@metriport/fhir-sdk 1.2.6 → 1.3.0

package/README.md

@@ -67,6 +67,170 @@ console.log(result.hasBrokenReferences); // true if at least one broken referenc
 console.log(result.brokenReferences); // All broken references in bundle
 ```
 
+### 5. Reverse Reference Lookup
+
+Find all resources that reference a given resource (reverse lookup). This is useful for discovering what refers to a specific resource.
+
+```typescript
+const patient = sdk.getPatientById("patient-123");
+
+// Find all resources that reference this patient
+const referencingResources = sdk.getResourcesReferencingId("patient-123");
+console.log(referencingResources); // [Observation, Encounter, DiagnosticReport, ...]
+
+// Filter by resource type
+const observations = sdk.getResourcesReferencingId("patient-123", {
+  resourceType: "Observation",
+});
+
+// Filter by reference field
+const subjectReferences = sdk.getResourcesReferencingId("patient-123", {
+  referenceField: "subject",
+});
+
+// Use smart resource method
+const backRefs = patient.getReferencingResources();
+const encounteredObs = patient.getReferencingResources({
+  resourceType: "Observation",
+  referenceField: "subject",
+});
+```
+
+**Key Features:**
+
+- **O(1) lookup** - constant time performance
+- **Flexible filtering** - by resource type and/or reference field
+- **Smart resources** - returns fully functional Smart resources
+- **Bi-directional** - complements forward reference navigation
+
+### 6. Date Range Search
+
+Search for resources by date range using an interval tree index. This is useful for filtering resources by clinical dates efficiently.
+
+```typescript
+const sdk = await FhirBundleSdk.create(bundle);
+
+// Basic date range search
+const results = sdk.searchByDateRange({
+  dateFrom: "2024-01-01",
+  dateTo: "2024-01-31",
+});
+
+// Filter by resource type
+const observations = sdk.searchByDateRange({
+  dateFrom: "2024-01-01",
+  dateTo: "2024-12-31",
+  resourceTypes: ["Observation", "Condition"],
+});
+
+// Filter by specific date field
+const recordedConditions = sdk.searchByDateRange({
+  dateFrom: "2024-01-01",
+  dateTo: "2024-12-31",
+  dateFields: ["recordedDate"],
+});
+
+// Use Date objects
+const recentResources = sdk.searchByDateRange({
+  dateFrom: new Date("2024-01-01"),
+  dateTo: new Date(),
+});
+```
+
+**Key Features:**
+
+- **O(log n + k) search** - efficient interval tree-based search where k is the number of matching resources
+- **Multiple date fields** - indexes primary clinical dates (effectiveDateTime, onset, performed) and recorded dates
+- **Flexible filtering** - by resource type and/or specific date fields
+- **Smart resources** - returns fully functional Smart resources
+- **Period support** - handles both single date fields and date periods/ranges
+
+**Indexed Resource Types:**
+
+The following resource types and date fields are automatically indexed:
+
+- **Observation**: effectiveDateTime, effectivePeriod, effectiveInstant, issued
+- **Condition**: onsetDateTime, onsetPeriod, abatementDateTime, abatementPeriod, recordedDate
+- **Encounter**: period
+- **Procedure**: performedDateTime, performedPeriod
+- **Immunization**: occurrenceDateTime, recorded
+- **DiagnosticReport**: effectiveDateTime, effectivePeriod, issued
+- **MedicationRequest**: authoredOn
+- **MedicationAdministration**: effectiveDateTime, effectivePeriod
+- **MedicationStatement**: effectiveDateTime, effectivePeriod
+- **MedicationDispense**: whenHandedOver, whenPrepared
+- **DocumentReference**: date, context.period
+- **Composition**: date
+- **Coverage**: period
+- **AllergyIntolerance**: onsetDateTime, onsetPeriod, lastOccurrence, recordedDate
+
+### 7. Reference Walking (BFS Traversal)
+
+Walk the reference graph starting from any resource using breadth-first search (BFS). This is useful for discovering all resources connected to a specific resource.
+
+```typescript
+const observation = sdk.getObservationById("obs-123");
+
+// Walk all reachable resources
+const result = sdk.walkReferences(observation);
+console.log(result.allResources); // All resources reachable from observation
+console.log(result.resourcesByDepth); // Resources organized by depth level
+console.log(result.depthReached); // Maximum depth traversed
+
+// Limit traversal depth
+const limitedResult = sdk.walkReferences(observation, { maxDepth: 2 });
+
+// Exclude the start resource from results
+const withoutStart = sdk.walkReferences(observation, { includeStartResource: false });
+```
+
+### 7. LLM Context Generation
+
+Generate comprehensive, LLM-friendly context from a resource and its related resources. This automatically performs BFS traversal, strips non-clinical metadata, and formats the output for optimal LLM consumption.
