test for web

arcovid19/__init__.py

@@ -29,4 +29,4 @@
 from .cache import CACHE, from_cache  # noqa
 from .cases import load_cases  # noqa
 from .models import load_infection_curve  # noqa
-from .web import  get_webapp  # noqa
+from . import web # noqa

arcovid19/cli.py

@@ -29,7 +29,7 @@
 import sys
 
 from .cases import load_cases, CASES_URL
-from .web import get_webapp
+from . import web
 
 
 # =============================================================================
@@ -98,7 +98,7 @@ def webserver(
         directory to the directory containing the first file found.
 
     """
-    app = get_webapp()
+    app = web.create_app()
     app.run(
         host=host, port=port,
         use_reloader=True,

arcovid19/models.py

@@ -447,7 +447,7 @@ class InfectionCurve:
     intervention_end: int = attr.ib(default=25)
     intervention_decrease: float = attr.ib(default=70)
     t_incubation: float = attr.ib(default=5.)
-    t_infectious = attr.ib(default=9.)
+    t_infectious: float = attr.ib(default=9.)
     t_death: float = attr.ib(default=32.)
     mild_recovery: float = attr.ib(default=11.)
     bed_stay: float = attr.ib(default=28.)

arcovid19/web/__init__.py

@@ -38,7 +38,7 @@
 # PUBLIC API
 # =============================================================================
 
-def get_webapp(**kwargs):
+def create_app(**kwargs):
     """Retrieve a flask app for arcovid 19 using the internal blueprint.
 
     """

arcovid19/web/bp.py

@@ -100,7 +100,8 @@ def get_context_data(self):
         context_data = {}
 
         form = forms.InfectionCurveForm()
-        if form.validate_on_submit():
+
+        if flask.request.method == "POST" and form.validate_on_submit():
             # get all the data as string
             data = form.data.copy()
 
@@ -139,6 +140,7 @@ class DownloadView(InfectionCurveView):
 
     def dispatch_request(self):
         context_data = self.get_context_data()
+
         result = context_data["result"]
 
         now = dt.datetime.now().isoformat()

arcovid19/web/templates/InfectionCurve.html

@@ -67,7 +67,7 @@
                             </a>
                     </tr>
                     {% for error in field.errors %}
-                    <tr class="text-danger">
+                    <tr class="field-error text-danger">
                         <td></td>
                         <td>{{error}}</td>
                     </tr>

tests/test_web.py

@@ -0,0 +1,153 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2020, Bruno Sanchez, Vanessa Daza,
+#                     Juan B Cabral, Marcelo Lares,
+#                     Nadia Luczywo, Dante Paz, Rodrigo Quiroga,
+#                     Martín de los Ríos, Federico Stasyszyn
+#                     Cristian Giuppone.
+# License: BSD-3-Clause
+#   Full Text: https://raw.githubusercontent.com/ivco19/libs/master/LICENSE
+
+
+# =============================================================================
+# DOCS
+# =============================================================================
+
+"""Test suite
+
+"""
+
+
+# =============================================================================
+# IMPORTS
+# =============================================================================
+
+import os
+import pathlib
+import tempfile
+import io
+
+import pytest
+
+import numpy as np
+
+import pandas as pd
+
+import arcovid19
+
+
+# =============================================================================
+# CONSTANTS
+# =============================================================================
+
+PATH = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
+
+
+# =============================================================================
+# SETUP
+# =============================================================================
+
+def setup_function(func):
+    arcovid19.CACHE.clear()
+
+
+# =============================================================================
+# FIXTURES
+# =============================================================================
+
+@pytest.fixture
+def webclient():
+    app = arcovid19.web.create_app()
+    db_fd, app.config['DATABASE'] = tempfile.mkstemp()
+    app.config['TESTING'] = True
+
+    with app.test_client() as client:
+        yield client
+
+    os.close(db_fd)
+    os.unlink(app.config['DATABASE'])
+
+
+# =============================================================================
+# TEST INDEX
+# =============================================================================
+
+def test_web_index(webclient):
+    index_response = webclient.get("/")
+    icurve_response = webclient.get("/icurve")
+
+    assert index_response.status_code == 200
+    assert icurve_response.status_code == 200
+    assert index_response.data == icurve_response.data
+
+
+def test_web_post_icurve(webclient):
+    data = {
+        'population': 600000, 'N_init': 10, 'R': 1.2,
+        'intervention_start': 15, 'intervention_end': 25,
+        'intervention_decrease': 70.0, 't_incubation': 5, 't_infectious': 9,
+        't_death': 32.0, 'mild_recovery': 11.0, 'bed_stay': 28.0,
+        'bed_rate': 0.2, 'bed_wait': 5, 'beta': 1.236, 'sigma': 1.1,
+        'gamma': 1.1, 't_max': 200, 'dt': 1.0}
+
+    response = webclient.post('/icurve', data=data)
+    assert response.status_code == 200
+    assert "field-error" not in str(response.data)
+
+
+def test_web_missing_data_post_icurve(webclient):
+    conf = {
+        'population': 600000, 'N_init': 10, 'R': 1.2,
+        'intervention_start': 15, 'intervention_end': 25,
+        'intervention_decrease': 70.0, 't_incubation': 5, 't_infectious': 9,
+        't_death': 32.0, 'mild_recovery': 11.0, 'bed_stay': 28.0,
+        'bed_rate': 0.2, 'bed_wait': 5, 'beta': 1.236, 'sigma': 1.1,
+        'gamma': 1.1, 't_max': 200, 'dt': 1.0}
+
+    for rk in conf.keys():
+        data = {k: v for k, v in conf.items() if k != rk}
+        post_response = webclient.post('/icurve', data=data)
+        assert post_response.status_code == 200
+        assert "field-error" in str(post_response.data)
+
+        get_response = webclient.get('/icurve', data=data)
+        assert get_response.status_code == 200
+        assert "field-error" not in str(get_response.data)
+
+
+def test_web_download_data(webclient):
+    curve_conf = {
+        'population': 600000, 'N_init': 10, 'R': 1.2,
+        'intervention_start': 15, 'intervention_end': 25,
+        'intervention_decrease': 70.0, 't_incubation': 5, 't_infectious': 9,
+        't_death': 32.0, 'mild_recovery': 11.0, 'bed_stay': 28.0,
+        'bed_rate': 0.2, 'bed_wait': 5, 'beta': 1.236, 'sigma': 1.1,
+        'gamma': 1.1}
+    sir_conf = {'t_max': 200, 'dt': 1.0}
+
+    curve = arcovid19.load_infection_curve(**curve_conf)
+    expected = curve.do_SIR(**sir_conf)
+
+    data = {"model": "do_SIR"}
+    data.update(curve_conf)
+    data.update(sir_conf)
+    response = webclient.post('/download_model', data=data)
+
+    ectype = (
+        'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+    assert response.status_code == 200
+    assert response.headers["Content-Type"] == ectype
+
+    # validate result
+    result = pd.read_excel(io.BytesIO(response.data), sheet_name="Data")
+    result = result.set_index("ts")
+
+    # validate in the 8 decimal place
+    np.testing.assert_array_almost_equal(result, expected.df, decimal=8)
+
+    config = pd.read_excel(io.BytesIO(response.data), sheet_name="Config")
+    config = config.set_index("Attribute")
+
+    assert config.to_dict()["Value"] == data

tox.ini

@@ -1,6 +1,6 @@
 # content of: tox.ini , put in same dir as setup.py
 [tox]
-envlist = py37, py38, style, coverage, docs
+envlist = style, py37, py38, docs, coverage
 
 [pytest]
 addopts = -n "auto" --mpl