Merge branch 'master' into engine-fhir-tests-improvements-7

cqframework · Oct 30, 2024 · b25912e · b25912e
2 parents 5c1b221 + 35668e9
commit b25912e
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Showing 79 changed files with 1,959 additions and 4,103 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -21,14 +21,23 @@ jobs:
       with:
         distribution: 'temurin'
         java-version: '21'
+        cache: gradle
+    - name: Cache SonarCloud packages
+      uses: actions/cache@v4
+      with:
+        path: ~/.sonar/cache
+        key: ${{ runner.os }}-sonar
+        restore-keys: ${{ runner.os }}-sonar
     - name: Setup Gradle
       uses: gradle/actions/setup-gradle@v3
     - name: Run Gradle Build
       working-directory: ./Src/java
-      run: ./gradlew check publish
+      run: ./gradlew check publish sonar
       env:
         OSSRH_USERNAME: ${{ vars.OSSRH_USERNAME }}
         OSSRH_TOKEN: ${{ secrets.OSSRH_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
     - name: Publish Test Report
       uses: mikepenz/action-junit-report@v4
       if: success() || failure() # always run even if the previous step fails

diff --git a/.github/workflows/check-pr.yml b/.github/workflows/check-pr.yml
@@ -23,11 +23,20 @@ jobs:
         distribution: 'temurin'
         java-version: '21'
         cache: gradle
+    - name: Cache SonarCloud packages
+      uses: actions/cache@v4
+      with:
+        path: ~/.sonar/cache
+        key: ${{ runner.os }}-sonar
+        restore-keys: ${{ runner.os }}-sonar
     - name: Setup Gradle
       uses: gradle/actions/setup-gradle@v3
     - name: Run Gradle Build
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       working-directory: ./Src/java
-      run: ./gradlew check -x spotlessCheck
+      run: ./gradlew check sonar -x spotlessCheck
     - name: Publish Test Report
       uses: mikepenz/action-junit-report@v4
       if: (success() || failure()) && matrix.os == 'ubuntu-latest'

diff --git a/Src/java/.sonarlint/connectedMode.json b/Src/java/.sonarlint/connectedMode.json
@@ -0,0 +1,4 @@
+{
+    "sonarCloudOrganization": "cqframework",
+    "projectKey": "cqframework_clinical_quality_language"
+}
diff --git a/Src/java/.vscode/settings.json b/Src/java/.vscode/settings.json
@@ -79,5 +79,9 @@
         ".git",
         "**/*.gradle",
         "**/test/resources/**"
-    ]
+    ],
+    "sonarlint.connectedMode.project": {
+        "connectionId": "cqframework",
+        "projectKey": "cqframework_clinical_quality_language"
+    }
 }
diff --git a/Src/java/build.gradle b/Src/java/build.gradle
@@ -1,6 +1,15 @@
 plugins {
     id 'idea'
     id 'eclipse'
+    id "org.sonarqube" version "4.4.1.3373"
+}
+
+sonar {
+  properties {
+    property "sonar.projectKey", "cqframework_clinical_quality_language"
+    property "sonar.organization", "cqframework"
+    property "sonar.host.url", "https://sonarcloud.io"
+  }
 }
 
 idea {

diff --git a/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmLibrarySourceProvider.java b/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmLibrarySourceProvider.java
@@ -6,7 +6,7 @@
 import java.util.List;
 import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.Library;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
@@ -15,16 +15,15 @@
  */
 public class NpmLibrarySourceProvider implements LibrarySourceProvider {
 
-    public NpmLibrarySourceProvider(
-            List<NpmPackage> packages, ILibraryReader reader, IWorkerContext.ILoggingService logger) {
+    public NpmLibrarySourceProvider(List<NpmPackage> packages, ILibraryReader reader, ILoggingService logger) {
         this.packages = packages;
         this.reader = reader;
         this.logger = logger;
     }
 
     private List<NpmPackage> packages;
     private ILibraryReader reader;
-    private IWorkerContext.ILoggingService logger;
+    private ILoggingService logger;
 
     @Override
     public InputStream getLibrarySource(VersionedIdentifier identifier) {
@@ -59,7 +58,7 @@ public InputStream getLibrarySource(VersionedIdentifier identifier) {
                 }
             } catch (IOException e) {
                 logger.logDebugMessage(
-                        IWorkerContext.ILoggingService.LogCategory.PROGRESS,
+                        ILoggingService.LogCategory.PROGRESS,
                         String.format(
                                 "Exceptions occurred attempting to load npm library source for %s",
                                 identifier.toString()));

diff --git a/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java b/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java
@@ -8,7 +8,7 @@
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.Library;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
@@ -17,16 +17,15 @@
  */
 public class NpmModelInfoProvider implements ModelInfoProvider {
 
