def get_dataset(inputDataset = None, inputID = None):
dbstore = DbStore()
if inputDataset is not None:
resultset = dbstore.find(Dataset, Dataset.name == inputDataset)
elif inputID is not None:
resultset = dbstore.find(Dataset, Dataset.dataset_id == inputID)
return list(resultset.values(Dataset.name, Dataset.dataset_id, Dataset.nevents, Dataset.process))
def get_sample(inputSample = None, inputID = None):
dbstore = DbStore()
if inputSample is not None:
resultset = dbstore.find(Sample, Sample.name == inputSample)
elif inputID is not None:
resultset = dbstore.find(Sample, Sample.sample_id == inputID)
return list(resultset.values(Sample.name, Sample.sample_id, Sample.source_dataset_id, Sample.code_version))
def compute_luminosity(sample, options):
print("Computing luminosity for %r") % str(sample.name)
lumi = 0
if not options.local:
print("Running brilcalc on lxplus... You'll probably need to enter your lxplus password in a moment")
print('')
cmds = ['brilcalc', 'lumi', '--normtag', '~lumipro/public/normtag_file/OfflineNormtagV2.json', '--output-style', 'csv', '-i', '"%s"' % str(sample.processed_lumi.replace('"', ''))]
cmd = 'export PATH="$HOME/.local/bin:/afs/cern.ch/cms/lumi/brilconda-1.0.3/bin:$PATH"; ' + ' '.join(cmds)
ssh_cmds = ['ssh', '*****@*****.**' % options.username, cmd]
brilcalc_result = subprocess.check_output(ssh_cmds)
lumi = parse_luminosity_csv(brilcalc_result)
else:
print("Running brilcalc locally...")
# FIXME one day
print("Error: running brilcalc locally is not supported for the moment.")
return 0
print("Sample luminosity: %.3f /pb" % lumi)
print('')
store = DbStore()
# Update luminosity in the database
store.find(Sample, Sample.sample_id == sample.sample_id).set(luminosity = lumi)
store.commit()
return lumi
def main():
"""Main function"""
# get the options
optmgr = MyOptionParser()
opts = optmgr.get_opt()
# connect to the MySQL database using default credentials
dbstore = DbStore()
# check that the LHCO exists and obtain the dataset id
check = dbstore.find(Sample,Sample.sample_id==opts.lhco_id)
if check.is_empty() or check.one().sampletype != "LHCO":
raise IndexError("No LHCO with such index: %d"%opts.lhco_id)
opts.dataset = findDataset(check.one())
if opts.dataset is None:
raise RuntimeError("Impossible to get the dataset id.")
# check that the process exists
check = dbstore.find(MadWeight,MadWeight.process_id==opts.process)
if check.is_empty():
raise IndexError("No process with such index: %d"%opts.process)
# create the MW run object
mw_run = MadWeightRun(opts.process,opts.lhco_id)
mw_run.systematics = unicode(opts.syst)
mw_run.user_comment = unicode(opts.comment)
mw_run.version = opts.version
if mw_run.version is None:
check = dbstore.find(MadWeightRun,(MadWeightRun.madweight_process==mw_run.madweight_process) & (MadWeightRun.lhco_sample_id==mw_run.lhco_sample_id))
if not check.is_empty():
mw_run.version = check.order_by(MadWeightRun.version).last().version + 1
else:
mw_run.version = 1
else:
check = dbstore.find(MadWeightRun,(MadWeightRun.madweight_process==mw_run.madweight_process) & (MadWeightRun.lhco_sample_id==mw_run.lhco_sample_id) & (MadWeightRun.version==mw_run.version))
if not check.is_empty():
raise RuntimeError("There is already one such MadWeight run with the same version number:\n%s\n"%str(check.one()))
# read the file
inputfile = open(opts.filepath)
count = 0
for line in inputfile:
data = line.rstrip('\n').split('\t')
# get the event
run_number = int(data[0].split('.')[0])
event_number = int(data[0].split('.')[1])
event_query = dbstore.find(Event, (Event.event_number==event_number) & (Event.run_number==run_number) & (Event.dataset_id==opts.dataset))
if event_query.is_empty():
event = Event(event_number,run_number,opts.dataset)
else:
event = event_query.one()
# create the weight
weight = Weight()
weight.event = event
weight.mw_run = mw_run
weight.value = float(data[1])
weight.uncertainty = float(data[2])
dbstore.add(weight)
count += 1
# confirm and commit
print mw_run
print "Adding weights to %d events."%count
if confirm(prompt="Insert into the database?", resp=True):
dbstore.commit()
def get_sample(id=None, name=None):
store = DbStore()
if (id):
result = store.find(Sample, Sample.sample_id == id)
else:
result = store.find(Sample, Sample.name == unicode(name))
return result.one()
def get_sample(id, name):
dbstore = DbStore()
if id is not None:
result = dbstore.find(Sample, Sample.sample_id == id)
elif name is not None:
result = dbstore.find(Sample, Sample.name.like(unicode(name.replace('*', '%').replace('?', '_'))))
return result.one()
def getSample(self, iSample):
""" Get sample from the DB, using the sample ID or name. """
sample = ""
dbstore = DbStore()
if isinstance(iSample, int):
sample = dbstore.find(Sample, Sample.sample_id == iSample).one()
elif isinstance(iSample, str):
sample = dbstore.find(Sample, Sample.name == unicode(iSample)).one()
else:
raise Exception("Argument should be sample ID or DB name.")
return sample
def getSampleFiles(self, iSample):
""" Get sample name/lit of sample files from the DB, using the sample ID or name. """
sample = ""
dbstore = DbStore()
if isinstance(iSample, int):
sample = dbstore.find(Sample, Sample.sample_id == iSample).one()
elif isinstance(iSample, str):
sample = dbstore.find(Sample, Sample.name == unicode(iSample)).one()
else:
raise Exception("Argument should be sample ID or DB name.")
return sample.name, [ "/storage/data/cms/" + str(file.lfn) for file in sample.files ]
def get_samples(name):
store = DbStore()
results = store.find(Sample,
Sample.name.like(unicode(name.replace('*', '%'))))
if results.count() == 0:
raise Exception("Could not find any sample matching {}".format(name))
print("Found samples: ")
for sample in results:
print(sample.name)
return results
def getSample(self, iSample):
""" Get sample from the DB, using the sample ID or name. """
sample = ""
dbstore = DbStore()
if isinstance(iSample, int):
sample = dbstore.find(Sample, Sample.sample_id == iSample).one()
elif isinstance(iSample, str):
sample = dbstore.find(Sample,
Sample.name == unicode(iSample)).one()
else:
raise Exception("Argument should be sample ID or DB name.")
