From d9b48a20a06e816a7d13293b3a95acc3e4341d33 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Wed, 11 Sep 2024 16:59:52 -0700
Subject: [PATCH] improve coverage

---
 .../src/main/nextflow/quilt/QuiltObserver.groovy    |  6 ++++--
 .../test/nextflow/quilt/QuiltObserverTest.groovy    | 13 ++++++++-----
 .../quilt/nio/QuiltFileSystemProviderTest.groovy    | 12 ++++++++++++
 3 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
index 3828e5f4..d7d85880 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
@@ -135,9 +135,11 @@ class QuiltObserver implements TraceObserver {
         String destString = QuiltPackage.osConvert(dest.toAbsolutePath().normalize().toString())
         // find pkgKey in destination.toString()
         int index = destString.indexOf(pkgKey)
+        println("pkgRelative[$index]: $pkgKey in $destString")
         // return the portion after the end of pkgKey
-        if (index >= 0) {
-            return destString.substring(index + pkgKey.length() + 1)
+        int len = index + pkgKey.length() + 1
+        if (index >= 0 && len < destString.length()) {
+            return destString.substring(len)
         }
         return null
     }
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
index 4b46d3be..c672261f 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
@@ -161,13 +161,16 @@ class QuiltObserverTest extends QuiltSpecification {
     void 'should addOverlay logical path with subfolders'() {
         given:
         QuiltObserver observer = makeObserver()
-        String file_path  = 'file.txt'
-        String full_path = "output/${file_path}"
-        Path source = Paths.get(TEST_KEY, file_path)
-        Path dest = Paths.get(TEST_KEY, full_path)
+        String file_path  = 'source'
+        Path source = Paths.get(root, file_path)
+        Path dest = Paths.get(root, path)
         expect:
         String relPath = observer.addOverlay(TEST_KEY, dest, source)
-        relPath == full_path
+        relPath == result
+        where:
+        root     | path     | result
+        TEST_KEY | SPEC_KEY | SPEC_KEY
+        SPEC_KEY | TEST_KEY | null
     }
 
     void 'should not error on onFlowComplete success'() {
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
index a8019693..a4a71f6c 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
@@ -95,6 +95,18 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
         Files.list(tempFolder).count() > 0
     }
 
+    void 'should fail to download a file if already exists'() {
+        given:
+        QuiltFileSystemProvider provider = new QuiltFileSystemProvider()
+        Path remoteFolder = parsedURIWithPath(false)
+        Path tempFolder = Files.createTempDirectory('quilt')
+        when:
+        provider.download(remoteFolder, tempFolder, null)
+
+        then:
+        thrown java.nio.file.FileAlreadyExistsException
+    }
+
     @IgnoreIf({ env.WRITE_BUCKET ==  null })
     void 'should upload file to test bucket'() {
         given: