fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-30 16:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Autoformat python to fix lint errors (#1470)

Browse Source 
* Autoformat python to fix lint errors

* Fix lint errors not caught by black
This commit is contained in:
Matt Weiden
2020-05-12 13:19:38 -07:00
committed by GitHub
parent e55595cc55
commit 730410c5e1
10 changed files with 50 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/data_common/data_adaptor.py
+6 -5
View File
@@ -230,18 +230,19 @@ class DataAdaptor(metaclass=ABCMeta):
# all labels must have a name, which must be unique and not used in obs column names
if not labels_df.columns.is_unique:
raise KeyError(f"All column names specified in user annotations must be unique.")
raise KeyError("All column names specified in user annotations must be unique.")
# the label index must be unique, and must have same values the anndata obs index
if not labels_df.index.is_unique:
raise KeyError(f"All row index values specified in user annotations must be unique.")
raise KeyError("All row index values specified in user annotations must be unique.")
obs_columns = self.get_obs_columns()
duplicate_columns = list(set(labels_df.columns) & set(obs_columns))
if len(duplicate_columns) > 0:
raise KeyError(
f"Labels file may not contain column names which overlap " f"with h5ad obs columns {duplicate_columns}"
"Labels file may not contain column names which overlap "
f"with h5ad obs columns {duplicate_columns}"
)
# labels must have same count as obs annotations
@@ -351,13 +352,13 @@ class DataAdaptor(metaclass=ABCMeta):
"""
embeddings = self.get_embedding_names() if fields is None or len(fields) == 0 else fields
layout_data = []
with ServerTiming.time(f"layout.query"):
with ServerTiming.time("layout.query"):
for ename in embeddings:
embedding = self.get_embedding_array(ename, 2)
normalized_layout = DataAdaptor.normalize_embedding(embedding)
layout_data.append(pd.DataFrame(normalized_layout, columns=[f"{ename}_0", f"{ename}_1"]))
with ServerTiming.time(f"layout.encode"):
with ServerTiming.time("layout.encode"):
if layout_data:
df = pd.concat(layout_data, axis=1, copy=False)
else:
server/data_common/matrix_loader.py
+2 -2
View File
@@ -228,7 +228,7 @@ class MatrixDataLoader(object):
self.matrix_data_type = self.__matrix_data_type()
if not self.__matrix_data_type_allowed(app_config):
raise DatasetAccessError(f"Dataset does not have an allowed type.")
raise DatasetAccessError("Dataset does not have an allowed type.")
if self.matrix_data_type == MatrixDataType.H5AD:
from server.data_anndata.anndata_adaptor import AnndataAdaptor
@@ -272,7 +272,7 @@ class MatrixDataLoader(object):
def pre_load_validation(self):
if self.matrix_data_type == MatrixDataType.UNKNOWN:
raise DatasetAccessError(f"Dataset does not have a recognized type: .h5ad or .cxg")
raise DatasetAccessError("Dataset does not have a recognized type: .h5ad or .cxg")
self.matrix_type.pre_load_validation(self.location)
def file_size(self):