nditech · takinbo · Nov 8, 2022 · Nov 8, 2022 · Nov 8, 2022 · Nov 8, 2022
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -29,7 +29,7 @@ jobs:
           key: deps-v3-1663187796-{{ checksum "requirements/dev.txt" }}
           paths:
             - "/home/circleci/.local"
-      - run: nosetests apollo/
+      - run: pytest -v apollo/
     resource_class: large
 
 workflows:

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,11 @@
 FROM python:3.6
+ARG ENV
 
 LABEL maintainer="Tim Akinbo <[email protected]>"
 
 ADD requirements/ /app/requirements/
-RUN pip install --no-cache-dir -r /app/requirements/prod.txt
+ADD build.sh /app/
+RUN /app/build.sh
 ADD . /app/
 RUN cd /app/ \
     && make babel-compile

diff --git a/apollo/core.py b/apollo/core.py
@@ -5,7 +5,6 @@
 from flask_admin import expose, Admin, AdminIndexView
 from flask_apispec import FlaskApiSpec
 from flask_babelex import Babel
-from flask_caching import Cache
 from flask_cors import CORS
 try:
     from flask_debugtoolbar import DebugToolbarExtension
@@ -40,7 +39,6 @@ def index(self):
 admin = Admin(
     name='Apollo', index_view=AdminHome(name='Dashboard'))
 babel = Babel()
-cache = Cache()
 cors = CORS()
 db = SQLAlchemy(session_options={'expire_on_commit': False})
 jwt_manager = JWTManager()

diff --git a/apollo/deployments/tests.py → apollo/deployments/test_deployments.py b/apollo/deployments/tests.py → apollo/deployments/test_deployments.py
diff --git a/apollo/factory.py b/apollo/factory.py
@@ -18,7 +18,7 @@
 from apollo import settings
 from apollo.api import hooks as jwt_hooks
 from apollo.core import (
-    babel, cache, db, cors, debug_toolbar, fdt_available, jwt_manager,
+    babel, db, cors, debug_toolbar, fdt_available, jwt_manager,
     mail, migrate, red, sentry, uploads)
 from apollo.helpers import register_blueprints
 
@@ -89,7 +89,6 @@ def create_app(
 
     sentry.init_app(app)
     babel.init_app(app)
-    cache.init_app(app)
     cors.init_app(app)
     db.init_app(app)
     jwt_manager.init_app(app)

diff --git a/apollo/formsframework/forms.py b/apollo/formsframework/forms.py
@@ -149,12 +149,12 @@ def __call__(self, form, field):
 
 class BaseQuestionnaireForm(wtforms.Form):
     form = wtforms.StringField(
-        'Form', validators=[wtforms.validators.required()],
+        'Form', validators=[wtforms.validators.DataRequired()],
         filters=[lambda data: filter_form(data)])
     form_serial = wtforms.StringField(
         'Form Serial', validators=[wtforms.validators.optional()])
     sender = wtforms.StringField('Sender',
-                                 validators=[wtforms.validators.required()])
+                                 validators=[wtforms.validators.DataRequired()])
     comment = wtforms.StringField('Comment',
                                   validators=[wtforms.validators.optional()])
 
@@ -339,7 +339,7 @@ def build_questionnaire(form, data=None):
     fields['participant'] = wtforms.StringField(
         'Participant',
         filters=[partial(filter_participants, form)],
-        validators=[wtforms.validators.required()])
+        validators=[wtforms.validators.DataRequired()])
 
     for group in form.data['groups']:
         groupspec = (group['name'], [])
@@ -397,15 +397,15 @@ def build_questionnaire(form, data=None):
 
