From d0a81b0d587276daf3d4038bf2c1ca1183962fc1 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Wed, 4 Sep 2024 21:27:06 -0700
Subject: [PATCH] QuiltPackage.osSep

---
 .../src/main/nextflow/quilt/jep/QuiltPackage.groovy   | 11 ++++++++++-
 .../src/main/nextflow/quilt/nio/QuiltPath.groovy      | 11 +----------
 .../src/test/nextflow/quilt/nio/QuiltPathTest.groovy  |  8 +++++---
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
index 7b6b5bb9..912f16f5 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -20,6 +20,7 @@ package nextflow.quilt.jep
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import java.nio.file.FileSystems
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.Paths
@@ -55,6 +56,14 @@ class QuiltPackage {
     private final Map meta
     private boolean installed
 
+    static String osSep() {
+        return FileSystems.getDefault().getSeparator()
+    }
+
+    static String osJoin(String... parts) {
+        return parts.join(osSep())
+    }
+
     static String today() {
         LocalDate date = LocalDate.now()
         return date.toString()
@@ -153,7 +162,7 @@ class QuiltPackage {
      */
     List<String> relativeChildren(String subpath) {
         Path subfolder = folder.resolve(subpath)
-        String base = subfolder.toString() + QuiltPath.osSep()
+        String base = subfolder.toString() + osSep()
         List<String> result = []
         final String[] children = subfolder.list().sort()
         //log.debug("relativeChildren[${base}] $children")
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
index 4e5b69e0..cc18e5ba 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -19,7 +19,6 @@ import nextflow.quilt.jep.QuiltPackage
 import nextflow.quilt.jep.QuiltParser
 import java.nio.file.Files
 import java.nio.file.FileSystem
-import java.nio.file.FileSystems
 import java.nio.file.LinkOption
 import java.nio.file.Path
 import java.nio.file.Paths
@@ -46,14 +45,6 @@ final class QuiltPath implements Path, Comparable {
     private final String[] paths
     private final boolean isFileName
 
-    static String osSep() {
-        return FileSystems.getDefault().getSeparator()
-    }
-
-    static String osJoin(String... parts) {
-        return parts.join(osSep())
-    }
-
     QuiltPath(QuiltFileSystem filesystem, QuiltParser parsed, boolean isFileName = false) {
         this.filesystem = filesystem
         this.parsed = parsed
@@ -223,7 +214,7 @@ final class QuiltPath implements Path, Comparable {
     Path relativize(Path other) {
         if (this == other) { return null }
         String file = (other in QuiltPath) ? ((QuiltPath)other).localPath() : other.toString()
-        String base = osJoin(pkg().toString(), parsed.getPath())
+        String base = QuiltPackage.osJoin(pkg().toString(), parsed.getPath())
         println("relativize[$base] in [$file]")
         int i = file.indexOf(base)
         if (i < 1) {
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy
index 72323dbf..f3637a8e 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy
@@ -261,13 +261,15 @@ class QuiltPathTest extends QuiltSpecification {
     @Unroll
     // @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') })
     void 'should validate relativize'() {
+        given:
+        String base = 'bucket#package=so%2fme'
         expect:
         pathify(path).relativize(pathify(other)).toString() == pathify(expected).toString()
         where:
         path                              | other                                      | expected
-        'bucket#package=so%2fme'          | 'bucket#package=so%2fme%2fdata%2ffile.txt' | 'data%2ffile.txt'
-        'bucket#package=so%2fme%2fdata'   | 'bucket#package=so%2fme%2fdata%2ffile.txt' | 'file.txt'
-        'bucket#package=so%2fme&path=foo' | 'bucket#package=so%2fme&path=foo%2fbar'    | 'bar'
+        base               | "${base}%2fdata%2ffile.txt" | QuiltPackage.osJoin('data', 'file.txt')
+        "${base}%2fdata"   | "${base}%2fdata%2ffile.txt" | 'file.txt'
+        "${base}&path=foo" | "${base}&path=foo%2fbar"    | 'bar'
     }
 
     void 'should reconstruct full URLs'() {