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From cphbrt <...@git.apache.org>
Subject [GitHub] beam pull request #3717: [BEAM-2750][BEAM-2751] Implement WholeFileIO
Date Fri, 11 Aug 2017 03:12:08 GMT
GitHub user cphbrt opened a pull request:

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

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

    Follow this checklist to help us incorporate your contribution quickly and easily:
    
     - [x] Make sure there is a [JIRA issue](https://issues.apache.org/jira/projects/BEAM/issues/)
filed for the change (usually before you start working on it).  Trivial changes like typos
do not require a JIRA issue.  Your pull request should address just this issue, without pulling
in other changes.
     - [x] Each commit in the pull request should have a meaningful subject line and body.
     - [x] Format the pull request title like `[BEAM-XXX] Fixes bug in ApproximateQuantiles`,
where you replace `BEAM-XXX` with the appropriate JIRA issue.
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pull request does, how, and why.
     - [ ] Run `mvn clean verify` to make sure basic checks pass. A more thorough check will
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     - [ ] If this contribution is large, please file an Apache [Individual Contributor License
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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 <chris.hebert-int@digitalreasoning.com>
Date:   2017-08-10T19:56:32Z

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

----


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