fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-25 18:18:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Auto format python, make sure it passes lint checks (#1401)

Browse Source
This commit is contained in:
Matt Weiden
2020-04-16 08:07:10 -07:00
committed by GitHub
parent 7e7ed74b92
commit 58e4c2489b
12 changed files with 66 additions and 78 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/app.py
+4 -2
View File
@@ -28,6 +28,7 @@ def _cache_control(always, **cache_kwargs):
See Werkzeug for attributes that can be set, eg, no_cache, private, max_age, etc.
https://werkzeug.palletsprojects.com/en/1.0.x/datastructures/#werkzeug.datastructures.ResponseCacheControl
"""
def inner_cache_control(f):
@wraps(f)
def wrapper(*args, **kwargs):
@@ -39,7 +40,9 @@ def _cache_control(always, **cache_kwargs):
for k, v in cache_kwargs.items():
setattr(response.cache_control, k, v)
return response
return wrapper
return inner_cache_control
@@ -126,8 +129,7 @@ def dataroot_test_index():
data += "<body><H1>Welcome to cellxgene</H1>"
config = current_app.app_config
locator = DataLocator(config.multi_dataset__dataroot,
region_name=config.data_locator__s3__region_name)
locator = DataLocator(config.multi_dataset__dataroot, region_name=config.data_locator__s3__region_name)
datasets = []
for fname in locator.ls():
location = path_join(config.multi_dataset__dataroot, fname)
server/cli/launch.py
+1 -1
View File
@@ -437,7 +437,7 @@ def launch(
port=app_config.server__port,
threaded=not app_config.server__debug,
use_debugger=False,
use_reloader=False
use_reloader=False,
)
except OSError as e:
if e.errno == errno.EADDRINUSE:
server/common/app_config.py
+3 -5
View File
@@ -446,9 +446,7 @@ class AppConfig(object):
cpu_multiplier = self.diffexp__alg_cxg__cpu_multiplier
cpu_count = os.cpu_count()
max_workers = min(max_workers, cpu_multiplier * cpu_count)
diffexp_tiledb.set_config(
max_workers,
self.diffexp__alg_cxg__target_workunit)
diffexp_tiledb.set_config(max_workers, self.diffexp__alg_cxg__target_workunit)
def handle_adaptor(self, context):
# cxg
@@ -537,8 +535,8 @@ class AppConfig(object):
config["links"] = links
config["parameters"] = parameters
config["limits"] = {
'column_request_max': self.limits__column_request_max,
'diffexp_cellcount_max': self.limits__diffexp_cellcount_max,
"column_request_max": self.limits__column_request_max,
"diffexp_cellcount_max": self.limits__diffexp_cellcount_max,
}
return c
server/common/data_locator.py
+1 -3
View File
@@ -43,9 +43,7 @@ class DataLocator:
# fsspec.filesystem will throw RuntimeError if the protocol is unsupported
if self.protocol == "s3" and region_name:
self.fs = fsspec.filesystem(
self.protocol, config_kwargs={"region_name": region_name}
)
self.fs = fsspec.filesystem(self.protocol, config_kwargs={"region_name": region_name})
else:
self.fs = fsspec.filesystem(self.protocol)
server/common/immutable_kvcache.py
+5 -5
View File
@@ -27,23 +27,23 @@ class ImmutableKVCache(MutableMapping):
return self.cache[key]
if key not in self.factory_calls:
creation_thr = True
self.factory_calls[key] = {'cv': threading.Condition(), 'is_done': False, 'error': None}
self.factory_calls[key] = {"cv": threading.Condition(), "is_done": False, "error": None}
factory_calls = self.factory_calls[key]
# with the CV, create the value (or wait for it to be created)
cv = factory_calls['cv']
cv = factory_calls["cv"]
with cv:
if creation_thr:
try:
self.cache[key] = self.factory(key)
except Exception as e:
factory_calls['error'] = e
factory_calls["error"] = e
factory_calls['is_done'] = True
factory_calls["is_done"] = True
cv.notify_all()
else:
""" wait for the value to be available """
while not factory_calls['is_done']:
while not factory_calls["is_done"]:
cv.wait()
with self.lock:
server/common/rest.py
+5 -7
View File
@@ -53,15 +53,15 @@ def _query_parameter_to_filter(args):
