adjust filter by context to exclude key words by tonywu1999 · Pull Request #111 · Vitek-Lab/MSstatsBioNet

tonywu1999 · 2026-09-23T15:13:02Z

Motivation and solution

Context-based filtering needs to exclude abstracts that contain unwanted keywords. This change adds optional keyword exclusion, allows filtering without a query, and returns abstracts for reuse in topic decomposition.

Changes

Add the optional exclude_keywords argument to filterSubnetworkByContext.
Make query optional. If query is omitted, abstracts are not scored and their score values are NA. Supplying cutoff without query, or omitting both query and exclude_keywords, raises an error.
Match keywords and tag-count terms case-insensitively as whole words or phrases. Escape regex metacharacters so they are treated literally.
Return an abstracts named character vector alongside nodes, edges, and evidence. Return an empty vector when no evidence or PMIDs are available.
Preserve data-frame dimensions when filtering nodes and edges.
Update the function documentation and vignette with usage examples and guidance for topic decomposition.
Raise the minimum suggested testthat version to 3.1.7.

Unit tests

Add tests for whole-word and phrase matching, including terms with regex metacharacters.
Add tests for keyword exclusion with and without a query, with tag-count and cosine scoring, and for argument validation.
Update result-shape expectations and test abstract selection and empty results.
Add an integration test that passes filtered output to topic decomposition while mocking INDRA and PubMed lookup functions.
Test execution results were not provided.

Coding guidelines

No coding guideline findings were provided. Guideline compliance cannot be determined.

coderabbitai · 2026-09-23T15:13:24Z

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

📝 Walkthrough

Walkthrough

The function supports case-insensitive keyword exclusion, including keyword-only filtering when query is omitted. It returns abstracts for retained evidence PMIDs. Callers can pass the returned evidence and abstracts to topic-decomposition functions.

Changes

Contextual Subnetwork Filtering

Layer / File(s)	Summary
Inputs and validation `R/filterSubnetworkByContext.R`, `man/filterSubnetworkByContext.Rd`, `tests/testthat/test-filterSubnetworkByContext.R`, `DESCRIPTION`	`query` is optional, and `exclude_keywords` accepts a non-empty character vector without missing or empty values. The function errors if both inputs are absent or if `cutoff` is supplied without `query`. The suggested minimum `testthat` version changes to 3.1.7.
Matching and filtering `R/filterSubnetworkByContext.R`, `tests/testthat/test-filterSubnetworkByContext.R`	Tag scoring and keyword exclusion use case-insensitive whole-word or phrase matching. The function applies keyword exclusion alone or with query scoring. Keyword-only filtering sets scores to `NA`.
Returned abstracts and topic-decomposition handoff `R/filterSubnetworkByContext.R`, `man/filterSubnetworkByContext.Rd`, `tests/testthat/test-filterSubnetworkByContext.R`, `vignettes/Filter-By-Context.Rmd`	The result includes abstracts for retained evidence PMIDs, including an empty vector on early returns. Documentation and tests pass the returned evidence and abstracts to topic-decomposition functions.

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

Sequence Diagram(s)

sequenceDiagram
  participant Caller
  participant filterSubnetworkByContext
  participant decomposeSubnetworkIntoHierarchicalTopics
  Caller->>filterSubnetworkByContext: Submit network and filter options
  filterSubnetworkByContext-->>Caller: Return filtered network, evidence, and abstracts
  Caller->>decomposeSubnetworkIntoHierarchicalTopics: Supply filtered network, evidence, and abstracts

Merge Risk: 🔵 Low · up to ef10d

Queries or exclusion keywords with surrounding spaces can produce unexpected filtering results. This narrow issue warrants a fix or explicit acceptance before merge.

🚥 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 description that includes the motivation and context, a detailed bullet list of changes, testing performed, and the completed checklist items from the repository template.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly identifies the primary change: adding keyword exclusion to context filtering.
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-commenter · 2026-09-23T15:15:22Z

Codecov Report

❌ Patch coverage is 96.82540% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.87%. Comparing base (0b9e217) to head (67bbe99).

Files with missing lines	Patch %	Lines
R/filterSubnetworkByContext.R	96.82%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #111      +/-   ##
==========================================
+ Coverage   71.54%   72.87%   +1.33%     
==========================================
  Files          14       14              
  Lines        1810     1851      +41     
==========================================
+ Hits         1295     1349      +54     
+ Misses        515      502      -13

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Actionable comments posted: 1

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Inline comments:
In `@tests/testthat/test-filterSubnetworkByContext.R`:
- Line 434: Update the testthat dependency requirement in DESCRIPTION to require
version 3.1.7 or newer, matching the local_mocked_bindings() API used by the
decomposition test.

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🪄 Fix CodeRabbit comments on this PR

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Inline comments:
In `@R/filterSubnetworkByContext.R`:
- Around line 275-276: Trim character values in query and exclude_keywords
before validation in the function containing .has_term(), so padded terms match
whole words or phrases correctly and whitespace-only terms are rejected as
empty.

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DESCRIPTION
R/filterSubnetworkByContext.R
man/filterSubnetworkByContext.Rd
tests/testthat/test-filterSubnetworkByContext.R
vignettes/Filter-By-Context.Rmd

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man/filterSubnetworkByContext.Rd
vignettes/Filter-By-Context.Rmd

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adjust filter by context to exclude key words

38fa608

coderabbitai Bot reviewed Sep 23, 2026

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Comment thread tests/testthat/test-filterSubnetworkByContext.R

tonywu1999 added 3 commits September 23, 2026 11:26

fix filtering by keywords to be whole keywords

c82a6da

fix tag count filtering for colon vs colonize

5b49b04

update testthat version

ef10d4a

coderabbitai Bot reviewed Sep 23, 2026

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Comment thread R/filterSubnetworkByContext.R

trim user input of whitespaces

67bbe99

tonywu1999 merged commit 409e9d4 into devel Sep 23, 2026
4 checks passed

tonywu1999 deleted the feature/filter-context-corpus-exclude branch September 23, 2026 20:57

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adjust filter by context to exclude key words - #111

adjust filter by context to exclude key words#111
tonywu1999 merged 5 commits into
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feature/filter-context-corpus-exclude

tonywu1999 commented Sep 23, 2026 •

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