@imranq2/fhirpatientsummary 0.0.1

package/LICENSE

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package/README.md

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+# FHIR Patient Summary Generator
+
+This project provides utilities to generate patient summaries from FHIR Bundles, including narrative generation and section extraction, following the International Patient Summary (IPS) specification.
+
+## Installation
+
+Clone the repository and install dependencies:
+
+```bash
+git clone <repo-url>
+cd fhir-patient-summary
+npm install
+```
+
+## Usage
+
+You can use the `ComprehensiveIPSCompositionBuilder` in your TypeScript or JavaScript project to generate an IPS-compliant FHIR Bundle. The builder supports both fluent section addition and a convenient `read_bundle()` method to extract all supported sections from a FHIR Bundle.
+
+### Example: Using setPatient and addSection
+
+```typescript
+import { ComprehensiveIPSCompositionBuilder } from './src/generators/fhir_summary_generator';
+import { IPSSections } from './src/structures/ips_sections';
+
+const builder = new ComprehensiveIPSCompositionBuilder()
+  .setPatient(patientResource)
+  .addSection(IPSSections.ALLERGIES, allergiesArray, 'America/New_York')
+  .addSection(IPSSections.MEDICATIONS, medicationsArray, 'America/New_York')
+  .addSection(IPSSections.PROBLEMS, problemsArray, 'America/New_York')
+  .addSection(IPSSections.IMMUNIZATIONS, immunizationsArray, 'America/New_York');
+
+const bundle = builder.build_bundle(
+  'example-organization',
+  'Example Organization',
+  'https://fhir.icanbwell.com/4_0_0/',
+  'America/New_York'
+);
+console.log(JSON.stringify(bundle, null, 2));
+```
+
+### Example: Using read_bundle()
+
+```typescript
+import { ComprehensiveIPSCompositionBuilder } from './src/generators/fhir_summary_generator';
+import testBundle from './test/fhir-summary-bundle/fixtures/test-bundle.json';
+
+const patientResource = testBundle.entry.find(e => e.resource.resourceType === 'Patient').resource;
+const builder = new ComprehensiveIPSCompositionBuilder()
+  .setPatient(patientResource)
+  .read_bundle(testBundle, 'Europe/London');
+
+const bundle = builder.build_bundle(
+  'org-1',
+  'Example Hospital',
+  'https://example.com/fhir',
+  'Europe/London'
+);
+console.log(JSON.stringify(bundle, null, 2));
+```
+
+- Use `setPatient(patientResource)` to set the patient.
+- Use `addSection(sectionType, resources, timezone)` to add each IPS section, or use `read_bundle(fhirBundle, timezone)` to extract all supported sections from a FHIR Bundle.
+- Use `build_bundle` to generate the final FHIR Bundle.
+
+## Running Tests
+
+To run the test suite:
+
+```bash
+npm test
+```
+
+## Project Structure
+
+- `src/generators/`: Main logic for summary and narrative generation
+- `src/types/`: FHIR resource TypeScript types
+- `test/`: Test suites and FHIR bundle fixtures
+
+## License
+
+See [LICENSE](./LICENSE).

package/lib/src/generators/fhir_summary_generator.d.ts

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+import { TPatient } from "../types/resources/Patient";
+import { TCompositionSection } from "../types/partials/CompositionSection";
+import { TDomainResource } from "../types/resources/DomainResource";
+import { IPSSections } from "../structures/ips_sections";
+import { TBundle } from "../types/resources/Bundle";
+export declare class ComprehensiveIPSCompositionBuilder {
+    private patient;
+    private sections;
+    private mandatorySectionsAdded;
+    private resources;
+    /**
+     * sets the patient resource for the IPS Composition.
+     * This is not needed if you are calling read_bundle, but can be used to set the patient resource directly.
+     * @param patient - FHIR Patient resource to set
+     */
+    setPatient(patient: TPatient): this;
+    addSection<T extends TDomainResource>(sectionType: IPSSections, resources: T[], timezone: string | undefined, options?: {
+        isOptional?: boolean;
+        customLoincCode?: string;
+    }): this;
+    /**
+     * Reads a FHIR Bundle and extracts resources for each section defined in IPSSections.
+     * @param bundle - FHIR Bundle containing resources
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    read_bundle(bundle: TBundle, timezone: string | undefined): this;
+    /**
+     * Builds the final Composition sections, ensuring all mandatory sections are present.
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    build(timezone: string | undefined): TCompositionSection[];
+    /**
+     * Builds a complete FHIR Bundle containing the Composition and all resources.
+     * @param authorOrganizationId - ID of the authoring organization (e.g., hospital or clinic)
+     * @param authorOrganizationName - Name of the authoring organization
+     * @param baseUrl - Base URL for the FHIR server (e.g., 'https://example.com/fhir')
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    build_bundle(authorOrganizationId: string, authorOrganizationName: string, baseUrl: string, timezone: string | undefined): TBundle;
+    /**
+     * Creates a narrative for the composition based on the patient and sections.
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     * @private
+     */
+    private createCompositionNarrative;
+}

