Fix AWS nio tests [ci fast]

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

.github/workflows/build.yml

@@ -84,6 +84,8 @@ jobs:
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_S3FS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_S3FS_SECRET_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
           NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
           NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
@@ -95,6 +97,7 @@ jobs:
           AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
 
       - name: Publish tests report
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: report-unit-tests-jdk-${{ matrix.java_version }}

modules/nf-commons/src/main/nextflow/file/FileHelper.groovy

@@ -49,6 +49,7 @@ import nextflow.extension.FilesEx
 import nextflow.plugin.Plugins
 import nextflow.util.CacheHelper
 import nextflow.util.Escape
+import nextflow.util.StringUtils
 /**
  * Provides some helper method handling files
  *
@@ -618,7 +619,7 @@ class FileHelper {
     }
 
     /**
-     *  Caches File system providers
+     * Caches File system providers
      */
     @PackageScope
     static final Map<String, FileSystemProvider> providersMap = [:]
@@ -722,7 +723,7 @@ class FileHelper {
             try { fs = provider.getFileSystem(uri) }
             catch( FileSystemNotFoundException e ) { fs=null }
             if( !fs ) {
-                log.debug "Creating a file system instance for provider: ${provider.class.simpleName}"
+                log.debug "Creating a file system instance for provider: ${provider.class.simpleName}; config=${StringUtils.stripSecrets(config)}"
                 fs = provider.newFileSystem(uri, config!=null ? config : envFor(uri.scheme))
             }
             return fs

modules/nf-commons/src/main/nextflow/util/StringUtils.groovy

@@ -87,6 +87,8 @@ class StringUtils {
 
 
     static Map stripSecrets(Map map) {
+        if( map==null )
+            return null
         final copy = new HashMap(map.size())
         for( Map.Entry entry : map.entrySet() ) {
             if( entry.value instanceof Map ) {

modules/nf-commons/src/test/nextflow/util/StringUtilsTest.groovy

@@ -83,6 +83,7 @@ class StringUtilsTest extends Specification {
 
         where:
         SECRET                                  | EXPECTED
+        null                                    | null
         [foo:'Hello']                           | [foo:'Hello']
         [foo: [bar: 'World']]                   | [foo: [bar: 'World']]
         [foo: [password:'hola', token:'hi']]    | [foo: [password:'****', token:'****']]

plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy

@@ -159,7 +159,7 @@ class AwsClientFactory {
             return new InstanceMetadataRegionProvider().getRegion()
         }
         catch (AmazonClientException e) {
-            log.debug "Cannot fetch AWS region", e
+            log.debug("Cannot fetch AWS region", e as Throwable)
             return null
         }
     }

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java

@@ -669,7 +669,8 @@ public <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V>
 				throw new RuntimeException("Unable read attributes for file: " + FilesEx.toUriString(s3Path), e);
 			}
 		}
-		throw new UnsupportedOperationException("Not a valid S3 file system provider file attribute view: " + type.getName());
+		log.trace("Unsupported S3 file system provider file attribute view: " + type.getName());
+        return null;
 	}
 
 

plugins/nf-amazon/src/test/nextflow/cloud/aws/nio/AwsS3NioTest.groovy

@@ -31,7 +31,6 @@ import java.nio.file.StandardOpenOption
 import java.nio.file.attribute.BasicFileAttributes
 
 import com.amazonaws.services.s3.AmazonS3
-import com.amazonaws.services.s3.model.AmazonS3Exception
 import com.amazonaws.services.s3.model.Tag
 import groovy.util.logging.Slf4j
 import nextflow.Global
@@ -58,22 +57,20 @@ import spock.lang.Unroll
 class AwsS3NioTest extends Specification implements AwsS3BaseSpec {
 
     @Shared
-    static AmazonS3 s3Client0
+    private AmazonS3 s3Client0
 
     AmazonS3 getS3Client() { s3Client0 }
 
-    static {
-        def fs = (S3FileSystem)FileHelper.getOrCreateFileSystemFor(URI.create("s3:///"), config0())
-        s3Client0 = fs.client.getClient()
-    }
-
     static private Map config0() {
         def accessKey = System.getenv('AWS_S3FS_ACCESS_KEY')
         def secretKey = System.getenv('AWS_S3FS_SECRET_KEY')
-        return [aws: [access_key: accessKey, secret_key: secretKey]]
+        return [aws:[accessKey: accessKey, secretKey: secretKey]]
     }
 
     def setup() {
+        def fs = (S3FileSystem)FileHelper.getOrCreateFileSystemFor(URI.create("s3:///"), config0().aws)
+        s3Client0 = fs.client.getClient()
+        and:
         def cfg = config0()
         Global.config = cfg
         Global.session = Mock(Session) { getConfig()>>cfg }
@@ -207,7 +204,6 @@ class AwsS3NioTest extends Specification implements AwsS3BaseSpec {
         if( bucketName ) deleteBucket(bucketName)
     }
 
-
     def 'should copy a stream to bucket' () {
         given:
         def TEXT = "Hello world!"
@@ -240,7 +236,6 @@ class AwsS3NioTest extends Specification implements AwsS3BaseSpec {
         if( bucketName ) deleteBucket(bucketName)
     }
 
-
     def 'copy local file to a bucket' () {
         given:
         def TEXT = "Hello world!"