Load the same automatic dependencies as SUSHI (#228)

* Load the same automatic dependencies as SUSHI Use SUSHI's function for loading automatic dependencies. There is a minor discrepancy in the expected type, but the FHIR definitions are only passed in so they can be passed to fhir-package-loader's mergeDependency function. So, the ts-ignore here should be safe. Add a note indicating the reason for the ts-ignore and the conditions under which it can be removed. * Refactor dependency loading operations All dependency loading is now handled by loadExternalDependencies. This function is used in both command-line and API modes. This function determines the core FHIR package, loads automatic dependencies (as defined by SUSHI), and loads configured dependencies. * Check for core package before adding it * Further update to FPL dependency
FHIR · Jul 25, 2023 · 5c8bec8 · 5c8bec8
1 parent 67472b7
commit 5c8bec8
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Showing 7 changed files with 270 additions and 85 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -73,7 +73,7 @@
     "diff": "^5.0.0",
     "diff2html": "^3.1.18",
     "fhir": "^4.10.0",
-    "fhir-package-loader": "^0.3.0",
+    "fhir-package-loader": "^0.5.0",
     "flat": "^5.0.2",
     "fs-extra": "^9.0.1",
     "fsh-sushi": "^3.1.0",

diff --git a/src/api/FhirToFsh.ts b/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);

diff --git a/src/app.ts b/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';
@@ -202,15 +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]}`);
-  const dependencyDefs = loadExternalDependencies(defs, allDependencies);
-
-  await Promise.all(dependencyDefs);
+  await loadExternalDependencies(defs, config);
 
   let pkg: Package;
   try {

diff --git a/src/utils/Processing.ts b/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 +113,28 @@ 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]);
+  if (!allDependencies.includes(`${fhirPackageId}@${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>[] {

diff --git a/test/api/FhirToFsh.test.ts b/test/api/FhirToFsh.test.ts
@@ -2,7 +2,7 @@ import fs from 'fs-extra';
 import path from 'path';
 import * as processing from '../../src/utils/Processing';
 import { fshtypes } from 'fsh-sushi';
-import { logger } from '../../src/utils';
+import { FHIRDefinitions, logger } from '../../src/utils';
 import { fhirToFsh, ResourceMap } from '../../src/api';
 import { loggerSpy } from '../helpers/loggerSpy';
 import { EOL } from 'os';
@@ -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,
@@ -111,50 +111,28 @@ 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([], {
+  it('should try to load external dependencies', async () => {
+    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(loadSpy).toHaveBeenCalledTimes(1);
+    expect(loadSpy).toHaveBeenCalledWith(
+      expect.any(FHIRDefinitions),
+      expect.objectContaining({
+        config: expect.objectContaining({
+          dependencies: [
+            {
+              packageId: 'hl7.fhir.us.core',
+              version: '3.1.0'
+            },
+            {
+              packageId: 'hl7.fhir.us.mcode',
+              version: '1.0.0'
+            }
+          ]
+        })
       })
-    ]);
-    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 () => {