Load the same automatic dependencies as SUSHI

src/api/FhirToFsh.ts

@@ -1,14 +1,13 @@
-import { fhirtypes, fshtypes, utils } from 'fsh-sushi';
+import { fshtypes, utils } from 'fsh-sushi';
 import {
-  determineCorePackageId,
   FHIRDefinitions,
   getResources,
   isProcessableContent,
-  loadExternalDependencies,
   MasterFisher,
   logger,
   errorsAndWarnings,
-  ErrorsAndWarnings
+  ErrorsAndWarnings,
+  loadExternalDependencies
 } from '../utils';
 import { FHIRProcessor, LakeOfFHIR, WildFHIR } from '../processor';
 import { FSHExporter } from '../export';
@@ -81,15 +80,7 @@ export async function fhirToFsh(
   );
 
   // Load dependencies, including those inferred from an IG file, and those given as input
-  const dependencies =
-    configuration.config.dependencies?.map(
-      (dep: fhirtypes.ImplementationGuideDependsOn) => `${dep.packageId}@${dep.version}`
-    ) ?? [];
-  const fhirPackageId = determineCorePackageId(configuration.config.fhirVersion[0]);
-  if (!dependencies.includes(`${fhirPackageId}@${configuration.config.fhirVersion[0]}`)) {
-    dependencies.push(`${fhirPackageId}@${configuration.config.fhirVersion[0]}`);
-  }
-  await Promise.all(loadExternalDependencies(defs, dependencies));
+  await loadExternalDependencies(defs, configuration);
 
   // Process the FHIR to rules, and then export to FSH
   const pkg = await getResources(processor, configuration, processingOptions);

src/app.ts

@@ -5,22 +5,21 @@ import fs from 'fs-extra';
 import program from 'commander';
 import chalk from 'chalk';
 import { pad, padStart, padEnd } from 'lodash';
-import { fhirtypes, utils } from 'fsh-sushi';
+import { utils } from 'fsh-sushi';
 import {
-  determineCorePackageId,
   ensureOutputDir,
   FHIRDefinitions,
   getInputDir,
   getAliasFile,
   getFhirProcessor,
   getResources,
-  loadExternalDependencies,
   writeFSH,
   logger,
   stats,
   fshingTrip,
   getRandomPun,
-  ProcessingOptions
+  ProcessingOptions,
+  loadExternalDependencies
 } from './utils';
 import { Package, AliasProcessor } from './processor';
 import { ExportableAlias } from './exportable';
@@ -202,21 +201,7 @@ async function app() {
   const config = processor.processConfig(dependencies, specifiedFHIRVersion);
 
   // Load dependencies from config for GoFSH processing
-  const allDependencies =
-    config.config.dependencies?.map(
-      (dep: fhirtypes.ImplementationGuideDependsOn) => `${dep.packageId}@${dep.version}`
-    ) ?? [];
-  const fhirPackageId = determineCorePackageId(config.config.fhirVersion[0]);
-  allDependencies.push(`${fhirPackageId}@${config.config.fhirVersion[0]}`);
-  await utils.loadAutomaticDependencies(
-    config.config.fhirVersion[0],
-    config.config.dependencies ?? [],
-    // @ts-ignore TODO: this can be removed once SUSHI changes the type signature for this function to use FPL's FHIRDefinitions type
-    defs
-  );
-  const dependencyDefs = loadExternalDependencies(defs, allDependencies);
-
-  await Promise.all(dependencyDefs);
+  await loadExternalDependencies(defs, config);
 
   let pkg: Package;
   try {

src/utils/Processing.ts

@@ -4,6 +4,7 @@ import ini from 'ini';
 import readlineSync from 'readline-sync';
 import { mergeDependency } from 'fhir-package-loader';
 import { logger, logMessage } from './GoFSHLogger';
+import { fhirtypes, utils } from 'fsh-sushi';
 import {
   Package,
   FHIRProcessor,
@@ -112,7 +113,26 @@ export function writeFSH(resources: Package, outDir: string, style: string): voi
   }
 }
 
-export function loadExternalDependencies(
+export async function loadExternalDependencies(
+  defs: FHIRDefinitions,
+  config: ExportableConfiguration
+) {
+  const allDependencies =
+    config.config.dependencies?.map(
+      (dep: fhirtypes.ImplementationGuideDependsOn) => `${dep.packageId}@${dep.version}`
+    ) ?? [];
+  const fhirPackageId = determineCorePackageId(config.config.fhirVersion[0]);
+  allDependencies.push(`${fhirPackageId}@${config.config.fhirVersion[0]}`);
+  await utils.loadAutomaticDependencies(
+    config.config.fhirVersion[0],
+    config.config.dependencies ?? [],
+    // @ts-ignore TODO: this can be removed once SUSHI changes the type signature for this function to use FPL's FHIRDefinitions type
+    defs
+  );
+  await Promise.all(loadConfiguredDependencies(defs, allDependencies));
+}
+
+export function loadConfiguredDependencies(
   defs: FHIRDefinitions,
   dependencies: string[] = []
 ): Promise<FHIRDefinitions | void>[] {

