class OWdictyExpress(OWWidget):
name = "dictyExpress"
description = "Time-course gene expression data"
icon = "../widgets/icons/OWdictyExpress.png"
want_main_area = True
priority = 3
class Inputs:
pass
class Outputs:
etc_data = Output("Data", Table)
class Error(OWWidget.Error):
unreachable_host = Msg('Host not reachable')
invalid_credentials = Msg('Invalid credentials')
username = settings.Setting('')
# password = settings.Setting('')
gene_as_attr_name = settings.Setting(0)
selected_item = settings.Setting(None, schema_only=True)
auto_commit = settings.Setting(False, schema_only=True)
def __init__(self):
super().__init__()
self.res = None
self.organism = '44689'
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.progress_bar = None
# threads
self.threadpool = QThreadPool()
# Login Section
box = gui.widgetBox(self.controlArea, 'Login')
self.namefield = gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"gene_as_attr_name",
["Genes in rows", "Genes in columns"],
callback=self.invalidate)
self.controlArea.layout().addWidget(h_line())
self.refresh_button = gui.button(self.controlArea,
self,
"Refresh",
callback=self.refresh)
self.handle_cache_button(True)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.mainArea.layout().addWidget(h_line())
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.on_selection_changed)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.auth_set()
self.connect()
self.sizeHint()
def sizeHint(self):
return QSize(1400, 680)
def auth_set(self):
self.passfield.setDisabled(not self.username)
def auth_changed(self):
self.auth_set()
self.connect()
def refresh(self):
self.reset()
self.load_experiments()
def reset(self):
self.experimentsWidget.clear() # clear QTreeWidget
self.items = []
# self.lastSelected = None
self.searchString = ""
def search_update(self):
parts = self.searchString.split()
for item in self.items:
item.setHidden(not all(s in item for s in parts))
def progress_advance(self):
# GUI should be updated in main thread. That's why we are calling advance method here
assert threading.current_thread() == threading.main_thread()
if self.progress_bar:
self.progress_bar.advance()
def handle_error(self, ex):
self.progress_bar.finish()
self.setStatusMessage('')
if isinstance(ex, ConnectionError) or isinstance(ex, ValueError):
self.Error.unreachable_host()
print(ex)
def load_experiments_result(self, experiments):
self.load_tree_items(experiments)
self.progress_bar.finish()
self.setStatusMessage('')
def connect(self):
self.res = None
self.Error.clear()
self.reset()
self.handle_cache_button(False)
user, password = resolwe.DEFAULT_EMAIL, resolwe.DEFAULT_PASSWD
if self.username or self.password:
user, password = self.username, self.password
try:
self.res = resolwe.connect(user, password, self.server, 'genesis')
except resolwe.ResolweAuthException:
self.Error.invalid_credentials()
else:
self.load_experiments()
self.handle_cache_button(True)
def load_experiments(self):
if self.res:
# init progress bar
self.progress_bar = gui.ProgressBar(self, iterations=2)
# status message
self.setStatusMessage('downloading experiments')
worker = Worker(self.res.fetch_etc_objects, progress_callback=True)
worker.signals.progress.connect(self.progress_advance)
worker.signals.result.connect(self.load_experiments_result)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def load_tree_items(self, list_of_exp):
self.items = [
CustomTreeItem(self.experimentsWidget, item)
for item in list_of_exp
]
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
self.set_cached_indicator()
self.set_selected()
def set_selected(self):
for item in self.items:
if self.selected_item and item.gen_data_id == self.selected_item:
self.experimentsWidget.setCurrentItem(item)
def on_selection_changed(self):
self.invalidate()
def invalidate(self):
self.commit()
def handle_cache_button(self, handle):
self.refresh_button.setEnabled(handle)
def send_to_output(self, result):
self.progress_bar.finish()
self.setStatusMessage('')
etc_json, table_name = result
# convert to table
data = etc_to_table(etc_json, bool(self.gene_as_attr_name))
# set table name
data.name = table_name
# match genes
gene_matcher = GeneMatcher(str(self.organism))
if not bool(self.gene_as_attr_name):
if 'Gene' in data.domain:
gene_column = data.domain['Gene']
gene_names = data.get_column_view(gene_column)[0]
gene_matcher.genes = gene_names
domain_ids = Domain([], metas=[StringVariable(ENTREZ_ID)])
data_ids = [[str(gene.gene_id) if gene.gene_id else '?']
