Feat: Move link implementation to the interactive session module

[l-mansouri]

Overview

This PR moves the link command implementation to the interactive session module and changes the --mountoption of cloudos interactive-session to --link --copy

JIRA

Please add here as many related tasks this PR covers with its brief description, if more than one ticket

https://lifebit.atlassian.net/browse/LP-110779

Changes

• Moves cloudos link into the interactive-session module as cloudos interactive-session link
• File Explorer paths now infer the project name from the first path segment (e.g. my-project/Data/folder); standard top-level folder names (Data, AnalysesResults, Analyses_Results, Analyses-Results, Cohorts) are treated as relative to the profile project
• Removes --mount from cloudos interactive-session create
• Introduces --copy as an optional flag of --link in cloudos interactive-session create to copy data into the session

Acceptance Criteria

Please add here as many scenarios as in the Story

At the time of opening the PR, this is only testable in DEV as the feature is not released to prod yet and it is not supported in Azure.

Scenario 1: cloudos interactive-session link replaces cloudos link with identical functionality

cloudos interactive-session link --session-id 6a29820299b736a9e2495d40 Data/ai_data_test/person.csv,leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt --profile internal-DEV

Scenario 2: create --link links a folder or file to the interactive session

cloudos interactive-session create --session-type vscode --name test-link --link Data/ai_data_test/person.csv,leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt --profile internal-DEV

Scenario 3: create --link --copy copies data into the interactive session

cloudos interactive-session create --session-type vscode --name test-mount --link Data/ai_data_test/person.csv,leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt  --copy --profile internal-DEV

Scenario 4: Files are linkable via cloudos interactive-session link if supported by the DEV endpoint

cloudos interactive-session link --session-id 6a29820299b736a9e2495d40 Data/ai_data_test/person.csv,leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt --profile internal-DEV

Scenario 5: Detailed API error messages are surfaced to the user on failure

cloudos interactive-session link --session-id 6a180a8a558610e459defb70 Data/ai_data_test/person.csv,leila-test/Data/MultiQC,Daniel_Test_Files/Data/20131219.populations.tsv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt --profile internal-DEV --apikey not-working-api-key

[Copilot]

Pull request overview

This PR relocates the legacy cloudos link functionality under the interactive-session module as cloudos interactive-session link, and updates interactive session creation to replace --mount with --link --copy for copying data into sessions.

Changes:

• Introduces cloudos interactive-session link with support for job-based linking and multi-project path inference.
• Reworks cloudos interactive-session create to remove --mount and add --copy (copy via --link paths).
• Updates documentation, changelog, and tests to reflect the new CLI surface and behaviors.

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/test_interactive_session/test_link_session.py	Adds tests for the new interactive-session link command and FE path normalization helpers.
tests/test_interactive_session/test_create_session.py	Updates create-session tests for --copy/--link behavior and removes --mount expectations.
tests/test_datasets/test_link.py	Updates datasets link tests to use the relocated Link implementation and adjusts expectations.
tests/test_datasets/test_link_files.py	Updates link-files tests for the relocated Link implementation and revised output/messages.
README.md	Documents interactive-session link and replaces --mount with --link --copy guidance.
cloudos_cli/link/init.py	Removes the legacy cloudos_cli.link package initializer/export.
cloudos_cli/jobs/cli.py	Switches imports to use cloudos_cli.interactive_session.link.Link.
cloudos_cli/interactive_session/link.py	Hosts the Link implementation; adds multi-batch support and path display updates.
cloudos_cli/interactive_session/interactive_session.py	Removes resolve_data_file_id and adjusts session output formatting for copied/link data display.
cloudos_cli/interactive_session/cli.py	Adds interactive-session link, removes --mount, introduces --copy, and implements FE path normalization/grouping.
cloudos_cli/interactive_session/init.py	Exposes Link from the interactive-session module.
cloudos_cli/datasets/cli.py	Updates imports to new Link location and modifies datasets link command docs/behavior.
cloudos_cli/_version.py	Bumps version to 2.92.0.
cloudos_cli/main.py	Removes the top-level cloudos link command registration.
CHANGELOG.md	Adds v2.92.0 entry describing the new command location and --copy change.

