diff --git a/main.path.nf b/main.path.nf index aa1f5894..a4f39c7e 100644 --- a/main.path.nf +++ b/main.path.nf @@ -4,8 +4,8 @@ nextflow.enable.dsl=2 test_file_local = 'README.md' -test_file_s3 = 's3://quilt-example/examples/protein-paint/README.md' -test_file_quilt = 'quilt+s3://quilt-example#package=examples/protein-paint&path=README.md' +test_file_s3 = 's3://quilt-example/examples/hurdat2/README.md' +test_file_quilt = 'quilt+s3://quilt-example#package=examples/hurdat2&path=README.md' myFileChannel = Channel.fromList([file(test_file_local), file(test_file_s3), file(test_file_quilt)]) diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy index 9c10afa7..24c8aff3 100644 --- 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 @@ -68,15 +66,12 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr private Map attributesCache = [:] static QuiltPath asQuiltPath(Path path) { - println("asQuiltPath.path: ${path}") if (path in QuiltPath) { return (QuiltPath)path } String pathString = path?.toString() ?: '-' - println("asQuiltPath.pathString: ${pathString}") if (pathString.startsWith(QuiltParser.SCHEME + ':/')) { QuiltPath qPath = QuiltPathFactory.parse(pathString) - println("asQuiltPath.qPath: ${qPath}") return qPath } String pathClassName = path?.class?.name ?: '-' @@ -116,16 +111,7 @@ 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.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.actualDestination: ${actualDestination}"*/ final CopyOptions opts = CopyOptions.parse(options) // delete target if it exists and REPLACE_EXISTING is specified diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy index c4a11aa3..b0a21eb5 100644 --- a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy +++ b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy @@ -40,16 +40,12 @@ class QuiltPathFactory extends FileSystemPathFactory { @Override protected Path parseUri(String uriString) { - println('parseUri.uriString: ' + uriString) if (!uriString.startsWith(QuiltParser.SCHEME)) { return null } String[] split = uriString.split('/') - println('parseUri.split: ' + split) String newString = (split[1] == '') ? uriString : uriString.replaceFirst(/\/+/, '//') - println('parseUri.newString: ' + newString) final uri = new URI(newString) - println('parseUri.uri: ' + uri) return FileHelper.getOrCreateFileSystemFor(uri).provider().getPath(uri) }