From 9b2d284ac2d614c5404a62d8d73fa6c9ea813915 Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 13:54:06 +0200
Subject: [PATCH 01/11] Added test coverage through coveralls in the travis
 system

---
 .travis.yml           |  1 +
 backend/settings.py   |  6 +++++-
 test/travis_script.sh | 10 ++++++++--
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index dc53665ad..e9d8926e4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,5 +7,6 @@ before_install:
     - test/travis_before_install.sh
 install:
     - pip install -r backend/requirements.txt
+    - pip install coverage coveralls
 script:
     - test/travis_script.sh
diff --git a/backend/settings.py b/backend/settings.py
index 4cbd431b3..b0a62ebc4 100644
--- a/backend/settings.py
+++ b/backend/settings.py
@@ -1,6 +1,10 @@
 import json
 
-json_settings_fh = open("../settings.json")
+try:
+    json_settings_fh = open("settings.json")
+except FileNotFoundError:
+    json_settings_fh = open("../settings.json")
+
 json_settings = json.load(json_settings_fh)
 json_settings_fh.close()
 
diff --git a/test/travis_script.sh b/test/travis_script.sh
index 1124cc748..f4ccef324 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -31,13 +31,14 @@ mysql -u swefreq -h 127.0.0.1 -P 3366 swefreq_test < test/data/load_dummy_data.s
 
 
 echo ">>> Test 3. Check that the backend starts"
-cd backend
 
+cd backend
 ../test/01_daemon_starts.sh
+cd ..
 
 
 echo ">>> Test 4. the backend API"
-python route.py --develop 1>http_log.txt 2>&1 &
+coverage run backend/route.py --develop 1>http_log.txt 2>&1 &
 BACKEND_PID=$!
 
 function exit_handler() {
@@ -51,3 +52,8 @@ trap exit_handler EXIT
 
 sleep 2 # Lets wait a little bit so the server has started
 python test.py -v
+
+kill -2 $BACKEND_PID
+sleep 2
+
+coveralls

From 93e116b2f006435e358f4d7b9b05be687b6e1e5c Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 15:01:39 +0200
Subject: [PATCH 02/11] Updated Dockerfile-backend to run from base dir instea

---
 Dockerfile-backend | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile-backend b/Dockerfile-backend
index c2f9361ba..2ccc0b728 100644
--- a/Dockerfile-backend
+++ b/Dockerfile-backend
@@ -6,8 +6,8 @@ RUN apt-get update && apt-get install -y \
         libmysqlclient-dev
 
 ADD . /code
-WORKDIR /code/backend
+WORKDIR /code
 
-RUN pip3 install -r requirements.txt
+RUN pip3 install -r backend/requirements.txt
 
-CMD ["python3", "route.py", "--develop"]
+CMD ["python3", "backend/route.py", "--develop"]

From 9dbc07d3f2961c22b694f578c2a3b3da33a90f66 Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 15:02:21 +0200
Subject: [PATCH 03/11] Run from base directory in travis test

---
 test/travis_script.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/travis_script.sh b/test/travis_script.sh
index f4ccef324..58e6dba3e 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -51,7 +51,7 @@ function exit_handler() {
 trap exit_handler EXIT
 
 sleep 2 # Lets wait a little bit so the server has started
-python test.py -v
+python backend/test.py -v
 
 kill -2 $BACKEND_PID
 sleep 2

From 6a520e9e9418c8d1338b42bb48bc5e68d7f7b415 Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 14:12:59 +0200
Subject: [PATCH 04/11] More coverage settings and show result in log

---
 .coveragerc           | 5 +++++
 test/travis_script.sh | 3 ++-
 2 files changed, 7 insertions(+), 1 deletion(-)
 create mode 100644 .coveragerc

diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 000000000..8db5982de
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,5 @@
+[run]
+omit = /usr/local/*,/home/travis/virtualenv/*
+
+[report]
+omit = /usr/local/*,/home/travis/virtualenv/*
diff --git a/test/travis_script.sh b/test/travis_script.sh
index 58e6dba3e..f6b7fe57e 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -38,7 +38,7 @@ cd ..
 
