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Feat: Multi file linking#317

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dapineyro merged 10 commits into
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multi-file-linking
Jun 3, 2026
Merged

Feat: Multi file linking#317
dapineyro merged 10 commits into
mainfrom
multi-file-linking

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@l-mansouri

@l-mansouri l-mansouri commented May 28, 2026

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Overview

This PR implement files linking. The CLI can now:

  • link individual files and folder (or multiples) in interactive session creation, both s3 files and File Explorer files (no virtual folders though!)
  • link multiple files and folders while an interactive session is running using cloudos link

JIRA

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

LP-107767

Changes

  • Implements linking of files in interactive session creation
  • Implements linking of files in cloudos link
  • Removes support for linking while resuming a paused interactive 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.

DEV

This Environment is interchangable with PROD if the acceptance criteria can only be tested in DEV for example. If that is the case please name this section PROD (or any new environment)

Scenario 1 - Successfully link individual S3 file via CLI
cloudos link --session-id 6a180a8a558610e459defb70 s3://lifebit-featured-datasets/pipelines/vep/agg_vcf/test_1_chr_121K_variants.csv --profile internal-DEV
Screenshot 2026-05-28 at 12 00 26
Scenario 2 - CLI automatically handles both files and folders
cloudos interactive-session create --name test_cli --session-type vscode --profile internal-DEV --link leila-test/Data/ai_data_test/person.csv,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/vcf_list.txt

cloudos link --session-id 6a180a8a558610e459defb70 Data/ai_data_test/measurements.csv,Data/results,s3://lifebit-featured-datasets/pipelines/VCF-s3table-ingestion/too_many_samples_input.txt --profile internal-DEV
Screenshot 2026-05-28 at 11 28 10 Screenshot 2026-05-28 at 11 34 27 Screenshot 2026-05-28 at 11 39 14 Screenshot 2026-05-28 at 11 39 26
Scenario 3 - Authentication failure handling
cloudos interactive-session create --name test_cli --session-type vscode --profile internal-DEV --link leila-test/Data/ai_data_test/person.csv --apikey not-working-api-key
Screenshot 2026-05-28 at 12 05 10
Scenario 4 - Authorization failure for file access
cloudos link --session-id 6a180a8a558610e459defb70 s3://lifebit-user-data-7088baee-f24b-4512-93cc-d35d0205ff9d/deploit/teams/687fb9905c45270e09db1e9a/users/651d2d387b9838932e40cf1b/projects/688351ab6be610972db54a8e/jobs/6a146f36e57a0d379c9c068a/work/72/d8fcaaa81768f441d932a5072b63b0/validated_vcf.txt --profile internal-DEV #file is a intermediate result file of a job from a different workspace
Screenshot 2026-05-28 at 12 24 16

Note that the file will appear anyway in the linked data with an error in the UI

Screenshot 2026-05-28 at 12 25 01
Scenario 5 - Private session access control
cloudos link --session-id 6a180a8a558610e459defb70 Daniel_Test_Files/Data/20131219.populations.tsv --profile internal-DEV-member
Screenshot 2026-05-28 at 12 22 36
Scenario 6 - Prevent duplicate file names
cloudos link --session-id 6a180a8a558610e459defb70 Data/ai_data_test/measurements.csv --profile internal-DEV
Screenshot 2026-05-28 at 12 26 29
Scenario 8 - Cross-platform session type support
cloudos interactive-session create --name test_cli-j --session-type jupyter --profile internal-DEV --link leila-test/Data/ai_data_test/person.csv 
cloudos interactive-session create --name test_cli-vs --session-type vscode --profile internal-DEV --link leila-test/Data/ai_data_test/person.csv 
cloudos interactive-session create --name test_cli-r --session-type Rstudio --profile internal-DEV --link leila-test/Data/ai_data_test/person.csv 
Screenshot 2026-05-28 at 12 29 33 Screenshot 2026-05-28 at 12 30 48 Screenshot 2026-05-28 at 12 29 15 Screenshot 2026-05-28 at 12 31 14 Screenshot 2026-05-28 at 12 28 54 Screenshot 2026-05-28 at 12 31 36
Scenario 10 - Backwards compatibility with folder linking
cloudos link --session-id 6a180a8a558610e459defb70 Data/MultiQC --profile internal-DEV
Screenshot 2026-05-28 at 12 38 04 Screenshot 2026-05-28 at 12 40 20
Scenario 11 - Missing required parameters
cloudos link --session-id 6a180a8a558610e459defb70 --profile internal-DEV 
Screenshot 2026-05-28 at 12 39 56
Scenario 12 - 100 items limit
cloudos link --session-id 6a180a8a558610e459defb70 --profile internal-DEV s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18939_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18940_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18941_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18942_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18943_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18944_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18945_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18946_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18947_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18948_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18949_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18950_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18951_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18952_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18953_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18956_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18957_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18959_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18960_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18961_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18962_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18963_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18964_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18965_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18966_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18967_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18968_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18969_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18970_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18971_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18972_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18973_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18974_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18975_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18976_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18977_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18978_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18979_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18980_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18981_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18982_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18983_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18984_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18985_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18986_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18987_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18988_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18989_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18990_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18991_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18992_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18993_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18994_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18995_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18997_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18998_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA18999_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19000_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19001_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19002_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19003_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19004_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19005_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19006_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19007_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19009_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19010_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19011_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19012_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19054_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19055_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19056_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19057_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19058_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19059_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19060_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19062_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19063_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19064_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19065_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19066_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19067_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19068_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19070_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19072_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19074_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19075_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19076_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19077_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19078_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19079_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19080_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19081_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19082_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19083_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19084_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19085_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19086_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19087_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19088_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19089_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19090_VEP_annotated.vcf.gz,s3://lifebit-featured-datasets/1000genomes-dragen/annotated_data/NA19091_VEP_annotated.vcf.gz
Screenshot 2026-05-28 at 12 43 40

Scenarios 7 and 9 are missing as they are not feasible as discussed in the ticket here

CLAUDE PR CHECK
PR Review (final): multi-file-linking → main
1. Style consistency ✓
Consistent naming, indentation, quote style, and imports throughout all changed files.

