fix(ENGKNOW-2956): Fix thread error in refbases. (#96)

* feat(ENGKNOW-2956):  Allow not quoted file names for rebases_with_build

* fix(ENGKNOW-2956): Fix threading issues refbases.

* fix(ENGKNOW-2956): Fix threading issues refbases.

* fix(ENGKNOW-2956): Fix threading issues refbases.

Author: gmagnu

VERSION

@@ -1 +1 @@
-5.8.0
+5.8.1

model/src/main/scala/org/gorpipe/model/gor/iterators/RefSeqFromChromSeq.scala

@@ -36,8 +36,12 @@ import org.slf4j.{Logger, LoggerFactory}
 
 import java.nio.file.{Files, Path, Paths}
 
+object RefSeqFromChromSeq {
+   var downloadTriggered : util.Map[String, java.lang.Boolean] =
+    new java.util.concurrent.ConcurrentHashMap[String, java.lang.Boolean]
+}
+
 class RefSeqFromChromSeq(ipath : String, fileReader : FileReader) extends RefSeq {
-  protected var download_triggered = false
   private val GOR_REFSEQ_CACHE_FOLDER = System.getProperty("gor.refseq.cache.folder")
   private val GOR_REFSEQ_CACHE_DOWNLOAD = Option(System.getProperty("gor.refseq.cache.download", "true")).exists(_.toBoolean)
 
@@ -66,8 +70,8 @@ class RefSeqFromChromSeq(ipath : String, fileReader : FileReader) extends RefSeq
       if (Files.exists(fullCachePath)) {
         log.debug("Using cached reference build {}", fullCachePath.toString)
         return fullCachePath.toString
-      } else if (GOR_REFSEQ_CACHE_DOWNLOAD && !download_triggered) {
-        download_triggered = true  // Only trigger download once per client
+      } else if (GOR_REFSEQ_CACHE_DOWNLOAD && (RefSeqFromChromSeq.downloadTriggered.putIfAbsent(fullRefPath.toString, true) == null)) {
+        // Only trigger download once per client
         triggerRefSeqDownload(fullRefPath, fullCachePath)
       }
     }

model/src/main/scala/org/gorpipe/model/gor/iterators/RefSeqFromConfigFactory.scala

@@ -24,19 +24,13 @@ package org.gorpipe.model.gor.iterators
 
 import org.gorpipe.gor.model.FileReader
 
-import java.util
-import java.util.Collections
-
 class RefSeqFromConfigFactory(path: String, reader: FileReader) extends RefSeqFactory {
-  var refSeqMap = Collections.synchronizedMap(new util.HashMap[String, RefSeq]())
 
   override def create(): RefSeq = {
-    refSeqMap.computeIfAbsent(path, _ => {
-      new RefSeqFromChromSeq(path, reader)})
+      new RefSeqFromChromSeq(path, reader)
   }
 
   def create(altPath: String): RefSeq = {
-    refSeqMap.computeIfAbsent(altPath, _ => {
-      new RefSeqFromChromSeq(altPath, reader)})
+      new RefSeqFromChromSeq(altPath, reader)
   }
 }

…gor/iterators/UTestRefSeqFromConfig.java …r/iterators/UTestRefSeqFromChromSeq.javamodel/src/test/java/org/gorpipe/model/gor/iterators/UTestRefSeqFromConfig.java renamed to model/src/test/java/org/gorpipe/model/gor/iterators/UTestRefSeqFromChromSeq.java model/src/test/java/org/gorpipe/model/gor/iterators/UTestRefSeqFromConfig.java renamed to model/src/test/java/org/gorpipe/model/gor/iterators/UTestRefSeqFromChromSeq.java

@@ -13,7 +13,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 
-public class UTestRefSeqFromConfig {
+public class UTestRefSeqFromChromSeq {
 
     @Rule
     public final ProvideSystemProperty cacheFolder
@@ -121,8 +121,7 @@ public void testGetRefbaseFromCache() throws InterruptedException {
 
         RefSeqFromChromSeq refseq = new RefSeqFromChromSeq("../tests/data/ref_mini/chromSeq", new DriverBackedFileReader(""));
 
-        refseq.download_triggered_$eq(false);
-
+        RefSeqFromChromSeq.downloadTriggered().clear();
 
         Assert.assertEquals('C', refseq.getBase("chr1", 101000));