Merge branch 'master' of https://github.com/srdc/onfhir

docker/docker-entrypoint.sh

@@ -1,6 +1,13 @@
 #!/usr/bin/env bash
 
-JAVA_CMD="java -Xms256m -Xmx3g -jar "
+# Set default Java options
+DEFAULT_JAVA_OPTIONS="-Xms256m -Xmx3g"
+
+# Use environment variable if provided, otherwise use default value
+JAVA_OPTIONS="${JAVA_OPTIONS:-$DEFAULT_JAVA_OPTIONS}"
+
+# Construct JAVA_CMD with Java options
+JAVA_CMD="java $JAVA_OPTIONS -jar "
 
 # Configure application.conf path
 if [ ! -z "$APP_CONF_FILE" ]; then

onfhir-common/src/main/scala/io/onfhir/api/util/IOUtil.scala

@@ -20,9 +20,10 @@ object IOUtil {
 
   /**
    * Read a FHIR resource from given path or default path (within project resources)
-   * @param resourcePath    Given file path
-   * @param defaultPath     Default resource path (within project resources)
-   * @param rtype           Resource type
+   *
+   * @param resourcePath Given file path
+   * @param defaultPath  Default resource path (within project resources)
+   * @param rtype        Resource type
    * @return
    */
   def readResource(resourcePath: Option[String], defaultPath: String, rtype: String): Resource = {
@@ -43,7 +44,8 @@ object IOUtil {
 
   /**
    * Read a FHIR resource from given File path
-   * @param filePath  File path
+   *
+   * @param filePath File path
    * @return
    */
   def readResource(filePath: String): Resource = {
@@ -52,7 +54,8 @@ object IOUtil {
 
   /**
    * Read a FHIR resource from project resources with a path
-   * @param resourcePath  Resource path
+   *
+   * @param resourcePath Resource path
    * @return
    */
   def readInnerResource(resourcePath: String): Resource = {
@@ -93,7 +96,7 @@ object IOUtil {
           if (!givenFile.isDirectory)
             throw new InitializationException(s"Given path '$path' is not a folder or zip file ...")
           //Given as folder
-          getFilesFromFolder(folder = givenFile, withExtension = None, recursively = Some(true))
+          getFilesFromFolder(folder = givenFile, recursively = true, ignoreHidden = true, withExtension = None)
             .map(file => {
               try {
                 parseResource(new InputStreamReader(BOMInputStream.builder.setInputStream(new FileInputStream(file)).get()), file.getAbsolutePath)
@@ -120,19 +123,30 @@ object IOUtil {
    * Get the list of files from the given folder.
    *
    * @param folder        The folder to retrieve the files from.
+   * @param recursively   If true, the folder will be searched recursively to retrieve all files within.
+   * @param ignoreHidden  If true, hidden files and directories will be excluded from the result.
    * @param withExtension An optional extension (e.g., .json) if the files need to be filtered.
-   * @param recursively   If exists and true, the folder will be searched recursively to retrieve all files within.
-   * @return
+   * @return A sequence of files matching the criteria.
    */
-  def getFilesFromFolder(folder: File, withExtension: Option[String], recursively: Option[Boolean]): Seq[File] = {
+  def getFilesFromFolder(
+                          folder: File,
+                          recursively: Boolean,
+                          ignoreHidden: Boolean,
+                          withExtension: Option[String]
+                        ): Seq[File] = {
     if (folder.exists && folder.isDirectory) {
       val files = folder.listFiles().toSeq // List all available files in the given folder
+
+      // Filter hidden files if ignoreHidden is true
+      val nonHiddenFiles = if (ignoreHidden) files.filterNot(f => f.isHidden || f.getName.startsWith(".")) else files
+
       val filteredFiles = withExtension
-        .map(ext => files.filter(_.getName.endsWith(ext))).getOrElse(files)
+        .map(ext => nonHiddenFiles.filter(_.getName.endsWith(ext))).getOrElse(nonHiddenFiles)
         .filterNot(_.isDirectory)
-      if (recursively.contains(true)) {
-        val subFolders = files.filter(_.isDirectory)
-        filteredFiles ++ subFolders.flatMap(f => getFilesFromFolder(f, withExtension, recursively))
+
+      if (recursively) {
+        val subFolders = nonHiddenFiles.filter(_.isDirectory)
+        filteredFiles ++ subFolders.flatMap(f => getFilesFromFolder(f, recursively, ignoreHidden, withExtension))
       } else {
         filteredFiles
       }
@@ -141,8 +155,10 @@ object IOUtil {
     }
   }
 