return sample
def getSampleFiles(self, iSample):
""" Get sample name/lit of sample files from the DB, using the sample ID or name. """
sample = ""
dbstore = DbStore()
if isinstance(iSample, int):
sample = dbstore.find(Sample, Sample.sample_id == iSample).one()
elif isinstance(iSample, str):
sample = dbstore.find(Sample,
Sample.name == unicode(iSample)).one()
else:
raise Exception("Argument should be sample ID or DB name.")
return sample.name, [
"/storage/data/cms/" + str(file.lfn) for file in sample.files
]
def main():
"""Main function"""
# get the options
optmgr = MyOptionParser()
opts = optmgr.get_opt()
# connect to the MySQL database using default credentials
dbstore = DbStore()
# build the query
if opts.objtype == "dataset":
objectClass = Dataset
objectId = Dataset.dataset_id
elif opts.objtype == "sample":
objectClass = Sample
objectId = Sample.sample_id
elif opts.objtype == "madweight":
objectClass = MadWeight
objectId = MadWeight.process_id
else:
objectClass = Result
objectId = Result.result_id
if opts.objid is not None:
result = dbstore.find(objectClass, objectId==opts.objid)
elif opts.path is not None:
result = dbstore.find(objectClass, objectClass.path.like(unicode(opts.path.replace('*', '%').replace('?', '_'))))
elif opts.name is not None:
result = dbstore.find(objectClass, objectClass.name.like(unicode(opts.name.replace('*', '%').replace('?', '_'))))
else:
result = dbstore.find(objectClass)
result = result.order_by(objectId)
# loop and print
if opts.longOutput:
for entry in result:
print entry
print "--------------------------------------------------------------------------------------"
else:
if opts.objtype != "result":
data = result.values(objectId, objectClass.name)
else:
data = result.values(objectId, objectClass.description)
for dset in data:
print "%i\t%s"%(dset[0], dset[1])
def main():
"""Main function"""
# get the options
optmgr = MyOptionParser()
opts = optmgr.get_opt()
# build the result from user input
result = Result(unicode(opts.path))
result.description = unicode(opts.desc)
result.author = unicode(opts.author)
result.creation_time = opts.datetime
# connect to the MySQL database using default credentials
dbstore = DbStore()
# unless the source is set, prompt the user and present a list to make a choice
if opts.inputSamples is None:
inputSamples = prompt_samples(dbstore)
else:
inputSamples = parse_samples(opts.inputSamples)
# create and store the relations
samples = dbstore.find(Sample,Sample.sample_id.is_in(inputSamples))
if samples.is_empty():
dbstore.add(result)
else:
for sample in samples:
sample.results.add(result)
print result
if confirm(prompt="Insert into the database?", resp=True):
dbstore.commit()
def main():
options = get_options()
print "Merging non-resonant HH samples: %s" % ', '.join(
str(i) for i in options.ids)
print("")
dbstore = DbStore()
print("Checking that the samples already exist in the database...")
samples = []
for id in options.ids:
sample = get_sample(id, dbstore)
if not sample:
raise AssertionError(
"Aborting: the sample %d does not exist in the database, please insert it first"
% id)
samples.append(sample)
print("All good. Continuing...")
# Sanity check. Ensure that all parent datasets have the same cross-section
dataset_xsec = None
for sample in samples:
if not dataset_xsec:
dataset_xsec = sample.source_dataset.xsection
else:
if dataset_xsec != sample.source_dataset.xsection:
raise AssertionError(
"Aborting: the parent datasets do not have the same cross-section. Merging would be ill-defined."
)
r = re.compile('(GluGluToHHTo2B2VTo2L2Nu_)node_.*(_13TeV-madgraph_.*)')
# Ensure that all samples match the regex
for sample in samples:
if not r.match(sample.name):
raise AssertionError(
"Aborting: sample %d's name (%s) does not match expected name."
% (sample.sample_id, sample.name))
merged_sample_name = r.sub(r'\g<1>all_nodes\g<2>', samples[0].name)
print "Constructing merged sample %r ..." % merged_sample_name
comment = 'Merging of SAMADhi samples %s' % ', '.join(
str(i) for i in options.ids)
add_merged_sample(samples, merged_sample_name, comment, dbstore)
def add_sample(NAME, localpath, type, dataset_nevents, nselected, AnaUrl, FWUrl, dataset_id):
# Large part of this imported from SAMADhi add_sample.py
sample = Sample(unicode(NAME), unicode(localpath), unicode(type), dataset_nevents)
sample.nevents = nselected
sample.normalization = 1.0
sample.luminosity = 40028954.499 / 1e6 # FIXME: figure out the fix for data whenever the tools will stabilize and be on cvmfs
sample.code_version = unicode(AnaUrl + ' ' + FWUrl) #NB: limited to 255 characters, but so far so good
# sample.user_comment =
sample.source_dataset_id = dataset_id
# sample.source_sample_id = None
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
# sample.creation_time =
# connect to the MySQL database using default credentials
dbstore = DbStore()
# check that source dataset exist
if dbstore.find(Dataset,Dataset.dataset_id==sample.source_dataset_id).is_empty():
raise IndexError("No dataset with such index: %d"%sample.source_dataset_id)
# check that there is no existing entry
checkExisting = dbstore.find(Sample,Sample.name==sample.name)
if checkExisting.is_empty():
print sample
if confirm(prompt="Insert into the database?", resp=True):
dbstore.add(sample)
# compute the luminosity, if possible
if sample.luminosity is None:
dbstore.flush()
sample.luminosity = sample.getLuminosity()
else:
existing = checkExisting.one()
prompt = "Replace existing "
prompt += str(existing)
prompt += "\nby new "
prompt += str(sample)
prompt += "\n?"
