Allow path-resource paths with a wildcard (#1427)

* Allow path-resource paths with wildcard to add deeply nested files

* Use what Node 16 knows

* Fix up tests

* Use what Node 18 knows

* Fix path separator and simplify logic

- Simplify logic when looking for one level and recurive directories
- Update comment to reflect new logic
- Use consitent / path separator in the path-resource parameter

* Allow parameters list to be empty in config

.github/workflows/ci-workflow.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        node-version: [16, 18]
+        node-version: [18, 20]
 
     steps:
     - uses: actions/checkout@v1

src/ig/IGExporter.ts

@@ -942,8 +942,8 @@ export class IGExporter {
    * capabilities, extensions, models, operations, profiles, resources, vocabulary, examples
    * Based on: https://build.fhir.org/ig/FHIR/ig-guidance/using-templates.html#root.input
    *
-   * NOTE: This does not include files nested in subfolders in supported paths since the
-   * IG Exporter does not handle those well.
+   * NOTE: This only includes files nested in subfolders when specified in the path-resource
+   * parameter, which is based on how the IG Publisher works.
    *
    * This function has similar operation to addResources, and both should be
    * analyzed when making changes to either.
@@ -963,14 +963,23 @@ export class IGExporter {
     const predefinedResourcePaths = pathEnds.map(pathEnd =>
       path.join(this.inputPath, 'input', pathEnd)
     );
-    let pathResourceDirectories: string[];
+    const pathResourceDirectories: string[] = [];
     const pathResources = this.config.parameters
       ?.filter(parameter => parameter.value && parameter.code === 'path-resource')
       .map(parameter => parameter.value);
     if (pathResources) {
-      pathResourceDirectories = pathResources
-        .map(directoryPath => path.join(this.inputPath, directoryPath))
-        .filter(directoryPath => existsSync(directoryPath));
+      pathResources.forEach(directoryPath => {
+        const fullPath = path.join(this.inputPath, ...directoryPath.split('/'));
+        if (existsSync(fullPath)) {
+          pathResourceDirectories.push(fullPath);
+        } else if (directoryPath.endsWith('/*') && existsSync(fullPath.slice(0, -2))) {
+          pathResourceDirectories.push(
+            ...readdirSync(fullPath.slice(0, -2), { withFileTypes: true, recursive: true })
+              .filter(file => file.isDirectory())
+              .map(dir => path.join(dir.path, dir.name))
+          );
+        }
+      });
       if (pathResourceDirectories) predefinedResourcePaths.push(...pathResourceDirectories);
     }
     const deeplyNestedFiles: string[] = [];
@@ -987,7 +996,9 @@ export class IGExporter {
             path.dirname(file) !== dirPath &&
             !pathResourceDirectories?.includes(path.dirname(file))
           ) {
-            deeplyNestedFiles.push(file);
+            if (!deeplyNestedFiles.includes(file)) {
+              deeplyNestedFiles.push(file);
+            }
             continue;
           }
           const resourceJSON: InstanceDefinition = this.fhirDefs.getPredefinedResource(file);

src/import/importConfiguration.ts

@@ -748,7 +748,7 @@ function parseParameters(
   }
   if (yamlConfig.parameters) {
     for (const [code, values] of Object.entries(yamlConfig.parameters)) {
-      normalizeToArray(values).forEach(value => parameters.push({ code, value: `${value}` }));
+      normalizeToArray(values)?.forEach(value => parameters.push({ code, value: `${value}` }));
     }
   } else if (parameters.length === 0) {
     return; // return undefined rather than an empty []