# on name and value.
try:
for key, value in args.items(multi=True):
axis, name = key.split(':')
axis, name = key.split(":")
if axis not in ("obs", "var"):
raise FilterError("unknown filter axis")
name = url_unquote(name)
current = filters[axis].setdefault(name, {"name": name})
val_split = value.split(',')
val_split = value.split(",")
if len(val_split) == 1:
if 'min' in current or 'max' in current:
if "min" in current or "max" in current:
raise FilterError("do not mix range and value filters")
value = url_unquote(value)
values = current.setdefault("values", [])
@@ -72,7 +72,7 @@ def _query_parameter_to_filter(args):
raise FilterError("duplicate range specification")
min = url_unquote(val_split[0])
max = url_unquote(val_split[1])
if min != '*':
if min != "*":
current["min"] = float(min)
if max != "*":
current["max"] = float(max)
@@ -89,9 +89,7 @@ def _query_parameter_to_filter(args):
for axis in ("obs", "var"):
axis_filter = filters[axis]
if len(axis_filter) > 0:
result[axis] = {
"annotation_value": [val for val in axis_filter.values()]
}
result[axis] = {"annotation_value": [val for val in axis_filter.values()]}
return result
server/compute/diffexp_cxg.py
+8 -5
View File
@@ -83,10 +83,10 @@ def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
try:
result = future.result()
part_meanA, part_varA, part_meanB, part_varB, cols = result
meanA[cols[0]: cols[1]] += part_meanA
varA[cols[0]: cols[1]] += part_varA
meanB[cols[0]: cols[1]] += part_meanB
varB[cols[0]: cols[1]] += part_varB
meanA[cols[0] : cols[1]] += part_meanA
varA[cols[0] : cols[1]] += part_varA
meanB[cols[0] : cols[1]] += part_meanB
varB[cols[0] : cols[1]] += part_varB
except Exception as e:
for future in futures:
future.cancel()
@@ -98,7 +98,10 @@ def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
nA,
meanB.astype(dtype),
varB.astype(dtype),
nB, top_n, diffexp_lfc_cutoff)
nB,
top_n,
diffexp_lfc_cutoff,
)
return r
server/data_common/matrix_loader.py
+1 -1
View File
@@ -167,7 +167,7 @@ class MatrixDataCacheManager(object):
self.datasets[location] = item
try:
assert(cache_item)
assert cache_item
if delete_adaptor:
delete_adaptor.delete()
if data_adaptor is None:
server/data_cxg/cxg_adaptor.py
+2 -4
View File
@@ -364,9 +364,7 @@ class CxgAdaptor(DataAdaptor):
user_anno_keys = frozenset(labels.columns.tolist()) if need_labels else frozenset()
return_keys = frozenset(fields)
label_join_index = (
frozenset([index_key]) if need_labels and (return_keys & user_anno_keys) else frozenset()
)
label_join_index = frozenset([index_key]) if need_labels and (return_keys & user_anno_keys) else frozenset()
unknown_fields = return_keys - (cxg_keys | user_anno_keys)
if unknown_fields:
@@ -376,7 +374,7 @@ class CxgAdaptor(DataAdaptor):
list((return_keys & cxg_keys) | label_join_index),
list(return_keys & user_anno_keys),
list(return_keys),
index_key
index_key,
)
def annotation_to_fbs_matrix(self, axis, fields=None, labels=None):
server/eb/app.py
+4 -9
View File
@@ -33,17 +33,12 @@ except Exception:
def get_flask_secret_key(region_name, secret_name):
session = boto3.session.Session()
