def main():
print(str(QStyleFactory.keys()))
app = QApplication(sys.argv)
dark(app)
stylesheet = """
QTableWidget {
background-color: rgb(80, 80, 80);
}
QPushButton {
background-color: rgb(90,70,0);
}
QCheckBox::indicator {
width: 15px;
height: 15px;
margin: 4px;
border-radius: 5px;
border: 3px solid rgb(120,90,0);
}
QCheckBox::indicator::unchecked {
background-color: transparent rgb(80, 80, 80);
}
QCheckBox::indicator::checked {
background-color: rgb(150,120,0);
}
"""
app.setStyleSheet(stylesheet)
window = MainWindow()
window.setWindowFlags(QtCore.Qt.CustomizeWindowHint
| QtCore.Qt.FramelessWindowHint | QtCore.Qt.Tool)
window.move(0, 0)
window.setGeometry(QtCore.QRect(300, 300, 640,
480)) # arbitrary size/location
# sizegrip = QtWidgets.QSizeGrip(window)
# window.horizontalLayout_2.addWidget(sizegrip, 0, QtCore.Qt.AlignBottom | QtCore.Qt.AlignRight)
mw = ModernWindow(window)
mw.show()
# main_window.show()
# main_window.show()
sys.exit(app.exec_())
def nove(proj_path: str):
os.environ["QT_AUTO_SCREEN_SCALE_FACTOR"] = "1"
app = QApplication([])
light(app)
app.setAttribute(Qt.AA_EnableHighDpiScaling)
rect = app.desktop().screenGeometry()
win = Main(proj_path)
area = QScrollArea()
area.setWidget(win)
area.setGeometry(100, 100, int(0.2 * rect.width()),
int(0.8 * rect.height()))
area.setWidgetResizable(True)
modern = ModernWindow(area)
modern.show()
sys.exit(app.exec_())
def __init__(self,
icon=None,
title=None,
text=None,
detailedText=None,
parent=None):
super().__init__(parent)
self.ui = Ui_MessageBox()
self.ui.setupUi(self)
# hide detail elements
self.ui.line.hide()
self.ui.errorDetails.hide()
self.ui.showDetailsBtn.clicked.connect(self.showDetails)
self.ui.okBtn.clicked.connect(self.close)
self.timer = QTimer()
self.detailsShown = False
if icon:
# requires QStyle.SP_MessageBox type of icon
self.setIcon(icon)
if title:
self.setWindowTitle(title)
if text:
self.setText(text)
if detailedText:
self.detailsEnabled = True
self.setDetailedText(detailedText)
else:
self.detailsEnabled = False
self.setShowDetailsEnabled(self.detailsEnabled)
self.mw = ModernWindow(self)
self.mw.btnMinimize.setEnabled(False)
self.mw.btnMinimize.setVisible(False)
self.mw.btnMaximize.setVisible(False)
self.mw.btnRestore.setVisible(False)
self.setupEvents()
def show_generate(self):
self.generate = Generate(self)
self.generate.setWindowModality(QtCore.Qt.ApplicationModal)
self.generate_modern = ModernWindow(self.generate)
self.generate_modern.show()
def show_preferences(self):
self.preferences = Preferences(self)
self.modern_pref = ModernWindow(self.preferences)
self.modern_pref.show()
class MainWindow(QMainWindow, Ui_MainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.setupUi(self)
self.label_3.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.SampleSheetCreator_settings = QSettings('vll',
'SampleSheetCreator')
# self.layout = QHBoxLayout(self)
# self.layout.setContentsMargins(0, 0, 0, 0)
# self.grip1 = QSizeGrip(self)
# self.grip2 = QSizeGrip(self)
# self.layout.addWidget(self.grip1, 0, Qt.AlignLeft | Qt.AlignTop)
# self.layout.addWidget(self.grip2, 0, Qt.AlignRight | Qt.AlignBottom)
yaml = YAML()
self.yconfig = ""
self.yindices = ""
self.yindices_mod = defaultdict(lambda: defaultdict(dict))
if self.SampleSheetCreator_settings.contains('path_config_file'):
self.path_config_file = self.SampleSheetCreator_settings.value(
'path_config_file', type=str)
if self.path_config_file:
if os.path.exists(self.path_config_file):
self.config_fh = open(self.path_config_file,
encoding="utf-8").read()
self.yconfig = yaml.load(self.config_fh)
print("loaded yconfig")
error_list = []
if self.SampleSheetCreator_settings.contains('path_indices_file'):
self.path_indices_file = self.SampleSheetCreator_settings.value(
'path_indices_file', type=str)
if self.path_config_file:
if os.path.exists(self.path_indices_file):
self.indices_fh = open(self.path_indices_file,
