From 266b9e0ee8e9d42887d535788ed93d7d5a93d734 Mon Sep 17 00:00:00 2001
From: Matthias Kleiner <matthias.kleiner@cern.ch>
Date: Thu, 8 Oct 2026 16:20:01 +0200
Subject: [PATCH] asyncReco: optional cosmics matching with raw-cluster output
 (EXTRACTCOSMICS)

JDL EXTRACTCOSMICS=1 enables the calibration workflows (ADD_CALIB, all other
calibrations stay off) and CALIB_ASYNC_EXTRACTCOSMICS, which makes O2's
calib-workflow.sh add o2-cosmics-match-workflow with the raw-cluster output
(o2_cosmics_full.root, to be added to the job's output files). Allowed in
async with TPC reconstructed, like the TPC time series. Optional JDL
variables:
- COSMICSPRESET: matcher preset (default physics-v1)
- COSMICSCONFIG: matcher settings on top of the preset (configKeyValues),
  e.g. cosmicsMatch.minSeedDCAxyTOF=0;cosmicsMatch.minSeedDCAxyNSigmaTOF=0
- COSMICSARGS: extra workflow options, e.g. --debug-tree
  (cosmics_collector_debug.root, also to be added to the output files)
- COSMICSPVVETO=0: no veto of legs belonging to primary-vertex contributors
  (on by default in calib-workflow.sh)
Needs the O2 counterpart in calib-workflow.sh.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 DATA/common/setenv_calib.sh                   |  2 ++
 .../configurations/asyncReco/async_pass.sh    |  4 ++++
 .../configurations/asyncReco/setenv_extra.sh  | 20 +++++++++++++++++++
 3 files changed, 26 insertions(+)

diff --git a/DATA/common/setenv_calib.sh b/DATA/common/setenv_calib.sh
index 59d457889..6ae6749cc 100755
--- a/DATA/common/setenv_calib.sh
+++ b/DATA/common/setenv_calib.sh
@@ -35,6 +35,7 @@ if [[ $SYNCMODE == 1 ]] && has_processing_step ENTROPY_ENCODER && [[ ! -z "$WORK
 if has_detector_calib EMC && has_detector_reco EMC && [[ $SYNCMODE != 1 ]]; then CAN_DO_CALIB_EMC_ASYNC_RECALIB=1; else CAN_DO_CALIB_EMC_ASYNC_RECALIB=0; fi
 if [[ $SYNCMODE != 1 ]] && has_detector_reco TPC; then CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS=1; else CAN_DO_CALIB_ASYNC_EXTRACTTPCCURRENTS=0; fi
 if [[ $SYNCMODE != 1 ]] && has_detector_reco TPC; then CAN_DO_CALIB_ASYNC_EXTRACTTIMESERIES=1; else CAN_DO_CALIB_ASYNC_EXTRACTTIMESERIES=0; fi
+if [[ $SYNCMODE != 1 ]] && has_detector_reco TPC; then CAN_DO_CALIB_ASYNC_EXTRACTCOSMICS=1; else CAN_DO_CALIB_ASYNC_EXTRACTCOSMICS=0; fi
 
 # additional individual settings for calibration workflows
 if has_detector CTP; then export CALIB_TPC_SCDCALIB_CTP_INPUT="--enable-ctp"; else export CALIB_TPC_SCDCALIB_CTP_INPUT=""; fi
@@ -222,6 +223,7 @@ fi
 ( [[ -z ${CALIB_ASYNC_DISABLE3DCURRENTS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_DISABLE3DCURRENTS == 0 ]] ) && CALIB_ASYNC_DISABLE3DCURRENTS=0
 : ${ON_SKIMMED_DATA:=0}
 ( [[ -z ${CALIB_ASYNC_EXTRACTTIMESERIES:-} ]] || [[ $CAN_DO_CALIB_ASYNC_EXTRACTTIMESERIES == 0 ]] ) && CALIB_ASYNC_EXTRACTTIMESERIES=0
+( [[ -z ${CALIB_ASYNC_EXTRACTCOSMICS:-} ]] || [[ $CAN_DO_CALIB_ASYNC_EXTRACTCOSMICS == 0 ]] ) && CALIB_ASYNC_EXTRACTCOSMICS=0
 
 
 if [[ "0${GEN_TOPO_VERBOSE:-}" == "01" ]]; then
diff --git a/DATA/production/configurations/asyncReco/async_pass.sh b/DATA/production/configurations/asyncReco/async_pass.sh
index 5a178344d..6b8e60c2c 100755
--- a/DATA/production/configurations/asyncReco/async_pass.sh
+++ b/DATA/production/configurations/asyncReco/async_pass.sh
@@ -205,6 +205,10 @@ if [[ "$ALIEN_JDL_EXTRACTTIMESERIES" == "1" ]]; then
   export ADD_CALIB=1
 fi
 
+if [[ "${ALIEN_JDL_EXTRACTCOSMICS:-}" == "1" ]]; then
+  export ADD_CALIB=1
+fi
+
 if [[ "$ALIEN_JDL_DOTPCTIMEGAINCALIB" == "1" ]]; then
   export ADD_CALIB=1
 fi
diff --git a/DATA/production/configurations/asyncReco/setenv_extra.sh b/DATA/production/configurations/asyncReco/setenv_extra.sh
index 5f6d70e7d..78f6885c1 100644
--- a/DATA/production/configurations/asyncReco/setenv_extra.sh
+++ b/DATA/production/configurations/asyncReco/setenv_extra.sh
@@ -797,6 +797,26 @@ if [[ $ADD_CALIB == "1" ]]; then
       export TPCTIMESERIES_MULT_MAX=$ALIEN_JDL_TPCTIMESERIESMULTMAX
     fi
   fi
+
+  # cosmic muons in collision data: matcher (TPC-only legs) + raw clusters of each cosmic -> o2_cosmics_full.root
+  if [[ -n ${ALIEN_JDL_EXTRACTCOSMICS:-} ]] ; then
+    echo "Adding cosmics matching and raw-cluster output in setenv_extra.sh"
+    export CALIB_ASYNC_EXTRACTCOSMICS=$ALIEN_JDL_EXTRACTCOSMICS
+    if [[ -n ${ALIEN_JDL_COSMICSPRESET:-} ]]; then
+      export COSMICS_PRESET=$ALIEN_JDL_COSMICSPRESET
+    fi
+    # optional: matcher settings on top of the preset (e.g. cosmicsMatch.minSeedDCAxyTOF=0), extra options (e.g. --debug-tree), and
+    # COSMICSPVVETO=0 to switch off the veto of legs belonging to primary-vertex contributors (on by default in calib-workflow.sh)
+    if [[ -n ${ALIEN_JDL_COSMICSCONFIG:-} ]]; then
+      export CONFIG_EXTRA_PROCESS_o2_cosmics_match_workflow+=";$ALIEN_JDL_COSMICSCONFIG"
+    fi
+    if [[ -n ${ALIEN_JDL_COSMICSARGS:-} ]]; then
+      export ARGS_EXTRA_PROCESS_o2_cosmics_match_workflow+=" $ALIEN_JDL_COSMICSARGS"
+    fi
+    if [[ -n ${ALIEN_JDL_COSMICSPVVETO:-} ]]; then
+      export COSMICS_PV_VETO=$ALIEN_JDL_COSMICSPVVETO
+    fi
+  fi
   if [[ $ALIEN_JDL_DOUPLOADSLOCALLY == 1 ]]; then
     export CCDB_POPULATOR_UPLOAD_PATH="file://$PWD"
   fi