feat: #231 fix pkg-input (#232)

#231 
> Files.copy -> FileUtils.copyDirectory
Because Java's Files.copy WILL copy a directory withOUT its contents.

---------

Co-authored-by: Dr. Ernie Prabhakar <[email protected]>

.github/workflows/test.yml

@@ -68,6 +68,6 @@ jobs:
       with:
         name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
         path: |
-            ${{ github.workspace }}/nf-quilt/plugins/nf-quilt/build/reports/tests/test/
+            ${{ github.workspace }}/plugins/nf-quilt/build/reports/tests/test/
         overwrite: true
 

README.md

@@ -6,7 +6,7 @@ Nextflow plugin for reading and writing Quilt packages as a FileSystem
 developed by [Quilt Data](https://quiltdata.com/) that enables you read and write directly
 to Quilt packages using `quilt+s3` URIs wherever your Nextflow pipeline currently use `s3` URIs.
 
-In v0.8.0, the plugin can even be used with "native" URIs, and it will automatically register a Quilt package at the root of the bucket.
+In v0.8+, the plugin can even be used with "native" URIs, and it will automatically register a Quilt package at the root of the bucket.
 
 Inspired by the original [`nf-quilt`](https://github.com/nextflow-io/nf-quilt) plugin (v0.2.0) developed by Seqera labs.
 
