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

@@ -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"

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