Repository: FHIR/sushi
Pull request #100 (2020-01-17 19:44:59)

Populate the dependsOn in generated ImplementationGuide resource
In order to get the fields I needed to populate in the generated IG, I needed to access the IG JSON from the dependencies, so this was added to FHIRDefinitions.


Patch:
diff --git a/src/app.ts b/src/app.ts
index e704649..690d111 100644
--- a/src/app.ts
+++ b/src/app.ts
@@ -87,7 +87,7 @@ async function app() {
   // If ig-data exists, generate an IG, otherwise, generate resources only
   const igDataPath = path.resolve(input, 'ig-data');
   if (fs.existsSync(igDataPath)) {
-    const igExporter = new IGExporter(outPackage, igDataPath);
+    const igExporter = new IGExporter(outPackage, defs, igDataPath);
     igExporter.export(program.out);
   } else {
     for (const sd of [
diff --git a/src/fhirdefs/FHIRDefinitions.ts b/src/fhirdefs/FHIRDefinitions.ts
index 1e0a97f..9440193 100644
--- a/src/fhirdefs/FHIRDefinitions.ts
+++ b/src/fhirdefs/FHIRDefinitions.ts
@@ -8,6 +8,7 @@ export class FHIRDefinitions implements Fishable {
   private types: Map<string, any>;
   private valueSets: Map<string, any>;
   private codeSystems: Map<string, any>;
+  private implementationGuides: Map<string, any>;
   packages: string[];
 
   constructor() {
@@ -18,6 +19,7 @@ export class FHIRDefinitions implements Fishable {
     this.types = new Map();
     this.valueSets = new Map();
     this.codeSystems = new Map();
+    this.implementationGuides = new Map();
   }
 
   size(): number {
@@ -27,7 +29,8 @@ export class FHIRDefinitions implements Fishable {
       this.extensions.size +
       this.types.size +
       this.valueSets.size +
-      this.codeSystems.size
+      this.codeSystems.size +
+      this.implementationGuides.size
     );
   }
 
@@ -57,28 +60,36 @@ export class FHIRDefinitions implements Fishable {
     return cloneJsonMapValues(this.codeSystems);
   }
 
+  allImplementationGuides(): any[] {
+    return cloneJsonMapValues(this.implementationGuides);
+  }
+
   add(definition: any): void {
-    if (
-      definition.type === 'Extension' &&
-      definition.baseDefinition !== 'http://hl7.org/fhir/StructureDefinition/Element'
-    ) {
-      addDefinitionToMap(definition, this.extensions);
-    } else if (
-      definition.kind === 'primitive-type' ||
-      definition.kind === 'complex-type' ||
-      definition.kind === 'datatype'
-    ) {
-      addDefinitionToMap(definition, this.types);
-    } else if (definition.kind === 'resource') {
-      if (definition.derivation === 'constraint') {
-        addDefinitionToMap(definition, this.profiles);
-      } else {
-        addDefinitionToMap(definition, this.resources);
+    if (definition.resourceType === 'StructureDefinition') {
+      if (
+        definition.type === 'Extension' &&
+        definition.baseDefinition !== 'http://hl7.org/fhir/StructureDefinition/Element'
+      ) {
+        addDefinitionToMap(definition, this.extensions);
+      } else if (
+        definition.kind === 'primitive-type' ||
+        definition.kind === 'complex-type' ||
+        definition.kind === 'datatype'
+      ) {
+        addDefinitionToMap(definition, this.types);
+      } else if (definition.kind === 'resource') {
+        if (definition.derivation === 'constraint') {
+          addDefinitionToMap(definition, this.profiles);
+        } else {
+          addDefinitionToMap(definition, this.resources);
+        }
       }
     } else if (definition.resourceType === 'ValueSet') {
       addDefinitionToMap(definition, this.valueSets);
     } else if (definition.resourceType === 'CodeSystem') {
       addDefinitionToMap(definition, this.codeSystems);
+    } else if (definition.resourceType === 'ImplementationGuide') {
+      addDefinitionToMap(definition, this.implementationGuides);
     }
   }
 
diff --git a/src/ig/IGExporter.ts b/src/ig/IGExporter.ts
index 35cf4a0..4fe89ef 100644
--- a/src/ig/IGExporter.ts
+++ b/src/ig/IGExporter.ts
@@ -1,11 +1,12 @@
 import fs from 'fs-extra';
 import path from 'path';
 import ini from 'ini';
+import sortBy from 'lodash/sortBy';
 import { ensureDirSync, copySync, outputJSONSync, outputFileSync } from 'fs-extra';
 import { Package } from '../export';
 import { ContactDetail, ImplementationGuide } from '../fhirtypes';
 import { logger } from '../utils/FSHLogger';
-import sortBy from 'lodash/sortBy';
+import { FHIRDefinitions } from '../fhirdefs';
 
