class ShortcutConfig(QWidget): # {{{
changed_signal = pyqtSignal()
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self._layout = l = QGridLayout()
self.setLayout(self._layout)
self.header = QLabel(_('Double click on any entry to change the'
' keyboard shortcuts associated with it'))
l.addWidget(self.header, 0, 0, 1, 3)
self.view = QTreeView(self)
self.view.setAlternatingRowColors(True)
self.view.setHeaderHidden(True)
self.view.setAnimated(True)
l.addWidget(self.view, 1, 0, 1, 3)
self.delegate = Delegate()
self.view.setItemDelegate(self.delegate)
self.delegate.sizeHintChanged.connect(self.editor_opened,
type=Qt.QueuedConnection)
self.delegate.changed_signal.connect(self.changed_signal)
self.search = SearchBox2(self)
self.search.initialize('shortcuts_search_history',
help_text=_('Search for a shortcut by name'))
self.search.search.connect(self.find)
l.addWidget(self.search, 2, 0, 1, 1)
self.nb = QPushButton(QIcon(I('arrow-down.png')), _('&Next'), self)
self.pb = QPushButton(QIcon(I('arrow-up.png')), _('&Previous'), self)
self.nb.clicked.connect(self.find_next)
self.pb.clicked.connect(self.find_previous)
l.addWidget(self.nb, 2, 1, 1, 1)
l.addWidget(self.pb, 2, 2, 1, 1)
l.setColumnStretch(0, 100)
def restore_defaults(self):
self._model.restore_defaults()
self.changed_signal.emit()
def commit(self):
if self.view.state() == self.view.EditingState:
self.delegate.accept_changes()
self._model.commit()
def initialize(self, keyboard):
self._model = ConfigModel(keyboard, parent=self)
self.view.setModel(self._model)
def editor_opened(self, index):
self.view.scrollTo(index, self.view.EnsureVisible)
@property
def is_editing(self):
return self.view.state() == self.view.EditingState
def find(self, query):
if not query:
return
try:
idx = self._model.find(query)
except ParseException:
self.search.search_done(False)
return
self.search.search_done(True)
if not idx.isValid():
info_dialog(self, _('No matches'),
_('Could not find any shortcuts matching %s')%query,
show=True, show_copy_button=False)
return
self.highlight_index(idx)
def highlight_index(self, idx):
self.view.scrollTo(idx)
self.view.selectionModel().select(idx,
self.view.selectionModel().ClearAndSelect)
self.view.setCurrentIndex(idx)
self.view.setFocus(Qt.OtherFocusReason)
def find_next(self, *args):
idx = self.view.currentIndex()
if not idx.isValid():
idx = self._model.index(0, 0)
idx = self._model.find_next(idx,
unicode(self.search.currentText()))
self.highlight_index(idx)
def find_previous(self, *args):
idx = self.view.currentIndex()
if not idx.isValid():
idx = self._model.index(0, 0)
idx = self._model.find_next(idx,
unicode(self.search.currentText()), backwards=True)
self.highlight_index(idx)
def highlight_group(self, group_name):
idx = self.view.model().index_for_group(group_name)
if idx is not None:
self.view.expand(idx)
self.view.scrollTo(idx, self.view.PositionAtTop)
self.view.selectionModel().select(idx,
self.view.selectionModel().ClearAndSelect)
self.view.setCurrentIndex(idx)
self.view.setFocus(Qt.OtherFocusReason)
class ShortcutConfig(QWidget): # {{{
changed_signal = pyqtSignal()
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self._layout = l = QVBoxLayout(self)
self.header = QLabel(
_('Double click on any entry to change the'
' keyboard shortcuts associated with it'))
l.addWidget(self.header)
self.view = QTreeView(self)
self.view.setAlternatingRowColors(True)
self.view.setHeaderHidden(True)
self.view.setAnimated(True)
l.addWidget(self.view)
self.delegate = Delegate()
self.view.setItemDelegate(self.delegate)
self.delegate.sizeHintChanged.connect(
self.editor_opened, type=Qt.ConnectionType.QueuedConnection)
self.delegate.changed_signal.connect(self.changed_signal)
self.search = SearchBox2(self)
self.search.initialize('shortcuts_search_history',
help_text=_('Search for a shortcut by name'))
self.search.search.connect(self.find)
self._h = h = QHBoxLayout()
l.addLayout(h)
h.addWidget(self.search)
self.nb = QPushButton(QIcon(I('arrow-down.png')), _('&Next'), self)
self.pb = QPushButton(QIcon(I('arrow-up.png')), _('&Previous'), self)
self.nb.clicked.connect(self.find_next)
self.pb.clicked.connect(self.find_previous)
h.addWidget(self.nb), h.addWidget(self.pb)
h.setStretch(0, 100)
def restore_defaults(self):
self._model.restore_defaults()
self.changed_signal.emit()
def commit(self):
if self.view.state() == self.view.EditingState:
self.delegate.accept_changes()
self._model.commit()
def initialize(self, keyboard):
self._model = ConfigModel(keyboard, parent=self)
self.view.setModel(self._model)
def editor_opened(self, index):
self.view.scrollTo(index, self.view.EnsureVisible)
@property
def is_editing(self):
return self.view.state() == self.view.EditingState
def find(self, query):
if not query:
return
try:
idx = self._model.find(query)
except ParseException:
self.search.search_done(False)
return
self.search.search_done(True)
if not idx.isValid():
info_dialog(self,
_('No matches'),
_('Could not find any shortcuts matching %s') % query,
show=True,
show_copy_button=False)
return
self.highlight_index(idx)
def highlight_index(self, idx):
self.view.scrollTo(idx)
self.view.selectionModel().select(
idx,
self.view.selectionModel().ClearAndSelect)
self.view.setCurrentIndex(idx)
self.view.setFocus(Qt.FocusReason.OtherFocusReason)
def find_next(self, *args):
idx = self.view.currentIndex()
if not idx.isValid():
idx = self._model.index(0, 0)
idx = self._model.find_next(idx,
unicode_type(self.search.currentText()))
self.highlight_index(idx)
def find_previous(self, *args):
idx = self.view.currentIndex()
if not idx.isValid():
idx = self._model.index(0, 0)
idx = self._model.find_next(idx,
unicode_type(self.search.currentText()),
backwards=True)
self.highlight_index(idx)
def highlight_group(self, group_name):
idx = self.view.model().index_for_group(group_name)
if idx is not None:
self.view.expand(idx)
self.view.scrollTo(idx, self.view.PositionAtTop)
self.view.selectionModel().select(
idx,
self.view.selectionModel().ClearAndSelect)
self.view.setCurrentIndex(idx)
self.view.setFocus(Qt.FocusReason.OtherFocusReason)
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)
