""" CCP4Utils.py: CCP4 GUI Project Copyright (C) 2001-2008 University of York, CCLRC Copyright (C) 2009-2010 University of York This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ """ Liz Potterton Jan 2010 - Copied from ccp4mg python/ui/utils.py and converted to Qt """ import types,os from CCP4Config import DEVELOPER from CCP4ErrorHandling import * class CUtils: ERROR_CODES = { 101 : {'description' :'Input is not etree element for output to' }, 102 : {'description' :'Failed creating XML text' }, 103 : {'description' :'Failed writing file' }, 104 : {'description' :'Failed parsing file' }, 105 : {'description' :'Error finding root in' }, 106 : {'description' :'Failed opening file to write' }, 107 : {'description' :'Error writing file' }, 108 : {'description' :'Failed opening file to read' }, 109 : {'description' :'Error reading file' }, 110 : {'description' :'Error opening file' }, 111 : {'description' :'Error reading limited number of lines from file' } } pass # bummer - need python 2.5 #from functools import partial """ # kludge .. def partial(func,arg): #print "partial func,arg",func,arg def callme(): return func(arg) return callme """ class partial(object): def __init__(*args, **kw): self = args[0] self.fn, self.args, self.kw = (args[1], args[2:], kw) def __call__(self, *args, **kw): if kw and self.kw: d = self.kw.copy() d.update(kw) else: d = kw or self.kw return self.fn(*(self.args), **d) class partialWithSignal(object): def __init__(*args, **kw): self = args[0] self.fn, self.args, self.kw = (args[1], args[2:], kw) def __call__(self, *args, **kw): if kw and self.kw: d = self.kw.copy() d.update(kw) else: d = kw or self.kw return self.fn(*(self.args + args), **d) ##Convert input string to int #@param value Input string #@param default Optional default value def safeInt(value,default=None): if isinstance(value,types.StringType): value = value.strip() if not value: return default try: i = int(value) except: i = default return i ##Convert input string to float #@param value Input string #@param default Optional default value def safeFloat(value,default=None): if isinstance(value,types.StringType): value = value.strip() if not value: return default try: i = float(value) except: i = default return i ##Convert input string to Boolean #@param value Input string #@param default Optional default value def safeBoolean(value,default=None): if isinstance(value,types.StringType): value = value.strip() if not value: return default try: i = bool(int(value)) except: i = default return i def safeOneWord(value): # Replace spaces and any 'odd' characters with underscore # Resulting word should be safe in a filename import re one_word_name = re.sub('[^a-zA-Z0-9_-]','_',value) return one_word_name def newLineFormat(fileName): f = openFile(fileName) line = f.readline() f.close() if line.endswith('\r\n'): return 'windows' else: return 'unix' def dos2unix(fileName,fileOut=None): import re,sys txt = readFile(fileName) txtout = re.sub(r'\r\n','\n',txt) if fileOut is None: fSplit = os.path.splitext(fileName) if sys.platform.startswith('darwin'): fileOut = fSplit[0]+'_macosx'+fSplit[1] else: fileOut = fSplit[0]+'_linux'+fSplit[1] saveFile(fileOut,txtout) return fileOut def unix2dos(fileName,fileOut=None): import re txt = readFile(fileName) txtout = re.sub(r'\n','\r\n',txt) if fileOut is None: fSplit = os.path.splitext(fileName) fileOut = fSplit[0]+'_windows'+fSplit[1] saveFile(fileOut,txtout) return fileOut #----------------------------------------------------------------- def readFile ( fileName=None,limit=None): #----------------------------------------------------------------- fileName = os.path.normpath(fileName) try: f = open(fileName,'r') except: raise CException(CUtils,108,str(fileName)) if limit is None: try: text = f.read() f.close() except: raise CException(CUtils,109,str(fileName)) else: #try: text = f.read(limit) f.close() #except: # raise CException(CUtils,111,str(fileName)) return text #----------------------------------------------------------------- def openFile ( fileName=None, mode='r',overwrite=1): #----------------------------------------------------------------- import sys import re fileName = os.path.normpath(fileName) if mode == 'w' and os.path.exists(fileName): if overwrite == 1: pass elif overwrite == -1: return '' elif overwrite == 0 : #NEED TO DELETE FILE pass if ['win32'].count(sys.platform): if re.search('b',mode)<0: mode = mode + 'b' try: f = open(fileName,mode) except: raise CException(CUtils,110,str(fileName)+" mode:"+str(mode)+" overwrite:"+str(overwrite)+" exists:"+str(os.path.exists(fileName))) return f #----------------------------------------------------------------- def saveFile(fileName=None,text=None,text_list=[],overwrite=0): #----------------------------------------------------------------- # If fileName is a CFilePath or CDataFile this will fix it fileName = os.path.normpath(str(fileName)) if os.path.exists(fileName): mode = 'w+' else: mode = 'w' f = openFile(fileName,mode,overwrite=overwrite) # Try writing to file try: if len(text_list)>0: f.writelines(text_list) elif text is not None: f.write(text) f.close() except: raise CException(CUtils,107,fileName) def etreeIndent(elem, level=0): i = "\n" + level*" " if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for elem in elem: indent(elem, level+1) if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i def saveEtreeToFile(tree=None,fileName=None): from lxml import etree if tree is None: raise CException(CUtils,101,filename) if DEVELOPER(): # No error trapping - we just want it to crash so we have to fix it! text = etree.tostring(tree, pretty_print=True, xml_declaration=True) saveFile(fileName=fileName,text=text,overwrite=1) else: try: text = etree.tostring(tree, pretty_print=True, xml_declaration=True) except: raise CException(CUtild,102,filename) try: saveFile(fileName=fileName,text=text,overwrite=1) except: raise CException(CUtils,103,filename) def openFileToEtree(fileName=None,printout=False): from lxml import etree # Use this as etree.parse() seg faults on some Linux try: parser = etree.XMLParser() f = open(os.path.normpath(fileName)) s = f.read() f.close() tree = etree.fromstring(s, parser) except: raise CException(CUtils,104,fileName) else: if printout: print etree.tostring(tree,pretty_print=True) return tree ''' if DEVELOPER(): tree = etree.parse(fileName) else: try: tree = etree.parse(fileName) except: raise CException(CUtils,104,filename) try: root = tree.getroot() except: raise CException(CUtils,105,filename) if printout: print etree.tostring(root,pretty_print=True) return root ''' def getHostName(): # From http://stackoverflow.com/questions/4271740/how-can-i-use-python-to-get-the-system-name import socket import socket if socket.gethostname().find('.')>=0: name=socket.gethostname() else: try: name=socket.gethostbyaddr(socket.gethostname())[0] except: name=socket.gethostbyaddr('localhost')[0] return name def getUserId(): name = os.environ.get('LOGNAME',None) if name is not None: return name name = os.environ.get('USERNAME',None) if name is not None: return name import getpass name = getpass.getuser() if name is not None: return name try: return os.getlogin() except: return None #-------------------------------------------------------------------- def getHOME(): #-------------------------------------------------------------------- import sys ''' print "HOME", os.environ.get('HOME') print "HOMEDRIVE", os.environ.get('HOMEDRIVE') print "HOMEPATH", os.environ.get('HOMEPATH') print "USERPROFILE", os.environ.get('USERPROFILE') # Expect HOME defined in LINUX and use it if exists in windows #homedir = os.environ.get('HOME') #if homedir and homedir != '' and os.path.exists(homedir): # return