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)
class Preferences(AutoPreferences):
""" Classe dérivée d'AutoPreferences qui va :
- déclarer la structure des préférences en appelant la méthode 'digest' de la classe mère
- redéfinir savePreferences et loadPreferences pour effectuer les sauvegardes/chargement
non prévus dans la classe mère (projets récents, modèle historique)
- définir les actions à effectuer lors de changement de valeurs des préférences (style, showTrayIcon ...)
- implémenter les fonctions d'accès aux valeurs des préférences (getMaxThreadNumber, getExecutablePath, getClusterExecutablepath ...)
"""
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)
def checkClusterValues(self, Qstr):
numSimulatedDatasetByJob = str(self.ui.numSimulatedDataSetByJobEdit.text()).strip()
if numSimulatedDatasetByJob != "":
try:
numSimulatedDatasetByJob = int(numSimulatedDatasetByJob)
except ValueError:
output.notify(
self,
"Value Error : numSimulatedDatasetByJob",
"Number of simulated data set by job must be a positive integer",
)
coresPerJob = str(self.ui.coresPerJobEdit.text()).strip()
if coresPerJob != "":
try:
coresPerJob = int(coresPerJob)
except ValueError:
output.notify(self, "Value Error : coresPerJob", "Number of cores per job must be a positive integer")
maxConcurrentJobs = str(self.ui.maxConcurrentJobsEdit.text()).strip()
if maxConcurrentJobs != "":
try:
maxConcurrentJobs = int(maxConcurrentJobs)
except ValueError:
output.notify(
self,
"Value Error : maxConcurrentJobs",
"Maximum number of concurrent job running on a cluster must be a positive integer",
)
seed = str(self.ui.seedEdit.text()).strip()
if seed not in ["", "None"]:
try:
seed = int(seed)
except ValueError:
output.notify(self, "Value Error : seed", "seed must be a positive integer or 'None' or blank")
if (self.ui.clusterBinLocationCombo.currentText() == "local") and (
not os.path.exists(self.ui.diyabcPathLocalPathEdit.text())
):
output.notify(
self,
"Value Error : cluster bin path",
"cluster binary not found. \n%s does not exists" % self.ui.diyabcPathLocalPathEdit.text(),
)
def saveTabsOrder(self):
tabconf = ""
for i in range(self.ui.tabWidget.count()):
widg = self.ui.tabWidget.widget(i)
tabconf += str(widg.objectName()).replace("tab_", "") + ","
tabconf = tabconf[:-1]
if not self.config.has_key("appearance"):
self.config["appearance"] = {}
self.config["appearance"]["tabsOrder"] = tabconf
def loadTabOrder(self):
cfg = self.config
if cfg.has_key("appearance") and cfg["appearance"].has_key("tabsOrder"):
tabconf = cfg["appearance"]["tabsOrder"].strip()
for tname in tabconf.split(","):
widg = self.ui.tabWidget.findChild(QWidget, QString("tab_" + tname))
self.ui.tabWidget.removeTab(self.ui.tabWidget.indexOf(widg))
self.ui.tabWidget.addTab(
self.ui.tabWidget.findChild(QWidget, QString("tab_" + tname)),
tname.replace("mmm", "MM Microsats").replace("mms", "MM Sequences"),
)
def getLastFolder(self, name):
res = ""
name_maj = name[0].upper() + name[1:]
exec("res = os.path.expanduser((str(self.ui.last%sFolderEdit.text())).encode(self.fsCoding))" % name_maj)
return res
def setLastFolder(self, name, path):
name_maj = name[0].upper() + name[1:]
exec("self.ui.last%sFolderEdit.setText(path)" % name_maj)
self.savePreferences()
def close(self):
if len(self.parent.project_list) == 0:
self.parent.switchToWelcomeStack()
else:
self.parent.switchToMainStack()
def savePreferences(self):
""" sauve les préférences si elles sont valides
"""
if self.allValid():
self.saveMMM()
self.saveMMS()
self.saveHM()
self.saveRecent()
# self.saveCluster()
self.saveTabsOrder()
super(Preferences, self).savePreferences()
# self.saveCluster()
self.close()
def loadPreferences(self):
""" charge les préférences de l'utilisateur si elles existent
"""
self.loadMMM()
self.loadMMS()
self.loadHM()
self.loadRecent()
self.loadToolBarPosition()
# self.loadCluster()
self.loadTabOrder()
super(Preferences, self).loadPreferences()
self.updateFont()
def setDefaultPreferences(self):
self.parent.setDefaultPreferences()
def changeLogLevel(self, index):
utilsPack.LOG_LEVEL = index + 1
def changeFontSize(self, size):
font = self.parent.app.font()
