Refines clinical context generation and corrects charting progress tracking

Standardizes pattern filtering to exclude metadata-heavy patterns like axioms and navigation from generated embeddings and clinical context. Additionally, ensures charting progress correctly increments the cumulative processed count and reports actual batch sizes during processing.

Author: aks8m

src/main/java/dev/ikm/server/cosmos/constellation/ConstellationEntity.java

@@ -28,7 +28,7 @@ public ConstellationEntity with(Instant completed) {
 	}
 
 	public ConstellationEntity with(long processed) {
-		return new ConstellationEntity(id, observatoryId, phase, name, scopes, portalPrompt, processed, created, completed);
+		return new ConstellationEntity(id, observatoryId, phase, name, scopes, portalPrompt, processed() + processed, created, completed);
 	}
 
 	public boolean isCompleted() {

src/main/java/dev/ikm/server/cosmos/constellation/charting/EmbeddingChartProcessor.java

@@ -155,13 +155,11 @@ private Set<String> generateSemanticFeatures(int nid, ChartingContext chartingCo
 				SemanticEntityVersion semanticEntityVersion = latestSemanticEntityVersion.get();
 				Latest<PatternEntityVersion> latestPatternEntityVersion = chartingContext.chart().stampCalculator()
 						.latest(semanticEntityVersion.patternNid());
-				if (latestPatternEntityVersion.isPresent()) {
+				if (latestPatternEntityVersion.isPresent() && !patternsToSkip().contains(latestPatternEntityVersion.get().nid())) {
 					PatternEntityVersion patternEntityVersion = latestPatternEntityVersion.get();
-					String semanticName = chartingContext.chart().languageCalculator()
-							.getDescriptionTextOrNid(patternEntityVersion.nid());
 					String purpose = chartingContext.chart().languageCalculator()
 							.getDescriptionTextOrNid(patternEntityVersion.semanticPurposeNid());
-					semanticFeaturesContext.add(semanticName + " which provides " + purpose + " data.");
+					semanticFeaturesContext.add(purpose + ", ");
 				}
 			}
 		});
@@ -170,6 +168,15 @@ private Set<String> generateSemanticFeatures(int nid, ChartingContext chartingCo
 		return semanticFeaturesContext;
 	}
 
+	private List<Integer> patternsToSkip() {
+        return List.of(TinkarTermV2.DESCRIPTION_PATTERN.nid(),
+                TinkarTermV2.EL_PLUS_PLUS_INFERRED_AXIOMS_PATTERN.nid(),
+                TinkarTermV2.EL_PLUS_PLUS_STATED_AXIOMS_PATTERN.nid(),
+                TinkarTermV2.STATED_NAVIGATION_PATTERN.nid(),
+                TinkarTermV2.INFERRED_NAVIGATION_PATTERN.nid(),
+                TinkarTermV2.OWL_AXIOM_SYNTAX_PATTERN.nid());
+    }
+
 	private void processBatch(List<EmbeddingData> embeddingBatch, ChartingContext chartingContext) {
 		// Generate embeddings values from string names
 		List<TextSegment> names = embeddingBatch.stream().map(EmbeddingData::name).toList();
@@ -179,6 +186,6 @@ private void processBatch(List<EmbeddingData> embeddingBatch, ChartingContext ch
 				.map(embeddingData -> TextSegment.from(embeddingData.name().text(), embeddingData.metadata()))
 				.toList();
 		embeddingStore.addAll(embeddings, segmentsWithMetaData);
-		chartingContext.progressUpdate().accept(chartingContext.batchSize());
+		chartingContext.progressUpdate().accept(embeddingBatch.size());
 	}
 }

src/main/java/dev/ikm/server/cosmos/portal/ContextGenerator.java

@@ -163,19 +163,22 @@ private void roleGroupContext(StringBuilder stringBuilder, RoleGroup roleGroup,
         roleGroup.roles().forEach(role -> roleContext(stringBuilder, role, true));
     }
 
-    private String semanticDataContext(int nid) {
-        List<Integer> patternFilter = List.of(TinkarTermV2.DESCRIPTION_PATTERN.nid(),
+    private List<Integer> patternsToSkip() {
+        return List.of(TinkarTermV2.DESCRIPTION_PATTERN.nid(),
                 TinkarTermV2.EL_PLUS_PLUS_INFERRED_AXIOMS_PATTERN.nid(),
                 TinkarTermV2.EL_PLUS_PLUS_STATED_AXIOMS_PATTERN.nid(),
                 TinkarTermV2.STATED_NAVIGATION_PATTERN.nid(),
                 TinkarTermV2.INFERRED_NAVIGATION_PATTERN.nid(),
                 TinkarTermV2.OWL_AXIOM_SYNTAX_PATTERN.nid());
+    }
+
+    private String semanticDataContext(int nid) {
         StringBuilder semanticDataBuilder = new StringBuilder();
         PrimitiveData.get().forEachSemanticNidForComponent(nid, semanticNid -> {
             Latest<SemanticEntityVersion> latestSemanticVersion = calculatorService.getStampCalculator()
                     .latest(semanticNid);
             if (latestSemanticVersion.isPresent()
-                    && !patternFilter.contains(latestSemanticVersion.get().patternNid())) {
+                    && !patternsToSkip().contains(latestSemanticVersion.get().patternNid())) {
                 SemanticEntityVersion semanticEntityVersion = latestSemanticVersion.get();
                 Latest<PatternEntityVersion> latestPattern = calculatorService.getStampCalculator()
                         .latest(semanticEntityVersion.patternNid());