diff --git a/server/app/__init__.py b/server/app/__init__.py index 8125c40d..0ebc4e71 100644 --- a/server/app/__init__.py +++ b/server/app/__init__.py @@ -34,7 +34,7 @@ app.config.update( DATASET_TITLE=TITLE ) -app.config['PROFILE'] = True +app.config["PROFILE"] = True # app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[15]) # Application Data @@ -54,8 +54,8 @@ 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", - 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') +app.add_url_rule("/", endpoint="index") diff --git a/server/app/rest_api/rest.py b/server/app/rest_api/rest.py index 4262957f..a44e5287 100644 --- a/server/app/rest_api/rest.py +++ b/server/app/rest_api/rest.py @@ -9,14 +9,14 @@ from ..util.filter import parse_filter class InitializeAPI(Resource): @swagger.doc({ - 'summary': 'get metadata schema, ranges for values, and cell count to initialize cellxgene app', - 'tags': ['initialize'], - 'parameters': [], - 'responses': { - '200': { - 'description': 'initialization data for UI', - 'examples': { - 'application/json': { + "summary": "get metadata schema, ranges for values, and cell count to initialize cellxgene app", + "tags": ["initialize"], + "parameters": [], + "responses": { + "200": { + "description": "initialization data for UI", + "examples": { + "application/json": { "data": { "cellcount": 3589, "options": { @@ -101,21 +101,21 @@ class InitializeAPI(Resource): class CellsAPI(Resource): @swagger.doc({ - 'summary': 'filter based on metadata fields to get a subset cells, expression data, and metadata', - 'tags': ['cells'], - 'description': "Cells takes query parameters defined in the schema retrieved from the /initialize enpoint. " + "summary": "filter based on metadata fields to get a subset cells, expression data, and metadata", + "tags": ["cells"], + "description": "Cells takes query parameters defined in the schema retrieved from the /initialize enpoint. " "
For categorical metadata keys filter based on `key=value`
" " For continuous metadata keys filter by `key=min,max`
Either value " "can be replaced by a \*. To have only a minimum value `key=min,\*` To have only a maximum " "value `key=\*,max`
Graph data (if retrieved) is normalized" " To only retrieve cells that don't have a value for the key filter by `key`", - 'parameters': [], + "parameters": [], - 'responses': { - '200': { - 'description': 'initialization data for UI', - 'examples': { - 'application/json': { + "responses": { + "200": { + "description": "initialization data for UI", + "examples": { + "application/json": { "data": { "badmetadatacount": 0, "cellcount": 0, @@ -185,8 +185,8 @@ class CellsAPI(Resource): }, }, - '400': { - 'description': 'bad query params', + "400": { + "description": "bad query params", } } }) @@ -212,21 +212,21 @@ class CellsAPI(Resource): class ExpressionAPI(Resource): @swagger.doc({ - 'summary': 'Json with gene list and expression data by cell, limited to first 40 cells', - 'tags': ['expression'], - 'parameters': [ + "summary": "Json with gene list and expression data by cell, limited to first 40 cells", + "tags": ["expression"], + "parameters": [ { - 'name': 'include_unexpressed_genes', - 'description': "Include genes that have 0 expression across all cells in set", - 'in': 'path', - 'type': 'bool', + "name": "include_unexpressed_genes", + "description": "Include genes that have 0 expression across all cells in set", + "in": "path", + "type": "bool", } ], - 'responses': { - '200': { - 'description': 'Json for heatmap', - 'examples': { - 'application/json': { + "responses": { + "200": { + "description": "Json for heatmap", + "examples": { + "application/json": { "data": { "cells": [ { @@ -258,12 +258,12 @@ class ExpressionAPI(Resource): return make_payload(expression_data) @swagger.doc({ - 'summary': 'Json with gene list and expression data by cell', - 'tags': ['expression'], - 'parameters': [ + "summary": "Json with gene list and expression data by cell", + "tags": ["expression"], + "parameters": [ { - 'name': 'body', - 'in': 'body', + "name": "body", + "in": "body", "schema": { "example": { "celllist": ["1001000173.G8", "1001000173.D4"], @@ -275,11 +275,11 @@ class ExpressionAPI(Resource): } }, ], - 'responses': { - '200': { - 'description': 'Json for expressiondata', - 'examples': { - 'application/json': { + "responses": { + "200": { + "description": "Json for expressiondata", + "examples": { + "application/json": { "data": { "cells": [ { @@ -305,24 +305,24 @@ class ExpressionAPI(Resource): } } }, - '400': { - 'description': 'Required parameter missing/incorrect', + "400": { + "description": "Required