[FHIR-Tools] [Bug fixes] Parse error at differential elements, VTL 2.0 syntax, special char in "short" field

.github/workflows/cd.yml

@@ -26,7 +26,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: wso2/open-healthcare-codegen-tool-framework
-          ref: v1.2.3
+          ref: v2.0.0
           path: './open-healthcare-codegen-tool-framework'
 
       - name: Setup Java and Maven

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: wso2/open-healthcare-codegen-tool-framework
-          ref: v1.2.3
+          ref: v2.0.0
           path: './open-healthcare-codegen-tool-framework'
 
       - name: Setup Maven

native/cds-bal-template/src/main/java/org/wso2/healthcare/cds/codegen/ballerina/tool/BallerinaCDSProjectConstants.java

@@ -30,12 +30,14 @@ public class BallerinaCDSProjectConstants {
     public static final String CONFIG = "config";
     public static final String PACKAGE = "package";
     public static final String DEPENDENCIES = "dependencies";
+    public static final String BASE_PACKAGE = "basePackage";
     public static final String DEPENDENT_PACKAGE = "dependentPackage";
     public static final String HOOKS = "hooks";
     public static final String CDS_SERVICES = "cds_services";
     public static final String META_CONFIG = "metaConfig";
     public static final String PROJECT_PACKAGE_ORG = "project.package.org";
     public static final String PROJECT_PACKAGE_VERSION = "project.package.version";
+    public static final String PROJECT_PACKAGE_BASE_PACKAGE = "project.package.basePackage";
     public static final String PROJECT_PACKAGE_DEPENDENT_PACKAGE = "project.package.dependentPackage";
     public static final String PROJECT_PACKAGE_NAME_PREFIX = "project.package.namePrefix";
     public static final String CMD_MESSAGE_OVERRIDE_OUTPUT_DIRECTORY = "Generated templates already exists. Do you want to overwrite? (y/n): ";

native/cds-bal-template/src/main/java/org/wso2/healthcare/cds/codegen/ballerina/tool/config/BallerinaCDSProjectToolConfig.java

@@ -43,7 +43,8 @@
 import static org.wso2.healthcare.cds.codegen.ballerina.tool.BallerinaCDSProjectConstants.PROJECT_PACKAGE_NAME_PREFIX;
 import static org.wso2.healthcare.cds.codegen.ballerina.tool.BallerinaCDSProjectConstants.PROJECT_PACKAGE_ORG;
 import static org.wso2.healthcare.cds.codegen.ballerina.tool.BallerinaCDSProjectConstants.PROJECT_PACKAGE_VERSION;
-
+import static org.wso2.healthcare.cds.codegen.ballerina.tool.BallerinaCDSProjectConstants.PROJECT_PACKAGE_BASE_PACKAGE;
+import static org.wso2.healthcare.cds.codegen.ballerina.tool.BallerinaCDSProjectConstants.BASE_PACKAGE;
 
 /**
  * Main config class to hold all the config objects.
@@ -53,6 +54,7 @@ public class BallerinaCDSProjectToolConfig extends AbstractToolConfig {
     private static final Log LOG = LogFactory.getLog(BallerinaCDSProjectToolConfig.class);
     private MetadataConfig metadataConfig;
     private final List<DependencyConfig> dependencyConfigs = new ArrayList<>();
+    private String basePackage;
     private String dependentPackage;
     private final List<CdsHook> cdsHooks = new ArrayList<>();
 
@@ -61,9 +63,16 @@ public void configure(ConfigType<?> configObj) throws CodeGenException {
         if (Constants.JSON_CONFIG_TYPE.equals(configObj.getType())) {
             JsonObject jsonConfigObj = ((JsonConfigType) configObj).getConfigObj();
             jsonConfigObj = jsonConfigObj.getAsJsonObject(CONFIG);
+
             this.metadataConfig = new MetadataConfig(jsonConfigObj.getAsJsonObject(PACKAGE));
             populateDependencyConfigs(jsonConfigObj.
                     getAsJsonArray(DEPENDENCIES));
+
+            if(jsonConfigObj.getAsJsonPrimitive((BASE_PACKAGE)) != null){
+                this.basePackage = jsonConfigObj
+                        .getAsJsonPrimitive(BASE_PACKAGE).getAsString();
+            }
+
             if (jsonConfigObj.getAsJsonPrimitive(DEPENDENT_PACKAGE) != null) {
                 this.dependentPackage = jsonConfigObj
                         .getAsJsonPrimitive(DEPENDENT_PACKAGE).getAsString();
@@ -95,6 +104,9 @@ public void overrideConfig(String jsonPath, JsonElement value) {
             case PROJECT_PACKAGE_NAME_PREFIX:
                 this.metadataConfig.setNamePrefix(value.getAsString());
                 break;
+            case PROJECT_PACKAGE_BASE_PACKAGE:
+                this.basePackage = value.getAsString();
+                break;
             case PROJECT_PACKAGE_DEPENDENT_PACKAGE:
                 this.dependentPackage = value.getAsString();
                 break;
@@ -121,6 +133,10 @@ public List<DependencyConfig> getDependencyConfigs() {
         return dependencyConfigs;
     }
 
+    public String getBasePackage() {
+        return basePackage;
+    }
+
     public String getDependentPackage() {
         return dependentPackage;
     }

native/cds-bal-template/src/main/java/org/wso2/healthcare/cds/codegen/ballerina/tool/generator/BallerinaCDSProjectGenerator.java

@@ -132,6 +132,6 @@ private String hookIdToCamelCase(String text) {
         StringBuilder textCopy = new StringBuilder(text);
         textCopy.setCharAt(ZERO, Character.toUpperCase(firstCharOfText));
         text = textCopy.toString();
-        return text.replaceAll(UNDERSCORE, "");
+        return text.replaceAll(UNDERSCORE, StringUtils.EMPTY);
     }
 }

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/BallerinaPackageGenTool.java

@@ -22,12 +22,13 @@
 import org.wso2.healthcare.codegen.tool.framework.commons.core.TemplateGenerator;
 import org.wso2.healthcare.codegen.tool.framework.commons.core.ToolContext;
 import org.wso2.healthcare.codegen.tool.framework.commons.exception.CodeGenException;
-import org.wso2.healthcare.codegen.tool.framework.fhir.core.model.FHIRDataTypeDef;
 import org.wso2.healthcare.fhir.ballerina.packagegen.tool.config.BallerinaPackageGenToolConfig;
-import org.wso2.healthcare.fhir.ballerina.packagegen.tool.modelgen.PackageContextGenerator;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.modelgen.PackageContextGeneratorFactory;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.modelgen.AbstractPackageContextGenerator;
 import org.wso2.healthcare.fhir.ballerina.packagegen.tool.templategen.PackageTemplateGenerator;
-import org.wso2.healthcare.codegen.tool.framework.fhir.core.common.FHIRSpecificationData;
 import org.wso2.healthcare.codegen.tool.framework.fhir.core.AbstractFHIRTool;
+import org.wso2.healthcare.codegen.tool.framework.fhir.core.common.FHIRSpecificationData;
+import org.wso2.healthcare.codegen.tool.framework.fhir.core.model.FHIRDataTypeDef;
 import org.wso2.healthcare.codegen.tool.framework.fhir.core.model.FHIRImplementationGuide;
 
 import java.util.HashMap;
@@ -37,7 +38,6 @@
  * Ballerina FHIR Package Generator Tool.
  */
 public class BallerinaPackageGenTool extends AbstractFHIRTool {
-
     private final Map<String, FHIRImplementationGuide> enabledIgs = new HashMap<>();
     private BallerinaPackageGenToolConfig packageGenToolConfig;
 
@@ -62,7 +62,8 @@ public TemplateGenerator execute(ToolContext toolContext) throws CodeGenExceptio
         if (packageGenToolConfig.isEnabled()) {
             String targetRoot = packageGenToolConfig.getTargetDir();
             Map<String, FHIRDataTypeDef> dataTypes = ((FHIRSpecificationData) toolContext.getSpecificationData()).getDataTypes();
-            PackageContextGenerator packageContextGenerator = new PackageContextGenerator(
+            AbstractPackageContextGenerator packageContextGenerator = PackageContextGeneratorFactory.getPackageContextGenerator(
+                    packageGenToolConfig.getPackageConfig().getFhirVersion(),
                     packageGenToolConfig,
                     enabledIgs, toolContext.getSpecificationData());
 

