Added get_evidence() with the backend chosen from backend_database

[tonywu1999]

• New exported generic get_evidence(); the INDRA method replaces .extract_evidence_text() and uses the backend's cogex_url
• New R/backend-registry.R splits edges by backend_database and calls each group's default backend
• filterSubnetworkByContext() and the four topic functions take backend = NULL
• New test-evidence.R; the old evidence tests moved there and mocks now target .fetch_evidence()

Context and solution

Evidence lookup previously used an INDRA-specific extraction path. This change adds a get_evidence() generic and moves evidence retrieval behind the NetworkBackend interface. When callers do not supply a backend, the code selects one from each edge group’s backend_database.

Changes

• Export get_evidence() and add a default NetworkBackend method.
• Add IndraBackend evidence retrieval from the CoGEx evidence endpoint. The method batches unique statement hashes and returns edge rows with evidence text and PMID.
• Add backend registry dispatch. It groups edges by backend_database when no backend is supplied and uses the registered default for each group.
• Add optional backend arguments to filterSubnetworkByContext() and four topic functions.
• Update topic evidence collection and context filtering to use the backend retrieval path.
• Document the new API and backend arguments in NEWS.md and the relevant help files.

Tests

• Add test-evidence.R coverage for evidence retrieval, backend dispatch, input validation, and backend propagation to context and topic functions.
• Update context-filtering and hierarchical-topic tests to mock .fetch_evidence() instead of .extract_evidence_text().
• Test execution results were not provided.

Coding guidelines

• No coding-guideline violations were identified in the supplied change summary.

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ℹ️ Recent review info

⚙️ Run configuration

• Configuration used: Organization UI
• Review profile: CHILL
• Plan: Advanced
• Run ID: aa4f3ea7-c555-4edc-aa6f-bc76c7df2f2b

📥 Commits

Reviewing files that changed from the base of the PR and between 4de7183 and d037861.

📒 Files selected for processing (21)

• NAMESPACE
• NEWS.md
• R/AllGenerics.R
• R/backend-indra-cogex.R
• R/backend-indra.R
• R/backend-registry.R
• R/bootstrapTopicModels.R
• R/compareTopicModels.R
• R/decomposeSubnetworkByTopic.R
• R/decomposeSubnetworkIntoHierarchicalTopics.R
• R/filterSubnetworkByContext.R
• R/utils_decomposeSubnetworkByTopic.R
• man/bootstrapTopicModels.Rd
• man/compareTopicModels.Rd
• man/decomposeSubnetworkByTopic.Rd
• man/decomposeSubnetworkIntoHierarchicalTopics.Rd
• man/filterSubnetworkByContext.Rd
• man/get_evidence.Rd
• tests/testthat/test-decomposeSubnetworkIntoHierarchicalTopics.R
• tests/testthat/test-evidence.R
• tests/testthat/test-filterSubnetworkByContext.R

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📝 Walkthrough

Walkthrough

The package adds get_evidence() as a backend-dispatched API, implements evidence retrieval for IndraBackend, and adds backend selection to context filtering and topic workflows. When no backend is supplied, edge backend_database values determine the default backend.

Changes

Evidence retrieval API

Layer / File(s)	Summary
Evidence API and INDRA retrieval NAMESPACE, NEWS.md, R/AllGenerics.R, R/backend-indra-cogex.R, R/backend-indra.R, R/filterSubnetworkByContext.R, man/get_evidence.Rd, tests/testthat/test-evidence.R	The package exports get_evidence() and adds a default method for unsupported backends. The IndraBackend method queries unique statement hashes through the backend CoGEx URL and returns rows containing edge fields, evidence text, and PMID. The old evidence-query helpers in context filtering are removed. Tests cover retrieval, validation, and empty results.

Backend routing and workflows

Layer / File(s)	Summary
Backend resolution and context filtering R/backend-registry.R, R/filterSubnetworkByContext.R, man/filterSubnetworkByContext.Rd, NEWS.md, tests/testthat/test-evidence.R, tests/testthat/test-filterSubnetworkByContext.R	The registry validates an explicit backend or resolves defaults from backend_database, groups edges, and fetches evidence for each group. Context filtering passes its optional backend to evidence fetching. Tests cover backend resolution, propagation, and context-filtering behavior.
Backend propagation through topic workflows R/bootstrapTopicModels.R, R/compareTopicModels.R, R/decomposeSubnetworkByTopic.R, R/decomposeSubnetworkIntoHierarchicalTopics.R, R/utils_decomposeSubnetworkByTopic.R, man/bootstrapTopicModels.Rd, man/compareTopicModels.Rd, man/decomposeSubnetworkByTopic.Rd, man/decomposeSubnetworkIntoHierarchicalTopics.Rd, tests/testthat/test-decomposeSubnetworkIntoHierarchicalTopics.R, tests/testthat/test-evidence.R	Topic functions add an optional backend argument and pass it to evidence and corpus construction. Documentation describes default backend selection and reuse of retrieved evidence. Tests check backend propagation and evidence reuse.

Priority: ➖ Normal

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

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant ContextAndTopicFunctions
  participant fetch_evidence
  participant BackendRegistry
  participant get_evidence
  participant IndraBackend
  ContextAndTopicFunctions->>fetch_evidence: Pass edges and optional backend
  fetch_evidence->>BackendRegistry: Resolve backend for edge groups
  BackendRegistry->>get_evidence: Fetch evidence for each group
  get_evidence->>IndraBackend: Dispatch evidence request

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Merge Risk: ⚪ Minimal · up to d0378

No identified issue currently blocks merging. The live CoGEx evidence request has not been validated.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The description summarizes the main code changes, but omits the required motivation and testing sections and does not address the review checklist.	Add a short motivation and context section, describe the tests added or modified and their results, and complete or explicitly address each checklist item.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly summarizes the new get_evidence() API and its backend selection from backend_database.

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_{I’m a rabbit with notes in my paws,
I hop through evidence, hash by hash.
New backends join the trail with care,
Edge rows bring sentences to share.
I thump for tidy results in the grass.}

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.33333% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.23%. Comparing base (4de7183) to head (d037861).
⚠️ Report is 1 commits behind head on devel.

Files with missing lines	Patch %	Lines
R/backend-indra-cogex.R	76.31%	9 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #124      +/-   ##
==========================================
+ Coverage   82.53%   85.23%   +2.70%     
==========================================
  Files          21       22       +1     
  Lines        2496     2547      +51     
==========================================
+ Hits         2060     2171     +111     
+ Misses        436      376      -60     

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