 
 echo ">>> Test 4. the backend API"
-coverage run backend/route.py --develop 1>http_log.txt 2>&1 &
+coverage run backend/route.py --port=4000 --develop 1>http_log.txt 2>&1 &
 BACKEND_PID=$!
 
 function exit_handler() {
@@ -57,3 +57,4 @@ kill -2 $BACKEND_PID
 sleep 2
 
 coveralls
+coverage report

From b0b5494245faf41b1a46f5fbfab3c81a8b9e4eec Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 14:31:33 +0200
Subject: [PATCH 05/11] Only run the test coverage stuff if we have the
 ".coverage" file

---
 test/travis_script.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/travis_script.sh b/test/travis_script.sh
index f6b7fe57e..66d7f3104 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -56,5 +56,7 @@ python backend/test.py -v
 kill -2 $BACKEND_PID
 sleep 2
 
-coveralls
-coverage report
+if [ -f .coverage ]; then
+    coveralls
+    coverage report
+fi

From 902c171db6c705e92af0d19e021fd51c954a840d Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 14:40:01 +0200
Subject: [PATCH 06/11] Added a way to quit the webapp in developer mode

---
 backend/application.py | 7 +++++++
 backend/route.py       | 1 +
 test/travis_script.sh  | 5 +++--
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/backend/application.py b/backend/application.py
index 4df01482d..49c0f90ce 100644
--- a/backend/application.py
+++ b/backend/application.py
@@ -8,6 +8,7 @@
 import smtplib
 import socket
 import tornado.web
+import tornado
 import random
 import string
 import uuid
@@ -41,6 +42,12 @@ def build_dataset_structure(dataset_version, user=None, dataset=None):
     return r
 
 
+class QuitHandler(handlers.UnsafeHandler):
+    def get(self):
+        ioloop = tornado.ioloop.IOLoop.instance()
+        ioloop.stop()
+
+
 class GetSchema(handlers.UnsafeHandler):
     """
     Returns the schema.org, and bioschemas.org, annotation for a given
diff --git a/backend/route.py b/backend/route.py
index 200b3b7a6..3b0c6de06 100644
--- a/backend/route.py
+++ b/backend/route.py
@@ -92,6 +92,7 @@ def __init__(self, settings):
         ## Adding developer login handler
         if settings.get('develop', False):
             self.declared_handlers.insert(-1, ("/developer/login", auth.DeveloperLoginHandler))
+            self.declared_handlers.insert(-1, ("/developer/quit",  application.QuitHandler))
 
         # google oauth key
         self.oauth_key = tornado_settings["google_oauth"]["key"]
diff --git a/test/travis_script.sh b/test/travis_script.sh
index 66d7f3104..b83c44003 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -52,10 +52,11 @@ trap exit_handler EXIT
 
 sleep 2 # Lets wait a little bit so the server has started
 python backend/test.py -v
-
-kill -2 $BACKEND_PID
 sleep 2
 
+# Quit the app
+curl localhost:4000/developer/quit
+
 if [ -f .coverage ]; then
     coveralls
     coverage report

From fe3a6808689ee9dfd7d096c7d00bb7837b591c18 Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 16:07:45 +0200
Subject: [PATCH 07/11] Added travis and coverage badges to readme

---
 README.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/README.md b/README.md
index 04b8d704e..9d563bfd4 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,8 @@
 SweFreq - Swedish Frequency database
 ====================================
+[![Travis Status][travis-badge]][travis-link]
+[![Coverage Status][coveralls-badge]][coverage-link]
+
 
 Running on a production system
 ------------------------------
@@ -70,3 +73,8 @@ Quick development mode
 ```bash
 $ docker-compose up
 ```
+
+[travis-badge]: https://travis-ci.org/NBISweden/swefreq.svg?branch=develop
+[travis-link]: https://travis-ci.org/NBISweden/swefreq
+[coveralls-badge]: https://coveralls.io/repos/github/NBISweden/swefreq/badge.svg?branch=develop
+[coveralls-link]: https://coveralls.io/github/NBISweden/swefreq?branch=release

From db0efb7e4349480c71550a7de3275a80413f443c Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Wed, 4 Apr 2018 16:12:14 +0200
Subject: [PATCH 08/11] Updated coveralls badge