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/ToolConstants.java

@@ -38,6 +38,8 @@ public class ToolConstants {
     public static final String CONFIG_PACKAGE_DISTRIBUTION_TOML = "tools.config.package.ballerina_distribution";
     public static final String CONFIG_PACKAGE_AUTHORS = "authors";
     public static final String CONFIG_PACKAGE_AUTHORS_TOML = "tools.config.package.authors";
+    public static final String CONFIG_PACKAGE_FHIR_VERSION = "fhirVersion";
+    public static final String CONFIG_PACKAGE_FHIR_VERSION_TOML = "tools.config.packageConfig.fhirVersion";
     public static final String CONFIG_PACKAGE_REPOSITORY = "repository";
     public static final String CONFIG_PACKAGE_REPOSITORY_TOML = "tools.config.package.repository";
     public static final String CONFIG_BASE_PACKAGE = "basePackage";
@@ -69,6 +71,7 @@ public class ToolConstants {
     public static final String CONFIG_BALLERINA_KEYWORD_REPLACE = "replace";
     public static final String CONFIG_BALLERINA_KEYWORD_REPLACE_TOML = "tools.config.ballerina_keyword.replace";
     public static final String TEMPLATE_PATH = "templates";
+    public static final String TEMPLATE_VERSION_PATH = "versions";
     public static final String BAL_EXTENSION = ".bal";
     public static final String TOML_EXTENSION = ".toml";
     public static final String MD_EXTENSION = ".md";
@@ -84,7 +87,8 @@ public enum TokenPosition {
         MIDDLE,
         END
     }
-    public static final String FHIR_R4_DEFINITION_URL = "http://hl7.org/fhir/StructureDefinition";
+    public static final String FHIR_R4_DEFINITION_URL = "https://hl7.org/fhir/R4/structuredefinition.html";
+    public static final String FHIR_R5_DEFINITION_URL = "https://hl7.org/fhir/R5/structuredefinition.html";
     public static final String LICENSE_YEAR = String.valueOf(LocalDate.now().getYear());
     public static final String DATA_TYPE_EXTENSION = "Extension";
 

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/config/BallerinaPackageGenToolConfig.java

@@ -113,6 +113,15 @@ public void overrideConfig(String jsonPath, JsonElement value) {
             case "packageConfig.name.append":
                 this.packageConfig.setName(packageConfig.getName() + "." + value.getAsString());
                 break;
+            case "packageConfig.fhirVersion":
+                this.packageConfig.setFhirVersion(value.getAsString());
+                break;
+            case "packageConfig.repository":
+                this.packageConfig.setRepository(value.getAsString());
+                break;
+            case "packageConfig.basePackage":
+                this.packageConfig.setBasePackage(value.getAsString());
+                break;
             case "packageConfig.dependent.igs":
                 List<String> dependentIgList = new ArrayList<>();
                 for (JsonElement dependentIgJsonElement : value.getAsJsonArray()) {