if confirm(prompt, resp=False):
existing.replaceBy(sample)
if existing.luminosity is None:
dbstore.flush()
existing.luminosity = existing.getLuminosity()
# commit
dbstore.commit()
def get_sample(name):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name == name)
return resultset.one()
def get_sample(inputSample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name==inputSample)
return list(resultset.values(Sample.path, Sample.normalization, Sample.nevents_processed))
def add_sample(NAME, localpath, type, nevents, nselected, AnaUrl, FWUrl, dataset_id, sumw, has_job_processed_everything, dataset_nevents, files, processed_lumi=None):
dbstore = DbStore()
sample = None
# check that source dataset exist
if dbstore.find(Dataset, Dataset.dataset_id == dataset_id).is_empty():
raise IndexError("No dataset with such index: %d" % sample.dataset_id)
# check that there is no existing entry
update = False
checkExisting = dbstore.find(Sample, Sample.name == unicode(NAME))
if checkExisting.is_empty():
sample = Sample(unicode(NAME), unicode(localpath), unicode(type), nevents)
else:
update = True
sample = checkExisting.one()
sample.removeFiles(dbstore)
sample.nevents_processed = nevents
sample.nevents = nselected
sample.normalization = 1
sample.event_weight_sum = sumw
# sample.luminosity = 40028954.499 / 1e6 # FIXME: figure out the fix for data whenever the tools will stabilize and be on cvmfs
sample.code_version = unicode(AnaUrl + ' ' + FWUrl) #NB: limited to 255 characters, but so far so good
if not has_job_processed_everything:
sample.user_comment = unicode("Sample was not fully processed, only " + str(nevents) + "/" + str(dataset_nevents) + " events were processed")
else:
sample.user_comment = u""
sample.source_dataset_id = dataset_id
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
if processed_lumi:
# Convert to json
import json
processed_lumi = json.dumps(processed_lumi, separators=(',', ':'))
sample.processed_lumi = unicode(processed_lumi)
else:
sample.processed_lumi = None
for f in files:
sample.files.add(f)
if not update:
dbstore.add(sample)
if sample.luminosity is None:
sample.luminosity = sample.getLuminosity()
print sample
if confirm(prompt="Insert into the database?", resp=True):
dbstore.commit()
return
else:
sample.luminosity = sample.getLuminosity()
prompt = "A sample with the same name already exists in the database. Replace by:\n"
prompt += str(sample)
prompt += "\n?"
if confirm(prompt, resp=False):
dbstore.commit()
return
# rollback
dbstore.rollback()
def get_sample(iSample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.sample_id == iSample)
return resultset.one()
def main():
"""Main function"""
# get the options
optmgr = MyOptionParser()
opts = optmgr.get_opt()
# build the configuration from user input
madweightCfg = MadWeight(unicode(opts.name))
for card in cards:
setattr(madweightCfg, card, unicode(open(opts.path+"/Cards/"+card+".dat","r").read()))
# get the transfert functions
madweightCfg.transfer_fctVersion = unicode(open('%s/Source/MadWeight/transfer_function/Transfer_FctVersion.txt'%opts.path,"r").read().strip('\n'))
theCfg = madweightCfg.transfer_fctVersion.split(':')[0]
if not os.path.exists("%s/Source/MadWeight/transfer_function/data/TF_%s.dat"%(opts.path,theCfg)):
raise RuntimeError("Could not find the transfert functions TF_%s.dat"%theCfg)
madweightCfg.transfer_function = unicode(open("%s/Source/MadWeight/transfer_function/data/TF_%s.dat"%(opts.path,theCfg),"r").read())
# find the generate line(s)
theCfg = filter(lambda x:x.startswith("generate"),map(lambda x:x.lstrip(' \t'),madweightCfg.proc_card_mg5.splitlines()))
if len(theCfg)!=1:
raise RuntimeError("Could not find a unique generate statement in proc_card_mg5.dat")
madweightCfg.diagram = theCfg[0][8:].lstrip(' \t')
# find the ISR correction parameter
theCfg = filter(lambda x:x.startswith("isr"),map(lambda x:x.lstrip(' \t'),madweightCfg.MadWeight_card.splitlines()))
if len(theCfg)!=1:
raise RuntimeError("Could not find a unique isr statement in MadWeight_card.dat")
madweightCfg.isr=int(theCfg[0].split(None,2)[1])
# find the NWA configuration parameter
theCfg = filter(lambda x:x.startswith("nwa"),map(lambda x:x.lstrip(' \t'),madweightCfg.MadWeight_card.splitlines()))
if len(theCfg)!=1:
raise RuntimeError("Could not find a unique nwa statement in MadWeight_card.dat")
nwa = theCfg[0].split(None,2)[1]
if nwa=='F':
madweightCfg.nwa=False
elif nwa=='T':
madweightCfg.nwa=True
else:
raise RuntimeError("Unrecognized value for the nwa parameter in MadWeight_card.dat: %s"%nwa)
# find the beam energy and store cm energy in TeV
theCfg = filter(lambda x:"ebeam1" in x,madweightCfg.run_card.splitlines())
try:
madweightCfg.cm_energy = float(theCfg[0].split()[0])*0.002
except:
print "Cannot find the beam energy in the run card"
raise
# find and add the Higgs weight (can be null, so no error if missing)
theCfg = filter(lambda x:x.startswith("DECAY"),map(lambda x:x.lstrip(' \t'),madweightCfg.param_card_1.splitlines()))
for cfg in theCfg:
fields = cfg.split()
if fields[1]=="25":
madweightCfg.higgs_width = float(fields[2])
# connect to the MySQL database using default credentials
dbstore = DbStore()
# check that there is no existing entry
checkExisting = dbstore.find(MadWeight,MadWeight.name==madweightCfg.name)
if checkExisting.is_empty():
print madweightCfg
if confirm(prompt="Insert into the database?", resp=True):
dbstore.add(madweightCfg)
else:
existing = checkExisting.one()
prompt = "Replace existing "
prompt += str(existing)
prompt += "\nby new "
prompt += str(madweightCfg)
prompt += "\n?"
