def update_usb_devices(self):
model = QStandardItemModel()
bus = dbus.SystemBus()
self.iface = 'org.freedesktop.DBus.ObjectManager'
#bus.add_signal_receiver(self.callback_function, signal, iface)
proxy = bus.get_object("org.freedesktop.UDisks2",
"/org/freedesktop/UDisks2")
self.iface = dbus.Interface(proxy, "org.freedesktop.UDisks2")
self.iface.connect_to_signal('DeviceAdded', self.device_added_callback)
self.iface.connect_to_signal('DeviceRemoved',
self.device_removed_callback)
self.iface.connect_to_signal('InterfacesAdded',
self.device_changed_callback)
dev1 = get_usb()
items = get_usb()
#for text, checked in items:
for text in sorted(items):
text_item = QStandardItem(text)
#checked_item = QStandardItem()
#checked_item.setData(QVariant(checked), Qt.CheckStateRole)
model.appendRow(text_item) #([text_item, checked_item])
view = QTreeView()
view.header().hide()
view.setRootIsDecorated(False)
combo = self.ui.comboBox_device
combo.setView(view)
combo.setModel(model)
combo.show()
class Navigation(QWidget):
"""a navigation widget,
displaying all known projects and samples
"""
changed_projects = pyqtSignal(str, str)
changed_allele = pyqtSignal(str, int, str)
change_view = pyqtSignal(int)
refresh = pyqtSignal(str)
def __init__(self, log, settings):
self.log = log
self.settings = settings
super().__init__()
self.init_UI()
self.create_model()
self.tree.expand(self.open_node)
self.tree.clicked.connect(self.onClicked)
self.tree.setContextMenuPolicy(Qt.CustomContextMenu)
self.tree.customContextMenuRequested.connect(self.open_menu)
def init_UI(self):
"""creates the UI
"""
self.log.debug("Setting up Navigation area UI...")
self.tree = QTreeView()
self.tree.doubleClicked.connect(self.onDoubleClick)
self.grid = QGridLayout()
self.setLayout(self.grid)
self.header_lbl = QLabel("Projects and Samples:", self)
self.header_lbl.setStyleSheet(general.label_style_2nd)
self.grid.addWidget(self.header_lbl, 0,0)
self.grid.addWidget(self.tree, 1, 0)
header = self.tree.header()
header.hide()
self.log.debug("\t=> Done!")
def create_model(self):
"""creates or recreates the model
"""
self.log.debug("Updating Navigation area...")
root_node = Node("All")
openNode = Node("Open", root_node)
closedNode = Node("Closed", root_node)
project_nodes = {}
query = """select distinct sample_id_int, projects.project_name, project_status, allele_status, allele_nr
from projects left join alleles
on projects.project_name = alleles.project_name
order by project_status desc, projects.project_name desc, sample_id_int
"""
q = QtSql.QSqlQuery()
q.exec_(query)
while q.next():
sample = q.value(0)
project = q.value(1)
pstatus = q.value(2)
astatus = q.value(3)
nr = q.value(4)
try:
pnode = project_nodes[project]
except KeyError:
if pstatus == "Closed":
topnode = closedNode
else:
topnode = openNode
pnode = Node(project, topnode, "Project")
project_nodes[project] = pnode
if sample:
if nr != 1:
sample = "{} ({})".format(sample, nr)
Node(sample, pnode, "Sample", astatus)
self.model = NavigationModel(root_node)
self.tree.setModel(self.model)
self.open_node = self.model.index(0, 0, QModelIndex())
self.closed_node = self.model.index(1, 0, QModelIndex())
self.root_node = self.open_node.parent()
self.log.debug("\t=> Done!")