parameter missing/incorrect", } } }) def post(self): from app import data args = request.get_json() - cell_list = args.get('celllist', []) - gene_list = args.get('genelist', []) + cell_list = args.get("celllist", []) + gene_list = args.get("genelist", []) 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) - if cell_list and len(expression_data['cells']) < len(cell_list): + if cell_list and len(expression_data["cells"]) < len(cell_list): return make_payload([], "Some cell ids not available", 400) - if gene_list and len(expression_data['genes']) < len(gene_list): + if gene_list and len(expression_data["genes"]) < len(gene_list): return make_payload([], "Some genes not available", 400) return make_payload(expression_data) @@ -330,13 +330,13 @@ class ExpressionAPI(Resource): class DifferentialExpressionAPI(Resource): @swagger.doc({ - 'summary': 'Get the top expressed genes for two cell sets. Calculated using t-test', - 'tags': ['expression'], - 'parameters': [ + "summary": "Get the top expressed genes for two cell sets. Calculated using t-test", + "tags": ["expression"], + "parameters": [ { - 'name': 'body', - 'in': 'body', - 'schema': { + "name": "body", + "in": "body", + "schema": { "example": { "celllist1": ["1001000176.C12", "1001000176.C7", "1001000177.F11"], "celllist2": ["1001000012.D2", "1001000017.F10", "1001000033.C3", "1001000229.D4"], @@ -347,10 +347,10 @@ class DifferentialExpressionAPI(Resource): } ], "responses": { - '200': { - 'description': 'top expressed genes for cellset1, cellset2', - 'examples': { - 'application/json': { + "200": { + "description": "top expressed genes for cellset1, cellset2", + "examples": { + "application/json": { "data": { "celllist1": { "ave_diff": [ @@ -419,10 +419,10 @@ class DifferentialExpressionAPI(Resource): def post(self): from app import data args = request.get_json() - cell_list_1 = args.get('celllist1', []) - cell_list_2 = args.get('celllist2', []) + cell_list_1 = args.get("celllist1", []) + cell_list_2 = args.get("celllist2", []) num_genes = args.get("num_genes", 7) - pval = args.get('pval', 0.5) + pval = args.get("pval", 0.5) if not (cell_list_1 and cell_list_2): return make_payload([], "must include celllist1 and celllist2 parameters", @@ -432,7 +432,7 @@ class DifferentialExpressionAPI(Resource): def get_api_resources(): - bp = Blueprint('api', __name__, url_prefix='/api/v2.0') + bp = Blueprint("api", __name__, url_prefix="/api/v2.0") api = Api(bp, add_api_spec_resource=False) api.add_resource(InitializeAPI, "/initialize") api.add_resource(CellsAPI, "/cells") diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py index a723c862..a7b63b7d 100644 --- a/server/app/scanpy_engine/scanpy_engine.py +++ b/server/app/scanpy_engine/scanpy_engine.py @@ -33,9 +33,9 @@ class ScanpyEngine(CXGDriver): return data_schema def _set_cell_ids(self): - self.data.obs['cxg_cell_id'] = list(range(self.data.obs.shape[0])) + self.data.obs["cxg_cell_id"] = list(range(self.data.obs.shape[0])) self.data.obs["cell_name"] = list(self.data.obs.index) - self.data.obs.set_index('cxg_cell_id', inplace=True) + self.data.obs.set_index("cxg_cell_id", inplace=True) def cells(self): return list(self.data.obs.index) @@ -78,7 +78,7 @@ class ScanpyEngine(CXGDriver): if self.schema[field]["variabletype"] == "categorical": group_by = field if group_by == "CellName": - group_by = 'cell_name' + group_by = "cell_name" metadata_ranges[field] = {"options": df.obs.groupby(group_by).size().to_dict()} else: metadata_ranges[field] = { diff --git a/server/app/web/webapp.py b/server/app/web/webapp.py index 045121a8..4717f155 100644 --- a/server/app/web/webapp.py +++ b/server/app/web/webapp.py @@ -2,10 +2,10 @@ from flask import ( Blueprint, render_template, url_for, current_app ) -bp = Blueprint('webapp', __name__, template_folder='templates') +bp = Blueprint("webapp", __name__, template_folder="templates") -@bp.route('/') +@bp.route("/") def index(): url_base = current_app.config["CXG_API_BASE"] dataset_title = current_app.config["DATASET_TITLE"] @@ -13,12 +13,12 @@ def index(): # renders swagger documentation -@bp.route('/swagger') +@bp.route("/swagger") def swag(): return render_template("swagger.html") # renders swagger documentation -@bp.route('/favicon.png') +@bp.route("/favicon.png") def favicon(): return url_for("static", filename="img/favicon.png") diff --git a/server/run.py b/server/run.py index 6a8dee0c..c7afec43 100644 --- a/server/run.py +++ b/server/run.py @@ -1,3 +1,3 @@ from app import app -app.run(host='0.0.0.0', debug=True, port=5005) +app.run(host="0.0.0.0", debug=True, port=5005)