if confirm(prompt, resp=False):
existing.replaceBy(madweightCfg)
# commit
dbstore.commit()
def add_merged_sample(NAME, type, AnaUrl, FWUrl, samples, comment):
# samples is a simple dict containing three keys: 'process', 'dataset_id', 'sample_id'
dbstore = DbStore()
sample = None
# check that source dataset exist
# Skip: should exist, the check has been done before calling this function
# check that there is no existing entry
update = False
localpath = ''
nevents = 0
checkExisting = dbstore.find(Sample, Sample.name == unicode(NAME))
if checkExisting.is_empty():
sample = Sample(unicode(NAME), unicode(localpath), unicode(type), nevents)
else:
update = True
sample = checkExisting.one()
sample.removeFiles(dbstore)
# collecting contents
sample.nevents_processed = 0
sample.nevents = 0
sample.normalization = 1
sample.event_weight_sum = 0
extras_event_weight_sum = {}
dataset_nevents = 0
processed_lumi = LumiList()
for i, s in enumerate(samples):
if i == 0:
sample.source_dataset_id = s['dataset_id']
sample.source_sample_id = s['sample_id']
results = dbstore.find(Sample, Sample.sample_id == s['sample_id'])
# Should exist, the check has been done before calling this function
sample.nevents_processed += results[0].nevents_processed
sample.nevents += results[0].nevents
sample.event_weight_sum += results[0].event_weight_sum
extra_sumw = results[0].extras_event_weight_sum
if extra_sumw is not None:
extra_sumw = json.loads(extra_sumw)
for key in extra_sumw:
try:
extras_event_weight_sum[key] += extra_sumw[key]
except KeyError:
extras_event_weight_sum[key] = extra_sumw[key]
tmp_processed_lumi = results[0].processed_lumi
if tmp_processed_lumi is not None:
tmp_processed_lumi = json.loads( tmp_processed_lumi )
processed_lumi = processed_lumi | LumiList(compactList = tmp_processed_lumi)
# Get info from file table
results = dbstore.find(File, File.sample_id == s['sample_id'])
for lfn, pfn, event_weight_sum, file_extras_event_weight_sum, nevents in list(results.values(File.lfn, File.pfn, File.event_weight_sum, File.extras_event_weight_sum, File.nevents)):
f = File(lfn, pfn, event_weight_sum, file_extras_event_weight_sum, nevents)
sample.files.add(f)
# Get info from parent datasets
results = dbstore.find(Dataset, Dataset.dataset_id == s['dataset_id'])
dataset_nevents += results[0].nevents
if len(extras_event_weight_sum) > 0:
sample.extras_event_weight_sum = unicode(json.dumps(extras_event_weight_sum))
if len(processed_lumi.getCompactList()) > 0:
sample.processed_lumi = unicode(json.dumps(processed_lumi.getCompactList()))
sample.code_version = unicode(AnaUrl + ' ' + FWUrl) #NB: limited to 255 characters, but so far so good
if sample.nevents_processed != dataset_nevents:
sample.user_comment = unicode("Sample was not fully processed, only " + str(sample.nevents_processed) + "/" + str(dataset_nevents) + " events were processed. " + comment)
else:
sample.user_comment = unicode(comment)
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
if not update:
dbstore.add(sample)
if sample.luminosity is None:
sample.luminosity = sample.getLuminosity()
print sample
dbstore.commit()
return
else:
sample.luminosity = sample.getLuminosity()
print("Sample updated")
print(sample)
dbstore.commit()
return
# rollback
dbstore.rollback()
def get_sample(iSample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.sample_id == iSample)
return resultset.one()
def main():
"""Main function"""
# get the options
optmgr = MyOptionParser()
opts = optmgr.get_opt()
# build the sample from user input
sample = Sample(unicode(opts.name), unicode(opts.path), unicode(opts.sampletype), opts.nevents_processed)
sample.nevents = opts.nevents
sample.normalization = opts.normalization
sample.luminosity = opts.luminosity
sample.code_version = unicode(opts.code_version)
sample.user_comment = unicode(opts.user_comment)
sample.source_dataset_id = opts.source_dataset_id
sample.source_sample_id = opts.source_sample_id
sample.author = unicode(opts.author)
sample.creation_time = opts.datetime
# connect to the MySQL database using default credentials
dbstore = DbStore()
# unless the source is set, prompt the user and present a list to make a choice
if sample.source_dataset_id is None:
prompt_dataset(sample,dbstore)
if sample.source_sample_id is None:
prompt_sample(sample,dbstore)
# check that source sample and dataset exist
if sample.source_dataset_id is not None:
checkExisting = dbstore.find(Dataset,Dataset.dataset_id==sample.source_dataset_id)
if checkExisting.is_empty():
raise IndexError("No dataset with such index: %d"%sample.source_dataset_id)
if sample.source_sample_id is not None:
checkExisting = dbstore.find(Sample,Sample.sample_id==sample.source_sample_id)
if checkExisting.is_empty():
raise IndexError("No sample with such index: %d"%sample.source_sample_id)
# if opts.nevents is not set, take #events from source sample (if set) or from source dataset (if set) in that order
if sample.nevents_processed is None and sample.source_sample_id is not None:
sample.nevents_processed = dbstore.find(Sample,Sample.sample_id==sample.source_sample_id).one().nevents_processed
if sample.nevents_processed is None and sample.source_dataset_id is not None:
sample.nevents_processed = dbstore.find(Dataset,Dataset.dataset_id==sample.source_dataset_id).one().nevents
if sample.nevents_processed is None:
print "Warning: Number of processed events not given, and no way to guess it."
# check that there is no existing entry
checkExisting = dbstore.find(Sample,Sample.name==sample.name)
if checkExisting.is_empty():
print sample
if confirm(prompt="Insert into the database?", resp=True):
dbstore.add(sample)
# compute the luminosity, if possible
if sample.luminosity is None:
dbstore.flush()
sample.luminosity = sample.getLuminosity()
else:
existing = checkExisting.one()
prompt = "Replace existing "
prompt += str(existing)
prompt += "\nby new "
prompt += str(sample)
prompt += "\n?"
