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Fix CVE-2026-33210: upgrade Ruby json gem in assemble, phylo, and mega images #1058

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Merged
dpark01 merged 2 commits into from
Mar 31, 2026
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Fix CVE-2026-33210: upgrade Ruby json gem in assemble, phylo, and mega images #1058

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fe939b2
Fix CVE-2026-33210: upgrade Ruby json gem to >=2.19.2
dpark01 Mar 31, 2026
44c3d2f
Apply Ruby json gem fix to phylo and mega Dockerfiles
dpark01 Mar 31, 2026
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11 changes: 8 additions & 3 deletions docker/Dockerfile.assemble
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

# Workaround: add sequip lib directory to PERL5LIB
# NOTE: sequip version here must match the version in requirements/assemble.txt
ENV PERL5LIB=$PERL5LIB:/opt/conda/share/sequip-0.11/lib

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GitHub Actions / build-assemble-amd64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-amd64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-arm64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-arm64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

# Copy requirements and dependency installation script
COPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt docker/requirements/assemble-x86.txt /tmp/requirements/
Expand All @@ -28,11 +28,16 @@

# Install conda dependencies (assembly tools)
# All files resolved together in single micromamba call; x86-only files skipped on ARM
# Remove mafft's dash_client (Go 1.22.1 binary with 11 Go stdlib CVEs) — we
# never use --dash mode; delete inline so it never appears in any layer.
# Post-install fixups (inline so vulnerable files never appear in a committed layer):
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4/sequip pull in Ruby (via yaggo), whose bundled json gem
# has CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt \
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The PR description says this affects assemble, phylo, and mega containers, but this change is only in Dockerfile.assemble. Dockerfile.mega and Dockerfile.phylo both build directly FROM main-core and run their own install-conda-deps.sh step, so they will not pick up this json-gem cleanup unless the same fix is applied there (notably mega installs assemble.txt, which is where sequip is pulled in).

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--x86-only:/tmp/requirements/assemble-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
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The cleanup command find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' ... will not traverse into the default gem payload under /opt/conda/lib/ruby/gems/<rubyver>/gems/json-* (depth is >3), so the vulnerable json gem files may remain on disk even after removing the default gemspec. If the goal is to eliminate CVE findings and the vulnerable code, also remove the json gem directories (and related cache/extensions/specs) under the RubyGems directory (ideally by querying gem env gemdir/ruby -e 'print Gem.default_dir' rather than relying on a fixed depth).

Suggested change
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
RUBY_GEM_DIRS="$(ruby -e 'print Gem.default_dir' 2>/dev/null || true) $(gem env gemdir 2>/dev/null || true)" && \
for d in $RUBY_GEM_DIRS; do \
if [ -d "$d" ]; then \
rm -rf "$d"/gems/json-* "$d"/cache/json-* "$d"/specifications/json-*.gemspec "$d"/extensions/*/*/json-* 2>/dev/null || true; \
rm -f "$d"/specifications/default/json-*.gemspec 2>/dev/null || true; \
fi; \
done && \

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These paths are hard-coded to /opt/conda/lib/ruby/.... To make this resilient to Ruby version / conda layout changes, consider deriving the RubyGems directory dynamically (e.g., via gem env gemdir or ruby -e 'print Gem.default_dir') and performing removals relative to that, rather than assuming /opt/conda/lib/ruby/gems/*/... exists.

Suggested change
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
RUBY_LIB_DIR="$(ruby -e 'require \"rbconfig\"; print RbConfig::CONFIG[\"rubylibdir\"]')" && \
RUBY_GEM_DIR="$(ruby -e 'print Gem.default_dir')" && \
find "$RUBY_LIB_DIR" -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f "$RUBY_GEM_DIR"/specifications/default/json-*.gemspec && \

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gem install json --version '>=2.19.2' --no-document
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To ensure the vulnerability fix actually takes effect (and catch cases where gem install silently installs a different version than expected), consider adding a build-time assertion right after installation (e.g., requiring json and checking JSON::VERSION is >= 2.19.2). This keeps the Docker build from succeeding with the old default gem still being used.

Suggested change
gem install json --version '>=2.19.2' --no-document
gem install json --version '>=2.19.2' --no-document && \
ruby -e "require 'rubygems'; require 'json'; min = Gem::Version.new('2.19.2'); if Gem::Version.new(JSON::VERSION) < min; abort(\"json gem version #{JSON::VERSION} is less than required #{min}\"); end"

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# Copy source code (includes assembly module)
COPY src/ /opt/viral-ngs/source/src/
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11 changes: 8 additions & 3 deletions docker/Dockerfile.mega
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Expand Up @@ -25,13 +25,18 @@ COPY docker/install-conda-deps.sh /tmp/

# Install ALL conda dependencies in single resolver call for proper dependency resolution
# All files resolved together; x86-only files skipped on ARM
# Remove mafft's dash_client (Go 1.22.1 binary with 11 Go stdlib CVEs) — we
# never use --dash mode; delete inline so it never appears in any layer.
# Post-install fixups (inline so vulnerable files never appear in a committed layer):
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4 → yaggo → Ruby, whose bundled json gem has CVE-2026-33210;
# remove the old default gem and install patched version (>=2.19.2)
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt /tmp/requirements/classify.txt /tmp/requirements/phylo.txt \
--x86-only:/tmp/requirements/assemble-x86.txt \
--x86-only:/tmp/requirements/classify-x86.txt \
--x86-only:/tmp/requirements/phylo-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
gem install json --version '>=2.19.2' --no-document

# Copy source code (includes all modules)
COPY src/ /opt/viral-ngs/source/src/
Expand Down
11 changes: 8 additions & 3 deletions docker/Dockerfile.phylo
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Expand Up @@ -25,11 +25,16 @@ COPY docker/install-conda-deps.sh /tmp/

# Install conda dependencies (phylo tools)
# All files resolved together in single micromamba call; x86-only files skipped on ARM
# Remove mafft's dash_client (Go 1.22.1 binary with 11 Go stdlib CVEs) — we
# never use --dash mode; delete inline so it never appears in any layer.
# Post-install fixups (inline so vulnerable files never appear in a committed layer):
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4 pulls in yaggo → Ruby, whose bundled json gem has
# CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/phylo.txt \
--x86-only:/tmp/requirements/phylo-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
gem install json --version '>=2.19.2' --no-document

# Copy source code (includes phylo module)
COPY src/ /opt/viral-ngs/source/src/
Expand Down
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