except pyAMI.exception.Error as e:
pyAMI.utils.safeprint('[ERROR] %s' % e)
sys.exit(1)
#####################################################################
print('#################### TEST 2 ####################')
try:
command = [
'GetUserInfo',
'-amiLogin=jodier',
]
pyAMI.utils.safeprint(client.execute(command))
print('[SUCCESS]')
except pyAMI.exception.Error as e:
pyAMI.utils.safeprint('[ERROR] %s' % e)
ret = 1
#####################################################################
print('#################### TEST 3 ####################')
try:
pyAMI.utils.safeprint(
client.execute('GetUserInfo -amiLogin=jodier', format='xml'))
# Get rid of comments
sample = asample.split('#')[0].strip()
# Skip blank linkes
if '' == sample: continue
if 'mc15_13TeV' not in sample or '_p' not in sample or not 'merge.DAOD_' in sample:
print "unexpected input %s, the script only runs over MC15 DAODs" % sample
continue
# strip mc15_13TeV: if present
sample = sample.replace('mc15_13TeV:', '')
print 'Checking sample', sample
result_DAOD = client.execute(
['GetDatasetInfo', '-logicalDatasetName=%s' % sample],
format='dict_object')
identifier = result_DAOD.get_rows('Element_Info')[0]['identifier']
# SQL query to retrieve nInputEvents and nInputEventsUsed for that DAOD
nInputEvents_DAOD = int(
client.execute(
['SearchQuery', MakeArg(identifier, 'nInputEvents')],
format='dict_object').get_rows('Element_Info')[0]['SUM'])
nInputEventsUsed_DAOD = int(
client.execute(
['SearchQuery',
MakeArg(identifier, 'nInputEventsUsed')],
format='dict_object').get_rows('Element_Info')[0]['SUM'])
def main():
logging.basicConfig(format='%(levelname)s:%(message)s')
import time, datetime
from pytz import timezone
import argparse
try:
import pyAMI.client
import pyAMI.atlas.api as AtlasAPI
import pyAMI.config
except ImportError:
logging.error(
"Unable to find pyAMI client. Please try this command first: lsetup pyAMI"
)
return -1
extraFieldDefaults = {
} #{"approx_crossSection":None,"approx_GenFiltEff":1.0}
fieldDefaults = {"subprocessID": 0, "dataset_number": 0}
#populate the fieldDefaults ... for all, assume 'None'
for field in pyAMI.config.tables['datasets'].keys():
if str(field) == "cross_section":
continue #special exception because this field only present in
if str(field) in fieldDefaults.keys(): continue
if str(field).startswith("@"): continue
fieldDefaults[str(field)] = None
import commands
#check the voms proxy
status, out = commands.getstatusoutput("voms-proxy-info -fqan -exists")
if status != 0:
logging.error(
"Please renew your certificate with this command: voms-proxy-init -voms atlas"
)
return -1
try:
client = pyAMI.client.Client('atlas')
AtlasAPI.init()
except:
logging.error(
"Could not establish pyAMI session. Are you sure you have a valid certificate? Do: voms-proxy-init -voms atlas"
)
return -1
#need to collect the ami dataset parameter defaults
paramExplains = [] #for the help message only
paramUnits = dict()
paramDefaults = {}
res = client.execute('ListPhysicsParameterDefs', format='dom_object')
for r in res.get_rows(): #r is OrderedDict
explainString = "%s: %s" % (r[u'PARAMNAME'], r[u'DESCRIPTION'])
if r[u'UNITS'] != u'NULL':
explainString += " (units: %s)" % r[u'UNITS']
paramUnits[r[u'PARAMNAME']] = r[u'UNITS']
if r[u'HASDEFAULT'] == u'N': paramDefaults[str(r[u'PARAMNAME'])] = None
else:
explainString += " (default value = %s)" % r[u'DEFAULTVALUE']
if r[u'PARAMTYPE'] == u'number':
paramDefaults[str(r[u'PARAMNAME'])] = float(
r[u'DEFAULTVALUE']
) #FIXME: Assumes all parameters are floats
elif r[u'PARAMTYPE'] == u'string':
paramDefaults[str(r[u'PARAMNAME'])] = str(r[u'DEFAULTVALUE'])
paramExplains += [explainString]
paramDefaults["crossSection_pb"] = None
paramUnits["crossSection_pb"] = "pb"
paramExplains += [
"crossSection_pb: Same as crossSection except in pb units (units: pb)"
]
cern_time = timezone('UCT')
current_time = datetime.datetime.fromtimestamp(
time.time(), cern_time).strftime('%Y-%m-%d %H:%M:%S')
from argparse import RawTextHelpFormatter
