Use new FPL API

package.json

@@ -73,10 +73,10 @@
     "diff": "^7.0.0",
     "diff2html": "^3.4.48",
     "fhir": "^4.12.0",
-    "fhir-package-loader": "^1.0.0",
+    "fhir-package-loader": "^2.0.1",
     "flat": "^5.0.2",
     "fs-extra": "^11.2.0",
-    "fsh-sushi": "^3.12.1",
+    "fsh-sushi": "^3.13.1",
     "ini": "^5.0.0",
     "lodash": "^4.17.21",
     "readline-sync": "^1.4.10",

src/api/FhirToFsh.ts

@@ -70,7 +70,9 @@ export async function fhirToFsh(
 
   // Set up the FHIRProcessor
   const lake = new LakeOfFHIR(docs);
+  await lake.prepareDefs();
   const defs = new FHIRDefinitions();
+  await defs.initialize();
   const fisher = new MasterFisher(lake, defs);
   const processor = new FHIRProcessor(lake, fisher);
 

src/app.ts

@@ -155,6 +155,7 @@ async function app() {
 
   // Load dependencies
   const defs = new FHIRDefinitions();
+  await defs.initialize();
 
   // Trim empty spaces from command line dependencies
   const dependencies = programOptions.dependency?.map((dep: string) => dep.trim());
@@ -197,7 +198,7 @@ async function app() {
     alias: programOptions.alias
   } as ProcessingOptions;
 
-  const processor = getFhirProcessor(inDir, defs, fileType);
+  const processor = await getFhirProcessor(inDir, defs, fileType);
   const config = processor.processConfig(dependencies, specifiedFHIRVersion);
 
   // Load dependencies from config for GoFSH processing

src/processor/FHIRProcessor.ts

@@ -16,14 +16,9 @@ import { InstanceProcessor } from './InstanceProcessor';
 export class FHIRProcessor {
   constructor(
     private readonly lake: LakeOfFHIR,
-    private readonly fisher?: MasterFisher,
+    private readonly fisher: MasterFisher,
     private readonly igPath: string = null
-  ) {
-    // If no fisher was passed in, just use the built-in lake fisher (usually for testing only)
-    if (fisher == null) {
-      fisher = new MasterFisher(lake);
-    }
-  }
+  ) {}
 
   getFisher(): MasterFisher {
     return this.fisher;

src/processor/LakeOfFHIR.ts

@@ -5,11 +5,16 @@ import { CONFORMANCE_AND_TERMINOLOGY_RESOURCES } from './InstanceProcessor';
 import { StructureDefinitionProcessor } from './StructureDefinitionProcessor';
 import { ValueSetProcessor } from './ValueSetProcessor';
 import { WildFHIR } from './WildFHIR';
-import { FHIRDefinitions, logger } from '../utils';
+import { FHIRDefinitions, logger, logMessage } from '../utils';
+import { InMemoryVirtualPackage } from 'fhir-package-loader';
 
 // Like FSHTank in SUSHI, but it doesn't contain FSH, it contains FHIR.  And who ever heard of a tank of FHIR?  But a lake of FHIR...
 export class LakeOfFHIR implements utils.Fishable {
-  constructor(public docs: WildFHIR[]) {}
+  readonly defs: FHIRDefinitions;
+
+  constructor(public docs: WildFHIR[]) {
+    this.defs = new FHIRDefinitions();
+  }
 
   /**
    * Gets all non-instance structure definitions (profiles, extensions, logicals, and resources) in the lake
@@ -111,32 +116,40 @@ export class LakeOfFHIR implements utils.Fishable {
     }
   }
 
