74 lines
3.4 KiB
Python
74 lines
3.4 KiB
Python
# ====================================================================================================
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# update the tribble code to the appropriate version, given the current GATK version.
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# this python script looks up the base version of the GATK, checks the date, and cross-references this
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# against the Tribble version.
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# ====================================================================================================
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import os, subprocess, re
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from subprocess import Popen, PIPE, STDOUT
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from datetime import datetime, date, time
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# test that we can use the SVN tool
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print "checking that we can use svn and svnversion commands..."
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outputSVN = Popen(["svn", "--version"], stdout=PIPE).communicate()[0]
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outputSVNVersion = Popen(["svnversion", "--version"], stdout=PIPE).communicate()[0]
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# match the regex
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m = re.search('version\s+(\d+\.\d+\.\d+)',outputSVN)
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m2 = re.search('version\s+(\d+\.\d+\.\d+)',outputSVNVersion)
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if ((not m) or (not m2)):
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raise Exception("Unable to find svn and svnversion commands")
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if (m.group(1) != m.group(1)):
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raise Exception('Unable to match versions for svn (version ' + m.group(1) + ') and svnversion (version ' + m2.group(1) + ') commands')
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# check that we're in the base GATK directory
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outputSVN = Popen(["svn","info"], stdout=PIPE).communicate()[0]
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m = re.search('URL:\s+(.+)\s+',outputSVN)
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print "checking that we're in the base directory of a SVN check-out of the GATK..."
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if (not m):
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raise Exception("Unable to find current working URL for this directory in SVN; make sure your in the base GATK directory when running this script")
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if (m.group(1) != "https://svn/Sting/trunk"):
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raise Exception("Not in the correct working directory; we expect to be in a directory pointing to the URL https://svn/Sting/trunk")
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# now get the version and date for the GATK checkout
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print "getting the GATK check-out version and date..."
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dateMatch = re.search('Last Changed Date:\s+(\S+)\s+(\S+)\s+',outputSVN)
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versionMatch = re.search('Last Changed Rev:\s+(.+)\s+(.+)\s+',outputSVN)
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if ((not dateMatch) or (not versionMatch)):
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raise Exception("Unable to match either the version or the check-out date from the svn -info output: " + outputSVN)
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dt = datetime.strptime(dateMatch.group(1)+" "+dateMatch.group(2), "%Y-%m-%d %H:%M:%S")
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print " The date of the current GATK check-out is = " + dt.strftime("%A, %d. %B %Y %I:%M%p")
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# now look through the tribble logs for the last version before the current GATK date
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# the log entries look like: r213 | hanna | 2010-09-22 11:28:16 -0400 (Wed, 22 Sep 2010) | 2 lines
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outputSVN = Popen(["svn","log","--quiet","tribble"], stdout=PIPE).communicate()[0]
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m = re.findall("r(\d+)\s\|\s\S+\s\|\s(\S+\s\S+)",outputSVN)
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diff = None
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bestRev = 0
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for match in m:
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rev = match
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tribbleDate = datetime.strptime(match[1] , "%Y-%m-%d %H:%M:%S")
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# print tribbleDate.strftime("%A, %d. %B %Y %I:%M%p")
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if (dt > tribbleDate):
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if (diff == None):
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diff = dt - tribbleDate
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bestRev = match[0]
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elif (dt - tribbleDate < diff):
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diff = dt - tribbleDate
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bestRev = match[0]
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if (bestRev == 0):
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raise Exception("Unable to find correct revision that predates the current GATK checkout...failing")
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# now update the tribble directory to the found revision
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print "attempting to update Tribble to the correct version of r" + bestRev
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print ""
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print "SVN update output:"
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print Popen(["svn","update","-r","r"+str(bestRev),"tribble"], stdout=PIPE).communicate()[0]
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