groovy4 fixes

quiltdata · Dec 6, 2024 · 4de2b84 · 4de2b84
1 parent a2d0ccd
commit 4de2b84
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Showing 10 changed files with 35 additions and 37 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,4 +1,4 @@
 {
-  "java.compile.nullAnalysis.mode": "disabled",
-  "java.configuration.updateBuildConfiguration": "disabled"
+  "java.compile.nullAnalysis.mode": "enabled",
+  "java.configuration.updateBuildConfiguration": "enabled"
 }
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy
@@ -33,7 +33,7 @@ class QuiltObserverFactory implements TraceObserverFactory {
     @Override
     Collection<TraceObserver> create(Session session) {
         //log.debug("`create` ${this}")
-        Collection<QuiltObserver> quiltObservers = new ArrayList<>()
+        Collection<QuiltObserver> quiltObservers = new ArrayList<QuiltObserver>()
         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 `${destRoot}`\n$e")
+            println("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e")
         }
     }
 
@@ -73,12 +73,12 @@ class QuiltPathify  {
      * - path: inputs/a_folder/THING_TWO.md
      */
     static String uriFromS3File(String s3path) {
-        log.debug("uriFromS3File: $s3path")
+        println("uriFromS3File: $s3path")
         String[] partsArray = s3path.split('/')
         List<String> parts = new ArrayList(partsArray.toList())
         // parts.eachWithIndex { p, i -> println("uriFromS3File.parts[$i]: $p") }
         if (parts.size() < 2) {
-            log.error("uriFromS3File: invalid path: $s3path")
+            println("uriFromS3File: invalid path: $s3path")
             return ''
         }
         parts.remove(0) // remove leading slash
@@ -90,7 +90,7 @@ class QuiltPathify  {
         String folder = parts.join('/')
         String sub_path = folder.length() > 0 ? folder + '/' + file : file
 
-        log.debug("uriFromS3File: $bucket/$prefix/$suffix/$sub_path")
+        // println("uriFromS3File: $bucket/$prefix/$suffix/$sub_path")
         String base = "quilt+s3://${bucket}#package=${prefix}%2f${suffix}"
         String uri = base + '&path=' + sub_path
         return uri
@@ -101,11 +101,11 @@ class QuiltPathify  {
         println("QuiltPathify: $path")
         if (path in QuiltPath) {
             this.path = (QuiltPath) path
-            println("\tQuiltPathify.QuiltPath: $this.path")
+            println("\tQuiltPathify.QuiltPath: ${this}.path")
             this.uri = this.path.toUriString()
-            println("\t\tQuiltPathify.QuiltPath.uri: $this.uri")
+            println("\t\tQuiltPathify.QuiltPath.uri: ${this}.uri")
             this.pkg = this.path.pkg()
-            println("\t\tQuiltPathify.QuiltPath.pkg: $this.pkg")
+            println("\t\tQuiltPathify.QuiltPath.pkg: ${this}.pkg")
         } else if (!findQuiltPath(path.getFileName().toString())) {
             makeQuiltPath(path.toString())
             this.isOverlay = true

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
@@ -96,7 +96,7 @@ ${nextflow}
     ]
 
     static void printMap(Map map, String title) {
-        log.info("\n\n\n# $title ${map.keySet()}")
+        println("\n\n\n# $title ${map.keySet()}")
         map.each {
             key, value -> log.info("\n## ${key}: ${value}")
         }
@@ -115,7 +115,7 @@ ${nextflow}
             Files.write(path, text.bytes)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$text` to `$path` for `${pkg}`\n$e")
+            println("writeString: cannot write `$text` to `$path` for `${pkg}`\n$e")
         }
     }
 
@@ -126,7 +126,7 @@ ${nextflow}
             Files.copy(source, dest)
         }
         catch (Exception e) {
-            log.error("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e.message()")
+            println("writeString: cannot write `$source` to `$dest` in `${destRoot}`\n$e.message()")
         }
     }
 
@@ -325,11 +325,11 @@ ${nextflow}
             return null
         }
         String raw_readme = flags.getProperty(KEY_README)
-        String nf = metadata['workflow']?['nextflow']
-        String nextflow = nf?.replace(', ', '```\n  - **')\
-            ?.replace('nextflow.NextflowMeta(', '  - **')\
-            ?.replace(')', '```')
-            ?.replace(':', '**: ```')
+        String nf = metadata['workflow']?.get('nextflow')
+        String nextflow = nf != null ? nf.replace(', ', '```\n  - **')
+            .replace('nextflow.NextflowMeta(', '  - **')
+            .replace(')', '```')
+            .replace(':', '**: ```') : null
         Map params = getTemplateArgs()
         params += [
             msg: msg,

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy
@@ -31,18 +31,18 @@ class QuiltID {
 
     static QuiltID fetch(String bucket, String packageName) {
         if (!bucket) {
-            log.error("null == QuiltID.fetch($bucket, $packageName)")
+            println("null == QuiltID.fetch($bucket, $packageName)")
             return null
         }
         String pkgName = packageName
         if (!packageName || packageName.size() < QuiltParser.MIN_SIZE) {
             pkgName = DEFAULT_PACKAGE.join(QuiltParser.SEP)
-            log.warn("QuiltID.fetch: setting missing package to $pkgName")
+            println("QuiltID.fetch: setting missing package to $pkgName")
         }
         String[] split = pkgName.split(QuiltParser.SEP)
         if (split.size() < QuiltParser.MIN_SIZE || split[1].size() < QuiltParser.MIN_SIZE) {
             split += DEFAULT_PACKAGE[1] as String
-            log.warn("QuiltID.fetch: setting missing suffix to $split[1]")
+            println("QuiltID.fetch: setting missing suffix to $split[1]")
         }
         String key = "${bucket}/${split[0]}/${split[1]}"
         if (!QIDS.containsKey(key)) {

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -78,12 +78,12 @@ class QuiltPackage {
         List<String> entries = dict.collect { key, value ->
             String prefix = JsonOutput.toJson(key)
             String suffix = "toJson.error: ${value}"
-            log.debug("QuiltPackage.toJson: ${prefix} [${suffix.length()}]")
+            println("QuiltPackage.toJson: ${prefix} [${suffix.length()}]")
             try {
                 suffix = JsonOutput.toJson(value)
             }
             catch (Exception e) {
-                log.error(suffix, e)
+                println("$suffix:\n$e")
             }
             return "${prefix}:${suffix}".toString()
         }
@@ -102,7 +102,7 @@ class QuiltPackage {
         }
 
         String pkgKey = parsed.toPackageString(true) // ignore metadata for Key
-        log.info("QuiltPackage.forParsed[${pkgKey}]")
+        println("QuiltPackage.forParsed[${pkgKey}]")
         def pkg = PKGS.get(pkgKey)
         if (pkg) { return pkg }
 
@@ -120,7 +120,7 @@ class QuiltPackage {
             if (!Files.exists(rootPath)) { return false }
         }
         catch (SecurityException e) {
-            log.warn("Cannnot verify whether `$rootPath` exists: $e")
+            println("Cannnot verify whether `$rootPath` exists: $e")
         }
         try {
             final List<Path> pathsToDelete = listDirectory(rootPath)
@@ -129,7 +129,7 @@ class QuiltPackage {
             }
         }
         catch (NoSuchFileException e) {
-            log.debug "deleteDirectory: ignore non-existent files\n$e"
+            println "deleteDirectory: ignore non-existent files\n$e"
         }
         return true
     }
@@ -233,9 +233,7 @@ class QuiltPackage {
             S3PhysicalKey registryPath = new S3PhysicalKey(bucket, '', null)
             Registry registry = new Registry(registryPath)
             Namespace namespace = registry.getNamespace(packageName)
-            String resolvedHash = (hash == 'latest' || hash == null || hash == 'null')
-              ? namespace.getHash('latest')
-              : hash
+            String resolvedHash = (hash == 'latest' || hash == null || hash == 'null') ? namespace.getHash('latest') : hash
             log.debug("hash: $hash -> $resolvedHash")
             Manifest manifest = namespace.getManifest(resolvedHash)
 
@@ -294,7 +292,7 @@ class QuiltPackage {
 
         Manifest.Builder builder = Manifest.builder()
 
-        Files.walk(packageDest()).filter(f -> Files.isRegularFile(f)).forEach(f -> {
+        Files.walk(packageDest()).filter({ f -> Files.isRegularFile(f) }).forEach({ f ->
             log.debug("push: ${f} -> ${packageDest()}")
             String logicalKey = packageDest().relativize(f)
             LocalPhysicalKey physicalKey = new LocalPhysicalKey(f)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy
@@ -60,7 +60,7 @@ class QuiltParser {
     }
 
     static QuiltParser forURI(URI uri) {
-        log.debug("forURI[${uri.scheme}] for ${uri}")
+        println("forURI[${uri.scheme}] for ${uri}")
         if (uri.scheme != SCHEME) {
             String msg =  "Scheme[${uri}] URI:${uri.scheme}] != SCHEME:${SCHEME}"
             throw new IllegalArgumentException(msg)

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy
@@ -106,14 +106,14 @@ final class QuiltFileSystem extends FileSystem implements Closeable {
     }
 
     static QuiltFileAttributes readAttributes(QuiltPath path)  {
-        log.debug("QuiltFileAttributes QuiltFileSystem.readAttributes($path)")
+        //println("QuiltFileAttributes QuiltFileSystem.readAttributes($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: ${installedPath}\n$e")
+            println("No attributes yet for: ${installedPath}\n$e")
         }
         return 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
@@ -63,7 +63,7 @@ import nextflow.file.FileHelper
 @CompileStatic
 class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTransferAware {
 
-    private final Map<String,String> myEnv = new HashMap<>(System.getenv())
+    private final Map<String,String> myEnv = new HashMap<String,String>(System.getenv())
     private final Map<String,QuiltFileSystem> fileSystems = [:]
     private Map<Path,BasicFileAttributes> attributesCache = [:]
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -55,19 +55,19 @@ final class QuiltPath implements Path, Comparable <Path> {
         }
         String base = filename
         if (n_package > 1) {
-            log.info("\tfindQuiltPath: multiple '#package' in $base")
+            println("\tfindQuiltPath: multiple '#package' in $base")
             println('\t\tTO MATCH')
             Matcher matches = (filename =~ /^([^#]+#package=.*)?(?:(?!%2f).)*#package=/)
             if (!matches) {
-                log.error("findQuiltPath: no match found for $filename")
+                println("findQuiltPath: no match found for $filename")
                 return null
             }
             println('\t\tDID MATCH')
             println("\tfindQuiltPath.matches: $matches")
             List<String> parts = matches[0] as List<String>
             println("\tfindQuiltPath.parts: $parts")
             base = parts[1]
-            log.info("\tfindQuiltPath: trimmed to $base")
+            println("\tfindQuiltPath: trimmed to $base")
         }
         return base
     }