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=RawTextHelpFormatter)
parser.add_argument('--inDS',
nargs='+',
default=[""],
help="List of datasets to retrieve parameters for")
parser.add_argument(
'--inDsTxt',
default="",
help=
"Alternative to --inDS, can specify the datasets from an input file")
parser.add_argument(
'--fields',
nargs='+',
help=
"List of parameters to extract. Available parameters are: \n\n %s\n\nYou can also include any from:\n %s\nYou can also do keyword_xxx to add a bool branch for keywords"
% ("\n ".join(paramExplains),
", ".join(fieldDefaults.keys() + extraFieldDefaults.keys())),
default=["dataset_number", "crossSection", "kFactor", "genFiltEff"])
parser.add_argument(
'--timestamp',
default=current_time,
help=
"The timestamp to query parameters at, specified in Universal Central Time (UCT). If left blank, will take the current time"
)
parser.add_argument(
'--physicsGroups',
nargs='+',
default=["PMG,MCGN"],
help=
"Physics group from which to retrieve parameters, listed in order of priority (highest first). Default value is 'PMG,MCGN' (i.e. try to use PMG values, fallback on MCGN values if unavailable). Allowed groups are:\n PMG (this is the PMG's group name), BPHY, COSM, DAPR, EGAM, EXOT, FTAG, HIGG, HION, IDET, IDTR, JETM, LARG, MCGN (this is the AMI default group name), MDET, MUON, PHYS, REPR, SIMU, STDM, SUSY, TAUP, TCAL, TDAQ, THLT, TOPQ, TRIG, UPGR, VALI"
)
parser.add_argument(
'--oldTimestamp',
default="",
help=
"If specified, will instead display a diff between the old and new timestamp, showing explanation of any changed parameters"
)
parser.add_argument(
'--explainFields',
nargs='+',
default=[],
help=
"The fields you would like explained .. will appear as comment lines after each row in the output"
)
parser.add_argument(
'--explainInfo',
nargs='+',
default=['explanation', 'insert_time'],
help=
"Properties of the parameter you want to show in the explanation. Can list from: explanation, insert_time, physicsGroup, createdby. Default is: explanation,insert_time"
)
parser.add_argument(
'--outFile',
default=sys.stdout,
type=argparse.FileType('w'),
help="Where to print the output to. Leave blank to print to stdout")
parser.add_argument(
'--delim',
default="",
help=
"The delimiter character. Defaults to spaces leading to nice formatting table"
)
parser.add_argument('-v',
action='store_true',
help="Verbose output for debugging")
args = parser.parse_args()
if args.v: logging.getLogger().setLevel(logging.DEBUG)
else: logging.getLogger().setLevel(logging.INFO)
logging.debug(args.inDS)
logging.debug(args.fields)
logging.debug(args.timestamp)
if args.timestamp == "the dawn of time":
logging.error(
"Unfortunately we don't know any parameters from this time period... but we're working on it!"
)
return 9999
#split elements of fields by comma to get full list
args.fields = sum((y.split(',') for y in args.fields), [])
args.fields = [x.strip() for x in args.fields] #strips whitespace
#look for keyword_ fields, these are special ...
args.keywords = []
for f in args.fields:
if f.startswith("keyword_"):
k = f[8:]
#and then add each keyword to the extraFieldDefaults so it is recognised thusly
extraFieldDefaults["keyword_%s" % k] = bool(False)
args.keywords += [k]
#same for physics groups
args.physicsGroups = sum((y.split(',') for y in args.physicsGroups), [])
args.physicsGroups = [x.strip()
for x in args.physicsGroups] #strips whitespace
#same for explainFields and explainInfo
args.explainFields = sum((y.split(',') for y in args.explainFields), [])
args.explainFields = [x.strip()
for x in args.explainFields] #strips whitespace
args.explainInfo = sum((y.split(',') for y in args.explainInfo), [])
args.explainInfo = [x.strip()
for x in args.explainInfo] #strips whitespace
if args.inDsTxt != '': args.inDS = readDsFromFile(args.inDsTxt)
#and same for inDS
args.inDS = sum((y.split(',') for y in args.inDS), [])
args.inDS = [x.strip() for x in args.inDS] #strips whitespace
#1. check field values are allowed, we obtain default field values at same time..
