Refactor Python and Orthanc Dockerfiles (#583)

Fixes #588 by de-duping the orthanc and PIXL dockerfiles. This was factored out from PR #400 which had become too big.
* Merge three pixl python dockerfiles into one multi-stage dockerfile to
avoid repetition.
* Merge orthanc dockerfiles, downloading dicom spec at a more separate stage.
* Specify healthcheck command in only one place

docker-compose.yml

@@ -74,8 +74,10 @@ services:
     hasher-api:
         build:
             context: .
-            dockerfile: ./docker/hasher-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: hasher_api
             args:
+                PIXL_PACKAGE_DIR: hasher
                 <<: *build-args-common
         environment:
             <<: [*proxy-common, *pixl-common-env]
@@ -93,7 +95,6 @@ services:
         networks:
             - pixl-net
         healthcheck:
-            test: ["CMD", "curl", "-f", "http://hasher-api:8000/heart-beat"]
             interval: 10s
             timeout: 30s
             retries: 5
@@ -102,9 +103,11 @@ services:
     orthanc-anon:
         build:
             context: .
-            dockerfile: ./docker/orthanc-anon/Dockerfile
+            dockerfile: ./docker/orthanc/Dockerfile
+            target: pixl_orthanc_anon
             args:
                 <<: *build-args-common
+                ORTHANC_DIR: orthanc-anon
                 ORTHANC_CONCURRENT_JOBS: ${ORTHANC_CONCURRENT_JOBS}
         platform: linux/amd64
         command: /run/secrets
@@ -171,9 +174,11 @@ services:
     orthanc-raw:
         build:
             context: .
-            dockerfile: ./docker/orthanc-raw/Dockerfile
+            dockerfile: ./docker/orthanc/Dockerfile
+            target: pixl_orthanc_raw
             args:
                 <<: *build-args-common
+                ORTHANC_DIR: orthanc-raw
                 ORTHANC_RAW_MAXIMUM_STORAGE_SIZE: ${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}
                 ORTHANC_RAW_JOB_HISTORY_SIZE: ${ORTHANC_RAW_JOB_HISTORY_SIZE}
                 ORTHANC_CONCURRENT_JOBS: ${ORTHANC_CONCURRENT_JOBS}
@@ -249,8 +254,10 @@ services:
     export-api:
         build:
             context: .
-            dockerfile: ./docker/export-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: export_api
             args:
+                PIXL_PACKAGE_DIR: pixl_export
                 <<: *build-args-common
         environment:
             <<:
@@ -297,8 +304,10 @@ services:
     imaging-api:
         build:
             context: .
-            dockerfile: ./docker/imaging-api/Dockerfile
+            dockerfile: ./docker/pixl-python/Dockerfile
+            target: imaging_api
             args:
+                PIXL_PACKAGE_DIR: pixl_imaging
                 <<: *build-args-common
         depends_on:
             queue:
@@ -308,7 +317,6 @@ services:
             orthanc-anon:
                 condition: service_healthy
         healthcheck:
-            test: curl -f http://0.0.0.0:8000/heart-beat
             interval: 10s
             timeout: 30s
             retries: 5

docker/orthanc-raw/Dockerfile → docker/orthanc/Dockerfile

@@ -11,7 +11,7 @@
 #  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.
-FROM orthancteam/orthanc:24.7.3@sha256:57a3d037729897331027ddc00c12695b50f1effbbf805f855396f3d0248d2d5f
+FROM orthancteam/orthanc:24.7.3@sha256:57a3d037729897331027ddc00c12695b50f1effbbf805f855396f3d0248d2d5f AS pixl_orthanc_apt
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 # Create a virtual environment, recommended since python 3.11 and Debian bookworm based images
@@ -20,6 +20,24 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && \
     apt-get install --yes --no-install-recommends python3-venv tzdata
 RUN python3 -m venv /.venv
+ENV PYTHONPATH=/.venv/lib64/python3.11/site-packages/
+
+# Install curl for now, but try to remove this dependency
+RUN apt-get --assume-yes install curl
+
+FROM pixl_orthanc_apt AS pixl_orthanc_with_spec
+# This part changes rarely, so do it nice and early to avoid redoing it every time we change our code.
+# It does have a dependency though, which would normally be fulfilled by our project files, so install that
+# manually.
+# Do it in dead end build stage to discard this environment afterwards,
+# and because the spec is only needed in orthanc-anon.
+RUN /.venv/bin/pip install dicom-validator
+COPY ./orthanc/orthanc-anon/plugin/download_dicom_spec.py /etc/orthanc/download_dicom_spec.py
+RUN --mount=type=cache,target=/root/.cache \
+    python3 /etc/orthanc/download_dicom_spec.py
+
+
+FROM pixl_orthanc_apt AS pixl_orthanc_base
 
 # Install requirements before copying modules
 COPY ./pixl_core/pyproject.toml /pixl_core/pyproject.toml
@@ -37,17 +55,22 @@ COPY ./pixl_dcmd/ /pixl_dcmd
 RUN --mount=type=cache,target=/root/.cache \
     /.venv/bin/pip install --no-cache-dir --force-reinstall --no-deps ./pixl_dcmd
 
