@onivoro/isomorphic-fhir 24.28.1

package/LICENSE

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+MIT License
+
+Copyright (c) 2024 Onivoro
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @onivoro/isomorphic-fhir
+
+A library for transforming FHIR (Fast Healthcare Interoperability Resources) bundles into normalized database tables following Third Normal Form (3NF).
+
+## Overview
+
+This library takes FHIR R4 bundles containing healthcare resources and transforms them into a set of normalized tables that can be used to populate a relational database. The transformation process:
+
+- Eliminates data redundancy across FHIR resources
+- Ensures referential integrity between healthcare entities
+- Creates proper foreign key relationships
+- Generates unique IDs for normalized records
+- Preserves FHIR resource relationships through reference tables
+- Handles complex nested structures like CodeableConcepts and Extensions
+
+## Supported FHIR Resources
+
+The library currently supports normalization of the following FHIR R4 resources:
+
+- **Patient**: Demographics, identifiers, names, contacts, addresses
+- **Practitioner**: Healthcare providers, qualifications, contact information
+- **Organization**: Healthcare organizations, types, contact details
+- **Encounter**: Healthcare encounters, participants, locations
+- **Condition**: Medical conditions, clinical status, evidence
+- **Observation**: Clinical measurements, vital signs, lab results
+- **MedicationRequest**: Medication prescriptions, dosage instructions
+- **Procedure**: Medical procedures, performers, outcomes
+- **Immunization**: Vaccinations, reactions, protocols
+- **AllergyIntolerance**: Allergies, reactions, manifestations
+- **DiagnosticReport**: Diagnostic test results, conclusions
+- **Location**: Healthcare facilities, positions, contact info
+- **Appointment**: Scheduled appointments, participants
+- **CareTeam**: Care team members, roles, periods
+- **CarePlan**: Care plans, activities, goals
+
+## Usage
+
+```typescript
+import { normalizeFhirBundle } from '@onivoro/isomorphic-fhir';
+
+const fhirBundle = {
+  resourceType: 'Bundle',
+  type: 'searchset',
+  entry: [
+    {
+      resource: {
+        resourceType: 'Patient',
+        id: 'patient-123',
+        name: [{ family: 'Doe', given: ['John'] }],
+        gender: 'male',
+        birthDate: '1985-03-15'
+      }
+    },
+    {
+      resource: {
+        resourceType: 'Observation',
+        id: 'observation-456',
+        status: 'final',
+        code: { coding: [{ code: '8867-4', display: 'Heart rate' }] },
+        subject: { reference: 'Patient/patient-123' },
+        valueQuantity: { value: 72, unit: 'beats/min' }
+      }
+    }
+  ]
+};
+
+const normalizedData = normalizeFhirBundle(fhirBundle);
+
+// normalizedData contains normalized tables:
+console.log(normalizedData.patients);      // Patient demographics
+console.log(normalizedData.patientNames);  // Patient names (separate table)
+console.log(normalizedData.observations);  // Clinical observations
+console.log(normalizedData.addresses);     // Addresses (deduplicated)
+console.log(normalizedData.telecoms);      // Contact points
+console.log(normalizedData.references);    // Resource relationships
+```
+
+## Normalized Tables Generated
+
+The library generates 30+ normalized tables following healthcare data patterns:
+
+### Core Resource Tables
+- **bundles**: FHIR bundle metadata
+- **bundleEntries**: Bundle entry information
+- **patients**: Patient demographics
+- **practitioners**: Healthcare provider information
+- **organizations**: Healthcare organizations
+- **encounters**: Healthcare encounters
+- **conditions**: Medical conditions and diagnoses
+- **observations**: Clinical measurements and findings
