pass path-input integration test

quiltdata · Jan 27, 2024 · 19a588c · 19a588c
1 parent b6c8387
commit 19a588c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,8 +2,9 @@
 
 ## [0.7.7] 2024-01-24
 
+- Properly implement and test getFilename()
 - Pre-install package if "&path" present
-- Add `path-input` integration test
+- Add and pass `path-input` integration test
 - Add unit test for "&path=" Quilt+ URIs
 
 ## [0.7.6] 2024-01-10 UNOFFICIAL

diff --git a/main.path.nf b/main.path.nf
@@ -20,9 +20,7 @@ process CHECK_INPUT {
     """
     ls -l
     echo $input
-    if [ "$input" != "README.md" ]; then
-        cp -f $input README.md
-    fi
+    cp -f $input ../../tmp
     """
 }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -33,7 +33,6 @@ import java.nio.file.LinkOption
 import java.nio.file.NoSuchFileException
 import java.nio.file.OpenOption
 import java.nio.file.Path
-import java.nio.file.Paths
 import java.nio.file.StandardOpenOption
 import java.nio.file.attribute.BasicFileAttributeView
 import java.nio.file.attribute.BasicFileAttributes
@@ -48,7 +47,6 @@ 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
@@ -101,28 +99,22 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
      */
 
     boolean canUpload(Path source, Path target) {
-        log.debug "QuiltFileSystemProvider.canUpload: ${source} -> ${target}"
+        // log.debug "QuiltFileSystemProvider.canUpload: ${source} -> ${target}"
         return FileSystems.getDefault().equals(source.getFileSystem()) && target instanceof QuiltPath
     }
 
     boolean canDownload(Path source, Path target) {
-        log.debug "QuiltFileSystemProvider.canDownload: ${source} -> ${target}"
+        // log.debug "QuiltFileSystemProvider.canDownload: ${source} -> ${target}"
         return source instanceof QuiltPath && FileSystems.getDefault().equals(target.getFileSystem())
     }
 
     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()
-        log.debug "download.cachedFile: ${cachedFile} [${qPath}]"
-
-        QuiltPackage pkg = qPath.pkg()
-        String pathName = pkg.parsed.getPath()
-
-        Path localRoot = localDestination.getParent().getParent().getParent().getParent()
-        Path finalDestination = Paths.get(localRoot.toUriString(), 'tmp', pathName)
-        log.debug "download.finalDestination: ${finalDestination} [${localRoot}]"
-        FileHelper.deletePath(finalDestination) // FIXME: be more intelligent about this
+        if (!Files.exists(cachedFile)) {
+            throw new NoSuchFileException(remoteFile.toString())
+        }
 
         final CopyOptions opts = CopyOptions.parse(options)
         // delete target if it exists and REPLACE_EXISTING is specified
@@ -133,15 +125,11 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             throw new FileAlreadyExistsException(localDestination.toString())
         }
 
-        log.info "download.Files.copy -> ${localDestination}"
         Files.copy(cachedFile, localDestination, options)
-        // log.info "download.Files.copy -> ${finalDestination}"
-        // Files.copy(localDestination, finalDestination, options)
-        log.info 'download.Files copied'
     }
 
     void upload(Path localFile, Path remoteDestination, CopyOption... options) throws IOException {
-        log.debug "QuiltFileSystemProvider.upload: ${localFile} -> ${remoteDestination}"
+        // log.debug "QuiltFileSystemProvider.upload: ${localFile} -> ${remoteDestination}"
         final CopyOptions opts = CopyOptions.parse(options)
         // delete target if it exists and REPLACE_EXISTING is specified
         if (opts.replaceExisting()) {
@@ -303,7 +291,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     QuiltPath getPath(URI uri) {
         QuiltParser parsed = QuiltParser.forURI(uri)
-        log.debug("QuiltFileSystemProvider.getPath`[${uri}]")
+        // log.debug("QuiltFileSystemProvider.getPath`[${uri}]")
         final fs = getFileSystem(parsed.quiltIDS(), true)
         return new QuiltPath(fs, parsed)
     }
@@ -334,7 +322,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     SeekableByteChannel newByteChannel(
       Path path, Set<? extends OpenOption> options, FileAttribute<?>... attrs) throws IOException {
-        //log.debug("Creating `newByteChannel`: ${path} <- ${options}")
+        // log.debug("Creating `newByteChannel`: ${path} <- ${options}")
         final modeWrite = options.contains(WRITE) || options.contains(APPEND)
 
