Record coverage for integration tests

api/api.py

+import atexit
 import json
+import os
 import sys
 import traceback
 
@@ -225,7 +227,8 @@ def app_factory(*_, **__):
     application = webapp2.WSGIApplication(routes, debug=config.__config['core']['debug'])
     application.router.set_dispatcher(dispatcher)
     application.request_class = SciTranRequest
-
+    if os.environ.get("SCITRAN_RUNTIME_COVERAGE") == "true":
+        start_coverage()
     # configure new relic
     if config.__config['core']['newrelic']:
         try:
@@ -241,3 +244,16 @@ def app_factory(*_, **__):
             sys.exit(1)
 
     return application
+
+# Functions to enable code coverage when API is started for testing
+def start_coverage():
+    import coverage
+    config.log.info("Enabling code coverage")
+    cov = coverage.coverage(source=["api"], data_suffix="integration-tests")
+    cov.start()
+    atexit.register(save_coverage, cov)
+
+def save_coverage(cov):
+    config.log.info("Saving coverage")
+    cov.stop()
+    cov.save()

bin/api.wsgi

 # vim: filetype=python
-import sys
-import os.path
-
 from api import api
 
 application = api.app_factory()

bin/run-dev-osx.sh

@@ -76,6 +76,7 @@ SCITRAN_RUNTIME_PORT=${SCITRAN_RUNTIME_PORT:-"8080"}
 SCITRAN_RUNTIME_UWSGI_INI=${SCITRAN_RUNTIME_UWSGI_INI:-""}
 SCITRAN_RUNTIME_BOOTSTRAP=${SCITRAN_RUNTIME_BOOTSTRAP:-"./bootstrap.json"}
 SCITRAN_RUNTIME_SSL_PEM=${SCITRAN_RUNTIME_SSL_PEM:-""}
+SCITRAN_RUNTIME_COVERAGE=${SCITRAN_RUNTIME_COVERAGE:-"false"}
 
 SCITRAN_CORE_DRONE_SECRET=${SCITRAN_CORE_DRONE_SECRET:-$( openssl rand -base64 32 )}
 
@@ -106,7 +107,7 @@ clean_up () {
     kill $MONGOD_PID || true
     kill $UWSGI_PID || true
     deactivate || true
-    wait
+    wait 2> /dev/null
 }
 trap clean_up EXIT
 

test/bin/run-integration-tests.sh

@@ -4,6 +4,8 @@ set -eu
 unset CDPATH
 cd "$( dirname "${BASH_SOURCE[0]}" )/../.."
 
+rm -f .coverage.integration-tests
+
 USAGE="
     Usage:\n
     $0 <api-base-url> <mongodb-uri>\n
@@ -40,7 +42,7 @@ rm -rf test/integration_tests/python/__pycache__
 
 BASE_URL="$SCITRAN_SITE_API_URL" \
     MONGO_PATH="$MONGODB_URI" \
-    py.test --cov=api --cov-append test/integration_tests/python
+    py.test test/integration_tests/python
 
 newman run test/integration_tests/postman/integration_tests.postman_collection -e test/integration_tests/postman/environments/integration_tests.postman_environment
 

test/bin/run-tests-osx.sh

@@ -13,7 +13,13 @@ SCITRAN_PERSISTENT_PATH="$( mktemp -d )"
 
 clean_up () {
   kill $API_PID || true
+  wait 2> /dev/null
   rm -rf "$SCITRAN_PERSISTENT_PATH"
+  # Report on unit tests and integration tests separately
+  coverage report -m
+  rm .coverage
+  coverage combine
+  coverage report -m
 }
 
 trap clean_up EXIT
@@ -29,6 +35,7 @@ trap clean_up EXIT
 
 SCITRAN_RUNTIME_PORT=8081 \
     SCITRAN_CORE_DRONE_SECRET=integration-tests \
+    SCITRAN_RUNTIME_COVERAGE="true" \
     ./bin/run-dev-osx.sh -T -U -I &
 API_PID=$!
 

test/bin/run-tests-ubuntu.sh

@@ -8,6 +8,19 @@ cd "$( dirname "${BASH_SOURCE[0]}" )/../.."
 
 ./test/bin/run-unit-tests.sh
 
+clean_up () {
+  kill $API_PID || true
+  wait 2> /dev/null
+  # Report on unit tests and integration tests separately
+  # Only submit integration test coverage to coveralls
+  coverage report -m
+  rm .coverage
+  coverage combine
+  coverage report -m
+}
+
+trap clean_up EXIT
+
 API_BASE_URL="http://localhost:8081/api"
 SCITRAN_PERSISTENT_DB_PORT=${SCITRAN_PERSISTENT_DB_PORT:-"9001"}
 SCITRAN_PERSISTENT_DB_URI=${SCITRAN_PERSISTENT_DB_URI:-"mongodb://localhost:$SCITRAN_PERSISTENT_DB_PORT/scitran"}
@@ -23,7 +36,9 @@ uwsgi --http "localhost:8081" --master --http-keepalive \
   --logformat '%(addr) - %(user) [%(ltime)] "%(method) %(uri) %(proto)" %(status) %(size) "%(referer)" "%(uagent)" request_id=%(request_id)' \
   --env "SCITRAN_PERSISTENT_DB_URI=$SCITRAN_PERSISTENT_DB_URI" \
   --env "SCITRAN_PERSISTENT_PATH=$SCITRAN_PERSISTENT_PATH" \
-  --env "SCITRAN_PERSISTENT_DATA_PATH=$SCITRAN_PERSISTENT_DATA_PATH" &
+  --env "SCITRAN_PERSISTENT_DATA_PATH=$SCITRAN_PERSISTENT_DATA_PATH" \
+  --env 'SCITRAN_RUNTIME_COVERAGE=true' &
+API_PID=$!
 
 ./test/bin/run-integration-tests.sh \
     "$API_BASE_URL" \

test/bin/run-unit-tests.sh

@@ -16,4 +16,6 @@ echo "Checking for files with windows style newline:"
 # Which have a mismatched __file__ attribute when loaded in docker container
 rm -rf test/unit_tests/python/__pycache__
 
-PYTHONPATH="$( pwd )"  py.test --cov=api --cov-append test/unit_tests/python
+rm -f .coverage
+
+PYTHONPATH="$( pwd )"  py.test --cov=api test/unit_tests/python

test/integration_tests/requirements-integration-test.txt

 coverage==4.0.3
 coveralls==1.1
 pylint==1.5.3
-pymongo==3.2
 pytest-cov==2.2.0
 pytest-watch==3.8.0
 pytest==2.8.5
-python-dateutil==1.5
-requests==2.9.1
 mock==2.0.0
 testfixtures==4.10.1