@metriport/fhir-sdk 0.30.0-alpha.1

package/dist/internal/graph-traversal.js

@@ -0,0 +1,89 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.walkReferences = void 0;
+const smart_resources_1 = require("../types/smart-resources");
+/**
+ * Walk references from a starting resource using BFS traversal.
+ * Discovers all reachable resources up to maxDepth levels.
+ *
+ * @param startResource - The smart resource to start traversal from
+ * @param options - Walk options including maxDepth and includeStartResource
+ * @returns WalkResult containing all discovered resources organized by depth
+ */
+function walkReferences(startResource, options) {
+    const maxDepth = options?.maxDepth ?? Infinity;
+    const includeStartResource = options?.includeStartResource ?? true;
+    const resourcesByDepth = new Map();
+    const visited = new Set();
+    const queue = [];
+    // Initialize with start resource at depth 0 - cast to avoid type complexity
+    queue.push({ resource: startResource, depth: 0 });
+    if (startResource.id) {
+        visited.add(startResource.id);
+    }
+    let maxDepthReached = 0;
+    while (queue.length > 0) {
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        const { resource, depth } = queue.shift();
+        // Track max depth reached
+        if (depth > maxDepthReached) {
+            maxDepthReached = depth;
+        }
+        // Add resource to current depth level
+        if (!resourcesByDepth.has(depth)) {
+            resourcesByDepth.set(depth, []);
+        }
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        resourcesByDepth.get(depth).push(resource);
+        // Stop if we've reached max depth
+        if (depth >= maxDepth) {
+            continue;
+        }
+        // Get all reference methods for this resource type
+        const referenceMethods = smart_resources_1.REFERENCE_METHOD_MAPPING[resource.resourceType];
+        if (!referenceMethods) {
+            continue;
+        }
+        // Iterate through all reference methods
+        for (const methodName of Object.keys(referenceMethods)) {
+            // Call the reference method
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const referencedResources = resource[methodName]();
+            if (!referencedResources) {
+                continue;
+            }
+            // Handle both single and array references
+            const resourceArray = Array.isArray(referencedResources)
+                ? referencedResources
+                : [referencedResources];
+            for (const referencedResource of resourceArray) {
+                if (!referencedResource?.id) {
+                    continue;
+                }
+                // Skip if already visited
+                if (visited.has(referencedResource.id)) {
+                    continue;
+                }
+                visited.add(referencedResource.id);
+                queue.push({ resource: referencedResource, depth: depth + 1 });
+            }
+        }
+    }
+    // Build flat array of all resources
+    const allResources = [];
+    for (const [depth, resources] of resourcesByDepth.entries()) {
+        // Skip depth 0 (start resource) if includeStartResource is false
+        if (depth === 0 && !includeStartResource) {
+            continue;
+        }
+        allResources.push(...resources);
+    }
+    return {
+        resourcesByDepth,
+        allResources,
+        startResource,
+        depthReached: maxDepthReached,
+    };
+}
+exports.walkReferences = walkReferences;
+//# sourceMappingURL=graph-traversal.js.map

package/dist/internal/graph-traversal.js.map

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package/dist/internal/indexing.d.ts

@@ -0,0 +1,17 @@
+import { Bundle, Resource } from "@medplum/fhirtypes";
+import { ReverseReference } from "../types/sdk-types";
+import { IntervalTree } from "../utils/interval-tree";
+import { DateIndexRecord } from "../types/sdk-types";
+/**
+ * Build O(1) indexes for resource lookup
+ */
+export declare function buildResourceIndexes(bundle: Bundle, resourcesById: Map<string, Resource>, resourcesByFullUrl: Map<string, Resource>, resourcesByType: Map<string, Resource[]>, reverseReferencesById: Map<string, ReverseReference[]>, dateRangeIndex: IntervalTree<DateIndexRecord, number>, resolutionStack: Set<string>): void;
+/**
+ * Build reverse reference index for O(1) reverse lookup
+ */
+export declare function buildReverseReferenceIndex(bundle: Bundle, reverseReferencesById: Map<string, ReverseReference[]>, resourcesByFullUrl: Map<string, Resource>): void;
+/**
+ * Build date range index for O(log n + k) date range searches
+ */
+export declare function buildDateRangeIndex(bundle: Bundle, dateRangeIndex: IntervalTree<DateIndexRecord, number>): void;
+//# sourceMappingURL=indexing.d.ts.map

package/dist/internal/indexing.d.ts.map

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package/dist/internal/indexing.js

@@ -0,0 +1,129 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildDateRangeIndex = exports.buildReverseReferenceIndex = exports.buildResourceIndexes = void 0;
+const reference_utils_1 = require("./reference-utils");
+const date_extraction_1 = require("./date-extraction");
+/**
+ * Build O(1) indexes for resource lookup
+ */
+function buildResourceIndexes(bundle, resourcesById, resourcesByFullUrl, resourcesByType, reverseReferencesById, dateRangeIndex, resolutionStack) {
+    if (!bundle.entry) {
+        return;
+    }
+    for (const entry of bundle.entry) {
+        if (!entry.resource) {
+            continue;
+        }
+        const resource = entry.resource;
+        // Index by resource.id if it exists
+        if (resource.id) {
+            resourcesById.set(resource.id, resource);
+        }
+        // Index by fullUrl if it exists
+        if (entry.fullUrl) {
+            resourcesByFullUrl.set(entry.fullUrl, resource);
+        }
+        // Index by resource type for type-specific getters
+        const resourceType = resource.resourceType;
+        if (!resourcesByType.has(resourceType)) {
+            resourcesByType.set(resourceType, []);
+        }
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        resourcesByType.get(resourceType).push(resource);
+    }
+    // Build reverse reference index
+    buildReverseReferenceIndex(bundle, reverseReferencesById, resourcesByFullUrl);
+    // Build date range index
+    buildDateRangeIndex(bundle, dateRangeIndex);
+    // Clear resolution stack after index building
+    resolutionStack.clear();
+}
+exports.buildResourceIndexes = buildResourceIndexes;
+/**
+ * Build reverse reference index for O(1) reverse lookup
+ */
+function buildReverseReferenceIndex(bundle, reverseReferencesById, resourcesByFullUrl) {
+    if (!bundle.entry) {
+        return;
+    }
+    for (const entry of bundle.entry) {
+        if (!entry.resource) {
+            continue;
+        }
+        const resource = entry.resource;
+        const sourceResourceId = resource.id ?? entry.fullUrl ?? "unknown";
+        const references = (0, reference_utils_1.findAllReferences)(resource);
+        for (const { field, reference } of references) {
+            // Extract target ID from reference
+            const targetId = (0, reference_utils_1.extractTargetIdFromReference)(reference);
+            if (!targetId) {
+                continue;
+            }
+            // Add to reverse index for both the extracted ID and the full reference
+            const reverseRef = {
+                sourceResourceId,
+                sourceResourceType: resource.resourceType,
+                referenceField: (0, reference_utils_1.normalizeReferenceField)(field),
+            };
+            // Index by extracted resource ID (e.g., "patient-123" from "Patient/patient-123")
+            if (!reverseReferencesById.has(targetId)) {
+                reverseReferencesById.set(targetId, []);
+            }
+            reverseReferencesById.get(targetId)?.push(reverseRef);
+            // Also index by full reference if it's different (e.g., "urn:uuid:patient-123")
+            if (targetId !== reference) {
+                if (!reverseReferencesById.has(reference)) {
+                    reverseReferencesById.set(reference, []);
+                }
+                reverseReferencesById.get(reference)?.push(reverseRef);
+            }
+            // Also try to index by the actual resource ID if we can find it efficiently
+            // Check if this reference can be resolved to a resource with a different ID
+            if (!reference.includes("/")) {
+                // This is likely a fullUrl reference (e.g., "urn:uuid:xxx")
+                // Check if we have a resource with this fullUrl
+                const targetResource = resourcesByFullUrl.get(reference);
+                if (targetResource?.id &&
+                    targetResource.id !== targetId &&
+                    targetResource.id !== reference) {
+                    if (!reverseReferencesById.has(targetResource.id)) {
+                        reverseReferencesById.set(targetResource.id, []);
+                    }
+                    reverseReferencesById.get(targetResource.id)?.push(reverseRef);
+                }
+            }
+        }
+    }
+}
+exports.buildReverseReferenceIndex = buildReverseReferenceIndex;
+/**
+ * Build date range index for O(log n + k) date range searches
+ */
+function buildDateRangeIndex(bundle, dateRangeIndex) {
+    if (!bundle.entry) {
+        return;
+    }
+    for (const entry of bundle.entry) {
+        if (!entry.resource || !entry.resource.id) {
+            continue;
+        }
+        const resource = entry.resource;
+        const dateIntervals = (0, date_extraction_1.extractDateIntervalsFromResource)(resource);
+        for (const interval of dateIntervals) {
+            try {
+                dateRangeIndex.insert(interval);
+            }
+            catch (error) {
+                // Handle bad data case where low > high
+                console.warn(`Error inserting date interval (${interval.low}, ${interval.high}) into index. Swapping values.`);
+                dateRangeIndex.insert({
+                    ...interval,
+                    low: interval.high,
+                    high: interval.low,
+                });
+            }
+        }
+    }
+}
+exports.buildDateRangeIndex = buildDateRangeIndex;
+//# sourceMappingURL=indexing.js.map

