version 2.1.0 updated libraries

build.sbt

@@ -1,7 +1,7 @@
 lazy val commonSettings = Seq(
   organization := "org.bireme",
   version := "1.0.0",
-  scalaVersion := "2.13.3" //"2.12.8"  // org.scala-lang.modules:scala-xml _2.13, _2.12
+  scalaVersion := "2.13.10" //"2.12.8"  // org.scala-lang.modules:scala-xml _2.13, _2.12
 )
 
 lazy val root = (project in file(".")).
@@ -10,14 +10,14 @@ lazy val root = (project in file(".")).
     name := "BVS-InfoButton"
   )
 
-val akkaVersion = "10.1.12" //"10.1.9"
-val playJsonVersion = "2.9.0" //"2.8.1"
-val scalaXmlVersion = "1.3.0" //"1.2.0"
-val dom4jVersion = "2.1.3" //"2.1.1"
-val scalaLoggingVersion = "3.9.2" //"3.9.0"
-val logbackVersion = "1.2.3"
-val scalaTestVersion = "3.2.0" //"3.1.2"
-val luceneVersion = "8.6.0" //"8.5.1"
+val akkaVersion = "10.5.0" //"10.1.12"
+val playJsonVersion = "2.9.4" //"2.9.0"
+val scalaXmlVersion = "2.1.0" //"1.3.0"
+val dom4jVersion = "2.1.4" //"2.1.3"
+val scalaLoggingVersion = "3.9.5" //"3.9.2"
+val logbackVersion = "1.4.6" //"1.2.3"
+val scalaTestVersion = "3.2.15" //"3.2.0"
+val luceneVersion = "9.5.0" //"8.6.0"
 val scalajHttpVersion = "2.4.2" //"2.4.1"
 
 libraryDependencies ++= Seq(
@@ -31,24 +31,25 @@ libraryDependencies ++= Seq(
   "org.scalactic" %% "scalactic" % scalaTestVersion,
   "org.scalatest" %% "scalatest" % scalaTestVersion % "test",
   "org.apache.lucene" % "lucene-core" % luceneVersion,
-  "org.apache.lucene" % "lucene-analyzers-common" % luceneVersion,
+  "org.apache.lucene" % "lucene-analysis-common" % luceneVersion,
+  //"org.apache.lucene" % "lucene-analyzers-common" % luceneVersion,
   "org.apache.lucene" % "lucene-queryparser" % luceneVersion,
   "org.apache.lucene" % "lucene-queries" % luceneVersion,
   "org.apache.lucene" % "lucene-backward-codecs" % luceneVersion,
   "org.scalaj" %% "scalaj-http" % scalajHttpVersion
 )
 
-logBuffered in Test := false
+Test / logBuffered := false
 trapExit := false  // To allow System.exit() without an exception (TestIndex.scala)
 
 scalacOptions ++= Seq("-unchecked", "-deprecation", "-feature", "-Ywarn-unused")
 
-assemblyMergeStrategy in assembly := {
+assembly / assemblyMergeStrategy := {
   case "module-info.class" => MergeStrategy.first //MergeStrategy.discard
   case x =>
-    val oldStrategy = (assemblyMergeStrategy in assembly).value
+    val oldStrategy = (assembly / assemblyMergeStrategy).value
     oldStrategy(x)
 }
 
-test in assembly := {}
+assembly / test := {}
 

src/main/scala/org/bireme/infob/MeshConverter.scala

@@ -25,7 +25,7 @@ import scala.util.{Either, Left, Right}
   */
 class MeshConverter(indexes: String) {
   //"ICD9CM", "ICD10CM", "IDC10", "SNOMED-CT", "RXNORM"
-  val thesauri: Map[String, String] = Map(
+  private val thesauri: Map[String, String] = Map(
     "ICD9-CM" -> "ICD9-CM",
     "ICD10-CM" -> "ICD10-CM",
     "ICD10" -> "ICD10",
@@ -34,13 +34,13 @@ class MeshConverter(indexes: String) {
   )
 
