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. 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.
To enable the dependency on lxml and/or PyYAML change False to True on the appropriate line(s) in goodruns/info.py and perform a manual installation as described below.
Automatic Installation
Automatically install the latest version of goodruns with pip:
pip install --user goodruns
or with easy_install:
easy_install --user goodruns
Omit the --user for a system-wide installation (requires root privileges). Add ${HOME}/.local/bin to your ${PATH} if using --user and if it is not there already (put this in your .bashrc):
export PATH=${HOME}/.local/bin${PATH:+:$PATH}
To upgrade an existing installation use the -U option in the pip or easy_install commands above.
Manual Installation
Get the latest tarball on PyPI
Untar and install (replace X appropriately):
tar -zxvf goodruns-X.tar.gz cd goodruns-X
To install goodruns into your home directory if using at least Python 2.6:
python setup.py install --user
or with older Python versions:
python setup.py install --prefix=~/.local
Add ${HOME}/.local/bin to your ${PATH} if it is not there already (put this in your .bashrc):
export PATH=${HOME}/.local/bin${PATH:+:$PATH}
To install the optional dependencies:
pip install -U -r optional-requirements.txt
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
grl find
grl find prints the GRLs containing a run number and lumiblock number (if any). The lumiblock number is optional, and if left unset all GRLs containing the run will be printed. For example, you can determine which ROOT file contains the run 215643 and lumiblock 400 with the following command:
grl find --path Lumi/tau --pattern "*.root*" --run 215643 --lb 400 globbed*path*
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