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package/dist/internal/llm-context.d.ts

@@ -0,0 +1,40 @@
+import { Resource } from "@medplum/fhirtypes";
+import { Smart } from "../types/smart-resources";
+import { LLMContextOptions, WalkResult } from "../types/sdk-types";
+/**
+ * Strip non-clinical metadata from a FHIR resource to reduce noise for LLM consumption.
+ * Removes: meta, extension, modifierExtension, text, id, identifier, and all reference fields
+ * defined in REFERENCE_METHOD_MAPPING
+ * Returns an immutable copy without mutating the original.
+ */
+export declare function stripNonClinicalData<T extends Resource>(resource: T): T;
+/**
+ * Group resources by their resource type
+ */
+export declare function groupResourcesByType(resources: Resource[]): Record<string, Resource[]>;
+/**
+ * Format a single resource as readable text
+ */
+export declare function formatResourceAsText(resource: Resource): string;
+/**
+ * Format resources as structured text for better LLM readability
+ */
+export declare function formatAsStructuredText(resourcesByDepth: Map<number, Resource[]>): string;
+/**
+ * Format resources as JSON with depth annotations
+ */
+export declare function formatAsJSON(resourcesByDepth: Map<number, Resource[]>): string;
+/**
+ * Generate LLM-friendly context from a starting resource and its related resources.
+ * Uses BFS to discover related resources, strips non-clinical data, and formats output.
+ *
+ * @param startResource - The smart resource to start traversal from
+ * @param options - Options for depth, inclusion, and format
+ * @param walkReferencesFn - Function to walk references (passed in to avoid circular dependency)
+ * @returns Formatted string suitable for LLM context
+ */
+export declare function generateLLMContext<T extends Resource>(startResource: Smart<T>, options: LLMContextOptions | undefined, walkReferencesFn: (startResource: Smart<T>, options: {
+    maxDepth: number;
+    includeStartResource: boolean;
+}) => WalkResult<T>): string;
+//# sourceMappingURL=llm-context.d.ts.map

package/dist/internal/llm-context.d.ts.map

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package/dist/internal/llm-context.js

