From cb59d970f6ed06d2c71243ec040e7c68c15e159d Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <ernest@quiltdata.io>
Date: Thu, 25 Jan 2024 20:39:25 -0800
Subject: [PATCH] handle single-slash URIs #PostelsLaw

---
 .../quilt/nio/QuiltFileSystemProvider.groovy  | 21 +++++++++++++------
 .../quilt/nio/QuiltPathFactory.groovy         | 10 +++++++--
 .../nio/QuiltFileSystemProviderTest.groovy    |  2 ++
 .../quilt/nio/QuiltPathFactoryTest.groovy     |  5 +++--
 4 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
index 55298d48..a2ea1d8f 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -68,13 +68,21 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     private Map<Path,BasicFileAttributes> attributesCache = [:]
 
     static QuiltPath asQuiltPath(Path path) {
-        if (path !in QuiltPath) {
-            String pathClassName = path?.class?.name ?: '-'
-            throw new IllegalArgumentException(
-                "Not a valid Quilt blob storage path object: `${path}` [${pathClassName}]"
-            )
+        println("asQuiltPath.path: ${path}")
+        if (path in QuiltPath) {
+            return (QuiltPath)path
+        }
+        String pathString = path?.toString() ?: '-'
+        println("asQuiltPath.pathString: ${pathString}")
+        if (pathString.startsWith(QuiltParser.SCHEME + ':/')) {
+            QuiltPath qPath = QuiltPathFactory.parse(pathString)
+            println("asQuiltPath.qPath: ${qPath}")
+            return qPath
         }
-        return (QuiltPath)path
+        String pathClassName = path?.class?.name ?: '-'
+        throw new IllegalArgumentException(
+            "Not a valid Quilt blob storage path object: `${path}` [${pathClassName}]"
+        )
     }
 
     static QuiltFileSystem getQuiltFilesystem(Path path) {
@@ -108,6 +116,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     void download(Path remoteFile, Path localDestination, CopyOption... options) throws IOException {
         log.debug "QuiltFileSystemProvider.download: ${remoteFile} -> ${localDestination}"
         QuiltPath qPath = asQuiltPath(remoteFile)
+        println("QuiltFileSystemProvider.download: ${qPath}")
         Path proxy = qPath.localPath()
         QuiltPackage pkg = qPath.pkg()
         String pathName = pkg.parsed.getPath()
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy
index 52a4716d..c4a11aa3 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy
@@ -40,10 +40,16 @@ class QuiltPathFactory extends FileSystemPathFactory {
 
     @Override
     protected Path parseUri(String uriString) {
-        if (!uriString.startsWith(QuiltParser.PREFIX)) {
+        println('parseUri.uriString: ' + uriString)
+        if (!uriString.startsWith(QuiltParser.SCHEME)) {
             return null
         }
-        final uri = new URI(uriString)
+        String[] split = uriString.split('/')
+        println('parseUri.split: ' + split)
+        String newString = (split[1] == '') ? uriString : uriString.replaceFirst(/\/+/, '//')
+        println('parseUri.newString: ' + newString)
+        final uri = new URI(newString)
+        println('parseUri.uri: ' + uri)
         return FileHelper.getOrCreateFileSystemFor(uri).provider().getPath(uri)
     }
 
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 2c5d0519..5ed36070 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
@@ -4,6 +4,8 @@ package nextflow.quilt.nio
 import nextflow.quilt.QuiltSpecification
 import groovy.transform.CompileDynamic
 import java.nio.file.Path
+import java.nio.file.Paths
+import java.nio.file.Files
 
 /**
  *
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
index 5343a39a..d0811b97 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
@@ -53,8 +53,9 @@ class QuiltPathFactoryTest extends QuiltSpecification {
         QuiltPathFactory.parse(PATH).toString() == STR
 
         where:
-        _ | PATH                                        | STR
-        _ | 'quilt+s3://reg#package=user/pkg'           | 'reg#package=user%2fpkg'
+        _ | PATH                                          | STR
+        _ | 'quilt+s3://reg#package=user/pkg'             | 'reg#package=user%2fpkg'
+        _ | 'quilt+s3:/reg#package=user/pkg&path=test.md' | 'reg#package=user%2fpkg&path=test.md'
     }
 
     void 'should create Channel from URL'() {