class Controller:
def __init__(self,viewType=None):
'''
construct an instance of the controller class
to use invoke the method initialize
'''
## determine location
cwd = os.getcwd()
if os.path.split(cwd)[1] == 'gdiqt4':
self.baseDir = cwd
elif os.path.split(cwd)[1] == 'tests':
self.baseDir = os.path.join(os.path.split(cwd)[0],'gdiqt4')
else:
print "ERROR: cannot determine current working directory"
## basic application wide variables
self.viewType = viewType
self.appName = "Gene Data Integrator"
self.fontName = 'Arial' #'Helvetica'
self.verbose = True
self.reset_workspace()
def reset_workspace(self):
self.projectID = None
self.homeDir = None
self.model = Model()
self.log = Logger()
self.subsampleIndices = None
def save(self):
self.log.write()
def initialize_project(self,projectID,loadExisting=False):
self.projectID = projectID
self.homeDir = os.path.join(self.baseDir,"projects",self.projectID)
self.log.initialize(self.projectID,self.homeDir,load=loadExisting)
self.model.initialize(self.projectID,self.homeDir)
##################################################################################################
#
# data dealings -- handling file, project, model and figure data
#
##################################################################################################
def create_new_project(self,view=None,projectID=None):
#fcsFileName = str(fcsFileName)
createNew = True
## create projects dir if necssary
if os.path.isdir(os.path.join(self.baseDir,'projects')) == False:
print "INFO: projects dir did not exist. creating..."
os.mkdir(os.path.join(self.baseDir,'projects'))
## get project id
if projectID != None:
pass
elif createNew == True and projectID == None:
projectID, ok = QtGui.QInputDialog.getText(view, self.appName, 'Enter the name of your new project:')
projectID = str(projectID)
if ok == False:
createNew = False
else:
createNew = False
print "ERROR: creating a new project"
if createNew == True:
print 'initializing project...'
self.initialize_project(projectID)
else:
print "WARNING: did not initialize project"
return False
# remove previous
if self.homeDir != None and os.path.exists(self.homeDir) == True and createNew == True:
print 'overwriting...', self.homeDir
self.remove_project(self.homeDir)
if createNew == True and self.homeDir != None:
os.mkdir(self.homeDir)
os.mkdir(os.path.join(self.homeDir,"data"))
os.mkdir(os.path.join(self.homeDir,"figs"))
os.mkdir(os.path.join(self.homeDir,"models"))
os.mkdir(os.path.join(self.homeDir,"results"))
return True
def remove_project(self,homeDir):
for fileOrDir in os.listdir(homeDir):
if os.path.isfile(os.path.join(homeDir,fileOrDir)) == True:
os.remove(os.path.join(homeDir,fileOrDir))
elif os.path.isdir(os.path.join(homeDir,fileOrDir)) == True:
for fileOrDir2 in os.listdir(os.path.join(homeDir,fileOrDir)):
if os.path.isfile(os.path.join(homeDir,fileOrDir,fileOrDir2)) == True:
os.remove(os.path.join(homeDir,fileOrDir,fileOrDir2))
elif os.path.isdir(os.path.join(homeDir,fileOrDir,fileOrDir2)) == True:
for fileOrDir3 in os.listdir(os.path.join(homeDir,fileOrDir,fileOrDir2)):
if os.path.isfile(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3)) == True:
os.remove(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3))
elif os.path.isdir(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3)) == True:
for fileName in os.listdir(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3)):
os.remove(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3,fileName))
os.rmdir(os.path.join(homeDir,fileOrDir,fileOrDir2,fileOrDir3))
os.rmdir(os.path.join(homeDir,fileOrDir,fileOrDir2))
os.rmdir(os.path.join(homeDir,fileOrDir))
os.rmdir(homeDir)
def rm_file(self,fileName):
if os.path.isfile(fileName) == False:
print "ERROR: could not rm file: %s"%fileName
else:
os.remove(fileName)
self.view.status.set("file removed")
def load_fcs_files(self,fileList,dataType='fcs',transform='log'):
if type(fileList) != type([]):
print "INPUT ERROR: load_fcs_files: takes as input a list of file paths"
script = os.path.join(self.baseDir,"LoadFile.py")
self.log.log['transform'] = transform
for filePath in fileList:
proc = subprocess.Popen("%s %s -f %s -h %s -d %s -t %s"%(pythonPath,script,filePath,self.homeDir,dataType,transform),
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
while True:
try:
next_line = proc.stdout.readline()
if next_line == '' and proc.poll() != None:
break
## to debug uncomment the following line
print next_line
except:
break
## check to see that files were made
newFileName = re.sub('\s+','_',os.path.split(filePath)[-1])
newFileName = re.sub('\.fcs|\.txt|\.out','',newFileName)
newDataFileName = newFileName +"_data_original.pickle"
newChanFileName = newFileName +"_channels_original.pickle"
newFileName = re.sub('\s+','_',filePath[-1])
if filePath == fileList[0]:
self.log.log['selectedFile'] = re.sub("\.pickle","",newDataFileName)
if os.path.isfile(os.path.join(self.homeDir,'data',newDataFileName)) == False:
print "ERROR: data file was not successfully created", os.path.join(self.homeDir,'data',newDataFileName)
if os.path.isfile(os.path.join(self.homeDir,'data',newChanFileName)) == False:
print "ERROR: channel file was not successfully created", os.path.join(self.homeDir,'data',newChanFileName)
#def load_additional_fcs_files(self,fileName=None,view=None):
# loadFile = True
# fcsFileName = None
# if fileName == None:
# fileName = QtGui.QFileDialog.getOpenFileName(self, 'Open FCS file')
#
# if not re.search('\.fcs',fileName):
# fcsFileName = None
# view.display_warning("File '%s' was not of type *.fcs"%fileName)
# else:
# fcsFileName = fileName
#
# if fcsFileName != None:
# self.load_fcs_file(fcsFileName)
# return True
# else:
# print "WARNING: bad attempt to load file name"
# return False
def get_component_states(self):
try:
return self.view.resultsNavigationLeft.get_component_states()
except:
return None
##################################################################################################
#
# log files
#
##################################################################################################
def run_selected_model(self,progressBar=None,view=None):
numItersMCMC = 1100
selectedModel = self.log.log['modelToRun']
numComponents = self.log.log['numComponents']
if self.subsampleIndices == None:
fileList = get_fcs_file_names(self.homeDir)
elif self.subsampleIndices != None:
fileList = get_fcs_file_names(self.homeDir,getPickles=True)
percentDone = 0
totalIters = float(len(fileList)) * numItersMCMC
percentagesReported = []
for fileName in fileList:
if selectedModel == 'dpmm':
script = os.path.join(self.baseDir,"RunDPMM.py")
if os.path.isfile(script) == False:
print "ERROR: Invalid model run file path ", script
proc = subprocess.Popen("%s %s -h %s -f %s -k %s"%(pythonPath,script,self.homeDir,fileName,numComponents),
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE)
while True:
try:
next_line = proc.stdout.readline()
if next_line == '' and proc.poll() != None:
break
## to debug uncomment the following 2 lines
if not re.search("it =",next_line):
print next_line
if re.search("it =",next_line):
progress = 1.0 / totalIters
percentDone+=progress * 100.0
if progressBar != None:
progressBar.move_bar(int(round(percentDone)))
else:
if int(round(percentDone)) not in percentagesReported:
percentagesReported.append(int(round(percentDone)))
if int(round(percentDone)) != 100:
print "\r",int(round(percentDone)),"percent complete",
else:
print "\r",int(round(percentDone)),"percent complete"
except:
break
else:
print "ERROR: invalid selected model", selectedModel