if confirm(prompt, resp=False):
existing.replaceBy(sample)
if existing.luminosity is None:
dbstore.flush()
existing.luminosity = existing.getLuminosity()
# commit
dbstore.commit()
def main(crabUsername, ingridUsername):
dbstore = DbStore()
print "##### Get the list of potential DB samples of interest"
list_allDBsamples = []
results = dbstore.find(Sample)
for r in results:
if r.author is None:
continue
for f in r.files:
if crabUsername in f.lfn:
p = '/storage/data/cms' + re.sub('/output.*root', '', f.lfn)
if p not in list_allDBsamples:
list_allDBsamples.append(p)
if crabUsername in r.path or ingridUsername in r.author:
if r.path == '':
continue
if r.path not in list_allDBsamples:
list_allDBsamples.append(r.path)
# print r.path
print ""
storageDir = join('/storage/data/cms/store/user/', crabUsername)
print "##### Get the list of user paths in %s" % storageDir
list_allUserDirs = {}
currentTime = dt.datetime.now()
tcut = getDateMinusT(currentTime, month = 1)
for d in listdir(storageDir):
if not isdir(join(storageDir, d)):
continue
if 'CRAB_PrivateMC' in d or 'testFiles' in d :
continue
for subd in listdir(join(storageDir, d)):
if not isdir(join(storageDir, d, subd)):
continue
for taskStamp in listdir(join(storageDir, d, subd)):
if not isdir(join(storageDir, d, subd, taskStamp)):
continue
try:
ttask = int(taskStamp.replace('_', ''))
except ValueError:
print("Warning: could not interpret path {}, skipping it...".format(taskStamp))
continue
if ttask >= tcut:
continue
for taskID in listdir(join(storageDir, d, subd, taskStamp)):
if not isdir(join(storageDir, d, subd, taskStamp, taskID)):
continue
myPath = join(storageDir, d, subd, taskStamp, taskID)
if myPath in list_allDBsamples:
continue
# print isFramework(myPath), myPath
try:
mySize = subprocess.check_output(["du", '-s', myPath]).split()[0].decode('utf-8')
except subprocess.CalledProcessError:
print("Error while accessing file in path {}, skipping it!".format(myPath))
continue
list_allUserDirs[ttask] = {'path': myPath, 'size': int(mySize) * 1024, 'is CP3-llbb': isFramework(myPath)}
print '# Tasks older than 6 months'
print '# timestamp= ', getDateMinusT(currentTime, month = 6)
totalSize = 0
finalprint = ''
for t in list_allUserDirs:
if t < getDateMinusT(currentTime, month = 6) and list_allUserDirs[t]['is CP3-llbb']:
totalSize += list_allUserDirs[t]['size']
finalprint += "# size= %s\nrm -r %s\n" % (sizeof_fmt(list_allUserDirs[t]['size']), list_allUserDirs[t]['path'])
print '# totalSize= ', sizeof_fmt(totalSize)
print finalprint
print '# Tasks between 3 and 6 months old'
print '# timestamp= ', getDateMinusT(currentTime, month = 3)
totalSize = 0
finalprint = ''
for t in list_allUserDirs:
if getDateMinusT(currentTime, month = 6) < t < getDateMinusT(currentTime, month = 3) and list_allUserDirs[t]['is CP3-llbb']:
totalSize += list_allUserDirs[t]['size']
finalprint += "# size= %s\nrm -r %s\n" % (sizeof_fmt(list_allUserDirs[t]['size']), list_allUserDirs[t]['path'])
print '# totalSize= ', sizeof_fmt(totalSize)
print finalprint
print '# Tasks between 1 and 3 months old'
print '# timestamp= ', getDateMinusT(currentTime, month = 1)
totalSize = 0
finalprint = ''
for t in list_allUserDirs:
if getDateMinusT(currentTime, month = 3) < t < getDateMinusT(currentTime, month = 1) and list_allUserDirs[t]['is CP3-llbb']:
totalSize += list_allUserDirs[t]['size']
finalprint += "# size= %s\nrm -r %s\n" % (sizeof_fmt(list_allUserDirs[t]['size']), list_allUserDirs[t]['path'])
print '# totalSize= ', sizeof_fmt(totalSize)
print finalprint
print '# The following tasks could not be asserted to be cp3_llbb framework tasks or not... deal with them as you see fit:'
totalSize = 0
finalprint = ''
for t in list_allUserDirs:
if not list_allUserDirs[t]['is CP3-llbb']:
totalSize += list_allUserDirs[t]['size']
finalprint += "# size= %s\tpath= %s\n" % (sizeof_fmt(list_allUserDirs[t]['size']), list_allUserDirs[t]['path'])
print '# totalSize= ', sizeof_fmt(totalSize)
print finalprint
def get_dataset(inputDataset):
dbstore = DbStore()
resultset = dbstore.find(Dataset, Dataset.name == inputDataset)
return list(
resultset.values(Dataset.name, Dataset.dataset_id, Dataset.nevents))
def add_sample(NAME, localpath, type, nevents, nselected, AnaUrl, FWUrl, dataset_id, sumw, extras_sumw, has_job_processed_everything, dataset_nevents, files, processed_lumi=None):
dbstore = DbStore()
sample = None
# check that source dataset exist
if dbstore.find(Dataset, Dataset.dataset_id == dataset_id).is_empty():
raise IndexError("No dataset with such index: %d" % sample.dataset_id)
# check that there is no existing entry
update = False
checkExisting = dbstore.find(Sample, Sample.name == unicode(NAME))
if checkExisting.is_empty():
sample = Sample(unicode(NAME), unicode(localpath), unicode(type), nevents)
else:
update = True
sample = checkExisting.one()
sample.removeFiles(dbstore)
sample.nevents_processed = nevents
sample.nevents = nselected
sample.normalization = 1
sample.event_weight_sum = sumw
sample.extras_event_weight_sum = unicode(json.dumps(extras_sumw, separators=(',', ':')))
sample.code_version = unicode(AnaUrl + ' ' + FWUrl) #NB: limited to 255 characters, but so far so good
if not has_job_processed_everything:
