def __init__(self, file, ui=None, expTime = 601, checkTime = 1, ):
self.fsCoding = getFsEncoding(logLevel=False)
self.expTime = expTime
self.checkTime = checkTime
self.file = file
self.ui = ui
QThread.__init__(self)
def __init__(self, name, dir=None, parent=None):
super(ProjectMsatSeq, self).__init__(name, dir, parent)
self.fsCoding = getFsEncoding(logLevel=False)
self.gen_data_win = SetGeneticDataMsatSeq(self)
self.gen_data_win.ui.okButton.setText("VALIDATE AND SAVE")
self.gen_data_win.hide()
self.verifyRefTableValid()
def __init__(self,sc_info_list=None,parent=None):
super(DrawScenario,self).__init__(parent)
self.parent=parent
self.fsCoding = getFsEncoding(logLevel=False)
self.createWidgets()
self.sc_info_list = sc_info_list
self.pixList = []
self.svgList = []
def treatment(csock,qued):
#filename = sys.argv[2]
filename = str(datetime.now())
filename = filename.replace(' ','_').replace(":",".")
filename+=".tar"
f=open( filename.encode(getFsEncoding(logLevel=False)), 'wb')
md5=csock.recv(33)
md5 = str(md5).strip()
print "md5 : '%s'"%md5
size=csock.recv(20)
print "size : '%s'"%size
received = 0
#data = csock.recv(int(size))
#f.write(data)
# 2. receive data
while received < int(size):
print "reception"
data = csock.recv(8192)
received = received + len(data)
if (not data):
print "je break, plus de data"
break
f.write(data)
print "sortie de boucle de reception"
#3.close file
f.close()
print filename.encode(getFsEncoding(logLevel=False)), "Received\n"
f=open(filename.encode(getFsEncoding(logLevel=False)),'r')
fdata = f.read()
f.close()
print str(hashlib.md5(fdata).hexdigest())
checkfile = (md5 == str(hashlib.md5(fdata).hexdigest()))
print "'%s' == '%s'"%(md5,hashlib.md5(fdata).hexdigest())
if checkfile:
dirname = filename.replace('.tar','')
os.mkdir((u"%s/%s"%(os.getcwd()).encode(getFsEncoding(logLevel=False)),dirname.encode(getFsEncoding(logLevel=False))))
#os.chdir("%s/%s"%(os.getcwd(),dirname))
a = os.popen("tar xvf %s -C ""%s"""%(filename.encode(getFsEncoding(logLevel=False)),dirname.encode(getFsEncoding(logLevel=False))))
a.close()
print "archive extracted"
#os.chdir("./SBCN_jm/")
f=open((u"%s/SBCN_jm/command_output"%dirname).encode(getFsEncoding(logLevel=False)),"w")
subprocess.Popen([u"sh".encode(getFsEncoding(logLevel=False)),u"./launch.sh".encode(getFsEncoding(logLevel=False))],stdout=f,cwd=(u"%s/SBCN_jm/"%dirname).encode(getFsEncoding(logLevel=False)))
while True:
time.sleep(2)
a=os.popen((u"tail -n 1 %s/SBCN_jm/command_output"%dirname).encode(getFsEncoding(logLevel=False)))
line = a.read()
print "[",dirname,"] ",line,"--------"
csock.send(line)
a.close()
if len(line.split("%%"))>1 and "100 %%" in line:
break
f.close()
csock.close()
def __init__(self,parent=None):
super(ShowLogFile,self).__init__(parent)
self.parent = parent
self.fsCoding = getFsEncoding(logLevel=False)
#dd = datetime.now()
#self.logfile = os.path.expanduser("~/.diyabc/logs/%02d_%02d_%s-%s.log"%(dd.day,dd.month,dd.year,os.getpid()))
#self.logfile = self.parent.logfile
self.createWidgets()
self.updateLogFile()
def __init__(self,analysis,directory,parent=None):
super(DrawComparisonAnalysisResult,self).__init__(parent)
self.parent=parent
self.directory=directory
self.analysis = analysis
self.fsCoding = getFsEncoding(logLevel=False)
self.createWidgets()
self.dicoPlot = {}
self.tab_colors = ["#0000FF","#00FF00","#FF0000","#00FFFF","#FF00FF","#FFFF00","#000000","#808080","#008080","#800080","#808000","#000080","#008000","#800000","#A4A0A0","#A0A4A0","#A0A0A4","#A00000","#00A000","#00A0A0"]
self.drawAll()
def __init__(self,analysis,directory,parent=None):
super(DrawPCAAnalysisResult,self).__init__(parent)
self.parent=parent
self.directory=directory
self.fsCoding = getFsEncoding(logLevel=False)
self.dico_points = {}
self.analysis = analysis
if self.directory.split('_')[-1] == "modelChecking":
self.acpFile = "%s/analysis/%s/mcACP.txt"%(self.parent.dir,self.directory)
else:
self.acpFile = "%s/analysis/%s/ACP.txt"%(self.parent.dir,self.directory)
self.createWidgets()
self.dicoPlot = {}
self.tab_colors = ["#0000FF","#00FF00","#FF0000","#00FFFF","#FF00FF","#FFFF00","#000000","#808080","#008080","#800080","#808000","#000080","#008000","#800000","#A4A0A0","#A0A4A0","#A0A0A4","#A00000","#00A000","#00A0A0"]
def __init__(self,parent=None,confFilePath=None,title="Settings"):
super(AutoPreferences,self).__init__(parent)
self.parent = parent
self.title = title
# dico indexé par le nom de la catégorie qui contient la liste des propriétés
self.dicoCategory = {}
# liste pour retenir l'ordre des catégories
self.categoryList = []
self.configFile = confFilePath.encode(getFsEncoding(logLevel=False))