@pyqtSlot(str, str)
def expand_project(self, project, status = None):
"""expands the node of the given project,
returns its index and parent-node's index
"""
self.log.debug("Expanding project {} ({})...".format(project, status))
if not status in (None, "Open", "Closed"):
return None, None
myindex = self.open_node
myparent_node = self.open_node
if status == "Open":
self.log.debug("Open")
parent_node = self.open_node
self.tree.expand(parent_node)
self.tree.collapse(self.closed_node)
elif status == "Closed":
self.log.debug("Closed")
parent_node = self.closed_node
self.tree.expand(parent_node)
self.tree.collapse(self.open_node)
else: # figure out whether project is open or closed
self.log.debug("Status unknown...")
try:
for i in range(self.model.rowCount(self.root_node)):
parent_node = self.model.index(i, 0, self.root_node)
status = self.model.data(parent_node, Qt.DisplayRole)
for row in range(self.model.rowCount(parent_node)):
index = self.model.index(row, 0, parent_node)
myproj = self.model.data(index, Qt.DisplayRole)
if myproj == project:
myindex = index
myparent_node = parent_node
self.tree.expand(myindex)
except Exception as E:
self.log.error(E)
self.log.exception(E)
self.select_project(project)
self.log.debug("\t=> project found ({}) and successfully expanded".format(status))
return myindex, myparent_node
@pyqtSlot(QModelIndex)
def onClicked(self, index):
"""emits signals when a project or sample is selected
"""
data = self.model.data(index, Qt.DisplayRole)
nodetype = self.model.nodeType(index)
if nodetype == "Sample":
if ("(") in data:
data = data.split("(")
sample = data[0].strip()
nr = int(data[1].strip()[:-1])
else:
sample = data
nr = 1
project = self.model.data(self.model.parent(index), Qt.DisplayRole)
self.changed_allele.emit(sample, nr, project)
self.log.debug("Navigation emitted 'Allele changed to {} #{} (project {})'".format(sample, nr, project))
elif nodetype == "Project":
status = self.model.data(self.model.parent(index), Qt.DisplayRole)
self.changed_projects.emit(data, status)
self.log.debug("Navigation emitted 'Project changed to {}'".format(data))
@pyqtSlot(QPoint)
def open_menu(self, pos):
"""provides a context menu
"""
index = self.tree.indexAt(pos)
nodetype = self.model.nodeType(index)
self.log.debug("Opening navigation menu...")
if nodetype == "Project":
menu = QMenu()
open_project_act = menu.addAction("Open Project View")
action = menu.exec_(self.tree.mapToGlobal(pos))
if action == open_project_act:
project = self.model.data(index, Qt.DisplayRole)
status = self.model.data(self.model.parent(index), Qt.DisplayRole)
self.changed_projects.emit(project, status)
self.change_view.emit(3)
self.log.debug("Navigation emitted changed_projects & change_view to ProjectView")
elif nodetype == "Sample":
menu = QMenu()
open_sample_act = menu.addAction("Open Sample View")
delete_sample_act = menu.addAction("Delete Allele (admin-only!)")
action = menu.exec_(self.tree.mapToGlobal(pos))
if action:
sample_list = self.model.data(index, Qt.DisplayRole).split()
sample = sample_list[0]
if len(sample_list) > 1:
nr = int(sample_list[1][1:-1])
else:
nr = 1
project = self.model.data(self.model.parent(index), Qt.DisplayRole)
status = self.model.data(self.model.parent(self.model.parent(index)), Qt.DisplayRole)
if action == open_sample_act:
try:
self.changed_allele.emit(sample, nr, project)
self.change_view.emit(4)
self.log.debug("Navigation emitted changed_alleles & change_view to AlleleView")
except Exception as E:
self.log.exception(E)
elif action == delete_sample_act:
self.log.info("Deleting {} #{} of project {}".format(sample, nr, project))
self.delete_sample(sample, nr, project, status)
@pyqtSlot(QModelIndex)
def onDoubleClick(self, index):
"""open SampleView or ProjectView
"""
nodetype = self.model.nodeType(index)
if nodetype == "Project":
project = self.model.data(index, Qt.DisplayRole)
status = self.model.data(self.model.parent(index), Qt.DisplayRole)
self.changed_projects.emit(project, status)
self.change_view.emit(3)
self.log.debug("Navigation emitted changed_projects & change_view to ProjectView")