+- **medicationRequests**: Medication prescriptions
+- **procedures**: Medical procedures performed
+- **immunizations**: Vaccination records
+- **allergyIntolerances**: Allergy and intolerance information
+- **diagnosticReports**: Diagnostic test reports
+- **locations**: Healthcare facility information
+- **appointments**: Scheduled appointments
+- **careTeams**: Care team compositions
+- **carePlans**: Patient care plans
+
+### Relationship and Detail Tables
+- **patientIdentifiers**: Patient identifier systems
+- **patientNames**: Patient name variations
+- **patientContacts**: Emergency/family contacts
+- **practitionerQualifications**: Provider credentials
+- **organizationTypes**: Organization classifications
+- **encounterParticipants**: Encounter participants
+- **observationComponents**: Multi-component observations
+- **medicationDosages**: Medication dosing instructions
+- **procedurePerformers**: Procedure performers
+- **allergyReactions**: Allergic reactions
+- **allergyManifestations**: Reaction manifestations
+- **diagnosticReportResults**: Report result references
+- **appointmentParticipants**: Appointment participants
+- **careTeamParticipants**: Care team member details
+- **carePlanActivities**: Care plan activity details
+
+### Common Data Type Tables
+- **addresses**: Physical addresses (deduplicated)
+- **telecoms**: Contact points (phone, email, etc.)
+- **codeableConcepts**: Coded concepts with text
+- **codings**: Individual coding systems
+- **notes**: Annotations and comments
+- **attachments**: Binary attachments and documents
+- **references**: Resource references and relationships
+
+## Key Features
+
+### FHIR Compliance
+- Full FHIR R4 resource support
+- Proper handling of FHIR data types (CodeableConcept, Reference, etc.)
+- Preservation of clinical terminology and coding systems
+- Support for complex nested structures
+
+### Data Integrity
+- Referential integrity through normalized foreign keys
+- Unique constraint handling for identifiers
+- Proper temporal data handling (effective periods, timestamps)
+- Clinical status and verification status preservation
+
+### Healthcare-Specific Patterns
+- Support for multiple identifier systems per resource
+- Proper handling of clinical hierarchies (conditions, observations)
+- Care team and care plan relationship modeling
+- Medication dosing and administration patterns
+- Allergy and adverse reaction tracking
+
+### Performance Optimized
+- Efficient deduplication of common entities (addresses, codings)
+- Bulk insert-friendly table structures
+- Indexed foreign key relationships
+- Minimal data redundancy
+
+## Testing
+
+The library includes comprehensive tests covering:
+- Complete FHIR bundle normalization
+- Individual resource type processing
+- Complex nested structure handling
+- Reference relationship preservation
+- Edge cases and error conditions
+
+Run tests with:
+```bash
+nx test lib-isomorphic-fhir
+```
+
+## FHIR Standards Compliance
+
+This library is designed to work with FHIR R4 resources and follows HL7 FHIR standards for:
+- Resource structure and cardinality
+- Data type handling and validation
+- Reference resolution and integrity
+- Clinical terminology bindings
+- Healthcare workflow patterns
+
+## Use Cases
+
+Perfect for:
+- **EHR Data Warehousing**: Normalize FHIR data for analytics
+- **Clinical Data Lakes**: Store FHIR resources in relational format
+- **Interoperability Solutions**: Transform FHIR for legacy systems
+- **Healthcare Analytics**: Enable SQL-based analysis of clinical data
+- **Compliance Reporting**: Structure data for regulatory requirements
+- **Research Databases**: Prepare clinical data for research queries
+
+## License
+
+This library is licensed under the MIT License. See the LICENSE file in this package for details.

