fix linting

quiltdata · Nov 13, 2024 · ddc3da0 · ddc3da0
1 parent 0e0cff2
commit ddc3da0
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Showing 10 changed files with 49 additions and 41 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy
@@ -33,7 +33,10 @@ class QuiltObserverFactory implements TraceObserverFactory {
     @Override
     Collection<TraceObserver> create(Session session) {
         //log.debug("`create` ${this}")
-        return (Collection<TraceObserver>) [new QuiltObserver()]
+        Collection<QuiltObserver> quiltObservers = new ArrayList<>()
+        quiltObservers.add(new QuiltObserver())
+
+        return quiltObservers as Collection<TraceObserver>
     }
 
 }
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy
@@ -51,7 +51,7 @@ class QuiltPathify  {
             Files.copy(source, dest)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`")
+            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e")
         }
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -110,7 +110,7 @@ ${nextflow}
             Files.write(path, text.bytes)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$text` to `$path` for `${pkg}`")
+            log.error("writeString: cannot write `$text` to `$path` for `${pkg}`\n$e")
         }
     }
 
@@ -121,7 +121,7 @@ ${nextflow}
             Files.copy(source, dest)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`")
+            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e.message()")
         }
     }
 
@@ -182,7 +182,7 @@ ${nextflow}
         Map<String, Object> cf_meta = quilt_cf.navigate(KEY_META) as Map<String, Object> ?: [:]
         quilt_cf.remove(KEY_META)
         // println("getMetadata.cf_meta: ${cf_meta}")
-        Map pkg_meta = pkg.meta
+        Map pkg_meta = pkg.getMetadata()
         updateFlags(pkg_meta, quilt_cf)
 
         Map params = session.getParams()

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy
@@ -15,9 +15,6 @@
  */
 package nextflow.quilt.jep
 
-/* groovylint-disable-next-line ImportFromSamePackage */
-import nextflow.quilt.jep.QuiltParser
-
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -49,8 +49,8 @@ class QuiltPackage {
     private static final String INSTALL_PREFIX = 'QuiltPackage'
     static final Path INSTALL_ROOT = Files.createTempDirectory(INSTALL_PREFIX)
 
+    public final String packageName
     private final String bucket
-    private final String packageName
     private final QuiltParser parsed
     private final String hash
     private final Path folder
@@ -220,6 +220,10 @@ class QuiltPackage {
         return folder
     }
 
+    Map getMetadata() {
+        return this.meta
+    }
+
     /*
      * Package methods
      */

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy
@@ -92,20 +92,21 @@ class QuiltParser {
     static Map<String, Object> parseQuery(String query) {
         if (!query) { return [:] } // skip for urls without query params
         def params = query.split('&')
-        def result = [:]
+        Map<String,List<String>> result = [:]
         params.each { param ->
             def keyValue = param.split('=')
             if (keyValue.size() == 2) {
                 String key = decode(keyValue[0])
                 String value = decode(keyValue[1])
                 if (result.containsKey(key)) {
-                    if (result[key] instanceof List) {
-                        result[key] += value
+                    List<String> listVal = result[key]
+                    if (listVal instanceof List) {
+                        listVal << value
                     } else {
-                        result[key] = [result[key], value]
+                        result[key] = [listVal, value] as List<String>
                     }
                 } else {
-                    result[key] = value
+                    result[key] = value as List<String>
                 }
             }
         }

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributesView.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributesView.groovy
@@ -49,7 +49,7 @@ class QuiltFileAttributesView implements BasicFileAttributeView {
 
     /**
      * This API is implemented is not supported but instead of throwing an exception just do nothing
-     * to not break the method {@link java.nio.file.CopyMoveHelper#copyToForeignTarget(...)}
+     * to not break the method {@link java.nio.file.CopyMoveHelper copyToForeignTarget(...)}
      *
      * @param lastModifiedTime
      * @param lastAccessTime

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy
@@ -58,11 +58,11 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
         return quiltIDS
     }
 
-    void copy(QuiltPath source, QuiltPath target) {
+    static void copy(QuiltPath source, QuiltPath target) {
         throw new UnsupportedOperationException("NOT Implemented 'QuiltFileSystem.copy' `$source` -> `$target`")
     }
 
-    void delete(QuiltPath path) {
+    static void delete(QuiltPath path) {
         //log.debug("QuiltFileSystem.delete: $path")
         path.deinstall()
     //throw new UnsupportedOperationException("Operation 'delete' is not supported by QuiltFileSystem")
@@ -93,7 +93,7 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
         return QuiltParser.SEP
     }
 
-    QuiltFileAttributesView getFileAttributeView(QuiltPath path) {
+    static QuiltFileAttributesView getFileAttributeView(QuiltPath path) {
         //log.debug("QuiltFileAttributesView QuiltFileSystem.getFileAttributeView($path)")
         String pathString = path.toUriString()
         try {
@@ -105,20 +105,20 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
         }
     }
 
-    QuiltFileAttributes readAttributes(QuiltPath path)  {
+    static QuiltFileAttributes readAttributes(QuiltPath path)  {
         log.debug("QuiltFileAttributes QuiltFileSystem.readAttributes($path)")
         Path installedPath = path.localPath()
         try {
             BasicFileAttributes attrs = Files.readAttributes(installedPath, BasicFileAttributes)
             return new QuiltFileAttributes(path, path.toString(), attrs)
         }
         catch (NoSuchFileException e) {
-            log.debug("No attributes yet for: ${installedPath}")
+            log.debug("No attributes yet for: ${installedPath}\n$e")
         }
         return null
     }
 
-    boolean exists(QuiltPath path) {
+    static boolean exists(QuiltPath path) {
         return path.pkg().isInstalled()
     }
 
