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feat(terraphim_types): implement dynamic ontology feature gates
- Add feature gates: ontology (default), medical (implies ontology), hgnc (implies medical) - Make EntityType and RelationshipType enums feature-gated with #[cfg(feature = "medical")] - Change ExtractedEntity and ExtractedRelationship to use String-based entity_type/relationship_type - Make hgnc module feature-gated with #[cfg(feature = "hgnc")] - Update example to demonstrate both string-based and feature-gated usage - Update tests to use string-based types This allows cross-domain use of Dynamic Ontology while keeping oncology-specific features optional via feature flags. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
1 parent 59da243 commit 0f443e2

11 files changed

Lines changed: 662 additions & 188 deletions

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‎.beads/issues.jsonl‎

Lines changed: 16 additions & 7 deletions
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‎.cachebro/cache.db-wal‎

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‎crates/terraphim_multi_agent/src/agents/ontology_agents.rs‎

Lines changed: 9 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,7 @@ use crate::{GenAiLlmClient, LlmMessage, LlmRequest, MultiAgentResult, ProviderCo
1010
use log::info;
1111
use serde::{Deserialize, Serialize};
1212
use std::sync::Arc;
13-
use terraphim_types::{
14-
CoverageSignal, EntityType, ExtractedEntity, GroundingMetadata, SchemaSignal,
15-
};
13+
use terraphim_types::{CoverageSignal, ExtractedEntity, GroundingMetadata, SchemaSignal};
1614
use tokio::sync::RwLock;
1715

1816
/// Configuration for ontology agents
@@ -108,13 +106,9 @@ Text to analyze:
108106

109107
let response = client.generate(request).await?;
110108

111-
let schema_signal: SchemaSignal =
112-
serde_json::from_str(&response.content).map_err(|e| {
113-
crate::MultiAgentError::LlmError(format!(
114-
"Failed to parse extraction response: {}",
115-
e
116-
))
117-
})?;
109+
let schema_signal: SchemaSignal = serde_json::from_str(&response.content).map_err(|e| {
110+
crate::MultiAgentError::LlmError(format!("Failed to parse extraction response: {}", e))
111+
})?;
118112

119113
info!(
120114
"Extracted {} entities and {} relationships",
@@ -136,10 +130,7 @@ pub struct NormalizationAgent {
136130

137131
impl NormalizationAgent {
138132
/// Create a new Normalization Agent
139-
pub fn new(
140-
config: OntologyAgentConfig,
141-
ontology_terms: Vec<String>,
142-
) -> MultiAgentResult<Self> {
133+
pub fn new(config: OntologyAgentConfig, ontology_terms: Vec<String>) -> MultiAgentResult<Self> {
143134
let llm_client = GenAiLlmClient::new(
144135
config.provider.clone(),
145136
ProviderConfig {
@@ -206,8 +197,7 @@ If no match found, respond with:
206197

207198
let response = client.generate(request).await?;
208199

209-
let grounding: Option<GroundingMetadata> =
210-
serde_json::from_str(&response.content).ok();
200+
let grounding: Option<GroundingMetadata> = serde_json::from_str(&response.content).ok();
211201

212202
let mut normalized_entity = entity;
213203
normalized_entity.grounding = grounding.clone();
@@ -359,8 +349,7 @@ Respond with ONLY valid JSON array:
359349
reason: Option<String>,
360350
}
361351

362-
if let Ok(suggestions) = serde_json::from_str::<Vec<ReviewSuggestion>>(&response.content)
363-
{
352+
if let Ok(suggestions) = serde_json::from_str::<Vec<ReviewSuggestion>>(&response.content) {
364353
for suggestion in suggestions {
365354
if let Some(entity) = entities
366355
.iter_mut()
@@ -397,7 +386,7 @@ mod tests {
397386
let agent = CoverageAgent::new(0.7);
398387
let entities = vec![
399388
ExtractedEntity {
400-
entity_type: EntityType::CancerDiagnosis,
389+
entity_type: "cancer_diagnosis".to_string(),
401390
raw_value: "lung carcinoma".to_string(),
402391
normalized_value: Some("lung carcinoma".to_string()),
403392
grounding: Some(GroundingMetadata::new(
@@ -409,7 +398,7 @@ mod tests {
409398
)),
410399
},
411400
ExtractedEntity {
412-
entity_type: EntityType::GenomicVariant,
401+
entity_type: "genomic_variant".to_string(),
413402
raw_value: "EGFR".to_string(),
414403
normalized_value: None,
415404
grounding: None,

‎crates/terraphim_multi_agent/src/workflows.rs‎

Lines changed: 0 additions & 83 deletions
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‎crates/terraphim_multi_agent/tests/ontology_integration_test.rs‎

Lines changed: 45 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -3,12 +3,10 @@
33
//! Integration tests for the Dynamic Ontology multi-agent pipeline.
44
//! These tests validate the end-to-end flow from text extraction to normalization.
55
6+
#[cfg(feature = "hgnc")]
67
#[cfg(test)]
78
mod tests {
89
use terraphim_types::hgnc::HgncNormalizer;
9-
use terraphim_types::{
10-
CoverageSignal, EntityType, ExtractedEntity, GroundingMetadata, SchemaSignal,
11-
};
1210

1311
/// Test the HGNC gene normalizer with known oncology genes
1412
#[test]
@@ -50,12 +48,45 @@ mod tests {
5048
assert_eq!(meta.normalized_label, Some("EGFR".to_string()));
5149
}
5250