#2. For each entry in inDS, if contains wildcard we obtain list of DS, otherwise check DS exists. During this time we obtain the datasetid and numEvents properties, incase we need them
#3. For each of these DS, get parameters from ami matching the timestamp. Organize into fields and index by subprocessID
#4. Output a line to our output file
#1.
#before adding all the ami parameters, identify which of provided fields are: 1). Obtained from list_datasets command (dsFields) 2). actual parameters
dsFields = [
x for x in args.fields
if x in fieldDefaults.keys() and x not in ["subprocessID", "ldn"]
]
extraFields = [x for x in args.fields if x in extraFieldDefaults.keys()]
paramFields = [x for x in args.fields if x in paramDefaults.keys()]
if len(paramFields) > 0 and args.physicsGroups == [""]:
logging.error(
"You must specify at least one physics group. See -h for allowed groups"
)
return -1
#combine paramDefaults with fieldDefaults
fieldDefaults.update(paramDefaults)
#and with extra fields
fieldDefaults.update(extraFieldDefaults)
for field in args.fields:
if field not in fieldDefaults:
logging.error("%s is not a recognised field. Allowed fields are:" %
field)
logging.error(fieldDefaults.keys())
return -1
if args.oldTimestamp != "":
logging.info("oldTimestamp option specified. Running in diff mode...")
args.explainFields = args.fields
args.explainInfo = [
"explanation", "insert_time", "physicsGroup", "createdby"
]
#2.
#replace all '*' with '%' and strip "/"
args.inDS = [ds.replace("*", "%") for ds in args.inDS]
args.inDS = [ds.rstrip("/") for ds in args.inDS]
if len(args.inDS) == 0 or (len(args.inDS) == 1 and args.inDS[0] == ""):
logging.error(
"No datasets provided. Please specify datasets with the --inDS or --inDsTxt options"
)
return -1
logging.info(
"Fetching list of datasets from AMI (this may take a few minutes)...")
#obtain list of datasets
res = AtlasAPI.list_datasets(
client,
patterns=args.inDS,
fields=dsFields + ['ldn'],
ami_status="VALID"
) #changed status from %, to only catch valid now: wb 08/2015
logging.info("...Found %d datasets matching your selection" % len(res))
if len(res) == 0:
return 0
#NOTE: Should we allow retrieval of the extra information: keyword, genfiltereff, approx crossection, .. these all come from GetDatasetInfo ami command
dataset_values = dict()
for r in res:
mydict = dict()
dataset_values[str(r['ldn'])] = mydict
for field in r.items():
if str(field[0]) == "ldn": continue
if str(field[0]) not in args.fields: continue
mydict[str(field[0])] = str(field[1])
#also if we have the 'extra fields or keywords' we will need to execute AtlasAPI.get_dataset_info ..