sample.user_comment = unicode("Sample was not fully processed, only " + str(nevents) + "/" + str(dataset_nevents) + " events were processed")
else:
sample.user_comment = u""
sample.source_dataset_id = dataset_id
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
if processed_lumi:
# Convert to json
processed_lumi = json.dumps(processed_lumi, separators=(',', ':'))
sample.processed_lumi = unicode(processed_lumi)
else:
sample.processed_lumi = None
for f in files:
sample.files.add(f)
if not update:
dbstore.add(sample)
if sample.luminosity is None:
sample.luminosity = sample.getLuminosity()
print sample
dbstore.commit()
return
else:
sample.luminosity = sample.getLuminosity()
print("Sample updated")
print(sample)
dbstore.commit()
return
# rollback
dbstore.rollback()
def get_sample(sample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name==sample)
return list(resultset.values(Sample.sample_id))
def main(crabUsername, ingridUsername, DEBUG = False, evaluateSize = False):
if DEBUG:
print "RUNNING IN DEBUG MODE"
print "Nothing will be deleted\n"
dbstore = DbStore()
print "##### Get the list of potential DB samples of interest"
list_allDBsamples = []
results = dbstore.find(Sample)
for r in results:
if crabUsername in r.path:
list_allDBsamples.append([r.name, r.source_dataset_id])
print ""
print "##### Get the list of existing productions"
# before anything else: get the list of tags to not touch
whitelist = requests.get('https://raw.githubusercontent.com/cp3-llbb/GridIn/master/data/SAMADhi_doNOTdelete_whitelist.json').json()
if DEBUG:
print "production whitelist= ", whitelist
list_all_productions = []
for i, s in enumerate(list_allDBsamples):
s_name, s_id = s
isProdAlreadyListed = False
isSampleProtected = False
for FWtag, Anatag in list_all_productions:
if FWtag in str(s_name) and Anatag in str(s_name):
# print "This prod is already in the list, FWtag= ", FWtag, "Anatag= ", Anatag
isProdAlreadyListed = True
break
if isProdAlreadyListed:
continue
tags = str(s_name)
# Get the tags:
# First of all: check if the sample is protected or not
for ana in whitelist:
part = str(ana)
for protectedtag in whitelist[ana]:
t = str(protectedtag).split('_%s_' % part)
if t[0] in tags and t[1] in tags:
if DEBUG:
print '\tSkipping whitelisted sample %s' % s_name
isSampleProtected = True
if not isSampleProtected:
tags = tags.replace(part, '') # remove HHAnalyzer and the like from the name of the sample
if isSampleProtected:
continue
# now extract the fw and analyzer tags
# for analyzer, this is always the last part of the sample name so we don't have to worry about naming conventions there (fortunately)
tags = tags.split('_')
Anatag = tags[-1]
tags = tags[:-1]
# for FW the following regex should work ((v\d+.\d+.\d+\+\d+X?)(-\d+-g[0-9a-f]{7,40})?)|([0-9a-f]{7,40})
# it matches either:
# - a framework tag (possibly with a final X): v1.2.0+7415
# - possibly followed by a number of commits and a 'g' plus 7 to 40 characters git hash: v1.2.0+7415-79-ga5b16ff
# - or alternatively a 7 to 40 characters git hash: f2f0a44
tags = [x for x in tags if re.match('((v\d+.\d+.\d+\+\d+X?)(-\d+-g[0-9a-f]{7,40})?)|([0-9a-f]{7,40})', x)]
if DEBUG:
print tags, Anatag
if len(tags) != 1:
print "ERROR, there are spurious things in the sample name, please figure out what is happening:"
print "FWtags= ", tags
return 1
FWtag = tags[0]
list_all_productions.append([FWtag, Anatag])
for i, p in enumerate(list_all_productions):
if DEBUG and i > 0:
break
FWtag, Anatag = p
extrastring = ''
if not evaluateSize:
extrastring = '(evaluation of the disk size is OFF by default)'
print "\n##### Now looking at prod FWtag= ", FWtag, 'Anatag= ', Anatag, 'and list the associated folders %s' % extrastring
totalSize = 0
totalSamples = 0
cannotManageToDeleteThisProd = False
for s_name, s_id in list_allDBsamples:
if FWtag in str(s_name) and Anatag in str(s_name):
result = dbstore.find(Sample, Sample.name == s_name)
s = result.one()
if evaluateSize:
totalSize += int(subprocess.check_output(["du", '-s', str(s.path)]).split()[0].decode('utf-8'))
totalSamples += 1
if s.source_sample is not None:
print "WARNING, the sample", s_name, "depend on another sample, aborting now"
cannotManageToDeleteThisProd = True
break
if s.derived_samples.count() > 0:
print "WARNING, the sample", s_name, "has derived samples, aborting now"
cannotManageToDeleteThisProd = True
break
if s.results.count() > 0:
print "WARNING, the sample", s_name, "has derived results, aborting now"
cannotManageToDeleteThisProd = True
break
print s.path
if cannotManageToDeleteThisProd:
continue
print '\tFWtag= ', FWtag, 'Anatag= ', Anatag, 'totalSamples= ', totalSamples, 'totalSize= ', totalSize, "(%s)" % sizeof_fmt(totalSize)
if confirm(prompt='\tDo you REALLY want to DELETE this prod from disk and from SAMADhi?', resp=False):
for s_name, s_id in list_allDBsamples:
if FWtag in str(s_name) and Anatag in str(s_name):
result = dbstore.find(Sample, Sample.name == s_name)
s = result.one()
if DEBUG:
print 'rm -r %s' % s.path
print 'rm -r %s' % str(s.path).rsplit('/0000', 1)[0]
print 'dbstore.remove()'
else:
try:
shutil.rmtree(s.path)
shutil.rmtree(str(s.path).rsplit('/0000', 1)[0])
except OSError:
print "Seems we have a buggy path: %s" % s.path
print "deleting the DB entry then moving on..."
