Merge pull request #11 from susom/development

Merge in dev branch

Author: jmesterh

.github/workflows/deployment.yaml

@@ -23,6 +23,11 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+      
+      - name: Update submodules
+        run: |
+          git submodule update --init --recursive
+          git submodule update --remote --merge
 
       - name: Authenticate with Google Cloud
         uses: google-github-actions/auth@v2
@@ -47,18 +52,10 @@ jobs:
       - name: Setup buildx so we can use GHA caching
         uses: docker/setup-buildx-action@v3
 
-      - name: Setup Java
-        uses: actions/setup-java@v4
-        with:
-          java-version: '8'
-          distribution: 'temurin'
-
-      - name: Run make
-        run: make install
-
       - name: Build and push image
         uses: docker/build-push-action@v6
         with:
+          platforms: linux/amd64,linux/arm64
           context: .
           cache-from: type=gha
           cache-to: type=gha,mode=max

.gitignore

@@ -65,3 +65,5 @@ DAT/dcm4che.jar
 DAT/log4j.jar
 DAT/pixelmed_codec.jar
 DAT/util.jar
+DICOM/
+DICOM-ANON/

CTP

@@ -1,17 +1,36 @@
 # Dockerfile for running CTP DicomAnonymizerTool with required dependencies
-FROM eclipse-temurin:8
+FROM eclipse-temurin:17-jdk AS build
 
-ENV HOME=/app
+ENV ANT_VERSION=1.10.15
+ENV ANT_HOME=/opt/ant
 
-WORKDIR /app
-ADD DAT /app/DAT
-ADD lib /app/lib
-ADD DicomAnonymizerTool/source/files/log4j.properties /app
+# change to tmp folder
+WORKDIR /tmp
 
-WORKDIR /opt/java/openjdk
-RUN chmod +x /app/lib/*.bin
-RUN echo yes | /app/lib/jai-1_1_3-lib-linux-amd64-jdk.bin
-RUN echo yes | /app/lib/jai_imageio-1_1-lib-linux-amd64-jdk.bin 
+# Download and extract apache ant to opt folder
+RUN wget --no-check-certificate --no-cookies http://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz \
+    && wget --no-check-certificate --no-cookies http://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz.sha512 \
+    && echo "$(cat apache-ant-${ANT_VERSION}-bin.tar.gz.sha512) apache-ant-${ANT_VERSION}-bin.tar.gz" | sha512sum -c \
+    && tar -zvxf apache-ant-${ANT_VERSION}-bin.tar.gz -C /opt/ \
+    && ln -s /opt/apache-ant-${ANT_VERSION} /opt/ant \
+    && rm -f apache-ant-${ANT_VERSION}-bin.tar.gz \
+    && rm -f apache-ant-${ANT_VERSION}-bin.tar.gz.sha512
 
-WORKDIR /app
-CMD ["java","-cp","/app/DAT/*","org.rsna.dicomanonymizertool.DicomAnonymizerTool"]
+# add executables to path
+RUN update-alternatives --install "/usr/bin/ant" "ant" "/opt/ant/bin/ant" 1 && \
+    update-alternatives --set "ant" "/opt/ant/bin/ant" 
+
+# Build CTP & DicomAnonymizerTool
+COPY CTP/ /build/CTP/
+COPY DicomAnonymizerTool/ /build/DicomAnonymizerTool/
+WORKDIR /build/CTP
+RUN ant
+WORKDIR /build/DicomAnonymizerTool
+RUN ant
+
+# Install
+FROM eclipse-temurin:17 AS dat
+COPY --from=build /build/DicomAnonymizerTool/build/DicomAnonymizerTool/ /opt/DAT/
+WORKDIR /opt/DAT
+ENV CLASSPATH=/opt/DAT/DAT.jar:/opt/DAT/imageio/*:/opt/DAT/libraries/*
+CMD ["java","org.rsna.dicomanonymizertool.DicomAnonymizerTool"]

DicomAnonymizerTool

@@ -1,28 +1,14 @@
 TARGET = install
-VERSION = 1.0.0
+VERSION = latest
 
-.PHONY: clean
-
-all: clean install docker
+all: submodule docker deinit
 
 docker:
-	docker build -f Dockerfile --pull -t starr-radio:$(VERSION) .
+	docker build -f Dockerfile --pull -t stanford-mirc-ctp:$(VERSION) .
 
-install: 
+submodule: 
 	git submodule update --init --recursive
 	git submodule update --remote --merge
-	cd CTP
-	git fetch
-	cd ..
-	cd DicomAnonymizerTool
-	git fetch
-	cd ..
-	$(MAKE) -C CTP
-	ant
-
-check: 
-	$(MAKE) -C tests check
-
-all: clean install
 
-	
+deinit:
+	git submodule deinit -f .

Dockerfile

@@ -37,7 +37,7 @@ shift $((OPTIND-1))
 [[ "${1:-}" = "--" ]] && shift
 
 docker run --rm  -e JAVA_TOOL_OPTIONS=${DEBUG} \
-    -p 8000:8000 -v ${PWD}/scripts:/scripts -v ${PWD}:/data/dicom mirc-ctp java ${VERBOSE} -cp /app/DAT/* org.rsna.dicomanonymizertool.DicomAnonymizerTool -v -n 8 \
+    -p 8000:8000 -v ${PWD}/scripts:/scripts -v ${PWD}:/data/dicom stanford-mirc-ctp:latest java ${VERBOSE} org.rsna.dicomanonymizertool.DicomAnonymizerTool -v -n 8 \
 	-in /data/dicom/DICOM \
 	-out /data/dicom/DICOM-ANON \
 	-dec \