 class FormForm(SecureForm):
     name = wtforms.StringField(
-        _('Name'), validators=[wtforms.validators.InputRequired()])
+        _('Name'), validators=[wtforms.validators.DataRequired()])
     prefix = wtforms.StringField(
-        _('Form Code'), validators=[wtforms.validators.InputRequired()],
+        _('Form Code'), validators=[wtforms.validators.DataRequired()],
         description=_('What code to identify this form in text messages.'))
     form_type = wtforms.SelectField(
         _('Form Type'), choices=Form.FORM_TYPES,
         coerce=choice_type_coerce_factory(
             Form.form_type.type),
-        validators=[wtforms.validators.InputRequired()])
+        validators=[wtforms.validators.DataRequired()])
     untrack_data_conflicts = wtforms.BooleanField(
         _("Don't Track Data Conflicts"),
         description=_('Whether data conflicts between observers in the same location are tracked or not.'))  # noqa

diff --git a/apollo/formsframework/parser.py b/apollo/formsframework/parser.py
@@ -75,9 +75,14 @@ def __init__(self):
         self.param = None
 
     def parse(self, source):
-        grammar = '\n'.join(v.__doc__ for k, v in list(vars(self.__class__).items())
-                            if '__' not in k and hasattr(v, '__doc__')
-                            and v.__doc__)
+        # using explicit raw-strings prevents a deprecation warning
+        # caused by the parsing of the escape sequences
+        grammar = r'''
+            expr = operator _ operand
+            operator = ">=" / "<=" / ">" / "<" / "=" / "!="
+            operand = ~"\\-?[0-9\\.]+" / "True" / "False"
+            _ = ~"\\s*"
+        '''
         return Grammar(grammar).parse(source)
 
     def eval(self, source, param=None):
@@ -89,20 +94,17 @@ def eval(self, source, param=None):
         return method(node, [self.eval(n) for n in node])
 
     def expr(self, node, children):
-        'expr = operator _ operand'
         operator, _, operand = children
         return operator(self.param, operand)
 
     def operator(self, node, children):
-        'operator = ">=" / "<=" / ">" / "<" / "=" / "!="'
         operators = {
             '>': op.gt, '>=': op.ge,
             '<': op.lt, '<=': op.le,
             '=': op.eq, '!=': op.ne}
         return operators[node.text]
 
     def operand(self, node, children):
-        'operand = ~"\-?[0-9\.]+" / "True" / "False"'
         if node.text == "True":
             return True
         elif node.text == "False":
@@ -111,5 +113,4 @@ def operand(self, node, children):
             return float(node.text)
 
     def _(self, node, children):
-        '_ = ~"\s*"'
         pass
diff --git a/apollo/formsframework/tests.py → apollo/formsframework/test_formsframework.py b/apollo/formsframework/tests.py → apollo/formsframework/test_formsframework.py
@@ -12,6 +12,7 @@
 from apollo.formsframework.models import Form
 from apollo.formsframework.parser import Comparator, grammar_factory
 from apollo.testutils import factory as test_factory, fixtures
+from sqlalchemy.orm.session import close_all_sessions
 
 DEFAULT_FIXTURE_PATH = pathlib.Path(__file__).parent / 'fixtures'
 
@@ -52,7 +53,7 @@ def setUp(self):
         self.incident_form.data = {'groups': [grp2]}
 
     def tearDown(self):
-        db.session.close_all()
+        close_all_sessions()
         db.drop_all()
 
     @mock.patch('apollo.formsframework.forms.filter_form')
@@ -98,7 +99,7 @@ def setUp(self):
         db.create_all()
 
     def tearDown(self):
-        db.session.close_all()
+        close_all_sessions()
         db.drop_all()
 
     def test_numeric_comparisons(self):
@@ -202,7 +203,7 @@ def setUp(self):
         db.create_all()
 
     def tearDown(self):
-        db.session.close_all()
+        close_all_sessions()
         db.drop_all()
 
     def test_active_form_selector(self):