   // Names of Lucene indexes to convert one thesaurus into another
-  val thes2thes: Map[String, String] = Map(
+  private val thes2thes: Map[String, String] = Map(
     "DeCS" -> s"$indexes/DeCS",
     "UMLS" -> s"$indexes/UMLS"
   )
 
   // Lucene index searchers to convert one system into another
-  val thes2thesSearchers: Map[String, IndexSearcher] = thes2thes.map {
+  private val thes2thesSearchers: Map[String, IndexSearcher] = thes2thes.map {
     case (k, v) =>
       val directory: FSDirectory = FSDirectory.open(new File(v).toPath)
       require(DirectoryReader.indexExists(directory))
@@ -49,7 +49,7 @@ class MeshConverter(indexes: String) {
       (k, new IndexSearcher(ireader))
   }
 
-  val analyzer: KeywordAnalyzer = new KeywordAnalyzer()
+  private val analyzer: KeywordAnalyzer = new KeywordAnalyzer()
 
   def close(): Unit = {
     thes2thesSearchers.foreach {
@@ -131,12 +131,14 @@ class MeshConverter(indexes: String) {
     */
   private def getCode(docIds: Array[Int],
                       searcher: IndexSearcher): Either[Option[Set[String]], String] = {
-    docIds.map(id => searcher.doc(id)).find(doc1 => doc1.get("meshCode") != null) match {
+    docIds.map(id => searcher.storedFields().document(id)).find(doc1 => doc1.get("meshCode") != null) match {
+    //docIds.map(id => searcher.storedFields().document(id)).find(doc1 => doc1.get("meshCode") != null) match {
       case Some(doc) => Right(doc.get("meshCode"))
       case None =>
         val labelSet: Set[String] = docIds.foldLeft(Set[String]()) {
           case (set, docId) =>
-            searcher.doc(docId).getValues("termLabel").foldLeft(set) {
+            searcher.storedFields().document(docId).getValues("termLabel").foldLeft(set) {
+            //searcher.doc(docId).getValues("termLabel").foldLeft(set) {
               case (set1, value) => set1 + value.trim.toLowerCase
             }
         }
@@ -164,7 +166,8 @@ class MeshConverter(indexes: String) {
         if (topDocs.totalHits.value == 0) {
           None
         } else {
-          val doc = searcher.doc(topDocs.scoreDocs.head.doc)
+          val doc = searcher.storedFields().document(topDocs.scoreDocs.head.doc)
+          //val doc = searcher.doc(topDocs.scoreDocs.head.doc)
           val eDescr = doc.get("ENGLISH_DESCR")
           if (eDescr == null) {
             val sDescr = doc.get("SPANISH_DESCR")

src/main/scala/org/bireme/infob/converters/MeSH_DeCS_Index.scala

@@ -27,7 +27,7 @@ import scala.jdk.CollectionConverters._
   */
 object MeSH_DeCS_Index extends App {
   val DEF_DECS_INDEX = "web/BVSInfoButton/indexes/DeCS"
-  val DEF_DECS_MASTER = "/usr/local/bireme/tabs/decs"
+  val DEF_DECS_MASTER = "isis/decs" //"/usr/local/bireme/tabs/decs"
 
   val MESH_ID_TAG = 480
   val HIERARCHICAL_CODE_TAG = 20

src/main/scala/org/bireme/infob/converters/UMLS_Index.scala

@@ -34,7 +34,7 @@ object UMLS_Index extends App {
 
   val DEF_UMLS_INDEX = "web/BVSInfoButton/indexes/UMLS"
   val DEF_UMLS_YEAR = 2020
-  val DEF_UMLS_MASTER =  s"/bases/umls/${DEF_UMLS_YEAR}AA/decsnamecuisty"
+  val DEF_UMLS_MASTER =  "isis/decsnamecuisty" //s"/bases/umls/${DEF_UMLS_YEAR}AA/decsnamecuisty"
 
   val thesauri = HashSet("ICD9CM", "ICD10CM", "ICD10", "SNOMEDCT_US", "RXNORM",
     "NDC", "LOINC")