package/lib/src/generators/fhir_summary_generator.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ComprehensiveIPSCompositionBuilder = void 0;
+const ips_sections_1 = require("../structures/ips_sections");
+const ips_section_loinc_codes_1 = require("../structures/ips_section_loinc_codes");
+const ips_section_resource_map_1 = require("../structures/ips_section_resource_map");
+const narrative_generator_1 = require("./narrative_generator");
+class ComprehensiveIPSCompositionBuilder {
+    constructor() {
+        this.sections = [];
+        this.mandatorySectionsAdded = new Set();
+        this.resources = new Set();
+    }
+    /**
+     * sets the patient resource for the IPS Composition.
+     * This is not needed if you are calling read_bundle, but can be used to set the patient resource directly.
+     * @param patient - FHIR Patient resource to set
+     */
+    setPatient(patient) {
+        if (!patient || patient.resourceType !== 'Patient') {
+            throw new Error('Invalid Patient resource');
+        }
+        this.patient = patient;
+        return this;
+    }
+    // Comprehensive method to add sections with validation
+    addSection(sectionType, resources, timezone, options) {
+        // Validate resources
+        const validResources = resources;
+        for (const resource of validResources) {
+            // Add resource to the internal set
+            this.resources.add(resource);
+        }
+        // Skip if no valid resources and not mandatory
+        if (validResources.length === 0) {
+            if (!(options === null || options === void 0 ? void 0 : options.isOptional)) {
+                throw new Error(`No valid resources for mandatory section: ${sectionType}`);
+            }
+            return this;
+        }
+        // Patient resource does not get a section, it is handled separately
+        if (sectionType !== ips_sections_1.IPSSections.PATIENT) {
+            // Create section entry
+            const narrative = narrative_generator_1.NarrativeGenerator.generateNarrative(sectionType, validResources, timezone);
+            const sectionEntry = {
+                title: ips_section_loinc_codes_1.IPS_SECTION_DISPLAY_NAMES[sectionType] || sectionType,
+                code: {
+                    coding: [{
+                            system: 'http://loinc.org',
+                            code: (options === null || options === void 0 ? void 0 : options.customLoincCode) || ips_section_loinc_codes_1.IPS_SECTION_LOINC_CODES[sectionType],
+                            display: ips_section_loinc_codes_1.IPS_SECTION_DISPLAY_NAMES[sectionType] || sectionType
+                        }],
+                    text: ips_section_loinc_codes_1.IPS_SECTION_DISPLAY_NAMES[sectionType] || sectionType
+                },
+                text: narrative,
+                entry: validResources.map(resource => ({
+                    reference: `${resource.resourceType}/${resource.id}`,
+                    display: resource.resourceType
+                }))
+            };
+            // Track mandatory sections
+            if (!(options === null || options === void 0 ? void 0 : options.isOptional)) {
+                this.mandatorySectionsAdded.add(sectionType);
+            }
+            this.sections.push(sectionEntry);
+        }
+        return this;
+    }
+    /**
+     * Reads a FHIR Bundle and extracts resources for each section defined in IPSSections.
+     * @param bundle - FHIR Bundle containing resources
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    read_bundle(bundle, timezone) {
+        if (!bundle.entry) {
+            return this;
+        }
+        // find the patient resource in the bundle
+        const patientEntry = bundle.entry.find(e => { var _a; return ((_a = e.resource) === null || _a === void 0 ? void 0 : _a.resourceType) === 'Patient'; });
+        if (!patientEntry || !patientEntry.resource) {
+            throw new Error('Patient resource not found in the bundle');
+        }
+        this.patient = patientEntry.resource;
+        // find resources for each section in IPSSections and add the section
+        for (const sectionType of Object.values(ips_sections_1.IPSSections)) {
+            const resourceTypesForSection = ips_section_resource_map_1.IPSSectionResourceHelper.getResourceTypesForSection(sectionType);
+            const customFilter = ips_section_resource_map_1.IPSSectionResourceHelper.getResourceFilterForSection(sectionType);
+            let resources = bundle.entry
+                .map(e => e.resource)
+                .filter(r => typeof (r === null || r === void 0 ? void 0 : r.resourceType) === 'string' && resourceTypesForSection.includes(r.resourceType));
+            if (customFilter) {
+                resources = resources.filter(customFilter);
+            }
+            if (resources.length > 0) {
+                this.addSection(sectionType, resources, timezone, { isOptional: true });
+            }
+        }
+        return this;
+    }
+    /**
+     * Builds the final Composition sections, ensuring all mandatory sections are present.
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    build(timezone) {
+        // Ensure all mandatory sections are present
+        const mandatorySections = [
+            ips_sections_1.IPSSections.ALLERGIES,
+            ips_sections_1.IPSSections.MEDICATIONS,
+            ips_sections_1.IPSSections.PROBLEMS,