-    public NpmModelInfoProvider(
-            List<NpmPackage> packages, ILibraryReader reader, IWorkerContext.ILoggingService logger) {
+    public NpmModelInfoProvider(List<NpmPackage> packages, ILibraryReader reader, ILoggingService logger) {
         this.packages = packages;
         this.reader = reader;
         this.logger = logger;
     }
 
     private List<NpmPackage> packages;
     private ILibraryReader reader;
-    private IWorkerContext.ILoggingService logger;
+    private ILoggingService logger;
 
     public ModelInfo load(ModelIdentifier modelIdentifier) {
         // VersionedIdentifier.id: Name of the model
@@ -60,7 +59,7 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
                 }
             } catch (IOException e) {
                 logger.logDebugMessage(
-                        IWorkerContext.ILoggingService.LogCategory.PROGRESS,
+                        ILoggingService.LogCategory.PROGRESS,
                         String.format(
                                 "Exceptions occurred attempting to load npm library for model %s",
                                 modelIdentifier.toString()));

diff --git a/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmPackageManager.java b/Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmPackageManager.java
@@ -4,15 +4,15 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class NpmPackageManager implements IWorkerContext.ILoggingService {
+public class NpmPackageManager implements ILoggingService {
     private static final Logger logger = LoggerFactory.getLogger(NpmPackageManager.class);
     private final ImplementationGuide sourceIg;
     private final FilesystemPackageCacheManager fspcm;
@@ -29,23 +29,10 @@ public NpmPackageManager(ImplementationGuide sourceIg, FilesystemPackageCacheMan
     public NpmPackageManager(
             ImplementationGuide sourceIg, FilesystemPackageCacheManager fspcm, List<NpmPackage> npmList) {
         this.sourceIg = sourceIg;
-
-        if (fspcm == null) {
-            try {
-                // userMode indicates whether the packageCache is within the working directory or in the user home
-                this.fspcm = new FilesystemPackageCacheManager(true);
-            } catch (IOException e) {
-                String message = "Error creating the FilesystemPackageCacheManager: " + e.getMessage();
-                logErrorMessage(message);
-                throw new NpmPackageManagerException(message, e);
-            }
-        } else {
-            this.fspcm = fspcm;
-        }
-
         this.npmList = npmList == null ? new ArrayList<>() : npmList;
 
         try {
+            this.fspcm = fspcm != null ? fspcm : new FilesystemPackageCacheManager.Builder().build();
             loadDependencies();
         } catch (Exception e) {
             logErrorMessage(e.getMessage());

diff --git a/Src/java/cqf-fhir-npm/src/test/java/org/cqframework/fhir/npm/NpmPackageManagerTests.java b/Src/java/cqf-fhir-npm/src/test/java/org/cqframework/fhir/npm/NpmPackageManagerTests.java
@@ -12,15 +12,15 @@
 import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
 import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
 import org.hl7.fhir.r4.model.Resource;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class NpmPackageManagerTests implements IWorkerContext.ILoggingService {
+public class NpmPackageManagerTests implements ILoggingService {
 
     private final Logger logger = LoggerFactory.getLogger(NpmPackageManagerTests.class);
     private final VersionConvertor_40_50 convertor = new VersionConvertor_40_50(new BaseAdvisor_40_50());
@@ -134,7 +134,7 @@ public void logMessage(String msg) {
     }
 
     @Override
-    public void logDebugMessage(IWorkerContext.ILoggingService.LogCategory category, String msg) {
+    public void logDebugMessage(ILoggingService.LogCategory category, String msg) {
         logMessage(msg);
     }
 

diff --git a/Src/java/cqf-fhir/src/main/java/org/cqframework/fhir/utilities/IGContext.java b/Src/java/cqf-fhir/src/main/java/org/cqframework/fhir/utilities/IGContext.java
@@ -9,7 +9,7 @@
 import org.hl7.fhir.convertors.conv30_50.VersionConvertor_30_50;
 import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.utilities.IniFile;
@@ -19,9 +19,9 @@
 
 public class IGContext {
 
-    private IWorkerContext.ILoggingService logger;
+    private ILoggingService logger;
 
-    public IWorkerContext.ILoggingService getLogger() {
+    public ILoggingService getLogger() {
         return logger;
     }
 
@@ -65,7 +65,7 @@ protected void setBinaryPaths(List<String> binaryPaths) {
         this.binaryPaths = binaryPaths;
     }
 