self.config = ConfigObj(self.configFile)
self.createWidgets()
def __init__(self,analysis,directory,parent=None):
super(DrawEstimationAnalysisResult,self).__init__(parent)
self.parent=parent
self.directory=directory
self.analysis = analysis
self.fsCoding = getFsEncoding(logLevel=False)
self.tab_colors = ["#0000FF","#00FF00","#FF0000","#00FFFF","#FF00FF","#FFFF00","#000000","#808080","#008080","#800080","#808000","#000080","#008000","#800000","#A4A0A0","#A0A4A0","#A0A0A4","#A00000","#00A000","#00A0A0"]
self.paramChoice = "o"
self.file_subname = "_original"
self.createWidgets()
self.dicoPlot = {}
self.dicoFrame = {}
self.svgList = []
self.drawAll()
def __init__(self,name,dir=None,parent=None):
super(ProjectSnp,self).__init__(name,dir,parent)
self.fsCoding = getFsEncoding(logLevel=False)
self.ui.nbMicrosatLabel.hide()
self.setGenValid(False)
self.ui.genDataLabel.setText("Summary statistics")
self.typesOrdered = ["A","H","X","Y","M"]
self.checkSNPbin = None
#self.ui.frame_11.show()
#self.ui.frame_12.show()
# until now set ascert bias functionality is not activated. (but waiting for further developpment)
# so self.ascert_state_valid is set to True
self.ascert_frame = ControlAscertBias(self)
self.ascert_frame.hide()
self.ascert_state_valid = True
self.setAscertValid(True)
QObject.connect(self.ui.ascertButton,SIGNAL("clicked()"),self.setAscertBias)
def __init__(self,name,dir=None,parent=None):
self.parent=parent
self.name=name
self.dir=dir
if self.dir != None :
self.dir = str(self.dir)
self.fsCoding = getFsEncoding(logLevel=False)
# objet data de cbgpUtils
self.data = None
self.hist_state_valid = False
self.gen_state_valid = False
self.MIN_NUM_DATA_SETS_BY_SCENARIO_FOR_ANALYSIS = 100000
# utile seulement si on derive de QTabWidget
super(Project,self).__init__(parent)
# on peut aussi instancier un tabwidget
#self.tab = QTabWidget()
self.createWidgets()
self.verifyRefTableValid()
def __init__(self,parent=None):
super(SetGeneticDataSimulation,self).__init__(parent)
self.fsCoding = getFsEncoding(logLevel=False)
self.ui.tableWidget.setColumnWidth(0,90)
self.ui.tableWidget.setColumnWidth(1,40)
self.ui.tableWidget.setColumnWidth(2,45)
self.ui.tableWidget.setColumnWidth(3,45)
self.ui.tableWidget.insertColumn(self.ui.tableWidget.columnCount())
self.ui.tableWidget.setColumnWidth(4,50)
self.ui.tableWidget.setHorizontalHeaderItem (4, QTableWidgetItem("length"))
self.ui.tableWidget.insertColumn(self.ui.tableWidget.columnCount())
self.ui.tableWidget.setColumnWidth(5,35)
self.ui.tableWidget.setHorizontalHeaderItem (5, QTableWidgetItem("%A"))
self.ui.tableWidget.insertColumn(self.ui.tableWidget.columnCount())
self.ui.tableWidget.setColumnWidth(6,35)
self.ui.tableWidget.setHorizontalHeaderItem (6, QTableWidgetItem("%C"))
self.ui.tableWidget.insertColumn(self.ui.tableWidget.columnCount())
self.ui.tableWidget.setColumnWidth(7,35)
self.ui.tableWidget.setHorizontalHeaderItem (7, QTableWidgetItem("%G"))
self.ui.tableWidget.insertColumn(self.ui.tableWidget.columnCount())
self.ui.tableWidget.setColumnWidth(8,35)
self.ui.tableWidget.setHorizontalHeaderItem (8, QTableWidgetItem("%T"))
# -*- coding: utf-8 -*-
import sys, codecs, traceback
from PyQt4 import QtCore, QtGui
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from utils.visualizescenario import *
from utils.data import *
from utils.cbgpUtils import log,getFsEncoding
import output
import variables
from variables import UIPATH
formControl,baseControl = uic.loadUiType((u"%s/controlAscertBias.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class ControlAscertBias(formControl,baseControl):
def __init__(self,parent=None):
super(ControlAscertBias,self).__init__(parent)
self.parent=parent
self.fsCoding = getFsEncoding(logLevel=False)
self.createWidgets()
def createWidgets(self):
#self.ui = Ui_Frame()
self.ui = self
self.ui.setupUi(self)
self.ui.verticalLayout_3.setAlignment(QtCore.Qt.AlignCenter)
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from historicalModel.setHistDrawnAnalysis import HistDrawn
from historicalModel.setHistFixedAnalysis import HistFixed
from setupEstimationBias import SetupEstimationBias
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding, Parents
formBiasScenarioSelection,baseBiasScenarioSelection = uic.loadUiType((u"%s/biasScenarioSelection.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class BiasNConfidenceScenarioSelection(formBiasScenarioSelection,baseBiasScenarioSelection):
""" Selection du scenario dans la cadre d'une analyse de type bias ou confidence
"""
def __init__(self,nb_sc,analysis,parent=None):
super(BiasNConfidenceScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.checklist = []
