Merge branch 'v0.22.2'

.github/workflows/ci.yml

@@ -0,0 +1,78 @@
+on: [pull_request]
+name: CI
+jobs:
+  # run python/js tests, coveralls and lint
+  integration-test:
+    name: python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: ci_db_test
+        ports:
+          - 5432:5432
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+        - ubuntu-20.04
+        python-version:
+        - 3.6
+        - 3.7
+        - 3.8
+        - 3.9
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up ruby for coveralls
+        uses: actions/setup-ruby@v1
+      - name: Set up js
+        uses: actions/setup-node@v1
+      - name: Install js dependencies
+        run: npm install [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
+      - name: Install opal
+        run: pip install -e .
+      - name: Install dependencies
+        run: pip install -r test-requirements.txt
+      - run: gem install coveralls-lcov
+      - name: run tests
+        run: opal test --coverage
+      - name: flake8
+        run: flake8
+      - name: combine coveralls
+        run: find coverage -name "lcov.info" -exec coveralls-lcov -v -n {} \; > coverage/coverage.json
+      - run: coveralls --merge=coverage/coverage.json
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}"
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+  # make sure the python side of things works on windows
+  other-os-tests:
+    name: ${{ matrix.os }} python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+        - windows-latest
+        python-version:
+        - 3.9
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install opal
+        run: pip install -e .
+      - name: Install dependencies
+        run: pip install -r test-requirements.txt
+      - name: run tests
+        run: opal test py

README.md

@@ -1,10 +1,11 @@
 Opal
 ====
 
-[![Build Status](https://travis-ci.org/openhealthcare/opal.svg?branch=v0.11.0)](https://travis-ci.org/openhealthcare/opal)
+![Build](https://github.com/openhealthcare/opal/workflows/.github/workflows/build.yml/badge.svg)
+
 [![Coverage Status](https://coveralls.io/repos/github/openhealthcare/opal/badge.svg?branch=v0.11.0)](https://coveralls.io/github/openhealthcare/opal?branch=v0.11.0)
-[![PyPI version](https://badge.fury.io/py/opal.svg)](https://badge.fury.io/py/opal)
 
+[![PyPI version](https://badge.fury.io/py/opal.svg)](https://badge.fury.io/py/opal)
 
 Opal is a full stack web framework that makes building digital tools for health care easy.
 

changelog.md

@@ -1,3 +1,11 @@
+### 0.22.2 (Minor Release)
+
+#### The future filter now accepts strings
+
+The filter `future` now accepts a string as outputted by the Opal date serialization
+e.g. 27/12/2022.
+
+
 ### 0.22.1 (Minor Release)
 
 #### Exclude many to one relationships from the advanced search

doc/mkdocs.yml

@@ -121,7 +121,7 @@ dev_addr: 0.0.0.0:8965
 include_next_prev: false
 
 extra:
-  version: v0.22.1
+  version: v0.22.2
 
 markdown_extensions:
     - fenced_code

opal/_version.py

@@ -1,4 +1,4 @@
 """
 Declare our current version string
 """
-__version__ = '0.22.1'
+__version__ = '0.22.2'

opal/core/search/extract.py

@@ -10,7 +10,6 @@
 import logging
 import os
 import tempfile
-import zipfile
 
 from django.template import loader
 from django.core.serializers.json import DjangoJSONEncoder
@@ -84,7 +83,9 @@ def get_field_names_to_render(self):
 
         # We should have id, patient_id, episode_id in every subrecord
         # CSV, if these fields are present, make them appear first.
-        id_fields = [f for f in ["id", "patient_id", "episode_id"] if f in result]
+        id_fields = [
+            f for f in ["id", "patient_id", "episode_id"] if f in result
+        ]
 
         for f in id_fields:
             result.remove(f)

opal/core/search/static/js/search/services/patient_summary.js

@@ -1,10 +1,9 @@
 //
 // This is the main PatientSummary class for OPAL.
 //
-angular.module('opal.services').factory('PatientSummary', function(UserProfile) {
+angular.module('opal.services').factory('PatientSummary', function() {
         var PatientSummary = function(jsonResponse){
             var startYear, endYear;
-            var self = this;
 
             if(jsonResponse.start_date){
                 startYear= moment(jsonResponse.start_date, 'DD/MM/YYYY').format("YYYY");
@@ -28,9 +27,6 @@ angular.module('opal.services').factory('PatientSummary', function(UserProfile)
             this.categories = jsonResponse.categories.join(", ");
             this.link = "/#/patient/" + jsonResponse.patient_id;
             this.hospitalNumber = jsonResponse.hospital_number;
-            UserProfile.load().then(function(user_profile){
-                self.canViewPatientNotes = _.contains(user_profile.roles.default, "micro_haem");
-            })
         };
 
         return PatientSummary;

opal/core/search/static/js/test/extract.controller.test.js

@@ -424,7 +424,6 @@ describe('ExtractCtrl', function(){
                     {categories: []}
                 ]
             });
-            $httpBackend.expectGET('/api/v0.1/userprofile/').respond({roles: {default: []}});
             $scope.criteria[0] = {
                 combine    : "and",
                 column     : "symptoms",