diff --git a/apollo/frontend/tests/__init__.py b/apollo/frontend/tests/__init__.py
diff --git a/apollo/frontend/tests/test_plain.py b/apollo/frontend/tests/test_plain.py
diff --git a/apollo/frontend/tests/test_ut.py b/apollo/frontend/tests/test_ut.py
diff --git a/apollo/locations/tasks.py b/apollo/locations/tasks.py
@@ -154,7 +154,7 @@ def update_locations(
     # spreadsheet structure
 
     for idx in data_frame.index:
-        current_row = data_frame.ix[idx]
+        current_row = data_frame.iloc[idx]
         location_path_helper_map = {}
         error_this_row = False
         warning_this_row = False

diff --git a/apollo/messaging/forms.py b/apollo/messaging/forms.py
@@ -29,8 +29,8 @@ class KannelForm(wtforms.Form):
     :param charset: (Optional) character set for handling incoming message.
     :param coding: (Optional) not being used at the moment.'''
 
-    sender = wtforms.StringField(validators=[wtforms.validators.required()])
-    text = wtforms.StringField(validators=[wtforms.validators.required()])
+    sender = wtforms.StringField(validators=[wtforms.validators.DataRequired()])
+    text = wtforms.StringField(validators=[wtforms.validators.DataRequired()])
     charset = wtforms.StringField()
     coding = wtforms.StringField()
     timestamp = wtforms.IntegerField()
@@ -60,8 +60,8 @@ class TelerivetForm(BaseHttpForm):
 
     id = wtforms.StringField()
     from_number = wtforms.StringField(
-        validators=[wtforms.validators.required()])
-    content = wtforms.StringField(validators=[wtforms.validators.required()])
+        validators=[wtforms.validators.DataRequired()])
+    content = wtforms.StringField(validators=[wtforms.validators.DataRequired()])
     time_created = wtforms.IntegerField()
 
     def get_message(self):

diff --git a/apollo/messaging/tests.py → apollo/messaging/test_messaging.py b/apollo/messaging/tests.py → apollo/messaging/test_messaging.py
diff --git a/apollo/odk/tests.py → apollo/odk/test_odk.py b/apollo/odk/tests.py → apollo/odk/test_odk.py
diff --git a/apollo/participants/tasks.py b/apollo/participants/tasks.py
@@ -156,7 +156,7 @@ def update_participants(dataframe, header_map, participant_set, task):
         db.session.commit()
 
     for idx in index:
-        record = dataframe.ix[idx]
+        record = dataframe.iloc[idx]
         participant_id = record[PARTICIPANT_ID_COL]
         try:
             participant_id = int(participant_id)

diff --git a/apollo/process_analysis/tests.py → ...process_analysis/test_process_analysis.py b/apollo/process_analysis/tests.py → ...process_analysis/test_process_analysis.py
diff --git a/apollo/process_analysis/voting.py b/apollo/process_analysis/voting.py
@@ -3,19 +3,19 @@
 
 
 def proportion(df, options, param):
-    m = df.ix[:, options].sum(axis=1)
+    m = df.loc[:, options].sum(axis=1)
     mbar = m.sum(axis=0) / m.size
-    return df.ix[:, param].sum(axis=0).sum(axis=0) / (mbar * m.size)
+    return df.loc[:, param].sum(axis=0).sum(axis=0) / (mbar * m.size)
 
 
 def variance(df, options, param):
     p = proportion(df, options, param)
     psquared = p * p
 
-    m = df.ix[:, options].sum(axis=1)
+    m = df.loc[:, options].sum(axis=1)
     msquared = m * m
 
