Add header removal for TextIO #29202

stankiewicz · 2023-10-30T18:37:23Z

Adds header removal for TextIO.Read / TextIO.ReadAll (with tests)

Related to ##28502 which may not work if number of lines is large.
Related to ##28728 which is not scalable if files are large.

github-actions · 2023-10-31T00:19:14Z

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stankiewicz · 2023-10-31T14:59:02Z

Run Java_GCP_IO_Direct PreCommit

ghost · 2023-10-31T15:41:46Z

Hi @stankiewicz, thanks so much for contributing to Beam!

Per our discussion, I would recommend the following additional changes.

Overloading the public functions to avoid breaking changes to the existed apis. (I see you have already submitted a new commit for that. Thanks for doing it!)
Your current code works great when the number of header lines to skip is 1. Would you please also add the logic for the case when we need to skip multiple header lines? Our Python SDK has a similar code path that you may find it useful.

beam/sdks/python/apache_beam/io/textio.py

Line 113 in c7dc5bd

skip_header_lines=0,

Notice that in this scenario, each reader will have to skip the header lines and make sure their start position is larger than the last position of the header. This may hurt the performance. Therefore, we will keep all 3 code paths (number of header lines to skip = 0/None, 1, >1) and choose the most efficient one based on user input.
Last but not least, I suggest using the same parameter name as our Python API, i.e.skipHeaderLines.

Again, great work!

Regards,

Shunping

stankiewicz · 2023-11-03T14:06:23Z

Run Java_GCP_IO_Direct PreCommit

Abacn · 2023-11-03T14:44:14Z

CHANGES.md

@@ -76,6 +76,7 @@ should handle this. ([#25252](https://github.com/apache/beam/issues/25252)).
 * `upload_graph` as one of the Experiments options for DataflowRunner is no longer required when the graph is larger than 10MB for Java SDK ([PR#28621](https://github.com/apache/beam/pull/28621).
 * state amd side input cache has been enabled to a default of 100 MB. Use `--max_cache_memory_usage_mb=X` to provide cache size for the user state API and side inputs. (Python) ([#28770](https://github.com/apache/beam/issues/28770)).
 * Beam YAML stable release. Beam pipelines can now be written using YAML and leverage the Beam YAML framework which includes a preliminary set of IO's and turnkey transforms. More information can be found in the YAML root folder and in the [README](https://github.com/apache/beam/blob/master/sdks/python/apache_beam/yaml/README.md).
+* `TextIO` supports skipping header.


this would go to beam 2.53.0. Also, link to the GitHub issue

Please append the the original issue link to this line, like

TextIO supports skipping header. (Java)(#17990).

ghost · 2023-11-03T14:53:13Z

sdks/java/core/src/main/java/org/apache/beam/sdk/io/TextSource.java

+    private void skipHeader(int headerLines, boolean skipFirstLine) throws IOException {
+      if (headerLines == 1) {
+        readNextRecord();
+      } else if (headerLines > 1) {


Could you also add a test to cover the skipping of multiple header lines?

ghost · 2023-11-03T15:07:04Z

sdks/java/core/src/main/java/org/apache/beam/sdk/io/TextSource.java

-          ((SeekableByteChannel) channel).position(requiredPosition);
-          startOfNextRecord = requiredPosition;
+          skipHeader(skipHeaderLines, false);
+          if (requiredPosition > startOfNextRecord) {


I am wondering what will happen if multiple readers having requiredPosition <= startOfNextRecord here.
In this case, more than one readers are assigned to a start position that falls in the header lines (assuming there are multiple long header lines). Not sure if the current code is handling this.

nvm. In this case, among those readers, only one will have an end position outside of the header lines, and will continue to read. So this should not be an issue then.

stankiewicz · 2023-11-03T18:01:48Z

Run Java_GCP_IO_Direct PreCommit

stankiewicz · 2023-11-03T19:11:30Z

Run Java PreCommit

stankiewicz · 2023-11-06T08:23:29Z

@shunping-google this is ready for review. after many retries of flaky tests, all green.

ghost

LGTM! Thanks again for contributing to Beam.

Abacn

Thanks for resolving this long standing feature request!

Please resolve the merge conflict then we can get this in

(not for this PR) Also this remind me that we should better check the correctness of our wordcount precommit test, not only run them

Abacn · 2023-11-08T14:58:48Z

testOrderedWithinKey (org.apache.beam.sdk.io.gcp.spanner.changestreams.it.SpannerChangeStreamOrderedWithinKeyIT) failed unrelated flaky test. merging for now

add header removal

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github-actions bot added the java label Oct 30, 2023

stankiewicz added 5 commits October 30, 2023 19:19

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ghost mentioned this pull request Oct 31, 2023

Add skipLines in FileIO.ReadableFile.readFullyAsUTF8String #28728

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avoiding breaking change

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stankiewicz added 9 commits November 2, 2023 22:41

add multiple header lines removal

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Merge branch 'master' into textio-header-removal

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Abacn reviewed Nov 3, 2023

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ghost reviewed Nov 3, 2023

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stankiewicz added 3 commits November 3, 2023 15:40

added new changes, fixed edge cases, added new test

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ghost approved these changes Nov 6, 2023

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Abacn approved these changes Nov 7, 2023

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Merge branch 'master' into textio-header-removal

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Abacn merged commit bf47289 into apache:master Nov 8, 2023
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Add header removal for TextIO #29202

Add header removal for TextIO #29202

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Add header removal for TextIO #29202

Add header removal for TextIO #29202

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