elif nodetype == "Sample":
sample_list = self.model.data(index, Qt.DisplayRole).split()
sample = sample_list[0]
if len(sample_list) > 1:
nr = int(sample_list[1][1:-1])
else:
nr = 1
project = self.model.data(self.model.parent(index), Qt.DisplayRole)
status = self.model.data(self.model.parent(self.model.parent(index)), Qt.DisplayRole)
self.changed_allele.emit(sample, nr, project)
self.change_view.emit(4)
self.log.debug("Navigation emitted changed_alleles & change_view to AlleleView")
@pyqtSlot(str)
def select_project(self, project):
"""looks for <project> in the tree-model and selects it if found;
selects it and returns its index
"""
for top_node in [self.open_node, self.closed_node]:
index = self.model.findValue(top_node, project)
if index.isValid():
self.tree.setCurrentIndex(index)
return index
return QModelIndex()
@pyqtSlot(str)
def select_sample(self, project, sample, nr):
"""looks for <sample> in <project> in the tree-model and selects it if found;
selects it and returns its index
"""
pindex = self.select_project(project)
if int(nr) > 1:
sample = "{} ({})".format(sample, nr)
index = self.model.findValue(pindex, sample)
if index.isValid():
self.tree.setCurrentIndex(index)
return index
return QModelIndex()
def delete_sample(self, sample, nr, project, status):
"""delete a sample from the database & file system
"""
self.log.debug("Attempting to delete sample '{}' allele {} of project '{}' from database...".format(sample, nr, project))
if self.settings["login"] == "admin":
pass
else:
pwd, ok = QInputDialog.getText(self, "Enter Password", "Please provide password:"******"ichdarfdas":
pass
else:
return
else:
return
self.log.debug("Asking for confirmation before deleting allele...")
reply = QMessageBox.question(self, 'Message',
"Are you really sure you want to delete sample {} allele #{} from project {}?".format(sample, nr, project), QMessageBox.Yes |
QMessageBox.No, QMessageBox.No)
if reply == QMessageBox.Yes:
# delete from database:
delete_q_alleles = "delete from alleles where sample_id_int = '{}' and allele_nr = {} and project_name = '{}'".format(sample, nr, project)
success, _ = db_internal.execute_query(delete_q_alleles, 0, self.log, "Deleting sample {} allele #{} from ALLELES table".format(sample, nr), "Sample Deletion Error", self)
if success:
self.log.debug("\t=> Successfully deleted sample from table ALLELES")
more_projects_query = "select project_name from alleles where sample_id_int = '{}'".format(sample)
success, data = db_internal.execute_query(more_projects_query, 1, self.log, "Finding more rows with sample {} in ALLELES table".format(sample), "Sample Deletion Error", self)
single_allele = False
if success:
if not data: # sample was only contained in this project and only had one allele
single_allele = True
delete_q_samples = "delete from SAMPLES where sample_id_int = '{}'".format(sample)
success, _ = db_internal.execute_query(delete_q_samples, 0, self.log, "Deleting sample {} from SAMPLES table".format(sample), "Sample Deletion Error", self)
if success:
self.log.debug("\t=> Successfully deleted sample from table SAMPLES")
files_q = "select raw_file, fasta, blast_xml, ena_file, ena_response_file, ipd_submission_file from FILES where sample_id_int = '{}' and allele_nr = {}".format(sample, nr)
success, files = db_internal.execute_query(files_q, 6, self.log, "Getting files of sample {} #{} from FILES table".format(sample, nr), "Sample Deletion Error", self)
if success:
delete_q_files = "delete from FILES where sample_id_int = '{}' and allele_nr = {}".format(sample, nr)
success, _ = db_internal.execute_query(delete_q_files, 0, self.log, "Deleting sample {} from FILES table".format(sample), "Sample Deletion Error", self)
if success:
self.log.debug("\t=> Successfully deleted sample from table FILES")
# delete from disk space:
self.log.debug("Attempting to delete sample {} allele #{} of project '{}' from file system...".format(sample, nr, project))
sample_dir = os.path.join(self.settings["projects_dir"], project, sample)
if files:
for myfile in files[0]:
if myfile:
self.log.debug("\tDeleting {}...".format(myfile))
