From 868418f4bcb64cc3bc81db8f74013af612c82a49 Mon Sep 17 00:00:00 2001
From: Jon Stutters <j.stutters@ucl.ac.uk>
Date: Wed, 31 Jan 2024 14:50:50 +0000
Subject: [PATCH] Improve orthanc-anon check

The existing test script checked the orthanc-anon log for receipt of a DICOM but
this was not catching that the received DICOM was not being stored due problems
during anonymisation.  The new check script queries the orthanc-anon API to make
sure it has received and stored the test DICOMs.
---
 test/run-system-test.sh                     |  2 +-
 test/scripts/check_entry_in_orthanc_anon.py | 15 +++++++++++++++
 test/scripts/check_entry_in_orthanc_anon.sh | 19 -------------------
 3 files changed, 16 insertions(+), 20 deletions(-)
 create mode 100755 test/scripts/check_entry_in_orthanc_anon.py
 delete mode 100755 test/scripts/check_entry_in_orthanc_anon.sh

diff --git a/test/run-system-test.sh b/test/run-system-test.sh
index 2817acd54..7a65e963f 100755
--- a/test/run-system-test.sh
+++ b/test/run-system-test.sh
@@ -32,7 +32,7 @@ pixl populate "${PACKAGE_DIR}/test/resources/omop"
 pixl start
 sleep 65  # need to wait until the DICOM image is "stable" = 60s
 ./scripts/check_entry_in_pixl_anon.sh
-./scripts/check_entry_in_orthanc_anon.sh
+./scripts/check_entry_in_orthanc_anon.py
 ./scripts/check_max_storage_in_orthanc_raw.sh
 
 pixl extract-radiology-reports "${PACKAGE_DIR}/test/resources/omop"
diff --git a/test/scripts/check_entry_in_orthanc_anon.py b/test/scripts/check_entry_in_orthanc_anon.py
new file mode 100755
index 000000000..88f7c9343
--- /dev/null
+++ b/test/scripts/check_entry_in_orthanc_anon.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python3
+
+# After pixl has run this script will query the orthanc-anon REST API to check
+# that the correct number of instances have been received.
+
+import json
+import shlex
+import subprocess
+
+
+instances_cmd = shlex.split('docker exec -it system-test-orthanc-anon-1 curl -u "orthanc_anon_username:orthanc_anon_password" http://orthanc-anon:8042/instances')
+instances_output = subprocess.run(instances_cmd, capture_output=True, check=True, text=True)
+instances = json.loads(instances_output.stdout)
+print("orthanc-anon instances:", instances)
+assert len(instances) == 2
diff --git a/test/scripts/check_entry_in_orthanc_anon.sh b/test/scripts/check_entry_in_orthanc_anon.sh
deleted file mode 100755
index 253e981df..000000000
--- a/test/scripts/check_entry_in_orthanc_anon.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/bin/bash
-#  Copyright (c) University College London Hospitals NHS Foundation Trust
-#
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-set -euxo pipefail
-
-# This could be much improved by having more realistic test data some of
-# which actually was persisted
-docker logs system-test-orthanc-anon-1 2>&1 | grep "DICOM instance received"