Use proper hurdat2 package (with README)

quiltdata · Jan 26, 2024 · 55aaa11 · 55aaa11
1 parent cb59d97
commit 55aaa11
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Showing 3 changed files with 11 additions and 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
@@ -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
@@ -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
@@ -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)