2. Test coverage ✓
447 tests pass across the full suite. All new paths (S3 file detection, File Explorer file resolution, 100-item cap, duplicate-name check against session, mixed batch, v2/v1 fallback) are covered in [test_link_files.py](vscode-webview://1rob5921kamjru37v842k4if5qgd1sef8snfma675k5ri3eb4mip/tests/test_datasets/test_link_files.py) and the updated [test_link.py](vscode-webview://1rob5921kamjru37v842k4if5qgd1sef8snfma675k5ri3eb4mip/tests/test_datasets/test_link.py).

3. Verbosity ✓
No unnecessary intermediates, redundant comments, or over-engineered abstractions.

4. Dead / unused code ✓

validate_file_explorer_folder — deleted
parse_file_explorer_path — deleted; its unused get_file_or_folder_id import in link.py removed
build_resume_payload(data_files, s3_mounts) dead parameters — removed; signature is now clean (instance_type, storage_size, cost_limit, shutdown_at only)
5. Maintainability & DRY ✓
_check_duplicate_mount_name helper defined at [cli.py:40](vscode-webview://1rob5921kamjru37v842k4if5qgd1sef8snfma675k5ri3eb4mip/cloudos_cli/interactive_session/cli.py#L40) and called from both the S3 branch ([line 506](vscode-webview://1rob5921kamjru37v842k4if5qgd1sef8snfma675k5ri3eb4mip/cloudos_cli/interactive_session/cli.py#L506)) and CloudOS branch ([line 560](vscode-webview://1rob5921kamjru37v842k4if5qgd1sef8snfma675k5ri3eb4mip/cloudos_cli/interactive_session/cli.py#L560)).

6. Changelog & README ✓
CHANGELOG.md has a correct v2.91.0 entry. README.md updates cover --link description, datasets link section, cloudos link section, resume (mount/link removed), and the 100-item cap.

7. nextflow.config — N/A

8. Security hygiene ✓
No hardcoded secrets, no eval, no shell passthrough. SSL verification plumbed correctly.

9. Performance ✓
Single pre-mount GET per link_folders_batch call; one list_folder_content per File Explorer item (unavoidable given the API contract). No hot-path issues.

Verdict: ✅ Approved — full suite green (447/447), all previously flagged issues resolved.

@l-mansouri l-mansouri marked this pull request as draft May 28, 2026 10:50
@l-mansouri l-mansouri marked this pull request as ready for review May 28, 2026 10:50
@dapineyro dapineyro self-requested a review June 1, 2026 11:02
@dapineyro dapineyro force-pushed the multi-file-linking branch from 8272e14 to cf236ff Compare June 1, 2026 12:37
@dapineyro dapineyro marked this pull request as draft June 1, 2026 12:47
@dapineyro dapineyro marked this pull request as ready for review June 1, 2026 12:47

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Pull request overview

This PR adds multi-item linking (files and folders) to interactive sessions across the CLI, enabling both S3 file linking and File Explorer file linking, plus batching and improved user feedback/error messaging. It also updates docs/changelog and removes data linking while resuming a paused session.

Changes:

  • Extend linking to support both files and folders (S3 + File Explorer), including batch linking and v2/v1 fallback behavior.
  • Enforce session link constraints (100-item cap, duplicate mount-name prevention) and add more actionable mount failure messaging.
  • Update CLI help/README/changelog and adjust/expand tests for the new linking behavior.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file
File Description
cloudos_cli/link/link.py Core implementation for multi-item linking, file detection/parsing, duplicate/limit checks, and mount verification/error translation.
cloudos_cli/link/cli.py Updates cloudos link UX/docs and uses the new boolean success signal to exit non-zero on verification failures.
cloudos_cli/datasets/cli.py Updates cloudos datasets link semantics/documentation to allow linking files and relative File Explorer paths.
cloudos_cli/interactive_session/cli.py Updates session creation flow to resolve/link both files and folders, plus duplicate-name handling reuse.
cloudos_cli/interactive_session/interactive_session.py Enhances link-path parsing to distinguish S3 file vs folder and updates display labels.
tests/test_datasets/test_link.py Adjusts existing link tests to account for the new pre-mount status GET checks and parsing changes.
tests/test_datasets/test_link_files.py Adds comprehensive new unit tests for file-level linking, mixed batches, limits, and error translation.
README.md Documents new file/folder linking behavior, relative File Explorer path rules, and the 100-item limit.
CHANGELOG.md Adds v2.91.0 release notes including breaking path-format change and new linking capabilities.
cloudos_cli/_version.py Bumps version to 2.91.0.

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Pull request overview

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Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.

Comment thread cloudos_cli/link/link.py
@dapineyro dapineyro merged commit 826dc3f into main Jun 3, 2026
161 of 165 checks passed
@dapineyro dapineyro deleted the multi-file-linking branch June 3, 2026 13:39
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3 participants