homedir if sys.platform == 'win32': # Try using HOMEDRIVE & HOMEPATH if os.environ.get('HOMEDRIVE'): if os.environ.get('HOMEPATH'): homedir = os.path.join(os.environ.get('HOMEDRIVE'), os.environ.get('HOMEPATH')) else: homedir = os.environ.get('HOMEDRIVE') else: # Last ditch effort - use USERPROFILE homedir = os.environ.get('USERPROFILE') if homedir and os.path.exists(homedir): print "get_HOME",homedir return homedir # Arghh - no HOME return "" ''' homedir = os.environ.get('CCP4_LOCAL_HOME',None) if homedir is not None: return homedir try: if sys.platform == 'win32': homedir = os.path.normpath(os.environ.get('USERPROFILE')) else: homedir = os.environ.get('HOME') except: homedir = '' if homedir and os.path.exists(homedir): return homedir else: return '' def getTMP(): # Return a temp directory #return os.path.join(getDotDirectory(),'tmp') import tempfile return tempfile.gettempdir() def getTestTmpDir(): tmp = os.environ.get('CCP4I2_TEST',None) if tmp is not None and not os.path.exists(tmp): try: os.mkdir(tmp) except: pass if tmp is None or not os.path.exists(tmp): tmp = os.path.join(getHOME(),'CCP4I2_TEST') if not os.path.exists(tmp): os.mkdir(tmp) for subDir in ['CCP4_JOBS','CCP4_PROJECT_FILES']: if not os.path.exists(os.path.join(tmp,subDir)): os.mkdir(os.path.join(tmp,subDir)) return tmp def makeTmpFile(name='tmp',extension='tmp',mode=None,dir=False): import time,os dotExtension = '' if extension : dotExtension = '.' + extension t = int(time.time()) n = 0 fileName = None while fileName is None or os.path.exists(fileName): n = n + 1 fileName = os.path.join(getTMP(),name+'_'+str(t)+'_'+str(n)+dotExtension) # Make the file to be sure if is reserved #print 'CCP4Utils.makeTmpFile',fileName if dir: os.mkdir( fileName ) return fileName elif mode is not None: fd = open(fileName,mode) return (fd,fileName) else: return fileName def backupFile(fileName=None,delete=False): import sys fileName = os.path.normpath(fileName) label = 'previous' labelLen = len(label) import shutil if not os.path.exists(fileName): return None backup = 0 ext1 = '' ext2 = '' base,ext0 = os.path.splitext(fileName) base,ext1 = os.path.splitext(base) if ext1[0:]==label: try: backup = int(ext1[labelLen+1:]) except: pass elif len(ext1)>0: ext2 = os.path.splitext(base) if ext2[0:labelLen]==label: try: backup = int(ext2[labelLen+1:]) except: pass #print 'CCP4Utils.backupFile',base,ext0,ext1,ext2,backup backup = backup + 1 newName = base + '.'+ label + '_'+str(backup)+ext1+ext0 while os.path.exists(newName): backup = backup + 1 newName = base + '.' + label + '_'+str(backup)+ext1+ext0 #print 'CCP4Utils.backupFile',newName if sys.platform == "win32" or not delete: shutil.copyfile(fileName,newName) else: shutil.move(fileName,newName) return newName def splitPath(path): pathList= [] while len(path)>0: path,tail = os.path.split(path) pathList.append(tail) pathList.reverse() return def pythonExecutable(): print 'into CCP4Utils.pythonExecutable' import sys # There is also os.path.join(os.environ["CCP4"],"libexec","ccp4i2") if os.path.exists(os.path.join(os.environ["CCP4"],"bin","ccp4-python")): return os.path.join(os.environ["CCP4"],"bin","ccp4-python") elif os.environ.has_key('PYTHONHOME'): return os.path.join(os.environ['PYTHONHOME'],'bin','python') else: return "python" ''' if sys.platform == 'darwin': return os.path.join(getCCP4I2Dir(),'bin','Python') else: return os.path.join(os.environ['CCP4MG'],'pythondist','bin','python') ''' ''' def getCCP4I2Dir(up=1): import sys target = os.environ.get('CCP4I2_TOP',None) #print 'CCP4Utils.getCCP4I2Dir environ',target if target is not None: return os.path.abspath(target) else: target = os.path.join(os.path.abspath(sys.argv[0]),"..") abstarget = os.path.abspath(target) splittarget = abstarget.split('/') if splittarget.count('ccp4i2'): splittarget.reverse() up = splittarget.index('ccp4i2') while up>0: abstarget = os.path.dirname(abstarget) up = up -1 #print 'CCP4Utils.getCCP4I2Dir Environment variable CCP4I2_TOP not defined - trying ',abstarget return abstarget ''' def getCCP4I2Dir(**kw): import os f = os.path.normpath(__import__('CCP4Utils').