package/package.json

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+{
+  "name": "@onivoro/isomorphic-fhir",
+  "version": "24.28.1",
+  "license": "MIT",
+  "type": "commonjs",
+  "main": "./src/index.js",
+  "types": "./src/index.d.ts",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/onivoro/monorepo.git"
+  },
+  "dependencies": {
+    "@nestjs/swagger": "*",
+    "tslib": "^2.3.0",
+    "uuid": "*"
+  },
+  "files": [
+    "**/*.js",
+    "**/*.d.ts",
+    "**/*.js.map",
+    "README.md"
+  ]
+}

package/src/index.d.ts

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+export * from './lib/interfaces/fhir-resources.interface';
+export * from './lib/interfaces/fhir-normalized-tables.interface';
+export * from './lib/functions/normalize-fhir-bundle.function';

package/src/index.js

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+// FHIR Resource Interfaces
+export * from './lib/interfaces/fhir-resources.interface';
+export * from './lib/interfaces/fhir-normalized-tables.interface';
+// Functions
+export * from './lib/functions/normalize-fhir-bundle.function';
+//# sourceMappingURL=index.js.map

package/src/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../../libs/isomorphic/fhir/src/index.ts"],"names":[],"mappings":"AAAA,2BAA2B;AAC3B,cAAc,2CAA2C,CAAC;AAC1D,cAAc,mDAAmD,CAAC;AAElE,YAAY;AACZ,cAAc,gDAAgD,CAAC"}

package/src/lib/functions/fhir-test-config.d.ts

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+import { AxiosInstance } from 'axios';
+/**
+ * Configuration and utilities for FHIR API integration tests
+ */
+export declare class FhirTestConfig {
+    static readonly FHIR_BASE_URL = "http://hapi.fhir.org/baseR4";
+    static readonly TEST_TIMEOUT = 30000;
+    private static testAxiosInstance;
+    /**
+     * Get or create the test axios instance
+     */
+    static getAxiosInstance(): AxiosInstance;
+    /**
+     * Clean up the axios instance
+     */
+    static cleanup(): void;
+    /**
+     * Common FHIR resource types for testing
+     */
+    static readonly RESOURCE_TYPES: {
+        readonly PATIENT: "Patient";
+        readonly PRACTITIONER: "Practitioner";
+        readonly ORGANIZATION: "Organization";
+        readonly ENCOUNTER: "Encounter";
+        readonly OBSERVATION: "Observation";
+        readonly CONDITION: "Condition";
+        readonly MEDICATION_REQUEST: "MedicationRequest";
+        readonly PROCEDURE: "Procedure";
+        readonly LOCATION: "Location";
+        readonly APPOINTMENT: "Appointment";
+        readonly CARE_TEAM: "CareTeam";
+        readonly CARE_PLAN: "CarePlan";
+        readonly IMMUNIZATION: "Immunization";
+        readonly ALLERGY_INTOLERANCE: "AllergyIntolerance";
+        readonly DIAGNOSTIC_REPORT: "DiagnosticReport";
+    };
+    /**
+     * Common search parameters for testing
+     */
+    static readonly SEARCH_PARAMS: {
+        readonly COUNT: "_count";
+        readonly FORMAT: "_format";
+        readonly INCLUDE: "_include";
+        readonly SORT: "_sort";
+        readonly TEXT: "_text";
+    };
+    /**
+     * Initialize axios defaults for testing
+     */
+    static initializeAxios(): void;
+    /**
+     * Build a FHIR search URL with parameters
+     */
+    static buildSearchUrl(resourceType: string, params?: Record<string, string | number>): string;
+    /**
+     * Get a resource by ID
+     */
+    static buildResourceUrl(resourceType: string, id: string): string;
+    /**
+     * Common assertion helpers for FHIR resources
+     */
+    static validateFhirResource(resource: any, expectedType: string): void;
+    /**
+     * Validate FHIR Bundle structure
+     */
+    static validateFhirBundle(bundle: any): void;
+    /**
+     * Wait for a condition to be met (useful for async operations)
+     */
+    static waitFor(condition: () => boolean | Promise<boolean>, timeout?: number): Promise<void>;
+    /**
+     * Retry a function with exponential backoff
+     */
+    static retry<T>(fn: () => Promise<T>, maxAttempts?: number, initialDelay?: number): Promise<T>;
+    /**
+     * Check if the FHIR server is available
+     */
+    static checkServerAvailability(): Promise<boolean>;
+    /**
+     * Get server capability statement
+     */
+    static getServerCapabilities(): Promise<any>;
+    /**
+     * Clean up test data (if the server supports it)
+     */
+    /**
+     * Clean up test data (placeholder - HAPI test server doesn't support DELETE)
+     */
+    static cleanupTestData(resourceType: string, identifiers: string[]): Promise<void>;
+    /**
+     * Generate test data patterns
+     */
+    static getTestPatterns(): {
+        searchPatterns: ({
+            params: {
+                _count: number;
+                _sort?: undefined;
+            };
+        } | {
+            params: {
+                _count: number;
+                _sort: string;
+            };
+        })[];
+        resourceCombinations: (("Patient" | "Encounter")[] | ("Practitioner" | "Organization")[] | ("Patient" | "Observation")[])[];
+        errorScenarios: {
+            url: string;
+            expectedStatus: number;
+        }[];
+    };
+}
+/**
+ * Test utilities for performance monitoring
+ */
+export declare class FhirTestPerformance {
+    private static measurements;
+    static startMeasurement(name: string): () => number;
+    static recordMeasurement(name: string, duration: number): void;
+    static getStatistics(name: string): {
+        avg: number;
+        min: number;
+        max: number;
+        count: number;
+    } | null;
+    static reset(): void;
+    static logStatistics(): void;
+}

