fix(pubmed): Reduce runtime for fetching pubmed abstracts

[tonywu1999]

Motivation and solution

Individual PubMed and INDRA evidence requests increase runtime. The change batches requests and adds pacing between INDRA evidence batches. PubMed parsing now supports article and book records.

Changes

• Import xml_find_first from xml2.
• Parse PubmedArticle and PubmedBookArticle records.
• Read PMIDs from article and book record paths.
• Join multiple abstract sections with spaces.
• Return empty strings for missing abstracts.
• Add pacing between non-final INDRA evidence batches.
• Skip empty or NULL INDRA responses during result matching.
• Ensure progress output is emitted after empty batches.

Unit tests

• Verify PubMed requests use batches of two PMIDs.
• Verify all requested PMIDs appear in the result.
• Verify missing abstracts map to empty strings.
• Verify multi-section abstract parsing.
• Verify articles without abstracts.
• Verify empty PubMed responses.

Coding guidelines

No coding guideline requirements were supplied. Compliance could not be assessed.

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📥 Commits

Reviewing files that changed from the base of the PR and between ff47371 and 7954c8b.

📒 Files selected for processing (2)

• R/filterSubnetworkByContext.R
• tests/testthat/test-filterSubnetworkByContext.R

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• R/filterSubnetworkByContext.R
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📝 Walkthrough

Walkthrough

The package updates INDRA evidence batching and PubMed XML parsing. PubMed book records are now supported. Tests cover batching, missing records, and abstract parsing.

Changes

Batched retrieval

Layer / File(s)	Summary
INDRA evidence batching R/filterSubnetworkByContext.R	.query_indra_evidence accepts a sleep interval, merges non-NULL parsed results, prints progress for empty batches, and pauses between non-final batches.
PubMed batching and XML parsing R/filterSubnetworkByContext.R, NAMESPACE, tests/testthat/test-filterSubnetworkByContext.R	.parse_pubmed_abstracts handles PubmedArticle and PubmedBookArticle records and extracts book PMIDs. The namespace imports xml_find_first. Tests cover batch sizes, missing PMIDs, multi-section abstracts, absent abstracts, and empty XML responses.

Priority: ⬇️ Low

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

Change: Refactor

Merge Risk: ⚪ Minimal · up to 7954c

The changes are mergeable; no concrete runtime or integration failure was identified.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	No pull request description was provided. The required motivation, changes, testing, and checklist sections are all missing.	Add a pull request description using the repository template. Include the motivation and context, a detailed list of changes, testing details, and the completed checklist items.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely describes the primary change: reducing runtime when fetching PubMed abstracts.
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.

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Codecov Report

❌ Patch coverage is 53.75000% with 37 lines in your changes missing coverage. Please review.
✅ Project coverage is 58.67%. Comparing base (c6cb932) to head (7954c8b).

Files with missing lines	Patch %	Lines
R/filterSubnetworkByContext.R	53.75%	37 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #109      +/-   ##
==========================================
+ Coverage   58.29%   58.67%   +0.38%     
==========================================
  Files          13       13              
  Lines        1561     1602      +41     
==========================================
+ Hits          910      940      +30     
- Misses        651      662      +11     

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Actionable comments posted: 1

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Inline comments:
In `@R/filterSubnetworkByContext.R`:
- Line 365: Update the article extraction to include both PubmedArticle and
PubmedBookArticle descendants, and update PMID lookup to use
MedlineCitation/PMID for articles or BookDocument/PMID for book records.
Preserve the existing downstream processing for both record types.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 65fb3e05-2023-4571-a44e-806e56a8c077

📥 Commits

Reviewing files that changed from the base of the PR and between c6cb932 and 31c0786.

📒 Files selected for processing (3)

• NAMESPACE
• R/filterSubnetworkByContext.R
• tests/testthat/test-filterSubnetworkByContext.R

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