feat: RG-A Sp19 Pass 2 QA (#242)

qa-physics/QA/modifyQaTree.groovy

@@ -7,29 +7,30 @@ Tools T = new Tools()
 
 // list of commands and description
 def usage = [:]
-usage["setBit"] = "setBit: overwrites stored defectBit(s) with specified bit"
-usage["addBit"] = "addBit: add specified bit to defectBit(s)"
-usage["delBit"] = "delBit: delete specified bit from defectBit(s)"
-usage["sectorLoss"] = "sectorLoss: specify a sector loss"
-usage["noBeam"] = "noBeam: add 'PossiblyNoBeam' bit"
-usage["setComment"] = "setComment: change or delete the comment"
-usage["addComment"] = "addComment: append a comment"
-usage["custom"] = "custom: do a custom action (see code)"
-usage["lossFT"] = "lossFT: specify a FT loss"
+usage["setbit"]     = "overwrites stored defectBit(s) with specified bit"
+usage["addbit"]     = "add specified bit to defectBit(s)"
+usage["delbit"]     = "delete specified bit from defectBit(s)"
+usage["sectorloss"] = "specify a sector loss"
+usage["lossft"]     = "specify a FT loss"
+usage["nobeam"]     = "add 'PossiblyNoBeam' bit"
+usage["setcomment"] = "change or delete the comment"
+usage["addcomment"] = "append a comment"
+usage["custom"]     = "do a custom action (see code)"
 println("\n\n")
 
 
 // check arguments and print usage
+def exe = "modify.sh"
 def cmd
-if(args.length>=1) cmd = args[0]
+if(args.length>=1) cmd = args[0].toLowerCase()
 else {
   System.err.println(
   """
-  syntax: modify.sh [command] [arguments]\n
+  SYNTAX: ${exe} [command] [arguments]\n
 List of Commands:
   """)
-  usage.each{ System.err.println("- "+it.value) }
-  System.err.println("\ntype any command without arguments for usage for that command\n")
+  usage.each{ key, value -> printf("%20s     %s\n", key, value) }
+  printf("\nType any command without arguments for usage guidance for that command\n\n")
   System.exit(101)
 }
 
@@ -66,15 +67,15 @@ def recomputeDefMask = { runnum,binnum ->
 ///////////////////////
 
 
-if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
+if( cmd=="setbit" || cmd=="addbit" || cmd=="delbit") {
   def rnum,bnumL,bnumR
   def bit
   def secList = []
-  if(args.length>4) {
+  if(args.length>2) {
     bit = args[1].toInteger()
     rnum = args[2].toInteger()
-    bnumL = args[3].toInteger()
-    bnumR = args[4].toInteger()
+    bnumL = args.length < 4 ?  0 : args[3].toInteger()
+    bnumR = args.length < 5 ? -1 : args[4].toInteger()
     if(args.length<6 || args[5]=="all") secList = (1..6).collect{it}
     else (5..<args.length).each{ secList<<args[it].toInteger() }
 
@@ -90,17 +91,17 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
       def qaFnum = k.toInteger()
       if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
 
-        if(cmd=="setBit") {
+        if(cmd=="setbit") {
           secList.each{
             qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] = [bit]
           }
         }
-        else if(cmd=="addBit") {
+        else if(cmd=="addbit") {
           secList.each{
             qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] += bit
           }
         }
-        else if(cmd=="delBit") {
+        else if(cmd=="delbit") {
           secList.each{
             qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= bit
           }
@@ -114,10 +115,10 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
 
   }
   else {
-    def helpStr = usage["$cmd"].tokenize(':')[1]
+    def helpStr = usage["$cmd"]
     System.err.println(
     """
-    SYNTAX: ${cmd} [defectBit] [run] [firstBin] [lastBin] [list_of_sectors (default=all)]
+    SYNTAX: ${exe} ${cmd} [defectBit] [run] [firstBin (default=0)] [lastBin (default=-1)] [list_of_sectors (default=all)]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - use \"all\" in place of [list_of_sectors] to apply to all sectors
@@ -132,7 +133,7 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
   }
 }
 
-else if(cmd=="sectorLoss") {
+else if(cmd=="sectorloss") {
   def rnum,bnumL,bnumR
   def secList = []
   if(args.length>3) {
@@ -168,10 +169,10 @@ else if(cmd=="sectorLoss") {
 
   }
   else {
-    def helpStr = usage["$cmd"].tokenize(':')[1]
+    def helpStr = usage["$cmd"]
     System.err.println(
     """
-    SYNTAX: ${cmd} [run] [firstBin] [lastBin] [list_of_sectors (default=all)]
+    SYNTAX: ${exe} ${cmd} [run] [firstBin] [lastBin] [list_of_sectors (default=all)]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - use \"all\" in place of [list_of_sectors] to apply to all sectors
@@ -183,7 +184,7 @@ else if(cmd=="sectorLoss") {
   }
 }
 
-else if(cmd=="noBeam") {
+else if(cmd=="nobeam") {
   def rnum,bnumL,bnumR
   def secList = (1..6).collect{it}
   if(args.length>3) {
@@ -221,10 +222,10 @@ else if(cmd=="noBeam") {
 
   }
   else {
-    def helpStr = usage["$cmd"].tokenize(':')[1]
+    def helpStr = usage["$cmd"]
     System.err.println(
     """
-    SYNTAX: ${cmd} [run] [firstBin] [lastBin]
+    SYNTAX: ${exe} ${cmd} [run] [firstBin] [lastBin]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - this will set the PossiblyNoBeam bit for specified time bins, and add
@@ -235,7 +236,7 @@ else if(cmd=="noBeam") {
   }
 }
 
-else if(cmd=="lossFT") {
+else if(cmd=="lossft") {
   def rnum,bnumL,bnumR
   if(args.length>4) {
     rnum = args[1].toInteger()
@@ -265,10 +266,10 @@ else if(cmd=="lossFT") {
 
   }
   else {
-    def helpStr = usage["$cmd"].tokenize(':')[1]
+    def helpStr = usage["$cmd"]
     println(
     """
-    SYNTAX: ${cmd} [run] [firstBin] [lastBin]
+    SYNTAX: ${exe} ${cmd} [run] [firstBin] [lastBin]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - this will set the LossFT bit for specified time bins;
@@ -279,7 +280,7 @@ else if(cmd=="lossFT") {
   }
 }
 
-else if( cmd=="addComment" || cmd=="setComment") {
+else if( cmd=="addcomment" || cmd=="setcomment") {
   def rnum,bnumL,bnumR
   def secList = []
   if(args.length==4) {
@@ -288,16 +289,16 @@ else if( cmd=="addComment" || cmd=="setComment") {
     bnumR = args[3].toInteger()
 
     println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) + ": $cmd")
-    if(cmd=="addComment")
+    if(cmd=="addcomment")
       println("Enter the new comment to be appended")
-    else if(cmd=="setComment")
+    else if(cmd=="setcomment")
       println("Enter the new comment, or leave it blank to delete any stored comment")
     print("> ")
     def cmt = System.in.newReader().readLine()
     qaTree["$rnum"].each { k,v ->
       def qaFnum = k.toInteger()
       if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
-        if (cmd=="addComment") {
+        if (cmd=="addcomment") {
           if(!qaTree["$rnum"]["$qaFnum"].containsKey("comment")) {
             qaTree["$rnum"]["$qaFnum"]["comment"] = cmt
           }
@@ -307,15 +308,15 @@ else if( cmd=="addComment" || cmd=="setComment") {
             qaTree["$rnum"]["$qaFnum"]["comment"] += cmt
           }
         }
-        else if (cmd=="setComment")
+        else if (cmd=="setcomment")
           qaTree["$rnum"]["$qaFnum"]["comment"] = cmt
       }
     }
   }
   else {
     System.err.println(
     """
-    SYNTAX: ${cmd} [run] [firstBin] [lastBin]
+    SYNTAX: ${exe} ${cmd} [run] [firstBin] [lastBin]
       - set [lastBin] to -1 to denote last time bin of run
       - you will be prompted to enter the comment
     """)
@@ -358,7 +359,7 @@ else if( cmd=="custom") {
 