+            ips_sections_1.IPSSections.IMMUNIZATIONS
+        ];
+        const missingMandatorySections = mandatorySections.filter(section => !this.mandatorySectionsAdded.has(section));
+        if (missingMandatorySections.length > 0) {
+            throw new Error(`Missing mandatory IPS sections: ${missingMandatorySections.join(', ')}`);
+        }
+        return this.sections;
+    }
+    /**
+     * Builds a complete FHIR Bundle containing the Composition and all resources.
+     * @param authorOrganizationId - ID of the authoring organization (e.g., hospital or clinic)
+     * @param authorOrganizationName - Name of the authoring organization
+     * @param baseUrl - Base URL for the FHIR server (e.g., 'https://example.com/fhir')
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     */
+    build_bundle(authorOrganizationId, authorOrganizationName, baseUrl, timezone) {
+        var _a, _b, _c;
+        if (baseUrl.endsWith('/')) {
+            baseUrl = baseUrl.slice(0, -1); // Remove trailing slash if present
+        }
+        if (!this.patient) {
+            throw new Error('Patient resource must be set before building the bundle');
+        }
+        // Create the Composition resource
+        const composition = {
+            id: `Composition-${this.patient.id}`,
+            resourceType: 'Composition',
+            status: 'final',
+            type: {
+                coding: [{
+                        system: 'http://loinc.org',
+                        code: '60591-5',
+                        display: 'Patient summary Document'
+                    }]
+            },
+            subject: {
+                reference: `Patient/${this.patient.id}`
+            },
+            author: [{
+                    reference: `Organization/${authorOrganizationId}`, // Assuming patient is also a practitioner for simplicity
+                    display: authorOrganizationName
+                }],
+            date: new Date().toISOString(),
+            title: 'International Patient Summary',
+            section: this.sections,
+            text: this.createCompositionNarrative(timezone)
+        };
+        // Create the bundle with proper document type
+        const bundle = {
+            resourceType: 'Bundle',
+            type: 'document',
+            timestamp: new Date().toISOString(),
+            identifier: {
+                "system": "urn:ietf:rfc:3986",
+                "value": "urn:uuid:4dcfd353-49fd-4ab0-b521-c8d57ced74d6"
+            },
+            entry: []
+        };
+        // Add Composition as first entry
+        (_a = bundle.entry) === null || _a === void 0 ? void 0 : _a.push({
+            fullUrl: `${baseUrl}/Composition/${composition.id}`,
+            resource: composition
+        });
+        // Add patient as second entry
+        (_b = bundle.entry) === null || _b === void 0 ? void 0 : _b.push({
+            fullUrl: `${baseUrl}/Patient/${this.patient.id}`,
+            resource: this.patient
+        });
+        // Extract and add all resources referenced in sections
+        this.resources.forEach(resource => {
+            var _a;
+            if (resource.resourceType !== "Patient") {
+                (_a = bundle.entry) === null || _a === void 0 ? void 0 : _a.push({
+                    fullUrl: `${baseUrl}/${resource.resourceType}/${resource.id}`,
+                    resource: resource
+                });
+            }
+        });
+        // add a bundle entry for Organization
+        (_c = bundle.entry) === null || _c === void 0 ? void 0 : _c.push({
+            fullUrl: `${baseUrl}/Organization/${authorOrganizationId}`,
+            resource: {
+                resourceType: 'Organization',
+                id: authorOrganizationId,
+                name: authorOrganizationName
+            }
+        });
+        return bundle;
+    }
+    /**
+     * Creates a narrative for the composition based on the patient and sections.
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     * @private
+     */
+    createCompositionNarrative(timezone) {
+        const patient = this.patient;
+        let fullNarrativeContent = "";
+        // generate narrative for the patient
+        const patientNarrative = narrative_generator_1.NarrativeGenerator.generateNarrativeContent(ips_sections_1.IPSSections.PATIENT, [patient], timezone);
+        fullNarrativeContent = fullNarrativeContent.concat(patientNarrative || '');
+        // now generate narrative for the sections and add to this narrative
+        for (const sectionType of Object.values(ips_sections_1.IPSSections)) {
+            const resourceTypesForSection = ips_section_resource_map_1.IPSSectionResourceHelper.getResourceTypesForSection(sectionType);
+            const allResources = Array.from(this.resources);
+            const resources = allResources
+                .filter(r => resourceTypesForSection.includes(r.resourceType));
+            if (resources.length > 0) {
+                const sectionNarrative = narrative_generator_1.NarrativeGenerator.generateNarrativeContent(sectionType, resources, timezone);
+                fullNarrativeContent = fullNarrativeContent.concat(sectionNarrative || '');
+            }
+        }
+        return {
+            status: 'generated',
+            div: narrative_generator_1.NarrativeGenerator.wrapInXhtml(fullNarrativeContent)
+        };
+    }
+}
+exports.ComprehensiveIPSCompositionBuilder = ComprehensiveIPSCompositionBuilder;