try:
os.remove(os.path.join(sample_dir, myfile))
except Exception:
self.log.debug("\t\t=> Could not delete")
if single_allele:
self.log.debug("\tDeleting sample dir {}...".format(sample_dir))
os.removedirs(sample_dir)
self.log.debug("=> Sample {} #{} of project {} successfully deleted from database and file system".format(sample, nr, project))
self.refresh.emit(project)
self.changed_projects.emit(project, status)
class BookWarriorHomepage ( QWidget,Ui_BookWarriorHomepage):
updateSelection = pyqtSignal()
def __init__ (self,model,parent=None):
super(BookWarriorHomepage,self).__init__(parent)
self.setupUi(self)
self.max_vignettes = 20
self.nb_col = 0
self.nb_row = 0
self.vignettes_liste = []
self.model = model
self.settings = Config().instance.settings
self.list_warrior = [] # utilise pour maj selection depuis warrrior layout
def setLeftPage(self):
self.treeView = QTreeView(self)
self.treeView.setObjectName("treeView")
self.left_page_Layout.addWidget(self.treeView)
self.treeView.activated.connect(self.changeCurrentSet)
self.tree_model = TreeModel(self.model)
self.treeView.setModel(self.tree_model)
self.treeView.setWindowTitle("Simple Tree Model")
self.treeView.header().hide()
self.treeView.setAlternatingRowColors(True)
# i = 0
# self.treeKingdom.setColumnCount(3)
# for faction in self.model.factions.values() :
# item_f = QTreeWidgetItem(self.treeKingdom)
# #self.treeKingdom.insertTopLevelItem(i,item_f)
# item_f.setText(i,faction.name)
# i = i +1
# for empire in faction.empires.values():
# item_e = QTreeWidgetItem()
# item_e.setText(i,empire.name)
# item_f.addChild(item_e)
# for kingdom in empire.kingdoms.values():
# item_k = QTreeWidgetItem()
# item_k.setText(i,kingdom.name)
# item_e.addChild(item_k)
# for groupe in kingdom.groupes.values():
# item_g = QTreeWidgetItem()
# item_g.setText(i,groupe.name)
# print ('groupe',groupe.name)
# item_k.addChild(item_g)
def setRightContent (self, list_warrior):
self.list_warrior = list_warrior
for v in self.vignettes_liste :
v.setParent(None)
self.gridLayout.removeWidget(v)
# while self.gridLayout.takeAt(0) != None :
# del self.gridLayout.takeAt(0).widget
# item = self.gridLayout.takeAt(0)
# print ('ll')
# del item
self.nb_col = 0
self.nb_row = 0
self.vignettes_liste = []
for i in range (min(len(list_warrior),self.max_vignettes)):
self.addVignette(list_warrior[i],i)
def updateContent(self):
pass
def addVignette (self,warrior,i):
widget_vignette = QWidget(self.vignettes)
layout_one_vignette = QVBoxLayout(widget_vignette)
layout_one_vignette.setSpacing(0)
layout_one_vignette.setContentsMargins(0, 0, 0, 0)
warrior_button = QPushButton(widget_vignette)
# on met plus car dans le cas du signal clicked on enverra True ou False (0 ou 1)
warrior_button.setObjectName(str(i+2))
warrior_button.clicked.connect(self.parent().goWarriorPage)
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
warrior_button.setFixedSize(QtCore.QSize(100,120))
warrior_button.setSizePolicy(sizePolicy)
layout_one_vignette.addWidget(warrior_button)
# label
warrior_label = HerosLabel(warrior,widget_vignette)
layout_one_vignette.addWidget(warrior_label)
max_col = 3
groupe_name = warrior.groupe().name
if warrior.masterGroupe() != None :
groupe_name = warrior.masterGroupe().name+"/"+groupe_name
#path = os.path.join(Config().instance.path_to_pic(),faction_name,empire_name,kingdom_name,"Picture",groupe_name,warrior_name
icon = QIcon(warrior.thumb)
#print (basepath+"/"+faction_name+"/"+empire_name+"/"+kingdom_name+"/Picture/"+groupe_name+"/"+warrior.name+"/portrait_thumbnail.jpg")
warrior_button.setIcon(icon)
warrior_button.setIconSize(QtCore.QSize(100,120))
if self.nb_col == 0:
self.nb_row = self.nb_row + 1
self.gridLayout.addWidget(widget_vignette,self.nb_row,self.nb_col)
self.vignettes_liste.append(widget_vignette)
self.nb_col = (self.nb_col +1)%max_col
def changeCurrentSet(self,index):
print ('changecurrentset:')
item = self.tree_model.metadata(index, QtCore.Qt.DecorationRole)
list_warrior = item.getWarriorList()
self.setRightContent(list_warrior)
self.updateSelection.emit()
