Files.copy(tempFile, installedFile)

quiltdata · Sep 10, 2023 · 3770b5d · 3770b5d
1 parent 51eb557
commit 3770b5d
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Showing 2 changed files with 46 additions and 12 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -46,6 +46,8 @@ import nextflow.Session
 import nextflow.file.FileSystemTransferAware
 import nextflow.quilt.jep.QuiltParser
 import nextflow.quilt.jep.QuiltPackage
+import sun.nio.fs.UnixFileSystemProvider
+import sun.nio.fs.MacOSXFileSystemProvider
 
 /**
  * Implements NIO File system provider for Quilt Blob Storage
@@ -85,22 +87,33 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         return path.getFileSystem().provider()
     }
 
-    boolean canUpload(Path source, Path target) {
-        log.debug("QuiltFileSystemProvider.canUpload[${source}] -> ${target}")
-        return false
+    static boolean localProvider(Path path) {
+        FileSystemProvider provider = provider(path)
+        log.debug("QuiltFileSystemProvider.localProvider[${path}] -> ${provider}")
+        return provider instanceof UnixFileSystemProvider ||
+               provider instanceof MacOSXFileSystemProvider
     }
 
     boolean canDownload(Path source, Path target) {
         log.debug("QuiltFileSystemProvider.canDownload[${source}] -> ${target}")
-        return false
+        return localProvider(target) && source instanceof QuiltPath
+    }
+
+    boolean canUpload(Path source, Path target) {
+        log.debug("QuiltFileSystemProvider.canUpload[${source}] -> ${target}")
+        return localProvider(source) && target instanceof QuiltPath
     }
 
     void download(Path source, Path target, CopyOption... options) throws IOException {
-        throw new UnsupportedOperationException("Operation 'download' is not supported by QuiltFileSystem")
+        QuiltPath qSource = asQuiltPath(source)
+        Path local_source = qSource.localPath()
+        Files.copy(local_source, target, options)
     }
 
     void upload(Path source, Path target, CopyOption... options) throws IOException {
-        throw new UnsupportedOperationException("Operation 'upload' is not supported by QuiltFileSystem")
+        QuiltPath qTarget = asQuiltPath(target)
+        Path local_target = qTarget.localPath()
+        Files.copy(source, local_target, options)
     }
 
     /**
@@ -359,7 +372,7 @@ 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

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
@@ -86,6 +86,31 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.exists(installPath)
     }
 
+    void 'should copy temp files into install folder'() {
+        given:
+        String filename = 'test.txt'
+        Path installPath = pkg.packageDest()
+        Path tempFile = File.createTempFile('test', '.txt').toPath()
+        println("tempFile: "+tempFile);
+        Path installedFile = Paths.get(installPath.toString(), filename)
+        expect:
+        Files.exists(tempFile)
+        Files.exists(installPath)
+        !Files.exists(installedFile)
+        Files.copy(tempFile, installedFile)
+        Files.exists(installedFile)
+    }
+
+    void 'should copy package files to temp Path'() {
+        given:
+        Path installPath = pkg.packageDest()
+        expect:
+        Files.exists(installPath)
+        Files.isDirectory(installPath)
+        Files.readAttributes(installPath, BasicFileAttributes)
+    }
+
+
     void 'should get attributes for package folder'() {
         given:
         def root = qpath.getRoot()
@@ -106,6 +131,7 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.readAttributes(qpath, BasicFileAttributes)
     }
 
+
     void 'should return null on failed install'() {
         given:
         def url2 = TEST_URL.replace('quilt-', 'quilted-')
@@ -125,11 +151,6 @@ class QuiltPackageTest extends QuiltSpecification {
         qpath.deinstall()
         then:
         !Files.exists(qpath.localPath(false))
-
-        /*when:
-        Files.readAttributes(qpath, BasicFileAttributes)
-        then:
-        thrown(java.nio.file.NoSuchFileException)*/
     }
 
     void 'should iterate over installed files '() {