self.radiolist = []
self.createWidgets()
self.putChoices()
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from biasScenarioSelection import BiasNConfidenceScenarioSelection
from historicalModel.setHistDrawnAnalysis import HistDrawn
from historicalModel.setHistFixedAnalysis import HistFixed
from setupComparisonConfidence import SetupComparisonConfidence
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding, Parents
formConfidenceTypeSelection,baseConfidenceTypeSelection = uic.loadUiType((u"%s/confidenceTypeSelection.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class ConfidenceTypeSelection(formConfidenceTypeSelection,baseConfidenceTypeSelection):
""" Selection du scenario dans la cadre d'une analyse de type bias ou confidence
"""
def __init__(self,nb_sc,analysis,parent=None):
super(ConfidenceTypeSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.createWidgets()
self.restoreAnalysisValues()
def createWidgets(self):
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setupComparisonConfidence_ui import Ui_Frame
from genericScenarioSelection import GenericScenarioSelection
import output
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding, Parents
formSetupComparisonConfidence,baseSetupComparisonConfidence = uic.loadUiType((u"%s/setupComparisonConfidence.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetupComparisonConfidence(formSetupComparisonConfidence,baseSetupComparisonConfidence):
""" dernière étape de définition d'une analyse de type comparison ou confidence
"""
def __init__(self,analysis,parent=None):
super(SetupComparisonConfidence,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.scNumList = []
self.dico_values = {}
self.createWidgets()
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_2.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4 import QtCore, QtGui
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setMutationModelSequences_ui import Ui_Frame
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding
formSetMutationModelSequences,baseSetMutationModelSequences = uic.loadUiType((u"%s/setMutationModelSequences.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetMutationModelSequences(formSetMutationModelSequences,baseSetMutationModelSequences):
""" définition du modèle mutationnel pour les séquences
"""
def __init__(self,parent=None,box_group=None):
super(SetMutationModelSequences,self).__init__(parent)
self.parent=parent
self.box_group = box_group
self.createWidgets()
if self.ui.jukesRadio.isChecked():
self.showJukes()
elif self.ui.haseRadio.isChecked() or self.ui.kimuraRadio.isChecked():
self.showKimuraHase()
elif self.ui.tamuraRadio.isChecked():
self.showTamura()
self.ui.verticalLayout_27.setAlignment(Qt.AlignTop)
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setHistFrame_ui import Ui_Frame
from utils.visualizescenario import *
from utils.history import *
from setCondition import SetCondition
from geneticData.setGenDataAnalysis import SetGeneticDataAnalysis
from analysis.setupEstimationBias import SetupEstimationBias
from analysis.setupComparisonConfidence import SetupComparisonConfidence
from utils.cbgpUtils import log, getFsEncoding, Parents
import variables
from variables import UIPATH
import output
formHistModelDrawn,baseHistModelDrawn = uic.loadUiType((u"%s/setHistFrame.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class HistDrawn(formHistModelDrawn,baseHistModelDrawn):
""" définition du modèle historique dans le cadre d'une analyse
les valeurs ne sont pas fixées
"""
def __init__(self,analysis,parent=None):
super(HistDrawn,self).__init__(parent)
self.parent=parent
self.parents = Parents(parent)
self.analysis = analysis
self.sc_to_show = self.analysis.chosenSc
self.list_selected_evaluate_sc = self.analysis.candidateScList
self.paramList = []
self.condList = []
def __init__(self,parent=None):
super(ControlAscertBias,self).__init__(parent)
self.parent=parent
self.fsCoding = getFsEncoding(logLevel=False)
self.createWidgets()
# -*- coding: utf-8 -*-
import sys, codecs
import os.path
import os
sys.path.append((u"/".join(os.getcwd().split('/')[:-1])).encode(getFsEncoding(logLevel=False)))
from project import *
#import time
import unittest
import shutil
from diyabc import Diyabc
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4.QtTest import QTest
from datetime import datetime
from utils.cbgpUtils import log,TeeLogger,getFsEncoding
import output
# pour eviter les popups de notification
output.debug = True
class testDiyabc(unittest.TestCase):
"""
A test class for DIYABC interface
"""
def setUp(self):
"""
set up data used in the tests.
setUp is called before each test function execution.