encoding="utf-8").read()
try:
self.yindices = yaml.load(self.indices_fh)
except yaml.constructor.DuplicateKeyError as e:
error_list.append(e)
if self.yindices:
for k, subdict1 in self.yindices.items():
for method, subdict2 in subdict1.items():
for instrument, subdict3 in subdict2.items(
):
for adapter_type, subdict4 in subdict3.items(
):
for set, subdict5 in subdict4.items(
):
if subdict5:
for index_name, value in subdict5.items(
):
try:
x = self.yindices_mod[
method][
instrument][
index_name]
error_list.append(
"duplicate index",
method,
instrument,
index_name)
except KeyError:
self.yindices_mod[
method][instrument][
index_name] = value
print("loaded yindices")
if len(error_list) > 0:
self.show_valerrordialog(error_list)
self.sdata_fields_constr = OrderedDict(
sorted(data_fields.data_fields.items(), key=lambda x: x[1]['c_p']))
self.sdata_fields_ss = OrderedDict(
sorted(data_fields.data_fields.items(),
key=lambda x: x[1]['ss_p']))
self.dateEdit.setDateTime(QtCore.QDateTime.currentDateTime())
max_fields = 0
for k in self.sdata_fields_constr:
if data_fields.data_fields[k]['construct']:
max_fields = data_fields.data_fields[k]['c_p']
self.tableWidget_construct.setColumnCount(max_fields + 1)
self.tableWidget_construct.setRowCount(64)
for r in range(64):
item = QTableWidgetItem()
item.setText(str(r + 1))
item.setTextAlignment(Qt.AlignCenter)
item.setToolTip("Hold down the CTRL key\nto select multiple rows")
self.tableWidget_construct.setVerticalHeaderItem(r, item)
self.tableWidget_construct.setAcceptDrops(True)
header_labels = []
for k in self.sdata_fields_constr:
if data_fields.data_fields[k]['construct']:
cnum = data_fields.data_fields[k]['c_p']
cwidth = data_fields.data_fields[k]['c_w']
self.tableWidget_construct.setColumnWidth(cnum, cwidth)
item = QTableWidgetItem()
item.setText(k)
try:
item.setToolTip(data_fields.data_fields[k]['tooltip'])
except KeyError:
pass
self.tableWidget_construct.setHorizontalHeaderItem(cnum, item)
#header_labels.append(k)
self.tableWidget_construct.horizontalHeader().setStretchLastSection(
True)
# self.tableWidget_construct.setHorizontalHeaderLabels(header_labels)
self.tableWidget_construct.verticalHeader().setMinimumWidth(30)
for row in range(64):
chk_bx = QCheckBox()
cell_widget = QWidget()
chk_bx.setCheckState(Qt.Unchecked)
lay_out = QHBoxLayout(cell_widget)
lay_out.addWidget(chk_bx)
lay_out.setAlignment(Qt.AlignCenter)
lay_out.setContentsMargins(0, 0, 0, 0)
cell_widget.setLayout(lay_out)
self.tableWidget_construct.setCellWidget(row, 0, cell_widget)
self.tableWidget_I5.horizontalHeader().setStretchLastSection(True)
self.tableWidget_I7.horizontalHeader().setStretchLastSection(True)
self.setWindowTitle("SampleSheetCreator v.0.3.8")
self.setWindowIcon(QtGui.QIcon('icons/icon.png'))
self.actionPreferences.triggered.connect(self.show_preferences)
self.comboBox_method.activated.connect(self.comboBox_method_activated)
self.comboBox_panel.activated.connect(self.comboBox_panel_activated)
self.comboBox_definition.activated.connect(
self.comboBox_definition_activated)
self.comboBox_P7.activated.connect(self.comboBox_P7_activated)
self.comboBox_P5.activated.connect(self.comboBox_P5_activated)
self.dateEdit.dateChanged.connect(self.onDateChanged)
self.pushButton_pasteall.clicked.connect(self.buttonClickedPasteAll)
self.pushButton_generate.clicked.connect(self.validateTable)
QApplication.clipboard().dataChanged.connect(self.clipboardChanged)
self.checkBox.stateChanged.connect(self.toggle_activated)
if self.yconfig and self.yindices:
self.populate_all()
self.toggle_activated()
self.clip = QApplication.clipboard()
def comboBox_method_activated(self, index):
self.populate_lineEdit_run()
self.populate_lineEdit_path()
self.populate_comboBox_P5()
self.populate_comboBox_P7()
self.populate_comboBox_panel()
self.populate_comboBox_definition()
self.populate_comboBox_analysis()
return 1