package/src/lib/functions/fhir-test-config.js

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+import { __awaiter } from "tslib";
+import axios from 'axios';
+import * as http from 'http';
+import * as https from 'https';
+/**
+ * Configuration and utilities for FHIR API integration tests
+ */
+export class FhirTestConfig {
+    /**
+     * Get or create the test axios instance
+     */
+    static getAxiosInstance() {
+        if (!this.testAxiosInstance) {
+            // Create HTTP/HTTPS agents that don't keep connections alive
+            const httpAgent = new http.Agent({
+                keepAlive: false,
+                maxSockets: 5
+            });
+            const httpsAgent = new https.Agent({
+                keepAlive: false,
+                maxSockets: 5
+            });
+            this.testAxiosInstance = axios.create({
+                timeout: this.TEST_TIMEOUT,
+                httpAgent,
+                httpsAgent,
+                headers: {
+                    'Accept': 'application/fhir+json',
+                    'Connection': 'close'
+                }
+            });
+        }
+        return this.testAxiosInstance;
+    }
+    /**
+     * Clean up the axios instance
+     */
+    static cleanup() {
+        if (this.testAxiosInstance) {
+            // Destroy any remaining connections
+            if (this.testAxiosInstance.defaults.httpAgent) {
+                this.testAxiosInstance.defaults.httpAgent.destroy();
+            }
+            if (this.testAxiosInstance.defaults.httpsAgent) {
+                this.testAxiosInstance.defaults.httpsAgent.destroy();
+            }
+        }
+    }
+    /**
+     * Initialize axios defaults for testing
+     */
+    static initializeAxios() {
+        // Just ensure our test instance is created
+        this.getAxiosInstance();
+    }
+    /**
+     * Build a FHIR search URL with parameters
+     */
+    static buildSearchUrl(resourceType, params = {}) {
+        const url = new URL(`${this.FHIR_BASE_URL}/${resourceType}`);
+        // Add default format parameter
+        url.searchParams.set(this.SEARCH_PARAMS.FORMAT, 'json');
+        // Add custom parameters, filtering out undefined values
+        Object.entries(params).forEach(([key, value]) => {
+            if (value !== undefined) {
+                url.searchParams.set(key, value.toString());
+            }
+        });
+        return url.toString();
+    }
+    /**
+     * Get a resource by ID
+     */
+    static buildResourceUrl(resourceType, id) {
+        return `${this.FHIR_BASE_URL}/${resourceType}/${id}?_format=json`;
+    }
+    /**
+     * Common assertion helpers for FHIR resources
+     */
+    static validateFhirResource(resource, expectedType) {
+        expect(resource).toBeDefined();
+        expect(resource.resourceType).toBe(expectedType);
+        expect(resource.id).toBeDefined();
+    }
+    /**
+     * Validate FHIR Bundle structure
+     */
+    static validateFhirBundle(bundle) {
+        expect(bundle).toBeDefined();
+        expect(bundle.resourceType).toBe('Bundle');
+        expect(bundle.type).toBeDefined();
+        expect(['searchset', 'collection', 'document', 'message', 'transaction', 'transaction-response', 'batch', 'batch-response', 'history'].includes(bundle.type)).toBe(true);
+    }
+    /**
+     * Wait for a condition to be met (useful for async operations)
+     */
+    static waitFor(condition_1) {
+        return __awaiter(this, arguments, void 0, function* (condition, timeout = 5000) {
+            const start = Date.now();