for gene in gene_matcher.genes]
table_ids = Table(domain_ids, data_ids)
data = Table.concatenate([data, table_ids])
data.attributes[GENE_ID_COLUMN] = ENTREZ_ID
else:
gene_matcher.match_table_attributes(data)
data.attributes[GENE_ID_ATTRIBUTE] = ENTREZ_ID
# add table attributes
data.attributes[TAX_ID] = str(self.organism)
data.attributes[GENE_AS_ATTRIBUTE_NAME] = bool(self.gene_as_attr_name)
# reset cache indicators
self.set_cached_indicator()
# send data to the output signal
self.Outputs.etc_data.send(data)
def commit(self):
self.Error.clear()
selected_item = self.experimentsWidget.currentItem(
) # get selected TreeItem
self.selected_item = selected_item.gen_data_id
if selected_item:
# init progress bar
self.progress_bar = gui.ProgressBar(self, iterations=1)
# status message
self.setStatusMessage('downloading experiment data')
worker = Worker(
self.res.download_etc_data,
selected_item.gen_data_id,
table_name=selected_item.data_name,
progress_callback=True,
)
worker.signals.progress.connect(self.progress_advance)
worker.signals.result.connect(self.send_to_output)
worker.signals.error.connect(self.handle_error)
# move download process to worker thread
self.threadpool.start(worker)
def set_cached_indicator(self):
cached = self.res.get_cached_ids()
for item in self.items:
if item.gen_data_id in cached:
item.setData(0, Qt.DisplayRole, " ")
else:
item.setData(0, Qt.DisplayRole, "")
class OWdictyExpress(OWWidget, ConcurrentWidgetMixin):
name = "dictyExpress"
description = "Time-course gene expression data"
icon = "../widgets/icons/OWdictyExpress.svg"
want_main_area = True
priority = 20
class Inputs:
pass
class Outputs:
etc_data = Output("Data", Table)
class Error(OWWidget.Error):
unreachable_host = Msg('Host not reachable')
invalid_credentials = Msg('Invalid credentials')
gene_as_attr_name = settings.Setting(0)
selected_item = settings.Setting(None, schema_only=True)
auto_commit = settings.Setting(False, schema_only=True)
def __init__(self):
super().__init__()
ConcurrentWidgetMixin.__init__(self)
self._res: Optional[genapi.GenAPI] = None
self.organism = '44689'
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.genapi_pub_auth = {
'url': genapi.DEFAULT_URL,
'username': genapi.DEFAULT_EMAIL,
'password': genapi.DEFAULT_PASSWD,
}
# Login Section
box = gui.widgetBox(self.controlArea, 'Sign in')
self.user_info = gui.label(box, self, '')
self.server_info = gui.label(box, self, '')
box = gui.widgetBox(box, orientation=Qt.Horizontal)
self.sign_in_btn = gui.button(box,
self,
'Sign In',
callback=self.sign_in,
autoDefault=False)
self.sign_out_btn = gui.button(box,
self,
'Sign Out',
callback=self.sign_out,
autoDefault=False)
box = gui.widgetBox(self.controlArea, "Output")
gui.radioButtonsInBox(box,
self,
"gene_as_attr_name",
["Genes in rows", "Genes in columns"],
callback=self.invalidate)
self.clear_cache_btn = gui.button(self.controlArea,
self,
"Clear cache",
autoDefault=False,
callback=self.clear_cache)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.on_selection_changed)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.sign_in(silent=True)
self.sizeHint()
def sizeHint(self):
return QSize(1400, 680)
@property
def res(self):
return self._res
@res.setter
def res(self, value: genapi.GenAPI):
if isinstance(value, genapi.GenAPI):
self._res = value
self.Error.clear()
self.reset()
self.load_experiments()
self.update_user_status()
self.Outputs.etc_data.send(None)
def sign_in(self, silent=False):
dialog = SignIn(self, server_type='genesis')