package/lib/src/generators/narrative_generator.d.ts

@@ -0,0 +1,40 @@
+import { TDomainResource } from "../types/resources/DomainResource";
+import { IPSSections } from "../structures/ips_sections";
+export interface Narrative {
+    status: 'generated' | 'extensions' | 'additional' | 'empty';
+    div: string;
+}
+/**
+ * Generates narrative content for FHIR resources using TypeScript templates
+ * Replaces the Nunjucks-based narrative generator
+ */
+export declare class NarrativeGenerator {
+    /**
+     * Generates narrative HTML content for a section
+     * @param section - IPS section type
+     * @param resources - Array of domain resources
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     * @returns Generated HTML content or undefined if no resources
+     */
+    static generateNarrativeContent<T extends TDomainResource>(section: IPSSections, resources: T[], timezone: string | undefined): string | undefined;
+    /**
+     * Creates a complete FHIR Narrative object
+     * @param content - HTML content
+     * @returns FHIR Narrative object
+     */
+    static createNarrative(content: string): Narrative;
+    /**
+     * Generates a complete FHIR Narrative object for a section
+     * @param section - IPS section type
+     * @param resources - Array of domain resources
+     * @param timezone - Optional timezone to use for date formatting (e.g., 'America/New_York', 'Europe/London')
+     * @returns FHIR Narrative object or undefined if no resources
+     */
+    static generateNarrative<T extends TDomainResource>(section: IPSSections, resources: T[], timezone: string | undefined): Narrative | undefined;
+    /**
+     * Wrap content in XHTML div with FHIR namespace
+     * @param content - HTML content to wrap
+     * @returns XHTML div string
+     */
+    static wrapInXhtml(content: string): string;
+}