     ///* // add misc bit to sector 6 only
     qaTree["$rnum"]["$bnum"]["sectorDefects"]["6"] += T.bit("Misc")
-    def cmt = "FADC failure in sector 6"
+    def cmt = "FADC failure in ECAL sector 6; see https://logbooks.jlab.org/entry/3678262"
     //*/
 
     if(!qaTree["$rnum"]["$bnum"].containsKey("comment")) {
@@ -369,7 +370,7 @@ else if( cmd=="custom") {
         qaTree["$rnum"]["$bnum"]["comment"] += "; "
       qaTree["$rnum"]["$bnum"]["comment"] += cmt
     }
-    println("modify $rnum $bnum")
+    // println("modify $rnum $bnum")
 
     recomputeDefMask(rnum,bnum)
 

qa-physics/epochs/epochs.rga_sp19_nSidis.txt

@@ -0,0 +1 @@
+epochs.rga_sp19.txt

qa-physics/epochs/epochs.rga_sp19_prescaled.txt

@@ -0,0 +1 @@
+epochs.rga_sp19.txt

qa-physics/notes/rga_sp19.md

@@ -0,0 +1,64 @@
+# Run Group A, Spring 2019, Pass 2
+
+## Produce prescaled trains
+
+> [!NOTE]
+> Bad tape 803771 (April, 2024) included DSTs that were not recooked;
+> this QA therefore did not check the 'prescale' train (but commands
+> are still written below)
+
+Check the commands carefully before you run; these are just notes...
+```bash
+cd qa-physics/prescaler
+cook-train.rb --dataset rga_sp19 --coatjava 10.1.1
+start-workflow.sh rga-a-sp19*.json  ## check that this is the correct JSON file before running
+```
+
+## Check prescaled trains
+
+> [!IMPORTANT]
+> To be sure the workflows succeeded and we have all the data, run `check-train.rb`.
+
+## Run monitoring
+
+> [!IMPORTANT]
+> Check any run-dependent settings in `qa-physics/monitorRead.groovy`, such as beam energy.
+
+For the prescaled train:
+```bash
+bin/run-monitoring.sh -d rga_sp19_prescaled --submit --focus-physics PATH_TO_PRESCALED_TRAIN
+```
+
+For the SIDIS train, `nSidis`, first make sure all skim files are cached:
+```bash
+bin/run-monitoring.sh -d rga_sp19_nSidis --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
+```
+If they are not:
+```bash
+ls /mss/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis/* | tee jlist.txt
+jcache get $(cat jlist.txt)
+# then wait for them to be cached
+```
+then run monitoring
+```bash
+bin/run-monitoring.sh -d rga_sp19_nSidis --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
+```
+
+## Make timelines
+
+Make the timelines:
+```bash
+bin/run-physics-timelines.sh -d rga_sp19_prescaled
+bin/run-physics-timelines.sh -d rga_sp19_nSidis
+```
+
+Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
+```bash
+# your area, for testing
+bin/deploy-timelines.sh -d rga_sp19_prescaled -t $LOGNAME -D
+bin/deploy-timelines.sh -d rga_sp19_nSidis -t $LOGNAME -D
+
+# common area
+bin/deploy-timelines.sh -d rga_sp19_prescaled -t rga/pass2/sp19/qa -D
+bin/deploy-timelines.sh -d rga_sp19_nSidis -t rga/pass2/sp19/qa -D
+```

qa-physics/notes/rgc_su22.md

@@ -1,4 +1,4 @@
-# Run Group C QA
+# Run Group C, Summer 2022, Pass 1
 
 This is the first QA to use the time bins and the prescaling.