def comboBox_panel_activated(self, index):
self.populate_comboBox_definition()
self.populate_comboBox_analysis()
return 1
def comboBox_P5_activated(self, index):
self.populate_tableWidget_I5()
return 1
def comboBox_P7_activated(self, index):
self.populate_tableWidget_I7()
return 1
def comboBox_definition_activated(self, index):
self.populate_comboBox_analysis()
return 1
def onDateChanged(self):
self.populate_lineEdit_run()
return 1
def populate_comboBox_investigator(self):
investigators_list = self.SampleSheetCreator_settings.value(
'investigators', type=list)
self.comboBox_investigator.clear()
self.comboBox_investigator.addItems(investigators_list)
def populate_comboBox_instrument(self):
if self.path_config_file and self.path_indices_file:
instrument = self.yconfig['Instrument']
self.comboBox_instrument.clear()
self.comboBox_instrument.addItems(instrument)
return 1
def populate_comboBox_method(self):
methods = list(self.yconfig['Methods'])
self.comboBox_method.clear()
self.comboBox_method.addItems(methods)
return 1
def populate_lineEdit_run(self):
cmethod = self.comboBox_method.currentText()
tmp_date = self.dateEdit.date()
date_var = tmp_date.toPyDate()
run_label = str(date_var) + "_" + str(cmethod)
self.lineEdit_run.setText(run_label)
return 1
def populate_lineEdit_reads(self):
cmethod = self.comboBox_method.currentText()
reads = self.yconfig['Methods'][cmethod]['Settings']['Reads']
self.lineEdit_reads.setText(str(reads))
return 1
def populate_lineEdit_manifest(self):
cmethod = self.comboBox_method.currentText()
cpanel = self.comboBox_panel.currentText()
manifests = self.yconfig['Methods'][cmethod]['Panels'][cpanel][
'Manifests']
jmanifests = " ".join(manifests)
self.lineEdit_manifest.setText(str(jmanifests))
return 1
def populate_lineEdit_adapter(self):
cmethod = self.comboBox_method.currentText()
adapter = self.yconfig['Methods'][cmethod]['Settings']['Adapter']
self.lineEdit_adapter.setText(str(adapter))
return 1
def populate_lineEdit_path(self):
cmethod = self.comboBox_method.currentText()
tmp_date = self.dateEdit.date()
date_var = tmp_date.toPyDate()
run_label = str(date_var) + "_" + cmethod
path_samplesheets_folder = self.SampleSheetCreator_settings.value(
'path_samplesheets_folder', type=str)
path = os.path.join(path_samplesheets_folder, run_label)
self.lineEdit_path.setText(path)
self.lineEdit_path.setToolTip(path)
return 1
def populate_comboBox_P5(self):
cmethod = self.comboBox_method.currentText()
cinstrument = self.comboBox_instrument.currentText()
if self.path_indices_file:
p5sets = list(self.yindices['Indices'][cmethod][cinstrument]['P5'])
self.comboBox_P5.clear()
self.comboBox_P5.addItems(p5sets)
cP5set = self.comboBox_P5.currentText()
if self.yindices['Indices'][cmethod][cinstrument]['P5'][cP5set]:
p5inds = list(self.yindices['Indices'][cmethod][cinstrument]
['P5'][cP5set])
lenp5inds = len(p5inds)
self.tableWidget_I5.setColumnCount(1)
self.tableWidget_I5.setRowCount(lenp5inds)
for index, item in enumerate(p5inds):
self.tableWidget_I5.setItem(index, 0,
QTableWidgetItem(item.strip()))
self.populate_tableWidget_I5()
else:
self.tableWidget_I5.clear()
return 1
def populate_comboBox_P7(self):
cmethod = self.comboBox_method.currentText()
cinstrument = self.comboBox_instrument.currentText()
p7sets = list(self.yindices['Indices'][cmethod][cinstrument]['P7'])
self.comboBox_P7.clear()
self.comboBox_P7.addItems(p7sets)
cP7set = self.comboBox_P7.currentText()
p7inds = list(
self.yindices['Indices'][cmethod][cinstrument]['P7'][cP7set])
lenp7inds = len(p7inds)
self.tableWidget_I7.setColumnCount(1)
self.tableWidget_I7.setRowCount(lenp7inds)
for index, item in enumerate(p7inds):
self.tableWidget_I7.setItem(index, 0,
QTableWidgetItem(item.strip()))
self.populate_tableWidget_I7()
return 1
def populate_tableWidget_I5(self):
cmethod = self.comboBox_method.currentText()
cinstrument = self.comboBox_instrument.currentText()