@@ -80,8 +80,8 @@ From the command-line, do, e.g.:
 ```bash
 # export NXF_VER=23.04.3
 export LOG4J_DEBUG=true  # for verbose logging
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.16/nf-quilt-0.7.16-meta.json
-nextflow run main.nf -plugins nf-quilt@0.7.16
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.8.0/nf-quilt-0.8.0-meta.json
+nextflow run main.nf -plugins nf-quilt@0.8.0
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

plugins/nf-quilt/build.gradle

@@ -85,6 +85,7 @@ dependencies {
     compileOnly 'black.ninia:jep:4.2.0'
     runtime 'black.ninia:jep:4.2.0'
     runtimeOnly 'org.junit.platform:junit-platform-launcher:1.11.0'
+    implementation 'commons-io:commons-io:2.11.0'
     implementation 'black.ninia:jep:4.2.0'
     testImplementation 'black.ninia:jep:4.2.0'
     //testImplementation(testFixtures('black.ninia:jep:4.0.3'))

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

@@ -42,6 +42,7 @@ import java.nio.file.spi.FileSystemProvider
 import java.nio.file.FileSystems
 import java.nio.file.FileAlreadyExistsException
 
+import org.apache.commons.io.FileUtils
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Global
@@ -139,7 +140,11 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             throw new FileAlreadyExistsException(localDestination.toString())
         }
 
-        Files.copy(cachedFile, localDestination, options)
+        if (Files.isDirectory(cachedFile)) {
+            FileUtils.copyDirectory(cachedFile.toFile(), localDestination.toFile())
+        } else {
+            Files.copy(cachedFile, localDestination, options)
+        }
     }
 
     void upload(Path localFile, Path remoteDestination, CopyOption... options) throws IOException {

plugins/nf-quilt/src/test/nextflow/quilt/QuiltSpecification.groovy

@@ -109,7 +109,7 @@ class QuiltSpecification extends Specification {
 
     Path makeObject(String url, String text) {
         assert url
-        Path path  = Paths.get(new URI(url))
+        Path path  = QuiltPathFactory.parse(url)
         return makeObject(path, text)
     }
 

plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy

@@ -111,7 +111,6 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.readAttributes(qpath, BasicFileAttributes)
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should successfully install files and get attributes'() {
         expect:
         pkg.install()
@@ -120,7 +119,6 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.readAttributes(qpath, BasicFileAttributes)
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should download the specified path'() {
         given:
         def qpath = factory.parseUri(TEST_URL)
@@ -167,7 +165,6 @@ class QuiltPackageTest extends QuiltSpecification {
         thrown(RuntimeException)
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should deinstall files'() {
         expect:
         Files.exists(qpath.localPath())

plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy

@@ -4,10 +4,10 @@ package nextflow.quilt.nio
 import nextflow.quilt.QuiltSpecification
 import groovy.transform.CompileDynamic
 import java.nio.file.Path
-import java.nio.file.Paths
 import java.nio.file.Files
+import java.nio.file.CopyOption
+import java.nio.file.StandardCopyOption
 import groovy.util.logging.Slf4j
-import spock.lang.IgnoreIf
 
 /**
  *
@@ -28,12 +28,11 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
     // newDirectoryStream returns package path for write
     // do we need a new schema for quilt+local?
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should download file from remote to local destination'() {
         given:
         QuiltFileSystemProvider provider = new QuiltFileSystemProvider()
         String filename = 'README.md'
-        Path remoteFile = Paths.get('quilt+s3://quilt-example#package=examples%2fhurdat2&path=' + filename)
+        Path remoteFile = QuiltPathFactory.parse('quilt+s3://quilt-example#package=examples%2fhurdat2&path=' + filename)
         Path tempFolder = Files.createTempDirectory('quilt')
         Path tempFile = tempFolder.resolve(filename)
 
@@ -45,4 +44,18 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
         Files.size(tempFile) > 0
     }
 
+    void 'should download folders from remote to local destination'() {
+        given:
+        QuiltFileSystemProvider provider = new QuiltFileSystemProvider()
+        Path remoteFolder = QuiltPathFactory.parse('quilt+s3://quilt-example#package=examples%2fhurdat2')
+        Path tempFolder = Files.createTempDirectory('quilt')
+        CopyOption opt = StandardCopyOption.REPLACE_EXISTING
+        when:
+        provider.download(remoteFolder, tempFolder, opt)
+
+        then:
+        Files.exists(tempFolder)
+        Files.list(tempFolder).count() > 0
+    }
+
 }

plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltNioTest.groovy

@@ -66,10 +66,9 @@ class QuiltNioTest extends QuiltSpecification {
         readObject(path).trim() == TEXT
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should read from a path'() {
         given:
-        QuiltPath path = Paths.get(new URI(READ_URL)) as QuiltPath
+        QuiltPath path = QuiltPathFactory.parse(READ_URL)
         path.pkg().install()
 
         when:
@@ -80,15 +79,15 @@ class QuiltNioTest extends QuiltSpecification {
         text.startsWith('id')
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('ux') })
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
+    @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') ||
+                System.getProperty('os.name').toLowerCase().contains('linux') })
     void 'should read file attributes'() {
         given:
         final start = System.currentTimeMillis()
         final root = 'folder'
         final start_path = "${root}/${start}.txt"
         final start_url = packagePath(start_path)
-        Path path = Paths.get(new URI(start_url))
+        Path path = QuiltPathFactory.parse(start_url)
 
         when:
         makeObject(path, TEXT)
@@ -513,7 +512,8 @@ class QuiltNioTest extends QuiltSpecification {
         list  == [ 'file4.txt' ]
     }
 
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
+    // \QuiltPackage.quilt_dev_null_test_null\foo
+    @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') })
     void 'should check walkTree'() {
         given:
         makeObject(null_path('foo/file1.txt'), 'A')
@@ -526,7 +526,7 @@ class QuiltNioTest extends QuiltSpecification {
         when:
         List<String> dirs = []
         Map<String,BasicFileAttributes> files = [:]
-        Path base = Paths.get(new URI(NULL_URL))
+        Path base = QuiltPathFactory.parse(NULL_URL)
         Files.walkFileTree(base, new SimpleFileVisitor<Path>() {
 
             @Override

plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy

@@ -6,7 +6,6 @@ import nextflow.quilt.jep.QuiltParser
 import nextflow.quilt.jep.QuiltPackage
 
 import java.nio.file.Path
-import java.nio.file.Paths
 import groovy.util.logging.Slf4j
 import groovy.transform.CompileDynamic
 
@@ -28,13 +27,12 @@ class QuiltPathTest extends QuiltSpecification {
 
     QuiltPath pathify(String path) {
         if (!path.contains(BKT)) {
-            URI uri = new URI(PKG_URL)
-            QuiltPath pkgPath = Paths.get(uri)
+            QuiltPath pkgPath = QuiltPathFactory.parse(PKG_URL)
             QuiltFileSystem qfs = pkgPath.getFileSystem()
             return qfs.getPath(path)
         }
         String url = QuiltParser.PREFIX + path
-        return Paths.get(new URI(url))
+        return QuiltPathFactory.parse(url)
     }
 
     @Unroll
@@ -240,7 +238,7 @@ class QuiltPathTest extends QuiltSpecification {
     }
 
     @Unroll
-    @IgnoreIf({ System.getProperty('os.name').contains('indows') })
+    @IgnoreIf({ System.getProperty('os.name').toLowerCase().contains('windows') })
     void 'should validate relativize'() {
         expect:
         pathify(path).relativize(pathify(other)).toString() == pathify(expected).toString()