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fix: Prevent broken report_href links by using deterministic report IDs with fixed prefix length#3889

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fix-report-href
Jan 8, 2026
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fix: Prevent broken report_href links by using deterministic report IDs with fixed prefix length#3889
johanneskoester merged 5 commits intomainfrom
fix-report-href

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@fxwiegand fxwiegand commented Dec 17, 2025 •
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This PR makes snakemake shorten report hashes to 16 characters and also makes report_href() use the 16 character long prefix which was not done before. Collisions are detected when shortening IDs and an error is raised directing users to open an issue to request a longer hash length. Fixes #3867.

Summary by CodeRabbit

  • New Features

    • Reports and generated links now use 16-character shortened file IDs for cleaner, more readable paths.

  • Bug Fixes

    • Added collision detection for shortened IDs; non-unique shortened IDs now produce a clear error with guidance to request longer hashes.
    • Removed prior silent-warning behavior in favor of explicit error handling.

  • Style

    • Minor formatting cleanup in generated report preambles (reduced extra blank lines).

✏️ Tip: You can customize this high-level summary in your review settings.

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coderabbitai Bot commented Dec 17, 2025 •
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📝 Walkthrough

Walkthrough

Replaces adaptive ID-shortening with a fixed 16-character truncation for report file IDs, applies those shortened IDs to FileRecord entries, adds collision detection that raises a WorkflowError with guidance, and updates ReportHref URL generation and tests to use 16-char IDs. (≤50 words)

Changes

Cohort / File(s) Summary
Report ID shortening logic
src/snakemake/report/__init__.py		 Replace prior dynamic shortening with unconditional 16-character truncation (constant used); check for collisions between shortened and full IDs and raise WorkflowError with a URL if collisions occur; apply shortened IDs to FileRecord entries in one pass; remove previous silent warning path.
Report href generation & formatting
src/snakemake/script/__init__.py		 Add FILE_HASH_PREFIX_LEN = 16; ReportHref.__str__ now uses the 16-char prefix when building relative paths; minor non-functional whitespace/formatting changes in R preambles.
Test expectations
tests/test_report_href/expected-results/test2.html		 Update expected HTML anchor hrefs to use 16-character directory hashes (shortened paths) for links.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

  • Inspect collision-detection logic, exception type, and the error message URL in src/snakemake/report/__init__.py.
  • Verify FILE_HASH_PREFIX_LEN usage and consistency between src/snakemake/report/__init__.py and src/snakemake/script/__init__.py.
  • Confirm tests in tests/test_report_href/ align with the new truncation and that no other code assumes full-length IDs.

Possibly related PRs

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❌ Failed checks (2 warnings)
Check name Status Explanation Resolution
Description check ⚠️ Warning The description explains the key changes and references the linked issue, but does not follow the required PR template with explicit QC checklist items. Add the QC checklist from the template explicitly documenting whether test cases exist and if documentation updates are needed.
Docstring Coverage ⚠️ Warning Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. You can run @coderabbitai generate docstrings to improve docstring coverage.
✅ Passed checks (3 passed)
Check name Status Explanation
Title check ✅ Passed The title clearly describes the main change: using fixed 16-character prefix for report IDs to prevent broken report_href links, which directly addresses the core issue.
Linked Issues check ✅ Passed The code changes successfully implement the core objective from issue #3867: report_href now uses deterministic 16-character prefix IDs that match Snakemake's file storage, fixing broken links [#3867].
Out of Scope Changes check ✅ Passed All changes are directly related to implementing the 16-character hash prefix: core logic in report/init.py, ReportHref.str in script/init.py, and test fixtures reflect expected output.
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  • Post copyable unit tests in a comment
  • Commit unit tests in branch fix-report-href

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Actionable comments posted: 0

🧹 Nitpick comments (1)
src/snakemake/report/__init__.py (1)

458-473: Simplify redundant ID slicing.

Since get_report_id returns exactly 16 characters, the [:16] slice on line 465 is redundant. Simplify to [rec.id for rec in file_records].

The strict=True parameter for zip() requires Python 3.10+, but the project's minimum version is Python 3.7, so it cannot be used.

