From b08f7270dbd95165fececfbedc4788ca55bce3cd Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Thu, 5 Sep 2024 14:13:31 -0700
Subject: [PATCH] Add dest key

---
 .../src/main/nextflow/quilt/QuiltObserver.groovy      | 11 ++++++++---
 .../src/test/nextflow/quilt/QuiltObserverTest.groovy  |  8 ++++----
 2 files changed, 12 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 febf3811..e9f5b2f1 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
@@ -62,6 +62,7 @@ class QuiltObserver implements TraceObserver {
     }
 
     static String quiltURIfromS3(String s3uri) {
+        println("quiltURIfromS3: $s3uri")
         String[] partsArray = s3uri.split('/')
         List<String> parts = new ArrayList(partsArray.toList())
         parts.eachWithIndex { p, i -> println("quiltURIfromS3.parts[$i]: $p") }
@@ -74,10 +75,14 @@ class QuiltObserver implements TraceObserver {
             parts = parts.drop(1)
         }
         String bucket = parts.remove(0)
-        String prefix = parts.size() > 0 ? parts.remove(0) : 'default_prefix'
-        String suffix = parts.size() > 0 ? parts.remove(0) : 'default_suffix'
+        String dest = parts.join('%2f')
+        println("quiltURIfromS3.bucket: $bucket dest: $dest from $parts")
+        String suffix = parts.size() > 1 ? parts.removeLast() : 'default_suffix'
+        println("quiltURIfromS3.suffix: $suffix from $parts")
+        String prefix = parts.size() > 0 ? parts.removeLast() : 'default_prefix'
+        println("quiltURIfromS3.prefix: $prefix from $parts")
         String base = "quilt+s3://${bucket}#package=${prefix}%2f${suffix}"
-        String uri = (parts.size() > 0) ? "${base}&path=${parts.join('/')}" : base
+        String uri = base + '&dest=' + ((dest) ?: '/')
         return uri
     }
 
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
index d6529f70..341378a0 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
@@ -69,10 +69,10 @@ class QuiltObserverTest extends QuiltSpecification {
         QuiltObserver.quiltURIfromS3(s3_uri) == quilt_uri
         where:
         s3_uri | quilt_uri
-        's3://bucket/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix'
-        's3://bucket/prefix'        | 'quilt+s3://bucket#package=prefix%2fdefault_suffix'
-        's3://bucket'               | 'quilt+s3://bucket#package=default_prefix%2fdefault_suffix'
-        // 's3://bucket/folder/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix&dest=folder/prefix/suffix'
+        's3://bucket/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix&dest=prefix%2fsuffix'
+        's3://bucket/prefix'        | 'quilt+s3://bucket#package=prefix%2fdefault_suffix&dest=prefix'
+        's3://bucket'               | 'quilt+s3://bucket#package=default_prefix%2fdefault_suffix&dest=/'
+        's3://bucket/folder/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix&dest=folder%2fprefix%2fsuffix'
     }
 
     void 'should findOutputParams'() {