Fix fetching new remote branch in multi-revision mode (nextflow-io#6733)

Co-authored-by: jorgee <jorge.ejarque@seqera.io>

Author: robsyme

modules/nextflow/src/main/groovy/nextflow/scm/MultiRevisionRepositoryStrategy.groovy

@@ -17,6 +17,7 @@
 package nextflow.scm
 
 import groovy.transform.CompileStatic
+import groovy.transform.Memoized
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.config.Manifest
@@ -333,20 +334,35 @@ class MultiRevisionRepositoryStrategy extends AbstractRepositoryStrategy {
     }
 
     private RefSpec refSpecForName(String revision) {
-        // Is it a local branch?
-        Ref branch = getBareGit().getRepository().findRef("refs/heads/" + revision)
+        // First, check if it's a local branch
+        final branchName = "refs/heads/$revision".toString()
+        final branch = getBareGit().getRepository().findRef(branchName)
         if( branch != null ) {
-            return new RefSpec("refs/heads/" + revision + ":refs/heads/" + revision)
+            return new RefSpec("$branchName:$branchName")
         }
 
-        // Is it a tag?
-        Ref tag = getBareGit().getRepository().findRef("refs/tags/" + revision)
+        // Check if it's a local tag
+        final tagName = "refs/tags/$revision".toString()
+        final tag = getBareGit().getRepository().findRef(tagName)
         if( tag != null ) {
-            return new RefSpec("refs/tags/" + revision + ":refs/tags/" + revision)
+            return new RefSpec("$tagName:$tagName")
         }
 
-        // It is a commit
-        return new RefSpec(revision + ":refs/tags/" + revision)
+        // Not found locally - check remote refs
+        final remoteRefs = lsRemote(false)
+
+        // Is it a remote branch?
+        if( remoteRefs.containsKey(branchName) ) {
+            return new RefSpec("$branchName:$branchName")
+        }
+
+        // Is it a remote tag?
+        if( remoteRefs.containsKey(tagName) ) {
+            return new RefSpec("$tagName:$tagName")
+        }
+
+        // Assume it's a commit SHA
+        return new RefSpec("$revision:$tagName")
     }
 
     @Override
@@ -422,7 +438,7 @@ class MultiRevisionRepositoryStrategy extends AbstractRepositoryStrategy {
     @Override
     Map<String, Ref> lsRemote(boolean tags) {
         final cmd = getBareGitWithLegacyFallback()?.lsRemote()?.setTags(tags)
-        if( provider.hasCredentials() )
+        if( provider?.hasCredentials() )
             cmd?.setCredentialsProvider(provider.getGitCredentials())
         return cmd?.callAsMap() ?: [:]
     }

modules/nextflow/src/test/groovy/nextflow/scm/MultiRevisionRepositoryStrategyTest.groovy

@@ -17,6 +17,7 @@
 package nextflow.scm
 
 import nextflow.config.Manifest
+import org.eclipse.jgit.api.Git
 
 import static MultiRevisionRepositoryStrategy.BARE_REPO
 import static MultiRevisionRepositoryStrategy.REVISION_SUBDIR
@@ -127,4 +128,87 @@ class MultiRevisionRepositoryStrategyTest extends Specification {
         folder.resolve(REPOS_SUBDIR + '/nextflow-io/hello/' + REVISION_SUBDIR + '/1c3e9e7404127514d69369cd87f8036830f5cf64/.git/objects/info/alternates').text == folder.resolve(REPOS_SUBDIR + '/nextflow-io/hello/' + BARE_REPO + '/objects').toAbsolutePath().toString()
     }
 
+    def 'should create correct RefSpec for branches tags and commits'() {
+        given:
+        def folder = tempDir.getRoot()
+        // Create a bare repo manually for testing
+        def bareRepoPath = folder.resolve(REPOS_SUBDIR + '/test/project/' + BARE_REPO).toFile()
+        bareRepoPath.mkdirs()
+        def git = Git.init().setDirectory(bareRepoPath).setBare(true).call()
+        // Configure origin to point to itself so lsRemote works (returns empty refs)
+        def config = git.getRepository().getConfig()
+        config.setString("remote", "origin", "url", bareRepoPath.absolutePath)
+        config.save()
+        git.close()
+
+        def strategy = new MultiRevisionRepositoryStrategy('test/project')
+
+        when:
+        // Access the private method via Groovy's metaclass
+        def refSpec = strategy.invokeMethod('refSpecForName', 'some-revision')
+
+        then:
+        // When revision is not found locally or remotely, it's treated as a commit
+        refSpec.toString() == 'some-revision:refs/tags/some-revision'
+    }
+
+    @IgnoreIf({ System.getenv('NXF_SMOKE') })
+    @Requires({ System.getenv('NXF_GITHUB_ACCESS_TOKEN') })
+    def 'should fetch new remote branch not in local bare repo'() {
+        given:
+        def folder = tempDir.getRoot()
+        def token = System.getenv('NXF_GITHUB_ACCESS_TOKEN')
+        // Use a test repo with known branches
+        def strategy = createStrategy('nextflow-io/hello', token)
+        def manifest = Mock(Manifest) {
+            getDefaultBranch() >> 'master'
+            getRecurseSubmodules() >> false
+        }
+
+        when:
+        // First, create bare repo with default branch only
+        strategy.checkBareRepo(manifest)
+
+        then:
+        folder.resolve(REPOS_SUBDIR + '/nextflow-io/hello/' + BARE_REPO).isDirectory()
+
+        when:
+        // Now try to download 'mybranch' which exists remotely but wasn't fetched initially
+        // Clear the local branch ref to simulate it not existing locally
+        def bareGit = Git.open(strategy.getBareRepo())
+        def localBranchRef = bareGit.getRepository().findRef("refs/heads/mybranch")
+        // If mybranch was fetched during clone, delete it to simulate fresh fetch scenario
+        if (localBranchRef) {
+            bareGit.branchDelete().setBranchNames("mybranch").setForce(true).call()
+        }
+        bareGit.close()
+
+        // This should succeed by querying remote refs
+        strategy.download('mybranch', 1, manifest)
+
+        then:
+        noExceptionThrown()
+        // mybranch commit is 1c3e9e7404127514d69369cd87f8036830f5cf64
+        folder.resolve(REPOS_SUBDIR + '/nextflow-io/hello/' + REVISION_SUBDIR + '/1c3e9e7404127514d69369cd87f8036830f5cf64/.git').isDirectory()
+
+        when:
+        // Now try to download tag 'v1.2' which exists remotely but wasn't fetched initially
+        // Clear the local tag ref to simulate it not existing locally
+        bareGit = Git.open(strategy.getBareRepo())
+        def localTagRef = bareGit.getRepository().findRef("refs/tags/v1.2")
+        // If v1.2 was fetched during clone, delete it to simulate fresh fetch scenario
+        if (localTagRef) {
+            bareGit.tagDelete().setTags("v1.2").call()
+        }
+        bareGit.close()
+
+        // This should succeed by querying remote refs
+        strategy.download('v1.2', 1, manifest)
+
+        then:
+        noExceptionThrown()
+        // v1.2 ref is 1b420d060d3fad67027154ac48e3bdea06f058
+        folder.resolve(REPOS_SUBDIR + '/nextflow-io/hello/' + REVISION_SUBDIR + '/1b420d060d3fad67027154ac48e3bdea06f058da/.git').isDirectory()
+    }
+
 }