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Code Issues Packages Projects Releases Wiki Activity

Add obs index to label file (#928)

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* remove debug logging

* load and save obs/row index in label file

* lint

* update tests
This commit is contained in:
Bruce Martin
2019-09-19 09:16:01 -07:00
committed by GitHub
parent 197ea9214a
commit 109c9e70ec
5 changed files with 23 additions and 26 deletions
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server/app/scanpy_engine/scanpy_engine.py
+18 -12
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@@ -22,15 +22,6 @@ from server.app.scanpy_engine.diffexp import diffexp_ttest
from server.app.util.fbs.matrix import encode_matrix_fbs, decode_matrix_fbs
from server.app.scanpy_engine.labels import read_labels, write_labels
"""
Sort order for methods
1. Initialize
2. Helper
3. Filter
4. Data & Metadata
5. Computation
"""
class ScanpyEngine(CXGDriver):
def __init__(self, data=None, args={}):
@@ -81,6 +72,8 @@ class ScanpyEngine(CXGDriver):
index column name to the front-end via the obs_names and var_names config
(which is incorporated into the schema).
"""
self.original_obs_index = self.data.obs.index
for (ax_name, config_name) in ((Axis.OBS, "obs_names"), (Axis.VAR, "var_names")):
name = self.config[config_name]
df_axis = getattr(self.data, str(ax_name))
@@ -255,7 +248,7 @@ class ScanpyEngine(CXGDriver):
self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1]
self._default_and_validate_layouts()
self._validate_label_file()
self._validate_label_data()
self._create_schema()
@requires_data
@@ -340,7 +333,7 @@ class ScanpyEngine(CXGDriver):
)
@requires_data
def _validate_label_file(self):
def _validate_label_data(self):
"""
labels is None if disabled, empty if enabled by no data
"""
@@ -350,6 +343,17 @@ class ScanpyEngine(CXGDriver):
# all lables must have a name, which must be unique and not used in obs column names
if not self.labels.columns.is_unique:
raise KeyError(f"All column names specified in {self.config['label_file']} must be unique.")
# the label index must be unique, and must have same values the anndata obs index
if not self.labels.index.is_unique:
raise KeyError(f"All row index values specified in the label file "
f"`{self.config['label_file']}` must be unique.")
if not self.labels.index.equals(self.original_obs_index):
raise KeyError("Label file row index does not match H5AD file index. "
"Please ensure that column zero (0) in the label file contain the same "
"index values as the H5AD file.")
duplicate_columns = list(set(self.labels.columns) & set(self.data.obs.columns))
if len(duplicate_columns) > 0:
raise KeyError(f"Labels file may not contain column names which overlap "
@@ -427,7 +431,7 @@ class ScanpyEngine(CXGDriver):
def annotation_to_fbs_matrix(self, axis, fields=None):
if axis == Axis.OBS:
if self.labels is not None and not self.labels.empty:
df = pandas.concat([self.data.obs, self.labels], axis=1, join_axes=[self.data.obs.index], copy=False)
df = self.data.obs.join(self.labels, self.config['obs_names'])
else:
df = self.data.obs
else:
@@ -446,6 +450,8 @@ class ScanpyEngine(CXGDriver):
raise ValueError("Only OBS dimension access is supported")
new_label_df = decode_matrix_fbs(fbs)
new_label_df.index = self.original_obs_index
self._validate_label_data() # paranoia
# if any of the new column labels overlap with our existing labels, raise error
duplicate_columns = list(set(new_label_df.columns) & set(self.data.obs.columns))