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126 lines
4.5 KiB
Python
126 lines
4.5 KiB
Python
# -*- coding: utf-8 -*-
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"""
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***************************************************************************
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RUtils.py
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---------------------
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Date : August 2012
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Copyright : (C) 2012 by Victor Olaya
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Email : volayaf at gmail dot com
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***************************************************************************
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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***************************************************************************
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"""
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__author__ = 'Victor Olaya'
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__date__ = 'August 2012'
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__copyright__ = '(C) 2012, Victor Olaya'
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# This will get replaced with a git SHA1 when you do a git archive
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__revision__ = '$Format:%H$'
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from PyQt4.QtGui import *
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from sextante.core.SextanteConfig import SextanteConfig
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import os
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from sextante.core.SextanteUtils import mkdir, SextanteUtils
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import subprocess
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from sextante.core.SextanteLog import SextanteLog
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import stat
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class RUtils:
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RSCRIPTS_FOLDER = "R_SCRIPTS_FOLDER"
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R_FOLDER = "R_FOLDER"
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R_USE64 = "R_USE64"
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@staticmethod
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def RFolder():
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folder = SextanteConfig.getSetting(RUtils.R_FOLDER)
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if folder == None:
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folder = ""
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return os.path.abspath(unicode(folder))
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@staticmethod
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def RScriptsFolder():
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folder = SextanteConfig.getSetting(RUtils.RSCRIPTS_FOLDER)
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if folder == None:
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folder = unicode(os.path.join(SextanteUtils.userFolder(), "rscripts"))
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mkdir(folder)
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return os.path.abspath(folder)
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@staticmethod
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def createRScriptFromRCommands(commands):
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scriptfile = open(RUtils.getRScriptFilename(), "w")
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for command in commands:
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scriptfile.write(command + "\n")
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scriptfile.close()
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@staticmethod
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def getRScriptFilename():
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return SextanteUtils.userFolder() + os.sep + "sextante_script.r"
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@staticmethod
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def getConsoleOutputFilename():
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return RUtils.getRScriptFilename()+".Rout"
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@staticmethod
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def executeRAlgorithm(alg, progress):
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RUtils.verboseCommands = alg.getVerboseCommands();
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RUtils.createRScriptFromRCommands(alg.getFullSetOfRCommands())
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if SextanteUtils.isWindows():
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if SextanteConfig.getSetting(RUtils.R_USE64):
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execDir = "x64"
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else:
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execDir = "i386"
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command = [RUtils.RFolder() + os.sep + "bin" + os.sep + execDir + os.sep + "R.exe", "CMD", "BATCH", "--vanilla",
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RUtils.getRScriptFilename(), RUtils.getConsoleOutputFilename()]
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else:
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os.chmod(RUtils.getRScriptFilename(), stat.S_IEXEC | stat.S_IREAD | stat.S_IWRITE)
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command = "R CMD BATCH --vanilla " + RUtils.getRScriptFilename() + " "+ RUtils.getConsoleOutputFilename()
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proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
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universal_newlines=True)
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proc.wait()
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RUtils.createConsoleOutput()
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loglines = []
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loglines.append("R execution console output")
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loglines += RUtils.allConsoleResults
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for line in loglines:
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progress.setConsoleInfo(line)
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SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)
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@staticmethod
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def createConsoleOutput():
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RUtils.consoleResults = []
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RUtils.allConsoleResults = []
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add = False
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if os.path.exists(RUtils.getConsoleOutputFilename()):
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lines = open(RUtils.getConsoleOutputFilename())
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for line in lines:
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line = line.strip("\n").strip(" ")
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if line.startswith(">"):
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line = line[1:].strip(" ")
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if line in RUtils.verboseCommands:
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add = True
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else:
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add = False
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elif add:
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RUtils.consoleResults.append("<p>" + line + "</p>\n");
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RUtils.allConsoleResults.append(line);
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@staticmethod
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def getConsoleOutput():
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s = "<font face=\"courier\">\n"
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s+="<h2> R Output</h2>\n"
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for line in RUtils.consoleResults:
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s+=line
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s+="</font>\n"
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return s
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