if silent:
dialog.sign_in()
if dialog.resolwe_instance is not None:
self.res = dialog.resolwe_instance
else:
self.res = connect(**self.genapi_pub_auth,
server_type=resolwe.GENESIS_PLATFORM)
if not silent and dialog.exec_():
self.res = dialog.resolwe_instance
def sign_out(self):
# Remove username and password
cm = get_credential_manager(resolwe.GENESIS_PLATFORM)
del cm.username
del cm.password
# Use public credentials when user signs out
self.res = connect(**self.genapi_pub_auth,
server_type=resolwe.GENESIS_PLATFORM)
def update_user_status(self):
cm = get_credential_manager(resolwe.GENESIS_PLATFORM)
if cm.username:
user_info = f"User: {cm.username}"
self.sign_in_btn.setEnabled(False)
self.sign_out_btn.setEnabled(True)
else:
user_info = 'User: Anonymous'
self.sign_in_btn.setEnabled(True)
self.sign_out_btn.setEnabled(False)
self.user_info.setText(user_info)
self.server_info.setText(f'Server: {self.res._gen.url[8:]}')
def clear_cache(self):
resolwe.GenAPI.clear_cache()
self.reset()
self.load_experiments()
def reset(self):
self.experimentsWidget.clear() # clear QTreeWidget
self.items = []
# self.lastSelected = None
self.searchString = ""
def search_update(self):
parts = self.searchString.split()
for item in self.items:
item.setHidden(not all(s in item for s in parts))
def on_exception(self, ex):
if isinstance(ex, ConnectionError) or isinstance(ex, ValueError):
self.Error.unreachable_host()
print(ex)
def on_done(self, results):
if isinstance(results, list):
self.load_tree_items(results)
elif isinstance(results, tuple):
self.send_to_output(results)
def load_experiments(self):
if self.res:
self.start(self.res.fetch_etc_objects)
def load_tree_items(self, list_of_exp):
self.items = [
CustomTreeItem(self.experimentsWidget, item)
for item in list_of_exp
]
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
self.set_cached_indicator()
self.set_selected()
def set_selected(self):
for item in self.items:
if self.selected_item and item.gen_data_id == self.selected_item:
self.experimentsWidget.setCurrentItem(item)
def on_selection_changed(self):
self.invalidate()
def invalidate(self):
self.commit()
def send_to_output(self, result):
etc_json, table_name = result
# convert to table
data = etc_to_table(etc_json, bool(self.gene_as_attr_name))
# set table name
data.name = table_name
# match genes
gene_matcher = GeneMatcher(str(self.organism))
if not bool(self.gene_as_attr_name):
if 'Gene' in data.domain:
data = gene_matcher.match_table_column(
data, 'Gene', StringVariable(ENTREZ_ID))
data.attributes[GENE_ID_COLUMN] = ENTREZ_ID
else:
data = gene_matcher.match_table_attributes(data)
data.attributes[GENE_ID_ATTRIBUTE] = ENTREZ_ID
# add table attributes
data.attributes[TAX_ID] = str(self.organism)
data.attributes[GENE_AS_ATTRIBUTE_NAME] = bool(self.gene_as_attr_name)
# reset cache indicators
self.set_cached_indicator()
# send data to the output signal
self.Outputs.etc_data.send(data)
def commit(self):
self.Error.clear()
selected_items = self.experimentsWidget.selectedItems(
) # get selected TreeItem
if len(selected_items) < 1:
self.Outputs.etc_data.send(None)
return
selected_item = selected_items[0]
self.selected_item = selected_item.gen_data_id
self.start(self.res.download_etc_data,
selected_item.gen_data_id,
table_name=selected_item.data_name)
def set_cached_indicator(self):
cached = self.res.get_cached_ids()
for item in self.items:
if item.gen_data_id in cached:
item.setData(0, Qt.DisplayRole, " ")
else:
item.setData(0, Qt.DisplayRole, "")