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/config/PackageConfig.java

@@ -42,6 +42,7 @@ public class PackageConfig {
     private String version;
     private String ballerinaDistribution;
     private String authors;
+    private String fhirVersion;
     private String repository;
     private String basePackage;
     private List<DependencyConfig> dependencyConfigList;
@@ -53,6 +54,7 @@ public PackageConfig(JsonObject packageConfigJson) {
         this.version = packageConfigJson.getAsJsonPrimitive(ToolConstants.CONFIG_PACKAGE_VERSION).getAsString();
         this.ballerinaDistribution = packageConfigJson.getAsJsonPrimitive(ToolConstants.CONFIG_PACKAGE_DISTRIBUTION).getAsString();
         this.authors = packageConfigJson.getAsJsonArray(ToolConstants.CONFIG_PACKAGE_AUTHORS).getAsString();
+        this.fhirVersion = packageConfigJson.getAsJsonPrimitive(ToolConstants.CONFIG_PACKAGE_FHIR_VERSION).getAsString();
         this.repository = packageConfigJson.getAsJsonPrimitive(ToolConstants.CONFIG_PACKAGE_REPOSITORY).getAsString();
         this.basePackage = packageConfigJson.getAsJsonPrimitive(ToolConstants.CONFIG_BASE_PACKAGE).getAsString();
         populateDependencies(packageConfigJson.getAsJsonArray(ToolConstants.CONFIG_PACKAGE_DEPENDENCY).getAsJsonArray());
@@ -64,6 +66,7 @@ public PackageConfig(TomlTable packageConfigToml) {
         this.version = packageConfigToml.getString(ToolConstants.CONFIG_PACKAGE_VERSION_TOML);
         this.ballerinaDistribution = packageConfigToml.getString(ToolConstants.CONFIG_PACKAGE_DISTRIBUTION_TOML);
         this.authors = packageConfigToml.getString(ToolConstants.CONFIG_PACKAGE_AUTHORS_TOML);
+        this.fhirVersion = packageConfigToml.getString(ToolConstants.CONFIG_PACKAGE_FHIR_VERSION_TOML);
         this.repository = packageConfigToml.getString(ToolConstants.CONFIG_PACKAGE_REPOSITORY_TOML);
         this.basePackage = packageConfigToml.getString(ToolConstants.CONFIG_BASE_PACKAGE_TOML);
         populateDependencies(packageConfigToml.getArrayOrEmpty(ToolConstants.CONFIG_PACKAGE_DEPENDENCY_TOML));
@@ -106,6 +109,10 @@ public String getAuthors() {
         return authors;
     }
 
+    public String getFhirVersion() {
+        return fhirVersion;
+    }
+
     public String getRepository() {
         return repository;
     }
@@ -149,6 +156,10 @@ public void setBallerinaDistribution(String ballerinaDistribution) {
         this.ballerinaDistribution = ballerinaDistribution;
     }
 
+    public void setFhirVersion(String fhirVersion) {
+        this.fhirVersion = fhirVersion;
+    }
+
     public void setBasePackage(String basePackage) {
         this.basePackage = basePackage;
     }

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/model/DataTypeProfile.java

@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2023, WSO2 LLC. (http://www.wso2.com).
+ *
+ * WSO2 LLC. licenses this file to you under the Apache License,
+ * Version 2.0 (the "License"); you may not use this file except
+ * in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
 package org.wso2.healthcare.fhir.ballerina.packagegen.tool.model;
 
 /**

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/model/ExtendedElement.java

@@ -31,6 +31,10 @@ public class ExtendedElement {
     private DataTypeDefinitionAnnotation annotation;
     private HashMap<String, Element> elements;
 
+    // Store datatype of extended elements extended from a primitive type
+    // e.g: FHIR R5 EuropeBase --> patient.birthDate
+    private String primitiveExtendedType;
+
     public String getTypeName() {
         return typeName;
     }
@@ -91,4 +95,12 @@ public boolean equals(Object o) {
         }
         return false;
     }
+
+    public String getPrimitiveExtendedType() {
+        return primitiveExtendedType;
+    }
+
+    public void setPrimitiveExtendedType(String primitiveExtendedType) {
+        this.primitiveExtendedType = primitiveExtendedType;
+    }
 }

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/model/ResourceTemplateContext.java

@@ -18,8 +18,6 @@
 
 package org.wso2.healthcare.fhir.ballerina.packagegen.tool.model;
 
-import org.hl7.fhir.r4.model.ElementDefinition;
-
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -39,7 +37,7 @@ public class ResourceTemplateContext {
     private ResourceDefinitionAnnotation resourceDefinitionAnnotation;
     // This was added to check the cardinality discrepancies of slice elements against their base elements
     // Related issue: https://github.com/wso2-enterprise/open-healthcare/issues/1504
-    private HashMap<String, ElementDefinition> snapshotElementDefinitions = new HashMap<>();
+    private HashMap<String, Object> snapshotElementDefinitions = new HashMap<>();
     private HashMap<String, Element> snapshotElements = new HashMap<>();
     private List<String> differentialElementIds = new ArrayList<>();
     private HashMap<String, Element> resourceElements = new HashMap<>();
@@ -95,11 +93,11 @@ public void setResourceDefinitionAnnotation(ResourceDefinitionAnnotation resourc
         this.resourceDefinitionAnnotation = resourceDefinitionAnnotation;
     }
 
