1/ Install and run ZeroLeptonRun2:
==================================

The instructions for installing and compiling are in ZeroLeptonRun2/INSTALL 

The cafe config file is in ZeroLeptonRun2/config/zerolepton.config, you can
copy it and modify it but for testing it is easier to just overwrite some 
configurations from the command line like:

for mc15 / data 15 :

cafe ZeroLeptonRun2/config/zerolepton.config Events: 100 Input: //eos/atlas/atlasdatadisk/rucio/mc15_13TeV/6d/97/DAOD_SUSY1.05556029._000058.pool.root.1

This run a simple job with no systematics. For systematics, turn 

Global.DoSystematics: TRUE

and adjust the systematics to run by changing the wilcard patterns (space
separated) in Global.SystematicsSelection:



To run the truth code, an example is given below : 

cafe ZeroLeptonRun2/config/zeroleptontruth.config Events: 100 Input: root://eosatlas.cern.ch//eos/atlas/user/c/conti/atlasreadable/datafiles/mc15_13TeV.361007.Pythia8EvtGen_A14NNPDF23LO_jetjet_JZ7.evgen.EVNT.e3569_tid04904951_00/DAOD_TRUTH1.DAOD.04904951._000779.pool.root



2/ Extract dataset informations from AMI:
=========================================
localSetupPyAMI
ZeroLeptonRun2/python/makeDatasetList.py --help

For example, 
ZeroLeptonRun2/python/makeDatasetList.py --baseline

will make the list of mc15_13TeV corresponding to the baseline samples.




3/ Running jobs on the grid:
============================
#to reduce the size of the tarball it's better to clear libraries etc 
rc clean
localSetupPandaClient
ZeroLeptonRun2/python/launch_jobs_on_grid.py --help

For example, with baseline.ds a text file with the list of dataset extracted with makeDatasetList.py:
ZeroLeptonRun2/python/launch_jobs_on_grid.py --prunopts='--nGBPerJob=10 --excludedSite=ANALY_UIO,SIGNET,LUNARC ' --prefix='user.lduflot.' --suffix='_test2' --tmpDir=/scratch/duflot  --inDSfile baseline.ds

If the inDS contains the string data11/data12, the job will be configured to 
read real data. For MC, if the inDS still has the AMI tags, the script can
figure out if ATLFAST was used. On the other hand, it knows about a limited 
pattern of signal datasets, to be safe use the --signal option.




4/ Creating an updated cross-section database:
==============================================
This step is necessary to produce a file in the correct format for merging.

Use the getMCInfo.py tools (slightly updated version of the Run1 tool)
to build the extended cross-section database from the un-merged small
ntuples. The tool will extract the number of events processed and the 
total sum of MC weights from the Counter and write an extended 
cross-section file that includes these informations.


   4.1/ From mini-tuples on disk
   -----------------------------

For example, one can list all downloaded small tuples in a file input.list
(the file path should allow to extract the dataset IDs) an do

ZeroLeptonRun2/python/getMCInfo.py --input input.list

this will create MCBackgroundDB.dat (and .tex) in the local directory.
You need to have the code compiled as it uses C++ code from SUSYTools.


   4.2/ From mini-tuples on (local) grid storage element
   -----------------------------------------------------

Alternatively, one may have subscribed the small ntuple datasets to a local
grid storage element. In this case a simple list of the file URLs does not 
allow to extract the dataset ID. A pickle file containing the datasets and 
files need to be built. This tools uses rucio so it is in general better to 
execute it from a fresh session.

ZeroLeptonRun2/python/buildRSEFileList --rse grid_storage  dids

or put the dataset names in a file and use --didfile. The resulting files.pkl
can be used with the getMCInfo.py commands (don't change the pkl extension):

ZeroLeptonRun2/python/getMCInfo.py --prefix mc15_13TeV --input files.pkl --xsecfile SUSYTools/data/susy_crosssections_13TeV.txt



5/ Merging small ntuples for ZeroLeptonHistFitter:
==================================================
The filter/merge/update step is done by FilterUpdateMerge.py:
ZeroLeptonRun2/python/FilterUpdateMerge.py --help  

For example:
ZeroLeptonRun2/python/FilterUpdateMerge.py --doBackground --input_mc=small.list --doNormWeight  --dbName updatedDB.dat

Where the --dbName option points to an updated cross-section database built 
with the previous step (needed as the previous steps adds the number of events
processed and corresponding sum weights.

The file path of input files for MC should allow to retreive the dataset ID, 
as for mini-tuple datasets downloaded on disk. Alternaltively, one can also 
point to a pickle file produced as explained in 4.2 if the dataset are on a
local grid storage element (keep the '.pkl' file extension).


You need to have the code compiled as it uses C++ code.



6/ Cleaning cuts:
================

Starting version ZeroLeptonRun2-00-00-36, the cleaning cuts have been removed
(except detector status) and a flag is added in the "cleaning" word

SR:
bit 0 : set if   bad jet veto
bit 1 : set if   bad MET muon
bit 2 : set if   bad Tile veto
bit 3 : set if   negative energy cell veto
bit 4 : set if   leading jet timing (not used in Run 1)
bit 5 : set if   chfTileVeto (8TeV)
bit 6 : set if   chfVeto (not used in Run 1)
suggested requirement:  '(cleaning&3)==0'


CRWT:
bit 0 : set if   bad jet veto
bit 1 : set if   bad muon
bit 2 : set if   cosmic muon
bit 3 : set if   bad MET muon
bit 4 : set if   bad Tile veto
bit 5 : set if   negative energy cell veto
bit 6 : set if   leading jet timing (not used in Run 1)
bit 7 : set if   chfVeto (not used in Run 1)
suggested requirement:  '(cleaning&15)==0'

CRZ:
bit 0 : set if   bad jet veto
bit 1 : set if   bad muon
bit 2 : set if   cosmic muon
bit 3 : set if   bad Tile veto
bit 4 : set if   negative energy cell veto
bit 5 : set if   leading jet timing (not used in Run 1)
bit 6 : set if   chfVeto (not used in Run 1)
suggested requirement:  '(cleaning&7)==0'

CRY:
bit 0 : set if   bad jet veto
bit 1 : set if   bad muon
bit 2 : set if   cosmic muon
bit 3 : set if   bad MET muon
bit 4 : set if   bad Tile veto
bit 5 : set if   negative energy cell veto
bit 6 : set if   leading jet timing (not used in Run 1)
bit 7 : set if   chfTileVeto (8TeV)
bit 8 : set if   chfVeto (not used in Run 1)
suggested requirement:  '(cleaning&15)==0'