From 55a47b29d05e051535a15ab8ba1add6d63f72046 Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <ernest@quiltdata.io>
Date: Fri, 26 Jan 2024 17:02:32 -0800
Subject: [PATCH] Install package just before download

---
 CHANGELOG.md                                                | 2 +-
 .../src/main/nextflow/quilt/jep/QuiltPackage.groovy         | 3 ---
 .../main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy  | 6 ++++++
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1ea4212b..c368343e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 ## [0.7.7] 2024-01-24
 
 - Properly implement and test getFilename()
-- Pre-install package if "&path" present
+- Install package just before download
 - Add and pass `path-input` integration test
 - Add unit test for "&path=" Quilt+ URIs
 
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 ef94562b..9123c622 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -162,9 +162,6 @@ class QuiltPackage {
     void setup() {
         Files.createDirectories(this.folder)
         this.installed = false
-        if (this.parsed.hasPath()) {
-            install()
-        }
     }
 
     boolean is_force() {
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 93464879..b7bb108d 100644
--- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
+++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -47,6 +47,7 @@ import groovy.util.logging.Slf4j
 import nextflow.Global
 import nextflow.Session
 import nextflow.quilt.jep.QuiltParser
+import nextflow.quilt.jep.QuiltPackage
 import nextflow.file.FileSystemTransferAware
 import nextflow.file.CopyOptions
 import nextflow.file.FileHelper
@@ -112,6 +113,11 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         // log.debug "QuiltFileSystemProvider.download: ${remoteFile} -> ${localDestination}"
         QuiltPath qPath = asQuiltPath(remoteFile)
         Path cachedFile = qPath.localPath()
+        QuiltPackage pkg = qPath.pkg()
+        if (!pkg.installed) {
+            pkg.install()
+        }
+
         if (!Files.exists(cachedFile)) {
             throw new NoSuchFileException(remoteFile.toString())
         }