+  async prepareDefs() {
+    this.assignMissingIds();
+    this.removeDuplicateDefinitions();
+    await this.defs.initialize();
+    const lakeMap = new Map<string, any>();
+    this.docs.forEach(wildFHIR => {
+      lakeMap.set(wildFHIR.path, wildFHIR.content);
+    });
+    const lakePackage = new InMemoryVirtualPackage(
+      { name: 'wild-fhir', version: '1.0.0' },
+      lakeMap,
+      {
+        log: (level: string, message: string) => {
+          logMessage(level, message);
+        }
+      }
+    );
+    return this.defs.loadVirtualPackage(lakePackage);
+  }
+
   fishForFHIR(item: string, ...types: utils.Type[]) {
-    // The simplest approach is just to re-use the FHIRDefinitions fisher.  But since this.docs can be modified by anyone at any time
-    // the only safe way to do this is by rebuilding a FHIRDefinitions object each time we need it.  If this becomes a performance
-    // concern, we can optimize it later -- but performance isn't a huge concern in GoFSH. Note also that this approach may need to be
-    // updated if we ever need to support fishing for Instances.
-    const defs = new FHIRDefinitions();
-    this.docs.forEach(d => defs.add(d.content));
-    return defs.fishForFHIR(item, ...types);
+    return this.defs.fishForFHIR(item, ...types);
   }
 
   fishForMetadata(item: string, ...types: utils.Type[]): utils.Metadata {
-    // The simplest approach is just to re-use the FHIRDefinitions fisher.  But since this.docs can be modified by anyone at any time
-    // the only safe way to do this is by rebuilding a FHIRDefinitions object each time we need it.  If this becomes a performance
-    // concern, we can optimize it later -- but performance isn't a huge concern in GoFSH. Note also that this approach may need to be
-    // updated if we ever need to support fishing for Instances.
-    const defs = new FHIRDefinitions();
-    this.docs.forEach(d => defs.add(d.content));
-    return defs.fishForMetadata(item, ...types);
+    return this.defs.fishForMetadata(item, ...types);
   }
 
   /**
    * Removes any definitions from this.docs that have the same resourceType and id as
    * a previous definition, as long as there is a defined id.
    * Logs an error when it finds a duplicate
    */
-  removeDuplicateDefinitions() {
+  private removeDuplicateDefinitions() {
     const dupPaths: string[] = [];
     this.docs = uniqWith(this.docs, (a, b) => {
       const isDuplicate =
@@ -165,7 +178,7 @@ export class LakeOfFHIR implements utils.Fishable {
    * If there is no name or if it is any other type of resource, we add a clearly generated id with a counter.
    * Log a warning if it finds any definitions without an id
    */
-  assignMissingIds() {
+  private assignMissingIds() {
     const createdIdPaths: string[] = [];
     let generatedId = 0;
     this.docs.forEach((d, index) => {

src/utils/FHIRDefinitions.ts

@@ -1,8 +1,12 @@
-import { FHIRDefinitions as BaseFHIRDefinitions, Type } from 'fhir-package-loader';
-import { utils } from 'fsh-sushi';
+import { utils, fhirdefs } from 'fsh-sushi';
+import { logMessage } from './GoFSHLogger';
 
-export class FHIRDefinitions extends BaseFHIRDefinitions implements utils.Fishable {
-  fishForMetadata(item: string, ...types: Type[]): utils.Metadata | undefined {
+export class FHIRDefinitions extends fhirdefs.FHIRDefinitions implements utils.Fishable {
+  constructor() {
+    super(undefined, undefined, { options: { log: logMessage } });
+  }
+
+  fishForMetadata(item: string, ...types: utils.Type[]): utils.Metadata | undefined {
     const result = this.fishForFHIR(item, ...types);
     if (result) {
       return {

src/utils/GoFSHLogger.ts

@@ -1,8 +1,14 @@
 import { createLogger, format, transports } from 'winston';
+import { TransformableInfo } from 'logform';
 import chalk from 'chalk';
 
 const { combine, printf } = format;
 
+interface LoggerInfo extends TransformableInfo {
+  file?: string;
+  location?: string;
+}
+
 const incrementCounts = format(info => {
   switch (info.level) {
     case 'info':
@@ -24,19 +30,19 @@ const incrementCounts = format(info => {
   return info;
 });
 