+            while (Date.now() - start < timeout) {
+                if (yield condition()) {
+                    return;
+                }
+                yield new Promise(resolve => setTimeout(resolve, 100));
+            }
+            throw new Error(`Condition not met within ${timeout}ms`);
+        });
+    }
+    /**
+     * Retry a function with exponential backoff
+     */
+    static retry(fn_1) {
+        return __awaiter(this, arguments, void 0, function* (fn, maxAttempts = 3, initialDelay = 1000) {
+            let lastError;
+            for (let attempt = 1; attempt <= maxAttempts; attempt++) {
+                try {
+                    return yield fn();
+                }
+                catch (error) {
+                    lastError = error;
+                    if (attempt === maxAttempts) {
+                        throw lastError;
+                    }
+                    const delay = initialDelay * Math.pow(2, attempt - 1);
+                    yield new Promise(resolve => setTimeout(resolve, delay));
+                }
+            }
+            throw lastError;
+        });
+    }
+    /**
+     * Check if the FHIR server is available
+     */
+    static checkServerAvailability() {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const axiosInstance = this.getAxiosInstance();
+                const response = yield axiosInstance.get(`${this.FHIR_BASE_URL}/metadata`, { timeout: 5000 });
+                return response.status === 200 && response.data.resourceType === 'CapabilityStatement';
+            }
+            catch (error) {
+                return false;
+            }
+        });
+    }
+    /**
+     * Get server capability statement
+     */
+    static getServerCapabilities() {
+        return __awaiter(this, void 0, void 0, function* () {
+            const axiosInstance = this.getAxiosInstance();
+            const response = yield axiosInstance.get(`${this.FHIR_BASE_URL}/metadata?_format=json`);
+            return response.data;
+        });
+    }
+    /**
+     * Clean up test data (if the server supports it)
+     */
+    /**
+     * Clean up test data (placeholder - HAPI test server doesn't support DELETE)
+     */
+    static cleanupTestData(resourceType, identifiers) {
+        return __awaiter(this, void 0, void 0, function* () {
+            // Note: HAPI FHIR test server typically doesn't allow DELETE operations
+            // This is a placeholder for when testing against a server that does support cleanup
+            const axiosInstance = this.getAxiosInstance();
+            for (const id of identifiers) {
+                try {
+                    yield axiosInstance.delete(`${this.FHIR_BASE_URL}/${resourceType}/${id}`);
+                }
+                catch (error) {
+                    // Ignore errors during cleanup as test servers may not support DELETE
+                    console.warn(`Could not delete ${resourceType}/${id}:`, error);
+                }
+            }
+        });
+    }
+    /**
+     * Generate test data patterns
+     */
+    static getTestPatterns() {
+        return {
+            // Common search patterns to test
+            searchPatterns: [
+                { params: { [FhirTestConfig.SEARCH_PARAMS.COUNT]: 5 } },
+                { params: { [FhirTestConfig.SEARCH_PARAMS.COUNT]: 1 } },
+                { params: { [FhirTestConfig.SEARCH_PARAMS.COUNT]: 10, [FhirTestConfig.SEARCH_PARAMS.SORT]: 'name' } },
+            ],
+            // Resource type combinations for mixed bundles