"""
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from utils.cbgpUtils import log,getFsEncoding,Parents
import variables
from variables import UIPATH
formGenericScenarioSelection,baseGenericScenarioSelection = uic.loadUiType((u"%s/genericScenarioSelection.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class GenericScenarioSelection(formGenericScenarioSelection,baseGenericScenarioSelection):
""" Sélection du scenario dans la cadre d'une analyse de type comparison ou estimate
"""
def __init__(self,nb_sc,label,next_widget,next_title,nb_min_sel,analysis,parent):
super(GenericScenarioSelection,self).__init__(parent)
self.parent=parent
self.parents = Parents(self.parent)
self.analysis = analysis
self.nb_sc = nb_sc
self.nb_min_sel = nb_min_sel
self.next_widget = next_widget
self.next_title = next_title
self.checklist = []
self.createWidgets()
self.ui.selectionLabel.setText(label)
self.ui.analysisTypeLabel.setText(self.next_title)
self.ui.projectDirEdit.setText(self.parents.dir)
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from setupComparisonConfidence import SetupComparisonConfidence
from setupEstimationBias import SetupEstimationBias
from genericScenarioSelection import GenericScenarioSelection
from biasScenarioSelection import BiasNConfidenceScenarioSelection
from confidenceTypeSelection import ConfidenceTypeSelection
from analysis import Analysis
import output
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding, Parents
formDefineNewAnalysis,baseDefineNewAnalysis = uic.loadUiType((u"%s/defineAnalysis.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class DefineNewAnalysis(formDefineNewAnalysis,baseDefineNewAnalysis):
""" écran de définition d'une nouvelle analyse. demande
le type d'analyse souhaitée
Si une analyse est fournie au constructeur, il passe directement à l'étape suivante : edition d'analyse
"""
def __init__(self,parent=None,nbScenario=0,analysis_to_edit=None):
super(DefineNewAnalysis,self).__init__(parent)
self.parent=parent
self.nbScenario = nbScenario
self.nb_sc = nbScenario
self.analysis_to_edit = analysis_to_edit
self.parents = Parents(self.parent)
self.createWidgets()
self.ui.verticalLayout_2.setAlignment(Qt.AlignHCenter)
## @package python_interface.project
# @author Julien Veyssier
#
# @brief Classe mère abstraite de tous les projets
import subprocess,shutil
import os, time, sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
from historicalModel.setHistoricalModel import SetHistoricalModel
from utils.cbgpUtils import log,addLine,getFsEncoding
import variables
from variables import UIPATH
formProject,baseProject = uic.loadUiType((u"%s/Project.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
## @class Project
# @brief Classe mère abstraite de tous les projets
class Project(baseProject,formProject):
""" classe qui représente un projet
par defaut, un projet est considéré comme nouveau, cad que l'affichage est celui d'un projet vierge
pour un projet chargé, on modifie l'affichage en conséquence dans loadFromDir
"""
def __init__(self,name,dir=None,parent=None):
self.parent=parent
self.name=name
self.dir=dir
if self.dir != None :
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.set_condition_ui import Ui_MainWindow
import output,os,shutil,tarfile,sys
import variables
from variables import VERSION,VERSION_DATE,UIPATH
import urllib, urllib2
from utils.cbgpUtils import getLastRevisionDate,getFsEncoding
formBugReport,baseBugReport= uic.loadUiType((u"%s/bugReport.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class BugReport(formBugReport,baseBugReport):
""" Fenetre de definition d'un rapport de bug
"""
def __init__(self,parent=None):
super(BugReport,self).__init__(parent)
self.parent=parent
self.createWidgets()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.cancelButton,SIGNAL("clicked()"),self.close)
QObject.connect(self.ui.validateButton,SIGNAL("clicked()"),self.valid)
self.ui.infoLabel.setText(str(self.ui.infoLabel.text()).replace("CONF","%s"%self.parent.configFile))
self.ui.cancelButton.setShortcut(QKeySequence(Qt.Key_Escape))
from PyQt4 import QtCore, QtGui
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setGenData_ui import Ui_Frame
#from mutationModel.setMutationModelMsatRefTable import SetMutationModelMsatRefTable
#from mutationModel.setMutationModelSequences import SetMutationModelSequences
from summaryStatistics.setSummaryStatisticsMsat import SetSummaryStatisticsMsat
from summaryStatistics.setSummaryStatisticsSeq import SetSummaryStatisticsSeq
from utils.visualizescenario import *
from utils.data import *
from utils.cbgpUtils import log,getFsEncoding,Parents
import variables
from variables import UIPATH
formGenData,baseGenData = uic.loadUiType((u"%s/setGenData.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetGeneticData(formGenData,baseGenData):
""" Frame qui est créée pour faire des groupes de locus,