if self.path_indices_file:
cP5set = self.comboBox_P5.currentText()
if self.yindices['Indices'][cmethod][cinstrument]['P5'][cP5set]:
p5inds = list(self.yindices['Indices'][cmethod][cinstrument]
['P5'][cP5set])
lenp5inds = len(p5inds)
self.tableWidget_I5.setColumnCount(1)
self.tableWidget_I5.setRowCount(lenp5inds)
for index, item in enumerate(p5inds):
self.tableWidget_I5.setItem(index, 0,
QTableWidgetItem(item.strip()))
else:
self.tableWidget_I5.clear()
return 1
def populate_tableWidget_I7(self):
cmethod = self.comboBox_method.currentText()
cinstrument = self.comboBox_instrument.currentText()
if self.path_indices_file:
cP7set = self.comboBox_P7.currentText()
p7inds = list(
self.yindices['Indices'][cmethod][cinstrument]['P7'][cP7set])
lenp7inds = len(p7inds)
self.tableWidget_I7.setColumnCount(1)
self.tableWidget_I7.setRowCount(lenp7inds)
for index, item in enumerate(p7inds):
self.tableWidget_I7.setItem(index, 0,
QTableWidgetItem(item.strip()))
return 1
def populate_comboBox_definition(self):
cmethod = self.comboBox_method.currentText()
cpanel = self.comboBox_panel.currentText()
print(cmethod, cpanel)
defpath = self.yconfig['Methods'][cmethod]['Panels'][cpanel][
'AnalysisDefPathWin']
print(defpath)
files = os.listdir(defpath)
self.comboBox_definition.clear()
self.comboBox_definition.addItems(files)
return 1
def populate_comboBox_panel(self):
cmethod = self.comboBox_method.currentText()
panels = list(self.yconfig['Methods'][cmethod]['Panels'])
self.comboBox_panel.clear()
self.comboBox_panel.addItems(panels)
return 1
def populate_comboBox_analysis(self):
def getanalyses(file):
anals = []
fh = open(file, encoding="utf-8")
for line in fh:
if line.startswith('>'):
l2 = line.strip()
anal = l2[1:]
anals.append(anal)
return anals
cdefinition = self.comboBox_definition.currentText()
cpanel = self.comboBox_panel.currentText()
cmethod = self.comboBox_method.currentText()
defpath = self.yconfig['Methods'][cmethod]['Panels'][cpanel][
'AnalysisDefPathWin']
file = os.path.join(defpath, cdefinition)
analyses = getanalyses(file)
self.comboBox_analysis.clear()
self.comboBox_analysis.addItems(analyses)
return 1
def show_preferences(self):
self.preferences = Preferences(self)
self.modern_pref = ModernWindow(self.preferences)
self.modern_pref.show()
def show_valerrordialog(self, incrows):
d = ValErrDialog()
for i in incrows:
print(i)
d.plainTextEdi_missing_fields.appendPlainText(i)
d.exec_()
def cell_contains_text(self, item):
if item != None:
item_txt = item.text()
if any(chr.isalnum() for chr in item_txt):
return True
else:
return False
else:
return False
def show_generate(self):
self.generate = Generate(self)
self.generate.setWindowModality(QtCore.Qt.ApplicationModal)
self.generate_modern = ModernWindow(self.generate)
self.generate_modern.show()
def validateTable(self):
rows = self.tableWidget_construct.rowCount()
columns = self.tableWidget_construct.columnCount()
required_fields_dict = {}
nonrequired_fields_dict = {}
fields_value_constraints = defaultdict(dict)
nodup_req_fields_dict = defaultdict(dict)
nodup_nonreq_fields_dict = defaultdict(dict)
dup_req_fields_dict = defaultdict(dict)
dup_nonreq_fields_dict = defaultdict(dict)
populated_required_fields_dict = defaultdict(dict)
unpopulated_required_fields_dict = defaultdict(dict)
populated_nonrequired_fields_dict = defaultdict(dict)
unpopulated_nonrequired_fields_dict = defaultdict(dict)
populated_false_value_constrained_fields_dict = defaultdict(dict)
error_log = []
""" structure fields and columns """
for cname, subdict in data_fields.data_fields.items():
if (subdict['c_p'] >= 0
or subdict['combine']) and subdict['required']:
if subdict['combine']:
tmp = subdict['combine'].split(",")
required_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']) + "," + str(
data_fields.data_fields[tmp[1]]['c_p'])
else:
required_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