+            resourceCombinations: [
+                [FhirTestConfig.RESOURCE_TYPES.PATIENT, FhirTestConfig.RESOURCE_TYPES.ENCOUNTER],
+                [FhirTestConfig.RESOURCE_TYPES.PRACTITIONER, FhirTestConfig.RESOURCE_TYPES.ORGANIZATION],
+                [FhirTestConfig.RESOURCE_TYPES.PATIENT, FhirTestConfig.RESOURCE_TYPES.OBSERVATION],
+            ],
+            // Error scenarios to test
+            errorScenarios: [
+                { url: `${FhirTestConfig.FHIR_BASE_URL}/Patient/non-existent-id-123456`, expectedStatus: 404 },
+                { url: `${FhirTestConfig.FHIR_BASE_URL}/InvalidResourceType`, expectedStatus: 404 },
+            ]
+        };
+    }
+}
+FhirTestConfig.FHIR_BASE_URL = 'http://hapi.fhir.org/baseR4';
+FhirTestConfig.TEST_TIMEOUT = 30000;
+/**
+ * Common FHIR resource types for testing
+ */
+FhirTestConfig.RESOURCE_TYPES = {
+    PATIENT: 'Patient',
+    PRACTITIONER: 'Practitioner',
+    ORGANIZATION: 'Organization',
+    ENCOUNTER: 'Encounter',
+    OBSERVATION: 'Observation',
+    CONDITION: 'Condition',
+    MEDICATION_REQUEST: 'MedicationRequest',
+    PROCEDURE: 'Procedure',
+    LOCATION: 'Location',
+    APPOINTMENT: 'Appointment',
+    CARE_TEAM: 'CareTeam',
+    CARE_PLAN: 'CarePlan',
+    IMMUNIZATION: 'Immunization',
+    ALLERGY_INTOLERANCE: 'AllergyIntolerance',
+    DIAGNOSTIC_REPORT: 'DiagnosticReport'
+};
+/**
+ * Common search parameters for testing
+ */
+FhirTestConfig.SEARCH_PARAMS = {
+    COUNT: '_count',
+    FORMAT: '_format',
+    INCLUDE: '_include',
+    SORT: '_sort',
+    TEXT: '_text'
+};
+/**
+ * Test utilities for performance monitoring
+ */
+export class FhirTestPerformance {
+    static startMeasurement(name) {
+        const start = performance.now();
+        return () => {
+            const duration = performance.now() - start;
+            this.recordMeasurement(name, duration);
+            return duration;
+        };
+    }
+    static recordMeasurement(name, duration) {
+        if (!this.measurements.has(name)) {
+            this.measurements.set(name, []);
+        }
+        this.measurements.get(name).push(duration);
+    }
+    static getStatistics(name) {
+        const measurements = this.measurements.get(name);
+        if (!measurements || measurements.length === 0) {
+            return null;
+        }
+        const avg = measurements.reduce((sum, val) => sum + val, 0) / measurements.length;
+        const min = Math.min(...measurements);
+        const max = Math.max(...measurements);
+        return { avg, min, max, count: measurements.length };
+    }
+    static reset() {
+        this.measurements.clear();
+    }
+    static logStatistics() {
+        for (const [name, measurements] of this.measurements.entries()) {
+            const stats = this.getStatistics(name);
+            if (stats) {
+                console.log(`${name}: avg=${stats.avg.toFixed(2)}ms, min=${stats.min.toFixed(2)}ms, max=${stats.max.toFixed(2)}ms, count=${stats.count}`);
+            }
+        }
+    }
+}
+FhirTestPerformance.measurements = new Map();
+//# sourceMappingURL=fhir-test-config.js.map

package/src/lib/functions/fhir-test-config.js.map

@@ -0,0 +1 @@
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package/src/lib/functions/normalize-fhir-bundle.function.d.ts

@@ -0,0 +1,3 @@
+import { IFhirBundle } from '../interfaces/fhir-resources.interface';
+import { INormalizedFhirData } from '../interfaces/fhir-normalized-tables.interface';
+export declare function normalizeFhirBundle(bundle: IFhirBundle): INormalizedFhirData;