-const trackErrorsAndWarnings = format(info => {
+const trackErrorsAndWarnings = format((info: LoggerInfo) => {
   if (!errorsAndWarnings.shouldTrack) {
     return info;
   }
   if (info.level === 'error') {
     errorsAndWarnings.errors.push({
-      message: info.message,
+      message: info.message as string,
       location: info.location,
       input: info.file
     });
   } else if (info.level === 'warn') {
     errorsAndWarnings.warnings.push({
-      message: info.message,
+      message: info.message as string,
       location: info.location,
       input: info.file
     });

src/utils/MasterFisher.ts

@@ -9,8 +9,8 @@ import { FHIRDefinitions } from '../utils';
  */
 export class MasterFisher implements utils.Fishable {
   constructor(
-    public lakeOfFHIR = new LakeOfFHIR([]),
-    public external = new FHIRDefinitions()
+    public lakeOfFHIR: LakeOfFHIR,
+    public external?: FHIRDefinitions
   ) {}
 
   fishForStructureDefinition(item: string) {
@@ -31,13 +31,15 @@ export class MasterFisher implements utils.Fishable {
   }
 
   fishForFHIR(item: string, ...types: utils.Type[]) {
-    return this.lakeOfFHIR.fishForFHIR(item, ...types) ?? this.external.fishForFHIR(item, ...types);
+    return (
+      this.lakeOfFHIR.fishForFHIR(item, ...types) ?? this.external?.fishForFHIR(item, ...types)
+    );
   }
 
   fishForMetadata(item: string, ...types: utils.Type[]): utils.Metadata {
     return (
       this.lakeOfFHIR.fishForMetadata(item, ...types) ??
-      this.external.fishForMetadata(item, ...types)
+      this.external?.fishForMetadata(item, ...types)
     );
   }
 }

src/utils/Processing.ts

@@ -2,8 +2,7 @@ import fs from 'fs-extra';
 import path from 'path';
 import ini from 'ini';
 import readlineSync from 'readline-sync';
-import { mergeDependency } from 'fhir-package-loader';
-import { logger, logMessage } from './GoFSHLogger';
+import { logger } from './GoFSHLogger';
 import { fhirtypes, utils } from 'fsh-sushi';
 import {
   Package,
@@ -58,14 +57,14 @@ export function ensureOutputDir(output = path.join('.', 'gofsh')): string {
   return output;
 }
 
-export function getFhirProcessor(inDir: string, defs: FHIRDefinitions, fileType: string) {
+export async function getFhirProcessor(inDir: string, defs: FHIRDefinitions, fileType: string) {
   const lake = getLakeOfFHIR(inDir, fileType);
+  await lake.prepareDefs();
 
-  // Assign any missing ids where we can before filtering out duplicates so that all
-  // the definitions with the same resourceType without an id don't get filtered out.
-  lake.assignMissingIds();
-  lake.removeDuplicateDefinitions();
-
+  if (defs == null) {
+    defs = new FHIRDefinitions();
+  }
+  await defs.initialize();
   const igIniIgPath = getIgPathFromIgIni(inDir);
   const fisher = new MasterFisher(lake, defs);
   return new FHIRProcessor(lake, fisher, igIniIgPath);
@@ -131,20 +130,19 @@ export async function loadExternalDependencies(
     // @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));
+  await loadConfiguredDependencies(defs, allDependencies);
 }
 
-export function loadConfiguredDependencies(
+export async function loadConfiguredDependencies(
   defs: FHIRDefinitions,
   dependencies: string[] = []
-): Promise<FHIRDefinitions | void>[] {
+): Promise<FHIRDefinitions | void> {
   // Automatically include FHIR R4 if no other versions of FHIR are already included
   if (!dependencies.some(dep => /hl7\.fhir\.r(4|5|4b|6)\.core/.test(dep))) {
     dependencies.push('hl7.fhir.r4.core@4.0.1');
   }
 
   // Load dependencies
-  const dependencyDefs: Promise<FHIRDefinitions | void>[] = [];
   for (const dep of dependencies) {
     const [packageId, version] = dep.split('@');
     if (version == null) {
@@ -154,17 +152,14 @@ export function loadConfiguredDependencies(
       );
       continue;
     }
-    dependencyDefs.push(
-      mergeDependency(packageId, version, defs, undefined, logMessage)
-        .then((def: FHIRDefinitions) => {
-          return def;
-        })
-        .catch(e => {
-          logger.error(`Failed to load ${dep}: ${e.message}`);
-        })
-    );
+    await defs.loadPackage(packageId, version).catch(e => {
+      logger.error(`Failed to load ${packageId}#${version}: ${e.message}`);
+      if (e.stack) {
+        logger.debug(e.stack);
+      }
+    });
   }
-  return dependencyDefs;
+  return defs;
 }
 
