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Style guide cleanup

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This commit is contained in:
Charlotte Weaver
2018-06-22 17:43:10 -07:00
parent 15ce4cc338
commit ca16447115
8 changed files with 930 additions and 45 deletions
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backend/app/__init__.py
+9 -8
View File
@@ -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",
description='An API connecting ExpressionMatrix2 clustering algorithm to cellxgene'))
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'))
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 -5
View File
@@ -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
+4 -2
View File
@@ -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
+8 -19
View File
@@ -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_2 = self.data.X[cells_idx_2,:]
expression_1 = self.data.X[cells_idx_1, :]
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
+2
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@@ -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
+4 -7
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@@ -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
+3 -1
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@@ -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():
backend/test/test_api.py
+898 -3
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