src/main/scala/org/bireme/infob/converters/UMLS_UpdateIndex.scala

@@ -27,22 +27,22 @@ import scala.io.Source
   * [-index=<UMLSIndex>] - path to Lucene index to be updated"
   */
 object UMLS_UpdateIndex extends App {
-  val DEF_LUCENE_INDEX = "web/BVSInfoButton/indexes/UMLS"
+  private val DEF_LUCENE_INDEX = "web/BVSInfoButton/indexes/UMLS"
   //val DEF_FILES = "ICD10:cid10/ver2010/all.txt,ICD10:cid10/espanhol/all.txt,ICD10:cid10/datasus/ver2008/all.txt,SNOMED-CT:Snomed-CT/all.txt"
   //val DEF_FILES = "ICD10:cid10/one.txt"
-  val DEF_FILES = "ICD10:cid10/ver2010/all.txt,ICD10:cid10/espanhol/all.txt,ICD10:cid10/datasus/ver2008/all.txt"
+  private val DEF_FILES = "ICD10:cid10/ver2010/all.txt,ICD10:cid10/espanhol/all.txt,ICD10:cid10/datasus/ver2008/all.txt"
 
-  val parameters = args.foldLeft[Map[String, String]](Map()) {
+  private val parameters = args.foldLeft[Map[String, String]](Map()) {
     case (map, par) =>
       val split = par.split(" *= *", 2)
       map + ((split(0).substring(1), split(1)))
   }
-  val files: Set[(String, String)] = parameters.getOrElse("files", DEF_FILES).split(" *, *")
+  private val files: Set[(String, String)] = parameters.getOrElse("files", DEF_FILES).split(" *, *")
     .map { elem =>
       val split = elem.split(" *: *")
       (split(0), split(1))
     }.toSet                                        // Set((thesaurus_name,path)...)
-  val index = parameters.getOrElse("index", DEF_LUCENE_INDEX)
+  private val index = parameters.getOrElse("index", DEF_LUCENE_INDEX)
 
   updateIndex(index, files)
 
@@ -99,7 +99,8 @@ object UMLS_UpdateIndex extends App {
           doc.add(new StringField("termLabelNorm", Tools.uniformString(termLabel), Field.Store.YES))
           writer.addDocument(doc)
         } else {
-          val doc1: Document = searcher2.doc(topDocs.scoreDocs.head.doc)
+          //val doc1: Document = searcher2.doc(topDocs.scoreDocs.head.doc)
+          val doc1: Document = searcher2.storedFields().document(topDocs.scoreDocs.head.doc)
           val labels = getLabels(doc1) + termLabel
           labels.foreach {
             label =>

src/main/scala/org/bireme/infob/parameters/Age.scala

@@ -12,13 +12,13 @@ import scala.util.{Try, Success, Failure}
 
 class Age(value: Option[String],
           unit: Option[String]) extends SearchParameter {
-  val value2: Int = value.getOrElse("0").toInt
+  private val value2: Int = value.getOrElse("0").toInt
   require(value2 > 0)
-  val unit2: String = unit.getOrElse("").toLowerCase
+  private val unit2: String = unit.getOrElse("").toLowerCase
   require(unit2.equals("min") || unit2.equals("h") || unit2.equals("d") ||
           unit2.equals("wk") || unit2.equals("mo") || unit2.equals("a"))
 
-  val agroup: Option[String] = convertToMonth(value.get, unit.get) match {
+  private val agroup: Option[String] = convertToMonth(value.get, unit.get) match {
     case Some(x) if (x >= 0) && (x <= 1)    => Some("infant, newborn")
     case Some(x) if (x > 1) && (x < 24)     => Some("infant")
     case Some(x) if (x >= 24) && (x < 72)   => Some("child, preschool")
@@ -29,7 +29,7 @@ class Age(value: Option[String],
     case Some(x) if (x >= 540) && (x < 780) => Some("middle aged")
     case Some(x) if (x >= 780) && (x < 960) => Some("aged")
     case Some(x) if x >= 960                => Some("aged, 80 and older")
-    case None                               => None
+    case _                                  => None
   }
 
   private def convertToMonth(value: String, unit: String): Option[Int] = {