client = session.client(
service_name='secretsmanager',
region_name=region_name
)
client = session.client(service_name="secretsmanager", region_name=region_name)
try:
get_secret_value_response = client.get_secret_value(
SecretId=secret_name
)
if 'SecretString' in get_secret_value_response:
var = get_secret_value_response['SecretString']
get_secret_value_response = client.get_secret_value(SecretId=secret_name)
if "SecretString" in get_secret_value_response:
var = get_secret_value_response["SecretString"]
secret = json.loads(var)
return secret.get("flask_secret_key")
except Exception:
server/test/test_anndata_adaptor.py
+1 -1
View File
@@ -42,7 +42,7 @@ class AdaptorTest(unittest.TestCase):
"adaptor__anndata_adaptor__backed": self.backed,
"single_dataset__datapath": self.data_locator,
"limits__diffexp_cellcount_max": None,
"limits__column_request_max": None
"limits__column_request_max": None,
}
config = AppConfig()
config.update(**args)
server/test/test_filter.py
+31 -35
View File
@@ -15,50 +15,46 @@ class FilterParseTests(unittest.TestCase):
def test_queryparam_to_filter_parse(self):
# categories
self.assertEqual(_query_parameter_to_filter(_qsparse("obs:foo=bar&var:baz=133&var:baz=A&obs:baz=foo")), {
"obs": {
"annotation_value": [
{"name": "foo", "values": ["bar"]},
{"name": "baz", "values": ["foo"]},
]
self.assertEqual(
_query_parameter_to_filter(_qsparse("obs:foo=bar&var:baz=133&var:baz=A&obs:baz=foo")),
{
"obs": {"annotation_value": [{"name": "foo", "values": ["bar"]}, {"name": "baz", "values": ["foo"]}]},
"var": {"annotation_value": [{"name": "baz", "values": ["133", "A"]}]},
},
"var": {
"annotation_value": [
{"name": "baz", "values": ["133", "A"]}
]
}
})
)
# ranges
self.assertEqual(_query_parameter_to_filter(_qsparse("obs:A=1,99&obs:B=*,100&obs:C=0,*")), {
"obs": {
"annotation_value": [
{"name": "A", "min": 1, "max": 99.},
{"name": "B", "max": 100.},
{"name": "C", "min": 0.},
]
self.assertEqual(
_query_parameter_to_filter(_qsparse("obs:A=1,99&obs:B=*,100&obs:C=0,*")),
{
"obs": {
"annotation_value": [
{"name": "A", "min": 1, "max": 99.0},
{"name": "B", "max": 100.0},
{"name": "C", "min": 0.0},
]
},
},
})
)
# combo
self.assertEqual(_query_parameter_to_filter(_qsparse("var:B=YES&var:A=1,99&var:B=NO")), {
"var": {
"annotation_value": [
{"name": "B", "values": ["YES", "NO"]},
{"name": "A", "min": 1., "max": 99.},
]
self.assertEqual(
_query_parameter_to_filter(_qsparse("var:B=YES&var:A=1,99&var:B=NO")),
{
"var": {
"annotation_value": [
{"name": "B", "values": ["YES", "NO"]},
{"name": "A", "min": 1.0, "max": 99.0},
]
},
},
})
)
def test_queryparam_to_filter_escaping(self):
self.assertEqual(_query_parameter_to_filter(_qsparse("obs:var=%2521%252C%253AOK%253D&obs:A%2521=YO")), {
"obs": {
"annotation_value": [
{"name": "var", "values": ["!,:OK="]},
{"name": "A!", "values": ["YO"]},
],
},
})
self.assertEqual(
_query_parameter_to_filter(_qsparse("obs:var=%2521%252C%253AOK%253D&obs:A%2521=YO")),
{"obs": {"annotation_value": [{"name": "var", "values": ["!,:OK="]}, {"name": "A!", "values": ["YO"]}]}},
)
def test_queryparam_to_filter_errors(self):