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Initial downstream THREDDS image with netCDF-Java patch framework
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‎.github/workflows/publish.yml‎

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name: Publish image
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on:
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push:
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tags: ['v*']
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permissions:
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contents: read
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packages: write
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ternaustralia/thredds-swiftfix
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jobs:
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publish:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- name: Read versions
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id: versions
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shell: bash
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run: |
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set -a
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source versions.env
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set +a
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echo "base=$THREDDS_BASE_IMAGE" >> "$GITHUB_OUTPUT"
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echo "commit=$NETCDF_JAVA_COMMIT" >> "$GITHUB_OUTPUT"
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echo "version=$IMAGE_VERSION" >> "$GITHUB_OUTPUT"
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- uses: docker/setup-buildx-action@v3
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- uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- id: meta
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uses: docker/metadata-action@v5
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with:
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images: ghcr.io/ternaustralia/thredds-swiftfix
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tags: |
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type=ref,event=tag
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type=sha,prefix=sha-
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- id: build
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uses: docker/build-push-action@v6
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with:
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context: .
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file: Containerfile
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push: true
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platforms: linux/amd64
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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THREDDS_BASE_IMAGE=${{ steps.versions.outputs.base }}
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NETCDF_JAVA_COMMIT=${{ steps.versions.outputs.commit }}
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IMAGE_VERSION=${{ steps.versions.outputs.version }}
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SOURCE_URL=${{ github.server_url }}/${{ github.repository }}
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VCS_REF=${{ github.sha }}
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BUILD_DATE=${{ github.event.repository.updated_at }}
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- name: Show digest
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run: echo 'ghcr.io/ternaustralia/thredds-swiftfix@${{ steps.build.outputs.digest }}'

‎.gitignore‎

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*.log

‎Containerfile‎

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ARG THREDDS_BASE_IMAGE
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FROM ${THREDDS_BASE_IMAGE} AS patch-builder
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USER root
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ARG NETCDF_JAVA_COMMIT
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WORKDIR /work
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COPY scripts/build-patched-jars.sh /usr/local/bin/build-patched-jars.sh
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RUN chmod 0755 /usr/local/bin/build-patched-jars.sh && \
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/usr/local/bin/build-patched-jars.sh "${NETCDF_JAVA_COMMIT}" /work/out
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ARG THREDDS_BASE_IMAGE
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FROM ${THREDDS_BASE_IMAGE}
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ARG NETCDF_JAVA_COMMIT
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ARG IMAGE_VERSION
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ARG SOURCE_URL
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ARG VCS_REF
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ARG BUILD_DATE
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LABEL org.opencontainers.image.source="${SOURCE_URL}" \
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org.opencontainers.image.revision="${VCS_REF}" \
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org.opencontainers.image.created="${BUILD_DATE}" \
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org.opencontainers.image.version="${IMAGE_VERSION}" \
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org.opencontainers.image.base.name="${THREDDS_BASE_IMAGE}" \
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io.thredds.netcdf-java.commit="${NETCDF_JAVA_COMMIT}"
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COPY --from=patch-builder /work/out/cdm-s3-5.9.1.jar \
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/usr/local/tomcat/webapps/thredds/WEB-INF/lib/cdm-s3-5.9.1.jar
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COPY --from=patch-builder /work/out/cdm-core-5.9.1.jar \
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/usr/local/tomcat/webapps/thredds/WEB-INF/lib/cdm-core-5.9.1.jar
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COPY --from=patch-builder /work/out/sha256sums.txt \
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/opt/thredds-swiftfix/sha256sums.txt

‎README.md‎

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# ternaustralia/thredds-swiftfix starter
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This starter builds an OCI image from a pinned official THREDDS 5.8 image and
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patches both bundled netCDF-Java 5.9.1 jars.
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Before building:
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1. Copy `versions.env.example` to `versions.env`.
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2. Replace the base-image digest.
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3. Replace the netCDF-Java commit SHA.
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4. Run:
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```bash
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docker build -f Containerfile --build-arg THREDDS_BASE_IMAGE="$(grep '^THREDDS_BASE_IMAGE=' versions.env | cut -d= -f2-)" --build-arg NETCDF_JAVA_COMMIT="$(grep '^NETCDF_JAVA_COMMIT=' versions.env | cut -d= -f2-)" --build-arg IMAGE_VERSION="$(grep '^IMAGE_VERSION=' versions.env | cut -d= -f2-)" --build-arg SOURCE_URL='https://github.com/ternaustralia/thredds-swiftfix' --build-arg VCS_REF="$(git rev-parse HEAD)" --build-arg BUILD_DATE="$(date -u +%Y-%m-%dT%H:%M:%SZ)" -t ternaustralia/thredds-swiftfix:local .
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```

