fix(ENGKNOW-2918): Allow using versioned link files with gord folders

gortools/src/main/scala/gorsat/Macros/PGor.scala

@@ -123,7 +123,7 @@ class PGor extends MacroInfo("PGOR", CommandArguments("-nowithin", "-gordfolder"
 
     val linkMetaOptions = LinkFileUtil.extractLinkMetaOptionData(queryAppend)
     if (!Strings.isNullOrEmpty(linkMetaOptions)) {
-      gordict += " -linkMeta " + linkMetaOptions
+      gordict += String.format(" -linkMeta '%s'", linkMetaOptions)
     }
 
     val cmd = splitManager.chromosomeSplits.keys.foldLeft(gordict)((x, y) => x + " [" + theKey + "_" + y + "] " +

gortools/src/main/scala/gorsat/Macros/Parallel.scala

@@ -133,7 +133,7 @@ class Parallel extends MacroInfo("PARALLEL", CommandArguments("-gordfolder", "-p
 
     val linkMetaOptions = LinkFileUtil.extractLinkMetaOptionData(create.query)
     if (!Strings.isNullOrEmpty(linkMetaOptions)) {
-      theCommand += " -linkMeta " + linkMetaOptions
+      theCommand += String.format(" -linkMeta '%s'", linkMetaOptions)
     }
     parGorCommands.put(createKey, ExecutionBlock(create.groupName, theCommand, create.signature, theDependencies.toArray, create.batchGroupName, cachePath, isDictionary = true, hasForkWrite = hasForkWrite))
 

gortools/src/test/java/gorsat/UTestGorWrite.java

@@ -293,6 +293,24 @@ public void testWriteLinkFileForGordFolder() throws IOException {
         Assert.assertEquals(linkresult1, linkresult3);
     }
 
+    @Test
+    public void testWriteLinkFileForGordFolderWithLinkMetaPgor() throws IOException {
+        Path p = Paths.get("../tests/data/gor/dbsnp_test.gor");
+        Files.copy(p, workDirPath.resolve("dbsnp.gor"));
+        TestUtils.runGorPipe("pgor dbsnp.gor | write -link dbsnp3.gord -linkmeta 'TEST1=T1,TEST2=T2' dbsnp2.gord", "-gorroot", workDirPath.toString());
+
+        var linkFile = LinkFile.load(new FileSource(workDirPath.resolve("dbsnp3.gord.link").toString()));
+
+        Assert.assertEquals(1, linkFile.getEntriesCount());
+        Assert.assertEquals(workDirPath.resolve("dbsnp2.gord"), Path.of(linkFile.getLatestEntry().url()));
+        Assert.assertEquals("T1", linkFile.getMeta().getProperty("TEST1"));
+        Assert.assertEquals("T2", linkFile.getMeta().getProperty("TEST2"));
+
+        String linkresult1 = TestUtils.runGorPipe("gor dbsnp.gor | top 1000", "-gorroot", workDirPath.toString());
+        String linkresult3 = TestUtils.runGorPipe("gor dbsnp3.gord | top 1000", "-gorroot", workDirPath.toString());
+        Assert.assertEquals(linkresult1, linkresult3);
+    }
+
     @Test
     public void testWriteLinkFileForGordFolderParallel() throws IOException {
         Path p = Paths.get("../tests/data/gor/dbsnp_test.gor");
@@ -309,6 +327,24 @@ public void testWriteLinkFileForGordFolderParallel() throws IOException {
         Assert.assertEquals(linkresult1, linkresult3);
     }
 
+    @Test
+    public void testWriteLinkFileForGordFolderParallelWithLinkMeta() throws IOException {
+        Path p = Paths.get("../tests/data/gor/dbsnp_test.gor");
+        Files.copy(p, workDirPath.resolve("dbsnp.gor"));
+        TestUtils.runGorPipe("parallel -parts <(nor dbsnp.gor | select chrom | distinct) <(gor -p #{col:Chrom} dbsnp.gor) | write -link dbsnp3.gord -linkmeta 'TEST1=T1,TEST2=T2' dbsnp2.gord", "-gorroot", workDirPath.toString());
+
+        var linkFile = LinkFile.load(new FileSource(workDirPath.resolve("dbsnp3.gord.link").toString()));
+
+        Assert.assertEquals(1, linkFile.getEntriesCount());
+        Assert.assertEquals(workDirPath.resolve("dbsnp2.gord"), Path.of(linkFile.getLatestEntry().url()));
+        Assert.assertEquals("T1", linkFile.getMeta().getProperty("TEST1"));
+        Assert.assertEquals("T2", linkFile.getMeta().getProperty("TEST2"));
+
+        String linkresult1 = TestUtils.runGorPipe("gor dbsnp.gor | top 1000", "-gorroot", workDirPath.toString());
+        String linkresult3 = TestUtils.runGorPipe("gor dbsnp3.gord | top 1000", "-gorroot", workDirPath.toString());
+        Assert.assertEquals(linkresult1, linkresult3);
+    }
+
     @Test
     public void testWriteLinkFileForGordFolderInferFilename() throws IOException {
         Path p = Paths.get("../tests/data/gor/dbsnp_test.gor");

model/src/main/java/org/gorpipe/gor/driver/meta/DataType.java

@@ -54,8 +54,8 @@ public enum DataType {
     GORP(TABLE, ".gorp", true),
     GORQ(REPORT, ".gorq"),
     LINK(REFERENCE, ".link"),
-    VERSIONED_LINK(REFERENCE, ".versioned.link"),
-    GORD_INTERNAL_LINK(REFERENCE, ".internal.link"),  // Gord internal link type
+    // VERSIONED_LINK(REFERENCE, ".versioned.link"),
+    GORD_INTERNAL_LINK(REFERENCE, ".link"),  // Gord internal link type
     CRAM(VARIANTS, ".cram", true),
     CRAI(INDEX, ".crai"),
     SPEC(VARIANTS, ".spec"),

model/src/main/java/org/gorpipe/gor/table/livecycle/TableInfoBase.java

@@ -78,7 +78,7 @@ protected TableInfoBase(String uri, FileReader inputFileReader, TableHeader head
             this.rootUri = realUri;
             this.folderPath = rootUri;
             this.linkPath = PathUtils.resolve(rootUri, DataUtil.toFile(GorOptions.DEFAULT_FOLDER_DICTIONARY_NAME, DataType.GORD_INTERNAL_LINK));
-            try (var linkFileSource = fileReader.resolveUrl(linkPath)) {
+            try (var linkFileSource = resolveGordUrl(linkPath)) {
                 this.path = linkFileSource != null ? linkFileSource.getFullPath() : getNewVersionedFileName();
             }
         } else if (safeCheckExists(PathUtils.resolve(realUri, GorOptions.DEFAULT_FOLDER_DICTIONARY_NAME))) {
@@ -354,4 +354,18 @@ protected String getNewVersionedFileName() {
         return PathUtils.resolve(getFolderPath(),
                 PathUtils.injectRandomStringIntoFileName("version" + DataType.GORD.suffix));
     }
+
+    /**
+     * Resolve gord path.  Traverses and fins thddict.gord files.
+     * @param path  path to resolve.  Should be gord path.
+     * @return the path to the acutal gord file.
+     */
+    protected DataSource resolveGordUrl(String path) {
+        var source = fileReader.resolveUrl(path);
+        while (source.isDirectory()) {
+            path = source.getPath().resolve(GorOptions.DEFAULT_FOLDER_DICTIONARY_NAME).toString();
+            source = fileReader.resolveUrl(path);
+        }
+        return source;
+    }
 }