@@ -145,15 +145,15 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
         return new QuiltPath(this, p)
     }
 
-    String toUriString(Path path) {
+    static String toUriString(Path path) {
         return path in QuiltPath ? ((QuiltPath)path).toUriString() : null
     }
 
-    String getBashLib(Path path) {
+    static String getBashLib(Path path) {
         return path in QuiltPath ? QuiltBashLib.script() : null
     }
 
-    String getUploadCmd(String source, Path target) {
+    static String getUploadCmd(String source, Path target) {
         return target in QuiltPath ?  QuiltFileCopyStrategy.uploadCmd(source, target) : null
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -34,7 +34,6 @@ 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
 import java.nio.file.attribute.FileAttribute
@@ -94,12 +93,12 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     boolean canUpload(Path source, Path target) {
         log.debug "QuiltFileSystemProvider.canUpload: ${source} -> ${target}"
-        return FileSystems.getDefault().equals(source.getFileSystem()) && target instanceof QuiltPath
+        return FileSystems.getDefault() == source.getFileSystem() && target instanceof QuiltPath
     }
 
     boolean canDownload(Path source, Path target) {
         log.debug "QuiltFileSystemProvider.canDownload: ${source} -> ${target}"
-        return source instanceof QuiltPath && FileSystems.getDefault().equals(target.getFileSystem())
+        return source instanceof QuiltPath && FileSystems.getDefault() == target.getFileSystem()
     }
 
     void download(Path remoteFile, Path localDestination, CopyOption... options) throws IOException {
@@ -161,7 +160,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         return QuiltParser.SCHEME
     }
 
-    String getQuiltIDS(URI uri) {
+    static String getQuiltIDS(URI uri) {
         assert uri
         QuiltParser parsed = QuiltParser.forURI(uri)
         return parsed.quiltID().toString()
@@ -213,6 +212,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     /* groovylint-disable-next-line UnusedMethodParameter */
     QuiltFileSystem newFileSystem(String quiltIDS, Map<String, ?> env) throws IOException {
+        log.debug("newFileSystem $env")
         final fs = new QuiltFileSystem(quiltIDS, this)
         fileSystems[quiltIDS] = fs
         return fs
@@ -301,7 +301,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         return new QuiltPath(fs, parsed)
     }
 
-    void checkRoot(Path path) {
+    static void checkRoot(Path path) {
         if (path == Paths.get('/')) {
             throw new UnsupportedOperationException("Operation 'checkRoot' not supported on root path")
         }
@@ -316,7 +316,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     * @return
     * @throws IOException
     */
-    void notifyFilePublish(QuiltPath destination) { //, Path source=null) {
+    static void notifyFilePublish(QuiltPath destination) { //, Path source=null) {
         final sess = Global.session
         /* groovylint-disable-next-line Instanceof */
         if (sess instanceof Session) {
@@ -345,12 +345,13 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             FileChannel channel = FileChannel.open(installedPath, options)
             return channel
         }
-        catch (java.nio.file.NoSuchFileException e) {
-            log.error("Failed `FileChannel.open`: ${installedPath} <- ${options}")
+        catch (NoSuchFileException e) {
+            log.error("Failed `FileChannel.open`: ${installedPath} <- ${options}\n$e")
         }
+        return null
       }
 
-    DirectoryStream<Path> emptyStream() throws IOException {
+    static DirectoryStream<Path> emptyStream() throws IOException {
         return new DirectoryStream<Path>() {
 
             @Override
@@ -450,32 +451,32 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     }
 
     @Override
-    def <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V> type, LinkOption... options) {
+    <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V> type, LinkOption... options) {
         // log.debug("Calling `getFileAttributeView`: ${path}")
         checkRoot(path)
         if (type == BasicFileAttributeView || type == QuiltFileAttributesView) {
             QuiltPath qPath = asQuiltPath(path)
-            QuiltFileSystem fs = qPath.filesystem
+            QuiltFileSystem fs = qPath.getFileSystem() as QuiltFileSystem
             return (V)fs.getFileAttributeView(qPath)
         }
         throw new UnsupportedOperationException("Operation 'getFileAttributeView' is not supported for type $type")
     }
 
     @Override
-    def <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type, LinkOption... options)
+    <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type, LinkOption... options)
          throws IOException {
         log.debug '<A>BasicFileAttributes QuiltFileSystemProvider.readAttributes()'
         def attr = attributesCache.get(path)
         if (attr) {
-            return attr
+            return attr as A
         }
         if (type == BasicFileAttributes || type == QuiltFileAttributes) {
             QuiltPath qPath = asQuiltPath(path)
-            QuiltFileSystem fs = qPath.filesystem
+            QuiltFileSystem fs = qPath.getFileSystem() as QuiltFileSystem
             def result = (A)fs.readAttributes(qPath)
             if (result) {
                 attributesCache[path] = result
-                return result
+                return result as A
             }
             log.debug("readAttributes: File ${qPath.localPath()} not found")
             if (!qPath.isNull()) {
@@ -484,7 +485,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             log.warn("readAttributes: Ignore ${qPath} for null bucket")
         }
         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 {

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -21,6 +21,7 @@ import nextflow.quilt.jep.QuiltParser
 import java.nio.file.Files
 import java.nio.file.FileSystem
 import java.nio.file.LinkOption
+import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 import java.nio.file.Paths
 import java.nio.file.ProviderMismatchException
@@ -112,10 +113,11 @@ final class QuiltPath implements Path, Comparable {
         log.debug("QuiltPath.deinstall: $path")
         try {
             Files.delete(path)
-        } catch (java.nio.file.NoSuchFileException e) {
+        } catch (NoSuchFileException e) {
             // Handle the exception here
             log.error("Failed to delete path: $path", e)
         }
+        return false
     }
 
     @Override