         final QuiltPath qPath = asQuiltPath(path)
@@ -348,7 +336,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
                 attributesCache = [:] // reset cache
                 notifyFilePublish(qPath)
             }
-            //log.debug("\tOpening channel to: $installedPath")
+            // log.debug("\tOpening channel to: $installedPath")
             FileChannel channel = FileChannel.open(installedPath, options)
             return channel
         }
@@ -374,10 +362,10 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     DirectoryStream<Path> newDirectoryStream(Path obj, DirectoryStream.Filter<? super Path> filter) throws IOException {
         final qPath = asQuiltPath(obj)
-        //final dirPath = qPath.localPath()
-        //Files.newDirectoryStream(dirPath, filter)
+        // final dirPath = qPath.localPath()
+        // Files.newDirectoryStream(dirPath, filter)
 
-        //log.debug("QuiltFileSystemProvider.newDirectoryStream[${qPath.file_key()}]: ${qPath}")
+        // log.debug("QuiltFileSystemProvider.newDirectoryStream[${qPath.file_key()}]: ${qPath}")
 
         return new DirectoryStream<Path>() {
 
@@ -396,7 +384,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     void createDirectory(Path dir, FileAttribute<?>... attrs) throws IOException {
         final path = asQuiltPath(dir).localPath()
-        //log.debug("Calling createDirectory[${path}]: ${dir} ")
+        // log.debug("Calling createDirectory[${path}]: ${dir} ")
         Files.createDirectories(path)
     }
     /* groovylint-enable BuilderMethodWithSideEffects */
@@ -411,7 +399,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     @Override
     void copy(Path from, Path to, CopyOption... options) throws IOException {
-        //log.debug("Attempting `copy`: ${from} -> ${to}")
+        // log.debug("Attempting `copy`: ${from} -> ${to}")
         assert provider(from) == provider(to)
         if (from == to) {
             return // nothing to do -- just return
@@ -447,7 +435,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     @Override
     void checkAccess(Path path, AccessMode... modes) throws IOException {
-        //log.debug("Calling `checkAccess`: ${path}")
+        // log.debug("Calling `checkAccess`: ${path}")
         checkRoot(path)
         QuiltPath qPath = asQuiltPath(path)
         readAttributes(qPath, QuiltFileAttributes)
@@ -458,7 +446,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     @Override
     def <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V> type, LinkOption... options) {
-        //log.debug("Calling `getFileAttributeView`: ${path}")
+        // log.debug("Calling `getFileAttributeView`: ${path}")
         checkRoot(path)
         if (type == BasicFileAttributeView || type == QuiltFileAttributesView) {
             QuiltPath qPath = asQuiltPath(path)
@@ -471,7 +459,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     def <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type, LinkOption... options)
          throws IOException {
-        //log.debug '<A>BasicFileAttributes QuiltFileSystemProvider.readAttributes()'
+        // log.debug '<A>BasicFileAttributes QuiltFileSystemProvider.readAttributes()'
         def attr = attributesCache.get(path)
         if (attr) {
             return attr
@@ -484,15 +472,15 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
                 attributesCache[path] = result
                 return result
             }
-            //log.debug("readAttributes: File ${qPath.localPath()} not found")
+            // log.debug("readAttributes: File ${qPath.localPath()} not found")
             throw new NoSuchFileException(qPath.toUriString())
         }
         throw new UnsupportedOperationException("Not a valid Quilt Storage file attribute type: $type")
-         }
+    }
 
     @Override
     Map<String, Object> readAttributes(Path path, String attributes, LinkOption... options) throws IOException {
-        //log.debug 'Map<String, Object> QuiltFileSystemProvider.readAttributes()'
+        // log.debug 'Map<String, Object> QuiltFileSystemProvider.readAttributes()'
         throw new UnsupportedOperationException("Operation Map 'readAttributes' is not supported by QuiltFileSystem")
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -219,11 +219,8 @@ final class QuiltPath implements Path, Comparable {
 
     @Override
     String toString() {
-        println("toString.parsed[isFileName=$isFileName]: $parsed")
-        String filename = paths.size() > 0 ? paths[-1] : ''
-        println("toString:filename: ${filename}")
         if (isFileName) {
-            return filename
+            return paths.size() > 0 ? paths[-1] : ''
         }
         return parsed.toString()
     }