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Refactor dependency loading operations
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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.
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@mint-thompson
mint-thompson committed Jul 18, 2023
1 parent f154fee commit 55feabf
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Showing 5 changed files with 98 additions and 87 deletions.
17 changes: 4 additions & 13 deletions src/api/FhirToFsh.ts
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Original file line number Diff line number Diff line change
@@ -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';
Expand Down Expand Up @@ -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);
Expand Down
23 changes: 4 additions & 19 deletions src/app.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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';
Expand Down Expand Up @@ -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 {
Expand Down
22 changes: 21 additions & 1 deletion src/utils/Processing.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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>[] {
Expand Down
48 changes: 1 addition & 47 deletions test/api/FhirToFsh.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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({
Expand Down
75 changes: 68 additions & 7 deletions test/utils/Processing.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ import {
ensureOutputDir,
getInputDir,
getResources,
loadExternalDependencies,
loadConfiguredDependencies,
writeFSH,
getIgPathFromIgIni,
getFhirProcessor,
Expand All @@ -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[] = [];
Expand All @@ -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();

Expand Down Expand Up @@ -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');
Expand All @@ -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');
Expand All @@ -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');
Expand All @@ -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');
Expand All @@ -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
Expand Down

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