test/ig/IGExporter.IG.test.ts

@@ -2921,7 +2921,7 @@ describe('IGExporter', () => {
       config.parameters = [];
       config.parameters.push({
         code: 'path-resource',
-        value: path.join('input', 'resources', 'path-resource-nest')
+        value: 'input/resources/path-resource-nest'
       });
       const pkg = new Package(config);
       exporter = new IGExporter(pkg, defs, path.resolve(fixtures));
@@ -2973,6 +2973,12 @@ describe('IGExporter', () => {
       );
       expect(warning).toInclude(path.join('nested1', 'StructureDefinition-MyTitlePatient.json'));
       expect(warning).toInclude(path.join('nested2', 'ValueSet-MyVS.json'));
+      expect(warning).toInclude(
+        path.join('path-resource-double-nest', 'john', 'Patient-John.json')
+      );
+      expect(warning).toInclude(
+        path.join('path-resource-double-nest', 'jack', 'examples', 'Patient-Jack.json')
+      );
       expect(warning).not.toInclude('Patient-BarPatient.json');
       expect(warning).not.toInclude('StructureDefinition-MyPatient.json');
     });
@@ -2989,10 +2995,63 @@ describe('IGExporter', () => {
       );
       expect(warning).toInclude(path.join('nested1', 'StructureDefinition-MyTitlePatient.json'));
       expect(warning).toInclude(path.join('nested2', 'ValueSet-MyVS.json'));
+      // path-resource-double-nest is not included in config
+      expect(warning).toInclude(
+        path.join('path-resource-double-nest', 'john', 'Patient-John.json')
+      );
+      expect(warning).toInclude(
+        path.join('path-resource-double-nest', 'jack', 'examples', 'Patient-Jack.json')
+      );
+      // path-resource-nest is included in config
       expect(warning).not.toInclude(
         path.join('path-resource-nest', 'StructureDefinition-MyCorrectlyNestedPatient.json')
       );
     });
+
+    it('should not warn on deeply nested resources that are included in the path-resource parameter with a directory and wildcard', () => {
+      const config = cloneDeep(minimalConfig);
+      config.parameters = [];
+      config.parameters.push({
+        code: 'path-resource',
+        value: 'input/resources/path-resource-double-nest/*'
+      });
+      const pkg = new Package(config);
+      exporter = new IGExporter(pkg, defs, path.resolve(fixtures));
+      exporter.export(tempOut);
+      expect(loggerSpy.getAllMessages('warn')).toHaveLength(1);
+      const warning = loggerSpy.getFirstMessage('warn');
+      expect(warning).not.toInclude(
+        path.join('path-resource-double-nest', 'john', 'Patient-John.json')
+      );
+      expect(warning).not.toInclude(
+        path.join('path-resource-double-nest', 'jack', 'examples', 'Patient-Jack.json')
+      );
+    });
+
+    it('should warn on deeply nested resources that are included in the path-resource parameter with a directory but NO wildcard', () => {
+      const config = cloneDeep(minimalConfig);
+      config.parameters = [];
+      config.parameters.push({
+        code: 'path-resource',
+        // NOTE: file path does not include the "*" portion (it just lists a directory), which is not sufficient
+        value: 'input/resources/path-resource-double-nest'
+      });
+      const pkg = new Package(config);
+      exporter = new IGExporter(pkg, defs, path.resolve(fixtures));
+      exporter.export(tempOut);
+      expect(loggerSpy.getAllMessages('warn')).toHaveLength(1);
+      const warning = loggerSpy.getFirstMessage('warn');
+      const warningLines = warning.split('\n');
+      const johnLine = warningLines.filter(w =>
+        w.includes(path.join('path-resource-double-nest', 'john', 'Patient-John.json'))
+      );
+      const jackLine = warningLines.filter(w =>
+        w.includes(path.join('path-resource-double-nest', 'john', 'Patient-John.json'))
+      );
+      // Check that both nested files are logged in the warning, but check that they're only there once
+      expect(johnLine).toHaveLength(1);
+      expect(jackLine).toHaveLength(1);
+    });
   });
 
   describe('#customized-ig-with-logical-model-example', () => {

test/ig/fixtures/customized-ig-with-nested-resources/input/resources/path-resource-double-nest/jack/examples/Patient-Jack.json

@@ -0,0 +1,13 @@
+{
+  "resourceType": "Patient",
+  "id": "Jack",
+  "name": [
+    {
+      "family": "Anyperson",
+      "given": [
+        "Jack",
+        "C."
+      ]
+    }
+  ]
+}

test/ig/fixtures/customized-ig-with-nested-resources/input/resources/path-resource-double-nest/john/Patient-John.json

@@ -0,0 +1,13 @@
+{
+  "resourceType": "Patient",
+  "id": "John",
+  "name": [
+    {
+      "family": "Anyperson",
+      "given": [
+        "John",
+        "B."
+      ]
+    }
+  ]
+}