déterminer leur modèle mutationnel et leur summary statistics
"""
def __init__(self,parent=None):
super(SetGeneticData,self).__init__(parent)
self.parent=parent
self.parents=Parents(self.parent)
# liste des box
self.groupList = []
# dicos de frames indexé par les box
self.setMutation_dico = {}
self.setMutationSeq_dico = {}
self.setSum_dico = {}
def generateBugReport(self):
current_project = str(self.parent.ui.tabWidget.currentWidget())
fsCoding = getFsEncoding(logLevel=False)
fileDial = QFileDialog(self,"Select location of the bug report","%s"%os.path.dirname(str(current_project.dir)))
fileDial.setAcceptMode(QFileDialog.AcceptSave)
fileDial.setLabelText(QFileDialog.Accept,"Save bug report")
fileDial.setLabelText(QFileDialog.FileName,"Bug report name")
ok = (fileDial.exec_() == 1)
if not ok:
return
result = fileDial.selectedFiles()
if len(result) > 0:
path = result[0]
tarname = u"%s"%path
if not tarname.endswith(u".tar.gz"):
tarname += u".tar.gz"
repIntoTar = tarname.split("/")[-1].replace(u".tar.gz","")
# creation du tar
dest = u"%s/bug_report_tmp/"%current_project.dir
if os.path.exists(dest.encode(fsCoding)):
try :
shutil.rmtree(dest.encode(fsCoding))
except :
QMessageBox.information(self,'Fatal Error', "Unable to remove previous bug report temporary directory: \n\n %s\n\n Please go to this folder, delete it and try again to create a bug report." % dest)
os.mkdir(dest.encode(fsCoding))
tar = tarfile.open(tarname.encode(fsCoding),"w:gz")
# copie du header
if self.ui.headerYesRadio.isChecked():
if os.path.exists((os.path.expanduser(u"%s/header.txt"%current_project.dir)).encode(fsCoding)):
tar.add(os.path.expanduser((u"%s/header.txt"%current_project.dir).encode(fsCoding)),u'%s/header.txt'%repIntoTar)
# copie du datafile
if self.ui.dataYesRadio.isChecked():
if os.path.exists(str(current_project.dataFileSource).encode(fsCoding)):
dataFileName = os.path.basename(current_project.dataFileSource)
tar.add(current_project.dataFileSource.encode(fsCoding),u'%s/%s'%(repIntoTar,dataFileName))
# copie du diyabcproject file
if os.path.exists((u"%s/%s.diyabcproject"%(current_project.dir,current_project.name)).encode(fsCoding)):
dataFileName = os.path.basename(u"%s/%s.diyabcproject"%(current_project.dir,current_project.name))
tar.add(current_project.dataFileSource.encode(fsCoding),u'%s/%s'%(repIntoTar,dataFileName))
# copie des logfiles
if os.path.exists(os.path.expanduser((u"%s"%self.parent.logfile)).encode(fsCoding)):
tar.add(os.path.expanduser((u"%s"%self.parent.logfile).encode(fsCoding)),u'%s/logfile.txt'%repIntoTar)
if os.path.exists((u"%s/command.txt"%(current_project.dir)).encode(fsCoding)):
tar.add(os.path.expanduser((u"%s/command.txt"%(current_project.dir)).encode(fsCoding)),u'%s/command.txt'%(repIntoTar))
# config file
if os.path.exists(os.path.expanduser((u"~/.diyabc/config.cfg")).encode(fsCoding)):
tar.add(os.path.expanduser((u"~/.diyabc/config.cfg").encode(fsCoding)),u'%s/config.cfg'%repIntoTar)
# creation de la desc
cause = ""
if self.ui.originInterfRadio.isChecked():
cause = "interface"
else:
cause = "computations"
osname = sys.platform
version_info = VERSION + " " + VERSION_DATE
name = "%s"%self.ui.nameLabel.text()
email = "%s"%self.ui.emailLabel.text()
desc = "%s"%self.ui.descEdit.toPlainText()
descf = open("%sdescription.txt"%dest,'w')
infos= "Name : %s\nEmail : %s\nVersion : %s\nOS : %s\nCause : %s\n\n"%(name,email,version_info,osname,cause)
descf.write(infos.encode('utf-8'))
descf.write(desc.encode('utf-8'))
descf.close()
tar.add(os.path.expanduser((u"%sdescription.txt"%dest).encode(fsCoding)),u'%s/description.txt'%repIntoTar)
# les .out
listf = os.listdir((u"%s"%current_project.dir).encode(fsCoding))
for fname in listf:
if fname.startswith("conf."):
tar.add(os.path.expanduser((u"%s/%s"%(current_project.dir,fname)).encode(fsCoding)),u'%s/%s'%(repIntoTar,fname))
if fname.endswith(u".out"):
tar.add(os.path.expanduser((u"%s/%s"%(current_project.dir,fname)).encode(fsCoding)),u'%s/%s'%(repIntoTar,fname))
tar.close()
shutil.rmtree(dest.encode(fsCoding))
output.notify(self,"Thank you","Thank you for creating a bug report : %s, please send it to the development team : [email protected]"%tarname)
## envoi par http :
#ft = open(tarname,'r')
#ftc = ft.read()
#ft.close()
#url = 'http://privas.dyndns.info/~julien/ff/write.php'
#values = {"file":ftc}
#data = urllib.urlencode(values)
#req = urllib2.Request(url, data)
#try:
# response = urllib2.urlopen(req)
#except Exception as e:
# output.notify(self,"Thank you","Thank you for creating a bug report, please send it to the development team because the sending process went wrong\n\n%s"%str(e).decode("utf-8"))
# self.close()
# return
#the_page = response.read()
#if the_page.strip() == "OK":
# output.notify(self,"Thank you","Thank you for creating a bug report, it was successfully sent to our development team !")
