# -*- coding: utf-8 -*-
"""
***************************************************************************
RUtils.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************
"""
from builtins import str
from builtins import object
__author__ = 'Victor Olaya'
__date__ = 'August 2012'
__copyright__ = '(C) 2012, Victor Olaya'
# This will get replaced with a git SHA1 when you do a git archive
__revision__ = '$Format:%H$'
import re
import os
import stat
import subprocess
from qgis.PyQt.QtCore import QSettings, QCoreApplication
from processing.core.ProcessingConfig import ProcessingConfig
from processing.core.ProcessingLog import ProcessingLog
from processing.tools.system import userFolder, isWindows, mkdir, getTempFilenameInTempFolder
class RUtils(object):
RSCRIPTS_FOLDER = 'R_SCRIPTS_FOLDER'
R_FOLDER = 'R_FOLDER'
R_USE64 = 'R_USE64'
R_LIBS_USER = 'R_LIBS_USER'
rscriptfilename = os.path.join(userFolder(), 'processing_script.r')
@staticmethod
def RFolder():
folder = ProcessingConfig.getSetting(RUtils.R_FOLDER)
if folder is None:
if isWindows():
if 'ProgramW6432' in list(os.environ.keys()) and os.path.isdir(os.path.join(os.environ['ProgramW6432'], 'R')):
testfolder = os.path.join(os.environ['ProgramW6432'], 'R')
elif 'PROGRAMFILES(x86)' in list(os.environ.keys()) and os.path.isdir(os.path.join(os.environ['PROGRAMFILES(x86)'], 'R')):
testfolder = os.path.join(os.environ['PROGRAMFILES(x86)'], 'R')
elif 'PROGRAMFILES' in list(os.environ.keys()) and os.path.isdir(os.path.join(os.environ['PROGRAMFILES'], 'R')):
testfolder = os.path.join(os.environ['PROGRAMFILES'], 'R')
else:
testfolder = 'C:\\R'
if os.path.isdir(testfolder):
subfolders = os.listdir(testfolder)
subfolders.sort(reverse=True)
for subfolder in subfolders:
if subfolder.startswith('R-'):
folder = os.path.join(testfolder, subfolder)
break
else:
folder = ''
else:
folder = ''
return os.path.abspath(str(folder))
@staticmethod
def RLibs():
folder = ProcessingConfig.getSetting(RUtils.R_LIBS_USER)
if folder is None:
folder = str(os.path.join(userFolder(), 'rlibs'))
try:
mkdir(folder)
except:
folder = str(os.path.join(userFolder(), 'rlibs'))
mkdir(folder)
return os.path.abspath(str(folder))
@staticmethod
def defaultRScriptsFolder():
folder = str(os.path.join(userFolder(), 'rscripts'))
mkdir(folder)
return os.path.abspath(folder)
@staticmethod
def RScriptsFolders():
folder = ProcessingConfig.getSetting(RUtils.RSCRIPTS_FOLDER)
if folder is not None:
return folder.split(';')
else:
return [RUtils.defaultRScriptsFolder()]
@staticmethod
def createRScriptFromRCommands(commands):
with open(RUtils.getRScriptFilename(), 'w') as scriptfile:
for command in commands:
scriptfile.write(command + '\n')
@staticmethod
def getRScriptFilename():
return RUtils.rscriptfilename
@staticmethod
def getConsoleOutputFilename():
return RUtils.getRScriptFilename() + '.Rout'
@staticmethod
def executeRAlgorithm(alg, progress):
# generate new R script file name in a temp folder
RUtils.rscriptfilename = getTempFilenameInTempFolder('processing_script.r')
# run commands
RUtils.verboseCommands = alg.getVerboseCommands()
RUtils.createRScriptFromRCommands(alg.getFullSetOfRCommands())
if isWindows():
if ProcessingConfig.getSetting(RUtils.R_USE64):
execDir = 'x64'
else:
execDir = 'i386'
command = [
os.path.join(RUtils.RFolder(), 'bin', execDir, 'R.exe'),
'CMD',
'BATCH',
'--vanilla',
RUtils.getRScriptFilename(),
RUtils.getConsoleOutputFilename()
]
else:
os.chmod(RUtils.getRScriptFilename(), stat.S_IEXEC | stat.S_IREAD
| stat.S_IWRITE)
command = 'R CMD BATCH --vanilla ' + RUtils.getRScriptFilename() \
+ ' ' + RUtils.getConsoleOutputFilename()
proc = subprocess.Popen(
command,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.DEVNULL,
stderr=subprocess.STDOUT,
universal_newlines=True,
)
proc.wait()
RUtils.createConsoleOutput()
loglines = []
loglines.append(RUtils.tr('R execution console output'))
loglines += RUtils.allConsoleResults
for line in loglines:
progress.setConsoleInfo(line)
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)
@staticmethod
def createConsoleOutput():
RUtils.consoleResults = []
RUtils.allConsoleResults = []
add = False
if os.path.exists(RUtils.getConsoleOutputFilename()):
with open(RUtils.getConsoleOutputFilename()) as lines:
for line in lines:
line = line.strip().strip(' ')
if line.startswith('>'):
line = line[1:].strip(' ')
if line in RUtils.verboseCommands:
add = True
else:
add = False
elif add:
RUtils.consoleResults.append('<p>' + line + '</p>\n')
RUtils.allConsoleResults.append(line)
@staticmethod
def getConsoleOutput():
s = '<font face="courier">\n'
s += RUtils.tr('<h2>R Output</h2>\n')
for line in RUtils.consoleResults:
s += line
s += '</font>\n'
return s
@staticmethod
def checkRIsInstalled(ignoreRegistrySettings=False):
if isWindows():
path = RUtils.RFolder()
if path == '':
return RUtils.tr('R folder is not configured.\nPlease configure '
'it before running R scripts.')
R_INSTALLED = 'R_INSTALLED'
settings = QSettings()
if not ignoreRegistrySettings:
if settings.contains(R_INSTALLED):
return
if isWindows():
if ProcessingConfig.getSetting(RUtils.R_USE64):
execDir = 'x64'
else:
execDir = 'i386'
command = [os.path.join(RUtils.RFolder(), 'bin', execDir, 'R.exe'), '--version']
else:
command = ['R --version']
proc = subprocess.Popen(
command,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.DEVNULL,
stderr=subprocess.STDOUT,
universal_newlines=True,
).stdout
for line in iter(proc.readline, ''):
if 'R version' in line:
settings.setValue(R_INSTALLED, True)
return
html = RUtils.tr(
'<p>This algorithm requires R to be run. Unfortunately, it '
'seems that R is not installed in your system, or it is not '
'correctly configured to be used from QGIS</p>'
'<p><a href="http://docs.qgis.org/testing/en/docs/user_manual/processing/3rdParty.html">Click here</a> '
'to know more about how to install and configure R to be used with QGIS</p>')
return html
@staticmethod
def getRequiredPackages(code):
regex = re.compile('[^#]library\("?(.*?)"?\)')
return regex.findall(code)
@staticmethod
def tr(string, context=''):
if context == '':
context = 'RUtils'
return QCoreApplication.translate(context, string)