-    public IGContext(IWorkerContext.ILoggingService logger) {
+    public IGContext(ILoggingService logger) {
         this.logger = logger;
     }
 
@@ -113,16 +113,17 @@ public void initializeFromIg(String rootDir, String igPath, String fhirVersion)
      * Initializes from an ig.ini file in the root directory
      */
     public void initializeFromIni(String iniFile) {
-        IniFile ini = new IniFile(new File(iniFile).getAbsolutePath());
-        String rootDir = Utilities.getDirectoryForFile(ini.getFileName());
-        String igPath = ini.getStringProperty("IG", "ig");
-        String specifiedFhirVersion = ini.getStringProperty("IG", "fhir-version");
-        if (specifiedFhirVersion == null || specifiedFhirVersion == "") {
-            logMessage("fhir-version was not specified in the ini file. Trying FHIR version 4.0.1");
-            specifiedFhirVersion = "4.0.1";
-        }
         try {
-            initializeFromIg(rootDir, igPath, specifiedFhirVersion);
+            IniFile ini = new IniFile(new File(iniFile).getAbsolutePath());
+            String iniDir = Utilities.getDirectoryForFile(ini.getFileName());
+            String igPath = ini.getStringProperty("IG", "ig");
+            String specifiedFhirVersion = ini.getStringProperty("IG", "fhir-version");
+            if (specifiedFhirVersion == null || specifiedFhirVersion == "") {
+                logMessage("fhir-version was not specified in the ini file. Trying FHIR version 4.0.1");
+                specifiedFhirVersion = "4.0.1";
+            }
+
+            initializeFromIg(iniDir, igPath, specifiedFhirVersion);
         } catch (Exception e) {
             String message = String.format(
                     "Exceptions occurred initializing refresh from ini file '%s':%s", iniFile, e.getMessage());

diff --git a/Src/java/cqf-fhir/src/main/java/org/cqframework/fhir/utilities/LoggerAdapter.java b/Src/java/cqf-fhir/src/main/java/org/cqframework/fhir/utilities/LoggerAdapter.java
@@ -1,9 +1,9 @@
 package org.cqframework.fhir.utilities;
 
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.slf4j.Logger;
 
-public class LoggerAdapter implements IWorkerContext.ILoggingService {
+public class LoggerAdapter implements ILoggingService {
     private Logger innerLogger;
 
     public LoggerAdapter(Logger innerLogger) {

diff --git a/Src/java/cqf-fhir/src/test/java/org/cqframework/fhir/utilities/TestIGContext.java b/Src/java/cqf-fhir/src/test/java/org/cqframework/fhir/utilities/TestIGContext.java
@@ -6,10 +6,10 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
-import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.junit.jupiter.api.Test;
 
-public class TestIGContext implements IWorkerContext.ILoggingService {
+public class TestIGContext implements ILoggingService {
 
     @Test
     void typesAndValuesIG() throws URISyntaxException {

diff --git a/Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/CqlCompiler.java b/Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/CqlCompiler.java
@@ -18,6 +18,7 @@
 import org.antlr.v4.runtime.tree.ParseTree;
 import org.cqframework.cql.cql2elm.elm.ElmEdit;
 import org.cqframework.cql.cql2elm.elm.ElmEditor;
+import org.cqframework.cql.cql2elm.elm.IElmEdit;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.cqframework.cql.cql2elm.preprocessor.CqlPreprocessor;
 import org.cqframework.cql.elm.IdObjectFactory;
@@ -234,7 +235,8 @@ public Library run(CharStream is) {
         var edits = allNonNull(
                 !options.contains(EnableAnnotations) ? ElmEdit.REMOVE_ANNOTATION : null,
                 !options.contains(EnableResultTypes) ? ElmEdit.REMOVE_RESULT_TYPE : null,
-                !options.contains(EnableLocators) ? ElmEdit.REMOVE_LOCATOR : null);
+                !options.contains(EnableLocators) ? ElmEdit.REMOVE_LOCATOR : null,
+                ElmEdit.REMOVE_CHOICE_TYPE_SPECIFIER_TYPE_IF_EMPTY);
 
         new ElmEditor(edits).edit(library);
 
@@ -248,7 +250,7 @@ public Library run(CharStream is) {
         return library;
     }
 
-    private List<ElmEdit> allNonNull(ElmEdit... ts) {
+    private List<IElmEdit> allNonNull(IElmEdit... ts) {
         return Arrays.stream(ts).filter(x -> x != null).collect(Collectors.toList());
     }
 }