210 dot path

.github/workflows/test.yml

@@ -47,7 +47,7 @@ jobs:
         cache: gradle
 
     - name: Setup Gradle
-      uses: gradle/gradle-build-action@v3
+      uses: gradle/actions/setup-gradle@v3
 
     - name: Run Gradle Tests
       run: make test

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.7.15] 2024-06-17
+
+- use null bucket for relative paths (e.g., nf-schema)
+
 ## [0.7.14] 2024-06-14
 
 - improve package name debugging

README.md

@@ -76,8 +76,8 @@ From the command-line, do, e.g.:
 ```bash
 # export NXF_VER=23.04.3
 export LOG4J_DEBUG=true  # for verbose logging
-export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.14/nf-quilt-0.7.14-meta.json
-nextflow run main.nf -plugins [email protected].14
+export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/0.7.15/nf-quilt-0.7.15-meta.json
+nextflow run main.nf -plugins [email protected].15
 ```
 
 For Tower, you can use the "Pre-run script" to set the environment variables.

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy

@@ -170,6 +170,10 @@ class QuiltPackage {
         return parsed.options[QuiltParser.P_FORCE]
     }
 
+    boolean isNull() {
+        return parsed.hasNullBucket()
+    }
+
     boolean isInstalled() {
         return installed
     }
@@ -179,6 +183,10 @@ class QuiltPackage {
     }
 
     Path install() {
+        if (isNull()) {
+            log.debug('null bucket: no need to install')
+            return null
+        }
         Path dest = packageDest()
 
         try {
@@ -229,6 +237,11 @@ class QuiltPackage {
     }
     // https://docs.quiltdata.com/v/version-5.0.x/examples/gitlike#install-a-package
     Manifest push(String msg = 'update', Map meta = [:]) {
+        if (isNull()) {
+            log.debug('null bucket: no need to push')
+            return null
+        }
+
         S3PhysicalKey registryPath = new S3PhysicalKey(bucket, '', null)
         Registry registry = new Registry(registryPath)
         Namespace namespace = registry.getNamespace(packageName)

plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy

@@ -28,6 +28,7 @@ class QuiltParser {
     static final String SEP = '/'
     static final String PREFIX = SCHEME + '://'
     static final int MIN_SIZE = 2
+    static final String NULL_BUCKET = 'nf-quilt-dev-null'
 
     static final String P_CAT = 'catalog'
     static final String P_DEST = 'dest'
@@ -58,6 +59,10 @@ class QuiltParser {
         return QuiltParser.forUriString(PREFIX + path)
     }
 
+    static QuiltParser forNullBucket() {
+        return new QuiltParser(NULL_BUCKET, 'dev/null', '')
+    }
+
     static QuiltParser forUriString(String uriString) {
         URI uri = new URI(uriString)
         return QuiltParser.forURI(uri)
@@ -268,6 +273,10 @@ class QuiltParser {
         return paths.size() > 0
     }
 
+    boolean hasNullBucket() {
+        return NULL_BUCKET == getBucket()
+    }
+
     String getOptions(String key) {
         return options?.get(key)
     }

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")
     }

plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy

@@ -66,7 +66,8 @@ final class QuiltPath implements Path, Comparable {
     }
 
     QuiltPackage pkg() {
-        return isAbsolute() ? QuiltPackage.forParsed(parsed) : null
+        QuiltParser source = isAbsolute() ? parsed : QuiltParser.forNullBucket()
+        return QuiltPackage.forParsed(source)
     }
 
     String file_key() {
@@ -104,6 +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())

plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.7.14
+Plugin-Version: 0.7.15
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=22.10.6
 

plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy

@@ -99,6 +99,18 @@ class QuiltPackageTest extends QuiltSpecification {
         Files.readAttributes(qroot, BasicFileAttributes)
     }
 
+    void 'should not raise error on null bucket'() {
+        given:
+        def qpath = factory.parseUri('quilt+s3://./')
+        def pkg = qpath.pkg()
+        expect:
+        pkg.isNull()
+        !pkg.install()
+        !pkg.isInstalled()
+        Files.exists(qpath.localPath())
+        Files.readAttributes(qpath, BasicFileAttributes)
+    }
+
     @IgnoreIf({ System.getProperty('os.name').contains('indows') })
     void 'should successfully install files and get attributes'() {
         expect:

plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy

@@ -259,4 +259,12 @@ class QuiltPathTest extends QuiltSpecification {
         fullPath.toUriString().contains('?')
     }
 
+    void 'should return a special-case null bucket on invalid paths'() {
+        when:
+        QuiltPath path = QuiltPathFactory.parse('quilt+s3://./')
+        then:
+        path.toString() == '.'
+        path.pkg() != null
+    }
+
 }