__file__) return os.path.split(os.path.split(f)[0])[0] def getOSDir(): import sys if sys.platform == 'darwin': return os.path.join(getCCP4I2Dir(),'MacOSX') elif sys.platform[0:5] == 'linux': return os.path.join(getCCP4I2Dir(),'Linux') elif sys.platform[0:3] == 'win': return os.path.normpath(os.path.join(getCCP4I2Dir(),'Windows')) else: return '' def getTestSysDir(): return os.path.join(getCCP4I2Dir(),'testsysdefs') def getCCP4Dir(): try: target = os.path.normpath(os.environ.get('CCP4',None)) except: target = '' return target def interpretPath(path='',currentDir=None): import re path = path.strip() # print 'interpretPath',path m = re.search(r'(.*?)\$(.*?)(\/|$)(.*)',path) while m is not None: #print 'interpretPath m',m.groups() reGroups = m.groups() envPath = os.environ.get(reGroups[1],'') path = reGroups[0] + os.environ.get(reGroups[1],'') + reGroups[2] + reGroups[3] m = re.search(r'(.*?)\$(.*?)(\/|$)(.*)',path) if currentDir is not None and path[0] == '.': if currentDir[-1] == '/' and path[0] == '/': path = currentDir[0:-1] + path elif currentDir[-1] != '/' and path[0] != '/': path = currentDir + '/' + path else: path = currentDir + path return os.path.abspath(path) def getDotDirectory(): import sys, shutil home = os.environ.get('CCP4_LOCAL_DOTDIR',None) if home is None: home = getHOME() ccp4i2 = os.path.join (home,'.CCP4I2') if not os.path.exists(ccp4i2) and sys.platform == 'win32': ccp4i2 = os.path.normpath( os.path.join (home,'CCP4I2')) if not os.path.exists(ccp4i2): try: os.mkdir(ccp4i2) except: print "ERROR creating .CCP4I2 directory" return "" # Make sure that we also have the subdirectories for subd in ['status','logs','configs','db','tmp','custom','demo_data','i1supplement']: path = os.path.join ( ccp4i2 , subd ) if not os.path.exists(path): try: os.mkdir(path) except: print "ERROR creating subdirectories in ",ccp4i2 for subd in ['workflows','comfilepatchs','importedjobs','tasks']: path = os.path.join ( ccp4i2 , 'custom', subd ) if not os.path.exists(path): try: os.mkdir(path) except: print "ERROR creating subdirectories in ",ccp4i2 #target = os.path.join ( ccp4i2 ,'configs', 'ccp4i2_config.params.xml') #if not os.path.exists(target): # source = os.path.join(getCCP4I2Dir(),'data','config_templates','ccp4i2_config.params.xml') # shutil.copyfile(source,target) return ccp4i2 def getProjectDirectory(): ccp4i2 = os.path.join (getHOME(),'CCP4I2_PROJECTS') if not os.path.exists(ccp4i2): try: os.mkdir(ccp4i2) except: print "ERROR creating CCP4I2_PROJECTS directory" return None return ccp4i2 def globSearchPath(searchPath=[],file='*'): import glob fileList = [] for path in searchPath: fileList.extend(glob.glob(os.path.join(path,file))) return fileList def importFileModule(pyFile,report=False): try: moduleName = os.path.splitext(os.path.basename(pyFile))[0] #print 'importFileModule moduleName',moduleName module = __import__(moduleName) return module,None except Exception as e: if report: print 'ERROR attempting to import module: ',moduleName,e module = None return module,str(e) def writeTarGzip(directory=None,tarFile=None): import tarfile if tarFile is None: tarFile = directory + '.tar.gz' try: tarObj = tarfile.open(tarFile,'w:gz') #tarObj.add(directory,arcname=os.path.split(directory)[1],exclude=excludeFromTarGzip) tarObj.add(directory,arcname=os.path.split(directory)[1]) tarObj.close() except: return None return tarFile def excludeFromTarGzip(fileName): #print 'excludeFromTarGzip',fileName return False def readTarGzip(fileName,destination=None): import tarfile if destination is None: destination = os.path.split(fileName)[0] tarObj = tarfile.open(fileName) next = tarObj.next().name print 'CCP4Utils. readTarGzip next',next tarObj.extractall(path=destination) tarObj.close() return next def getProgramVersion(programName,mode='version'): # Run CCP4 program with -i to get either explicit version info # or version as part of the program banner header which appears before program fails import re,os,copy import CCP4Modules bin = copy.deepcopy(programName) programName = programName.lower() logFile = makeTmpFile(extension='log') if programName == 'ccp4i2': import CCP4File versionHeader = CCP4File.CI2XmlHeader() versionHeader.loadFromXml(os.path.join(getCCP4I2Dir(),'core','version.params.xml')) if mode == 'version': return versionHeader.ccp4iVersion.__str__() elif mode == 'date': return versionHeader.creationTime.date() elif programName == 'ccp4': CCP4Modules.PROCESSMANAGER().startProcess('fft',['-i'],logFile=logFile) text = readFile(logFile) m1 = re.search('(.*)patch level(.*)',text) if m1 is None: return None text = m1.groups()[1].strip() return text elif programName == 'python': import sys return sys.version.split()[0] elif programName == 'qt': from PyQt4 import QtCore return QtCore.qVersion() elif programName == 'arp_warp': # Need to get the it exit return None elif programName.startswith('phenix'): testArgList = [['--version'],['-version']] else: testArgList = [['-i'],['--version'],['-version']] for argList in testArgList: CCP4Modules.PROCESSMANAGER().startProcess(bin,argList,logFile=logFile) #print 'CCP4Utils.getProgramVersion programName',programName,logFile text = readFile(logFile) if arglist == ['-i']: ret = searchVersion(text,programName) else: ret = searchVersion(text) if ret is not None: return ret def searchVersion(text,programName=None): import re if programName is not None: #Split text at program name - for CCP4 progs expect the version on same line m1 = re.search('(.*)'+programName+'(.*)',text) if m1 is not None: text = m1.groups()[1] print 'CCP4Utils.getProgramVersion m1',m1.groups() m2 = re.search('(.*)(V|v)ersion([ :\.]*)([0123456789.]*)',text) if m2 is not None and len(m2.groups()[3])>0: return m2.groups()[3] m2 = re.search('(.*)(V|v)er([ :\.]*)([0123456789.]*)',text) if m2 is not None and len(m2.groups()[3])>0: return m2.groups()[3] m2 = re.search('(.*)([V|v])([0123456789.]*)',text) if m2 is not None and len(m2.groups()[2])>0: return m2.groups()[2] return None def versionLogHeader(): import sys text = 'CCP4i2 version: '+getProgramVersion('ccp4i2')+'\n'+ \ 'Running CCP4 version: '+getProgramVersion('ccp4')+'\n'+ \ 'Using Python version: '+sys.version+'\n'+ \ 'Using Qt version: ' + getProgramVersion('qt')+'\n' return text def listReMatch(lst,reExp): # search list of strings with reg expression and return hit string and index # More genius code brought to you by # http://stackoverflow.com/questions/23229675/search-list-of-string-with-wildcard-and-return-matches-indexes-python import re regex=re.compile(reExp) locs, matches = zip(*[(idx, string) for idx, string in enumerate(lst) if re.match(regex, string)]) #print 'listSearch matches', matches #print 'listSearch locs', locs return locs, matches import pickle class QtUnpickler(pickle.Unpickler): def __init__(self, file): pickle.Unpickler.__init__(self, file) def load_global(self): module = self.readline()[:-1] name = self.readline()[:-1] if module == "sip" and name == "_unpickle_enum": module = __name__ klass = self.find_class(module, name) self.append(klass) pickle.Unpickler.dispatch[pickle.GLOBAL] = load_global def isAlive(qobj): import sip try: sip.unwrapinstance(qobj) except RuntimeError: return False return True # Slightly modified from http://timgolden.me.uk/python/win32_how_do_i/see_if_two_files_are_the_same_file.html def get_read_handle (filename): import win32file if os.path.isdir(filename): dwFlagsAndAttributes = win32file.FILE_FLAG_BACKUP_SEMANTICS else: dwFlagsAndAttributes = 0 return win32file.CreateFile ( filename, win32file.GENERIC_READ, win32file.FILE_SHARE_READ, None, win32file.OPEN_EXISTING, dwFlagsAndAttributes, None ) def get_unique_id (hFile): import win32file ( attributes, created_at, accessed_at, written_at, volume, file_hi, file_lo, n_links, index_hi, index_lo ) = win32file.GetFileInformationByHandle (hFile) return volume, index_hi, index_lo def files_are_equal (filename1, filename2,default=False): try: hFile1 = get_read_handle (filename1) except: return default try: hFile2 = get_read_handle (filename2) except: return default try: are_equal = (get_unique_id (hFile1) == get_unique_id (hFile2)) hFile2.Close () hFile1.Close () except: return default return are_equal def samefile(f1,f2,default=False): import sys if sys.platform != 'win32': return os.path.samefile(f1,f2) else: return files_are_equal(f1,f2,default=default) def zipDirectory(zip,sourceDirectory,rootRelPath=None): if rootRelPath is None: rootRelPath=sourceDirectory # Beware the 'sourceDirectory' could be a file if os.path.isfile(sourceDirectory): root,file = os.path.split(sourceDirectory) arcname = os.path.join(os.path.relpath(root,rootRelPath ), file) zip.write(sourceDirectory, arcname) else: for root, dirs, files in os.walk(sourceDirectory): # add directory (needed for empty dirs) # Beware relpath can barf on Windows if comparing paths on differnt drives # - this should not be the case here zip.write(root, os.path.relpath(root, rootRelPath)) for file in files: filename = os.path.join(root, file) if os.path.isfile(filename): # regular files only arcname = os.path.join(os.path.relpath(root,rootRelPath ), file) zip.write(filename, arcname) def findDaBirdy(): import sys import CCP4Modules # This is the default install path for ccp4 6.4.0 # Except windows release does not include coot and this is default install for coot if path is not None and os.path.exists(path): return path if sys.platform == 'win32': path = os.path.normpath(os.path.join('C:','WinCoot','runwincoot')) elif sys.platform == 'darwin': path = os.path.normpath(os.path.join(os.environ['CCP4'],'coot')) else: path = os.path.normpath(os.path.join(os.environ['CCP4'],'bin','coot')) if os.path.exists(path): return path return None def getCCP4Exe(program): import sys if sys.platform == 'win32': exe = program+'.exe' else: exe = program bin = os.path.join( getOSDir(), 'bin', exe ) if not os.path.exists(bin): bin = os.path.join(getCCP4Dir(), 'bin', exe ) return bin def which(program, mode=os.F_OK | os.X_OK, path=None): ''' From shutil.which in python 3.3 back ported for local use here in 2.7 via Tom Burnley and the CCP4EM GUI. Given a command, mode, and a PATH string, return the path which conforms to the given mode on the PATH, or None if there is no such file. `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result of os.environ.get("PATH"), or can be overridden with a custom search path. ''' # Check ccpem settings for specified bins. E.g. if bin is set via alias # it will not be located via which function. import sys,os cmd = program # Check that a given file can be accessed with the correct mode. # Additionally check that `file` is not a directory, as on Windows # directories pass the os.access check. def _access_check(fn, mode): return (os.path.exists(fn) and os.access(fn, mode) and not os.path.isdir(fn)) # If we're given a path with a directory part, look it up directly rather # than referring to PATH directories. This includes checking relative to the # current directory, e.g. ./script if os.path.dirname(cmd): if _access_check(cmd, mode): return cmd return None if path is None: path = os.environ.get("PATH", os.defpath) if not path: return None path = path.split(os.pathsep) if sys.platform == "win32": # The current directory takes precedence on Windows. if not os.curdir in