remove extraneous debugging

quiltdata · Jan 26, 2024 · 3c9a552 · 3c9a552
1 parent 55aaa11
commit 3c9a552
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Showing 3 changed files with 2 additions and 20 deletions.
diff --git 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
@@ -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<Path,BasicFileAttributes> 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
@@ -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)
     }