Rename com.upplication.s3fs package to nextflow.cloud.aws.nio

Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Apr 13, 2023 · a2f3bb2 · a2f3bb2
1 parent cc59596
commit a2f3bb2
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diff --git a/changelog.txt b/changelog.txt
@@ -2426,7 +2426,7 @@ NEXTFLOW CHANGE-LOG
 0.16.1 - 7 Nov 2015
 - Fixed issue #85. Directive `publishDir` can't access process local variables.
 - Fixed wrong error message when trying to run a project sticked on a specific revision.
-- Fixed `IllegalArgumentException: other must be an instance of com.upplication.s3fs.S3Path` exception when publishing to a S3 path.
+- Fixed `IllegalArgumentException: other must be an instance of nextflow.cloud.aws.nio.S3Path` exception when publishing to a S3 path.
 - Fixed indentation in repo info command.
 
 0.16.0 - 4 Nov 2015

diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -168,7 +168,7 @@ class LoggerHelper {
         packages[MAIN_PACKAGE] = quiet ? Level.WARN : Level.INFO
 
         // -- add the S3 uploader by default
-        if( !containsClassName(debugConf,traceConf, 'com.upplication.s3fs') )
+        if( !containsClassName(debugConf,traceConf, 'nextflow.cloud.aws.nio') )
             debugConf << S3_UPLOADER_CLASS
         if( !containsClassName(debugConf,traceConf, 'io.seqera') )
             debugConf << 'io.seqera'

diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -126,7 +126,7 @@ class Const {
       http://nextflow.io
 """
 
-    static public final String S3_UPLOADER_CLASS = 'com.upplication.s3fs'
+    static public final String S3_UPLOADER_CLASS = 'nextflow.cloud.aws.nio'
 
     static public final String ROLE_WORKER = 'worker'
 

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/AmazonPlugin.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/AmazonPlugin.groovy
@@ -15,7 +15,7 @@
  */
 package nextflow.cloud.aws
 
-import com.upplication.s3fs.S3FileSystemProvider
+import nextflow.cloud.aws.nio.S3FileSystemProvider
 import groovy.transform.CompileStatic
 import nextflow.file.FileHelper
 import nextflow.plugin.BasePlugin

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy
@@ -23,7 +23,7 @@ import com.amazonaws.services.batch.AWSBatch
 import com.amazonaws.services.batch.model.AWSBatchException
 import com.amazonaws.services.ecs.model.AccessDeniedException
 import com.amazonaws.services.logs.model.ResourceNotFoundException
-import com.upplication.s3fs.S3Path
+import nextflow.cloud.aws.nio.S3Path
 import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope

diff --git a/...c/main/com/upplication/s3fs/S3Client.java → ...main/nextflow/cloud/aws/nio/S3Client.java b/...c/main/com/upplication/s3fs/S3Client.java → ...main/nextflow/cloud/aws/nio/S3Client.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnáiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.File;
 import java.io.IOException;
@@ -101,15 +78,15 @@
 import com.amazonaws.services.s3.transfer.TransferManagerBuilder;
 import com.amazonaws.services.s3.transfer.Upload;
 import com.amazonaws.services.s3.transfer.UploadContext;
-import com.upplication.s3fs.util.S3MultipartOptions;
+import nextflow.cloud.aws.nio.util.S3MultipartOptions;
 import nextflow.cloud.aws.util.AwsHelper;
 import nextflow.util.Duration;
 import nextflow.util.ThreadPoolHelper;
 import nextflow.util.ThreadPoolManager;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static com.upplication.s3fs.util.S3UploadHelper.*;
+import static nextflow.cloud.aws.nio.util.S3UploadHelper.*;
 
