Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix flake8 issue raised following the Rocky Linux 9 image upgrade #84

Merged
merged 4 commits into from
Jan 15, 2024
Merged

Fix flake8 issue raised following the Rocky Linux 9 image upgrade #84

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
9412168
Fix flake8 issue raised following the Rocky Linux 9 image upgrade
sbesson Jan 11, 2024
c1c3476
Fix DeprecationWarning and use log.warning
sbesson Jan 12, 2024
11254d1
Add additional assert to test command output
sbesson Jan 12, 2024
cd4f657
Fix the assert by being less sensitive to the logging level
sbesson Jan 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 21 additions & 20 deletions src/omero_metadata/populate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -650,7 +650,7 @@ def resolve_plate(self, column, row, value):
try:
return self.plates_by_name[value].id.val
except KeyError:
log.warn('Screen is missing plate: %s' % value)
log.warning('Screen is missing plate: %s' % value)
return Skip()

def _load(self):
Expand All @@ -673,7 +673,8 @@ def _load(self):
self.plates_by_id = dict()
images_by_id = dict()
self.images_by_id[self.target_object.id.val] = images_by_id
for plate in (l.child for l in self.target_object.copyPlateLinks()):
plates = [link.child for link in self.target_object.copyPlateLinks()]
for plate in plates:
parameters = omero.sys.ParametersI()
parameters.addId(plate.id.val)
plate = query_service.findByQuery((
Expand Down Expand Up @@ -774,10 +775,10 @@ def resolve_roi(self, column, row, value):
try:
return self.rois_by_id[int(value)].id.val
except KeyError:
log.warn('Dataset is missing ROI: %s' % value)
log.warning('Dataset is missing ROI: %s' % value)
return -1
except ValueError:
log.warn('Wrong input type for ROI ID: %s' % value)
log.warning('Wrong input type for ROI ID: %s' % value)
return -1

def resolve_shape(self, value):
Expand All @@ -787,10 +788,10 @@ def resolve_shape(self, value):
try:
return self.shapes_by_id[int(value)].id.val
except KeyError:
log.warn('Dataset is missing Shape: %s' % value)
log.warning('Dataset is missing Shape: %s' % value)
return -1
except ValueError:
log.warn('Wrong input type for Shape ID: %s' % value)
log.warning('Wrong input type for Shape ID: %s' % value)
return -1

def get_image_id_by_name(self, iname, dname=None):
Expand Down Expand Up @@ -900,7 +901,7 @@ def resolve_dataset(self, column, row, value):
else:
return self.datasets_by_name[value].id.val
except KeyError:
log.warn('Project is missing dataset: %s' % value)
log.warning('Project is missing dataset: %s' % value)
return Skip()

def _load(self):
Expand Down Expand Up @@ -982,20 +983,20 @@ def resolve_shape(self, value):
try:
return self.shapes_by_id[int(value)].id.val
except KeyError:
log.warn('Image is missing Shape: %s' % value)
log.warning('Image is missing Shape: %s' % value)
return -1
except ValueError:
log.warn('Wrong input type for Shape ID: %s' % value)
log.warning('Wrong input type for Shape ID: %s' % value)
return -1

def resolve_roi(self, column, row, value):
try:
return self.rois_by_id[int(value)].id.val
except KeyError:
log.warn('Image is missing ROI: %s' % value)
log.warning('Image is missing ROI: %s' % value)
return -1
except ValueError:
log.warn('Wrong input type for ROI ID: %s' % value)
log.warning('Wrong input type for ROI ID: %s' % value)
return -1

def _load(self):
Expand Down Expand Up @@ -1035,7 +1036,7 @@ def _load(self):
rois_by_id[rid] = roi
shapes_by_id[shape.id.val] = shape
if unwrap(roi.name) in rois_by_name.keys():
log.warn('Conflicting ROI names.')
log.warning('Conflicting ROI names.')
self.ambiguous_naming = True
rois_by_name[unwrap(roi.name)] = roi
self.rois_by_id = rois_by_id
Expand Down Expand Up @@ -1153,7 +1154,7 @@ def preprocess_from_handle(self, data):
self.columns = self.header_resolver.create_columns()
log.debug('Columns: %r' % self.columns)
if len(self.columns) > MAX_COLUMN_COUNT:
log.warn("Column count exceeds max column count")
log.warning("Column count exceeds max column count")

self.preprocess_data(reader)

Expand Down Expand Up @@ -1366,7 +1367,7 @@ def post_process(self):
for column in self.columns:
columns_by_name[column.name.lower()] = column
if column.__class__ is PlateColumn:
log.warn("PlateColumn is unimplemented")
log.warning("PlateColumn is unimplemented")
elif column.__class__ is WellColumn:
well_column = column
elif column.name == WELL_NAME_COLUMN:
Expand Down Expand Up @@ -1416,7 +1417,7 @@ def post_process(self):
plate = columns_by_name["plate"].values[i]
v = self.value_resolver.get_well_name(well_id, plate)
except KeyError:
log.warn(
log.warning(
'Skipping table row %d! Missing well row or column '
'for well name population!' % i, exc_info=True
)
Expand Down Expand Up @@ -1444,7 +1445,7 @@ def post_process(self):
iname = self.value_resolver.get_image_name_by_id(
iid, did)
except KeyError:
log.warn(
log.warning(
"%d not found in image ids" % iid)
assert i == len(image_name_column.values)
image_name_column.values.append(iname)
Expand All @@ -1470,7 +1471,7 @@ def post_process(self):
iid = self.value_resolver.get_image_id_by_name(
iname, did)
except KeyError:
log.warn(
log.warning(
"%d not found in image ids" % iid)
assert i == len(image_column.values)
image_column.values.append(iid)
Expand Down Expand Up @@ -1509,7 +1510,7 @@ def post_process(self):
if rname is None:
rname = ""
except KeyError:
log.warn(
log.warning(
"%d not found in roi ids" % rid)
assert i == len(roi_name_column.values)
roi_name_column.values.append(rname)
Expand All @@ -1526,7 +1527,7 @@ def post_process(self):
rname = roi_name_column.values[i]
rid = self.value_resolver.get_roi_id_by_name(rname)
except KeyError:
log.warn(
log.warning(
"%d not found in roi names" % rname)
assert i == len(roi_column.values)
roi_column.values.append(rid)
Expand Down Expand Up @@ -1899,7 +1900,7 @@ def idcolumn_to_omeroclass(col):
targets.append(obj)
targets.extend(self._get_additional_targets(obj))
else:
log.warn("Invalid Id:%d found in row %s", row[n], row)
log.warning("Invalid Id:%d found in row %s", row[n], row)
if targets:
for tr in trs:
rowkvs = tr.transform(row)
Expand Down
4 changes: 2 additions & 2 deletions test/integration/clitest/test_metadata.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -245,9 +245,9 @@ def test_deletebulkanns(self, capfd):
o = self.invoke(capfd)
assert "FileAnnotation:" in o

# Should be empty since it's deleted
# Should have no FileAnnotation since it's deleted
o = self.invoke(capfd)
assert len(o.strip()) == 0
assert "FileAnnotation:" not in o

@pytest.mark.parametrize('report', [False, True])
def test_measures(self, capfd, report):
Expand Down