skip if hasNullBucket

quiltdata · Jun 17, 2024 · c7399c9 · c7399c9
1 parent ab2fba5
commit c7399c9
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Showing 5 changed files with 19 additions and 12 deletions.
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
@@ -170,8 +170,8 @@ class QuiltPackage {
         return parsed.options[QuiltParser.P_FORCE]
     }
 
-    boolean is_null() {
-        return parsed.isNullBucket()
+    boolean isNull() {
+        return parsed.hasNullBucket()
     }
 
     boolean isInstalled() {
@@ -183,8 +183,8 @@ class QuiltPackage {
     }
 
     Path install() {
-        if (is_null()) {
-            log.debug("null bucket: no need to install")
+        if (isNull()) {
+            log.debug('null bucket: no need to install')
             return null
         }
         Path dest = packageDest()
@@ -237,8 +237,8 @@ class QuiltPackage {
     }
     // https://docs.quiltdata.com/v/version-5.0.x/examples/gitlike#install-a-package
     Manifest push(String msg = 'update', Map meta = [:]) {
-        if (is_null()) {
-            log.debug("null bucket: no need to push")
+        if (isNull()) {
+            log.debug('null bucket: no need to push')
             return null
         }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy
@@ -273,7 +273,7 @@ class QuiltParser {
         return paths.size() > 0
     }
 
-    boolean isNullBucket() {
+    boolean hasNullBucket() {
         return NULL_BUCKET == getBucket()
     }
 

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
@@ -473,7 +473,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
     @Override
     def <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type, LinkOption... options)
          throws IOException {
-        // log.debug '<A>BasicFileAttributes QuiltFileSystemProvider.readAttributes()'
+        log.debug '<A>BasicFileAttributes QuiltFileSystemProvider.readAttributes()'
         def attr = attributesCache.get(path)
         if (attr) {
             return attr
@@ -486,8 +486,11 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
                 attributesCache[path] = result
                 return result
             }
-            // log.debug("readAttributes: File ${qPath.localPath()} not found")
-            throw new NoSuchFileException(qPath.toUriString())
+            log.debug("readAttributes: File ${qPath.localPath()} not found")
+            if (!qPath.isNull()) {
+                throw new NoSuchFileException(qPath.toUriString())
+            }
+            log.warn("readAttributes: Ignore ${qPath} for null bucket")
         }
         throw new UnsupportedOperationException("Not a valid Quilt Storage file attribute type: $type")
     }

diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
@@ -69,7 +69,7 @@ final class QuiltPath implements Path, Comparable {
         QuiltParser source = isAbsolute() ? parsed : QuiltParser.forNullBucket()
         return QuiltPackage.forParsed(source)
     }
-    
+
     String file_key() {
         return sub_paths()
     }
@@ -105,6 +105,10 @@ final class QuiltPath implements Path, Comparable {
         return !parsed.hasPath()
     }
 
+    boolean isNull() {
+        return parsed.hasNullBucket()
+    }
+
     QuiltPath getJustPackage() {
         if (isJustPackage()) { return this }
         QuiltParser packageParsed = QuiltParser.forBarePath(parsed.toPackageString())

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
@@ -104,7 +104,7 @@ class QuiltPackageTest extends QuiltSpecification {
         def qpath = factory.parseUri('quilt+s3://./')
         def pkg = qpath.pkg()
         expect:
-        pkg.is_null()
+        pkg.isNull()
         !pkg.install()
         !pkg.isInstalled()
         Files.exists(qpath.localPath())