Security updates to containers

[nedvedba]

PR Description

This PR serves to reduce image sizes and drastically reduce CVEs in built images, along with fixing a deprecation warning to the python API.

BEFORE

Container Name	Size	Critical CVEs	High CVEs	Medium CVEs	Low CVEs	Unspecified CVEs
datafed/core	200.37MB	0	0	5	52	0
datafed/web	610.28MB	1	8	1211	59	0
datafed/repo	181.30MB	0	0	5	12	0
datafed/gcs	6.16GB	2	23	30	19	0

AFTER

Container Name	Size	Critical CVEs	High CVEs	Medium CVEs	Low CVEs	Unspecified CVEs
datafed/core	159.88MB	0	0	0	33	0
datafed/web	747.02MB	0	2	1	75	2
datafed/repo	141.48MB	0	0	0	33	0
datafed/gcs	1.57GB	1	14	13	53	0

Tasks

• - A description of the PR has been provided, and a diagram included if it is a new feature.
• - Formatter has been run
• - CHANGELOG comment has been added
• - Labels have been assigned to the pr
• - A reviwer has been added
• - A user has been assigned to work on the pr
• - If new feature a unit test has been added

Summary by Sourcery

Updates dependencies, base images, and protobuf handling to reduce image sizes and CVEs, and fixes a deprecation warning in the Python API.

Bug Fixes:

• Fixes a deprecation warning in the Python API related to protobuf messages by using MessageFactory to create protobuf message instances.

Enhancements:

• Updates the base image for the GCS container to debian:bookworm-slim, reducing image size and potential security vulnerabilities.
• Updates dependencies including Node.js, protobuf, libcurl, and Boost to address security vulnerabilities and improve performance.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR updates dependency versions, addresses a protobuf deprecation warning, and modifies the base image used for building containers. These changes aim to reduce image sizes, mitigate CVEs, and improve the overall security and compatibility of the DataFed system.

Updated class diagram for protobuf message handling

classDiagram
  class Connection {
    +recv(self, a_timeout=1000)
    +makeMessage(self, msg_name)
  }
  note for Connection.recv "Uses MessageFactory to create message instances"
  note for Connection.makeMessage "Uses MessageFactory to create message instances"
  class MessageFactory {
    +GetMessageClass(desc)
  }
  Connection -- MessageFactory : uses

Loading

File-Level Changes

Change	Details	Files
Updated dependency versions in dependency_versions.sh to address security vulnerabilities and improve compatibility.	Updated DATAFED_NVM_VERSION to v0.40.1. Updated DATAFED_NODE_VERSION to v20.18.2. Updated DATAFED_BOOST to 1.74.0. Updated DATAFED_GCS_SUBMODULE_VERSION to ff7167860345e9b994110dfabdb251fe4dea8c00.	scripts/dependency_versions.sh
Addressed a deprecation warning in the Python API related to protobuf message creation.	Replaced google.protobuf.reflection.ParseMessage with MessageFactory().GetMessageClass(desc)() and reply.ParseFromString(data) in recv method. Replaced google.protobuf.reflection.MakeClass with MessageFactory().GetMessageClass(self._msg_desc_by_name[msg_name])() in makeMessage method.	python/datafed_pkg/datafed/Connection.py
Modified the base image and submodule checkout in compose_build_images.sh to reduce image sizes and CVEs.	Set BASE_IMAGE to debian:bookworm-slim. Updated the docker build command to use Dockerfile.debian-12 instead of Dockerfile.ubuntu-20.04.	scripts/compose_build_images.sh
Passed arguments to the compose build images script.	Added $@ to the end of the compose build images script call.	compose/all/build_images_for_compose.sh
Updated the protobuf dependency version in requirements.txt.	Updated protobuf to 5.27.1.	python/datafed_pkg/requirements.txt
Added libopenssl to the list of external dependencies in install_authz_dependencies.sh.	Added libopenssl to the externals array.	scripts/install_authz_dependencies.sh
Added libboost-program-options-dev to the list of packages in install_core_dependencies.sh.	Added libboost-program-options-dev to the packages array.	scripts/install_core_dependencies.sh

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[sourcery-ai]

Hey @nedvedba - I've reviewed your changes - here's some feedback:

Overall Comments:

• It looks like you're updating dependencies - consider adding a comment to the changelog about these dependency updates.
• It looks like you're using a specific commit hash for the gcs submodule - is there a reason not to use a tagged release?

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[t-ramz]

Does this come with any breakages? I know @AronPerez was exploring an upgrade

[nedvedba]

I have not noticed any, maybe @AronPerez can point out what he was running into?

[AronPerez]

We can upgrade node, but we need to keep our web dependencies locked at their version

What I was running into was with node ~v16: #1245

That being said v20.18.2 looks like clean install

[AronPerez]

I have been pinged

[JoshuaSBrown]

Can these be deleted?

[nedvedba]

Anything that is commented out will be removed once I get the CI to pass.