71 support path in input uri (#178)

debug build
v0.7.8

CHANGELOG.md

@@ -1,6 +1,14 @@
 # Changelog
 
-## [0.7.7] 2024-01-24
+## [0.7.9] 2024-01-30
+
+- Auto-install (needed for < 23.12?)
+
+## [0.7.8] 2024-01-30 UNOFFICIAL
+
+- Add debugging for installs
+
+## [0.7.7] 2024-01-24 UNOFFICIAL
 
 - Properly implement and test getFilename()
 - Install package just before download

Makefile

@@ -4,6 +4,7 @@ WRITE_BUCKET ?= quilt-example
 FRAGMENT ?= &path=.
 NF_DIR ?= ../nextflow
 NF_BIN ?= ./launch.sh
+PATH_NF ?= ./main.path.nf
 PID ?= $$$$
 PIPELINE ?= sarek
 QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
@@ -67,7 +68,7 @@ pkg-fail: compile
 
 path-input: clean compile #-all
 	echo "$(TEST_URI)"
-	$(NF_BIN) run ./main.path.nf -profile standard -plugins $(PROJECT) --outdir "./results"
+	$(NF_BIN) run $(PATH_NF) -profile standard -plugins $(PROJECT) --outdir "./results"
 
 tower-test: $(NF_BIN)
 	$(NF_BIN) run "https://github.com/quiltdata/nf-quilt" -name local_einstein  -with-tower -r main -latest --pub "$(TEST_URI)"

README.md

@@ -75,8 +75,8 @@ From the command-line, do, e.g.:
 
 ```bash
 # export NXF_VER=23.04.3
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.7/nf-quilt-0.7.7-meta.json
-nextflow run main.nf -plugins nf-quilt@0.7.7
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.9/nf-quilt-0.7.9-meta.json
+nextflow run main.nf -plugins nf-quilt@0.7.9
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

main.gallery.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+/* groovylint-disable CompileStatic */
+
+nextflow.enable.dsl=2
+
+test_file_local = 'README.md'
+test_file_s3 = 's3://nf-core-gallery/nf-core/hlatyping/README_NF_QUILT.md'
+test_file_quilt = 'quilt+s3://nf-core-gallery#package=nf-core/hlatyping&path=README_NF_QUILT.md'
+// file(test_file_local), file(test_file_s3), file(test_file_quilt)
+myFileChannel = Channel.fromList([file(test_file_s3), file(test_file_quilt)])
+
+process CHECK_INPUT {
+    input:
+        path input
+
+    output:
+        path 'README_NF_QUILT.md', emit: output
+
+    script:
+    """
+    ls -l
+    echo $input
+    cp -f $input ../../tmp
+    """
+}
+
+workflow {
+    CHECK_INPUT(myFileChannel)
+}

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

@@ -162,6 +162,7 @@ class QuiltPackage {
     void setup() {
         Files.createDirectories(this.folder)
         this.installed = false
+        install() // FIXME: only needed for nextflow < 23.12?
     }
 
     boolean is_force() {
@@ -197,7 +198,7 @@ class QuiltPackage {
             log.error("failed to install $packageName")
             // this is non-fatal error, so we don't want to stop the pipeline
             /* groovylint-disable-next-line ReturnNullFromCatchBlock */
-            return
+            return null
         }
 
         installed = true

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy

@@ -103,7 +103,6 @@ class QuiltParser {
                     result[key] = value
                 }
             }
-
         }
         return result
     }

plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy

@@ -110,15 +110,22 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     }
 
     void download(Path remoteFile, Path localDestination, CopyOption... options) throws IOException {
-        // log.debug "QuiltFileSystemProvider.download: ${remoteFile} -> ${localDestination}"
+        log.debug "QuiltFileSystemProvider.download: ${remoteFile} -> ${localDestination}"
         QuiltPath qPath = asQuiltPath(remoteFile)
         Path cachedFile = qPath.localPath()
         QuiltPackage pkg = qPath.pkg()
         if (!pkg.installed) {
-            pkg.install()
+            log.info "download.install Quilt package: ${pkg}"
+            Path dest = pkg.install()
+            if (!dest) {
+                log.error "download.install failed: ${pkg}"
+                throw new IOException("Failed to install Quilt package: ${pkg}")
+            }
+            log.info "download.installed Quilt package to: $dest"
         }
 
         if (!Files.exists(cachedFile)) {
+            log.error "download: File ${cachedFile} not found"
             throw new NoSuchFileException(remoteFile.toString())
         }
 
@@ -128,6 +135,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             FileHelper.deletePath(localDestination)
         }
         else if (Files.exists(localDestination)) {
+            log.error "download: File ${localDestination} already exists"
             throw new FileAlreadyExistsException(localDestination.toString())
         }
 

plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.7.7
+Plugin-Version: 0.7.9
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6