path: path.insert(0, os.curdir) # PATHEXT is necessary to check on Windows. pathext = os.environ.get("PATHEXT", "").split(os.pathsep) # See if the given file matches any of the expected path extensions. # This will allow us to short circuit when given "python.exe". # If it does match, only test that one, otherwise we have to try # others. if any([cmd.lower().endswith(ext.lower()) for ext in pathext]): files = [cmd] else: files = [cmd + ext for ext in pathext] else: # On other platforms you don't have things like PATHEXT to tell you # what file suffixes are executable, so just pass on cmd as-is. files = [cmd] seen = set() for dir in path: normdir = os.path.normcase(dir) if not normdir in seen: seen.add(normdir) for thefile in files: name = os.path.join(dir, thefile) if _access_check(name, mode): return name return None def nonWhiteDifferences(file1,file2): retDiffs = [] retCount = [] import re import diff_match_patch dmp = diff_match_patch.diff_match_patch() text1= readFile(file1) text2 = readFile(file2) text1 = re.sub(r' +\n','\n',text1) text2 = re.sub(r' +\n','\n',text2) diffs = dmp.diff_main(text1,text2) #dmp.diff_cleanupSemantic(diffs) for n in range(len(diffs)): if diffs[n][0] != 0 and len(diffs[n][1].strip())>0 : d = [ diffs[n][0],diffs[n][1] ] if retDiffs.count(d): idx = retDiffs.index(d) retCount[idx] += 1 else: retDiffs.append(d) retCount.append(1) for n in range(len(retDiffs)): retDiffs[n].append(retCount[n]) #print 'nonWhiteDifferences',retDiffs return retDiffs #=================================================================================================== import unittest def TESTSUITE(): suite = unittest.defaultTestLoader.loadTestsFromTestCase(testEtreeTools) suite.addTests(unittest.defaultTestLoader.loadTestsFromTestCase(testFileOpen)) suite.addTests(unittest.defaultTestLoader.loadTestsFromTestCase(testBackup)) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite) class testEtreeTools(unittest.TestCase): def test1(self): import os fileName = os.path.join(getCCP4I2Dir(),'test','data','test_job_104.def.xml') root = openFileToEtree(fileName=fileName) self.assertEqual(root.tag,'ccp4i2','Failed to read first item in eTree') def test2(self): import os fileName = os.path.join(getTestTmpDir(),'CCP4Utils_test.def.xml') import CCP4Data x = CCP4Data.CFloat(42,default=0) ele = x.getEtree() saveEtreeToFile(tree=ele,fileName=fileName) if not os.path.exists(fileName): self.fail('Failed to write eTree file') class testFileOpen(unittest.TestCase): def test1(self): import os fileName = os.path.join(getCCP4I2Dir(),'test','data','test_job_104.def.xml') text = readFile(fileName) textLines = text.split('\n') self.assertEqual(textLines[0],"",'Error reading file with readFile') def test2(self): import os text = 'The quick brown fox jumped over the lazy dog' fileName = os.path.join(getTMP(),'fox.dog') saveFile(fileName,text) self.assertTrue(os.path.exists(fileName),'Failed to save file with saveFile') def test3(self): import os text = 'The quick brown fox jumped over the lazy dog' fileName = '/foo/bar/fox.dog' try: saveFile(fileName,text) except CException as e: #print 'testFileOpen.test3',e.report() self.assertEqual(e[0]['code'],110,'saveFile gives unexpected CException code') except: self.fail('saveFile gives unexpected Python exception') class testBackup(unittest.TestCase): def test1(self): import os tempdir = getTMP() fileName = os.path.join(tempdir,'fox.PARAMS.xml') try: os.remove(os.path.join(tempdir,'fox.backup_1.PARAMS.xml')) except: pass saveFile(fileName,'whatever') newFile = backupFile(fileName=fileName,delete=True) self.assertEqual(newFile,os.path.join(tempdir,'fox.backup_1.PARAMS.xml'),'backupFile gives wrong file name') if not os.path.exists(newFile): self.fail('backupFile does not create new file') if os.path.exists(fileName): self.fail('backupFile old file still exists')