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fix: properly handle remote storage when waiting for pipes#3317

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johanneskoester merged 3 commits intomainfrom
fix/wait-for-pipe
Feb 27, 2025
Merged

fix: properly handle remote storage when waiting for pipes#3317
johanneskoester merged 3 commits intomainfrom
fix/wait-for-pipe

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@johanneskoester johanneskoester commented Feb 27, 2025

Before it could fail with certain storage plugins (e.g. fs), in combination with local execution.

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

Summary by CodeRabbit

  • New Features
    • Refined file storage behavior by excluding certain flagged files from retention.
    • Enhanced file waiting functionality with an additional option for local file evaluation and clearer notifications when files are missing.
    • Upgraded job processing by tracking special outputs and providing improved error reporting for smoother operations.

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coderabbitai bot commented Feb 27, 2025

📝 Walkthrough

Walkthrough

This pull request refines file handling and job processing logic. In the DAG, the handle_storage method now excludes files marked as "pipe" or "service" from being stored. The IO module adds a new constant and parameter to better manage local file considerations and improves logging for missing files. Additionally, the Jobs module now tracks pipe/service outputs with a new class field and method, updates job preparation to accommodate these inputs, and enhances error handling during postprocessing by capturing multiple exceptions.

Changes

File(s) Change Summary
snakemake/dag.py Extended file storage logic in handle_storage to now exclude files flagged as "pipe" or "service" from being stored.
snakemake/io.py Introduced _CONSIDER_LOCAL_DEFAULT and updated wait_for_files to include a new consider_local parameter. Enhanced get_missing by adding a condition for _IOFile and improved logging.
snakemake/jobs.py Added pipe_or_service_output field and is_pipe_or_service_input method in the Job class. Modified job preparation to account for pipe/service inputs and adjusted error handling in postprocess for group jobs.

Sequence Diagram(s)

sequenceDiagram
    participant U as User/Job
    participant D as DAG.handle_storage
    participant S as Storage Service

    U->>D: Trigger file storage
    D->>D: Evaluate file condition (is storage & not flagged as pipe/service)
    alt Eligible for storage
        D->>S: Store file
    else Not eligible (flagged as pipe/service)
        D-->>U: Skip storage operation
    end
Loading
sequenceDiagram
    participant A as Async Caller
    participant I as wait_for_files
    participant L as Logger

    A->>I: Call wait_for_files(files, consider_local)
    I->>I: Iterate over files and check if _IOFile not in consider_local
    I->>L: Log detailed missing files information
    I-->>A: Return formatted missing files list
Loading
sequenceDiagram
    participant J as Job
    participant P as Pipe/Service Processor
    participant E as Error Handler

    J->>J: Initialize Job (populate pipe_or_service_output)
    J->>P: Process outputs, flagging pipe/service files
    J->>J: Invoke is_pipe_or_service_input() during job preparation
    J->>E: In postprocess, catch ExceptionGroup for error handling
Loading

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Actionable comments posted: 0

🧹 Nitpick comments (1)
snakemake/jobs.py (1)

1598-1602: Enhanced error handling for group job postprocessing.

The code now properly catches ExceptionGroup exceptions, which provides better error reporting when multiple exceptions occur during parallel postprocessing of group jobs.

Consider using raise ... from e to preserve the exception chain, which helps with debugging by showing the original cause:

-            except ExceptionGroup as e:
-                raise WorkflowError(
-                    f"Error postprocessing group job {self.jobid}.",
-                    *e.exceptions,
-                )
+            except ExceptionGroup as e:
+                raise WorkflowError(
+                    f"Error postprocessing group job {self.jobid}.",
+                    *e.exceptions,
+                ) from e
🧰 Tools
🪛 Ruff (0.8.2)

1599-1602: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 77ef176 and 3336f7d.

📒 Files selected for processing (3)
  • snakemake/dag.py (1 hunks)
  • snakemake/io.py (3 hunks)
  • snakemake/jobs.py (6 hunks)
🧰 Additional context used
📓 Path-based instructions (1)
`**/*.py`: Do not try to improve formatting. Do not suggest ...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

  • snakemake/dag.py
  • snakemake/jobs.py
  • snakemake/io.py
🪛 Ruff (0.8.2)
snakemake/jobs.py

1599-1602: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

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🔇 Additional comments (11)
snakemake/dag.py (1)

916-921: Improved handling of pipe and service files in storage operations.

The additional conditions to exclude files flagged as "pipe" or "service" from being stored in storage is a valuable improvement. These file types serve as communication channels between jobs and don't need to be persisted in storage, avoiding unnecessary storage operations.

snakemake/jobs.py (4)

291-291: Good addition for tracking pipe or service outputs.