if not subdict['duplicates_ok']:
if subdict['combine']:
tmp = subdict['combine'].split(",")
nodup_req_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']
) + "," + str(data_fields.data_fields[tmp[1]]['c_p'])
else:
nodup_req_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
if subdict['value_constraints']:
fields_value_constraints[cname]['c_p'] = subdict['c_p']
fields_value_constraints[cname]['constraints'] = subdict[
'value_constraints']
else:
if subdict['combine']:
tmp = subdict['combine'].split(",")
dup_req_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']
) + "," + str(data_fields.data_fields[tmp[1]]['c_p'])
else:
dup_req_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
elif (subdict['c_p'] >= 0
or subdict['combine']) and not subdict['required']:
if subdict['combine']:
tmp = subdict['combine'].split(",")
nonrequired_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']) + "," + str(
data_fields.data_fields[tmp[1]]['c_p'])
else:
nonrequired_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
if not subdict['duplicates_ok']:
if subdict['combine']:
tmp = subdict['combine'].split(",")
nodup_nonreq_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']
) + "," + str(data_fields.data_fields[tmp[1]]['c_p'])
else:
nodup_nonreq_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
else:
if subdict['combine']:
tmp = subdict['combine'].split(",")
dup_nonreq_fields_dict[cname] = str(
data_fields.data_fields[tmp[0]]['c_p']
) + "," + str(data_fields.data_fields[tmp[1]]['c_p'])
else:
dup_nonreq_fields_dict[cname] = str(
data_fields.data_fields[cname]['c_p'])
""" remove spaces from empty cells """
for r in range(rows):
for c in range(columns):
if c != data_fields.data_fields['N']['c_p']:
curr_item = self.tableWidget_construct.item(r, c)
if not self.cell_contains_text(curr_item):
self.tableWidget_construct.setItem(
r, c, QtWidgets.QTableWidgetItem(""))
""" verify that required fields are populated """
for r in range(rows):
for cname in required_fields_dict:
c = required_fields_dict[cname]
c_list = c.split(',')
item_txt_list = []
for tmp_c in c_list:
curr_item = self.tableWidget_construct.item(r, int(tmp_c))
if self.cell_contains_text(curr_item):
item_txt = curr_item.text()
item_txt_list.append(item_txt)
if (len(item_txt_list) > 0):
item_txt_join = ','.join(item_txt_list)
populated_required_fields_dict[r][cname] = item_txt_join
else:
unpopulated_required_fields_dict[r][cname] = 1
for cname in nonrequired_fields_dict:
c = nonrequired_fields_dict[cname]
c_list = c.split(',')
item_txt_list = []
for tmp_c in c_list:
curr_item = self.tableWidget_construct.item(r, int(tmp_c))
if self.cell_contains_text(curr_item):
item_txt = curr_item.text()
item_txt_list.append(item_txt)
if (len(item_txt_list) > 0):
item_txt_join = ','.join(item_txt_list)
populated_nonrequired_fields_dict[r][cname] = item_txt_join
else:
unpopulated_nonrequired_fields_dict[r][cname] = 1
for cname, subdict in fields_value_constraints.items():
c = subdict['c_p']
item_txt_list = []
curr_item = self.tableWidget_construct.item(r, int(c))
if self.cell_contains_text(curr_item):
item_txt = curr_item.text()
item_txt_list.append(item_txt)
if (len(item_txt_list) > 0):
item_txt_join = ','.join(item_txt_list)
accepted_values = subdict['constraints'].split(",")
if item_txt_join not in accepted_values:
populated_false_value_constrained_fields_dict[r][
cname] = item_txt_join
for r in range(rows):
if len(unpopulated_required_fields_dict[r]) > 0 and len(
populated_required_fields_dict[r]) > 0:
unpop_req_list = unpopulated_required_fields_dict[r].keys()
error_log.append(
"Required fields are partially unpopulated in row " +
str(r + 1) + ", fields: [" +
", ".join(str(x) for x in unpop_req_list) + "]")
if len(populated_required_fields_dict[r]) == 0 and len(
populated_nonrequired_fields_dict[r]):
pop_nonreq_list = populated_nonrequired_fields_dict[r].keys()