@@ -0,0 +1,214 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateLLMContext = exports.formatAsJSON = exports.formatAsStructuredText = exports.formatResourceAsText = exports.groupResourcesByType = exports.stripNonClinicalData = void 0;
+const smart_resources_1 = require("../types/smart-resources");
+/**
+ * Build a set of all reference field names from REFERENCE_METHOD_MAPPING.
+ * Extracts base field names, handling nested paths (e.g., "participant.individual" -> "participant")
+ */
+function buildReferenceFieldSet() {
+    const fields = new Set();
+    for (const resourceMapping of Object.values(smart_resources_1.REFERENCE_METHOD_MAPPING)) {
+        for (const fieldPath of Object.values(resourceMapping)) {
+            // Handle nested paths - take the first part
+            const parts = fieldPath.split(".");
+            const baseField = parts[0];
+            if (baseField !== undefined) {
+                fields.add(baseField);
+            }
+        }
+    }
+    return fields;
+}
+const REFERENCE_FIELDS = buildReferenceFieldSet();
+/**
+ * Strip non-clinical metadata from a FHIR resource to reduce noise for LLM consumption.
+ * Removes: meta, extension, modifierExtension, text, id, identifier, and all reference fields
+ * defined in REFERENCE_METHOD_MAPPING
+ * Returns an immutable copy without mutating the original.
+ */
+function stripNonClinicalData(resource) {
+    function deepCloneAndStrip(obj, resourceType) {
+        if (obj === null || obj === undefined) {
+            return obj;
+        }
+        if (Array.isArray(obj)) {
+            return obj.map(item => deepCloneAndStrip(item, resourceType));
+        }
+        if (typeof obj === "object") {
+            const result = {};
+            for (const [key, value] of Object.entries(obj)) {
+                // Skip non-clinical fields, identifiers, and reference fields
+                if (key === "meta" ||
+                    key === "extension" ||
+                    key === "modifierExtension" ||
+                    key === "text" ||
+                    key === "id" ||
+                    key === "identifier" ||
+                    REFERENCE_FIELDS.has(key)) {
+                    continue;
+                }
+                result[key] = deepCloneAndStrip(value, resourceType);
+            }
+            return result;
+        }
+        return obj;
+    }
+    return deepCloneAndStrip(resource, resource.resourceType);
+}
+exports.stripNonClinicalData = stripNonClinicalData;
+/**
+ * Group resources by their resource type
+ */
+function groupResourcesByType(resources) {
+    const grouped = {};
+    for (const resource of resources) {
+        const type = resource.resourceType;
+        if (!grouped[type]) {
+            grouped[type] = [];
+        }
+        const resourceArray = grouped[type];
+        if (resourceArray) {
+            resourceArray.push(resource);
+        }
+    }
+    return grouped;
+}
+exports.groupResourcesByType = groupResourcesByType;
+/**
+ * Format a single resource as readable text
+ */
+function formatResourceAsText(resource) {
+    const lines = [];
+    lines.push(`[Type: ${resource.resourceType}, ID: ${resource.id ?? "unknown"}]`);
+    function formatValue(value, indent = 2) {
+        const prefix = " ".repeat(indent);
+        const result = [];
+        if (value === null || value === undefined) {
+            return [`${prefix}(none)`];
+        }
+        if (Array.isArray(value)) {
+            if (value.length === 0) {
+                return [`${prefix}[]`];
+            }
+            for (const [index, item] of value.entries()) {
+                result.push(`${prefix}[${index}]:`);
+                result.push(...formatValue(item, indent + 2));
+            }
+            return result;
+        }
+        if (typeof value === "object") {
+            for (const [key, val] of Object.entries(value)) {
+                result.push(`${prefix}${key}:`);
+                result.push(...formatValue(val, indent + 2));
+            }
+            return result;
+        }
+        return [`${prefix}${String(value)}`];
+    }
+    // Format key fields
+    for (const [key, value] of Object.entries(resource)) {
+        if (key === "resourceType" || key === "id")
+            continue; // Already shown in header
+        lines.push(`  ${key}:`);
+        lines.push(...formatValue(value, 4));
+    }
+    return lines.join("\n");
+}
+exports.formatResourceAsText = formatResourceAsText;
+/**
+ * Format resources as structured text for better LLM readability
+ */
+function formatAsStructuredText(resourcesByDepth) {
+    const lines = [];
+    // Primary resource section
+    const primaryResources = resourcesByDepth.get(0) ?? [];
+    if (primaryResources.length > 0) {
+        lines.push("PRIMARY RESOURCE:");
+        lines.push("=".repeat(80));
+        for (const resource of primaryResources) {
+            lines.push(formatResourceAsText(resource));
+            lines.push("");
+        }
+    }
+    // Related resources by depth
+    for (const [depth, resources] of resourcesByDepth.entries()) {
+        if (depth === 0)
+            continue; // Already handled above
+        const depthLabel = depth === 1 ? "DIRECTLY REFERENCED" : `INDIRECTLY REFERENCED (Depth ${depth})`;
+        lines.push(`${depthLabel} RESOURCES:`);
+        lines.push("=".repeat(80));
+        // Group by resource type for better organization
+        const groupedByType = groupResourcesByType(resources);
+        for (const [resourceType, typeResources] of Object.entries(groupedByType)) {
+            lines.push(`\n--- ${resourceType} (${typeResources.length}) ---\n`);
+            for (const resource of typeResources) {
+                lines.push(formatResourceAsText(resource));
+                lines.push("");
+            }
+        }
+    }
+    return lines.join("\n");
+}
+exports.formatAsStructuredText = formatAsStructuredText;
+/**
+ * Format resources as JSON with depth annotations
+ */
+function formatAsJSON(resourcesByDepth) {
+    const relatedResourcesByDepth = {};
+    for (const [depth, resources] of resourcesByDepth.entries()) {
+        if (depth === 0)
+            continue; // Skip primary resource (already at top)
+        relatedResourcesByDepth[`depth_${depth}`] = resources;
+    }
+    const output = {
+        primaryResource: resourcesByDepth.get(0)?.[0],
+        relatedResourcesByDepth,
+    };
+    return JSON.stringify(output, null, 2);
+}
+exports.formatAsJSON = formatAsJSON;
+/**
+ * Generate LLM-friendly context from a starting resource and its related resources.
+ * Uses BFS to discover related resources, strips non-clinical data, and formats output.
+ *
+ * @param startResource - The smart resource to start traversal from
+ * @param options - Options for depth, inclusion, and format
+ * @param walkReferencesFn - Function to walk references (passed in to avoid circular dependency)
+ * @returns Formatted string suitable for LLM context
+ */
+function generateLLMContext(startResource, options, walkReferencesFn) {
+    const maxDepth = options?.maxDepth ?? 2;
+    const includeStartResource = options?.includeStartResource ?? true;
+    const format = options?.format ?? "structured-text";
+    // Walk the reference graph
+    const walkResult = walkReferencesFn(startResource, {
+        maxDepth,
+        includeStartResource,
+    });
+    // Log resource counts for debugging
+    console.log(`[LLM Context] Total resources discovered: ${walkResult.allResources.length}`);
+    for (const [depth, resources] of walkResult.resourcesByDepth.entries()) {
+        console.log(`[LLM Context] Depth ${depth}: ${resources.length} resources`);
+    }
+    // Strip non-clinical data from all resources
+    const cleanedResourcesByDepth = new Map();
+    for (const [depth, resources] of walkResult.resourcesByDepth.entries()) {
+        // Skip depth 0 if includeStartResource is false
+        if (depth === 0 && !includeStartResource) {
+            continue;
+        }
+        cleanedResourcesByDepth.set(depth, 
+        // Cast to Resource to satisfy type checker - Smart extends Resource
+        resources.map(r => stripNonClinicalData(r)));
+    }
+    // Format based on selected format
+    if (format === "json") {
+        return formatAsJSON(cleanedResourcesByDepth);
+    }
+    else {
+        return formatAsStructuredText(cleanedResourcesByDepth);
+    }
+}
+exports.generateLLMContext = generateLLMContext;
+//# sourceMappingURL=llm-context.js.map

