Shorter outputs, new summary mode
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4440 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
d841f260eb
commit
effcd26977
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@ -31,6 +31,10 @@ def main():
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action='store_true', default=False,
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help="if provided, only records not coming from a dev version of GATK will be included")
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parser.add_option("", "--stingExceptionsOnly", dest="stingExceptionsOnly",
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action='store_true', default=False,
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help="if provided, only records with StingExceptions will be generated in report")
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parser.add_option("", "--max_days", dest="maxDays",
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type='int', default=None,
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help="if provided, only records generated within X days of today will be included")
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@ -215,10 +219,11 @@ class Archive(RecordAsXML):
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def finalize(self, args):
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RecordAsXML.finalize(self, args)
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for arg in args:
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print 'Deleting file: ', arg
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if OPTIONS.verbose: print 'Deleting file: ', arg
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if OPTIONS.reallyDeleteInArchiveMode:
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os.remove(arg)
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print 'Deleted', len(args), 'files'
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addHandler('archive', Archive)
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class ExceptionReport(StageHandler):
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@ -253,7 +258,10 @@ class ExceptionReport(StageHandler):
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for common in commonExceptions:
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msg, at, svns, walkers, counts, ids, duration, users, userError = common.toStrings()
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if OPTIONS.stingExceptionsOnly and userError == "true":
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continue
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print >> self.out, ''.join(['*'] * 80)
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print >> self.out, 'Exception :', msg
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print >> self.out, ' is-user-exception? :', userError
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@ -275,7 +283,7 @@ class CommonException:
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self.users = set([ex['user-name']])
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self.userError = ex['is-user-exception']
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self.counts = 1
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self.times = set([decodeTime(ex['start-time'])])
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self.times = set([decodeTime(ex['end-time'])])
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self.walkers = set([ex['walker-name']])
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self.ids = set([ex['id']])
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@ -288,7 +296,7 @@ class CommonException:
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self.users.add(ex['user-name'])
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self.counts += 1
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self.walkers.add(ex['walker-name'])
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self.times.add(decodeTime(ex['start-time']))
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self.times.add(decodeTime(ex['end-time']))
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self.ids.add(ex['id'])
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def bestExample(self, examples):
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@ -319,38 +327,39 @@ class CommonException:
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addHandler('exceptions', ExceptionReport)
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class SummaryReport(StageHandler):
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#FIELDS = ["Msg", "At", "SVN.versions", "Walkers", 'Occurrences', 'IDs']
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def __init__(self, name, out):
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StageHandler.__init__(self, name, out)
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self.reports = []
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#
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# def long_substr(data):
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# substr = ''
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# if len(data) > 1 and len(data[0]) > 0:
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# for i in range(len(data[0])):
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# for j in range(len(data[0])-i+1):
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# if j > len(substr) and is_substr(data[0][i:i+j], data):
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# substr = data[0][i:i+j]
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# return substr
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#
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# def is_substr(find, data):
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# if len(data) < 1 and len(find) < 1:
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# return False
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# for i in range(len(data)):
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# if find not in data[i]:
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# return False
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# return True
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#
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# def parameterizeStrings( strings ):
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# example = strings[0]
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# para = ''
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#
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# lcs = long_substr(strings)
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# if lcs == '':
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# # nothing common at all, we are done
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# return para
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# else:
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# # we need to remove the LCS from all strings
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# strings = map( lambda x: x.replace(lcs, ''), strings)
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#
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def initialize(self, args):
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self.decoder = RecordDecoder()
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#print >> self.out, "\t".join(self.FIELDS)
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def processRecord(self, record):
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self.reports.append(self.decoder.decode(record))
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def finalize(self, args):
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print >> self.out, 'GATK run summary for :', datetime.datetime.today()
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print >> self.out, ' number of runs :', len(self.reports)
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print >> self.out, ' number of StingExceptions :', len(filter(isStingException, self.reports))
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print >> self.out, ' number of UserExceptions :', len(filter(isUserException, self.reports))
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print >> self.out, ' users :', ', '.join(set(map(userID, self.reports)))
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def userID(rec):
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return rec['user-name']
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def isStingException(rec):
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return rec['exception-at'] != "NA" and rec['is-user-exception'] == "false"
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def isUserException(rec):
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return rec['exception-at'] != "NA" and rec['is-user-exception'] == "true"
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addHandler('summary', SummaryReport)
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#
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# utilities
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#
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@ -393,7 +402,7 @@ def passesFilters(elt):
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now = datetime.datetime.today()
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now = datetime.datetime(now.year, now.month, now.day)
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# <start-time>2010/08/31 15.38.00</start-time>
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eltTime = decodeTime(elt.find('start-time').text)
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eltTime = decodeTime(elt.find('end-time').text)
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diff = now - eltTime
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#print eltTime, now, diff, diff.days
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if diff.days > OPTIONS.maxDays:
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@ -409,8 +418,8 @@ def readReports(files):
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try:
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tree = ElementTree(file=input)
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except:
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print "EXCEPTING FILE", file
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raise
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print "Ignoring excepting file", file
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continue
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elem = tree.getroot()
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if elem.tag == RUN_REPORT_LIST:
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