Adding a dedicated set to track outputs flagged as pipe or service will make it easier to handle these special file types throughout the job lifecycle.


301-302: Properly populating the pipe_or_service_output set.

The code correctly identifies pipe or service outputs during initialization and adds them to the dedicated tracking set.


949-953: Well-implemented helper method for identifying pipe or service inputs.

This method efficiently determines if an input file is a pipe or service output from one of the job's dependencies by checking against the newly added tracking set.


858-860: Improved handling of pipe/service inputs during job preparation.

The consider_local parameter now properly includes pipe and service inputs, which ensures these files are correctly handled when waiting for inputs during job preparation.

snakemake/io.py (6)

944-945: Good addition of a new constant.

This constant provides a clean default value for the new consider_local parameter.


947-953: Function signature updated appropriately with type annotation.

The new parameter consider_local has been added with proper type annotation and default value, maintaining backward compatibility.


964-966: Good addition to handle pipe/service files as local files.

This check now considers files in the consider_local set to bypass storage checks, which properly addresses the issue with pipe/service files in remote storage scenarios.


970-971: Improved error message formatting.

The error message for missing files in storage now uses f-string formatting, which is more readable and Pythonic.


988-994: Enhanced logging with better formatting.

The log message for missing files has been improved with better formatting and structure.


1001-1002: Consistent error formatting.

This change maintains consistency with the earlier logging improvements by using the same formatting approach for missing files in the error message.

@johanneskoester johanneskoester merged commit 9f7e092 into main Feb 27, 2025
41 checks passed
@johanneskoester johanneskoester deleted the fix/wait-for-pipe branch February 27, 2025 10:52
johanneskoester pushed a commit that referenced this pull request Feb 27, 2025
🤖 I have created a release *beep* *boop*
---


##
[8.29.0](v8.28.0...v8.29.0)
(2025-02-27)


### Features

* provide mechanism to link between report items (snakemake.report_href,
see docs) ([#3224](#3224))
([a024e60](a024e60))
* toggles for binary labels in report
([#3296](#3296))
([7690998](7690998))


### Bug Fixes

* add missing [@conda](https://github.com/conda) annotations
([#3298](#3298))
([0b541cc](0b541cc))
* properly handle remote storage when waiting for pipes
([#3317](#3317))
([9f7e092](9f7e092))
* provide proper error messages if output file preparation (pipe, mkdir)
fails ([#3309](#3309))
([77ef176](77ef176))
* record file extension (e.g. .tsv) in between workflow cache records in
order to avoid that files of the wrong format are erroneously returned
by the cache. This will lead to some cache misses. But avoiding errors
induced by the previous behavior of ignoring file extensions when
seeking for cache records is more important.
([#3314](#3314))
([4912f00](4912f00))
* sort results lexicographically by labels in their order of appearance
([#3293](#3293))
([a19a0ac](a19a0ac))


### Documentation

* update best practices
([7270eb3](7270eb3))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
…#3317)

Before it could fail with certain storage plugins (e.g. fs), in
combination with local execution.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Refined file storage behavior by excluding certain flagged files from
retention.
- Enhanced file waiting functionality with an additional option for
local file evaluation and clearer notifications when files are missing.
- Upgraded job processing by tracking special outputs and providing
improved error reporting for smoother operations.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
🤖 I have created a release *beep* *boop*
---


##
[8.29.0](snakemake/snakemake@v8.28.0...v8.29.0)
(2025-02-27)


### Features

* provide mechanism to link between report items (snakemake.report_href,
see docs) ([snakemake#3224](snakemake#3224))
([a024e60](snakemake@a024e60))
* toggles for binary labels in report
([snakemake#3296](snakemake#3296))
([7690998](snakemake@7690998))


### Bug Fixes

* add missing [@conda](https://github.com/conda) annotations
([snakemake#3298](snakemake#3298))
([0b541cc](snakemake@0b541cc))
* properly handle remote storage when waiting for pipes
([snakemake#3317](snakemake#3317))
([9f7e092](snakemake@9f7e092))
* provide proper error messages if output file preparation (pipe, mkdir)
fails ([snakemake#3309](snakemake#3309))
([77ef176](snakemake@77ef176))
* record file extension (e.g. .tsv) in between workflow cache records in
order to avoid that files of the wrong format are erroneously returned
by the cache. This will lead to some cache misses. But avoiding errors
induced by the previous behavior of ignoring file extensions when
seeking for cache records is more important.
([snakemake#3314](snakemake#3314))
([4912f00](snakemake@4912f00))
* sort results lexicographically by labels in their order of appearance
([snakemake#3293](snakemake#3293))
([a19a0ac](snakemake@a19a0ac))


### Documentation

* update best practices
([7270eb3](snakemake@7270eb3))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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