chore: upgrade backend dependencies (#2641)

chore: upgrade backend dependencies (#2641)

server/common/annotations/local_file_csv.py

@@ -145,7 +145,7 @@ class AnnotationsLocalFile(Annotations):
     def write_gene_sets(self, gene_sets, tid, data_adaptor):
         self.check_gene_sets_save_enabled()  # raises
 
-        if type(tid) != int or tid < 0:
+        if type(tid) is not int or tid < 0:
             raise ValueError("tid must be a positive integer")
 
         # may raise
@@ -175,7 +175,7 @@ class AnnotationsLocalFile(Annotations):
 
             # update the cache
             self.last_geneset_fname = fname
-            self.last_geneset = gene_sets if type(gene_sets) == dict else {g["geneset_name"]: g for g in gene_sets}
+            self.last_geneset = gene_sets if isinstance(gene_sets, dict) else {g["geneset_name"]: g for g in gene_sets}
 
     def _get_userdata_idhash(self, data_adaptor):
         """

server/common/compute/diffexp_generic.py

@@ -56,7 +56,7 @@ def diffexp_ttest_from_mean_var(meanA, varA, nA, meanB, varB, nB, top_n, diffexp
 
     # degrees of freedom for Welch's t-test
     with np.errstate(divide="ignore", invalid="ignore"):
-        dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
+        dof = sum_vn**2 / (vnA**2 / (nA - 1) + vnB**2 / (nB - 1))
     dof[np.isnan(dof)] = 1
 
     # Welch's t-test score calculation

server/common/compute/estimate_distribution.py

@@ -97,7 +97,7 @@ def estimate_approximate_distribution(X) -> XApproximateDistribution:
     if Xdata.size > CHUNKSIZE:
         min_val = max_val = Xdata[0]
         with concurrent.futures.ThreadPoolExecutor() as tp:
-            for (_min, _max) in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
+            for _min, _max in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
                 min_val = min(_min, min_val)
                 max_val = max(_max, max_val)
 

server/common/config/__init__.py

@@ -1,2 +1,2 @@
 DEFAULT_SERVER_PORT = 5005
-BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20  # 100MB
+BIG_FILE_SIZE_THRESHOLD = 100 * 2**20  # 100MB

server/common/config/app_config.py

@@ -19,7 +19,6 @@ class AppConfig(object):
     """
 
     def __init__(self):
-
         # the default configuration (see default_config.py)
         # TODO @madison -- if we always read from the default config (hard coded path) can we set those values as
         #  defaults within the config class?

server/common/config/base_config.py

@@ -50,7 +50,7 @@ class BaseConfig(object):
                     f"Invalid type for attribute: {attrname}, expected types ({tnames}), got {type(val).__name__}"
                 )
         else:
-            if type(val) != vtype:
+            if type(val) is not vtype:
                 raise ConfigurationError(
                     f"Invalid type for attribute: {attrname}, "
                     f"expected type {vtype.__name__}, got {type(val).__name__}"
@@ -70,7 +70,7 @@ class BaseConfig(object):
             if not hasattr(self, key):
                 raise ConfigurationError(f"unknown config parameter {key}.")
             try:
-                if type(value) == tuple:
+                if type(value) is tuple:
                     # convert tuple values to list values
                     value = list(value)
                 setattr(self, key, value)

server/common/config/external_config.py

@@ -29,7 +29,7 @@ class ExternalConfig(BaseConfig):
             if name is None:
                 raise ConfigurationError("environment: 'name' is missing")
             required = envdict.get("required", False)
-            if type(required) != bool:
+            if type(required) is not bool:
                 raise ConfigurationError("environment: 'required' must be a bool")
             path = envdict.get("path")
             if path is None:

server/common/fbs/matrix.py

@@ -19,7 +19,7 @@ import server.common.fbs.NetEncoding.Uint32Array as Uint32Array
 
 # Serialization helper
 def serialize_column(builder, typed_arr):
-    """ Serialize NetEncoding.Column """
+    """Serialize NetEncoding.Column"""
 
     (u_type, u_value) = typed_arr
     Column.ColumnStart(builder)
@@ -30,7 +30,7 @@ def serialize_column(builder, typed_arr):
 
 # Serialization helper
 def serialize_matrix(builder, n_rows, n_cols, columns, col_idx):
-    """ Serialize NetEncoding.Matrix """
+    """Serialize NetEncoding.Matrix"""
 
     Matrix.MatrixStart(builder)
     Matrix.MatrixAddNRows(builder, n_rows)

server/common/genesets.py

@@ -136,7 +136,7 @@ def write_gene_sets_tidycsv(f, genesets):
 
 
 def summarizeQueryHash(raw_query):
-    """ generate a cache key (hash) from the raw query string """
+    """generate a cache key (hash) from the raw query string"""
     return hashlib.sha1(raw_query).hexdigest()
 
 
@@ -187,7 +187,7 @@ def validate_gene_sets(genesets, var_names, context=None):
     # 1. check gene set character set and format
     illegal_name = re.compile(r"^\s|  |[\u0000-\u001F\u007F-\uFFFF]|\s$")
     for name in geneset_names:
-        if type(name) != str or len(name) == 0:
+        if type(name) is not str or len(name) == 0:
             raise KeyError("Gene set names must be non-null string.")
         if illegal_name.search(name):
             messagefn(

server/common/rest.py

@@ -6,7 +6,7 @@ import zlib
 import json
 
 from flask import make_response, jsonify, current_app, abort
-from werkzeug.urls import url_unquote
+from urllib.parse import unquote
 
 from server.common.config.client_config import get_client_config
 from server.common.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
@@ -64,22 +64,22 @@ def _query_parameter_to_filter(args):
             axis, name = key.split(":")
             if axis not in ("obs", "var"):
                 raise FilterError("unknown filter axis")
-            name = url_unquote(name)
+            name = unquote(name)
             current = filters[axis].setdefault(name, {"name": name})
 
             val_split = value.split(",")
             if len(val_split) == 1:
                 if "min" in current or "max" in current:
                     raise FilterError("do not mix range and value filters")
-                value = url_unquote(value)
+                value = unquote(value)
                 values = current.setdefault("values", [])
                 values.append(value)
 
             elif len(val_split) == 2:
                 if len(current) > 1:
                     raise FilterError("duplicate range specification")
-                min = url_unquote(val_split[0])
-                max = url_unquote(val_split[1])
+                min = unquote(val_split[0])
+                max = unquote(val_split[1])
                 if min != "*":
                     current["min"] = float(min)
                 if max != "*":
@@ -379,7 +379,7 @@ def summarize_var_helper(request, data_adaptor, key, raw_query):
             HTTPStatus.OK,
             {"Content-Type": "application/octet-stream"},
         )
-    except (ValueError) as e:
+    except ValueError as e:
         return abort(HTTPStatus.NOT_FOUND, description=str(e))
     except (UnsupportedSummaryMethod, FilterError) as e:
         return abort(HTTPStatus.BAD_REQUEST, description=str(e))

server/common/utils/utils.py

@@ -8,7 +8,7 @@ import socket
 from urllib.parse import urlsplit, urljoin
 
 import numpy as np
-from flask import json
+import json
 
 from server.common.errors import ConfigurationError
 
@@ -100,6 +100,7 @@ def custom_format_warning(msg, *args, **kwargs):
 def jsonify_strict(data):
     return StrictJSONEncoder().encode(data)
 
+
 def import_plugins(plugin_module):
     """
     Load optional plugin modules from server.common.plugins