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Code Issues Packages Projects Releases Wiki Activity

Consistency with quotes

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' -> "
This commit is contained in:
Charlotte Weaver
2018-06-29 13:14:58 -07:00
parent ba13e32206
commit 40f5b94075
5 changed files with 73 additions and 73 deletions
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server/app/__init__.py
+4 -4
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@@ -34,7 +34,7 @@ app.config.update(
DATASET_TITLE=TITLE DATASET_TITLE=TITLE
) )
app.config['PROFILE'] = True app.config["PROFILE"] = True
# app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[15]) # app.wsgi_app = ProfilerMiddleware(app.wsgi_app, restrictions=[15])
# Application Data # Application Data
@@ -54,8 +54,8 @@ docs.append(resources.get_swagger_doc())
app.register_blueprint(webapp.bp) app.register_blueprint(webapp.bp)
app.register_blueprint(resources.blueprint) app.register_blueprint(resources.blueprint)
app.register_blueprint( app.register_blueprint(
get_swagger_blueprint(docs, '/api/swagger', produces=["application/json"], title="cellxgene rest api", get_swagger_blueprint(docs, "/api/swagger", produces=["application/json"], title="cellxgene rest api",
description='An API connecting ExpressionMatrix2 clustering algorithm to cellxgene')) description="An API connecting ExpressionMatrix2 clustering algorithm to cellxgene"))
app.add_url_rule('/', endpoint='index') app.add_url_rule("/", endpoint="index")
server/app/rest_api/rest.py
+61 -61
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@@ -9,14 +9,14 @@ from ..util.filter import parse_filter
class InitializeAPI(Resource): class InitializeAPI(Resource):
@swagger.doc({ @swagger.doc({
'summary': 'get metadata schema, ranges for values, and cell count to initialize cellxgene app', "summary": "get metadata schema, ranges for values, and cell count to initialize cellxgene app",
'tags': ['initialize'], "tags": ["initialize"],
'parameters': [], "parameters": [],
'responses': { "responses": {
'200': { "200": {
'description': 'initialization data for UI', "description": "initialization data for UI",
'examples': { "examples": {
'application/json': { "application/json": {
"data": { "data": {
"cellcount": 3589, "cellcount": 3589,
"options": { "options": {
@@ -101,21 +101,21 @@ class InitializeAPI(Resource):
class CellsAPI(Resource): class CellsAPI(Resource):
@swagger.doc({ @swagger.doc({
'summary': 'filter based on metadata fields to get a subset cells, expression data, and metadata', "summary": "filter based on metadata fields to get a subset cells, expression data, and metadata",
'tags': ['cells'], "tags": ["cells"],
'description': "Cells takes query parameters defined in the schema retrieved from the /initialize enpoint. " "description": "Cells takes query parameters defined in the schema retrieved from the /initialize enpoint. "
"<br>For categorical metadata keys filter based on `key=value` <br>" "<br>For categorical metadata keys filter based on `key=value` <br>"
" For continuous metadata keys filter by `key=min,max`<br> Either value " " For continuous metadata keys filter by `key=min,max`<br> Either value "
"can be replaced by a \*. To have only a minimum value `key=min,\*` To have only a maximum " "can be replaced by a \*. To have only a minimum value `key=min,\*` To have only a maximum "
"value `key=\*,max` <br>Graph data (if retrieved) is normalized" "value `key=\*,max` <br>Graph data (if retrieved) is normalized"
" To only retrieve cells that don't have a value for the key filter by `key`", " To only retrieve cells that don't have a value for the key filter by `key`",
'parameters': [], "parameters": [],
'responses': { "responses": {
'200': { "200": {
'description': 'initialization data for UI', "description": "initialization data for UI",
'examples': { "examples": {
'application/json': { "application/json": {
"data": { "data": {
"badmetadatacount": 0, "badmetadatacount": 0,
"cellcount": 0, "cellcount": 0,
@@ -185,8 +185,8 @@ class CellsAPI(Resource):
}, },
}, },
'400': { "400": {
'description': 'bad query params', "description": "bad query params",
} }
} }
}) })
@@ -212,21 +212,21 @@ class CellsAPI(Resource):
class ExpressionAPI(Resource): class ExpressionAPI(Resource):
@swagger.doc({ @swagger.doc({
'summary': 'Json with gene list and expression data by cell, limited to first 40 cells', "summary": "Json with gene list and expression data by cell, limited to first 40 cells",
'tags': ['expression'], "tags": ["expression"],
'parameters': [ "parameters": [
{ {
'name': 'include_unexpressed_genes', "name": "include_unexpressed_genes",
'description': "Include genes that have 0 expression across all cells in set", "description": "Include genes that have 0 expression across all cells in set",
'in': 'path', "in": "path",
'type': 'bool', "type": "bool",
} }
], ],
'responses': { "responses": {
'200': { "200": {
'description': 'Json for heatmap', "description": "Json for heatmap",
'examples': { "examples": {
'application/json': { "application/json": {
"data": { "data": {
"cells": [ "cells": [
{ {
@@ -258,12 +258,12 @@ class ExpressionAPI(Resource):
return make_payload(expression_data) return make_payload(expression_data)
@swagger.doc({ @swagger.doc({
'summary': 'Json with gene list and expression data by cell', "summary": "Json with gene list and expression data by cell",
'tags': ['expression'], "tags": ["expression"],
'parameters': [ "parameters": [
{ {
'name': 'body', "name": "body",
'in': 'body', "in": "body",