 export function getLakeOfFHIR(inDir: string, fileType: string): LakeOfFHIR {

test/api/FhirToFsh.test.ts

@@ -6,6 +6,7 @@ import { FHIRDefinitions, logger } from '../../src/utils';
 import { fhirToFsh, ResourceMap } from '../../src/api';
 import { loggerSpy } from '../helpers/loggerSpy';
 import { EOL } from 'os';
+import { InMemoryVirtualPackage } from 'fhir-package-loader';
 describe('fhirToFsh', () => {
   let loadSpy: jest.SpyInstance;
   let defaultConfig: fshtypes.Configuration;
@@ -37,9 +38,19 @@ describe('fhirToFsh', () => {
         'utf-8'
       )
     );
-    loadSpy = jest.spyOn(processing, 'loadExternalDependencies').mockImplementation(defs => {
-      defs.add(sd);
-      defs.add(patient);
+
+    loadSpy = jest.spyOn(processing, 'loadExternalDependencies').mockImplementation(async defs => {
+      const resourceMap: Map<string, any> = new Map();
+      resourceMap.set('StructureDefinition', sd);
+      resourceMap.set('Patient', patient);
+      const testPackage = new InMemoryVirtualPackage(
+        {
+          name: 'fhir-to-fsh-test',
+          version: '1.0.0'
+        },
+        resourceMap
+      );
+      await defs.loadVirtualPackage(testPackage);
       return Promise.resolve();
     });
     defaultConfig = {

test/extractor/CardRuleExtractor.test.ts

@@ -6,14 +6,15 @@ import { ExportableCardRule } from '../../src/exportable';
 import { ProcessableElementDefinition } from '../../src/processor';
 import { loadTestDefinitions } from '../helpers/loadTestDefinitions';
 import { FHIRDefinitions } from '../../src/utils';
+import '../helpers/loggerSpy'; // suppresses logs in test output
 
 describe('CardRuleExtractor', () => {
   let looseSD: any;
   let looseSDWithSlices: any;
   let looseSDWithInheritedSlices: any;
   let defs: FHIRDefinitions;
 
-  beforeAll(() => {
+  beforeAll(async () => {
     looseSD = JSON.parse(
       fs.readFileSync(path.join(__dirname, 'fixtures', 'card-profile.json'), 'utf-8').trim()
     );
@@ -30,7 +31,7 @@ describe('CardRuleExtractor', () => {
         )
         .trim()
     );
-    defs = loadTestDefinitions();
+    defs = await loadTestDefinitions();
   });
   describe('#process', () => {
     it('should extract a card rule with a min and a max', () => {

test/extractor/CaretValueRuleExtractor.test.ts

@@ -20,8 +20,8 @@ describe('CaretValueRuleExtractor', () => {
   let config: fshtypes.Configuration;
   let defs: FHIRDefinitions;
 
-  beforeAll(() => {
-    defs = loadTestDefinitions();
+  beforeAll(async () => {
+    defs = await loadTestDefinitions();
     config = {
       canonical: 'http://hl7.org/fhir/sushi-test',
       fhirVersion: ['4.0.1']

test/extractor/ContainsRuleExtractor.test.ts

@@ -15,11 +15,11 @@ describe('ContainsRuleExtractor', () => {
   let looseSD: any;
   let defs: FHIRDefinitions;
 
-  beforeAll(() => {
+  beforeAll(async () => {
     looseSD = JSON.parse(
       fs.readFileSync(path.join(__dirname, 'fixtures', 'contains-profile.json'), 'utf-8').trim()
     );
-    defs = loadTestDefinitions();
+    defs = await loadTestDefinitions();
   });
 
   it('should extract a ContainsRule with cardinality', () => {

test/extractor/InvariantExtractor.test.ts

@@ -13,8 +13,8 @@ describe('InvariantExtractor', () => {
   let defs: FHIRDefinitions;
   let looseSD: ProcessableStructureDefinition;
 
-  beforeAll(() => {
-    defs = loadTestDefinitions();
+  beforeAll(async () => {
+    defs = await loadTestDefinitions();
     looseSD = JSON.parse(
       fs.readFileSync(path.join(__dirname, 'fixtures', 'obeys-profile.json'), 'utf-8').trim()
     );