added alessio/shellescape and changed prepareEnvs to use envfile

[antoinetran]

Fixes #27

STATUS: READY for code review and merge

Summary

Fixes #27 by moving all env variables to inside a envfile.properties, which fixes the file command limit of 4096 characters, and bash-quoting it, which fixes all quote issues.
This does not fix the missing prefix docker:/docker.io/

This has not been tested yet. The CI/CD gives some error: https://github.com/antoinetran/interlink-slurm-plugin/actions for lint and build. This is my first time programming in GO, and I don't understand why the branch has issue with lint (clone , which has nothing to do with the modifications I did).

The docker builds fails too, https://github.com/antoinetran/interlink-slurm-plugin/actions/runs/11219763886 , because I did not modify the go.sum . Will do it now.

---

Related issue :
#27

[antoinetran]

Status: the build docker is OK (https://github.com/antoinetran/interlink-slurm-plugin/actions/runs/11274890712) . The release binary https://github.com/antoinetran/interlink-slurm-plugin/releases/tag/0.3.4 has been tested by me. It works.

The results (some name has been anonymized):
For InterLink slurm plugin log:

time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_PROGRESS_FILE value /var/run/argo/progress"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_PROGRESS_PATCH_TICK_DURATION value 1m0s"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_POD_NAME value appname-lsdsharedfs-template-gnj4q
-group-block-1706385343"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_POD_UID value 61d92d8b-2052-47c0-84c9-aba0efcb949a"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key GODEBUG value x509ignoreCN=0"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_WORKFLOW_NAME value appname-lsdsharedfs-template-
gnj4q"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_CONTAINER_NAME value wait"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_DEADLINE value 0001-01-01T00:00:00Z"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_WORKFLOW_UID value dc412cb8-3f0a-4a1a-b2d3-a9677c935173
"
time="2024-10-10T13:30:33Z" level=debug msg="---- Written envfile file /home/username/.interlink/argo-workflows-61d92d8b-2052-47c0-84c9-aba0efcb949a/envfile.properties key ARGO_TEMPLATE value '{\"name\":\"group-block\",\"inputs\":{\
"parameters\":[{\"name\":\"input_data\",\"value\":\"stub2_output_preprocessed_signal.h5\"},{\"name\":\"pipeline_run_id\",\"value\":\"appname-lsdsharedfs-template-gnj4q\"},{\"name\":\"block_label\",\"value\":\"282\"},{\"name\":
\"group_label\",\"value\":\"stub2\"},{\"name\":\"block_static_configuration_reference\",\"value\":\"dummy_config.json\"},{\"name\":\"workdir\",\"value\":\"/work\"},{\"name\":\"bus_uri\",\"value\":\"nats://my-nats.nats:4222\"},{\"nam
e\":\"n_steps_per_iteration\",\"value\":\"1000\"},{\"name\":\"current_iteration\",\"value\":\"0\"}]},\"outputs\":{},\"affinity\":{\"nodeAffinity\":{\"preferredDuringSchedulingIgnoredDuringExecution\":[{\"weight\":1,\"preference\":{\
"matchExpressions\":[{\"key\":\"kubernetes.io/hostname\",\"operator\":\"In\",\"values\":[\"interlink-slurm\"]}]}}]}},\"metadata\":{},\"container\":{\"name\":\"\",\"image\":\"gitlabaddress/projectname-sgs/componentName/framework:0.4.0\",\
"command\":[\"appcmd\"],\"args\":[\"--workdir=/work\",\"--pipeline-run-id=appname-lsdsharedfs-template-gnj4q\",\"--servers=nats://my-nats.nats:4222\",\"start-block\",\"--input-data=stub2_output_preprocessed_signal.h5\",\"--i
nput-group-configuration-path=/work/stub2_group_configuration.json\",\"--block-label=282\",\"--group-label=stub2\",\"--n-steps=1000\",\"--current-iteration=0\",\"--output-checkpoint=/work/stub2_282_mcmc.dump\"],\"resources\":{\"limi
ts\":{\"cpu\":\"500m\",\"memory\":\"256Mi\"},\"requests\":{\"cpu\":\"500m\",\"memory\":\"256Mi\"}},\"volumeMounts\":[{\"name\":\"working-volume\",\"mountPath\":\"/work\"}]},\"tolerations\":[{\"key\":\"virtual-node.interlink/no-sched
ule\",\"operator\":\"Exists\"}]}'"
time

The created envfile.properties

ARGO_NODE_ID=appname-lsdsharedfs-template-gnj4q-2986436489
ARGO_INCLUDE_SCRIPT_OUTPUT=false
ARGO_DEADLINE=0001-01-01T00:00:00Z
ARGO_PROGRESS_FILE=/var/run/argo/progress
ARGO_PROGRESS_PATCH_TICK_DURATION=1m0s
ARGO_PROGRESS_FILE_TICK_DURATION=3s
ARGO_CONTAINER_NAME=main
ARGO_TEMPLATE='{"name":"group-block","inputs":{"parameters":[{"name":"input_data","value":"stub2_output_preprocessed_signal.h5"},{"name":"pipeline_run_id","value":"appname-lsdsharedfs-template-gnj4q"},{"name":"block_label","value":"160"},{"name":"group_label","value":"stub2"},{"name":"block_static_configuration_reference","value":"dummy_config.json"},{"name":"workdir","value":"/work"},{"name":"bus_uri","value":"nats://my-nats.nats:4222"},{"name":"n_steps_per_iteration","value":"1000"},{"name":"current_iteration","value":"0"}]},"outputs":{},"affinity":{"nodeAffinity":{"preferredDuringSchedulingIgnoredDuringExecution":[{"weight":1,"preference":{"matchExpressions":[{"key":"kubernetes.io/hostname","operator":"In","values":["interlink-slurm"]}]}}]}},"metadata":{},"container":{"name":"","image":"gitlabaddress/projectname-sgs/componentName/framework:0.4.0","command":["appcmd"],"args":["--workdir=/work","--pipeline-run-id=appname-lsdsharedfs-template-gnj4q","--servers=nats://my-nats.nats:4222","start-block","--input-data=stub2_output_preprocessed_signal.h5","--input-group-configuration-path=/work/stub2_group_configuration.json","--block-label=160","--group-label=stub2","--n-steps=1000","--current-iteration=0","--output-checkpoint=/work/stub2_160_mcmc.dump"],"resources":{"limits":{"cpu":"500m","memory":"256Mi"},"requests":{"cpu":"500m","memory":"256Mi"}},"volumeMounts":[{"name":"working-volume","mountPath":"/work"}]},"tolerations":[{"key":"virtual-node.interlink/no-schedule","operator":"Exists"}]}'

[antoinetran]

ping @dciangot for review and merge

[dciangot]

LGTM