+
   /**
    * Given a filename, removes its extension if an extension exists (e.g., admissions.json -> admissions)
+   *
    * @param fileName
    * @return
    */
@@ -254,8 +270,9 @@ object IOUtil {
 
   /**
    * Parse a JSON resource
-   * @param reader  Reader
-   * @param path  File path it is read from
+   *
+   * @param reader Reader
+   * @param path   File path it is read from
    * @return
    */
   private def parseResource(reader: Reader, path: String): Resource = {

onfhir-config/src/main/scala/io/onfhir/config/BaseFhirConfigurator.scala

@@ -54,7 +54,7 @@ abstract class BaseFhirConfigurator extends IFhirVersionConfigurator {
     //Get the parser for parsing FHIR foundation resources
     val foundationResourceParser = getFoundationResourceParser(fhirConfig.FHIR_COMPLEX_TYPES, fhirConfig.FHIR_PRIMITIVE_TYPES)
 
-    logger.info("Reading FHIR foundation resources to start configuration of onFhir server ...")
+    logger.info("Reading FHIR foundation resources to start configuration of onFHIR server ...")
     //Read the StructureDefinitions for all supported profiles
     val profileResources = configReader.getInfrastructureResources(FHIR_STRUCTURE_DEFINITION)
     //Read the ValueSet definitions to be used in this server (within the profiles)

onfhir-core/src/main/scala/io/onfhir/Onfhir.scala

@@ -136,7 +136,7 @@ class Onfhir(
               logger.info("OnFhir server is gracefully terminated...")
             case Failure(exception) => logger.error("Problem while gracefully terminating OnFhir server!", exception)
           }
-          logger.info("OnFhir FHIR server started on host {} and port {}", OnfhirConfig.serverHost, OnfhirConfig.serverPort)
+          logger.info("onFHIR FHIR server started on host {} and port {}", OnfhirConfig.serverHost, OnfhirConfig.serverPort)
           //Wait for a shutdown signal
           Await.ready(waitForShutdownSignal(), Duration.Inf)
           fhirServerBinding.terminate(FiniteDuration.apply(60L, TimeUnit.SECONDS))

onfhir-path/src/main/scala/io/onfhir/path/FhirPathAggFunctions.scala

@@ -142,7 +142,7 @@ class FhirPathAggFunctions(context:FhirPathEnvironment, current:Seq[FhirPathResu
       .flatMap(c => {
         val result = new FhirPathExpressionEvaluator(context, Seq(c)).visit(expr)
         if (result.length > 1)
-          throw new FhirPathException(s"Invalid function call 'min', the expression ${expr.getText} does not return a single value or Nil!")
+          throw new FhirPathException(s"Invalid function call 'max', the expression ${expr.getText} does not return a single value or Nil!")
         result.headOption
       })
 

pom.xml

@@ -113,7 +113,7 @@
         <akka.version>2.8.5</akka.version>
         <!--mongodb.scala.version>4.11.1</mongodb.scala.version-->
         <mongodb.scala.version>5.1.3</mongodb.scala.version>
-        <mongo.embedded.version>4.12.0</mongo.embedded.version>
+        <mongo.embedded.version>4.18.1</mongo.embedded.version>
         <json4s.version>3.7.0-M11</json4s.version>
         <scala.xml.version>2.2.0</scala.xml.version>
         <logback.version>1.4.14</logback.version>
@@ -122,9 +122,9 @@
         <specs2.version>4.20.4</specs2.version>
         <nimbus-jose.version>9.37.3</nimbus-jose.version>
         <nimbus-oidc.version>11.9.1</nimbus-oidc.version>
-        <apache-commons-lang.version>3.14.0</apache-commons-lang.version>
-        <apache-commons-io.version>2.15.1</apache-commons-io.version>
-        <apache-commons-text.version>1.11.0</apache-commons-text.version>
+        <apache-commons-lang.version>3.17.0</apache-commons-lang.version>
+        <apache-commons-io.version>2.18.0</apache-commons-io.version>
+        <apache-commons-text.version>1.13.0</apache-commons-text.version>
         <reflections.version>0.10.2</reflections.version>
 
         <!-- release plugin versions -->