From a1bcd500e98fec2163289926cbf4f31ce00f56dc Mon Sep 17 00:00:00 2001 From: "Dr. Ernie Prabhakar" Date: Wed, 24 Jan 2024 14:32:16 -0800 Subject: [PATCH] try pre-install --- CHANGELOG.md | 6 ++++-- .../src/main/nextflow/quilt/jep/QuiltPackage.groovy | 3 +++ .../src/main/nextflow/quilt/nio/QuiltFileSystem.groovy | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cd6693e2..2d633f03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,10 @@ # Changelog -## [0.7.6] 2024-01-10 UNOFFICIAL +## [0.7.6] 2024-01-24 -- Fix "&path=" Quilt+ URIs +- Pre-install package if "&path" present +- Add `path-input` integration test +- Add unit test for "&path=" Quilt+ URIs - Re-enable crash on failure ## [0.7.5] 2023-10-17 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 d54c0b80..da63ec59 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy @@ -162,6 +162,9 @@ 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/QuiltFileSystem.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy index 62d71e00..dc8d22b0 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy @@ -106,7 +106,7 @@ final class QuiltFileSystem extends FileSystem implements Closeable { } QuiltFileAttributes readAttributes(QuiltPath path) { - //log.debug("QuiltFileAttributes QuiltFileSystem.readAttributes($path)") + log.debug("QuiltFileAttributes QuiltFileSystem.readAttributes($path)") Path installedPath = path.localPath() try { BasicFileAttributes attrs = Files.readAttributes(installedPath, BasicFileAttributes)