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9d563bfd4..a9591ac71 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 SweFreq - Swedish Frequency database
 ====================================
 [![Travis Status][travis-badge]][travis-link]
-[![Coverage Status][coveralls-badge]][coverage-link]
+[![Coverage Status][coveralls-badge]][coveralls-link]
 
 
 Running on a production system
@@ -77,4 +77,4 @@ $ docker-compose up
 [travis-badge]: https://travis-ci.org/NBISweden/swefreq.svg?branch=develop
 [travis-link]: https://travis-ci.org/NBISweden/swefreq
 [coveralls-badge]: https://coveralls.io/repos/github/NBISweden/swefreq/badge.svg?branch=develop
-[coveralls-link]: https://coveralls.io/github/NBISweden/swefreq?branch=release
+[coveralls-link]: https://coveralls.io/github/NBISweden/swefreq?branch=develop

From a02753fe2cc8160dd92e7db7721e4e5a47a40f4d Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Thu, 5 Apr 2018 09:44:26 +0200
Subject: [PATCH 09/11] Moved the sleeps around

---
 test/travis_script.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/travis_script.sh b/test/travis_script.sh
index b83c44003..b3a98b970 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -41,6 +41,8 @@ echo ">>> Test 4. the backend API"
 coverage run backend/route.py --port=4000 --develop 1>http_log.txt 2>&1 &
 BACKEND_PID=$!
 
+sleep 2 # Lets wait a little bit so the server has started
+
 function exit_handler() {
     kill -9 $BACKEND_PID
 
@@ -50,12 +52,12 @@ function exit_handler() {
 
 trap exit_handler EXIT
 
-sleep 2 # Lets wait a little bit so the server has started
+
 python backend/test.py -v
-sleep 2
 
 # Quit the app
 curl localhost:4000/developer/quit
+sleep 2 # Lets wait a little bit so the server has stopped
 
 if [ -f .coverage ]; then
     coveralls

From 0ea9885713cf6e703c2cb9885a62f6eb7bdc01ff Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Thu, 5 Apr 2018 09:54:05 +0200
Subject: [PATCH 10/11] Better exit handler

---
 test/travis_script.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/travis_script.sh b/test/travis_script.sh
index b3a98b970..a187e9604 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -44,10 +44,14 @@ BACKEND_PID=$!
 sleep 2 # Lets wait a little bit so the server has started
 
 function exit_handler() {
+    rv=$?
+    # Ignore errors in the exit handler
+    set +e 
     kill -9 $BACKEND_PID
 
     echo "THE HTTP LOG WAS:"
     cat http_log.txt
+    exit $rv
 }
 
 trap exit_handler EXIT

From 209ba62db381b953c39178d925c60d0d9741d589 Mon Sep 17 00:00:00 2001
From: Johan Viklund <johan.viklund@nbis.se>
Date: Thu, 5 Apr 2018 11:12:19 +0200
Subject: [PATCH 11/11] Updated travis script

---
 .pylintrc             | 3 ++-
 test/travis_script.sh | 8 ++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.pylintrc b/.pylintrc
index 3e4f6d1d3..5b77e41e8 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -138,7 +138,8 @@ disable=print-statement,
         keyword-arg-before-vararg,
         arguments-differ,
         line-too-long,
-        import-error
+        import-error,
+        no-self-use
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
diff --git a/test/travis_script.sh b/test/travis_script.sh
index a187e9604..34f904dc0 100755
--- a/test/travis_script.sh
+++ b/test/travis_script.sh
@@ -32,9 +32,7 @@ mysql -u swefreq -h 127.0.0.1 -P 3366 swefreq_test < test/data/load_dummy_data.s
 
 echo ">>> Test 3. Check that the backend starts"
 
-cd backend
-../test/01_daemon_starts.sh
-cd ..
+(cd backend && ../test/01_daemon_starts.sh)
 
 
 echo ">>> Test 4. the backend API"
@@ -43,10 +41,12 @@ BACKEND_PID=$!
 
 sleep 2 # Lets wait a little bit so the server has started
 
-function exit_handler() {
+exit_handler() {
     rv=$?
     # Ignore errors in the exit handler
     set +e 
+    # We want to make sure the background process has stopped, otherwise the
+    # travis test will stall for a long time.
     kill -9 $BACKEND_PID
 
     echo "THE HTTP LOG WAS:"