

src/main/java/org/jlab/clas/timeline/analysis/alert/alert_atof_tdc.groovy

@@ -1,12 +1,14 @@
 package org.jlab.clas.timeline.analysis
 import java.util.concurrent.ConcurrentHashMap
+import java.util.concurrent.atomic.AtomicBoolean
 import org.jlab.groot.data.TDirectory
 import org.jlab.groot.data.GraphErrors
 import org.jlab.clas.timeline.fitter.ALERTFitter
 
 class alert_atof_tdc {
 
 def data = new ConcurrentHashMap()
+def has_data = new AtomicBoolean(false)
 
   def processRun(dir, run) {
 
@@ -22,19 +24,27 @@ def data = new ConcurrentHashMap()
       if (component <= 10) file_index = String.format('sector%d_layer%d_component%d_order0', sector, layer, component)
       else file_index = String.format('sector%d_layer%d_component%d_order1', sector, layer, component-1)
       def h1 = dir.getObject(String.format('/ALERT/TDC_%s', file_index))
-      data[run].put(String.format('atof_tdc_%s', file_index),  h1)
-      def f1 = ALERTFitter.tdcfitter(h1)
-      data[run].put(String.format('fit_atof_tdc_%s', file_index),  f1)
-      data[run].put(String.format('peak_location_atof_tdc_%s', file_index),  f1.getParameter(1))
-      data[run].put(String.format('sigma_atof_tdc_%s', file_index),  f1.getParameter(2))
-      data[run].put(String.format('integral_normalized_to_trigger_atof_tdc_%s', file_index),  Math.sqrt(2*3.141597f) * f1.getParameter(0) * f1.getParameter(2)/trigger.getBinContent(reference_trigger_bit) )
+      if(h1!=null && h1.getEntries()>10) {
+        data[run].put(String.format('atof_tdc_%s', file_index),  h1)
+        def f1 = ALERTFitter.tdcfitter(h1)
+        data[run].put(String.format('fit_atof_tdc_%s', file_index),  f1)
+        data[run].put(String.format('peak_location_atof_tdc_%s', file_index),  f1.getParameter(1))
+        data[run].put(String.format('sigma_atof_tdc_%s', file_index),  f1.getParameter(2))
+        data[run].put(String.format('integral_normalized_to_trigger_atof_tdc_%s', file_index),  Math.sqrt(2*3.141597f) * f1.getParameter(0) * f1.getParameter(2)/trigger.getBinContent(reference_trigger_bit) )
+        has_data.set(true)
+      }
     }
   }
 
 
 
   def write() {
 
+    if(!has_data.get()) {
+      System.err.println "ERROR: no data for this ALERT timeline, not producing"
+      return
+    }
+
     ['peak_location', 'sigma', 'integral_normalized_to_trigger'].each{variable->
       (0..<15).collect{sector->
         (0..<4).collect{layer->
@@ -67,4 +77,4 @@ def data = new ConcurrentHashMap()
       }
     }
   }
-}
+}

src/main/java/org/jlab/clas/timeline/run_analysis.groovy

@@ -144,6 +144,7 @@ def eng = engines.collectMany{key,engs->engs.collect{[key,it]}}
 if(eng) {
   def (name,engine) = eng
   def input = new File(args[1])
+  def allow_timeline = true
   println([name,args[0],engine.getClass().getSimpleName(),input])
   def fnames = []
   input.traverse {
@@ -163,17 +164,36 @@ if(eng) {
       def m = fname =~ /\d+/
       def run = m[0].toInteger()
 
-      engine.processRun(dir, run)
+      // allow / disallow certain timelines, based on run number
+      if(run < 21317) { // before RG-L
+        if(args[0] == "alert_atof_tdc") { allow_timeline = false }
+      }
+
+      // run the analysis for this run
+      if(allow_timeline) {
+        engine.processRun(dir, run)
+        println("debug: "+engine.getClass().getSimpleName()+" finished $arg")
+      }
+      else {
+        println("debug: "+engine.getClass().getSimpleName()+" is not allowed for run $run")
+      }
 
-      println("debug: "+engine.getClass().getSimpleName()+" finished $arg")
     } catch(Exception ex) {
       System.err.println("error: "+engine.getClass().getSimpleName()+" didn't process $arg, due to exception:")
       ex.printStackTrace()
       System.exit(100)
     }
   }
-  engine.write()
-  println("debug: "+engine.getClass().getSimpleName()+" ended")
+
+  // write the timeline HIPO file
+  if(allow_timeline) {
+    engine.write()
+    println("debug: "+engine.getClass().getSimpleName()+" ended")
+  }
+  else {
+    println("debug: "+engine.getClass().getSimpleName()+" was not produced, since not allowed for these data")
+  }
+
 } else {
   System.err.println("error: "+args[0]+" not found")
   System.exit(100)