51+
/// Test multiple HGNC genes
52+
#[test]
53+
fn test_hgnc_multiple_genes() {
54+
let normalizer = HgncNormalizer::new();
55+
56+
let genes = ["EGFR", "TP53", "KRAS", "BRAF", "ALK", "ROS1", "MET"];
57+
58+
for gene in genes {
59+
let result = normalizer.normalize(gene);
60+
assert!(
61+
result.is_some(),
62+
"Expected to find {} in HGNC database",
63+
gene
64+
);
65+
}
66+
}
67+
}
68+
69+
#[cfg(not(feature = "hgnc"))]
70+
#[cfg(test)]
71+
mod tests {
72+
// Stub tests when hgnc feature is not enabled
73+
#[test]
74+
fn test_hgnc_stub() {
75+
// HGNC tests require the hgnc feature
76+
assert!(true);
77+
}
78+
}
79+
80+
#[cfg(test)]
81+
mod generic_tests {
82+
use terraphim_types::{CoverageSignal, ExtractedEntity, GroundingMetadata, SchemaSignal};
83+
5384
/// Test coverage signal calculation
5485
#[test]
5586
fn test_coverage_signal_calculation() {
5687
let entities = vec![
5788
ExtractedEntity {
58-
entity_type: EntityType::CancerDiagnosis,
89+
entity_type: "cancer_diagnosis".to_string(),
5990
raw_value: "lung carcinoma".to_string(),
6091
normalized_value: Some("lung carcinoma".to_string()),
6192
grounding: Some(GroundingMetadata::new(
@@ -67,13 +98,13 @@ mod tests {
6798
)),
6899
},
69100
ExtractedEntity {
70-
entity_type: EntityType::GenomicVariant,
101+
entity_type: "genomic_variant".to_string(),
71102
raw_value: "EGFR".to_string(),
72103
normalized_value: None,
73104
grounding: None,
74105
},
75106
ExtractedEntity {
76-
entity_type: EntityType::Drug,
107+
entity_type: "drug".to_string(),
77108
raw_value: "Osimertinib".to_string(),
78109
normalized_value: Some("Osimertinib".to_string()),
79110
grounding: Some(GroundingMetadata::new(
@@ -106,7 +137,7 @@ mod tests {
106137
fn test_coverage_above_threshold() {
107138
let entities = vec![
108139
ExtractedEntity {
109-
entity_type: EntityType::CancerDiagnosis,
140+
entity_type: "cancer_diagnosis".to_string(),
110141
raw_value: "lung carcinoma".to_string(),
111142
normalized_value: Some("lung carcinoma".to_string()),
112143
grounding: Some(GroundingMetadata::new(
@@ -118,7 +149,7 @@ mod tests {
118149
)),
119150
},
120151
ExtractedEntity {
121-
entity_type: EntityType::Drug,
152+
entity_type: "drug".to_string(),
122153
raw_value: "Osimertinib".to_string(),
123154
normalized_value: Some("Osimertinib".to_string()),
124155
grounding: Some(GroundingMetadata::new(
@@ -150,7 +181,7 @@ mod tests {
150181
fn test_schema_signal_creation() {
151182
let entities = vec![
152183
ExtractedEntity {
153-
entity_type: EntityType::CancerDiagnosis,
184+
entity_type: "cancer_diagnosis".to_string(),
154185
raw_value: "non-small cell lung carcinoma".to_string(),
155186
normalized_value: Some("Non-Small Cell Lung Carcinoma".to_string()),
156187
grounding: Some(GroundingMetadata::new(
@@ -162,7 +193,7 @@ mod tests {
162193
)),
163194
},
164195
ExtractedEntity {
165-
entity_type: EntityType::GenomicVariant,
196+
entity_type: "genomic_variant".to_string(),
166197
raw_value: "EGFR L858R".to_string(),
167198
normalized_value: None,
168199
grounding: None,
@@ -191,7 +222,10 @@ mod tests {
191222
terraphim_types::NormalizationMethod::Exact,
192223
);
193224

194-
assert_eq!(grounding.normalized_uri, Some("http://example.org/egfr".to_string()));
225+
assert_eq!(
226+
grounding.normalized_uri,
227+
Some("http://example.org/egfr".to_string())
228+
);
195229
assert_eq!(grounding.normalized_label, Some("EGFR".to_string()));
196230
assert_eq!(grounding.normalized_prov, Some("HGNC".to_string()));
197231
assert_eq!(grounding.normalized_score, Some(1.0));
@@ -200,21 +234,4 @@ mod tests {
200234
Some(terraphim_types::NormalizationMethod::Exact)
201235
);
202236
}
203-
204-
/// Test multiple HGNC genes
205-
#[test]
206-
fn test_hgnc_multiple_genes() {
207-
let normalizer = HgncNormalizer::new();
208-
209-
let genes = ["EGFR", "TP53", "KRAS", "BRAF", "ALK", "ROS1", "MET"];
210-
211-
for gene in genes {
212-
let result = normalizer.normalize(gene);
213-
assert!(
214-
result.is_some(),
215-
"Expected to find {} in HGNC database",
216-
gene
217-
);
218-
}
219-
}
220237
}

‎crates/terraphim_types/Cargo.toml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -34,4 +34,8 @@ uuid = { version = "1.19.0", features = ["v4", "serde", "js"] }
3434
getrandom = { version = "0.3", features = ["wasm_js"] }
3535

3636
[features]
37+
default = ["ontology"]
38+
ontology = [] # Core generic ontology (string-based types)
39+
medical = ["ontology"] # Medical/oncology extensions
40+
hgnc = ["medical"] # HGNC gene normalization
3741
typescript = ["tsify", "wasm-bindgen"]

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