-COPY ./orthanc/orthanc-raw/plugin/pixl.py /etc/orthanc/pixl.py
+ARG ORTHANC_DIR
+COPY ./orthanc/${ORTHANC_DIR}/plugin/pixl.py /etc/orthanc/pixl.py
+COPY ./orthanc/${ORTHANC_DIR}/config /run/secrets
 
 # Orthanc can't substitute environment veriables as integers so copy and replace before running
+ARG ORTHANC_CONCURRENT_JOBS
+RUN sed -i "s/\${ORTHANC_CONCURRENT_JOBS}/${ORTHANC_CONCURRENT_JOBS:-5}/g" /run/secrets/orthanc.json
+
+FROM pixl_orthanc_base AS pixl_orthanc_raw
+
 ARG ORTHANC_RAW_MAXIMUM_STORAGE_SIZE
 ARG ORTHANC_RAW_JOB_HISTORY_SIZE
-ARG ORTHANC_CONCURRENT_JOBS
 ARG PIXL_DICOM_TRANSFER_TIMEOUT
-COPY ./orthanc/orthanc-raw/config /run/secrets
 RUN sed -i "s/\${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE}/${ORTHANC_RAW_MAXIMUM_STORAGE_SIZE:-0}/g" /run/secrets/orthanc.json
 RUN sed -i "s/\${ORTHANC_RAW_JOB_HISTORY_SIZE}/${ORTHANC_RAW_JOB_HISTORY_SIZE:-100}/g" /run/secrets/orthanc.json
-RUN sed -i "s/\${ORTHANC_CONCURRENT_JOBS}/${ORTHANC_CONCURRENT_JOBS:-5}/g" /run/secrets/orthanc.json
 RUN sed -i "s/\${ORTHANC_RAW_STABLE_SECONDS}/${PIXL_DICOM_TRANSFER_TIMEOUT:-600}/g" /run/secrets/orthanc.json
 
-ENV PYTHONPATH=/.venv/lib64/python3.11/site-packages/
+FROM pixl_orthanc_base AS pixl_orthanc_anon
+COPY --from=pixl_orthanc_with_spec /root/dicom-validator /root/dicom-validator

docker/export-api/Dockerfile → docker/pixl-python/Dockerfile

@@ -11,7 +11,7 @@
 #  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.
-FROM python:3.12.4-slim-bullseye@sha256:26ce493641ad3b1c8a6202117c31340c7bbb2dc126f1aeee8ea3972730a81dc6
+FROM python:3.12.4-slim-bullseye@sha256:26ce493641ad3b1c8a6202117c31340c7bbb2dc126f1aeee8ea3972730a81dc6 AS pixl_python_base
 SHELL ["/bin/bash", "-o", "pipefail", "-e", "-u", "-x", "-c"]
 
 ARG TEST="false"
@@ -31,20 +31,32 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
 RUN sed -i '/en_GB.UTF-8/s/^# //g' /etc/locale.gen && locale-gen
 RUN  apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
 
+HEALTHCHECK CMD /usr/bin/curl -f http://0.0.0.0:8000/heart-beat || exit 1
+
 WORKDIR /app
+# specify what we're installing using build time arg
+ARG PIXL_PACKAGE_DIR
 
 # Install requirements before copying modules
 COPY ./pixl_core/pyproject.toml ./pixl_core/pyproject.toml
-COPY ./pixl_export/pyproject.toml ./pixl_export/pyproject.toml
+COPY ./$PIXL_PACKAGE_DIR/pyproject.toml ./$PIXL_PACKAGE_DIR/pyproject.toml
 RUN pip3 install --no-cache-dir pixl_core/ \
-    && pip3 install --no-cache-dir pixl_export/
+    && pip3 install --no-cache-dir $PIXL_PACKAGE_DIR/
 
+# Install our code
 COPY ./pixl_core/ pixl_core/
-COPY ./pixl_export/ .
+COPY ./$PIXL_PACKAGE_DIR/ .
 RUN pip install --no-cache-dir --force-reinstall --no-deps pixl_core/ \
     --no-cache-dir --force-reinstall --no-deps . && \
     if [ "$TEST" = "true" ]; then pip install --no-cache-dir pixl_core/[test] .[test]; fi
 
-HEALTHCHECK CMD /usr/bin/curl -f http://0.0.0.0:8000/heart-beat || exit 1
 
+# Each container should be run with a different entry point
+FROM pixl_python_base AS export_api
 ENTRYPOINT ["uvicorn", "pixl_export.main:app", "--host", "0.0.0.0", "--port", "8000"]
+
+FROM pixl_python_base AS hasher_api
+ENTRYPOINT ["uvicorn", "hasher.main:app", "--host", "0.0.0.0", "--port", "8000"]
+
+FROM pixl_python_base AS imaging_api
+ENTRYPOINT ["/app/scripts/migrate_and_run.sh"]

pixl_imaging/tests/docker-compose.yml

@@ -68,9 +68,11 @@ services:
     orthanc-raw:
         build:
             context: ../../
-            dockerfile: ./docker/orthanc-raw/Dockerfile
+            dockerfile: ./docker/orthanc/Dockerfile
+            target: pixl_orthanc_raw
             args:
                 PIXL_DICOM_TRANSFER_TIMEOUT: 30
+                ORTHANC_DIR: orthanc-raw
         environment:
             ORTHANC_NAME: "PIXL: Raw"
             ORTHANC_USERNAME: "orthanc"