if len(extraFields) > 0 or len(args.keywords) > 0:
info_res = AtlasAPI.get_dataset_info(client, str(r['ldn']))
#print(info_res)
if len(info_res) == 0:
logging.error("Unable to retrieve dataset info for %s" %
str(r['ldn']))
return -1
for field in extraFields:
#ignore the keyword_ fields
if field.startswith("keyword_"): continue
mydict[field] = float(info_res[0][unicode(field)]) if isfloat(
info_res[0][unicode(field)]) else extraFieldDefaults[field]
for k in args.keywords:
mydict["keyword_%s" % k] = int(
(k in str(info_res[0][unicode('keyword')]).split(",")))
#sort dataset_values as well as possible
from collections import OrderedDict
sorted_values = OrderedDict()
for ds in args.inDS:
if ds in dataset_values.keys():
sorted_values[ds] = dataset_values[ds]
for ds in sorted(dataset_values):
if ds not in sorted_values.keys():
sorted_values[ds] = dataset_values[ds]
dataset_values = sorted_values
logging.debug(dataset_values)
#res = client.execute(['GetDatasetInfo
for ds in args.inDS:
if '%' not in ds and ds not in dataset_values.keys():
logging.warning("Unknown dataset: %s" % ds)
datasetsToQuery = ",".join(dataset_values.keys())
#if using inDsTxt, retain any comment or blank lines in structure of output
complete_values = OrderedDict()
if args.inDsTxt != "":
# read lines
commentcount = 0
import re
txt = open(args.inDsTxt)
for tmpLine in txt:
# remove \n
tmpLine = re.sub('\n', '', tmpLine)
# remove white spaces
tmpLine = tmpLine.strip()
# skip comment or empty
if tmpLine.startswith('#') or tmpLine == '':
complete_values['comment%d' % (commentcount)] = tmpLine
commentcount = commentcount + 1
continue
# append
tmpLine = tmpLine.rstrip("/")
if tmpLine in dataset_values.keys():
complete_values[tmpLine] = dataset_values[tmpLine]
else:
print("cannot find %s" % tmpLine)
# close file
txt.close()
dataset_values = complete_values
logging.info(
"Obtaining %s for selected datasets at timestamp=%s... (please be patient)"
% (args.fields, args.timestamp))
#do as one query, to be efficient
if (args.timestamp == current_time):
res = client.execute([
'GetPhysicsParamsForDataset',
"--logicalDatasetName=%s" % datasetsToQuery,
"--timestamp='%s'" % args.timestamp
],
format='dom_object')
else:
res = client.execute([
'GetPhysicsParamsForDataset',
"--logicalDatasetName=%s" % datasetsToQuery,
"--timestamp='%s'" % args.timestamp, "--history=true"
],
format='dom_object')
#organize results by dataset
parameterQueryResults = dict()
for r in res.get_rows():
if r[u'logicalDatasetName'] not in parameterQueryResults.keys():
parameterQueryResults[r[u'logicalDatasetName']] = []
parameterQueryResults[r[u'logicalDatasetName']] += [
r
] #puts row in the list for this dataset
if args.oldTimestamp != "":
logging.info(
"Obtaining %s for selected datasets at timestamp=%s... (please be patient)"
% (args.fields, args.oldTimestamp))
res2 = client.execute([
'GetPhysicsParamsForDataset',
"--logicalDatasetName=%s" % datasetsToQuery,
"--timestamp='%s'" % args.oldTimestamp, "--history=true"
],
format='dom_object')
old_parameterQueryResults = dict()
for r in res2.get_rows():
if r[u'logicalDatasetName'] not in old_parameterQueryResults.keys(
):
old_parameterQueryResults[r[u'logicalDatasetName']] = []
old_parameterQueryResults[r[u'logicalDatasetName']] += [
r
] #puts row in the list for this dataset
headerString = ""
doneHeader = False
commentCache = ""
commentCount = 0
#result is a list of lists (each list is 1 row)
outputTable = []
tableHeaders = []
for ds in dataset_values.keys():
if ds.startswith('comment'):
if commentCount > 0: commentCache += "\n"
commentCache += dataset_values[ds]
commentCount = commentCount + 1
continue
#obtain list of parameters for this dataset
#if(args.timestamp==current_time):
# res = client.execute(['GetPhysicsParamsForDataset',"--logicalDatasetName=%s"% ds,"--timestamp='%s'"%args.timestamp], format='dom_object')
#else:
# res = client.execute(['GetPhysicsParamsForDataset',"--logicalDatasetName=%s"% ds,"--timestamp='%s'"%args.timestamp,"--history=true"], format='dom_object')
res = parameterQueryResults.get(ds, [])
if args.oldTimestamp != "":
res2 = old_parameterQueryResults.get(ds, [])
#first we have to determine how many subprocesses this ds has
dsSubprocesses = [0] #always have the 0 subprocess
for r in res:
sp = int(r[u'subprocessID'])
if sp not in dsSubprocesses: dsSubprocesses += [sp]
#now for each subprocess we have to locate each required field value (in paramFields)
#rank by physicsGroup
for sp in dsSubprocesses:
paramVals = dict()
paramVals2 = dict()
groupsWithVals = dict() #held for helpful output
#need to keep explanations for requested fields
explainInfo = dict()
for i in args.explainFields:
explainInfo[i] = dict()
for param in paramFields:
groupsWithVals[param] = []
bestGroupIndex = len(args.physicsGroups)
import copy
paramVals[param] = copy.copy(fieldDefaults[param])
for r in res:
if int(r[u'subprocessID']) != sp: continue
if str(r[u'paramName']) != param and not (
param == "crossSection_pb"
and str(r[u'paramName']) == "crossSection"):
continue
if str(r[u'physicsGroup']) not in args.physicsGroups:
groupsWithVals[param] += [(str(r[u'physicsGroup']),
str(r[u'paramValue']))]
continue
if args.physicsGroups.index(str(
r[u'physicsGroup'])) > bestGroupIndex:
continue
if args.physicsGroups.index(str(
r[u'physicsGroup'])) == bestGroupIndex:
logging.warning(
"Duplicate parameter %s for group %s in dataset %s (subprocess %d). Please report this!"
