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refactor: Make generic backend exported from MSstatsBioNet - #122
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📝 WalkthroughWalkthroughThe package exposes its network-building API and documents entity preparation, selection, queries, and backend capabilities. The INDRA backend now reports supported operations, describes subnetwork queries, and applies optional confidence filtering to returned edges. ChangesNetwork-building API
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~25 minutes Change: Feature Sequence Diagram(s)sequenceDiagram
participant Caller
participant get_network
participant IndraBackend
participant CoGEx
Caller->>get_network: Provide entities, query, and confidence cutoff
get_network->>IndraBackend: Request subnetwork
IndraBackend->>CoGEx: Query subnetwork relations
CoGEx-->>IndraBackend: Return network relations
IndraBackend-->>get_network: Return confidence-filtered network
get_network-->>Caller: Return nodes and edges
Merge Risk: 🟡 Moderate · up to The package check depends on a live network service, and callers can receive an error at the advertised query limit. Fix both before merging unless the check dependency is explicitly accepted. 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## devel #122 +/- ##
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+ Coverage 81.85% 82.17% +0.31%
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Files 20 21 +1
Lines 2409 2451 +42
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+ Hits 1972 2014 +42
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Actionable comments posted: 2
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Inline comments:
Review comments at @R/AllGenerics.R:
- Around line 53-55: Wrap the CoGEx-dependent example using indra_backend(),
convert_ids(), and get_network() in \donttest{} so routine package checks do not
run live requests; leave the standalone conversion and property examples
unchanged.
Review comments at @R/backend-indra.R:
- Line 90: Update the reported subnetwork limit in INDRA_MAX_NODES so
max_nodes[["subnetwork"]] reports 399, and keep the validation and capability
test consistent with that accepted maximum.
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📒 Files selected for processing (20)
NAMESPACENEWS.mdR/AllClasses.RR/AllGenerics.RR/backend-indra.RR/entities.RR/filter-edges.RR/queries.Rman/NetworkBackend-class.Rdman/NetworkQuery-class.Rdman/backend_capabilities.Rdman/convert_ids.Rdman/get_entity_properties.Rdman/get_network.Rdman/indra_backend.Rdman/network_queries.Rdman/prepare_entities.Rdman/select_entities.Rdman/subnetwork_query.Rdtests/testthat/test-backend-indra.R
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Motivation and solution
The generic network backend API was not fully exposed for use by MSstatsBioNet users and extension packages. This change exports the backend classes, generics, and helper functions. It also documents the API and adds confidence filtering to network retrieval.
Changes
NetworkBackend,IndraBackend,NetworkQuery, andSubnetworkQuery.backend_capabilities(),indra_backend(),prepare_entities(),select_entities(), andsubnetwork_query(), along with the existing backend generics.backend_capabilities()methods that report backend support and a default method that errors when a backend does not describe its capabilities.min_confidenceargument toget_network(). The INDRA backend validates the cutoff, drops edges with missing confidence when a cutoff is set, and retains edges at or above the cutoff.get_network()messages and subnetwork query validation to report entity counts and use the configured INDRA node limit.Unit tests
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