+
+```typescript
+const observation = sdk.getObservationById("obs-123");
+
+// Generate structured text context (default, best for LLMs)
+const llmContext = sdk.generateLLMContext(observation, {
+  maxDepth: 2, // Default: 2
+  format: "structured-text", // Default: 'structured-text'
+});
+
+// Send to your LLM
+await llm.chat({
+  messages: [
+    { role: "system", content: "You are a medical data analyst." },
+    { role: "user", content: `Analyze this patient data:\n\n${llmContext}` },
+  ],
+});
+
+// Alternative: JSON format
+const jsonContext = sdk.generateLLMContext(observation, {
+  format: "json",
+});
+```
+
+**Features:**
+
+- Automatically discovers all related resources via BFS traversal
+- Strips non-clinical metadata (`meta`, `extension`, `text`) to reduce tokens by ~30-40%
+- Organizes resources hierarchically (primary → directly referenced → indirectly referenced)
+- Groups resources by type within each depth level
+- Logs resource counts for debugging (not included in output)
+
+**Static Helper:**
+
+You can also strip non-clinical data from any resource independently:
+
+```typescript
+import { FhirBundleSdk } from "@metriport/fhir-sdk";
+
+const cleanedPatient = FhirBundleSdk.stripNonClinicalData(patient);
+// Removes: meta, extension, modifierExtension, text
+// Returns immutable copy
+```
+
 ## Example Use Cases
 
 ### Patient Summary
@@ -91,6 +255,28 @@ const buildPatientSummary = (patientId: string) => {
 const orgName = sdk.getPatients()[0]?.getManagingOrganization()?.name;
 ```
 
+### Extract Related Resources
+
+```typescript
+// Get all resources related to a specific observation
+const extractRelatedResources = (observationId: string) => {
+  const observation = sdk.getObservationById(observationId);
+  if (!observation) return null;
+
+  // Walk the graph to find all related resources up to 2 levels deep
+  const result = sdk.walkReferences(observation, { maxDepth: 2 });
+
+  return {
+    observation,
+    relatedResourceCount: result.allResources.length,
+    resourcesByType: result.allResources.reduce((acc, resource) => {
+      acc[resource.resourceType] = (acc[resource.resourceType] || 0) + 1;
+      return acc;
+    }, {} as Record<string, number>),
+  };
+};
+```
+
 ### Example Use Case: Processing a bundle
 
 ```typescript
@@ -122,3 +308,24 @@ const processBundle = async (bundle: Bundle) => {
 - **getById**: O(1) lookup
 - **getByType**: O(n) where n = resources of that type
 - **Reference resolution**: O(1) traversal
+- **Reverse reference lookup**: O(1) lookup
+
+## Demo
+
+To see reverse reference functionality in action, run:
+
+```bash
+# From the utils package
+cd packages/utils
+npx ts-node src/fhir-sdk/demo-reverse-references.ts --bundle-path /path/to/your/bundle.json
+```
+
+The demo will:
+
+- Automatically find the first patient in your bundle
+- Showcase all reverse reference capabilities:
+  - Finding all resources that reference a specific resource
+  - Filtering by resource type and reference field
+  - Using smart resource methods
+  - Bi-directional navigation
+  - Performance characteristics

package/dist/__tests__/date-range-performance.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=date-range-performance.test.d.ts.map

package/dist/__tests__/date-range-performance.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"date-range-performance.test.d.ts","sourceRoot":"","sources":["../../src/__tests__/date-range-performance.test.ts"],"names":[],"mappings":""}

package/dist/__tests__/date-range-performance.test.js

@@ -0,0 +1,218 @@
+"use strict";
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
+Object.defineProperty(exports, "__esModule", { value: true });
+const index_1 = require("../index");
+// Skip these tests by default as its a performance test that is slow and will slow down CI.