opal/core/search/static/js/test/search.controller.test.js

@@ -57,7 +57,6 @@ describe('SearchCtrl', function (){
             $httpBackend.expectGET('/search/simple/?query=jane').respond(
                 {object_list: [{categories: []}]}
             );
-            $httpBackend.expectGET('/api/v0.1/userprofile/').respond({roles: {default: []}});
             expect($scope.query.searchTerm.length).toBe(0);
             $scope.query.autocompleteSearchTerm = 'jane';
             expect($scope.getQueryParam()).toEqual('jane');

opal/core/test_runner.py

@@ -10,7 +10,10 @@
 
 from opal.utils import write
 
-TRAVIS = os.environ.get('TRAVIS', False)
+# We're using the GITHUB_WORKFLOW env variable
+# to determine that we are running in a github action.
+# GITHUB_WORKFLOW is set in the env by github.
+GITHUB_ACTION = os.environ.get('GITHUB_WORKFLOW', False)
 
 
 def _has_file(where, filename):
@@ -84,7 +87,7 @@ def _run_js_tests(args):
     # to a string
     env["OPAL_LOCATION"] = str(args.opal_location)
 
-    if TRAVIS:
+    if GITHUB_ACTION:
         karma = './node_modules/karma/bin/karma'
     else:
         karma = 'karma'

opal/static/js/opal/filters.js

@@ -120,13 +120,13 @@ filters.filter('daysSince', function(daysToFilter){
 });
 
 
-filters.filter('future', function(){
+filters.filter('future', function(toMomentFilter){
     return function(i, includeToday){
       if(!i){
         return false;
       }
       var today = new moment();
-      var input = moment(i);
+      var input = toMomentFilter(i);
 
 			if(includeToday && input.isSame(today, "day")){
         return true;

opal/static/js/test/filters.test.js

@@ -278,6 +278,10 @@ describe('filters', function() {
       expect(futureFilter(tomorrow)).toBe(true);
     });
 
+    it('should work for strings that look like dates', function(){
+      expect(futureFilter('27/12/5000')).toBe(true);
+    });
+
     it('should return true if today if we include today', function(){
       expect(futureFilter(new Date(), true)).toBe(true);
     });

opal/tests/js_config/karma_defaults.js

@@ -63,8 +63,8 @@ module.exports = function(includedFiles, baseDir, coverageFiles){
       }
     ];
 
-    if(process.env.TRAVIS){
-        browsers = ["Firefox"];
+    if(process.env.GITHUB_WORKFLOW){
+        browsers = ["FirefoxHeadless"];
         plugins.push("karma-firefox-launcher");
         plugins.push("karma-coveralls");
         if(useCoverage){

opal/tests/test_core_test_runner.py

@@ -10,6 +10,7 @@
 
 from opal.core import test_runner
 
+
 class RunPyTestsTestCase(OpalTestCase):
 
     @patch('subprocess.check_call')
@@ -148,10 +149,10 @@ def test_run_tests_for_unknown_config(self, sysexit, writer, has_file):
 class RunJSTestsTestCase(OpalTestCase):
 
     def setUp(self):
-        self.TRAVIS = test_runner.TRAVIS
+        self.GITHUB_ACTION = test_runner.GITHUB_ACTION
 
     def tearDown(self):
-        test_runner.TRAVIS = self.TRAVIS
+        test_runner.GITHUB_ACTION = self.GITHUB_ACTION
 
     @patch('subprocess.check_call')
     def test_run_tests(self, check_call):
@@ -160,21 +161,21 @@ def test_run_tests(self, check_call):
         mock_args.coverage = False
         mock_args.test = None
         mock_args.failfast = False
-        test_runner.TRAVIS = False
+        test_runner.GITHUB_ACTION = False
         test_runner._run_js_tests(mock_args)
         self.assertEqual(
             ['karma', 'start', 'config/karma.conf.js', '--single-run'],
             check_call.call_args[0][0]
         )
 
     @patch('subprocess.check_call')
-    def test_run_tests_travis(self, check_call):
+    def test_run_tests_github(self, check_call):
         mock_args = MagicMock(name="args")
         mock_args.userland_here = ffs.Path('.')
         mock_args.coverage = False
         mock_args.test = None
         mock_args.failfast = False
-        test_runner.TRAVIS = True
+        test_runner.GITHUB_ACTION = True
         test_runner._run_js_tests(mock_args)
         self.assertEqual(
             [
@@ -198,7 +199,7 @@ def test_run_tests_failfast(self, check_call):
         mock_args.coverage = False
         mock_args.test = None
         mock_args.failfast = True
-        test_runner.TRAVIS = False
+        test_runner.GITHUB_ACTION = False
         test_runner._run_js_tests(mock_args)
         self.assertEqual(
             [

runtests.py

@@ -113,13 +113,13 @@
     }
 )
 
-if 'TRAVIS' in os.environ:
+if os.environ.get('GITHUB_WORKFLOW') and not os.environ.get('RUNNER_OS') == 'Windows':
     test_settings_config["DATABASES"] = {
         'default': {
             'ENGINE': 'django.db.backends.postgresql_psycopg2',
-            'NAME': 'travis_ci_test',
+            'NAME': 'ci_db_test',
             'USER': 'postgres',
-            'PASSWORD': '',
+            'PASSWORD': 'postgres',
             'HOST': 'localhost',
         }
     }

setup.py

@@ -45,6 +45,8 @@
         ]
     },
     install_requires=[
+        # We pin kombu because kombu 5.3 imports does not work on python 3.6.9
+        'kombu==5.1.0',
         'ffs>=0.0.8.2',
         'Jinja2==2.10.1',
         'django==2.2.16',