package/dist/internal/llm-context.js.map

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package/dist/internal/reference-resolution.d.ts

@@ -0,0 +1,29 @@
+import { Resource } from "@medplum/fhirtypes";
+import { Smart } from "../types/smart-resources";
+import { ReverseReferenceOptions } from "../types/sdk-types";
+/**
+ * Check if a reference field expects an array of references.
+ * Handles both simple paths ("performer") and nested paths ("diagnosis.condition").
+ *
+ * For nested paths, if the intermediate level is an array, the method returns an array.
+ * For example, "diagnosis.condition" returns an array because diagnosis is an array field.
+ */
+export declare function isArrayReferenceField(fieldName: string): boolean;
+/**
+ * Resolve a single reference object to a resource
+ * FR-5.5: Reference resolution methods handle both resource.id and fullUrl matching
+ */
+export declare function resolveReferenceObject(referenceObj: unknown, resourcesById: Map<string, Resource>, resourcesByFullUrl: Map<string, Resource>, resolutionStack: Set<string>): Resource | undefined;
+/**
+ * Resolve a reference method call to actual resources
+ * FR-5.2-5.6: Handle different reference types and patterns
+ */
+export declare function resolveReference(methodName: string, resource: Resource, resourcesById: Map<string, Resource>, resourcesByFullUrl: Map<string, Resource>, resolutionStack: Set<string>, createSmartResourceFn: <T extends Resource>(resource: T) => Smart<T>): Smart<Resource> | Smart<Resource>[] | undefined;
+/**
+ * Create a smart resource with reference resolution methods
+ * FR-5.1: Resources returned by SDK have additional getter methods for each Reference field
+ * FR-5.7: Reference resolution operates in O(1) time complexity per reference
+ * FR-5.8: Original reference fields remain unchanged
+ */
+export declare function createSmartResource<T extends Resource>(resource: T, smartResourceCache: WeakMap<Resource, Smart<Resource>>, resourcesById: Map<string, Resource>, resourcesByFullUrl: Map<string, Resource>, resolutionStack: Set<string>, getResourcesReferencingIdFn: (targetId: string, options?: ReverseReferenceOptions) => Smart<Resource>[]): Smart<T>;
+//# sourceMappingURL=reference-resolution.d.ts.map

package/dist/internal/reference-resolution.d.ts.map

@@ -0,0 +1 @@
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