"schema": { "schema": {
"example": { "example": {
"celllist": ["1001000173.G8", "1001000173.D4"], "celllist": ["1001000173.G8", "1001000173.D4"],
@@ -275,11 +275,11 @@ class ExpressionAPI(Resource):
} }
}, },
], ],
'responses': { "responses": {
'200': { "200": {
'description': 'Json for expressiondata', "description": "Json for expressiondata",
'examples': { "examples": {
'application/json': { "application/json": {
"data": { "data": {
"cells": [ "cells": [
{ {
@@ -305,24 +305,24 @@ class ExpressionAPI(Resource):
} }
} }
}, },
'400': { "400": {
'description': 'Required parameter missing/incorrect', "description": "Required parameter missing/incorrect",
} }
} }
}) })
def post(self): def post(self):
from app import data from app import data
args = request.get_json() args = request.get_json()
cell_list = args.get('celllist', []) cell_list = args.get("celllist", [])
gene_list = args.get('genelist', []) 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) return make_payload([], "must include celllist and/or genelist parameter", 400)
expression_data = data.expression(cell_list, gene_list) 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) 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([], "Some genes not available", 400)
return make_payload(expression_data) return make_payload(expression_data)
@@ -330,13 +330,13 @@ class ExpressionAPI(Resource):
class DifferentialExpressionAPI(Resource): class DifferentialExpressionAPI(Resource):
@swagger.doc({ @swagger.doc({
'summary': 'Get the top expressed genes for two cell sets. Calculated using t-test', "summary": "Get the top expressed genes for two cell sets. Calculated using t-test",
'tags': ['expression'], "tags": ["expression"],
'parameters': [ "parameters": [
{ {
'name': 'body', "name": "body",
'in': 'body', "in": "body",
'schema': { "schema": {
"example": { "example": {
"celllist1": ["1001000176.C12", "1001000176.C7", "1001000177.F11"], "celllist1": ["1001000176.C12", "1001000176.C7", "1001000177.F11"],
"celllist2": ["1001000012.D2", "1001000017.F10", "1001000033.C3", "1001000229.D4"], "celllist2": ["1001000012.D2", "1001000017.F10", "1001000033.C3", "1001000229.D4"],
@@ -347,10 +347,10 @@ class DifferentialExpressionAPI(Resource):
} }
], ],
"responses": { "responses": {
'200': { "200": {
'description': 'top expressed genes for cellset1, cellset2', "description": "top expressed genes for cellset1, cellset2",
'examples': { "examples": {
'application/json': { "application/json": {
"data": { "data": {
"celllist1": { "celllist1": {
"ave_diff": [ "ave_diff": [
@@ -419,10 +419,10 @@ class DifferentialExpressionAPI(Resource):
def post(self): def post(self):
from app import data from app import data
args = request.get_json() args = request.get_json()
cell_list_1 = args.get('celllist1', []) cell_list_1 = args.get("celllist1", [])
cell_list_2 = args.get('celllist2', []) cell_list_2 = args.get("celllist2", [])
num_genes = args.get("num_genes", 7) 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): if not (cell_list_1 and cell_list_2):
return make_payload([], return make_payload([],
"must include celllist1 and celllist2 parameters", "must include celllist1 and celllist2 parameters",
@@ -432,7 +432,7 @@ class DifferentialExpressionAPI(Resource):
def get_api_resources(): 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 = Api(bp, add_api_spec_resource=False)
api.add_resource(InitializeAPI, "/initialize") api.add_resource(InitializeAPI, "/initialize")
api.add_resource(CellsAPI, "/cells") api.add_resource(CellsAPI, "/cells")
server/app/scanpy_engine/scanpy_engine.py
+3 -3
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@@ -33,9 +33,9 @@ class ScanpyEngine(CXGDriver):
return data_schema return data_schema
def _set_cell_ids(self): 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["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): def cells(self):
return list(self.data.obs.index) return list(self.data.obs.index)
@@ -78,7 +78,7 @@ class ScanpyEngine(CXGDriver):
if self.schema[field]["variabletype"] == "categorical": if self.schema[field]["variabletype"] == "categorical":
group_by = field group_by = field
if group_by == "CellName": if group_by == "CellName":
group_by = 'cell_name' group_by = "cell_name"
metadata_ranges[field] = {"options": df.obs.groupby(group_by).size().to_dict()} metadata_ranges[field] = {"options": df.obs.groupby(group_by).size().to_dict()}
else: else:
metadata_ranges[field] = { metadata_ranges[field] = {
server/app/web/webapp.py
+4 -4
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@@ -2,10 +2,10 @@ from flask import (
Blueprint, render_template, url_for, current_app 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(): def index():
url_base = current_app.config["CXG_API_BASE"] url_base = current_app.config["CXG_API_BASE"]
dataset_title = current_app.config["DATASET_TITLE"] dataset_title = current_app.config["DATASET_TITLE"]
@@ -13,12 +13,12 @@ def index():
# renders swagger documentation # renders swagger documentation
@bp.route('/swagger') @bp.route("/swagger")
def swag(): def swag():
return render_template("swagger.html") return render_template("swagger.html")
# renders swagger documentation # renders swagger documentation
@bp.route('/favicon.png') @bp.route("/favicon.png")
def favicon(): def favicon():
return url_for("static", filename="img/favicon.png") return url_for("static", filename="img/favicon.png")
server/run.py
+1 -1
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@@ -1,3 +1,3 @@
from app import app 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)