font.setPointSize(int(size))
self.parent.app.setFont(font)
def changeFontFamily(self, family):
font = self.parent.app.font()
font.setFamily(family)
self.parent.app.setFont(font)
def changeFontOptions(self):
self.qfd.setCurrentFont(self.parent.app.font())
i = self.qfd.exec_()
if i != 0:
font = self.qfd.currentFont()
self.fontFamilyEdit.setText(str(font.family()))
self.fontSizeEdit.setText(str(font.pointSize()))
self.fontStrikeOutEdit.setText(str(font.strikeOut()))
self.fontUnderlineEdit.setText(str(font.underline()))
self.fontBoldEdit.setText(str(font.bold()))
self.fontItalicEdit.setText(str(font.italic()))
self.updateFont(font)
def updateFont(self, font=None):
if font != None:
self.parent.app.setFont(font)
else:
fofo = QFont()
fofo.setFamily(self.fontFamilyEdit.text())
fofo.setPointSize(int(str(self.fontSizeEdit.text())))
fofo.setStrikeOut(str(self.fontStrikeOutEdit.text()) == "True")
fofo.setUnderline(str(self.fontUnderlineEdit.text()) == "True")
fofo.setBold(str(self.fontBoldEdit.text()) == "True")
fofo.setItalic(str(self.fontItalicEdit.text()) == "True")
self.parent.app.setFont(fofo)
def toggleCluster(self, state):
self.ui.numSimulatedDataSetByJobEdit.setDisabled(not state)
self.ui.coresPerJobEdit.setDisabled(not state)
self.ui.maxConcurrentJobsEdit.setDisabled(not state)
self.ui.seedEdit.setDisabled(not state)
# kkpz
self.ui.scriptMasterFirstTextEdit.setDisabled(not state)
self.ui.scriptMasterLastTextEdit.setDisabled(not state)
self.ui.clusterBinLocationCombo.setDisabled(not state)
self.ui.diyabcPathClusterEdit.setDisabled(not state)
self.ui.diyabcPathLocalPathEdit.setDisabled(not state)
def toggleBinClusterPath(self, pathPlace):
if self.ui.clusterBinLocationCombo.currentText() == "cluster":
self.ui.frame_cluster_diyabcPathCluster.show()
self.ui.frame_cluster_diyabcPathLocal.hide()
elif self.ui.clusterBinLocationCombo.currentText() == "local":
self.ui.frame_cluster_diyabcPathCluster.hide()
self.ui.frame_cluster_diyabcPathLocal.show()
else:
raise Exception("Place to find the cluster bin not allowed")
def toggleExeSelection(self, state):
self.ui.execPathBrowseButton.setDisabled(state)
self.ui.execPathPathEdit.setDisabled(state)
def toggleWtSelection(self, state):
self.parent.toggleWt(state)
self.debugWhatsThisCheck.setDisabled(not state)
self.debugWhatsThisCheck.setChecked(False)
def toggleTrayIconCheck(self, state):
self.parent.systrayHandler.toggleTrayIcon(state)
def getMaxThreadNumber(self):
return int(self.ui.maxThreadCombo.currentText())
def getExecutablePath(self):
exPath = ""
if self.ui.useDefaultExecutableCheck.isChecked():
# LINUX
if "linux" in sys.platform:
if "86" in platform.machine() and "64" not in platform.machine():
exPath = "%s/bin/diyabc-comput-linux-i386" % DATAPATH
else:
exPath = "%s/bin/diyabc-comput-linux-x64" % DATAPATH
# si on a le paquet deb installé et qu'aucun binaire n'est dans le datapath
if (
os.path.exists(u"/usr/bin/diyabc".encode(self.fsCoding))
and not os.path.exists((u"%s/bin/diyabc-comput-linux-x64" % DATAPATH).encode(self.fsCoding))
and not os.path.exists((u"%s/bin/diyabc-comput-linux-i386" % DATAPATH).encode(self.fsCoding))
):
exPath = "/usr/bin/diyabc"
# WINDOWS
elif "win" in sys.platform and "darwin" not in sys.platform:
if os.environ.has_key("PROCESSOR_ARCHITECTURE") and "86" not in os.environ["PROCESSOR_ARCHITECTURE"]:
exPath = "%s\\bin\diyabc-comput-win-x64" % DATAPATH.replace("/", "\\")
else:
exPath = "%s\\bin\diyabc-comput-win-i386" % DATAPATH.replace("/", "\\")
# MACOS
elif "darwin" in sys.platform:
if "86" in platform.machine() and "64" not in platform.machine():
exPath = os.path.join(DATAPATH, "bin/diyabc-comput-mac-i386")
else:
exPath = os.path.join(DATAPATH, "bin/diyabc-comput-mac-x64")
else:
if not os.path.exists(str(self.ui.execPathPathEdit.text()).encode(self.fsCoding)):
output.notify(
self,
"executable not found",
"The executable set in DIYABC settings cannot be found\n%s\n\If, and only if, 'use default executable' is checked, then this is a bug. We apologize !\n Please send us a b!ug report.\n\n Next, check if no analysis or reftable are running and restart diyabc.\nIt should work again."