-    a = df.ix[:, param].sum(axis=1)
+    a = df.loc[:, param].sum(axis=1)
     asquared = a * a
 
     mbar = m.sum(axis=0) / m.size

diff --git a/apollo/result_analysis/views_results.py b/apollo/result_analysis/views_results.py
@@ -141,12 +141,12 @@ def _voting_results(form_id, location_id=None):
 
     try:
         overall_summation = dataset.groupby(
-            location.location_type.name).sum().ix[location.name]
+            location.location_type.name).sum().loc[location.name]
         reported_subset = dataset[dataset.reported == True]     # noqa
         valid_dataframe = reported_subset[
             reported_subset[location.location_type.name] == location.name]
         valid_summation = reported_subset.fillna(0).groupby(
-            location.location_type.name).sum().ix[location.name]
+            location.location_type.name).sum().loc[location.name]
         reporting = overall_summation[['missing', 'reported']]
         reporting['reported_pct'] = reporting['reported']/(
             reporting['reported'] + reporting['missing'])
@@ -278,9 +278,9 @@ def _voting_results(form_id, location_id=None):
 
             for sublocation in location_tree[location_type]:
                 try:
-                    _overall = grouped_summation.ix[sublocation.name]
+                    _overall = grouped_summation.loc[sublocation.name]
                     _valid = grouped_valid_summation.fillna(
-                        0).ix[sublocation.name]
+                        0).loc[sublocation.name]
                     _reported_subset = dataset[dataset.reported==True]  # noqa
                     _valid_dataframe = _reported_subset[
                         _reported_subset[location_type] == sublocation.name]
@@ -526,22 +526,22 @@ def results_analysis_with_location(form_id, location_id):
 def _point_estimate(dataframe, numerator, denominator):
     if not isinstance(numerator, list):
         numerator = [numerator]
-    m = dataframe.ix[:, denominator].sum(axis=1)
+    m = dataframe.loc[:, denominator].sum(axis=1)
     mbar = m.sum(axis=0) / m.size
-    return dataframe.ix[:, numerator].sum(axis=0).sum(axis=0) / (mbar * m.size)
+    return dataframe.loc[:, numerator].sum(axis=0).sum(axis=0) / (mbar * m.size)
 
 
 def _variance(dataframe, numerator, denominator):
     p = _point_estimate(dataframe, numerator, denominator)
     psquared = p * p
 
-    m = dataframe.ix[:, denominator].sum(axis=1)
+    m = dataframe.loc[:, denominator].sum(axis=1)
     msquared = m * m
 
     if isinstance(numerator, list):
-        a = dataframe.ix[:, numerator].sum(axis=1)
+        a = dataframe.loc[:, numerator].sum(axis=1)
     else:
-        a = dataframe.ix[:, [numerator]].sum(axis=1)
+        a = dataframe.loc[:, [numerator]].sum(axis=1)
     asquared = a * a
 
     mbar = m.sum(axis=0) / m.size

diff --git a/apollo/submissions/incidents.py b/apollo/submissions/incidents.py
@@ -7,10 +7,10 @@ def incidents_csv(df, groupby, options):
         for group in list(grouped.groups.keys()):
             entry = {}
             entry['LOC'] = group
-            entry['TOT'] = int(df.ix[grouped.groups[group]].ix[:, options].fillna(0).sum().sum())
+            entry['TOT'] = int(df.loc[grouped.groups[group]].loc[:, options].fillna(0).sum().sum())
             for option in options:
                 try:
-                    entry[option] = int(df.ix[grouped.groups[group]][option].fillna(0).sum())
+                    entry[option] = int(df.loc[grouped.groups[group]][option].fillna(0).sum())
                 except KeyError:
                     entry[option] = 0
             incidents.append(entry)

diff --git a/apollo/submissions/tests.py → apollo/submissions/test_submissions.py b/apollo/submissions/tests.py → apollo/submissions/test_submissions.py
diff --git a/build.sh b/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+if [ "${ENV}" = "DEV" ]; then
+  pip install --no-cache-dir -r /app/requirements/dev.txt
+else
+  pip install --no-cache-dir -r /app/requirements/prod.txt
+fi
diff --git a/requirements/dev.in b/requirements/dev.in
@@ -3,7 +3,7 @@ autopep8
 coverage
 flake8
 flask-debugtoolbar==0.10.1
-flask-testing==0.7.1
+flask-testing==0.8.1
 mimesis
-nose==1.3.7
 pip-tools
+pytest==7.0.1