test/api/FhirToFsh.test.ts

@@ -40,7 +40,7 @@ describe('fhirToFsh', () => {
     loadSpy = jest.spyOn(processing, 'loadExternalDependencies').mockImplementation(defs => {
       defs.add(sd);
       defs.add(patient);
-      return [undefined];
+      return Promise.resolve();
     });
     defaultConfig = {
       FSHOnly: true,
@@ -111,52 +111,6 @@ describe('fhirToFsh', () => {
     expect(results.configuration).toEqual(defaultConfig);
   });
 
-  it('should load dependencies from user input', async () => {
-    // Should be able to accept both # and @ style for dependencies
-    const results = await fhirToFsh([], {
-      dependencies: ['hl7.fhir.us.core#3.1.0', 'hl7.fhir.us.mcode@1.0.0']
-    });
-    expect(results.errors).toHaveLength(0);
-    expect(results.warnings).toHaveLength(1);
-    expect(results.warnings[0].message).toMatch('Could not determine FHIR version. Using 4.0.1.');
-    expect(results.fsh).toEqual('');
-    expect(results.configuration).toEqual({
-      ...defaultConfig,
-      dependencies: [
-        { packageId: 'hl7.fhir.us.core', version: '3.1.0' },
-        { packageId: 'hl7.fhir.us.mcode', version: '1.0.0' }
-      ]
-    });
-
-    expect(loadSpy.mock.calls).toHaveLength(1);
-    expect(loadSpy.mock.calls[0][1]).toEqual([
-      'hl7.fhir.us.core@3.1.0',
-      'hl7.fhir.us.mcode@1.0.0',
-      'hl7.fhir.r4.core@4.0.1'
-    ]);
-  });
-
-  it('should load FHIR R4B when specified in config fhirVersion', async () => {
-    // Loads R4B from fhirVersion
-    const results = await fhirToFsh([
-      JSON.stringify({
-        resourceType: 'StructureDefinition',
-        name: 'Foo',
-        baseDefinition: 'http://hl7.org/fhir/StructureDefinition/Patient',
-        derivation: 'constraint',
-        fhirVersion: '4.3.0' // FHIR R4B
-      })
-    ]);
-    expect(results.errors).toHaveLength(0);
-    expect(results.warnings).toHaveLength(0);
-    expect(results.configuration).toEqual({
-      ...defaultConfig,
-      fhirVersion: ['4.3.0']
-    });
-    expect(loadSpy.mock.calls).toHaveLength(1);
-    expect(loadSpy.mock.calls[0][1]).toEqual(['hl7.fhir.r4b.core@4.3.0']);
-  });
-
   it('should parse a string input into JSON', async () => {
     const results = await fhirToFsh([
       JSON.stringify({

test/utils/Processing.test.ts

@@ -9,7 +9,7 @@ import {
   ensureOutputDir,
   getInputDir,
   getResources,
-  loadExternalDependencies,
+  loadConfiguredDependencies,
   writeFSH,
   getIgPathFromIgIni,
   getFhirProcessor,
@@ -25,7 +25,7 @@ import {
   ExportableProfile,
   ExportableAssignmentRule
 } from '../../src/exportable';
-import { FHIRDefinitions } from '../../src/utils';
+import { FHIRDefinitions, loadExternalDependencies } from '../../src/utils';
 import * as loadOptimizers from '../../src/optimizer/loadOptimizers';
 
 let loadedPackages: string[] = [];
@@ -51,6 +51,22 @@ jest.mock('fhir-package-loader', () => {
   return newStyle;
 });
 
+jest.mock('fsh-sushi', () => {
+  const original = jest.requireActual('fsh-sushi');
+  const newStyle = {
+    ...original,
+    utils: {
+      ...original.utils,
+      loadAutomaticDependencies: jest.fn(async () => {
+        // this is just one of the usual automatic depencies, as an example
+        loadedPackages.push('hl7.terminology.r4#1.0.0');
+        return Promise.resolve();
+      })
+    }
+  };
+  return newStyle;
+});
+
 describe('Processing', () => {
   temp.track();
 
@@ -527,10 +543,55 @@ describe('Processing', () => {
       loadedPackages = [];
     });
 
