fix: apply transforms after a canonicalization and remove only the verified Signature

[cjbarth]

Summary

This PR fixes two related problems with transform chains that include enveloped-signature.

Transforms after a canonicalization were skipped

getCanonXml stopped applying transforms as soon as one returned a string, which every built-in canonicalization does. Every transform after a canonicalization was silently skipped on both sides:

• [exc-c14n, enveloped-signature] with the Signature inside the referenced element signed, but no version of this library could verify it, and it rejected the same chain signed by other implementations.
• [exc-c14n, <custom transform>] never called the custom transform, although SignedInfo declares it.

When a transform returns a string and another transform follows, getCanonXml now parses the octets into a new document and applies the next transform to its root, as the reference processing model requires. The parsed document has no ancestors, so the referenced node's ancestorNamespaces and defaultNs are dropped for the rest of the chain. Octets that are not well-formed XML now throw instead of being skipped.

Copies of the enveloped signature were removed too (security)

enveloped-signature removed every Signature element in the signed content whose SignatureValue matched the signature being verified. checkSignature() parses its own copy of the document, so the loaded signature was never part of the digested tree, and verification always took that path. A copy of the signature pasted into the signed content, with other content inside it, was left out of the digest, and the document verified. getSignedReferences() never contained the copy, but code that read the verified document itself could.

This affects [enveloped-signature, canonicalization] in 6.1.2 and earlier. The first fix above would have extended it to [canonicalization, enveloped-signature], as review pointed out. XMLDSig 6.6.4 removes only "the whole Signature element containing" the transform, so now:

• The loaded signature is found in the document being checked by its SignatureValue, and checkSignature() throws when more than one Signature element carries it.
• EnvelopedSignature removes that element by identity only.
• After octets are parsed for the next transform, the signature is found again by its SignatureValue in the parsed document, with the same refusal of duplicates. (.NET uses the signature's position among the Signature elements instead, but a custom transform that reorders or removes Signature elements moves that position.) Signing needs no fallback: the new signature is not in the document when input references are digested.

Testing

• Duplicate-signature tests for both transform orders, with the signature loaded from the document and from a string, plus a copy inside a signed element that the signature sits outside of. All fail before the fix.
• The existing parent/child counter-signing tests now also run with enveloped-signature after canonicalization, and a custom transform that returns octets with its Signature elements reordered is followed by enveloped-signature. Both need the post-parse lookup.
• Two signatures created by .NET's SignedXml with client.pem are committed as fixtures ([exc-c14n, enveloped-signature] over URI="", and [c14n, enveloped-signature] over an element that inherits namespaces), so a mistake shared by this library's signer and verifier cannot hide behind a round trip. Both fail on master.

Signing and verifying against .NET's SignedXml in both directions agrees for [exc, env], [c14n, env], [exc#WithComments, env], [exc, c14n], [exc, env, c14n] and [env, exc, c14n], with the Signature inside and outside the referenced element.

Compatibility

Measured against 6.1.2:

• A canonicalization followed by enveloped-signature with the Signature inside the referenced element now verifies. 6.1.2 could not verify these, including its own.
• These chains now produce a different digest, so signatures created by 6.1.2 no longer verify, and the reverse. In each case the new digest is the one .NET computes.
  • A #WithComments canonicalization followed by enveloped-signature: the trailing node-set is canonicalized without comments.
  • Inclusive canonicalization followed by exclusive canonicalization, when the referenced element inherits namespaces it does not use.
  • Any canonicalization followed by a custom transform.
• [exc, env], [c14n, env] and [exc, c14n] with the Signature outside the referenced element are unchanged.
• checkSignature() throws for a document with more than one Signature element carrying the SignatureValue being verified. getCanonXml() finds the loaded signature the same way and removes nothing when it is not in the node's document.
• A test from 2013 asserted that transforms after a string are skipped. It now asserts the enveloped signature is removed.

This PR, #588 and #589 merge cleanly in any order, and the combined suite passes.

Fixes #111

🤖 Generated with Claude Code

Summary by CodeRabbit

• Bug Fixes

  • Transforms following canonicalization now run correctly instead of being skipped.
  • Enveloped signatures can be processed when located inside the referenced element.
  • Namespace handling is corrected when chaining inclusive and exclusive canonicalization.
  • Malformed XML returned by a transform now produces a clear error.
  • Ambiguous signature selection now produces a clear error.
  • Documents with copied signatures sharing the same value are handled correctly.