 /**
  * Client Amazon S3

diff --git a/...om/upplication/s3fs/S3FileAttributes.java → ...tflow/cloud/aws/nio/S3FileAttributes.java b/...om/upplication/s3fs/S3FileAttributes.java → ...tflow/cloud/aws/nio/S3FileAttributes.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnáiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.FileTime;

diff --git a/...pplication/s3fs/S3FileAttributesView.java → ...w/cloud/aws/nio/S3FileAttributesView.java b/...pplication/s3fs/S3FileAttributesView.java → ...w/cloud/aws/nio/S3FileAttributesView.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,9 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
+ *
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.IOException;
 import java.nio.file.attribute.BasicFileAttributeView;

diff --git a/...in/com/upplication/s3fs/S3FileSystem.java → .../nextflow/cloud/aws/nio/S3FileSystem.java b/...in/com/upplication/s3fs/S3FileSystem.java → .../nextflow/cloud/aws/nio/S3FileSystem.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnáiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.IOException;
 import java.net.URI;

diff --git a/...pplication/s3fs/S3FileSystemProvider.java → ...w/cloud/aws/nio/S3FileSystemProvider.java b/...pplication/s3fs/S3FileSystemProvider.java → ...w/cloud/aws/nio/S3FileSystemProvider.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnáiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -101,9 +78,9 @@
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Sets;
-import com.upplication.s3fs.util.IOUtils;
-import com.upplication.s3fs.util.S3MultipartOptions;
-import com.upplication.s3fs.util.S3ObjectSummaryLookup;
+import nextflow.cloud.aws.nio.util.IOUtils;
+import nextflow.cloud.aws.nio.util.S3MultipartOptions;
+import nextflow.cloud.aws.nio.util.S3ObjectSummaryLookup;
 import nextflow.cloud.aws.AwsClientFactory;
 import nextflow.cloud.aws.config.AwsConfig;
 import nextflow.extension.FilesEx;

diff --git a/...main/com/upplication/s3fs/S3Iterator.java → ...in/nextflow/cloud/aws/nio/S3Iterator.java b/...main/com/upplication/s3fs/S3Iterator.java → ...in/nextflow/cloud/aws/nio/S3Iterator.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnáiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.nio.file.Path;
 import java.util.ArrayList;

diff --git a/.../com/upplication/s3fs/S3OutputStream.java → ...extflow/cloud/aws/nio/S3OutputStream.java b/.../com/upplication/s3fs/S3OutputStream.java → ...extflow/cloud/aws/nio/S3OutputStream.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,9 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
+ *
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -52,8 +53,8 @@
 import com.amazonaws.services.s3.model.Tag;
 import com.amazonaws.services.s3.model.UploadPartRequest;
 import com.amazonaws.util.Base64;
-import com.upplication.s3fs.util.ByteBufferInputStream;
-import com.upplication.s3fs.util.S3MultipartOptions;
+import nextflow.cloud.aws.nio.util.ByteBufferInputStream;
+import nextflow.cloud.aws.nio.util.S3MultipartOptions;
 import nextflow.util.Duration;
 import nextflow.util.ThreadPoolHelper;
 import nextflow.util.ThreadPoolManager;

diff --git a/...src/main/com/upplication/s3fs/S3Path.java → ...c/main/nextflow/cloud/aws/nio/S3Path.java b/...src/main/com/upplication/s3fs/S3Path.java → ...c/main/nextflow/cloud/aws/nio/S3Path.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,33 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- */
-
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2014 Javier Arnaiz @arnaix
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
  */
 
-package com.upplication.s3fs;
+package nextflow.cloud.aws.nio;
 
 import java.io.File;
 import java.io.IOException;

diff --git a/.../com/upplication/s3fs/ng/ChunkBuffer.java → ...extflow/cloud/aws/nio/ng/ChunkBuffer.java b/.../com/upplication/s3fs/ng/ChunkBuffer.java → ...extflow/cloud/aws/nio/ng/ChunkBuffer.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2023, Seqera Labs
+ * Copyright 2020-2022, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,9 +12,10 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
+ *
  */
 
-package com.upplication.s3fs.ng;
+package nextflow.cloud.aws.nio.ng;
 
 import java.io.IOException;
 import java.io.InputStream;