From d1d08b94e3068ff9e2a57540a145d290551170ff Mon Sep 17 00:00:00 2001
From: Gisli Magnusson <gmagnusson@genedx.com>
Date: Fri, 8 May 2026 15:41:05 +0000
Subject: [PATCH] fix(ENGKNOW-3472): include meta sources in query
 fingerprinting

---
 .../scala/gorsat/process/GorPrePipe.scala     |  2 +-
 .../java/gorsat/Script/UTestSignature.java    | 34 +++++++++++++++++++
 .../gorsat/Utilities/UTestGorPrePipe.scala    |  8 +++++
 3 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/gortools/src/main/scala/gorsat/process/GorPrePipe.scala b/gortools/src/main/scala/gorsat/process/GorPrePipe.scala
index 3a181305..41c75dd8 100644
--- a/gortools/src/main/scala/gorsat/process/GorPrePipe.scala
+++ b/gortools/src/main/scala/gorsat/process/GorPrePipe.scala
@@ -45,7 +45,7 @@ object GorPrePipe {
   val availNorCommands: Array[String] = GorPipeCommands.getNorCommands ++ GorInputSources.getInputSources
 
   private val supportedGorSQLFileEndings = Array[String](".json",".csv",".tsv",".gor",".gorz",".gor.gz",".gord",".txt",".vcf",".bgen",".parquet",".adam",".mt",".xml")
-  private val commandsContainingInputSources = Array[String]("PARALLEL", "GOR","NOR","SPARK","MAP","MULTIMAP","INSET","MERGE","JOIN","LEFTJOIN","VARJOIN","GORIF", "NORIF", "EXEC"/*,"CSVSEL","CSVCC","GTGEN"*/)
+  private val commandsContainingInputSources = Array[String]("PARALLEL", "GOR","NOR","SPARK","MAP","MULTIMAP","INSET","MERGE","JOIN","LEFTJOIN","VARJOIN","GORIF", "NORIF", "META", "EXEC"/*,"CSVSEL","CSVCC","GTGEN"*/)
   val gorpred = (p: String) => supportedGorSQLFileEndings.map(e => p.toLowerCase.endsWith(e)).reduce((a,b) => a || b)
 
   private def getCommandArgument(command: String) : Option[CommandArguments] = {
diff --git a/gortools/src/test/java/gorsat/Script/UTestSignature.java b/gortools/src/test/java/gorsat/Script/UTestSignature.java
index b9eea927..c0173e1c 100644
--- a/gortools/src/test/java/gorsat/Script/UTestSignature.java
+++ b/gortools/src/test/java/gorsat/Script/UTestSignature.java
@@ -15,6 +15,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.Arrays;
 
 public class UTestSignature {
 
@@ -31,6 +32,17 @@ public void setUp() {
         GorInputSources.register();
     }
 
+    private String extractSingleValue(String output) {
+        var lines = Arrays.stream(output.split("\n"))
+                .map(String::trim)
+                .filter(line -> !line.isEmpty())
+                .toArray(String[]::new);
+
+        Assert.assertEquals("Expected a header row and one data row", 2, lines.length);
+        var values = lines[1].split("\t");
+        return values[values.length - 1];
+    }
+
     @Test
     public void testQuerySignatureAfterUpdate() throws IOException, InterruptedException {
         var cachePath = workPath.resolve("cache");
@@ -50,6 +62,28 @@ public void testQuerySignatureAfterUpdate() throws IOException, InterruptedExcep
         Assert.assertEquals(3, res.length);
     }
 
+    @Test
+    public void testQuerySignatureAfterUpdateWithMetaVirtualRelation() throws IOException {
+        var cachePath = workPath.resolve("cache");
+        Files.createDirectory(cachePath);
+
+        var dataPath = workPath.resolve("data_meta.gor");
+        Files.writeString(dataPath, "#Chrom\tPos\nchr1\t1\n");
+
+        var query = "create meta_size = meta " + dataPath
+                + " | where source='FILE' and name='SIZE' | rename value file_size | select file_size; nor [meta_size]";
+
+        var before = extractSingleValue(TestUtils.runGorPipe(query, workPath.toString(), cachePath.toString(), false, "", null));
+        Assert.assertEquals(String.valueOf(Files.size(dataPath)), before);
+
+        Files.writeString(dataPath, "chr1\t2\n", StandardOpenOption.APPEND);
+
+        var after = extractSingleValue(TestUtils.runGorPipe(query, workPath.toString(), cachePath.toString(), false, "", null));
+        Assert.assertEquals("META virtual relation should be invalidated when the source file size changes",
+                String.valueOf(Files.size(dataPath)), after);
+        Assert.assertNotEquals("META virtual relation should not reuse stale cached results", before, after);
+    }
+
     @Test
     public void testQuerySignatureAfterUpdateWithLink() throws IOException, InterruptedException {
         var cachePath = workPath.resolve("cache");
diff --git a/gortools/src/test/scala/gorsat/Utilities/UTestGorPrePipe.scala b/gortools/src/test/scala/gorsat/Utilities/UTestGorPrePipe.scala
index 4a29356d..194b39da 100644
--- a/gortools/src/test/scala/gorsat/Utilities/UTestGorPrePipe.scala
+++ b/gortools/src/test/scala/gorsat/Utilities/UTestGorPrePipe.scala
@@ -92,6 +92,14 @@ class UTestGorPrePipe extends AnyFunSuite with BeforeAndAfterAll {
     assert(result.head == "../tests/data/gor/dbsnp_test.gorz")
   }
 
+  test("Get used file from meta query") {
+    val query = "meta ../tests/data/gor/dbsnp_test.gorz | where source='FILE' and name='SIZE'"
+    val result = process.GorPrePipe.getUsedFiles(query, session)
+
+    assert(result.length == 1)
+    assert(result.head == "../tests/data/gor/dbsnp_test.gorz")
+  }
+
   test("Get used file from gor query with join") {
     val query = "nor ../tests/data/gor/dbsnp_test.gorz | join -snpsnp multicolumns.gor"
     val result = process.GorPrePipe.getUsedFiles(query, session)