Style guide cleanup

backend/app/__init__.py

@@ -1,12 +1,10 @@
 import os
 
-from flask import Flask, url_for, g
+from flask import Flask
 from flask_compress import Compress
 from flask_cors import CORS
 from flask_restful_swagger_2 import get_swagger_blueprint
 
-# from werkzeug.contrib.profiler import ProfilerMiddleware
-
 from .web import webapp
 from .rest_api.rest import get_api_resources
 
@@ -14,11 +12,12 @@ app = Flask(__name__)
 Compress(app)
 CORS(app)
 
-#Config
+# Config
 CONFIG_FILE = os.environ.get("CXG_CONFIG_FILE", default="scanpy-test.cfg")
 CXG_DIR = os.environ.get("CXG_DIRECTORY", default="/Users/charlotteweaver/Documents/Git/cxg-v2/data/")
 SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
 ENGINE = os.environ.get("CXG_ENGINE", default="scanpy")
+TITLE = os.environ.get("DATASET_TITLE", default="PBMC 3K")
 # TODO remove the 2 when this is prod
 CXG_API_BASE = os.environ.get("CXG_API_BASE2", default="http://0.0.0.0:5005/api/")
 
@@ -30,7 +29,8 @@ app.config.update(
     SECRET_KEY=SECRET_KEY,
     CXG_API_BASE=CXG_API_BASE,
     ENGINE=ENGINE,
-    DATA=CXG_DIR
+    DATA=CXG_DIR,
+    DATASET_TITLE=TITLE
 )
 
 app.config['PROFILE'] = True
@@ -52,12 +52,13 @@ docs.append(resources.get_swagger_doc())
 
 app.register_blueprint(webapp.bp)
 app.register_blueprint(resources.blueprint)
-app.register_blueprint(get_swagger_blueprint(docs, '/api/swagger', produces=["application/json"], title="cellxgene rest api", 
+app.register_blueprint(
-          description='An API connecting ExpressionMatrix2 clustering algorithm to cellxgene'))
+    get_swagger_blueprint(docs, '/api/swagger', produces=["application/json"], title="cellxgene rest api",
+                          description='An API connecting ExpressionMatrix2 clustering algorithm to cellxgene'))
 
 
 app.add_url_rule('/', endpoint='index')
 
 
 if __name__ == "__main__":
-    app.run(host='0.0.0.0', debug=True, port=5005)
+    app.run(host='0.0.0.0', debug=True, port=5005)

backend/app/driver/driver.py

@@ -2,7 +2,6 @@ from abc import ABCMeta, abstractmethod
 
 
 class CXGDriver(metaclass=ABCMeta):
-
 	def __init__(self, data, schema=None, graph_method=None, diffexp_method=None):
 		self.data = self._load_data(data)
 
@@ -51,10 +50,8 @@ class CXGDriver(metaclass=ABCMeta):
 		:param fields: list of keys for metadata to return, returns all metadata values if not set.
 		:return: Iterator for cellid + list of cells metadata values  ex. [cell-id, val1, val2, val3]
 		"""
-
 		pass
 
-
 	@abstractmethod
 	def create_graph(self, df):
 		"""
@@ -64,7 +61,6 @@ class CXGDriver(metaclass=ABCMeta):
 		"""
 		pass
 
-
 	@abstractmethod
 	def diffexp(self, df1, df2):
 		"""
@@ -72,7 +68,8 @@ class CXGDriver(metaclass=ABCMeta):
 
 		:param df1: First set of cells
 		:param df2: Second set of cells
-		:return: Up in the air: I recommend [gene name, mean_expression_cells1, mean_expression_cells2, average_difference, statistic_value]
+		:return: Up in the air: I recommend [gene name, mean_expression_cells1,
+											mean_expression_cells2, average_difference, statistic_value]
 		"""
 		pass
 

backend/app/rest_api/rest.py

@@ -315,7 +315,7 @@ class ExpressionAPI(Resource):
         args = request.get_json()
         cell_list = args.get('celllist', [])
         gene_list = args.get('genelist', [])
-        if not (cell_list) and not (gene_list):
+        if not cell_list and not gene_list:
             return make_payload([], "must include celllist and/or genelist parameter", 400)
 
         expression_data = data.expression(cell_list, gene_list)
@@ -327,6 +327,7 @@ class ExpressionAPI(Resource):
 
         return make_payload(expression_data)
 
+
 class DifferentialExpressionAPI(Resource):
     @swagger.doc({
         'summary': 'Get the top expressed genes for two cell sets. Calculated using t-test',
@@ -429,6 +430,7 @@ class DifferentialExpressionAPI(Resource):
         data = data.diffexp(cell_list_1, cell_list_2, pval, num_genes)
         return make_payload(data)
 
+
 def get_api_resources():
     bp = Blueprint('api', __name__, url_prefix='/api/v2.0')
     api = Api(bp, add_api_spec_resource=False)
@@ -436,4 +438,4 @@ def get_api_resources():
     api.add_resource(CellsAPI, "/cells")
     api.add_resource(ExpressionAPI, "/expression")
     api.add_resource(DifferentialExpressionAPI, "/diffexp")
-    return api
+    return api

backend/app/scanpy_engine/scanpy_engine.py

@@ -1,8 +1,9 @@
-import scanpy.api as sc
-import numpy as np
-from scipy import stats
 import os
 