+describe.skip("Date Range Search - Large Scale Performance", () => {
+    const ONE_MILLION = 1000000;
+    describe("1 Million Resources", () => {
+        let largeBundle;
+        let sdk;
+        beforeAll(() => {
+            console.log(`\n🔨 Building bundle with ${ONE_MILLION.toLocaleString()} resources...`);
+            const startBuild = performance.now();
+            largeBundle = {
+                resourceType: "Bundle",
+                type: "searchset",
+                entry: [],
+            };
+            // Generate 1 million observations spread over 2024
+            // Each observation has a date somewhere in the year
+            const startDate = new Date("2024-01-01").getTime();
+            const endDate = new Date("2024-12-31").getTime();
+            const dateRange = endDate - startDate;
+            for (let i = 0; i < ONE_MILLION; i++) {
+                // Distribute dates across the year
+                const randomOffset = (i / ONE_MILLION) * dateRange;
+                const date = new Date(startDate + randomOffset).toISOString();
+                largeBundle.entry.push({
+                    resource: {
+                        resourceType: "Observation",
+                        id: `obs-${i}`,
+                        status: "final",
+                        code: { text: `Test ${i % 100}` },
+                        effectiveDateTime: date,
+                    },
+                });
+                // Log progress every 100k resources
+                if ((i + 1) % 100000 === 0) {
+                    console.log(`  ✓ Generated ${(i + 1).toLocaleString()} resources`);
+                }
+            }
+            const endBuild = performance.now();
+            console.log(`✅ Bundle built in ${((endBuild - startBuild) / 1000).toFixed(2)}s\n`);
+        });
+        it("should index 1 million resources efficiently", () => {
+            console.log("📊 Indexing 1 million resources...");
+            const start = performance.now();
+            sdk = index_1.FhirBundleSdk.createSync(largeBundle);
+            const end = performance.now();
+            const duration = end - start;
+            const durationSeconds = duration / 1000;
+            const resourcesPerSecond = ONE_MILLION / durationSeconds;
+            console.log(`\n⏱️  Indexing Performance:`);
+            console.log(`  • Total time: ${durationSeconds.toFixed(2)}s`);
+            console.log(`  • Resources/second: ${Math.round(resourcesPerSecond).toLocaleString()}`);
+            console.log(`  • Average time per resource: ${(duration / ONE_MILLION).toFixed(3)}ms\n`);
+            expect(sdk).toBeDefined();
+            // Should index at least 10,000 resources per second
+            expect(resourcesPerSecond).toBeGreaterThan(10000);
+        });
+        describe("Search Performance", () => {
+            it("should search 1 month range efficiently", () => {
+                console.log("🔍 Searching 1-month range...");
+                const start = performance.now();
+                const results = sdk.searchByDateRange({
+                    dateFrom: "2024-06-01",
+                    dateTo: "2024-06-30",
+                });
+                const end = performance.now();
+                const duration = end - start;
+                console.log(`\n⏱️  1-Month Search:`);
+                console.log(`  • Time: ${duration.toFixed(2)}ms`);
+                console.log(`  • Results: ${results.length.toLocaleString()}`);
+                console.log(`  • Time per result: ${(duration / results.length).toFixed(3)}ms\n`);
+                expect(results.length).toBeGreaterThan(0);
+                // Should complete in under 100ms
+                expect(duration).toBeLessThan(100);
+            });
+            it("should search 1 week range efficiently", () => {
+                console.log("🔍 Searching 1-week range...");
+                const start = performance.now();
+                const results = sdk.searchByDateRange({
+                    dateFrom: "2024-06-01",
+                    dateTo: "2024-06-07",
+                });
+                const end = performance.now();
+                const duration = end - start;
+                console.log(`\n⏱️  1-Week Search:`);
+                console.log(`  • Time: ${duration.toFixed(2)}ms`);
+                console.log(`  • Results: ${results.length.toLocaleString()}`);
+                console.log(`  • Time per result: ${(duration / results.length).toFixed(3)}ms\n`);
+                expect(results.length).toBeGreaterThan(0);
+                // Should complete in under 50ms
+                expect(duration).toBeLessThan(50);
+            });
+            it("should search 1 day range efficiently", () => {
+                console.log("🔍 Searching 1-day range...");
+                const start = performance.now();
+                const results = sdk.searchByDateRange({
+                    dateFrom: "2024-06-15",
+                    dateTo: "2024-06-15",
+                });
+                const end = performance.now();
+                const duration = end - start;
+                console.log(`\n⏱️  1-Day Search:`);
+                console.log(`  • Time: ${duration.toFixed(2)}ms`);
+                console.log(`  • Results: ${results.length.toLocaleString()}`);
+                if (results.length > 0) {
+                    console.log(`  • Time per result: ${(duration / results.length).toFixed(3)}ms`);
+                }
+                console.log();
+                // Should complete very quickly even if no results
+                expect(duration).toBeLessThan(20);
+            });
+            it("should search full year range efficiently", () => {
+                console.log("🔍 Searching full year range...");
+                const start = performance.now();
+                const results = sdk.searchByDateRange({
+                    dateFrom: "2024-01-01",