+    it('should load automatic and configured dependencies', async () => {
+      const config = new ExportableConfiguration({
+        FSHOnly: true,
+        canonical: 'http://example.org',
+        fhirVersion: ['4.0.1'],
+        id: 'example',
+        name: 'Example',
+        applyExtensionMetadataToRoot: false,
+        dependencies: [{ packageId: 'hl7.fhir.us.core', version: '3.1.0' }]
+      });
+      const defs = new FHIRDefinitions();
+      await loadExternalDependencies(defs, config);
+      expect(loadedPackages).toHaveLength(3);
+      expect(loadedPackages).toContain('hl7.fhir.r4.core#4.0.1');
+      expect(loadedPackages).toContain('hl7.fhir.us.core#3.1.0');
+      expect(loadedPackages).toContain('hl7.terminology.r4#1.0.0');
+      expect(loggerSpy.getAllMessages('error')).toHaveLength(0);
+    });
+
+    it('should load FHIR R4B when specified in config fhirVersion', async () => {
+      const config = new ExportableConfiguration({
+        FSHOnly: true,
+        canonical: 'http://example.org',
+        fhirVersion: ['4.3.0'],
+        id: 'example',
+        name: 'Example',
+        applyExtensionMetadataToRoot: false,
+        dependencies: [{ packageId: 'hl7.fhir.us.core', version: '3.1.0' }]
+      });
+      const defs = new FHIRDefinitions();
+      await loadExternalDependencies(defs, config);
+      expect(loadedPackages).toHaveLength(3);
+      expect(loadedPackages).toContain('hl7.fhir.r4b.core#4.3.0');
+      expect(loadedPackages).toContain('hl7.fhir.us.core#3.1.0');
+      expect(loadedPackages).toContain('hl7.terminology.r4#1.0.0');
+      expect(loggerSpy.getAllMessages('error')).toHaveLength(0);
+    });
+  });
+
+  describe('loadConfiguredDependencies', () => {
+    beforeEach(() => {
+      loggerSpy.reset();
+      loadedPackages = [];
+    });
+
     it('should load specified dependencies', () => {
       const defs = new FHIRDefinitions();
       const dependencies = ['hl7.fhir.us.core@3.1.0'];
-      const dependencyDefs = loadExternalDependencies(defs, dependencies);
+      const dependencyDefs = loadConfiguredDependencies(defs, dependencies);
       return Promise.all(dependencyDefs).then(() => {
         expect(loadedPackages).toHaveLength(2);
         expect(loadedPackages).toContain('hl7.fhir.r4.core#4.0.1');
@@ -542,7 +603,7 @@ describe('Processing', () => {
     it('should log an error when it fails to load a dependency', () => {
       const defs = new FHIRDefinitions();
       const badDependencies = ['hl7.does.not.exist@current'];
-      const dependencyDefs = loadExternalDependencies(defs, badDependencies);
+      const dependencyDefs = loadConfiguredDependencies(defs, badDependencies);
       return Promise.all(dependencyDefs).then(() => {
         expect(loadedPackages).toHaveLength(1);
         expect(loadedPackages).toContain('hl7.fhir.r4.core#4.0.1');
@@ -556,7 +617,7 @@ describe('Processing', () => {
     it('should log an error when a dependency has no specified version', () => {
       const defs = new FHIRDefinitions();
       const badDependencies = ['hl7.fhir.us.core']; // No version
-      const dependencyDefs = loadExternalDependencies(defs, badDependencies);
+      const dependencyDefs = loadConfiguredDependencies(defs, badDependencies);
       return Promise.all(dependencyDefs).then(() => {
         expect(loadedPackages).toHaveLength(1);
         expect(loadedPackages).toContain('hl7.fhir.r4.core#4.0.1');
@@ -570,7 +631,7 @@ describe('Processing', () => {
     it('should load only FHIR if no dependencies specified', () => {
       const defs = new FHIRDefinitions();
       // No dependencies specified on CLI will pass in undefined
-      const dependencyDefs = loadExternalDependencies(defs, undefined);
+      const dependencyDefs = loadConfiguredDependencies(defs, undefined);
       return Promise.all(dependencyDefs).then(() => {
         expect(loadedPackages).toHaveLength(1);
         expect(loadedPackages).toContain('hl7.fhir.r4.core#4.0.1');
@@ -581,7 +642,7 @@ describe('Processing', () => {
     it('should load FHIR R4B if specified', () => {
       const defs = new FHIRDefinitions();
       const dependencies = ['hl7.fhir.r4b.core@4.3.0-snapshot1'];
-      const dependencyDefs = loadExternalDependencies(defs, dependencies);
+      const dependencyDefs = loadConfiguredDependencies(defs, dependencies);
       return Promise.all(dependencyDefs).then(() => {
         expect(loadedPackages).toHaveLength(1);
         expect(loadedPackages).toContain('hl7.fhir.r4b.core#4.3.0-snapshot1'); // Only contains r4b, doesn't load r4