Apply this diff:

-    shortened_ids = [rec.id[:16] for rec in file_records]
+    shortened_ids = [rec.id for rec in file_records]
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🔇 Additional comments (2)
src/snakemake/common/__init__.py (1)

62-66: LGTM! Hash truncation aligns with report generation.

The 16-character prefix provides 64 bits of entropy, which should be sufficient for most workflows. This change ensures consistency with the shorten_ids function in the report module.

tests/test_report_href/expected-results/test2.html (1)

7-8: Test expectations correctly reflect the 16-character hash fix.

The shortened hash paths in the expected HTML output validate that report_href now generates links consistent with Snakemake's report storage paths.

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Actionable comments posted: 1

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🧠 Learnings (2)
📓 Common learnings 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3159
File: docs/tutorial/interaction_visualization_reporting/workdir/workflow/Snakefile:1-1
Timestamp: 2024-10-20T19:42:16.694Z
Learning: The `report` directive at the workflow level is still valid in Snakemake and is not deprecated.
📚 Learning: 2024-10-06T14:09:54.370Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3117
File: tests/test_wrapper/Snakefile:11-11
Timestamp: 2024-10-06T14:09:54.370Z
Learning: Changes made within test cases, such as in `tests/test_wrapper/Snakefile`, are for testing purposes and do not require updates to the project documentation.

Applied to files:

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🪛 Ruff (0.14.8)
src/snakemake/report/__init__.py

471-474: Avoid specifying long messages outside the exception class

(TRY003)

476-476: zip() without an explicit strict= parameter

Add explicit value for parameter strict=

(B905)

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src/snakemake/script/__init__.py (1)

89-103: LGTM!

The 16-character truncation of self._id correctly aligns ReportHref.__str__ with the shorten_ids function in report/__init__.py, ensuring generated links match the actual stored report paths. This directly addresses the broken report_href links described in issue #3867.

Comment thread src/snakemake/report/__init__.py
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Actionable comments posted: 0

🧹 Nitpick comments (1)
src/snakemake/report/__init__.py (1)

465-475: Collision detection logic is now correct.

The fix properly detects collisions caused by shortening by comparing the number of unique shortened IDs against unique full IDs. This addresses the issue from the previous review.

One minor lint suggestion per static analysis (Ruff B905): consider adding strict=True to the zip call for defensive coding, though both lists are guaranteed to have the same length here.

-    for rec, short_id in zip(file_records, shortened_ids):
+    for rec, short_id in zip(file_records, shortened_ids, strict=True):
         rec.id = short_id
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📚 Learning: 2024-11-12T12:08:20.342Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3148
File: snakemake/dag.py:1332-1336
Timestamp: 2024-11-12T12:08:20.342Z
Learning: In `snakemake/dag.py`, when code is outdated and will disappear upon resolving merge conflicts, avoid making code review suggestions on that code.

Applied to files:

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📚 Learning: 2024-10-14T09:42:11.571Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3140
File: snakemake/dag.py:1308-1308
Timestamp: 2024-10-14T09:42:11.571Z
Learning: In `snakemake/dag.py`, avoid flagging missing lines or indentation issues when there is no clear syntax or logical error to prevent false positives.

Applied to files:

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🪛 Ruff (0.14.8)
src/snakemake/report/__init__.py

469-472: Avoid specifying long messages outside the exception class

(TRY003)

474-474: zip() without an explicit strict= parameter

Add explicit value for parameter strict=

(B905)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (46)
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johanneskoester
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Actionable comments posted: 0

🧹 Nitpick comments (1)
src/snakemake/report/__init__.py (1)

465-475: LGTM! Fixed-length shortening correctly implemented.

The function now uses a deterministic 16-character prefix for all report IDs and includes collision detection with clear error guidance. The logic correctly identifies collisions introduced by shortening.

Optional refinements for clarity and defensive programming

Consider these minor improvements:

     full_ids = [rec.id for rec in file_records]
-    shortened_ids = [rec.id[:FILE_HASH_PREFIX_LEN] for rec in file_records]
+    shortened_ids = [rec.id[:FILE_HASH_PREFIX_LEN] for rec in file_records]
     # We only need to check for collisions that appear because of the shortening
-    if len(set(shortened_ids)) != len(set(full_ids)):
+    if len(set(shortened_ids)) < len(set(full_ids)):
         raise WorkflowError(
             "Collision detected when shortening report file hashes to 16 characters. "
             "Please open an issue at https://github.com/snakemake/snakemake/issues/new to request a greater hash length."
         )
 
-    for rec, short_id in zip(file_records, shortened_ids):
+    for rec, short_id in zip(file_records, shortened_ids, strict=True):
         rec.id = short_id

Changes:

  1. Use < instead of != for more explicit intent (collision means fewer unique shortened IDs)
  2. Add strict=True to zip() for defensive programming (satisfies B905 linter)

Both changes are optional refinements—the current implementation is functionally correct.

