--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/LaunchMatcherInParallel.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,285 @@
+#!/usr/bin/env python
+
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+from commons.core.LoggerFactory import LoggerFactory
+from commons.core.sql.DbFactory import DbFactory
+from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
+from commons.core.launcher.Launcher import Launcher
+from commons.core.launcher.LauncherUtils import LauncherUtils
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+from commons.core.checker.ConfigChecker import ConfigRules, ConfigChecker
+from commons.core.coord.AlignUtils import AlignUtils
+import shutil
+import os
+
+LOG_DEPTH = "repet.tools"
+
+
+class LaunchMatcherInParallel(object):
+    def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", alignPattern = ".*\.align", \
+                 config = "", groupId = "", maxFileSize = 1000000, mergeResults=True, workingDir="tmpMatcher", doClean = False, verbosity = 0):
+        self._alignFileName = align
+        self._queryFileName = queryFileName
+        self.setSubjectFileName(subjectFileName)
+        self.setOutPrefix(prefix)
+        self._alignPattern = alignPattern
+        self._doJoin = doJoin
+        self._eValue = evalue
+        self._keepConflict = keepConflict
+        self._configFileName = config
+        self.setGroupId(groupId)
+        self._maxFileSize = maxFileSize
+        self._mergeResults = mergeResults
+        self._doClean = doClean
+        self._workingDir = workingDir
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+        self._jobSectionName = "jobs"
+        
+    def setAttributesFromCmdLine(self):
+        description = "Launch Matcher in parallel."
+        epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
+        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -v 0"
+        epilog += "\n\t"
+        epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
+        epilog += "\t$ python LaunchMatcherInParallel.py -a in.align -q query.fa -s subject.fa -o query -c -v 2"
+        parser = RepetOptionParser(description = description, epilog = epilog)
+        parser.add_option("-a", "--align",      dest = "align",         action = "store",       type = "string", help = "input align file name [compulsory] [format: align]",       default = "")
+        parser.add_option("-q", "--query",      dest = "query",         action = "store",       type = "string", help = "query fasta file name [optional] [format: fasta]",         default = "")
+        parser.add_option("-s", "--subject",    dest = "subject",       action = "store",       type = "string", help = "subject fasta file name [optional] [format: fasta]",       default = "")
+        parser.add_option("-e", "--evalue",     dest = "evalue",        action = "store",       type = "string", help = "E-value filter [default: 1e10]",                           default = "1e-10")
+        parser.add_option("-j", "--join",       dest = "doJoin",        action = "store_true",                   help = "join matches [default: False]",                            default = False)
+        parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true",                   help = "keep conflicting subjects [default: False]",               default = False)
+        parser.add_option("-o", "--outPrefix",  dest = "outPrefix",     action = "store",       type = "string", help = "output file prefix [default: align file name]",            default = "")
+        parser.add_option("-p", "--alignPattern",dest = "alignPattern", action = "store",       type = "string", help = "align file pattern [default: .*\.align]",                  default = ".*\.align")
+        parser.add_option("-n", "--maxFileSize",dest = "maxFileSize",   action = "store",       type = "int",    help = "max file size (1 file for 1 job) [default: 100000]",       default = 10000)
+        parser.add_option("-m", "--notMergeResults",dest = "notMergeResults", action = "store_false",            help = "don't merge results files [default: True]",                default = True)
+        parser.add_option("-w", "--workingDir",dest = "workingDir",     action = "store",       type = "string", help = "working directory [default: tmpMatcher]",                  default = "tmpMatcher")
+        parser.add_option("-c", "--clean",      dest = "doClean",       action = "store_true",                   help = "clean temporary files [default: False]",                   default = False)