error_log.append(
"Required fields unpopulated, nonrequired fields populated in row "
+ str(r + 1) + ", fields: [" +
", ".join(str(x) for x in pop_nonreq_list) + "]")
for cname in populated_false_value_constrained_fields_dict[r]:
value = populated_false_value_constrained_fields_dict[r][cname]
error_log.append("Incorrect value-constrained field. Field: " +
cname + ", row: " + str(r + 1) +
", value: [" + str(value) + "]")
for cname, positions in nodup_req_fields_dict.items():
field_values_list = []
for r in range(rows):
c = required_fields_dict[cname]
c_list = c.split(',')
item_txt_list = []
for tmp_c in c_list:
curr_item = self.tableWidget_construct.item(r, int(tmp_c))
if self.cell_contains_text(curr_item):
item_txt = curr_item.text()
item_txt_list.append(item_txt)
if (len(item_txt_list) > 0):
item_txt_join = ','.join(item_txt_list)
field_values_list.append(item_txt_join)
dups = [
item for item, count in Counter(field_values_list).items()
if count > 1
]
if len(dups) > 0:
error_log.append(
"Required field, duplicates not allowed contain duplicate values. Field: "
+ cname + ", values: [" + ", ".join(str(x)
for x in dups) + "]")
for cname, positions in nodup_nonreq_fields_dict.items():
field_values_list = []
for r in range(rows):
c = required_fields_dict[cname]
c_list = c.split(',')
item_txt_list = []
for tmp_c in c_list:
curr_item = self.tableWidget_construct.item(r, int(tmp_c))
if self.cell_contains_text(curr_item):
item_txt = curr_item.text()
item_txt_list.append(item_txt)
if (len(item_txt_list) > 0):
item_txt_join = ','.join(item_txt_list)
field_values_list.append(item_txt_join)
dups = [
item for item, count in Counter(field_values_list).items()
if count > 1
]
if len(dups) > 0:
error_log.append(
"Nonrequired field, duplicates not allowed contain duplicate values. Field: "
+ cname + ", values: [" + ", ".join(str(x)
for x in dups) + "]")
""" disallow multiple panels in the same batch """
batch2panel = defaultdict(dict)
for r in range(rows):
batch_c = required_fields_dict['Group']
panel_c = required_fields_dict['Panel']
batch_item_list = []
panel_item_list = []
batch_item = self.tableWidget_construct.item(r, int(batch_c))
if self.cell_contains_text(batch_item):
item_txt = batch_item.text()
batch_item_list = item_txt.split(",")
panel_item = self.tableWidget_construct.item(r, int(panel_c))
if self.cell_contains_text(panel_item):
item_txt = panel_item.text()
panel_item_list = item_txt.split(",")
if len(batch_item_list) > 0 and len(panel_item_list) > 0:
for b in batch_item_list:
for p in panel_item_list:
batch2panel[b][p] = 1
for b in batch2panel:
if len(batch2panel[b]) > 1:
panels_list = batch2panel[b].keys()
error_log.append(
"Different panels cannot be analyzed in one batch. Batch "
+ b + ", panels: " + "[" +
", ".join(str(x) for x in panels_list) + "]")
if len(error_log) > 0:
self.show_valerrordialog(error_log)
else:
# print("hej")
self.show_generate()
def keyPressEvent(self, e):
if e.key() == Qt.Key_Delete:
indexes = self.tableWidget_construct.selectionModel(
).selectedIndexes()
for index in indexes:
self.tableWidget_construct.setItem(index.row(), index.column(),
QTableWidgetItem(""))
if e.matches(QtGui.QKeySequence.Paste):
crow = self.tableWidget_construct.currentRow()
ccolumn = self.tableWidget_construct.currentColumn()
if ccolumn > 0:
cb_rows = QApplication.clipboard().text().split('\n')
for rnum, rdat in enumerate(cb_rows):
cb_columns = rdat.split('\t')
for cnum, cdat in enumerate(cb_columns):
paste_row = crow + rnum
paste_column = ccolumn + cnum
self.tableWidget_construct.setItem(
paste_row, paste_column, QTableWidgetItem(cdat))
if e.matches(QtGui.QKeySequence.Copy):
selected = self.tableWidget_construct.selectedRanges()
s = ""
for r in range(selected[0].topRow(), selected[0].bottomRow() + 1):
for c in range(selected[0].leftColumn(),
selected[0].rightColumn() + 1):
try:
s += str(self.tableWidget_construct.item(
r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" #eliminate last '\t'
clip = QApplication.clipboard()
self.clip.setText(s)
def clipboardChanged(self):
text = QApplication.clipboard().text().split('\n')
def buttonClickedPasteAll(self):
indexes = self.tableWidget_construct.selectionModel().selectedRows()
cpanel = self.comboBox_panel.currentText()
canalysis = self.comboBox_analysis.currentText()
canalysisdef = self.comboBox_definition.currentText()
for index in sorted(indexes):
row = index.row()
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Definition']['c_p'],
QTableWidgetItem(canalysisdef))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Panel']['c_p'],
QTableWidgetItem(cpanel))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Analysis']['c_p'],
QTableWidgetItem(canalysis))
def populate_all(self):
self.populate_comboBox_investigator()
self.populate_comboBox_instrument()
self.populate_comboBox_method()
self.populate_comboBox_P5()
self.populate_comboBox_P7()
self.populate_comboBox_panel()
self.populate_comboBox_definition()
self.populate_comboBox_analysis()
self.populate_lineEdit_reads()
self.populate_lineEdit_run()
self.populate_lineEdit_manifest()
self.populate_lineEdit_adapter()
self.populate_lineEdit_path()
self.comboBox_method.setEnabled(True)
self.comboBox_instrument.setEnabled(True)
self.comboBox_instrument.setEnabled(True)
self.dateEdit.setEnabled(True)
self.comboBox_investigator.setEnabled(True)
self.lineEdit_adapter.setEnabled(True)
self.lineEdit_manifest.setEnabled(True)
self.lineEdit_run.setEnabled(True)
self.lineEdit_reads.setEnabled(True)
self.lineEdit_path.setEnabled(True)
self.tableWidget_I5.setEnabled(False)
self.tableWidget_I7.setEnabled(False)
self.comboBox_P5.setEnabled(False)
self.comboBox_P7.setEnabled(False)
self.comboBox_definition.setEnabled(False)
self.comboBox_panel.setEnabled(False)
self.comboBox_analysis.setEnabled(False)
self.pushButton_pasteall.setEnabled(False)
self.plainTextEdit.setEnabled(False)
self.tableWidget_construct.setEnabled(False)
self.pushButton_generate.setEnabled(False)
return 1
def toggle_activated(self):
if self.checkBox.isChecked():
self.comboBox_method.setEnabled(False)
self.lineEdit_adapter.setEnabled(False)
self.lineEdit_manifest.setEnabled(False)
self.lineEdit_run.setEnabled(False)
self.lineEdit_reads.setEnabled(False)
self.lineEdit_path.setEnabled(False)
self.tableWidget_I5.setEnabled(True)
self.tableWidget_I7.setEnabled(True)
self.comboBox_P5.setEnabled(True)
self.comboBox_P7.setEnabled(True)
self.comboBox_definition.setEnabled(True)
self.comboBox_panel.setEnabled(True)
self.comboBox_analysis.setEnabled(True)
self.pushButton_pasteall.setEnabled(True)
self.plainTextEdit.setEnabled(True)
self.tableWidget_construct.setEnabled(True)
self.pushButton_generate.setEnabled(True)
else:
self.comboBox_method.setEnabled(True)
self.lineEdit_adapter.setEnabled(True)
self.lineEdit_manifest.setEnabled(True)
self.lineEdit_run.setEnabled(True)
self.lineEdit_reads.setEnabled(True)
self.lineEdit_path.setEnabled(True)
self.tableWidget_I5.setEnabled(False)
self.tableWidget_I7.setEnabled(False)
self.comboBox_P5.setEnabled(False)
self.comboBox_P7.setEnabled(False)
self.comboBox_definition.setEnabled(False)
self.comboBox_panel.setEnabled(False)
self.comboBox_analysis.setEnabled(False)
self.pushButton_pasteall.setEnabled(False)
self.plainTextEdit.setEnabled(False)
self.tableWidget_construct.setEnabled(False)
self.pushButton_generate.setEnabled(False)
for row in range(64):
self.tableWidget_construct.setItem(
row, data_fields.data_fields['I5_Index_ID']['c_p'],
QTableWidgetItem(""))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['I7_Index_ID']['c_p'],
QTableWidgetItem(""))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Definition']['c_p'],
QTableWidgetItem(""))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Panel']['c_p'],
