Patch: fix for non-extension files

[dapineyro]

Overview

Bug to fix: Files without file extension are not recognised as files when they are submitted as parameters in Bash jobs and array jobs.

JIRA

• HSM-8316

Changes

• Resolve extensionless Data/ paths as file references.
• Correct project detection for nested Data/ paths.
• Add regression tests, update docs/changelog, and bump to 2.96.1.

Acceptance Criteria

• Extensionless files resolve across current and explicit projects; missing files fail before submission.
• Text values, existing file parameters, and glob patterns retain their behavior.
• 608 tests passed locally; five logging tests required a temporary log directory.

PROD (ADAPT)

Before the fix 🔴

We try to add a parameter file: --parameter --file=ci-testing/Data/bash_array/input

(testpip) dpineyro@Lifebit-QXDXLP41DQ cloudos-cli % cloudos bash array-job \
          --instance-type m4.xlarge \
          --memory 2 \
          --parameter -test=value \
          --parameter --gaq=test \
          --array-parameter --array_var=title \
          --job-name "before_fix" \
          --command "echo 'test' > new_file.txt" \
          --project-name "cloudos-cli-tests" \
          --workflow-name "plink2-lifebiai-dockerhub" \
          --array-file Data/bash_array/sampleArray.csv \
          --separator "," \
          --parameter --file=ci-testing/Data/bash_array/input \
          --last
CloudOS CLI python package: a package for interacting with Lifebit Platform.

Version: 2.95.1

Lifebit Platform bash-specific job functionality.


Checking columns in the array file vs parameters added...

Found column 'title' in the array file.
	Job successfully launched to Lifebit Platform, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1b0399aa89690e55e3be
	Your assigned job id is: 6aad1b0399aa89690e55e3be

	Your current job status is: initializing
	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1b0399aa89690e55e3be or use the following command:
	cloudos job status \
		--profile my_profile \
		--job-id 6aad1b0399aa89690e55e3be

But it is not recognised as a file and instead recognised as a string:
https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1b0399aa89690e55e3be

No FileTransfers

After the fix 🟢

(cloudos-cli) dpineyro@Lifebit-QXDXLP41DQ cloudos-cli % cloudos bash array-job \                      
          --instance-type m4.xlarge \
          --memory 2 \
          --parameter -test=value \
          --parameter --gaq=test \
          --array-parameter --array_var=title \
          --job-name "after_fix" \
          --command "echo 'test' > new_file.txt" \
          --project-name "cloudos-cli-tests" \
          --workflow-name "plink2-lifebiai-dockerhub" \
          --array-file Data/bash_array/sampleArray.csv \
          --separator "," \
          --parameter --file=ci-testing/Data/bash_array/input \
          --last
CloudOS CLI python package: a package for interacting with Lifebit Platform.

Version: 2.96.1

Lifebit Platform bash-specific job functionality.


Checking columns in the array file vs parameters added...

Found column 'title' in the array file.
	Job successfully launched to Lifebit Platform, please check the following link: https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1c1d985c161657184102
	Your assigned job id is: 6aad1c1d985c161657184102

	Your current job status is: scheduled
	To further check your job status you can either go to https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1c1d985c161657184102 or use the following command:
	cloudos job status \
		--profile my_profile \
		--job-id 6aad1c1d985c161657184102

The parameter is now recognised as a file and staged into the process:
https://cloudos.lifebit.ai/app/advanced-analytics/analyses/6aad1c1d985c161657184102

AZURE

Not relevant

Interactive Analysis

Not relevant

[Copilot]

🟢 Approval recommended

No unresolved blocking issues were identified.

Pull request overview

Fixes resolution of extensionless File Explorer paths in Bash and Bash array jobs.

Changes:

• Corrects nested Data/ path and project extraction.
• Adds regression tests for Bash and array jobs.
• Updates documentation, changelog, and version.

File summaries

File	Reviewed change
tests/test_bash/test_send_bash_array_job_multi_project.py	Verifies array-job file references.
tests/test_bash/test_docker_workflow_param_processing.py	Adds regression coverage.
README.md	Documents extensionless file parameters.
cloudos_cli/utils/array_job.py	Corrects project extraction for nested paths.
cloudos_cli/jobs/job.py	Resolves extensionless Data/ files.
cloudos_cli/_version.py	Bumps the package version.
CHANGELOG.md	Records the fix.

Review details

• Files reviewed: 7/7 changed files
• Comments generated: 0
• Review effort level: Lite

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[danielboloc]

LGTM