Dockerize tests

.dockerignore

@@ -1,4 +1,8 @@
+.git
+
+# --- Below Should mirror .gitignore, without leading '/' --- #
 .DS_Store
 .*sw[op]
 *.py[co]
 *.egg-info
+testdata

.gitignore

@@ -2,3 +2,4 @@
 .*sw[op]
 *.py[co]
 *.egg-info
+testdata

.travis.yml

@@ -1,39 +1,29 @@
 sudo: false
-language: python
-python:
-    - "2.7"
+dist: trusty
+services:
+    - docker
 
 env:
     global:
-        - DCMTK_VERSION="dcmtk-3.6.1_20150924"
-        - DCMTK_DB_DIR="dcmtk_dicom_db"
-        - TESTDATA_DIR="testdata"
-        - ORTHANC_VERSION="Orthanc-1.1.0"
+        - TESTDATA_DIR="$HOME/.cache/testdata"
+        - DOCKER_DIR="$HOME/.cache/docker"
         - secure: tLyIDfETpHCDRyEqF2ROM8ue+D+fl/IeOdFBY/Mov7zhAHpgBdQQJi+HQ1/RK+G7DDsnM/FIjvCcf4etphmBHK3xs8vDM1oPntYs+3iE2AbTcVGglHYoX1++H76xPt3eXyf1S0frgVg6qYCNmuP0chhDUkYXPydcKvq1ANjfTQU= # BUILD_TRIGGER_URL
 
 cache:
-    pip: true
     directories:
-        - $DCMTK_VERSION
-        - $DCMTK_DB_DIR
         - $TESTDATA_DIR
-        - $ORTHANC_VERSION
+        - $DOCKER_DIR
 
-addons:
-    apt:
-        packages:
-            - uuid-dev
 
-before_install:
-    - ln -s bin $VIRTUAL_ENV/sbin
-
-install:
-    - pip install .
-    - pip install -r test/requirements.txt
-    - ./test/install_deps.sh
+install: true
 
 script:
-    - ./test/lint.sh && ./test/test.sh
+    - test -f "$DOCKER_DIR/image.tar" && sudo docker load -i "$DOCKER_DIR/image.tar" || true
+    - docker build -t my_image .
+    - docker save -o "$DOCKER_DIR/image.tar" $(docker history -q my_image | grep -v '<missing>')
+    - mkdir -p "$TESTDATA_DIR"
+    - curl -L https://github.com/scitran/testdata/archive/master.tar.gz | tar xz -C "$TESTDATA_DIR" --strip-components 1
+    - ./docker/test.sh --testdata "$TESTDATA_DIR"
 
 after_success:
     - if [ "$TRAVIS_TAG" ]; then

bin/dicom_sniper

@@ -44,6 +44,7 @@ auth_group.add_argument('--key', help='user API key')
 args = arg_parser.parse_args(sys.argv[1:] or ['--help'])
 args.query = dict(args.query)
 
+
 args.timezone = reaper.util.validate_timezone(args.timezone)
 if args.timezone is None:
     log.error('invalid timezone')
@@ -60,7 +61,7 @@ matched_series = {}
 for study in scu_studies:
     scu_series = scu_.find(reaper.scu.SeriesQuery(**reaper.scu.SCUQuery(StudyInstanceUID=study.StudyInstanceUID)))
     for series in scu_series:
-        if series.NumberOfSeriesRelatedInstances is None:
+        if not series.NumberOfSeriesRelatedInstances:
             scu_images = scu_.find(reaper.scu.ImageQuery(**reaper.scu.SCUQuery(SeriesInstanceUID=series.SeriesInstanceUID)))
             series.NumberOfSeriesRelatedInstances = len(scu_images)
         matched_series[series.SeriesInstanceUID] = {

docker/Dockerfile-orthanc

@@ -0,0 +1,20 @@
+#
+# Image used for hosting .
+#
+# Example usage is in README.md
+#
+
+FROM ubuntu:16.04
+
+
+# Install pre-requisites
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+		ca-certificates curl \
+		dcmtk \
+		orthanc \
+	&& rm -rf /var/lib/apt/lists/*
+
+COPY orthanc-config.json /etc/orthanc/orthanc-reaper-config.json
+
+ENTRYPOINT ["Orthanc", "/etc/orthanc/orthanc-reaper-config.json"]

docker/orthanc-config.json

@@ -0,0 +1,7 @@
+{
+  "UnknownSopClassAccepted" : true,
+  "RemoteAccessAllowed" : true,
+  "DicomModalities" : {
+    "reaper"  : [ "REAPER", "reaper-test", 5104]
+  }
+}

