def test_task_compress_and_repack_strip_issue19(qtbot, monkeypatch):
"""Same test as above, only tests whether repack and strip logs works"""
path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
path_out = path.with_name("compressed")
path_out.mkdir()
# Monkeypatch
monkeypatch.setattr(QDialog, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([path])
mw.checkBox_repack.setChecked(True)
pouts, invalid = mw.on_task_compress()
assert len(pouts) == 1
assert len(invalid) == 0
with dclab.new_dataset(pouts[0]) as ds, dclab.new_dataset(path) as ds0:
assert len(ds) == len(ds0)
assert len(ds.logs) == 0
scf = list(set(ds.features_scalar + ds0.features_scalar))
for feat in scf:
assert feat in ds0
assert feat in ds
assert np.all(ds[feat] == ds0[feat])
def test_integrity_shapein_issue3(qtbot, monkeypatch):
"""Shape-In did not store the medium correctly
https://github.com/ZELLMECHANIK-DRESDEN/ShapeIn_Issues/issues/3
We don't do anything in this test. We just make sure that
CellCarrierB is set automatically.
"""
h5path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
with h5py.File(h5path, "a") as h5:
h5.attrs["setup:software version"] = "2.2.2.0"
h5.attrs["setup:medium"] = "CellCarrierB"
h5path_m = h5path.with_name("M001_data.rtdc")
h5path.rename(h5path_m)
# Create SoftwareSettings.ini
sinipath = h5path_m.with_name("M001_SoftwareSettings.ini")
sinipath.write_text("Buffer_Medium_ID=0\nBuffer_Medium=CellCarrierB")
# Proceed with loading
path_out = pathlib.Path(h5path_m).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([h5path_m])
assert mw.tableWidget.rowCount() == 1, "sanity check"
# Now edit the medium (create dialog manually)
with pytest.warns(MetadataEditedWarning):
dlg = IntegrityCheckDialog(mw, h5path_m)
assert dlg.get_metadata_value("setup", "medium") == "CellCarrier"
assert "setup" in dlg.user_widgets, "setup section must be there"
assert "medium" in dlg.user_widgets["setup"], "medium must be there"
# finish the dialog
dlg.done(True)
# 1. Get metadata from dict (just to be sure)
dlg2 = IntegrityCheckDialog(mw, h5path_m)
assert dlg2.get_metadata_value("setup", "medium") == "CellCarrier"
# 2. Make sure the combobox is set correctly (just to be sure)
wid2 = dlg2.user_widgets["setup"]["medium"]
assert wid2.currentText() == "CellCarrier"
# 3. Compress and check (just to be sure)
paths_compressed, invalid = mw.on_task_compress()
assert len(invalid) == 0
assert len(paths_compressed) == 1
with dclab.new_dataset(paths_compressed[0]) as ds:
assert ds.config["setup"]["medium"] == "CellCarrier"
def test_integrity_shapein_issue3_control(qtbot, monkeypatch):
"""Shape-In did not store the medium correctly
https://github.com/ZELLMECHANIK-DRESDEN/ShapeIn_Issues/issues/3
With a functional Shape-In version, DCKit should not attempt anything.
"""
h5path = retrieve_data("rtdc_data_hdf5_rtfdc.zip")
with h5py.File(h5path, "a") as h5:
h5.attrs["setup:software version"] = "2.2.3.0" # [sic]
h5.attrs["setup:medium"] = "CellCarrierB"
h5path_m = h5path.with_name("M001_data.rtdc")
# Create SoftwareSettings.ini (should not have any effect, because
# the Shape-In version is expected to be safe.
sinipath = h5path_m.with_name("M001_SoftwareSettings.ini")
sinipath.write_text("Buffer_Medium_ID=0\nBuffer_Medium=CellCarrierB")
h5path.rename(h5path_m)
# Proceed with loading
path_out = pathlib.Path(h5path_m).parent
# Monkeypatch message box to always return OK
monkeypatch.setattr(QMessageBox, "exec_", lambda *args: QMessageBox.Ok)
monkeypatch.setattr(QFileDialog, "getExistingDirectory",
lambda *args: str(path_out))
mw = DCKit(check_update=False)
qtbot.addWidget(mw)
mw.append_paths([h5path_m])
assert mw.tableWidget.rowCount() == 1, "sanity check"
# Now edit the medium (create dialog manually)
dlg = IntegrityCheckDialog(mw, h5path_m)
assert dlg.get_metadata_value("setup", "medium") == "CellCarrierB"
assert "setup" not in dlg.user_widgets, "setup section must not be there"
# finish the dialog
dlg.done(True)
# 1. Get metadata from dict (just to be sure)
dlg2 = IntegrityCheckDialog(mw, h5path_m)
assert dlg2.get_metadata_value("setup", "medium") == "CellCarrierB"
# 2. Compress and check (just to be sure)
paths_compressed, invalid = mw.on_task_compress()
assert len(invalid) == 0
assert len(paths_compressed) == 1
with dclab.new_dataset(paths_compressed[0]) as ds:
assert ds.config["setup"]["medium"] == "CellCarrierB"