-    public HashMap<String, ElementDefinition> getSnapshotElementDefinitions() {
+    public HashMap<String, Object> getSnapshotElementDefinitions() {
         return snapshotElementDefinitions;
     }
 
-    public void setSnapshotElementDefinitions(HashMap<String, ElementDefinition> snapshotElementDefinitions) {
+    public void setSnapshotElementDefinitions(HashMap<String, Object> snapshotElementDefinitions) {
         this.snapshotElementDefinitions = snapshotElementDefinitions;
     }
 

native/fhir-to-bal-lib/src/main/java/org/wso2/healthcare/fhir/ballerina/packagegen/tool/modelgen/AbstractDatatypeContextGenerator.java

@@ -0,0 +1,88 @@
+/*
+ * Copyright (c) 2025, WSO2 LLC. (http://www.wso2.com).
+ *
+ * WSO2 LLC. licenses this file to you under the Apache License,
+ * Version 2.0 (the "License"); you may not use this file except
+ * in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.wso2.healthcare.fhir.ballerina.packagegen.tool.modelgen;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.wso2.healthcare.codegen.tool.framework.fhir.core.common.FHIRSpecificationData;
+import org.wso2.healthcare.codegen.tool.framework.fhir.core.model.FHIRDataTypeDef;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.model.BallerinaDataType;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.model.DatatypeTemplateContext;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.model.Element;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.model.ExtendedElement;
+import org.wso2.healthcare.fhir.ballerina.packagegen.tool.utils.GeneratorUtils;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Abstract class for generating context for FHIR data types.
+ * This class provides methods to populate and manage the context for FHIR data types.
+ * Extended by R4DatatypeContextGenerator and R5DatatypeContextGenerator
+ */
+
+public abstract class AbstractDatatypeContextGenerator {
+    private static final Log LOG = LogFactory.getLog(AbstractDatatypeContextGenerator.class);
+    private final Map<String, FHIRDataTypeDef> datatypeDefnMap;
+    private final Map<String, DatatypeTemplateContext> dataTypeTemplateContextMap;
+
+    public AbstractDatatypeContextGenerator(FHIRSpecificationData fhirSpecificationData) {
+        this.datatypeDefnMap = fhirSpecificationData.getDataTypes();
+        this.dataTypeTemplateContextMap = new HashMap<>();
+        populateDatatypeContext();
+    }
+
+    public Map<String, FHIRDataTypeDef> getDatatypeDefnMap() {
+        return datatypeDefnMap;
+    }
+
+    public Map<String, DatatypeTemplateContext> getDataTypeTemplateContextMap() {
+        return dataTypeTemplateContextMap;
+    }
+
+    protected Map<String, FHIRDataTypeDef> getDataTypeDefnMap() {
+        return datatypeDefnMap;
+    }
+
+    protected Map<String, DatatypeTemplateContext> datatypeTemplateContextMap() {
+        return dataTypeTemplateContextMap;
+    }
+
+    protected void populateExtendedElementsMap(Element element, DatatypeTemplateContext context) {
+        LOG.debug("Started: Resource Extended Element Map population");
+        if (!element.getDataType().equals("Extension")) {
+            if (element.hasChildElements()) {
+                for (Map.Entry<String, Element> childEntry : element.getChildElements().entrySet()) {
+                    populateExtendedElementsMap(childEntry.getValue(), context);
+                }
+            }
+            ExtendedElement extendedElement;
+            String elementDataType = element.getDataType();
+            if (elementDataType.equals("code") && element.hasChildElements()) {
+                extendedElement = GeneratorUtils.getInstance().populateExtendedElement(element, BallerinaDataType.Enum, elementDataType,
+                        context.getName());
+                context.getExtendedElements().putIfAbsent(element.getName(), extendedElement);
+                element.setExtended(true);
+            }
+        }
+        LOG.debug("Ended: Resource Extended Element Map population");
+    }
+
+    protected abstract void populateDatatypeContext();
+}