def test_settings(qtbot):
widget = sequana_gui.SequanaGUI(ipython=False)
qtbot.addWidget(widget)
widget.read_settings()
#widget.menuHelp()
widget.close()
def test_standalone_generic_with_noconfig_2(qtbot):
"""mimics:
sequanix -s path_to_snakefile
followed by selection of a working directory in the GUI + forceall + run
"""
# From the command line argument
snakefile = sequana_data("test_gui_generic_snakefile_noconfig.rules")
wkdir = TemporaryDirectory()
args = Namespace(snakefile=snakefile)
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
assert widget.mode == "generic"
assert widget.generic_factory.is_runnable() is False
assert widget.ui.run_btn.isEnabled() == False
widget.generic_factory._directory_browser.set_filenames(wkdir.name)
widget.force = True
widget.save_project()
# check that it worked:
widget.snakemake_dialog.ui.snakemake_options_general_forceall_value.setChecked(
True)
widget.click_run()
time.sleep(2)
widget.click_stop()
time.sleep(4)
widget.show_dag()
time.sleep(4)
widget.diag.close()
# in the GUI, we see when it stops. Here, we need to wait a few seconds
time.sleep(5)
def test_others(qtbot, mock):
widget = sequana_gui.SequanaGUI(ipython=True)
qtbot.addWidget(widget)
# level and pipeline attribute
widget.set_level()
assert widget.sequana_factory.pipeline is None
# The repr functions
widget.sequana_factory.__repr__()
widget.generic_factory.__repr__()
# menuQuit
import sequana.gui.messages
mock.patch.object(sequana.gui.messages.WarningMessage,
"exec_",
return_value=QW.QMessageBox.Yes)
widget.menuQuit()
# menu Help and About
import sequana.gui.about
mock.patch.object(sequana.gui.about.About,
"exec_",
return_value=QW.QMessageBox.Ok)
widget.menuAbout()
mock.patch.object(sequana.gui.help.HelpDialog,
"exec_",
return_value=QW.QMessageBox.Ok)
widget.menuHelp()
def test_standalone_generic(qtbot, tmpdir, module):
wkdir = TemporaryDirectory()
# Standalone for generic case given a wkdir and snakefile (no config)
args = Namespace(wkdir=wkdir.name, snakefile=module.snakefile)
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
assert widget.mode == "generic"
def test_progress_bar(qtbot):
widget = sequana_gui.SequanaGUI(ipython=False)
qtbot.addWidget(widget)
widget.click_run() # defines the regex
widget.update_progress_bar("0 of 10 steps ")
widget.update_progress_bar("10 of 10 steps ")
widget.start_progress()
widget.end_run()
def test_open_report(qtbot, tmpdir, module):
p = tmpdir.mkdir("sub").join('test.html')
p.write("hello")
args = Namespace(wkdir=str(p.dirpath()), snakefile=module.snakefile)
# Open a valid HTML file
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
widget.preferences_dialog.ui.preferences_options_general_htmlpage_value.setText(
"test.html")
widget.open_report()
assert widget.browser.isVisible()
widget.close()
# a wrong filename
widget.preferences_dialog.ui.preferences_options_general_htmlpage_value.setText(
"dummy.html")
widget.open_report()
assert widget.browser.isVisible() is False
# Now, we unset the working dir and this should just return without openning
# any report
widget.sequana_factory._directory_browser.set_empty_path()
widget.generic_factory._directory_browser.set_empty_path()
assert widget.working_dir is None
widget.open_report()
assert widget.browser.isVisible() is False
# try using firefox
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
widget.preferences_dialog.ui.preferences_options_general_htmlpage_value.setText(
"test.html")
widget.preferences_dialog.ui.preferences_options_general_browser_value.setCurrentText(
"firefox")
def simple_execute(cmd):
pass
@patch("easydev.execute", side_effects=simple_execute)
def runthis(qtbot):
widget.open_report()
runthis()
def test_generic_copy_nodir(qtbot):
# _copy does not work if directory not set
snakefile = sequana_data("test_gui_generic_snakefile_noconfig.rules")
configfile = sequana_data("test_gui_generic_config.yaml")
args = Namespace(snakefile=snakefile, configfile=configfile)
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
widget.generic_factory._copy_configfile()
widget.generic_factory._copy_snakefile()
def test_standalone_generic_with_config(qtbot, tmpdir, module):
# Standalone for generic case given a wkdir and snakefile (no config)
wkdir = TemporaryDirectory()
args = Namespace(wkdir=wkdir.name,
snakefile=module.snakefile,
configfile=module.config)
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
assert widget.mode == "generic"
assert widget.generic_factory.is_runnable() == True
widget.save_project()
widget.unlock_snakemake()
with TempFile() as fh:
widget.report_issues(fh.name)
def test_standalone_generic_with_config(qtbot, tmpdir):
# Standalone for generic case given a wkdir and snakefile
wkdir = TemporaryDirectory()
args = Namespace(wkdir=wkdir.name,
snakefile=sequana_data("test_generic.rules"),
configfile=sequana_data("test_generic.yaml"))
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
assert widget.mode == "generic"
assert widget.generic_factory.is_runnable() == True
widget.save_project()
# read back.
yaml = SequanaConfig(wkdir.name + "/test_generic.yaml").config
assert yaml['test']["mylist"] == [1, 2, 3]
def test_import_config_from_menu(qtbot):
widget = sequana_gui.SequanaGUI(ipython=True)
qtbot.addWidget(widget)
assert widget.sequana_factory._imported_config is None
# while an existing config file should
# First, we simulate selection of quality control pipeline
index = widget.sequana_factory._choice_button.findText("quality_control")
widget.sequana_factory._choice_button.setCurrentIndex(index)
widget.ui.tabs_pipeline.setCurrentIndex(0) # set sequana pipeline mode
widget._update_sequana("quality_control")
qc = Module("quality_control")
widget.menuImportConfig(qc.config)
assert widget.sequana_factory._imported_config is not None
widget.close()
def test_user_interface_sequana(qtbot):
widget = sequana_gui.SequanaGUI(ipython=False)
qtbot.addWidget(widget)
assert widget.form.count() == 0
# simulate selection of quality control pipeline
index = widget.sequana_factory._choice_button.findText("quality_control")
widget.sequana_factory._choice_button.setCurrentIndex(index)
widget.ui.tabs_pipeline.setCurrentIndex(0) # set sequana pipeline mode
widget._update_sequana("quality_control")
# we should have the focus on the config file now
assert widget.ui.tabs.currentIndex() == 2
assert widget.form.count() == 5
widget.clear_form()
assert widget.form.count() == 0
# select no pipeline
widget._update_sequana('Select a Sequana pipeline')
assert widget.form.count() == 0
def _test_standalone_sequana(qtbot, tmpdir):
wkdir = TemporaryDirectory()
inputdir = os.path.realpath(
sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")).rsplit(os.sep, 1)[0]
# Standalone for sequana given a wkdir and pipeline and input_dir
args = Namespace(pipeline="quality_control",
wkdir=wkdir.name,
input_directory=inputdir)
widget = sequana_gui.SequanaGUI(ipython=False, user_options=args)
qtbot.addWidget(widget)
assert widget.mode == "sequana"
widget.force = True
widget.save_project()
widget.click_run()
count = 0
while widget.process.state() and count < 5:
time.sleep(0.5)
count += 0.5
widget.click_stop()
time.sleep(1)