% self.ui.execPathPathEdit.text(),
)
return ""
return str(self.ui.execPathPathEdit.text())
if not os.path.exists(exPath.encode(self.fsCoding)):
output.notify(
self,
"executable not found",
"The executable set in DIYABC settings cannot be found\n%s\n\If, and only if, 'use default executable' is checked, then this is a bug. We apologize !\n Pleasesend us a bug report.\n\n Next, check if no analysis or reftable are running and restart diyabc.\nIt should work again."
% exPath,
)
return ""
return os.path.abspath(str(exPath).encode(self.fsCoding))
def changeBackgroundColor(self, colorstr):
if str(colorstr) in self.tabColor.keys():
self.parent.setStyleSheet("background-color: %s;" % self.tabColor[str(colorstr)])
elif colorstr == "default":
output.notify(self, "advice", "Restart DIYABC in order to load the default color scheme")
else:
self.parent.setStyleSheet("background-color: %s;" % colorstr)
def changeStyle(self, stylestr):
""" change le style de l'application (toutes les fenêtres)
"""
self.parent.app.setStyle(str(stylestr))
def saveToolBarPosition(self, pos):
if pos == Qt.LeftToolBarArea:
c = 1
elif pos == Qt.RightToolBarArea:
c = 2
elif pos == Qt.TopToolBarArea:
c = 3
elif pos == Qt.BottomToolBarArea:
c = 4
if not self.config.has_key("various"):
self.config["various"] = {}
self.config["various"]["toolBarOrientation"] = c
def loadToolBarPosition(self):
cfg = self.config
if cfg.has_key("various") and cfg["various"].has_key("toolBarOrientation"):
c = cfg["various"]["toolBarOrientation"].strip()
if c == "1":
self.parent.setToolBarPosition(Qt.LeftToolBarArea)
elif c == "2":
self.parent.setToolBarPosition(Qt.RightToolBarArea)
elif c == "3":
self.parent.setToolBarPosition(Qt.TopToolBarArea)
elif c == "4":
self.parent.setToolBarPosition(Qt.BottomToolBarArea)
def loadRecent(self):
recent_list = []
if self.config.has_key("recent") and self.config["recent"].has_key("projectPathList"):
log(3, "Loading recent list")
for rec in self.config["recent"]["projectPathList"].split("\n"):
if len(rec) > 0 and rec.strip() != "":
recent_list.append(rec.strip())
log(4, "Loading recent : %s" % rec.strip())
self.parent.setRecent(recent_list)
def getMaxRecentNumber(self):
return int(str(self.ui.nbMaxRecentEdit.text()))
def saveRecent(self):
log(3, "Saving recent list")
if not self.config.has_key("recent"):
self.config["recent"] = {}
recList = self.parent.getRecent()
cfgRecentIndex = 0
rec_cfg = ""
for rec in recList:
log(4, "Saving into recent list : %s" % rec)
rec_cfg += "{0}\n".format(rec)
# delete last '\n'
rec_cfg = rec_cfg[:-1]
self.config["recent"]["projectPathList"] = rec_cfg
def saveMMM(self):
""" sauvegarde de la partie mutation model microsats des préférences
"""
if not self.config.has_key("mutation_m_default_values"):
self.config["mutation_m_default_values"] = {}
lines = self.mutmodM.getMutationConf()
for l in lines.strip().split("\n"):
ll = l.strip()
if ll != "":
ti = ll.split()[0]
law = ll.split()[1].split("[")[0]
zero = ll.split("[")[1].split(",")[0]
one = ll.split(",")[1]
two = ll.split(",")[2]
three = ll.split(",")[3].split("]")[0]
for f in ["law", "zero", "one", "two", "three"]:
exec("self.config['mutation_m_default_values'][ti+'_{0}'] = {0}".format(f))
def loadMMM(self):
""" chargement de la partie mutation model microsats des préférences
"""
lines = []
dico = {}
cfg = self.config
if cfg.has_key("mutation_m_default_values"):
try:
for param in ["MEANMU", "GAMMU", "MEANP", "GAMP", "MEANSNI", "GAMSNI"]:
exec(
'lines.append("{0} %s[%s,%s,%s,%s]"%(cfg["mutation_m_default_values"]["{0}_law"],cfg["mutation_m_default_values"]["{0}_zero"],cfg["mutation_m_default_values"]["{0}_one"],cfg["mutation_m_default_values"]["{0}_two"],cfg["mutation_m_default_values"]["{0}_three"]))'.format(