% (param, str(r[u'physicsGroup']), ds, sp))
paramVals[param] = str(r[u'paramValue'])
if param == "crossSection_pb":
paramVals[param] = str(
float(paramVals[param]) * 1000.0)
bestGroupIndex = args.physicsGroups.index(
str(r[u'physicsGroup']))
#keep the explanation info for the requested fields
if param in explainInfo.keys():
for e in args.explainInfo:
if unicode(e) not in r:
logging.error(
"Unrecognised explainInfo field: %s" % e)
return -1
explainInfo[param][e] = str(r[unicode(e)])
if args.oldTimestamp != "":
bestGroupIndex = len(args.physicsGroups)
paramVals2[param] = copy.copy(fieldDefaults[param])
for r in res2:
if int(r[u'subprocessID']) != sp: continue
if str(r[u'paramName']) != param and not (
param == "crossSection_pb"
and str(r[u'paramName']) == "crossSection"):
continue
if str(r[u'physicsGroup']) not in args.physicsGroups:
continue
if args.physicsGroups.index(str(
r[u'physicsGroup'])) > bestGroupIndex:
continue
if args.physicsGroups.index(str(
r[u'physicsGroup'])) == bestGroupIndex:
logging.warning(
"Duplicate parameter %s for group %s in dataset %s (subprocess %d). Please report this!"
% (param, str(r[u'physicsGroup']), ds, sp))
paramVals2[param] = str(r[u'paramValue'])
if param == "crossSection_pb":
paramVals2[param] = str(
float(paramVals2[param]) * 1000.0)
bestGroupIndex = args.physicsGroups.index(
str(r[u'physicsGroup']))
#at this stage, parameters reside in paramVals dict or dataset_values[ds] dict
#print them in the requested order .. if any is "None" then stop, because it doesn't have a default value and didn't find a value for it either
rowString = ""
rowList = []
firstPrint = False
for param in args.fields:
val = None
if param == "ldn": val = ds
elif param == "subprocessID": val = sp
elif param in dataset_values[ds].keys():
val = dataset_values[ds][param]
else:
val = paramVals.get(param, None)
if val == None:
if args.outFile != sys.stdout:
logging.warning(
"dataset %s (subprocess %d) does not have parameter %s, which has no default."