‎scripts/build-patched-jars.sh‎

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#!/usr/bin/env bash
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set -Eeuo pipefail
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COMMIT="${1:?Missing netCDF-Java commit}"
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OUT="${2:?Missing output directory}"
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LIB=/usr/local/tomcat/webapps/thredds/WEB-INF/lib
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JAVA_HOME="${JAVA_HOME:-/opt/java/openjdk}"
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WORK=/tmp/netcdf-java-swiftfix
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rm -rf "$WORK" "$OUT"
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mkdir -p "$WORK/src/thredds/filesystem/s3" \
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"$WORK/src/ucar/nc2/internal/ncml" \
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"$WORK/classes/s3" "$WORK/classes/core" "$OUT"
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S3="$WORK/src/thredds/filesystem/s3/ControllerS3.java"
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CORE="$WORK/src/ucar/nc2/internal/ncml/AggregationExisting.java"
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curl -fsSL "https://raw.githubusercontent.com/Unidata/netcdf-java/${COMMIT}/cdm/s3/src/main/java/thredds/filesystem/s3/ControllerS3.java" -o "$S3"
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curl -fsSL "https://raw.githubusercontent.com/Unidata/netcdf-java/${COMMIT}/cdm/core/src/main/java/ucar/nc2/internal/ncml/AggregationExisting.java" -o "$CORE"
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awk '
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{
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print
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if ($0 ~ /^[[:space:]]*String continuationToken = useV2 \? responseV2\.nextContinuationToken\(\) : responseV1\.nextMarker\(\);[[:space:]]*$/) {
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print ""
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print " // OpenStack Swift may omit NextMarker for a truncated V1 response."
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print " if (!useV2"
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print " && continuationToken == null"
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print " && responseV1.isTruncated()"
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print " && !objects.isEmpty()) {"
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print " continuationToken = objects.get(objects.size() - 1).key();"
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print " }"
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}
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}
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' "$S3" > "$S3.patched"
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mv "$S3.patched" "$S3"
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grep -Fq 'continuationToken = objects.get(objects.size() - 1).key();' "$S3"
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OLD='Parse.readRootElement("file:" + cacheFile.getPath())'
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NEW='Parse.readRootElement(cacheFile.toURI().toString())'
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grep -Fq "$OLD" "$CORE"
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sed -i "s@${OLD}@${NEW}@" "$CORE"
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grep -Fq "$NEW" "$CORE"
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"$JAVA_HOME/bin/javac" -proc:none -cp "$LIB/*" -d "$WORK/classes/s3" "$S3"
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"$JAVA_HOME/bin/javac" -proc:none -cp "$LIB/*" -d "$WORK/classes/core" "$CORE"
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cp "$LIB/cdm-s3-5.9.1.jar" "$OUT/cdm-s3-5.9.1.jar"
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cp "$LIB/cdm-core-5.9.1.jar" "$OUT/cdm-core-5.9.1.jar"
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"$JAVA_HOME/bin/jar" --update --file "$OUT/cdm-s3-5.9.1.jar" \
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-C "$WORK/classes/s3" thredds/filesystem/s3
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"$JAVA_HOME/bin/jar" --update --file "$OUT/cdm-core-5.9.1.jar" \
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-C "$WORK/classes/core" ucar/nc2/internal/ncml/AggregationExisting.class
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"$JAVA_HOME/bin/javap" -classpath "$OUT/cdm-core-5.9.1.jar" -c -p \
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ucar.nc2.internal.ncml.AggregationExisting | grep -q 'java/io/File.toURI'
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sha256sum "$OUT/cdm-s3-5.9.1.jar" "$OUT/cdm-core-5.9.1.jar" \
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> "$OUT/sha256sums.txt"
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cat "$OUT/sha256sums.txt"

‎versions.env‎

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THREDDS_BASE_IMAGE=docker.io/unidata/thredds-docker:5.8@sha256:5dcec410058ee0fa4f55debe5152ee53fe0e82f5e4d9bccf70f05ca1a228d95f
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NETCDF_JAVA_COMMIT=647155bae55ff3ce7ce2d518ffa7621d721d4f0f
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IMAGE_VERSION=5.8-ncj5.9.1-r1

‎versions.env.example‎

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THREDDS_BASE_IMAGE=docker.io/unidata/thredds-docker:5.8@sha256:REPLACE_ME
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NETCDF_JAVA_COMMIT=REPLACE_WITH_FULL_40_CHARACTER_SHA
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IMAGE_VERSION=5.8-ncj5.9.1-r1

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