ATLAS "good run list" utilities
Project description
About
goodruns provides an implementation of an ATLAS “good run list” (GRL) reader/writer in Python, and collection of useful command-line tools.
Requirements
goodruns requires at least Python 2.5 and only depends on modules in the standard library. Unlike the standard ATLAS GoodRunsLists package, goodruns does not depend on ROOT for XML processing unless you are reading from or writing to a ROOT file (see below). For better XML reading/writing goodruns will optionally use lxml if installed. Install PyYAML if you would like to convert GRLs into YAML format.
Installation
The easiest way to install goodruns is with pip. To install for all users:
sudo pip install goodruns
To install in your user site-packages directory (also see below):
pip install --user goodruns
If you have obtained a copy of goodruns yourself use the setup.py script to install. To install for all users:
sudo python setup.py install
or to install in your user base directory:
python setup.py install --user
To install the optional dependencies:
pip install -U -r optional-requirements.txt
Post-Installation
If installing in your user site-packages directory be sure to add ~/.local/bin to your $PATH:
export PATH=${HOME}/.local/bin${PATH:+:$PATH}
You may specify a different location for your user site-packages directory with:
export PYTHONUSERBASE=/path/to/alternate/.local
Warning
goodruns uses Python’s built-in XML libraries by default unless you first change this in goodruns/info.py:
USE_LXML = False
to:
USE_LXML = True
before installing. This enables the dependency on lxml for XML parsing and formatting. iLumiCalc unfortunately treats whitespace as significant in text-only nodes like <Run> 123456 </Run> which you will see if using Python’s built-in libraries (see issue 4147). To avoid problems with iLumiCalc please enable lxml support before installing goodruns.
Usage
An example of how to use goodruns:
from goodruns import GRL
grl = GRL('grl.xml')
# or:
grl = GRL('http://atlasdqm.web.cern.ch/atlasdqm/grlgen/path/to/grl.xml')
# or (if '/path/to/grl' is a ROOT.TObjString in data.root):
grl = GRL('data.root:/path/to/grl')
# check if the GRL contains the lumiblock 231 in run 186356:
if (186356, 231) in grl:
# do something
pass
The GRL is automatically optimized (lumiblocks are merged and sorted):
>>> from goodruns import GRL >>> a = GRL() >>> a.insert(1, (1,4)) >>> a.insert(1, (7,10)) >>> a --------------- RUN: 1 LUMIBLOCKS: 1 - 4 7 - 10 >>> a.insert(1, (6,7)) >>> a --------------- RUN: 1 LUMIBLOCKS: 1 - 4 6 - 10 >>> a.insert(1, (5,5)) >>> a --------------- RUN: 1 LUMIBLOCKS: 1 - 10
Command-line Tools
goodruns also provides a collection of command-line tools for combining, manipulating, and inspecting GRLs. As above GRLs may be XML files, URLs, or in ROOT files.
grl diff
Use grl diff to determine the GRL containing the runs/lumiblocks in A.xml but not in B.xml:
grl diff A.xml B.xml
In other words, B.xml is subtracted from A.xml. All command-line tools print on stdout. Redirect stdout to a file to save the result:
grl diff A.xml B.xml > C.xml
You may supply more than two GRLs to grl diff:
grl diff A.xml B.xml C.xml D.xml > E.xml
which results in the GRL E=((A-B)-C)-D). This is equivalent to:
grl diff A.xml B.xml | grl diff C.xml | grl diff D.xml > E.xml
The output of one command can be piped into any of the other commands in goodruns.
grl and, grl or, grl xor
These scripts implement logical combinations of GRLs. Logical AND:
grl and A.xml B.xml > C.xml
OR:
grl or A.xml B.xml > C.xml
and XOR (exclusive OR):
grl xor A.xml B.xml > C.xml
Again, these commands can be combined arbitrarily:
grl and A.xml B.xml | grl or C.xml | grl xor D.xml > E.xml
and any GRL argument can also be a ROOT file or URL:
grl and data.root:/path/to/grl http://atlasdqm.web.cern.ch/path/to/grl.xml
grl clip
Use grl clip to truncate a GRL between a starting run/lumiblock and ending run/lumiblock:
> grl clip --help
usage: grl clip [-h] [-o OUTPUT] [-f FORMAT] [--startrun STARTRUN]
[--startlb STARTLB] [--endrun ENDRUN] [--endlb ENDLB]
[grl]
positional arguments:
grl
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Output filename (optional)
-f FORMAT, --format FORMAT
Output format: xml, yml, txt, py, cut
--startrun STARTRUN Start run
--startlb STARTLB Start lumiblock
--endrun ENDRUN End run
--endlb ENDLB End lumiblock
grl convert
grl convert can convert a GRL from XML format into YAML:
> grl convert -f yml A.xml 186178: - !!python/tuple [125, 156] - !!python/tuple [158, 161] 186179: - !!python/tuple [382, 388] - !!python/tuple [390, 390] - !!python/tuple [396, 396] - !!python/tuple [398, 415] - !!python/tuple [417, 431] - !!python/tuple [433, 453] - !!python/tuple [455, 469] - !!python/tuple [471, 474] - !!python/tuple [476, 479] 186180: - !!python/tuple [114, 116] - !!python/tuple [118, 124] - !!python/tuple [126, 140] - !!python/tuple [144, 149] - !!python/tuple [151, 170] - !!python/tuple [173, 176] ...
or plain text:
> grl convert -f txt A.xml --------------- RUN: 186178 LUMIBLOCKS: 125 - 156 158 - 161 --------------- RUN: 186179 LUMIBLOCKS: 382 - 388 390 396 398 - 415 417 - 431 433 - 453 455 - 469 471 - 474 476 - 479 --------------- RUN: 186180 LUMIBLOCKS: 114 - 116 118 - 124 126 - 140 144 - 149 151 - 170 173 - 176 ...
grl convert will also convert a GRL into Python code (dict of lists of tuples) or (as a joke) a ROOT TCut expression.
grl runs
grl runs simply prints the run numbers, one per line, contained within a GRL:
> grl runs A.xml 186178 186179 186180 ...
Quickly print the runs contained in a GRL from a URL:
> grl runs http://atlasdqm.web.cern.ch/path/to/grl.xml
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