param
)
)
self.mutmodM.setMutationConf(lines)
except Exception as e:
log(3, "Malformed mutation_m_default_values in configuration")
else:
log(3, "No MMM conf found")
def saveMMS(self):
""" sauvegarde de la partie mutation model sequences des préférences
"""
if not self.config.has_key("mutation_s_default_values"):
self.config["mutation_s_default_values"] = {}
lines = self.mutmodS.getMutationConf()
for l in lines.strip().split("\n"):
ll = l.strip()
if ll != "":
ti = ll.split()[0]
if ti == "MODEL":
model = ll.split()[1]
inv_sites_pc = ll.split()[2]
gamma_shape = ll.split()[3]
for f in ["model", "inv_sites_pc", "gamma_shape"]:
exec("self.config['mutation_s_default_values'][ti+'_{0}'] = {0}".format(f))
else:
law = ll.split()[1].split("[")[0]
zero = ll.split("[")[1].split(",")[0]
one = ll.split(",")[1]
two = ll.split(",")[2]
three = ll.split(",")[3].split("]")[0]
for f in ["law", "zero", "one", "two", "three"]:
exec("self.config['mutation_s_default_values'][ti+'_{0}'] = {0}".format(f))
def loadMMS(self):
""" chargement de la partie mutation model sequences des préférences
"""
lines = []
cfg = self.config
if cfg.has_key("mutation_s_default_values"):
try:
for param in ["MEANMU", "GAMMU", "MEANK1", "GAMK1", "MEANK2", "GAMK2"]:
exec(
'lines.append("{0} %s[%s,%s,%s,%s]"%(cfg["mutation_s_default_values"]["{0}_law"],cfg["mutation_s_default_values"]["{0}_zero"],cfg["mutation_s_default_values"]["{0}_one"],cfg["mutation_s_default_values"]["{0}_two"],cfg["mutation_s_default_values"]["{0}_three"]))'.format(
param
)
)
lines.append(
"MODEL %s %s %s"
% (
cfg["mutation_s_default_values"]["MODEL_model"],
cfg["mutation_s_default_values"]["MODEL_inv_sites_pc"],
cfg["mutation_s_default_values"]["MODEL_gamma_shape"],
)
)
self.mutmodS.setMutationConf(lines)
except Exception as e:
log(3, "Malformed mutation_s_default_values in configuration")
else:
log(3, "No MMS conf found")
def saveHM(self):
""" sauvegarde de la partie historical model des préférences
"""
if not self.config.has_key("hist_model_default_values"):
self.config["hist_model_default_values"] = {}
for type_letter in ["n", "t", "a"]:
for law_name in ["UN", "LU", "NO", "LN"]:
exec(
"if self.hist_model.{0}{1}Radio.isChecked(): {2}law = '{1}'".format(
type_letter.upper(), law_name, type_letter
)
)
toSave = {}
for key in [
"nmin",
"nmax",
"nmean",
"nstdev",
"tmin",
"tmax",
"tmean",
"tstdev",
"amin",
"amax",
"amean",
"astdev",
]:
editname = key[0].upper() + key[1:]
exec('toSave["%s"] = float(self.hist_model.%sEdit.text())' % (key, editname))
toSave["nlaw"] = nlaw
toSave["tlaw"] = tlaw
toSave["alaw"] = alaw
for k in toSave:
self.config["hist_model_default_values"][k] = toSave[k]
def loadHM(self):
""" chargement de la partie historical model des préférences
"""
cfg = self.config
if cfg.has_key("hist_model_default_values"):
dico_val = {}
pairs = cfg["hist_model_default_values"].items()
for p in pairs:
dico_val[p[0]] = p[1]
try:
for key in [
"nmin",
"nmax",
"nmean",
"nstdev",
"tmin",
"tmax",
"tmean",
"tstdev",
"amin",
"amax",
"amean",
"astdev",
]:
editname = key[0].upper() + key[1:]
exec('self.hist_model.%sEdit.setText(str(dico_val["%s"]))' % (editname, key))
for pair in [
("nlaw", "UN"),
("nlaw", "LN"),
("nlaw", "NO"),
("nlaw", "LU"),
("alaw", "UN"),
("alaw", "LN"),
("alaw", "NO"),
("alaw", "LU"),
("tlaw", "UN"),
("tlaw", "LN"),
("tlaw", "NO"),
("tlaw", "LU"),
]:
exec(
'if dico_val["%s"] == "%s": self.hist_model.%sRadio.setChecked(True)'
% (pair[0], pair[1], pair[0][0].upper() + pair[1])
)
except Exception as e:
log(3, "Malformed hist_model_default_values section in configuration\n\n%s" % e)
else:
log(3, "No hist conf found")