self.close()
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.set_condition_ui import Ui_MainWindow
import variables
from variables import UIPATH
from utils.cbgpUtils import getLastRevisionDate,getFsEncoding
formSetCondition,baseSetCondition= uic.loadUiType((u"%s/setCondition.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetCondition(formSetCondition,baseSetCondition):
""" Fenetre de definition d'une condition
"""
def __init__(self,param,target_list,parent=None):
super(SetCondition,self).__init__(parent)
self.parent=parent
self.param = param
self.target_list = target_list
self.createWidgets()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
self.ui.paramLabel.setText(self.param)
for t in self.target_list:
self.ui.targetComboBox.addItem(t)
QObject.connect(self.ui.cancelButton,SIGNAL("clicked()"),self.close)
QObject.connect(self.ui.validateButton,SIGNAL("clicked()"),self.valid)
# -*- coding: utf-8 -*-
import sys, codecs
from PyQt4 import QtCore, QtGui
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setMutationModelMsat_ui import Ui_Frame
import variables
from variables import UIPATH
from utils.cbgpUtils import getFsEncoding
formSetMutationModelMsat,baseSetMutationModelMsat = uic.loadUiType((u"%s/setMutationModelMsat.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetMutationModelMsat(formSetMutationModelMsat,baseSetMutationModelMsat):
""" définition du modèle mutationnel pour les microsats
"""
def __init__(self,parent=None,box_group=None):
super(SetMutationModelMsat,self).__init__(parent)
self.parent=parent
self.box_group = box_group
self.createWidgets()
def createWidgets(self):
self.ui=self
self.ui.setupUi(self)
QObject.connect(self.ui.exitButton,SIGNAL("clicked()"),self.exit)
QObject.connect(self.ui.clearButton,SIGNAL("clicked()"),self.clear)
QObject.connect(self.ui.okButton,SIGNAL("clicked()"),self.validate)
import re, sys, codecs
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
#from uis.setupEstimationBias_ui import Ui_Frame
from genericScenarioSelection import GenericScenarioSelection
from summaryStatistics.setSummaryStatisticsMsatAnalysis import SetSummaryStatisticsMsatAnalysis
from summaryStatistics.setSummaryStatisticsSeqAnalysis import SetSummaryStatisticsSeqAnalysis
from summaryStatistics.setSummaryStatisticsSnpAnalysis import SetSummaryStatisticsSnpAnalysis
import output
from utils.cbgpUtils import log,getFsEncoding
import variables
from variables import UIPATH
formSetupEstimationBias,baseSetupEstimationBias = uic.loadUiType((u"%s/setupEstimationBias.ui"%UIPATH).encode(getFsEncoding(logLevel=False)))
class SetupEstimationBias(formSetupEstimationBias,baseSetupEstimationBias):
""" dernière étape de définition d'une analyse de type estimation ou bias precision ou model checking
"""
def __init__(self,analysis,parent=None):
super(SetupEstimationBias,self).__init__(parent)
self.parent=parent
self.analysis = analysis
self.scNumList = []
self.dico_values = {}
self.createWidgets()
self.ui.verticalLayout_3.setAlignment(Qt.AlignHCenter)
self.ui.verticalLayout_3.setAlignment(Qt.AlignTop)
self.restoreAnalysisValues()
def __init__(self, parent=None, configfile=None):
super(Preferences, self).__init__(parent, configfile)
self.fsCoding = getFsEncoding(logLevel=False)
f = open((DATAPATH + u"/txt/launch_header_cluster.sh").encode(self.fsCoding), "r")
self.DEFAULT_FIRST_PART_SCRIPT_CLUSTER = f.read()
f.close()
f = open((DATAPATH + u"/txt/launch_body_cluster.sh").encode(self.fsCoding), "r")
self.DEFAULT_SECOND_PART_SCRIPT_CLUSTER = f.read()
f.close()
self.tabColor = {
"green": "#c3ffa6",
"blue": "#7373ff",
"red": "#ffb2a6",
"yellow": "#ffffb2",
"pink": "#ffbff2",
}
# initialisation du combo pour le nombre max de thread
try:
nb_core = multiprocessing.cpu_count()
except Exception as e:
nb_core = 1
log(3, "Impossible to count core number on this computer")
dicoValTxtMaxThread = {}
for i in range(1, nb_core + 1):
dicoValTxtMaxThread[str(i)] = str(i)
dicoValTxtLogLvl = {
"1": "1 : Human actions",
"2": "2 : High level actions (file read, checks)",
"3": "3 : Small actions",
"4": "4 : Details",
}
formats = ["pdf", "svg", "jpg", "png"]
dicoValTxtFormat = {}
for i in formats:
dicoValTxtFormat[i] = i
self.styles = []
for i in QStyleFactory.keys():
self.styles.append(str(i))
default_style = None
if "Cleanlooks" in self.styles:
default_style = "Cleanlooks"
dicoValTxtStyle = {}
for i in self.styles:
dicoValTxtStyle[i] = i
colors = ["default", "white"]
colors.extend(self.tabColor.keys())
dicoValTxtColor = {}
for i in colors:
dicoValTxtColor[i] = i
default_font_family = str(self.parent.app.font().family())
if "linux" in sys.platform:
default_Psize = "10"
default_font_family = "DejaVu Sans"
elif "win" in sys.platform and "darwin" not in sys.platform:
default_Psize = "8"
elif "darwin" in sys.platform:
default_Psize = "12"
BETWEEN_BRACKETS = re.compile("{.*}")
# hashtable contenant les informations des champs
dico_fields = OrderedDict(
[
(
"various",
[
{
"proptype": "check",
"propname": "useDefaultExecutable",
"labelText": "Use default executable",
"defaultState": True,
},
{
"proptype": "pathEdit",
"propname": "execPath",
"labelText": "Path to the executable file",
"default_value": "",
"default_explore_path": "~/",
},
{
"proptype": "combo",
"propname": "maxThread",
"labelText": "Maximum thread number",
"dicoValTxt": dicoValTxtMaxThread,
"l_ordered_val": [str(i) for i in range(1, nb_core + 1)],
"default_value": str(nb_core),
},
{
"proptype": "lineEdit",
"propname": "particleLoopSize",
"labelText": "Particle loop size",
"default_value": "100",
},
{
"proptype": "combo",
"propname": "maxLogLvl",
"labelText": "Maximum log level",
"dicoValTxt": dicoValTxtLogLvl,
"l_ordered_val": ["1", "2", "3", "4"],
"default_value": "3",
},
{
"proptype": "check",
"propname": "activateWhatsThis",
"labelText": "Activate " "what's this" " help functionnality",
"defaultState": True,
"visible": False,
},
{
"proptype": "check",
"propname": "debugWhatsThis",
"labelText": "Show object name in what's this\\n(needs restart)",
"defaultState": True,
"visible": False,
},
{
"proptype": "lineEdit",
"propname": "nbMaxRecent",
"labelText": "Maximum number of memorized recent projects",
"default_value": "20",
},
{
"proptype": "combo",
"propname": "picturesFormat",
"labelText": "Graphics and pictures save format \\n(scenario trees, PCA graphics)",
"dicoValTxt": dicoValTxtFormat,
"l_ordered_val": formats,
"default_value": "pdf",
},
{
"proptype": "lineEdit",
"propname": "lastOpenFolder",
"labelText": "",
"default_value": "~/",
"visibility": invisible,
},
],
),
(
"appearance",
[
{
"proptype": "check",
"propname": "showTrayIcon",
"labelText": "Show tray icon",
"defaultState": False,
},
{
"proptype": "combo",
"propname": "style",
"labelText": "Style",
"dicoValTxt": dicoValTxtStyle,
"l_ordered_val": self.styles,
"default_value": default_style,
},
{
"proptype": "lineEdit",
"propname": "fontFamily",
"labelText": "Application font family\\n(needs restart)",
"default_value": default_font_family,
"visibility": invisible,
},
{
"proptype": "lineEdit",
"propname": "fontSize",
"labelText": "Application point font size\\n(needs restart)",
"default_value": default_Psize,
"visibility": invisible,
},
{
"proptype": "lineEdit",
"propname": "fontStrikeOut",
"labelText": "rien",
"default_value": "False",
"visibility": invisible,
},
{
"proptype": "lineEdit",
"propname": "fontUnderline",
"labelText": "rien",
"default_value": "False",
"visibility": invisible,
},
{
"proptype": "lineEdit",
"propname": "fontBold",
"labelText": "rien",
"default_value": "False",
"visibility": invisible,
},
{
"proptype": "lineEdit",
"propname": "fontItalic",
"labelText": "rien",
"default_value": "False",
"visibility": invisible,
},
{
"proptype": "combo",
"propname": "backgroundColor",
"labelText": "Window background color",
"dicoValTxt": dicoValTxtColor,
"l_ordered_val": colors,
"default_value": "default",
},
],
),
(
"cluster",
[
{
"proptype": "check",
"propname": "useCluster",
"labelText": "Use a cluster (don't check if you don't know what it is)",
"defaultState": False,
},
{
"proptype": "lineEdit",
"propname": "numSimulatedDataSetByJob",
"labelText": "Number of simulations per job (granularity)",
"default_value": "50000",
},
{
"proptype": "lineEdit",
"propname": "coresPerJob",
"labelText": "Number of CPU cores per job",
"default_value": "1",
},
{
"proptype": "lineEdit",
"propname": "maxConcurrentJobs",
"labelText": "Maximum number of jobs running a the same time in the cluster (number of RNG's to generate)",
"default_value": "200",
},
{
"proptype": "lineEdit",
"propname": "seed",
"labelText": "First seed of the random number generators (if set to negative then a random seed will be used)",
"default_value": "-1",
},
{
"proptype": "combo",
"propname": "clusterBinLocation",
"labelText": "The diyabc binary is on :",