QTableWidgetItem(""))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Analysis']['c_p'],
QTableWidgetItem(""))
self.tableWidget_construct.setItem(
row, data_fields.data_fields['Method']['c_p'],
QTableWidgetItem(""))
def repopulate(self):
yaml = YAML()
self.yconfig = ""
self.yindices = ""
if self.SampleSheetCreator_settings.contains('path_config_file'):
self.path_config_file = self.SampleSheetCreator_settings.value(
'path_config_file', type=str)
if self.path_config_file:
if os.path.exists(self.path_config_file):
self.config_fh = open(self.path_config_file,
encoding="utf-8").read()
self.yconfig = yaml.load(self.config_fh)
print("reloaded yconfig")
if self.SampleSheetCreator_settings.contains('path_indices_file'):
self.path_indices_file = self.SampleSheetCreator_settings.value(
'path_indices_file', type=str)
if self.path_indices_file:
if os.path.exists(self.path_indices_file):
self.indices_fh = open(self.path_indices_file,
encoding="utf-8").read()
self.yindices = yaml.load(self.indices_fh)
print("reloaded yindices")
self.populate_all()
class MessageBox(QDialog):
def __init__(self,
icon=None,
title=None,
text=None,
detailedText=None,
parent=None):
super().__init__(parent)
self.ui = Ui_MessageBox()
self.ui.setupUi(self)
# hide detail elements
self.ui.line.hide()
self.ui.errorDetails.hide()
self.ui.showDetailsBtn.clicked.connect(self.showDetails)
self.ui.okBtn.clicked.connect(self.close)
self.timer = QTimer()
self.detailsShown = False
if icon:
# requires QStyle.SP_MessageBox type of icon
self.setIcon(icon)
if title:
self.setWindowTitle(title)
if text:
self.setText(text)
if detailedText:
self.detailsEnabled = True
self.setDetailedText(detailedText)
else:
self.detailsEnabled = False
self.setShowDetailsEnabled(self.detailsEnabled)
self.mw = ModernWindow(self)
self.mw.btnMinimize.setEnabled(False)
self.mw.btnMinimize.setVisible(False)
self.mw.btnMaximize.setVisible(False)
self.mw.btnRestore.setVisible(False)
self.setupEvents()
def show(self):
super().show()
self.mw.show()
def showEvent(self, event):
super().showEvent(event)
# keep button from shrinking
if self.detailsEnabled:
self.ui.showDetailsBtn.setMinimumWidth(
self.ui.showDetailsBtn.width())
def close(self):
super().close()
self.mw.close()
def setupEvents(self):
flags = self.mw.windowFlags()
flags |= Qt.WindowStaysOnTopHint
self.mw.setWindowFlags(flags)
# keep focus on messagebox only
self.mw.setWindowModality(Qt.ApplicationModal)
self.mw.layout().setSizeConstraint(QLayout.SetFixedSize)
def setIcon(self, icon):
''' Icon can be any one of these
QStyle::SP_MessageBoxInformation
QStyle::SP_MessageBoxWarning
QStyle::SP_MessageBoxCritical
QStyle::SP_MessageBoxQuestion
'''
icon = self.style().standardIcon(icon).pixmap(96, 96)
self.ui.boxIcon.setPixmap(icon)
def setShowDetailsEnabled(self, flag):
self.detailsEnabled = flag
if flag:
self.ui.showDetailsBtn.show()
else:
self.ui.showDetailsBtn.hide()
self.timer.singleShot(0, lambda: self.mw.resize(0, 0))
def showDetails(self):
if not self.detailsShown:
self.ui.line.show()
self.ui.errorDetails.show()
self.ui.showDetailsBtn.setText('Hide Details...')
self.detailsShown = True
self.timer.singleShot(0, lambda: self.mw.resize(0, 0))
else:
self.ui.errorDetails.hide()
self.ui.line.hide()
self.ui.showDetailsBtn.setText('Show Details...')
self.detailsShown = False
self.timer.singleShot(0, lambda: self.mw.resize(0, 0))
def setText(self, text):
self.ui.message.setText(text)
def setDetailedText(self, text):
self.ui.errorDetails.setPlainText(text)
from PyQt5.QtWidgets import QApplication
from sys import argv as sys_argv, exit as sys_exit
from gui.main import ApplicationWindow
from qtmodern.styles import dark as qtdark
from qtmodern.windows import ModernWindow
if __name__ == '__main__':
app = QApplication(sys_argv)
main = ApplicationWindow()
qtdark(app)
window_main = ModernWindow(main)
window_main.show()
sys_exit(app.exec_())