Limit orthanc raw storage size (#181)

* Fix env variable names in `delete_oldest_n_studies.py` These new variable names are consistent with what is set in `.env` and `test/.env.test` * Add MaximumStorageSize config for orthanc-raw * MaximumStorageSize needs to be an integer * Revert "Fix env variable names in `delete_oldest_n_studies.py`" This reverts commit 0842f43. * Set orthanc raw maximum storage in Dockerfile (#179) * Set orthanc raw maximum storage in Dockerfile * Orthanc raw defaults to no limit on storage Saves us from faffing around with build args for other tests * Format README * Document `ORTHANC_RAW_MAXIMUM_STORAGE_SIZE` * Add simple test for `ORTHANC_RAW_MAXIMUM_STORAGE_SIZE` --------- Co-authored-by: Milan Malfait <[email protected]> --------- Co-authored-by: Milan Malfait <[email protected]>
SAFEHR-data · Dec 13, 2023 · 44c9226 · 44c9226
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diff --git a/.env.sample b/.env.sample
@@ -39,6 +39,7 @@ ORTHANC_RAW_USERNAME=
 ORTHANC_RAW_PASSWORD=
 ORTHANC_RAW_AE_TITLE=
 ORTHANC_AUTOROUTE_RAW_TO_ANON=true
+ORTHANC_RAW_MAXIMUM_STORAGE_SIZE= // MB
 
 # PIXL Orthanc anon instance
 ORTHANC_ANON_USERNAME=

diff --git a/README.md b/README.md
@@ -159,8 +159,14 @@ on the target storage account. The storage account must also allow network acces
 
 #### Ports
 
-Most services need to expose ports that must be mapped to ports on the host. The host port is specified in `.env`
-Ports need to be configured such that they don't clash with any other application running on that GAE.
+Most services need to expose ports that must be mapped to ports on the host. The host port is specified in `.env`  
+Ports need to be configured such that they don't clash with any other application running on that GAE.  
+
+#### Storage size
+
+The maximum storage size of the `orthanc-raw` instance can be configured through the `ORTHANC_RAW_MAXIMUM_STORAGE_SIZE`
+environment variable in `.env`. This limits the storage size to the specified value (in MB). When the storage is full
+[Orthanc will automatically recycle older studies in favour of new ones](https://orthanc.uclouvain.be/book/faq/features.html#id8).
 
 ## Run
 
@@ -199,8 +205,10 @@ select count(*) from emap_data.ehr_anon where xray_report is not null;
 ## Develop
 
 See each service's README for instructions for individual developing and testing instructions.
+
 For Python development we use [ruff](https://docs.astral.sh/ruff/) alongside [pytest](https://www.pytest.org/).
 There is support (sometimes through plugins) for these tools in most IDEs & editors.
+
 Before raising a PR, **run the full test suite** from the _PIXL_ directory with
 
 ```bash

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -157,6 +157,7 @@ services:
       dockerfile: ./docker/orthanc-raw/Dockerfile
       args:
         <<: *build-args-common
+        ORTHANC_RAW_MAXIMUM_STORAGE_SIZE: ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}
     command: /run/secrets
     environment:
       <<: [*pixl-db, *proxy-common, *pixl-common-env]
@@ -165,6 +166,7 @@ services:
       ORTHANC_PASSWORD: ${ORTHANC_RAW_PASSWORD}
       ORTHANC_RAW_AE_TITLE: ${ORTHANC_RAW_AE_TITLE}
       ORTHANC_AUTOROUTE_RAW_TO_ANON: ${ORTHANC_AUTOROUTE_RAW_TO_ANON}
+      ORTHANC_RAW_MAXIMUM_STORAGE_SIZE: ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}
       VNA_AE_TITLE : ${VNA_AE_TITLE}
       VNA_DICOM_PORT: ${VNA_DICOM_PORT}
       VNA_IP_ADDR: ${VNA_IP_ADDR}
@@ -181,7 +183,6 @@ services:
       - type: volume
         source: orthanc-raw-data
         target: /var/lib/orthanc/db
-      - ${PWD}/orthanc/orthanc-raw/config:/run/secrets:ro
     networks:
       - pixl-net
     depends_on:

diff --git a/docker/orthanc-raw/Dockerfile b/docker/orthanc-raw/Dockerfile
@@ -14,4 +14,9 @@
 FROM osimis/orthanc:22.9.0-full-stable
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
-COPY ./orthanc/orthanc-raw/plugin/pixl.py /etc/orthanc/pixl.py
+ARG ORTHANC_RAW_MAXIMUM_STORAGE_SIZE
+
+COPY ./orthanc/orthanc-raw/plugin/pixl.py /etc/orthanc/pixl.py
+# Orthanc can't substitute environment veriables as integers so copy and replace before running
+COPY ./orthanc/orthanc-raw/config /run/secrets
+RUN sed -i "s/\${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}/${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE:-0}/g" /run/secrets/orthanc.json
diff --git a/orthanc/orthanc-raw/config/orthanc.json b/orthanc/orthanc-raw/config/orthanc.json
@@ -10,8 +10,11 @@
   // doubling them, or replaced by forward slashes "/".
   "StorageDirectory" : "/var/lib/orthanc/db",
 
-  // Limit the maximum number of instances
-  "MaximumPatientCount": 20000,
+  // Limit the maximum storage size
+  "MaximumPatientCount" : 0, // no limit
+  "MaximumStorageSize" : ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}, // MB, replaced in Dockerfile because its an integer
+  "MaximumStorageMode" : "Recycle",
+
 
   // Path to the directory that holds the SQLite index (if unset, the
   // value of StorageDirectory is used). This index could be stored on

diff --git a/test/.env.test.sample b/test/.env.test.sample
@@ -37,6 +37,7 @@ ORTHANC_RAW_USERNAME=orthanc_raw_username
 ORTHANC_RAW_PASSWORD=orthanc_raw_password
 ORTHANC_RAW_AE_TITLE=ORTHANCRAW
 ORTHANC_AUTOROUTE_RAW_TO_ANON=true
+ORTHANC_RAW_MAXIMUM_STORAGE_SIZE=1
 
 # PIXL Orthanc anon instance
 ORTHANC_ANON_USERNAME=orthanc_anon_username

diff --git a/test/run-system-test.sh b/test/run-system-test.sh
@@ -31,6 +31,7 @@ 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_max_storage_in_orthanc_raw.sh
 
 cd "${PACKAGE_DIR}"
 docker compose -f docker-compose.yml -f ../docker-compose.yml -p test down

diff --git a/test/scripts/check_max_storage_in_orthanc_raw.sh b/test/scripts/check_max_storage_in_orthanc_raw.sh
@@ -0,0 +1,21 @@
+#!/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 -eux pipefail
+
+# This could be much improved by having more realistic test data some of
+# which actually was persisted
+source ./.env.test
+docker logs test-orthanc-raw-1 2>&1 | grep "At most ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}MB will be used for the storage area"
+