"dicoValTxt": {"cluster": "cluster", "local": "local"},
"l_ordered_val": ["cluster", "local"],
"default_value": "cluster",
},
{
"proptype": "lineEdit",
"propname": "diyabcPathCluster",
"labelText": "Absolute path to the diyabc binary on the cluster",
"default_value": "",
},
{
"proptype": "pathEdit",
"propname": "diyabcPathLocal",
"labelText": "Path to the diyabc binary on your computer (local)",
"default_value": "",
},
{
"proptype": "textEdit",
"propname": "scriptMasterFirst",
"labelText": "NOT EDITABLE !\\nFirst part of the script\\n to run on your cluster master node\\n\\n(this first part will be merged\\nwith the second part in order\\nto obtain the launch.sh script)",
"default_value": """\\n""".join(
BETWEEN_BRACKETS.sub("", self.DEFAULT_FIRST_PART_SCRIPT_CLUSTER).splitlines()
),
"visibility": False,
"readOnly": True,
"toBeSaved": False,
},
{
"proptype": "textEdit",
"propname": "scriptMasterLast",
"labelText": "Second part of the script\\nto run on master node\\n\\nModify it in order to fit\\n your cluster scheduler\\n(ask your cluster administrator)",
"default_value": """\\n""".join(self.DEFAULT_SECOND_PART_SCRIPT_CLUSTER.splitlines()),
"visibility": True,
},
],
),
]
)
self.digest(dico_fields)
QObject.connect(self.ui.styleCombo, SIGNAL("currentIndexChanged(QString)"), self.changeStyle)
self.changeStyle(self.ui.styleCombo.currentText())
QObject.connect(self.ui.maxLogLvlCombo, SIGNAL("currentIndexChanged(int)"), self.changeLogLevel)
QObject.connect(
self.ui.backgroundColorCombo, SIGNAL("currentIndexChanged(QString)"), self.changeBackgroundColor
)
self.changeLogLevel(self.ui.maxLogLvlCombo.currentIndex())
QObject.connect(self.ui.useClusterCheck, SIGNAL("toggled(bool)"), self.toggleCluster)
QObject.connect(self.ui.numSimulatedDataSetByJobEdit, SIGNAL("textChanged(QString)"), self.checkClusterValues)
QObject.connect(self.ui.coresPerJobEdit, SIGNAL("textChanged(QString)"), self.checkClusterValues)
QObject.connect(self.ui.maxConcurrentJobsEdit, SIGNAL("textChanged(QString)"), self.checkClusterValues)
QObject.connect(self.ui.seedEdit, SIGNAL("textChanged(QString)"), self.checkClusterValues)
QObject.connect(
self.ui.clusterBinLocationCombo, SIGNAL("currentIndexChanged(QString)"), self.toggleBinClusterPath
)
QObject.connect(self.ui.diyabcPathLocalPathEdit, SIGNAL("textChanged(QString)"), self.checkClusterValues)
QObject.connect(self.ui.useDefaultExecutableCheck, SIGNAL("toggled(bool)"), self.toggleExeSelection)
QObject.connect(self.ui.activateWhatsThisCheck, SIGNAL("toggled(bool)"), self.toggleWtSelection)
QObject.connect(self.ui.showTrayIconCheck, SIGNAL("toggled(bool)"), self.toggleTrayIconCheck)
self.qfd = QFontDialog(self.parent.app.font())
fontButton = QPushButton("Change font options (needs restart)")
self.verticalLayoutScroll_appearance.addWidget(fontButton)
QObject.connect(fontButton, SIGNAL("clicked()"), self.changeFontOptions)
self.updateFont()
self.toggleCluster(self.ui.useClusterCheck.isChecked())
self.toggleBinClusterPath(self.ui.clusterBinLocationCombo.currentText())
self.toggleExeSelection(self.ui.useDefaultExecutableCheck.isChecked())
self.toggleWtSelection(self.ui.activateWhatsThisCheck.isChecked())
self.hist_model = uic.loadUi("%s/historical_preferences_frame.ui" % UIPATH)
self.hist_model.setObjectName("tab_historical")
self.ui.tabWidget.addTab(self.hist_model, "Historical")
self.hist_model.verticalLayout.setAlignment(Qt.AlignTop)
self.mutmodM = SetMutationModelMsat(self)
self.mutmodS = SetMutationModelSequences(self)
self.mutmodM.setObjectName("tab_mmm")
self.mutmodS.setObjectName("tab_mms")
self.ui.tabWidget.addTab(self.mutmodM, "MM Microsats")
self.ui.tabWidget.addTab(self.mutmodS, "MM Sequences")
self.ui.tabWidget.setMovable(True)
self.mutmodM.ui.frame_6.hide()
self.mutmodM.ui.setMutMsLabel.setText("Default values for mutation model of Microsatellites")
self.mutmodS.ui.frame_6.hide()
self.mutmodS.ui.setMutSeqLabel.setText("Default values for mutation model of Sequences")
# gestion du bouton "set default values"
self.ui.defaultPreferencesButton = QPushButton(self.frame_button)
self.ui.defaultPreferencesButton.setText("Reset default values")
self.ui.defaultPreferencesButton.setObjectName("defaultPreferencesButton")
self.ui.bottomButtonsLayout.insertWidget(1, self.ui.defaultPreferencesButton)
QObject.connect(self.ui.defaultPreferencesButton, SIGNAL("clicked()"), self.setDefaultPreferences)