dbstore.remove(s)
dbstore.commit()
def add_sample(NAME,
localpath,
type,
nevents,
nselected,
AnaUrl,
FWUrl,
dataset_id,
sumw,
extras_sumw,
has_job_processed_everything,
dataset_nevents,
files,
processed_lumi=None):
dbstore = DbStore()
sample = None
# check that source dataset exist
if dbstore.find(Dataset, Dataset.dataset_id == dataset_id).is_empty():
raise IndexError("No dataset with such index: %d" % sample.dataset_id)
# check that there is no existing entry
update = False
checkExisting = dbstore.find(Sample, Sample.name == unicode(NAME))
if checkExisting.is_empty():
sample = Sample(unicode(NAME), unicode(localpath), unicode(type),
nevents)
else:
update = True
sample = checkExisting.one()
sample.removeFiles(dbstore)
sample.nevents_processed = nevents
sample.nevents = nselected
sample.normalization = 1
sample.event_weight_sum = sumw
sample.extras_event_weight_sum = unicode(
json.dumps(extras_sumw, separators=(',', ':')))
sample.code_version = unicode(
AnaUrl + ' ' +
FWUrl) #NB: limited to 255 characters, but so far so good
if not has_job_processed_everything:
sample.user_comment = unicode("Sample was not fully processed, only " +
str(nevents) + "/" +
str(dataset_nevents) +
" events were processed")
else:
sample.user_comment = u""
sample.source_dataset_id = dataset_id
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
if processed_lumi:
# Convert to json
processed_lumi = json.dumps(processed_lumi, separators=(',', ':'))
sample.processed_lumi = unicode(processed_lumi)
else:
sample.processed_lumi = None
for f in files:
sample.files.add(f)
if not update:
dbstore.add(sample)
if sample.luminosity is None:
sample.luminosity = sample.getLuminosity()
print sample
dbstore.commit()
return
else:
sample.luminosity = sample.getLuminosity()
print("Sample updated")
print(sample)
dbstore.commit()
return
# rollback
dbstore.rollback()
def get_sample(name):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name == name)
return resultset.one()
def get_sample(iSample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.sample_id == iSample)
return list(resultset.values(Sample.name, Sample.path))
)
CMSSW_BASE = os.environ['CMSSW_BASE']
SCRAM_ARCH = os.environ['SCRAM_ARCH']
sys.path.append(os.path.join(CMSSW_BASE, 'bin', SCRAM_ARCH))
from SAMADhi import Dataset, Sample, DbStore
import inspect
scriptDir = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
sys.path.append(scriptDir)
from sampleList import samples_dict, number_of_bases, analysis_tags
# Connect to the database
dbstore = DbStore()
def build_sample_name(name, tag):
return "{}*{}".format(name, tag)
def get_sample_ids_from_name(name):
results = dbstore.find(Sample,
Sample.name.like(unicode(name.replace('*', '%'))))
if results.count() == 0:
return None
if results.count() > 1:
print(
def get_sample(self, name, tag):
dbstore = DbStore()
resultset = dbstore.find(Sample,
Sample.name.like(unicode(name + "%_" + tag)))
return resultset.one()
def get_dataset(inputDataset):
dbstore = DbStore()
resultset = dbstore.find(Dataset, Dataset.name==inputDataset)
return list(resultset.values(Dataset.name, Dataset.dataset_id, Dataset.nevents))
def main():
"""Main function"""
# get the options
optmgr = DASOptionParser()
opts = optmgr.get_opt()
host = opts.host
debug = opts.verbose
sample = opts.sample
query1 = "dataset="+sample+" | grep dataset.name, dataset.nevents, dataset.size, dataset.tag, dataset.datatype, dataset.creation_time"
query2 = "release dataset="+sample+" | grep release.name"
idx = opts.idx
thr = opts.threshold
ckey = opts.ckey
cert = opts.cert
das_h = opts.das_headers
# perform the DAS queries
jsondict1 = get_data(host, query1, idx, 1, debug, thr, ckey, cert, das_h)
jsondict2 = get_data(host, query2, idx, 1, debug, thr, ckey, cert, das_h)
# check the result
if len(jsondict1)>1: print "Error: more than one element in jsondict1..."
tmp = [{u'dataset' : [{}]},]
for i in range(0,len(jsondict1[0]["dataset"])):
if jsondict1[0]["dataset"][i]["name"]==sample:
for key in jsondict1[0]["dataset"][i]:
tmp[0]["dataset"][0][key] = jsondict1[0]["dataset"][i][key]
if not "tag" in tmp[0]["dataset"][0]:
print "global tag not found: looks to be always the case now, value will be 'None'"
tmp[0]["dataset"][0][u'tag']=None
print "****das query:", tmp
jsondict1 = tmp
if not(isinstance(jsondict1, list) and
len(jsondict1)==1 and
isinstance(jsondict1[0], dict) and
isinstance(jsondict1[0]["dataset"],list) and
len(jsondict1[0]["dataset"])==1 and
isinstance(jsondict1[0]["dataset"][0],dict) and
isinstance(jsondict2, list) and
len(jsondict2)==1 and
isinstance(jsondict2[0], dict) and
isinstance(jsondict2[0]["release"],list) and
len(jsondict2[0]["release"])==1 and
isinstance(jsondict2[0]["release"][0],dict)):
raise RuntimeError("Incorrect response from DAS:\n"+str(jsondict1)+"\n"+str(jsondict2))
# prepare the summary json object
jsondict1[0]["dataset"][0][u"release"] = jsondict2[0]["release"][0]["name"]
jsondict1[0]["dataset"][0].update({ u"process":unicode(opts.process),
u"xsection":opts.xsection, u"energy":opts.energy,
u"comment":unicode(opts.comment) })
# convert the jsondict into a Dataset
dataset = asDataset(jsondict1[0]["dataset"][0])
# connect to the MySQL database using default credentials
dbstore = DbStore()
# check that there is no existing entry
checkExisting = dbstore.find(Dataset,Dataset.name==dataset.name)
if checkExisting.is_empty():
print dataset
if confirm(prompt="Insert into the database?", resp=True):
dbstore.add(dataset)
else:
existing = checkExisting.one()
prompt = "Replace existing entry:\n"
prompt += str(existing)
prompt += "\nby new entry:\n"
prompt += str(dataset)
prompt += "\n?"
if confirm(prompt, resp=False):
existing.replaceBy(dataset)
# commit
dbstore.commit()
def get_sample(sample):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name == sample)
return list(resultset.values(Sample.sample_id))
def add_sample(NAME,
localpath,
type,
nevents,
nselected,
AnaUrl,
FWUrl,
dataset_id,
sumw,
has_job_processed_everything,
dataset_nevents,
files,
processed_lumi=None):
dbstore = DbStore()
sample = None
# check that source dataset exist
if dbstore.find(Dataset, Dataset.dataset_id == dataset_id).is_empty():
raise IndexError("No dataset with such index: %d" % sample.dataset_id)
# check that there is no existing entry
update = False
checkExisting = dbstore.find(Sample, Sample.name == unicode(NAME))
if checkExisting.is_empty():
sample = Sample(unicode(NAME), unicode(localpath), unicode(type),
nevents)
else:
update = True
sample = checkExisting.one()
sample.removeFiles(dbstore)
sample.nevents_processed = nevents
sample.nevents = nselected
sample.normalization = 1
sample.event_weight_sum = sumw
# sample.luminosity = 40028954.499 / 1e6 # FIXME: figure out the fix for data whenever the tools will stabilize and be on cvmfs
sample.code_version = unicode(
AnaUrl + ' ' +
FWUrl) #NB: limited to 255 characters, but so far so good
if not has_job_processed_everything:
sample.user_comment = unicode("Sample was not fully processed, only " +
str(nevents) + "/" +
str(dataset_nevents) +
" events were processed")
else:
sample.user_comment = u""
sample.source_dataset_id = dataset_id
sample.author = unicode(getpwuid(os.stat(os.getcwd()).st_uid).pw_name)
if processed_lumi:
# Convert to json
import json
processed_lumi = json.dumps(processed_lumi, separators=(',', ':'))
sample.processed_lumi = unicode(processed_lumi)
else:
sample.processed_lumi = None
for f in files:
sample.files.add(f)
if not update:
dbstore.add(sample)
if sample.luminosity is None:
sample.luminosity = sample.getLuminosity()
print sample
if confirm(prompt="Insert into the database?", resp=True):
dbstore.commit()
return
else:
sample.luminosity = sample.getLuminosity()
prompt = "A sample with the same name already exists in the database. Replace by:\n"
prompt += str(sample)
prompt += "\n?"