+import numpy as np
+import scanpy.api as sc
+from scipy import stats
+
 from ..util.schema_parse import parse_schema
 from ..driver.driver import CXGDriver
 
@@ -14,12 +15,10 @@ class ScanpyEngine(CXGDriver):
 		self.schema = self._load_or_infer_schema(data, schema)
 		self._set_cell_ids()
 		self.cell_count = self.data.shape[0]
-		# TODO Do I need this?
 		self.gene_count = self.data.shape[1]
 		self.graph_method = graph_method
 		self.diffexp_method = diffexp_method
 
-
 	@staticmethod
 	def _load_data(data):
 		return sc.read(os.path.join(data, "data.h5ad"))
@@ -30,7 +29,7 @@ class ScanpyEngine(CXGDriver):
 		if not schema:
 			pass
 		else:
-			data_schema = parse_schema(os.path.join(data,schema))
+			data_schema = parse_schema(os.path.join(data, schema))
 		return data_schema
 
 	def _set_cell_ids(self):
@@ -102,7 +101,6 @@ class ScanpyEngine(CXGDriver):
 			metadata[idx]["CellName"] = metadata[idx].pop("cell_name", None)
 		return metadata
 
-
 	def create_graph(self, df):
 		"""
 		Computes a n-d layout for cells through dimensionality reduction.
@@ -112,12 +110,11 @@ class ScanpyEngine(CXGDriver):
 		normalized_graph = (graph - graph.min()) / (graph.max() - graph.min())
 		return np.hstack((df.obs["cell_name"].values.reshape(len(df.obs.index), 1), normalized_graph)).tolist()
 
-
 	def diffexp(self, cell_list_1, cell_list_2, pval, num_genes):
 		cells_idx_1 = np.in1d(self.data.obs["cell_name"], cell_list_1)
 		cells_idx_2 = np.in1d(self.data.obs["cell_name"], cell_list_2)
-		expression_1 = self.data.X[cells_idx_1,:]
+		expression_1 = self.data.X[cells_idx_1, :]
-		expression_2 = self.data.X[cells_idx_2,:]
+		expression_2 = self.data.X[cells_idx_2, :]
 		diff_exp = stats.ttest_ind(expression_1, expression_2)
 		set1 = np.logical_and(diff_exp.pvalue < pval, diff_exp.statistic > 0)
 		set2 = np.logical_and(diff_exp.pvalue < pval, diff_exp.statistic < 0)
@@ -151,7 +148,7 @@ class ScanpyEngine(CXGDriver):
 				"ave_diff": mean_diff2.tolist()[:num_genes]
 			},
 		}
-	
+
 	def expression(self, cells=None, genes=None):
 		"""
 		:param df:
@@ -185,11 +182,3 @@ class ScanpyEngine(CXGDriver):
 			"cells": cell_data,
 			"nonzero_gene_count": int(np.sum(expression.any(axis=0)))
 		}
-
-
-
-
-
-
-
-

backend/app/util/filter.py

@@ -1,6 +1,7 @@
 class QueryStringError(Exception):
     pass
 
+
 def _convert_variable(datatype, variable):
     """
     Convert variable to number (float/int)
@@ -19,6 +20,7 @@ def _convert_variable(datatype, variable):
     except ValueError:
         raise
 
+
 def parse_filter(filter, schema):
     """
     {key: variable_type

backend/app/util/utils.py

@@ -1,7 +1,9 @@
 import json
+
 from numpy import float32, integer
 from flask import make_response, jsonify, Response
 
+
 class Float32JSONEncoder(json.JSONEncoder):
     def default(self, obj):
         if isinstance(obj, float32):
@@ -10,6 +12,7 @@ class Float32JSONEncoder(json.JSONEncoder):
             return int(obj)
         return json.JSONEncoder.default(self, obj)
 
+
 def make_payload(data, errormessage="", errorcode=200):
     """
     Creates JSON respons for requests
@@ -31,13 +34,7 @@ def make_payload(data, errormessage="", errorcode=200):
         }
     }), errorcode)
 
+
 def make_streaming_response(data_generator, errorcode=200, content_type="application/json"):
     # TODO headers
     return Response(data_generator, status=errorcode, content_type=content_type)
-
-
-
-
-
-
-

backend/app/web/webapp.py

@@ -1,9 +1,10 @@
 from flask import (
-    Blueprint, render_template, request, url_for, current_app
+    Blueprint, render_template, url_for, current_app
 )
 
 bp = Blueprint('webapp', __name__, template_folder='templates')
 
+
 @bp.route('/')
 def index():
     url_base = current_app.config["CXG_API_BASE"]
@@ -16,6 +17,7 @@ def index():
 def swag():
     return render_template("swagger.html")
 
+
 # renders swagger documentation
 @bp.route('/favicon.png')
 def favicon():