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Do not suggest type annotations for functions that are defined inside of functions or methods.
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🧠 Learnings (4)
📚 Learning: 2024-10-06T14:09:54.370Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3117
File: tests/test_wrapper/Snakefile:11-11
Timestamp: 2024-10-06T14:09:54.370Z
Learning: Changes made within test cases, such as in `tests/test_wrapper/Snakefile`, are for testing purposes and do not require updates to the project documentation.

Applied to files:

  • src/snakemake/report/__init__.py
📚 Learning: 2024-11-12T12:08:20.342Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3148
File: snakemake/dag.py:1332-1336
Timestamp: 2024-11-12T12:08:20.342Z
Learning: In `snakemake/dag.py`, when code is outdated and will disappear upon resolving merge conflicts, avoid making code review suggestions on that code.

Applied to files:

  • src/snakemake/report/__init__.py
📚 Learning: 2024-10-14T09:42:11.571Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3140
File: snakemake/dag.py:1308-1308
Timestamp: 2024-10-14T09:42:11.571Z
Learning: In `snakemake/dag.py`, avoid flagging missing lines or indentation issues when there is no clear syntax or logical error to prevent false positives.

Applied to files:

  • src/snakemake/report/__init__.py
📚 Learning: 2024-10-29T09:26:26.636Z 
Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 3171
File: snakemake/cli.py:106-145
Timestamp: 2024-10-29T09:26:26.636Z
Learning: Avoid adding input validation or error handling that unnecessarily complicates the code in the `snakemake` codebase, especially when the cases handled don't make sense.

Applied to files:

  • src/snakemake/report/__init__.py
🪛 Ruff (0.14.8)
src/snakemake/report/__init__.py

469-472: Avoid specifying long messages outside the exception class

(TRY003)

474-474: zip() without an explicit strict= parameter

Add explicit value for parameter strict=

(B905)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (46)
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🔇 Additional comments (1)
src/snakemake/report/__init__.py (1)

48-48: FILE_HASH_PREFIX_LEN import is valid.

FILE_HASH_PREFIX_LEN is correctly defined in snakemake.script as 16, and the import at line 48 is properly used in the shorten_ids function.

@johanneskoester johanneskoester merged commit 6d8f4d8 into main Jan 8, 2026
60 checks passed
@johanneskoester johanneskoester deleted the fix-report-href branch January 8, 2026 16:34
@snakemake-bot snakemake-bot mentioned this pull request Jan 8, 2026
Merged
johanneskoester pushed a commit that referenced this pull request Jan 8, 2026
@snakemake-bot
chore(main): release 9.14.6 (#3893)
0130fc8 
🤖 I have created a release *beep* *boop*
---


##
[9.14.6](v9.14.5...v9.14.6)
(2026-01-08)


### Bug Fixes

* create local clone of git repos for source files from hosting
providers ([#3643](#3643))
([d2f8aba](d2f8aba))
* create potentially missing .snakemake folder in case of very long
command lines for spawned jobs
([#3894](#3894))
([4b431dd](4b431dd))
* make ilp solver enumeration lazy
([#3900](#3900))
([30e1509](30e1509))
* Prevent broken report_href links by using deterministic report IDs
with fixed prefix length
([#3889](#3889))
([6d8f4d8](6d8f4d8))
* refactor LoggerManager setup and scope
([#3851](#3851))
([f46d904](f46d904))
* yield proper error message in case a local git source file is not
retrievable
([#3892](#3892))
([ed79cae](ed79cae))


### Documentation

* explain how to pass nested config via CLI
([#3885](#3885))
([9d8c539](9d8c539))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
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report_href generates broken links because it doesn't match Snakemake's shortened report paths

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@fxwiegand @johanneskoester