Merge branch 'nextflow-io:master' into master

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -757,7 +757,7 @@ class BashWrapperBuilder {
         result += copyFileToWorkDir(TaskRun.CMD_ERRFILE) + ' || true' + ENDL
         if( statsEnabled )
             result += copyFileToWorkDir(TaskRun.CMD_TRACE) + ' || true' + ENDL
-        if(  outputEnvNames )
+        if( outputEnvNames || outputEvals )
             result += copyFileToWorkDir(TaskRun.CMD_ENV) + ' || true' + ENDL
         return result
     }

modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy

@@ -305,6 +305,15 @@ class FilePorter {
             }
         }
 
+        protected void cleanup(Path path) {
+            try {
+                FileHelper.deletePath(path)
+            }
+            catch (IOException e) {
+                log.warn "Unable to cleanup file path: ${path.toUriString()} - cause: ${e.message}"
+            }
+        }
+
         /**
          * Download a foreign file (ie. remote) storing it the current pipeline execution directory
          *
@@ -319,8 +328,11 @@ class FilePorter {
                     return stageForeignFile0(filePath, stagePath)
                 }
                 catch( IOException e ) {
+                    // remove the target file that could be have partially downloaded
+                    cleanup(stagePath)
+                    // check if a stage/download retry is allowed
                     if( count++ < maxRetries && e !instanceof NoSuchFileException && e !instanceof InterruptedIOException && !Thread.currentThread().isInterrupted() ) {
-                        def message = "Unable to stage foreign file: ${filePath.toUriString()} (try ${count}) -- Cause: $e.message"
+                        def message = "Unable to stage foreign file: ${filePath.toUriString()} (try ${count} of ${maxRetries}) -- Cause: $e.message"
                         log.isDebugEnabled() ? log.warn(message, e) : log.warn(message)
 
                         sleep (10 + RND.nextInt(300))

modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy

@@ -1320,6 +1320,46 @@ class BashWrapperBuilderTest extends Specification {
 
     }
 
+    def 'should get unstage control script'(){
+        given:
+        BashWrapperBuilder builder
+        when:
+        builder = newBashWrapperBuilder()
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                '''.stripIndent()
+
+
+        when:
+        builder = newBashWrapperBuilder(statsEnabled: true)
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.trace /work/dir/.command.trace || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEnvNames: ['some-data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEvals: [some:'data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+    }
+
 
     def 'should create wrapper with podman' () {
         when:

modules/nf-httpfs/src/main/nextflow/file/http/FixedInputStream.groovy

@@ -0,0 +1,73 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * 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 nextflow.file.http
+
+import groovy.transform.CompileStatic
+
+/**
+ * Implements a {@link FilterInputStream} that checks the expected length of bytes have been
+ * read when closing the stream or throws an error otherwise
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+class FixedInputStream extends FilterInputStream {
+
+    private final long length
+    private long bytesRead
+
+    FixedInputStream(InputStream inputStream, long len) {
+        super(inputStream)
+        this.length = len
+    }
+
+    @Override
+    int read() throws IOException {
+        final result = super.read()
+        if( result!=-1 )
+            bytesRead++
+        return result
+    }
+
+    @Override
+    int read(byte[] b, int off, int len) throws IOException {
+        final result = super.read(b, off, len)
+        if( result!=-1 )
+            bytesRead += result
+        return result
+    }
+
+    @Override
+    long skip(long n) throws IOException {
+        long skipped = super.skip(n)
+        bytesRead += skipped
+        return skipped
+    }
+
+    @Override
+    int available() throws IOException {
+        super.available()
+    }
+
+    @Override
+    void close() throws IOException {
+        if( bytesRead != length )
+            throw new IOException("Read data length does not match expected size - bytes read: ${bytesRead}; expected: ${length}")
+        super.close()
+    }
+}

modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy

@@ -245,7 +245,11 @@ abstract class XFileSystemProvider extends FileSystemProvider {
         }
 
         final conn = toConnection(path)
-        final stream = new BufferedInputStream(conn.getInputStream())
+        final length = conn.getContentLengthLong()
+        final target = length>0
+                ? new FixedInputStream(conn.getInputStream(),length)
+                : conn.getInputStream()
+        final stream = new BufferedInputStream(target)
 
         new SeekableByteChannel() {
 
@@ -346,7 +350,11 @@ abstract class XFileSystemProvider extends FileSystemProvider {
             }
         }
 
-        return toConnection(path).getInputStream()
+        final conn = toConnection(path)
+        final length = conn.getContentLengthLong()
+        return length>0
+            ? new FixedInputStream(conn.getInputStream(), length)
+            : conn.getInputStream()
     }
 
     /**

modules/nf-httpfs/src/test/nextflow/file/http/FixedInputStreamTest.groovy

@@ -0,0 +1,79 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * 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 nextflow.file.http
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+class FixedInputStreamTest extends Specification {
+
+    def 'should read byte by byte' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def ch
+        def result = new StringBuilder()
+        while( (ch=stream.read())!=-1 )
+            result.append(ch as char)
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        result.toString() == 'Hello world'
+    }
+
+    def 'should read byte buffer' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def buffer = new byte[5]
+        def result = new StringBuilder()
+        def c
+        while( (c=stream.read(buffer))!=-1 ) {
+            for( int i=0; i<c; i++ )
+                result.append(buffer[i] as char)
+        }
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        result.toString() == 'Hello world'
+    }
+
+    def 'should read all bytes' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def result = stream.readAllBytes()
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        and:
+        new String(result) == "Hello world"
+    }
+}

modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy

@@ -42,6 +42,7 @@ class XFileSystemProviderTest extends Specification {
 
     def "should return input stream from path"() {
         given:
+        def DATA = 'Hello world'
         def fsp = Spy(new HttpFileSystemProvider())
         def path = fsp.getPath(new URI('http://host.com/index.html?query=123'))
         def connection = Mock(URLConnection)
@@ -54,7 +55,8 @@ class XFileSystemProviderTest extends Specification {
             return connection
         }
         and:
-        connection.getInputStream() >> new ByteArrayInputStream('Hello world'.bytes)
+        connection.getInputStream() >> new ByteArrayInputStream(DATA.bytes)
+        connection.getContentLengthLong() >> DATA.size()
         and:
         stream.text == 'Hello world'
     }