% (ds, sp, param))
if len(groupsWithVals.get(param, [])) > 0:
logging.warning(
"The follow physicsGroups have defined that parameter though:"
)
logging.warning(groupsWithVals[param])
val = "#UNKNOWN#"
#return -1
#if isfloat(str(val)): val = "%.6g" % float(val)
if args.oldTimestamp != "":
#diff val to old val
val2 = None
if param == "ldn": val2 = ds
elif param == "subprocessID": val2 = sp
elif param in dataset_values[ds].keys():
val2 = dataset_values[ds][param]
else:
val2 = paramVals2.get(param, None)
if val2 == None: val2 = "#UNKNOWN#"
#if isfloat(str(val2)): val2 = "%.6g" % float(val)
if (str(val) != str(val2)):
if not firstPrint: print("%s:" % ds)
firstPrint = True
print(" %s : %s ---> %s" %
(param, str(val2), str(val)))
print(" insert_time : %s" %
explainInfo[param]['insert_time'])
print(" explanation : %s" %
explainInfo[param]['explanation'])
print(" createdby : %s" %
explainInfo[param]['createdby'])
print(" physicsGroup : %s" %
explainInfo[param]['physicsGroup'])
continue
rowList += [str(val)]
if rowString != "" and args.delim != "":
rowString += args.delim
rowString += str(val)
#inspect the type of str(val) to build up the header
if not doneHeader:
headerString += param
if args.outFile != sys.stdout:
if type(fieldDefaults[param]) == bool:
headerString += "/O:"
elif type(fieldDefaults[param]) == int:
headerString += "/I:"
elif type(fieldDefaults[param]) == float:
headerString += "/D:"
elif isfloat(str(val)):
headerString += "/D:"
#elif isint(str(val)): headerString += "/I:" TO BE SAFE WE MAKE ALL NUMERIC FIELDS FLOATS, EXCEPT if the default value is type int
else:
headerString += "/C:"
else:
v = param
if param in paramUnits:
headerString += " [%s]" % paramUnits[param]
v += " [%s]" % paramUnits[param]
tableHeaders += [v]
headerString += " "
if args.oldTimestamp != "":
continue #print nothing more for diff mode
if not doneHeader:
doneHeader = True
if args.outFile != sys.stdout:
print(headerString[:-1], file=args.outFile)
if commentCount > 0:
if args.outFile != sys.stdout and args.delim != "":
print(commentCache, file=args.outFile)
outputTable += [["COMMENT", commentCache]]
commentCache = ''
commentCount = 0
if args.outFile != sys.stdout and args.delim != "":
print(rowString, file=args.outFile)
outputTable += [rowList]
#also print the required explanations
for (field, expl) in explainInfo.items():
outString = "#%s: { " % field
doneFirst = False
for eField in args.explainInfo:
if doneFirst: outString += " , "
if not eField in expl.keys():
outString += " %s: <NONE .. value is default>" % eField
else:
outString += "%s: %s" % (eField, expl[eField])
doneFirst = True
outString += " }"
#print(outString,file=args.outFile)
outputTable += [["COMMENT", outString]]
if args.oldTimestamp != "":
args.outFile.close()
return 0
#print the table in nicely formatted state
if args.outFile == sys.stdout or args.delim == "":
#determine column widths
columnWidths = [0] * len(args.fields)
for i in range(0, len(tableHeaders)):
columnWidths[i] = len(tableHeaders[i])
for r in outputTable:
if len(r) > 0 and r[0] == "COMMENT": continue
for i in range(0, len(r)):
if len(r[i]) > columnWidths[i]: columnWidths[i] = len(r[i])
lineout = ""
for i in range(0, len(tableHeaders)):
lineout += tableHeaders[i].ljust(columnWidths[i]) + " "
print(lineout)
for r in outputTable:
lineout = ""
if len(r) > 0 and r[0] == "COMMENT": lineout = r[1]
else:
for i in range(0, len(r)):
lineout += r[i].ljust(columnWidths[i]) + " "
print(lineout, file=args.outFile)
#print the footer, which is the command to reproduce this output
import os
if args.outFile != sys.stdout:
#remove comment from dataset_values
datasetss = [
x for x in dataset_values.keys() if not x.startswith("comment")
]
print("", file=args.outFile)
print("#lsetup \"asetup %s,%s\" pyAMI" %
(os.environ.get('AtlasProject', 'UNKNOWN!'),
os.environ.get('AtlasVersion', 'UNKNOWN!')),
file=args.outFile)
print(
"#getMetadata.py --timestamp=\"%s\" --physicsGroups=\"%s\" --fields=\"%s\" --inDS=\"%s\""
% (args.timestamp, ",".join(args.physicsGroups), ",".join(
args.fields), ",".join(datasetss)),
file=args.outFile)
logging.info("Results written to: %s" % args.outFile.name)
args.outFile.close()