Comments suppressed due to low confidence (3)

cloudos_cli/interactive_session/link.py:647

• _parse_file_explorer_item now calls generate_datasets_for_project(), which can sys.exit(1) on common errors (missing project / Forbidden). That can terminate the whole CLI process (or any caller using Link as a library) instead of surfacing a normal ValueError that link/copy commands can handle and report cleanly.
  cloudos_cli/interactive_session/link.py:729
• get_fuse_filesystems_status treats HTTP 401 as "Forbidden". 401 is "Unauthorized" (authentication), while 403 is "Forbidden" (authorization). This makes the error misleading and inconsistent with other handlers in this file.
  cloudos_cli/interactive_session/link.py:482
• _handle_mount_error maps "401/unauthorized" to a message starting with "Forbidden". This is incorrect for 401 responses and will confuse users when an API key is invalid/expired.

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[Copilot]

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (3)

cloudos_cli/interactive_session/link.py:621

• _parse_file_explorer_item calls generate_datasets_for_project(), which can sys.exit(1) on project-not-found / forbidden. That makes Link unusable as a library helper (and bypasses the CLI’s structured error handling), and can abruptly terminate tests/callers instead of raising a catchable exception.
  cloudos_cli/interactive_session/link.py:702
• 401 responses are labeled as "Forbidden" here, but 401 is Unauthorized. This message is also inconsistent with the v1 mount handler above in this file, which uses "Unauthorized..." for 401.
  cloudos_cli/interactive_session/link.py:461
• _handle_mount_error treats 401 as "Forbidden", which is misleading and inconsistent with other 401 handling in this module (e.g., _mount_single_folder_v1 raises "Unauthorized...").

[Copilot]

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (4)

cloudos_cli/interactive_session/link.py:125

• link_folders_batch returns True for any non-204 response, which can report success even when the mount request wasn’t accepted or when verification never ran (e.g., v1 success codes other than 204, or future API changes). This breaks the method’s contract (“verified as mounted”) and can cause callers (e.g., datasets link / interactive-session link) to miss failures.
  cloudos_cli/interactive_session/link.py:461
• _handle_mount_error maps 401/unauthorized to a "Forbidden" message. That’s both semantically incorrect (401 != 403) and currently contradicts the unit tests expecting an invalid API key/unauthorized message.
  cloudos_cli/interactive_session/link.py:702
• get_fuse_filesystems_status raises a "Forbidden" message on HTTP 401. This is misleading (401 is Unauthorized) and inconsistent with other 401 handling in this module (e.g., _mount_single_folder_v1).
  cloudos_cli/interactive_session/link.py:621
• _parse_file_explorer_item calls generate_datasets_for_project(), which can sys.exit(1) internally on common errors (missing project / Forbidden). That makes Link hard to use safely from other code paths (and prevents Click from formatting a clean error), since SystemExit bypasses normal exception handling.

[Copilot]

Pull request overview

Copilot reviewed 18 out of 18 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (6)

cloudos_cli/interactive_session/link.py:125

• link_folders_batch returns True for any non-204 status code, which can incorrectly report success without verifying mounts (e.g., if the mount endpoint returns 200/202 or an unexpected 2xx). This also contradicts the method docstring that says mounts are verified as mounted.
  cloudos_cli/interactive_session/link.py:462
• The 401 handling reports "Forbidden" (403) even though this branch is for 401/unauthorized. This makes CLI output misleading and can confuse users troubleshooting API key vs. authorization issues.
  cloudos_cli/interactive_session/link.py:703
• This 401 branch raises a "Forbidden" error message. 401 indicates authentication failure (invalid/missing API key), while 403 indicates the key is valid but lacks access. Using the wrong status text makes it harder to debug API issues.
  cloudos_cli/interactive_session/link.py:621
• generate_datasets_for_project(...) can call sys.exit(1) (see cloudos_cli/utils/array_job.py), which will terminate the CLI abruptly from inside _parse_file_explorer_item and bypass the normal Click error handling / messaging. Converting that to a ValueError here keeps error handling consistent and prevents hard exits from a library-style helper.
  cloudos_cli/interactive_session/cli.py:495
• When --copy is used, S3 inputs are treated as files without validating that the provided path is actually a file (e.g. a trailing / would be sent as an S3File object key). This can lead to confusing API failures; it should be rejected early with a clear usage error, and the name should be the basename rather than the full key/prefix.

                        s3_file_item = {
                            "type": "S3File",
                            "data": {
                                "name": parsed["s3_prefix"],
                                "s3BucketName": parsed["s3_bucket"],

cloudos_cli/datasets/cli.py:766

• cloudos datasets link documents File Explorer paths as relative to --project-name, but there is no guard against users passing my-project/Data/... (which is now encouraged by interactive-session link). Without a check, the CLI will attempt to resolve a folder named my-project inside project my-project, producing a confusing "not found" error.

    if not path.startswith("s3://") and project_name is None:
        raise click.UsageError("When using File Explorer paths '--project-name' needs to be defined")