 /**
  * The IG Exporter exports the FSH artifacts into a file structure supported by the IG Publisher.
@@ -16,7 +17,11 @@ import sortBy from 'lodash/sortBy';
  */
 export class IGExporter {
   private ig: ImplementationGuide;
-  constructor(public readonly pkg: Package, public readonly igDataPath: string) {}
+  constructor(
+    private readonly pkg: Package,
+    private readonly fhirDefs: FHIRDefinitions,
+    private readonly igDataPath: string
+  ) {}
 
   /**
    * Export the IG structure to the location specified by the outPath argument
@@ -72,6 +77,7 @@ export class IGExporter {
       packageId: config.name,
       license: config.license,
       fhirVersion: ['4.0.1'],
+      dependsOn: [],
       definition: {
         resource: [],
         page: {
@@ -88,6 +94,29 @@ export class IGExporter {
         }
       }
     };
+
+    // Add the dependencies
+    if (this.pkg.config.dependencies) {
+      const igs = this.fhirDefs.allImplementationGuides();
+      for (const key of Object.keys(this.pkg.config.dependencies)) {
+        if (key === 'hl7.fhir.r4.core') {
+          continue;
+        }
+        const depIG = igs.find(
+          ig => ig.packageId === key && ig.version == this.pkg.config.dependencies[key]
+        );
+        if (depIG) {
+          this.ig.dependsOn.push({
+            uri: `${depIG.url}|${depIG.version}`,
+            packageId: depIG.packageId,
+            version: depIG.version
+          });
+        }
+      }
+      if (this.ig.dependsOn.length === 0) {
+        delete this.ig.dependsOn;
+      }
+    }
   }
 
   /**


Test patch:
diff --git a/test/export/StructureDefinitionExporter.test.ts b/test/export/StructureDefinitionExporter.test.ts
index 08d818a..d0960a0 100644
--- a/test/export/StructureDefinitionExporter.test.ts
+++ b/test/export/StructureDefinitionExporter.test.ts
@@ -21,7 +21,6 @@ import {
 import { loggerSpy, TestFisher } from '../testhelpers';
 import { ElementDefinitionType } from '../../src/fhirtypes';
 import path from 'path';
-import { logger } from '../../src/utils';
 import { withDebugLogging } from '../testhelpers/withDebugLogging';
 
 describe('StructureDefinitionExporter', () => {
diff --git a/test/ig/IGExporter.test.ts b/test/ig/IGExporter.test.ts
index c1fbe9c..78e4e29 100644
--- a/test/ig/IGExporter.test.ts
+++ b/test/ig/IGExporter.test.ts
@@ -7,6 +7,7 @@ import { StructureDefinition, InstanceDefinition, CodeSystem } from '../../src/f
 import { Package } from '../../src/export';
 import { Config } from '../../src/fshtypes';
 import { loggerSpy } from '../testhelpers/loggerSpy';
+import { FHIRDefinitions, loadFromPath } from '../../src/fhirdefs';
 
 describe('IGExporter', () => {
   // Track temp files/folders for cleanup
@@ -18,6 +19,12 @@ describe('IGExporter', () => {
     let tempOut: string;
 
     beforeAll(() => {
+      const defs = new FHIRDefinitions();
+      loadFromPath(
+        path.join(__dirname, '..', 'testhelpers', 'testdefs', 'package'),
+        'testPackage',
+        defs
+      );
       const fixtures = path.join(__dirname, 'fixtures', 'simple-ig');
       const config: Config = fs.readJSONSync(path.join(fixtures, 'package.json'));
       pkg = new Package(config);
@@ -47,7 +54,7 @@ describe('IGExporter', () => {
       codeSystemDef.description = 'A code system description';
       pkg.codeSystems.push(codeSystemDef);
 
