From 55aaa11f2d32ce7d39a6c2faa23167d3be66f8ca Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <ernest@quiltdata.io>
Date: Thu, 25 Jan 2024 20:55:03 -0800
Subject: [PATCH] Use proper hurdat2 package (with README)

---
 .../main/nextflow/quilt/jep/QuiltPackage.groovy   |  1 +
 .../quilt/nio/QuiltFileSystemProvider.groovy      | 15 +++++++++------
 .../quilt/nio/QuiltFileSystemProviderTest.groovy  |  2 +-
 3 files changed, 11 insertions(+), 7 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 0cc72db7..ef94562b 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -195,6 +195,7 @@ class QuiltPackage {
 
             manifest.install(dest)
             log.debug("done: installed into $dest)")
+            println("Children: ${relativeChildren('')}")
         } catch (IOException e) {
             log.error("failed to install $packageName")
             // this is non-fatal error, so we don't want to stop the pipeline
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 a2ea1d8f..9c10afa7 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -116,27 +116,30 @@ 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}")
+        println("QuiltFileSystemProvider.qPath: ${qPath}")
         Path proxy = qPath.localPath()
+        println("QuiltFileSystemProvider.proxy: ${proxy}")
         QuiltPackage pkg = qPath.pkg()
+        println("QuiltFileSystemProvider.pkg[installed=${pkg.installed}]: ${pkg}")
+        /*QuiltPackage pkg = qPath.pkg()
         String pathName = pkg.parsed.getPath()
         Path localFolder = localDestination.getParent()
         Path actualDestination = Paths.get(localFolder.toUriString(), pathName)
-        log.debug "QuiltFileSystemProvider.download: ${proxy} -> ${actualDestination}"
+        log.debug "QuiltFileSystemProvider.actualDestination: ${actualDestination}"*/
 
         final CopyOptions opts = CopyOptions.parse(options)
         // delete target if it exists and REPLACE_EXISTING is specified
         if (opts.replaceExisting()) {
-            FileHelper.deletePath(actualDestination)
+            FileHelper.deletePath(localDestination)
         }
-        else if (Files.exists(actualDestination)) {
-            throw new FileAlreadyExistsException(actualDestination.toString())
+        else if (Files.exists(localDestination)) {
+            throw new FileAlreadyExistsException(localDestination.toString())
         }
 
         if (!Files.exists(proxy)) {
             throw new NoSuchFileException(remoteFile.toString())
         }
-        Files.copy(proxy, actualDestination, options)
+        Files.copy(proxy, localDestination, options)
     }
 
     void upload(Path localFile, Path remoteDestination, CopyOption... options) throws IOException {
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 5ed36070..c6ee7af1 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
+++ b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
@@ -29,7 +29,7 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
         given:
         QuiltFileSystemProvider provider = new QuiltFileSystemProvider()
         String filename = 'README.md'
-        Path remoteFile = Paths.get('quilt+s3://quilt-example#package=examples%2fhurdat&path=' + filename)
+        Path remoteFile = Paths.get('quilt+s3://quilt-example#package=examples%2fhurdat2&path=' + filename)
         Path tempFolder = Files.createTempDirectory('quilt')
         Path tempFile = tempFolder.resolve(filename)