+                    dateTo: "2024-12-31",
+                });
+                const end = performance.now();
+                const duration = end - start;
+                const durationSeconds = duration / 1000;
+                console.log(`\n⏱️  Full Year Search:`);
+                console.log(`  • Time: ${durationSeconds.toFixed(2)}s`);
+                console.log(`  • Results: ${results.length.toLocaleString()}`);
+                console.log(`  • Time per result: ${(duration / results.length).toFixed(3)}ms\n`);
+                expect(results.length).toBe(ONE_MILLION);
+                // Should complete in under 5 seconds even for all results
+                expect(duration).toBeLessThan(5000);
+            });
+            it("should handle multiple consecutive searches efficiently", () => {
+                console.log("🔍 Running 100 consecutive searches...");
+                const searches = 100;
+                const start = performance.now();
+                for (let i = 0; i < searches; i++) {
+                    // Search different months
+                    const month = (i % 12) + 1;
+                    const monthStr = month.toString().padStart(2, "0");
+                    sdk.searchByDateRange({
+                        dateFrom: `2024-${monthStr}-01`,
+                        dateTo: `2024-${monthStr}-28`,
+                    });
+                }
+                const end = performance.now();
+                const duration = end - start;
+                const avgDuration = duration / searches;
+                console.log(`\n⏱️  100 Consecutive Searches:`);
+                console.log(`  • Total time: ${duration.toFixed(2)}ms`);
+                console.log(`  • Average per search: ${avgDuration.toFixed(2)}ms`);
+                console.log(`  • Searches per second: ${Math.round(1000 / avgDuration)}\n`);
+                // Average should be under 50ms per search
+                expect(avgDuration).toBeLessThan(50);
+            });
+        });
+        describe("Comparison with Linear Search", () => {
+            function linearSearchByDate(bundle, dateFrom, dateTo) {
+                const fromMs = new Date(dateFrom).getTime();
+                const toMs = new Date(dateTo).getTime();
+                let count = 0;
+                for (const entry of bundle.entry ?? []) {
+                    if (entry.resource?.resourceType === "Observation") {
+                        const obs = entry.resource;
+                        if (obs.effectiveDateTime) {
+                            const dateMs = new Date(obs.effectiveDateTime).getTime();
+                            if (dateMs >= fromMs && dateMs <= toMs) {
+                                count++;
+                            }
+                        }
+                    }
+                }
+                return count;
+            }
+            it("should be significantly faster than linear search", () => {
+                console.log("⚖️  Comparing interval tree vs linear search...");
+                // Test with 1-month range
+                const dateFrom = "2024-06-01";
+                const dateTo = "2024-06-30";
+                // Interval tree search
+                console.log("\n  Testing interval tree...");
+                const treeStart = performance.now();
+                const treeResults = sdk.searchByDateRange({ dateFrom, dateTo });
+                const treeEnd = performance.now();
+                const treeDuration = treeEnd - treeStart;
+                // Linear search
+                console.log("  Testing linear search...");
+                const linearStart = performance.now();
+                const linearCount = linearSearchByDate(largeBundle, dateFrom, dateTo);
+                const linearEnd = performance.now();
+                const linearDuration = linearEnd - linearStart;
+                const speedup = linearDuration / treeDuration;
+                console.log(`\n📊 Performance Comparison (1-month search):`);
+                console.log(`  • Interval Tree: ${treeDuration.toFixed(2)}ms`);
+                console.log(`  • Linear Search: ${linearDuration.toFixed(2)}ms`);
+                console.log(`  • Speedup: ${speedup.toFixed(1)}x faster`);
+                console.log(`  • Results matched: ${treeResults.length === linearCount}\n`);
+                expect(treeResults.length).toBe(linearCount);
+                // Interval tree should be significantly faster (at least 5x)
+                expect(speedup).toBeGreaterThan(5);
+            });
+        });
+        describe("Memory Efficiency", () => {
+            it("should report memory usage", () => {
+                if (typeof process !== "undefined" && process.memoryUsage) {
+                    const memUsage = process.memoryUsage();
+                    console.log(`\n💾 Memory Usage:`);
+                    console.log(`  • Heap Used: ${(memUsage.heapUsed / 1024 / 1024).toFixed(2)} MB`);
+                    console.log(`  • Heap Total: ${(memUsage.heapTotal / 1024 / 1024).toFixed(2)} MB`);
+                    console.log(`  • External: ${(memUsage.external / 1024 / 1024).toFixed(2)} MB`);
+                    console.log(`  • Per resource: ${((memUsage.heapUsed / ONE_MILLION) * 1024).toFixed(2)} bytes\n`);
+                }
+                expect(true).toBe(true);
+            });
+        });
+    });
+});
+//# sourceMappingURL=date-range-performance.test.js.map

package/dist/__tests__/date-range-performance.test.js.map

@@ -0,0 +1 @@
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package/dist/__tests__/date-range-search.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=date-range-search.test.d.ts.map

package/dist/__tests__/date-range-search.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"date-range-search.test.d.ts","sourceRoot":"","sources":["../../src/__tests__/date-range-search.test.ts"],"names":[],"mappings":""}