docker/test.sh

@@ -0,0 +1,130 @@
+#!/usr/bin/env bash
+
+set -e
+
+unset CDPATH
+cd "$( dirname "${BASH_SOURCE[0]}" )/.."
+
+function usage() {
+cat >&2 <<EOF
+Run scitran-reaper tests
+
+Usage:
+    $0 [OPTION...] [-- TEST_ARGS...]
+
+Options:
+    -B, --no-build      Skip Docker Builds
+    -h, --help          Print this help and exit
+    --testdata path     Path to testdata.
+    -- TEST_ARGS        Arguments passed to test/bin/test.sh
+
+EOF
+}
+
+function main() {
+  local DOCKER_BUILD=true
+  local TEST_ARGS=
+  local TESTDATA_DIR=
+
+  while [[ "$#" > 0 ]]; do
+      case "$1" in
+          -B|--no-build)    DOCKER_BUILD=false;              ;;
+          -h|--help)        usage;                    exit 0 ;;
+          --testdata)
+            TESTDATA_DIR="$2";
+            if [ ! "$(ls -A $TESTDATA_DIR)" ] ; then
+              >&2 echo "ERROR: --testdata must exist and not be empty."
+              exit 1
+            fi
+            shift
+            ;;
+          --)               TEST_ARGS="${@:2}";     break;;
+          *) echo "Invalid argument: $1" >&2; usage;  exit 1 ;;
+      esac
+      shift
+  done
+
+  if $DOCKER_BUILD ; then
+    # build this repo
+    docker build -t reaper-test .
+
+    # build dependencies
+    docker build -t orthanc-test -f docker/Dockerfile-orthanc docker/
+  fi
+
+  #Spin up dependencies
+  docker network create reaper-test
+
+
+  # Orthanc
+  #   calledAE = ORTHANC 4242
+  #   REST port = 8042
+  docker run -d --name orthanc-test --network reaper-test orthanc-test
+
+
+  # scitran-core
+  docker run -d --name scitran-core-mongo --network reaper-test mongo
+  docker run -d --name scitran-core \
+    --network reaper-test \
+    -e "SCITRAN_PERSISTENT_DB_URI=mongodb://scitran-core-mongo:27017/scitran" \
+    -e "SCITRAN_PERSISTENT_DB_LOG_URI=mongodb://scitran-core-mongo:27017/logs" \
+    -e "SCITRAN_CORE_DRONE_SECRET=secret" \
+    scitran/core
+
+
+  # Fetch test data
+  if [ -z ${TESTDATA_DIR} ]; then
+    TESTDATA_DIR="./testdata"
+    mkdir -p $TESTDATA_DIR
+    if [ ! "$(ls -A $TESTDATA_DIR)" ]; then
+        curl -L https://github.com/scitran/testdata/archive/master.tar.gz | tar xz -C "$TESTDATA_DIR" --strip-components 1
+    fi
+  fi
+
+  # Make sure testdata path is absolute. Could be either absolute or relative.
+  TESTDATA_DIR="$(cd "$(dirname "$TESTDATA_DIR")" && pwd)/$(basename "$TESTDATA_DIR")"
+
+  set +e
+  docker run -it \
+    --rm \
+    --name reaper-test \
+    --network reaper-test \
+    -v "$TESTDATA_DIR:/testdata" \
+    -v "$(pwd)/bin:/src/reaper/bin" \
+    -v "$(pwd)/reaper:/src/reaper/reaper" \
+    -v "$(pwd)/tests:/src/reaper/tests" \
+    reaper-test \
+      /src/reaper/tests/bin/test.sh \
+      --testdata /testdata \
+      --core-url http://scitran-core:8080 \
+      --core-secret secret \
+      --dicom-scp-host orthanc-test \
+      --dicom-scp-port 4242 \
+      --dicom-scp-aet ORTHANC \
+      --orthanc http://orthanc-test:8042 \
+      $TEST_ARGS
+
+  TEST_RESULT_CODE=$?
+  >&2 echo
+  >&2 echo "INFO: Test return code = $TEST_RESULT_CODE"
+  if [ "${TEST_RESULT_CODE}" != "0" ] ; then
+    >&2 echo "INFO: Printing container logs..."
+    docker logs scitran-core-mongo
+    docker logs scitran-core
+    docker logs orthanc-test
+    >&2 echo
+    >&2 echo "ERROR: Test return code = $TEST_RESULT_CODE. Container logs printed above."
+  fi
+}
+
+clean_up () {(
+  set +e
+  # Spin down dependencies
+  docker rm -f -v scitran-core-mongo
+  docker rm -f -v scitran-core
+  docker rm -f -v orthanc-test
+  docker network rm reaper-test
+)}
+trap clean_up EXIT
+
+main "$@"

setup.py

@@ -6,7 +6,7 @@
     'pydicom',
     'python-dateutil',
     'pytz',
-    'requests',
+    'requests<2.16',
     'requests_toolbelt',
     'tzlocal',
 ]