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [default: 1]",                                   default = 1)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+        
+    def _setAttributesFromOptions(self, options):
+        self.setAlignFileName(options.align)
+        self.setQueryFileName(options.query)
+        self.setSubjectFileName(options.subject)
+        self.setEvalue(options.evalue)
+        self.setDoJoin(options.doJoin)
+        self.setKeepConflicts(options.keepConflict)
+        self.setOutPrefix(options.outPrefix)
+        self.setAlignPattern(options.alignPattern)
+        self.setMaxFileSize(options.maxFileSize)
+        self.setMergeResults(options.notMergeResults)
+        self.setWorkingDir(options.workingDir)
+        self.setDoClean(options.doClean)
+        self.setVerbosity(options.verbosity)
+        
+    def setAlignFileName(self, alignFileName):
+        self._alignFileName = alignFileName
+        
+    def setQueryFileName(self, queryFileName):
+        self._queryFileName = queryFileName
+        
+    def setSubjectFileName(self, subjectFileName):
+        self._subjectFileName = subjectFileName
+        
+    def setEvalue(self, evalue):
+        self._eValue = evalue
+        
+    def setDoJoin(self, doJoin):
+        self._doJoin = doJoin
+        
+    def setKeepConflicts(self, keepConflict):
+        self._keepConflict = keepConflict
+        
+    def setOutPrefix(self, outPrefix):
+        if outPrefix == "":
+            self._outPrefix = self._alignFileName
+        else:
+            self._outPrefix = outPrefix
+        
+    def setAlignPattern(self, alignPattern):
+        self._alignPattern = alignPattern
+        
+    def setGroupId(self, groupId):
+        if groupId == "":
+            self._groupId = "Matcher_%s" % os.getpid()
+        else:
+            self._groupId = groupId
+            
+    def setMaxFileSize(self, maxFileSize):
+        self._maxFileSize = maxFileSize
+        
+    def setMergeResults(self, mergeResults):
+        self._mergeResults = mergeResults
+    
+    def setWorkingDir(self, workingDir):
+        self._workingDir = workingDir
+        
+    def setDoClean(self, doClean):
+        self._doClean = doClean
+        
+    def setVerbosity(self, verbosity):
+        self._verbosity = verbosity
+        
+    def _checkOptions(self):
+        if self._alignFileName == "":
+            self._logAndRaise("ERROR: Missing input align file name")
+        
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+    
+    def _checkConfig(self):       
+        iConfigRules = ConfigRules()
+        iConfigRules.addRuleSection(section=self._jobSectionName, mandatory=True)
+        iConfigRules.addRuleOption(section=self._jobSectionName, option ="resources", mandatory=True, type="string")
+        iConfigRules.addRuleOption(section=self._jobSectionName, option ="tmpDir", mandatory=True, type="string")
+        iConfigRules.addRuleOption(section=self._jobSectionName, option ="copy", mandatory=True, type="bool")
+        iConfigRules.addRuleOption(section=self._jobSectionName, option ="clean", mandatory=True, type="bool")
+
+        iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
+        self._iConfig = iConfigChecker.getConfig()
+        self._setAttributesFromConfig()
+        
+    def _setAttributesFromConfig(self):
+        self._resources = self._iConfig.get(self._jobSectionName, "resources")
+        self._tmpDir = self._iConfig.get(self._jobSectionName, "tmpDir")
+        self._isCopyOnNode = self._iConfig.get(self._jobSectionName, "copy")
+        self._doClean = self._iConfig.get(self._jobSectionName, "clean")
+        
+        if self._isCopyOnNode and not self._tmpDir:
+            self._isCopyOnNode = False
+        self._log.debug("The copy option is: %s." % self._isCopyOnNode)
+
+    def _getLaunchMatcherCmd(self, iLauncher, file):
+        lArgs = []
+        lArgs.append("-a %s" % file)
+        if self._queryFileName:
+            lArgs.append("-q %s" % self._queryFileName)
+        if self._subjectFileName:
+            lArgs.append("-s %s" % self._subjectFileName)
+        lArgs.append("-e %s" % self._eValue)
+        lArgs.append("-o %s" % file)
+        if self._doJoin:
+            lArgs.append("-j")
+        if self._keepConflict:
+            lArgs.append("-k")
+        lArgs.append("-v %i" % (self._verbosity - 1))
+        return iLauncher.getSystemCommand("LaunchMatcher.py", lArgs)
+    
+    def _splitAlignFilePerSeq(self):
+        lAlign = AlignUtils.getAlignListFromFile(self._alignFileName)
+        lAlignList = AlignUtils.splitAlignListByQueryName(lAlign)
+        inputFileNameWithoutExtension = os.path.splitext(os.path.basename(self._alignFileName))[0]
+        AlignUtils.createAlignFiles(lAlignList, inputFileNameWithoutExtension, self._workingDir)
+        
+    def _writeTabHeader(self, outTabFileName):
+        with open(outTabFileName, 'w') as f:
+            f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
+
+    def run(self):
+        LoggerFactory.setLevel(self._log, self._verbosity)
+        self._checkConfig()
+        self._checkOptions()
+        
+        self._log.info("START LaunchMatcherInParallel")
+        self._log.debug("Align file name: %s" % self._alignFileName)
+        self._log.debug("Query file name: %s" % self._queryFileName)
+        self._log.debug("Subject file name: %s" % self._subjectFileName)
+        if not os.path.exists(self._workingDir):
+            os.makedirs(self._workingDir)
+        else:
+            self._doClean = False
+        self._splitAlignFilePerSeq()
+        os.chdir(self._workingDir)
+        os.symlink("../%s" % self._queryFileName, self._queryFileName)
+        if self._queryFileName != self._subjectFileName:
+            os.symlink("../%s" % self._subjectFileName, self._subjectFileName)
+            
+        cDir = os.getcwd()
+        if not self._tmpDir:
+            self._tmpDir = cDir
+        
+        acronym = "Matcher"
+        iDb = DbFactory.createInstance()
+        jobdb = TableJobAdaptatorFactory.createInstance(iDb, "jobs")
+        iLauncher = Launcher(jobdb, os.getcwd(), "", "", cDir, self._tmpDir, "jobs", self._resources, self._groupId, acronym, chooseTemplateWithCopy = self._isCopyOnNode)
+
+        lCmdsTuples = []
+        lCmdSize = []
+        lCmdCopy = []
+
+        lFiles = FileUtils.getFileNamesList(".", self._alignPattern)
+        lFileSizeTuples = []
+        for fileName in lFiles:
+            fileSize = os.path.getsize(fileName)
+            lFileSizeTuples.append((fileName, fileSize))
+        lFileSizeList = LauncherUtils.createHomogeneousSizeList(lFileSizeTuples, self._maxFileSize)
+        
+        for lFiles in lFileSizeList:
+            lCmds = []
+            lCmdStart = []
+            lCmdFinish = []
+            if self._queryFileName:
+                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._queryFileName, self._queryFileName))
+            if self._subjectFileName and self._subjectFileName != self._queryFileName:
+                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, self._subjectFileName, self._subjectFileName))
+            for file in lFiles:
+                lCmds.append(self._getLaunchMatcherCmd(iLauncher, file))
+                lCmdStart.append("os.symlink(\"%s/%s\", \"%s\")" % (cDir, file, file))
+                lCmdFinish.append("if os.path.exists(\"%s.match.path\"):" % file)
+                lCmdFinish.append("\tshutil.move(\"%s.match.path\", \"%s/.\" )" % (file, cDir))
+                lCmdFinish.append("if os.path.exists(\"%s.match.tab\"):" % file)
+                lCmdFinish.append("\tshutil.move(\"%s.match.tab\", \"%s/.\" )" % (file, cDir))
+            lCmdsTuples.append(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish, lCmdSize, lCmdCopy))
+        
+        iLauncher.runLauncherForMultipleJobs("Matcher", lCmdsTuples, self._doClean, self._isCopyOnNode)
+
+        if self._mergeResults:
+            FileUtils.catFilesByPattern("*.match.path", "../%s.match.path" % self._outPrefix)
+            if self._queryFileName or self._subjectFileName:
+                outTabFileName = "../%s.match.tab" % self._outPrefix
+                self._writeTabHeader(outTabFileName)
+                FileUtils.catFilesByPattern("*.match.tab", outTabFileName, skipHeaders = True)
+        os.chdir("..")
+        if self._doClean and self._mergeResults:
+            self._log.warning("Working directory will be cleaned")
+            shutil.rmtree(self._workingDir)
+        self._log.info("END LaunchMatchInParallel")
+
+if __name__ == "__main__":
+    iLaunch = LaunchMatcherInParallel()
+    iLaunch.setAttributesFromCmdLine()
+    iLaunch.run()