• Documentation

  • Updated guidance on transform chains and enveloped-signature handling.

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📒 Files selected for processing (3)

• README.md
• src/signed-xml.ts
• test/signature-integration-tests.spec.ts

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• README.md

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📝 Walkthrough

Walkthrough

The transform pipeline now parses string output before applying later transforms. It rejects malformed XML, preserves signature identity across parsed documents, removes only the verified signature, and rejects duplicate matching signatures. Tests and README documentation cover the behavior.

Changes

Signature transform processing

Layer / File(s)	Summary
Transform execution and XML parsing src/signed-xml.ts, test/canonicalization-unit-tests.spec.ts, README.md	String transform output is parsed before later transforms. Malformed XML raises an error. The README documents transform chaining behavior.
Loaded signature selection and removal src/signed-xml.ts, src/enveloped-signature.ts, README.md	The code locates the loaded signature by SignatureValue, rejects duplicate matching signatures, and removes only the supplied signature element.
Transform and signature validation test/signature-integration-tests.spec.ts, test/static/*	Tests cover transform order, reordered signatures, duplicate signatures, parent signatures, tampering, canonicalization behavior, and .NET XML fixtures.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Bug fix · Severity of issue fixed: Medium

Suggested reviewers: shunkica

Sequence Diagram(s)

sequenceDiagram
  participant SignedXml
  participant Transform
  participant ParsedDocument
  participant EnvelopedSignature
  SignedXml->>Transform: Apply canonicalization or custom transform
  Transform-->>SignedXml: Return XML string
  SignedXml->>ParsedDocument: Parse transform output
  ParsedDocument-->>SignedXml: Return XML document
  SignedXml->>SignedXml: Locate loaded Signature by SignatureValue
  SignedXml->>EnvelopedSignature: Remove supplied Signature node
  EnvelopedSignature-->>SignedXml: Return transformed XML

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Merge Risk: ⚪ Minimal · up to 6e6b3

The transform-chain compatibility change is covered for both transform orders and signature-selection edge cases, with no current merge-blocking risk identified.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 5 functions across 4 files. (1 skipped: 1 …	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes satisfy issue #111. getCanonXml() now parses octets returned by a transform before it applies the next transform, and it resets transform options for the new document. `enveloped-signatu…
Out of Scope Changes check	✅ Passed	The changes remain within issue #111. Signature re-identification, duplicate SignatureValue rejection, custom-transform coverage, compatibility fixtures, and documentation support correct transform …
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the two main changes: applying transforms after canonicalization and removing only the verified Signature.

Full details: Docstring Coverage

Explanation

Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 5 functions across 4 files. (1 skipped: 1 unsupported.)

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[codecov]

Codecov Report

❌ Patch coverage is 96.55172% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.44%. Comparing base (f5c4d22) to head (6e6b3a2).
⚠️ Report is 14 commits behind head on master.

Files with missing lines	Patch %	Lines
src/signed-xml.ts	96.42%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #585      +/-   ##
==========================================
+ Coverage   75.95%   79.44%   +3.48%     
==========================================
  Files           9        9              
  Lines        1048     1109      +61     
  Branches      273      281       +8     
==========================================
+ Hits          796      881      +85     
+ Misses        144      131      -13     
+ Partials      108       97      -11     

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Actionable comments posted: 1

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Inline comments:
In `@src/signed-xml.ts`:
- Line 1352: Update the signature-node resolution around findSignatureElements
and signaturePosition to first locate the parsed signature by its SignatureValue
after custom transforms, preserving identity when signatures are removed or
reordered. Retain ordinal lookup only as a fallback for signing flows where no
SignatureValue exists, then continue using options.signatureNode as the final
fallback.

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📒 Files selected for processing (6)

• README.md
• src/enveloped-signature.ts
• src/signed-xml.ts
• test/signature-integration-tests.spec.ts
• test/static/dotnet_enveloped_signature_after_c14n.xml
• test/static/dotnet_enveloped_signature_after_exc_c14n.xml

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