if confirm(prompt, resp=False):
dbstore.commit()
return
# rollback
dbstore.rollback()
def main(crabUsername, ingridUsername, DEBUG=False, evaluateSize=False):
if DEBUG:
print "RUNNING IN DEBUG MODE"
print "Nothing will be deleted\n"
dbstore = DbStore()
print "##### Get the list of potential DB samples of interest"
list_allDBsamples = []
results = dbstore.find(Sample)
for r in results:
if crabUsername in r.path:
list_allDBsamples.append([r.name, r.source_dataset_id])
print ""
print "##### Get the list of existing productions"
# before anything else: get the list of tags to not touch
whitelist = requests.get(
'https://raw.githubusercontent.com/cp3-llbb/GridIn/master/data/SAMADhi_doNOTdelete_whitelist.json'
).json()
if DEBUG:
print "production whitelist= ", whitelist
list_all_productions = []
for i, s in enumerate(list_allDBsamples):
s_name, s_id = s
isProdAlreadyListed = False
isSampleProtected = False
for FWtag, Anatag in list_all_productions:
if FWtag in str(s_name) and Anatag in str(s_name):
# print "This prod is already in the list, FWtag= ", FWtag, "Anatag= ", Anatag
isProdAlreadyListed = True
break
if isProdAlreadyListed:
continue
tags = str(s_name)
# Get the tags:
# First of all: check if the sample is protected or not
for ana in whitelist:
part = str(ana)
for protectedtag in whitelist[ana]:
t = str(protectedtag).split('_%s_' % part)
if t[0] in tags and t[1] in tags:
if DEBUG:
print '\tSkipping whitelisted sample %s' % s_name
isSampleProtected = True
if not isSampleProtected:
tags = tags.replace(
part, ''
) # remove HHAnalyzer and the like from the name of the sample
if isSampleProtected:
continue
# now extract the fw and analyzer tags
# for analyzer, this is always the last part of the sample name so we don't have to worry about naming conventions there (fortunately)
tags = tags.split('_')
Anatag = tags[-1]
tags = tags[:-1]
# for FW the following regex should work ((v\d+.\d+.\d+\+\d+X?)(-\d+-g[0-9a-f]{7,40})?)|([0-9a-f]{7,40})
# it matches either:
# - a framework tag (possibly with a final X): v1.2.0+7415
# - possibly followed by a number of commits and a 'g' plus 7 to 40 characters git hash: v1.2.0+7415-79-ga5b16ff
# - or alternatively a 7 to 40 characters git hash: f2f0a44
tags = [
x for x in tags if re.match(
'((v\d+.\d+.\d+\+\d+X?)(-\d+-g[0-9a-f]{7,40})?)|([0-9a-f]{7,40})',
x)
]
if DEBUG:
print tags, Anatag
if len(tags) != 1:
print "ERROR, there are spurious things in the sample name, please figure out what is happening:"
print "FWtags= ", tags
return 1
FWtag = tags[0]
list_all_productions.append([FWtag, Anatag])
for i, p in enumerate(list_all_productions):
if DEBUG and i > 0:
break
FWtag, Anatag = p
extrastring = ''
if not evaluateSize:
extrastring = '(evaluation of the disk size is OFF by default)'
print "\n##### Now looking at prod FWtag= ", FWtag, 'Anatag= ', Anatag, 'and list the associated folders %s' % extrastring
totalSize = 0
totalSamples = 0
cannotManageToDeleteThisProd = False
for s_name, s_id in list_allDBsamples:
if FWtag in str(s_name) and Anatag in str(s_name):
result = dbstore.find(Sample, Sample.name == s_name)
s = result.one()
if evaluateSize:
totalSize += int(
subprocess.check_output(["du", '-s',
str(s.path)
]).split()[0].decode('utf-8'))
totalSamples += 1
if s.source_sample is not None:
print "WARNING, the sample", s_name, "depend on another sample, aborting now"
cannotManageToDeleteThisProd = True
break
if s.derived_samples.count() > 0:
print "WARNING, the sample", s_name, "has derived samples, aborting now"
cannotManageToDeleteThisProd = True
break
if s.results.count() > 0:
print "WARNING, the sample", s_name, "has derived results, aborting now"
cannotManageToDeleteThisProd = True
break
print s.path
if cannotManageToDeleteThisProd:
continue
print '\tFWtag= ', FWtag, 'Anatag= ', Anatag, 'totalSamples= ', totalSamples, 'totalSize= ', totalSize, "(%s)" % sizeof_fmt(
totalSize)
if confirm(
prompt=
'\tDo you REALLY want to DELETE this prod from disk and from SAMADhi?',
resp=False):
for s_name, s_id in list_allDBsamples:
if FWtag in str(s_name) and Anatag in str(s_name):
result = dbstore.find(Sample, Sample.name == s_name)
s = result.one()
if DEBUG:
print 'rm -r %s' % s.path
print 'rm -r %s' % str(s.path).rsplit('/0000', 1)[0]
print 'dbstore.remove()'
else:
try:
shutil.rmtree(s.path)
shutil.rmtree(str(s.path).rsplit('/0000', 1)[0])
except OSError:
print "Seems we have a buggy path: %s" % s.path
print "deleting the DB entry then moving on..."
dbstore.remove(s)
dbstore.commit()
def get_sample(self, name, tag):
dbstore = DbStore()
resultset = dbstore.find(Sample, Sample.name.like(unicode(name + "%_" + tag)))
return resultset.one()
