[jira] [Commented] (BEAM-2750) Read whole files as one PCollection element each

["ASF GitHub Bot (JIRA)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/BEAM-2750?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16122761#comment-16122761 ] 

ASF GitHub Bot commented on BEAM-2750:
--------------------------------------

GitHub user cphbrt opened a pull request:

    https://github.com/apache/beam/pull/3717

    [BEAM-2750][BEAM-2751] Implement WholeFileIO

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    ---
    
    ## Narrative
    
    WholeFileIO fulfills the requests of [BEAM-2750] and [BEAM-2751] for a way to read and write individual files as individual elements of a PCollection to and from specific filenames.
    
    ## Description
    
    `WholeFileIO.Read` receives a file pattern (glob) of input files. The file pattern is expanded into a `PCollection` of `ResourceId`s, each pointing to a single file. The bytes at the file location specified by the `ResourceId`s are read in and attached to their originating filename in a `KV`.
    
    `WholeFileIO.Write` receives a `PCollection` of `KV`s containing byte arrays and their corresponding filenames. The byte arrays are written to the output directory with their corresponding filename.
    
    ## Example Usage
    
    This example pipeline will read in files according to a given file glob and write them to the specified output directory unmodified other than "-copy" appended to their filenames. If the input file glob specifies files spread through a directory hierarchy, they will still be written out all into the same flat output directory.
    
    Example pipeline:
    ```java
    public class WholeFileIOPipeline {
    
        public interface FileIOOptions extends PipelineOptions {
            @Description("File glob of the files to read from")
            @Validation.Required
            String getInputFiles();
            void setInputFiles(String value);
    
            @Description("Path of the directory to write files to")
            @Validation.Required
            String getOutputDir();
            void setOutputDir(String value);
        }
    
        public static void main(String[] args) {
            final FileIOOptions options = PipelineOptionsFactory.fromArgs(args).withValidation()
                    .as(FileIOOptions.class);
            Pipeline p = Pipeline.create(options);
    
            PCollection<KV<String, byte[]>> files = p.apply(
                "Read Bytes and filenames of input files",
                WholeFileIO.read().from(options.getInputFiles())
            );
    
            PCollection<KV<String, byte[]>> renamedFiles = files.apply(
                    ParDo.of(
                            new DoFn<KV<String, byte[]>, KV<String, byte[]>>() {
                                @ProcessElement
                                public void processElement(ProcessContext c) {
                                    KV<String, byte[]> file = c.element();
                                    c.output(KV.of(file.getKey() + "-copy", file.getValue()));
                                }
                            }
                    )
            );
    
            renamedFiles.apply(
                    "Write Bytes to filenames in Output Directory",
                    WholeFileIO.write().to(options.getOutputDir())
            );
    
            p.run().waitUntilFinish();
        }
    }
    ```
    
    Example command to run example pipeline:
    ```bash
    mvn clean compile exec:java -Dexec.mainClass=com.example.WholeFileIOPipeline \
      -Dexec.args=" \
        --inputFiles=/path/to/input/files/** \
        --outputDir=/path/to/output/directory/ \
        " \
      -Pdirect-runner
    ```
    
    ## ToDo
    
    - [ ] Add comments
    - [ ] Add unit tests
    - [ ] Scale test for performance
    - [ ] Find out if `FileSystems.resolve()` will resolve multiple intermediary directories if a user provides a path that doesn't fully exist yet. (`WholeFileIO -> Write -> expand() -> ParDo -> ResourceId logic`)
    - [ ] Make sure that the `OutputStream` automatically closes when an `Exception` occurs in `WholeFileIO -> Write -> expand() -> ParDo -> try/catch`. If not, close it in a `finally` statement.

You can merge this pull request into a Git repository by running:

    $ git pull https://github.com/cphbrt/beam master+WholeFileIO

Alternatively you can review and apply these changes as the patch at:

    https://github.com/apache/beam/pull/3717.patch

To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:

    This closes #3717
    
----
commit 42f8b991512aa01019013d64e167b5e5782f87bf
Author: Chris Hebert <ch...@digitalreasoning.com>
Date:   2017-08-10T19:56:32Z

    [BEAM-2750][BEAM-2751] Implement WholeFileIO

----


> Read whole files as one PCollection element each
> ------------------------------------------------
>
>                 Key: BEAM-2750
>                 URL: https://issues.apache.org/jira/browse/BEAM-2750
>             Project: Beam
>          Issue Type: New Feature
>          Components: sdk-java-core
>            Reporter: Christopher Hebert
>            Assignee: Davor Bonaci
>
> I'd like to read whole files as one element each.
> If my input files are hi.txt, what.txt, and yes.txt, then the whole contents of hi.txt are an element of the returned PCollection, the whole contents of what.txt are the next element, etc., giving me a PCollection with three elements.
> This contrasts with TextIO which reads a new element for every line of text in the input files.
> This read (I'll call it WholeFileIO for now) would work like so:
> {code:java}
> PCollection<KV<String, Byte[]>> fileNamesAndBytes = p.apply("Read", WholeFileIO.read().from("/path/to/input/dir/*"));
> {code}
> The above example passes the raw file contents and the filename.
> Alternatively, we could pass a PCollection of some sort of FileWrapper around an InputStream to support lazy loading.
> This ticket complements [BEAM-2751].



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