-      exporter = new IGExporter(pkg, path.resolve(fixtures, 'ig-data'));
+      exporter = new IGExporter(pkg, defs, path.resolve(fixtures, 'ig-data'));
       tempOut = temp.mkdirSync('sushi-test');
       // No need to regenerate the IG on every test -- generate it once and inspect what you
       // need to in the tests
@@ -138,6 +145,13 @@ describe('IGExporter', () => {
         packageId: 'sushi-test',
         license: 'CC0-1.0',
         fhirVersion: ['4.0.1'],
+        dependsOn: [
+          {
+            uri: 'http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core|3.1.0',
+            packageId: 'hl7.fhir.us.core',
+            version: '3.1.0'
+          }
+        ],
         definition: {
           resource: [
             {
@@ -254,7 +268,7 @@ describe('IGExporter', () => {
       const fixtures = path.join(__dirname, 'fixtures', 'customized-ig');
       const config: Config = fs.readJSONSync(path.join(fixtures, 'package.json'));
       pkg = new Package(config);
-      exporter = new IGExporter(pkg, path.resolve(fixtures, 'ig-data'));
+      exporter = new IGExporter(pkg, new FHIRDefinitions(), path.resolve(fixtures, 'ig-data'));
       tempOut = temp.mkdirSync('sushi-test');
       // No need to regenerate the IG on every test -- generate it once and inspect what you
       // need to in the tests
@@ -340,7 +354,7 @@ describe('IGExporter', () => {
       const fixtures = path.join(__dirname, 'fixtures', 'invalid-data-ig');
       const config: Config = fs.readJSONSync(path.join(fixtures, 'package.json'));
       pkg = new Package(config);
-      exporter = new IGExporter(pkg, path.resolve(fixtures, 'ig-data'));
+      exporter = new IGExporter(pkg, new FHIRDefinitions(), path.resolve(fixtures, 'ig-data'));
       tempOut = temp.mkdirSync('sushi-test');
       // No need to regenerate the IG on every test -- generate it once and inspect what you
       // need to in the tests
diff --git a/test/ig/fixtures/simple-ig/package.json b/test/ig/fixtures/simple-ig/package.json
index b9a1a0f..26afaa2 100644
--- a/test/ig/fixtures/simple-ig/package.json
+++ b/test/ig/fixtures/simple-ig/package.json
@@ -6,7 +6,8 @@
   "title" : "FSH Test IG",
   "description": "Provides a simple example of how FSH can be used to create an IG",
   "dependencies": {
-     "hl7.fhir.core": "4.0.1"
+     "hl7.fhir.core": "4.0.1",
+     "hl7.fhir.us.core": "3.1.0"
   },
   "language": "en",
   "author": "James Tuna",
diff --git a/test/testhelpers/testdefs/package/ImplementationGuide-hl7.fhir.us.core.json b/test/testhelpers/testdefs/package/ImplementationGuide-hl7.fhir.us.core.json
new file mode 100644
index 0000000..653462d
--- /dev/null
+++ b/test/testhelpers/testdefs/package/ImplementationGuide-hl7.fhir.us.core.json
@@ -0,0 +1,1 @@
+{"resourceType":"ImplementationGuide","id":"hl7.fhir.us.core","text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>USCore</h2><p>The official URL for this implementation guide is: </p><pre>http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core</pre></div>"},"url":"http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core","version":"3.1.0","name":"USCore","title":"US Core","status":"active","date":"2019-11-06T12:37:38+11:00","publisher":"HL7 International - US Realm Steering Committee","contact":[{"telecom":[{"system":"url","value":"http://www.hl7.org/Special/committees/usrealm/index.cfm"}]}],"jurisdiction":[{"coding":[{"system":"urn:iso:std:iso:3166","code":"US","display":"United States of America"}]}],"copyright":"Used by permission of HL7 International, all rights reserved Creative Commons License","packageId":"hl7.fhir.us.core","license":"CC0-1.0","fhirVersion":["4.0.1"],"definition":{"grouping":[{"name":"base"}],"resource":[{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-urine-glucose.html"}],"reference":{"reference":"Observation/urine-glucose"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Procedure"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Procedure-rehab.html"}],"reference":{"reference":"Procedure/rehab"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"CareTeam"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"CareTeam-example.html"}],"reference":{"reference":"CareTeam/example"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-urine-leukocyte-esterase.html"}],"reference":{"reference":"Observation/urine-leukocyte-esterase"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Bundle"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Bundle-66c8856b-ba11-4876-8aa8-467aad8c11a2.html"}],"reference":{"reference":"Bundle/66c8856b-ba11-4876-8aa8-467aad8c11a2"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-urine-bilirubin.html"}],"reference":{"reference":"Observation/urine-bilirubin"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Condition"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Condition-hc1.html"}],"reference":{"reference":"Condition/hc1"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-urine-sediment.html"}],"reference":{"reference":"Observation/urine-sediment"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Immunization"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Immunization-imm-1.html"}],"reference":{"reference":"Immunization/imm-1"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-pediatric-wt-example.html"}],"reference":{"reference":"Observation/pediatric-wt-example"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Organization"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Organization-saint-luke-w-endpoint.html"}],"reference":{"reference":"Organization/saint-luke-w-endpoint"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-urine-ph.html"}],"reference":{"reference":"Observation/urine-ph"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Encounter"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Encounter-example-1.html"}],"reference":{"reference":"Encounter/example-1"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"DiagnosticReport"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"DiagnosticReport-chest-xray-report.html"}],"reference":{"reference":"DiagnosticReport/chest-xray-report"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Observation"},{"url":"http://hl7.org/fhir/StructureDefinition/implementationguide-page","valueUri":"Observation-serum-sodium.html"}],"reference":{"reference":"Observation/serum-sodium"},"exampleBoolean":true},{"extension":[{"url":"http://hl7.org/fhir/tools/StructureDefinition/resource-information","valueString":"Diagnosti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